Hypothesis

24,814 Matching Annotations

Apr 2022
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273320

1
1. sciscore 09 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273320: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Molecular quantification by digital RT-PCR: A panel of oligonucleotides was designed using AlleleID software vers. 7</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>AlleleID</div><div>suggested: (AlleleID, RRID:SCR_014790)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data analysis was performed using the Galaxy tools.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Galaxy</div><div>suggested: (Galaxy, RRID:SCR_006281)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Reads were mapped with BWA-MEM (version 0.7.17.1) against reference genome (NC_45512).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BWA-MEM</div><div>suggested: (Sniffles, RRID:SCR_017619)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Variant calling was performed using Lofreq (version 2.1.5) and annotation of SARS-CoV-2 variants using SnpEff eff version 4.5 covid19).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Lofreq</div><div>suggested: (LoFreq, RRID:SCR_013054)</div></div><div style="margin-bottom:8px"><div>SnpEff</div><div>suggested: (SnpEff, RRID:SCR_005191)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mathematical and statistical methods: Dynamics of mutations (concentration or mutation frequency) were modeled based on daily average concentration (when multiple locations were sampled on the same day) using a LOWESS smoothing method on 10 adjacent points (GraphPad Prism v9.0), allowing to limit outlier effects.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">First derivative of dynamics curves was calculated using dedicated function of GraphPad Prism software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Variant identification results from sequencing, but such approach faces limitations for application in wastewater with respect to RNA quality and quantity (Lou et al., 2022), but also mathematical tools to deconvolute isolated mutations to reconstruct the original genomes in a mixture of variants (Agrawal et al., 2022b; Jahn et al., 2021; Smyth et al., 2022). Different studies have shown that it is also possible to monitor specific mutations suggestive of VOC to identify the emergence of VOC in a territory and to explain the predominance of certain VOC in epidemic waves (Caduff et al., 2022; Carcereny et al., 2022; Erster et al., 2022; Wurtzer et al., 2022). RT-qPCR approaches require calibration tools for absolute quantification or allelic discrimination (wild-type vs mutated) for relative quantification. Digital PCR allows more flexibility by offering a most probable number estimation (in accordance with Poisson’s law), by avoiding the realization of a standard curve and by allowing multiplexing of reactions. The del69-70 mutation was shared by Alpha and Omicron BA.1 VOCs. However, Alpha VOC has been chronologically replaced by Delta VOC, to the point of disappearance as confirmed by the absence of del69-70 mutation detection since summer 2021 in wastewater. In this regard, the WHO no longer identifies Alpha VOC as a circulating VOC (World Health Organization, 2022). On the other hand, Omicron BA.1 VOC carries the synonymous mutation C21762T, the presence of which confers a...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273320
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273334

1
1. sciscore 09 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273334: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Positive samples with known Ct value were selected by simple random sampling technique, from 9,520 positive samples within one month, which is obtained from 28.4% prevalence of Covid-19 in Ethiopia as of August 20/2020.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After viral heat inactivation, NA extraction was done from 0.6 ml sample volume on the Abbott m2000SP instrument by using the Abbott mSample Preparation System Deoxyribonucleic acid (DNA) according to the manufacturer’s recommendations [1].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Abbott</div><div>suggested: (Abbott, RRID:SCR_010477)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitation of the study: Performance has only been established with the specimen types listed in the Intended Use. Other specimen types have not been evaluated and should not be used with this assay. The small sample size can affect the conclusion. Since our study conducted analysis from stored positive samples, weak positive samples may be affected by repeated thaw and refreezing.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273334
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.05.22273483

1
1. sciscore 09 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.22273483: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.05.22273483
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.05.487186

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.487186: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Since scores calculated by the SYFPEITHI server vary, we identified peptides that have been experimentally validated to bind to C57BL/6 and BALB/CJ supertypes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>C57BL/6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Retrieval of SARS-CoV-2 sequence: We retrieved the reference S protein sequence of SARS-CoV-2 Wuhan isolates from the NCBI database using accession number YP_009724390.1.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NCBI</div><div>suggested: (NCBI, RRID:SCR_006472)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antigenicity prediction: VaxiJen v2.0 [29] was used to predict antigenic CD8 and CD4 epitopes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>VaxiJen</div><div>suggested: (VaxiJen, RRID:SCR_018514)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Allergenicity prediction: AllerTop v2.0 [30] was used to predict allergenicity for both CD8 and CD4 epitopes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>AllerTop</div><div>suggested: (AllerTop, RRID:SCR_018496)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Using ProtParam [32] tool on ExPASy, the chemical and physical properties of the top CD8 and CD4 peptides were assessed.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ProtParam</div><div>suggested: (ProtParam Tool, RRID:SCR_018087)</div></div><div style="margin-bottom:8px"><div>ExPASy</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Since scores calculated by the SYFPEITHI server vary, we identified peptides that have been experimentally validated to bind to C57BL/6 and BALB/CJ supertypes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SYFPEITHI</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We then spatially docked the predicted epitope in the MHC groove using PyMOL and FlexPepDock [39].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PyMOL</div><div>suggested: (PyMOL, RRID:SCR_000305)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Additionally, the PCOptim tool allowed us to determine the caveats in population coverage and thus identify the populations that may receive less coverage. The PCOptim tool provided us with an optimal set of epitopes that reaches the maximum possible population coverage given our raw dataset. Comparing this optimal dataset to our set of top epitopes revealed some overlap, confirming the success of our selection procedure. A total of three epitopes were found in both the optimal dataset and our top epitope datasets. Out of the 27 most common HLA alleles in the human population, we identified 5 alleles that are unaccounted for in the immunogenic, antigenic, non-allergenic, non-toxic, and stable epitope dataset (HLA-B*07:02, HLA-B*08:01, HLA-A*31:01, HLA-A*33:01, and HLA-B*51:01). The difference in population coverage between that optimal dataset and our set of 8 CD8 Omicron-related epitopes can be attributed to the five aforementioned HLA alleles. The only way to increase population coverage further is to include new epitopes that are predicted to be strong binders to the desired HLA alleles and pass the clinical checkpoint filters. While PCOptim does not account for the clinical checkpoint parameters we address in this study, it is a useful tool in determining several epitopes that are useful in obtaining high population coverage. The population coverage that we obtained from our top epitope dataset is substantially high, so adding new epitopes will make a very small impact on...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.04.05.487186
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.06.487215

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.06.487215: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

biorxiv.org/cgi/content/10.1101/2022.04.06.487215
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.06.22273080

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.06.22273080: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The study was approved by the Monash Health Human Research Ethics Committee (RES-21-0000-364L – 76466) and registered with the Australian New Zealand Clinical Trials Registry (ACTRN12621001467820).<br>Consent: Potential participants who accessed the survey link and gave informed consent were directed to the survey, hosted on the Qualtrics® secure data capture platform.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses were performed using SPSS Statistics Version 27.0 (IBM, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengths and limitations: In addition to the use of validated instruments, the strengths of the present study include the broad and diverse sampling of pre-defined, high-risk participants with three disease types within a range of demographics. The three-month recruitment period spanned changing levels of community transmission and social restriction measures, including strict state-wide lockdowns, giving a broader perspective than a short ‘snapshot’ survey. Importantly, data collection commenced at least three months after the availability of vaccines to high-risk groups, allowing sufficient time for vaccination if willing. Finally, the low prevalence of COVID-19 disease in Australia at the time of the study gives insight into attitudes and actions in the setting where there is less immediate threat from COVID-19. Study limitations include recall and misclassification bias inherent in a survey-based study and availability only in English. Additionally, people who had a greater interest in COVID-19 vaccinations may have been more likely to respond. These issues should be considered when generalising findings. Given that Australia had one of the highest vaccination rates globally and relatively low community transmission during most of the period studied, results may not be directly translatable to global regions with lower vaccination rates and/or high transmission. However, within one year of the study, a period of extremely high community transmission occurred throughout A...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.06.22273080
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.05.22273434

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.22273434: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: 12 Our study received approval from the local Institutional Review Board /Ref.;26022021-CN-1e-CI) and was conducted per the Code of Ethics of the World Medical Association (Declaration of Helsinki) for experiments that involve humans.<br>Consent: Every participant signed an informed consent where the study was explained.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">The inclusion criteria were healthcare professionals of both genders and any age who consented to participate, with a complete BNT162b2 national vaccination regimen, the application of the third BNT162b2 dose 4-6 months after the original vaccination scheme, and an additional BNT162b2 booster 4-6 months following the third dose.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Specific anti S1-S2 IgG antibodies against SARS-CoV-2 were measured by laboratory personnel using a chemiluminescence immunoassay (CLIA) by DiaSorin.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti S1-S2 IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>SARS-CoV-2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We performed a Friedman test to compare the anti S1 and S2 antibody titers through time and a Mann Whitney U test to compare antibody levels between subjects previously exposed to SARS-CoV-2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti S1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>S2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We performed an individual variation as a random effect, and the fixed effects were the time of every anti S1-S2 antibody, gender, and age.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti S1-S2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SPSS version 25 and R v 4.0.4 was the statistical program used to analyze data.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  As for limitations of our study, this is an observational study, so we lack randomization and a control group; however, we were able to compare our information with previously published data. A larger sample size would be of interest for testing for other predictors of antibody change; however, the changes of antibody titers between doses were so different that we could achieve enough statistical power for the inferences addressed in the present manuscript. This study did not include basal antibody measurement because, unfortunately, we could not obtain these samples since our protocol was accepted after all participants had received the first dose. However, we think this manuscript is valuable since new SARS-COV2 variants are emerging, and scarce information exists concerning a fourth dose that could help prevent infection or severe cases. Future studies about new generation vaccines against SARS-CoV-2 are required to compare the results with this regimen. In conclusion, the fourth dose of BNT162b2mRNA produced a humoral response by increasing 33.6 times S1/S2 IgG compared to one dose, with mild adverse events. Women had more AEFI after the fourth dose, and there is a small effect related to the antibody level. Even though the Omicron variant is contagious, we found a similar infection rate to the Delta variant after subjects received the fourth dose. All the infected cases were mild and treated ambulatory.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT05228912</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Immunization of 7 Different Vaccines Against SARS-COV-2 Acro…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.05.22273434
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.05.22273450

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.22273450: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Following the written informed consent process, participants answered questions detailing their demographics, lifestyle habits, past medical history (including COVID-19), and COVID-19 infection symptoms.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">The selected predictors from each of the best-fitting cross-validated LASSO models were then included as fixed effects in follow-up LMMs with by-participant random intercepts, allowing us to control for individual differences.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were washed three times with 0.1% PBST followed by addition of a 1:3,000 dilution of goat anti-human IgG–horseradish peroxidase (HRP) conjugated secondary antibody (50μl) well and incubated 1h.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG–horseradish</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plots were produced using the ggplot2 [30].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ggplot2</div><div>suggested: (ggplot2, RRID:SCR_014601)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study has several limitations. Sample sizes for each cohort examined were small due to variability in vaccination timelines and participant scheduling. Some individuals were excluded due to a confounding effect on our predictive modeling, which is controlled by the fixed effect of time. The natural infection group was further limited by the study timeline, as the first SARS-CoV-2 vaccination became available shortly after enrollment began and therefore limited the number of individuals we were able to follow longitudinally. Additionally, our analysis only included quantitative antibody binding titers. Although recent work has demonstrated that higher binding antibodies correlate to higher neutralizing antibodies [13], expansive, multi-center longitudinal studies are needed. An ideal analysis would consist of a multivariate analysis of reactogenicity, demographics, and quantitatively characterized antibody, B-cell and T-cell responses, as immune protection seems to be contingent on all three tiers of the immune response [50]. Further, some of the predictors used in our statistical analysis were found to be significant in one test but not in post-hoc tests. Large, longitudinal studies are required to confirm a significant group difference, but the predictors utilized herein should be included in future analyses. Our bivariate analysis of symptoms experienced following the 1st and 2nd doses failed to demonstrate that individual symptoms can influence peak antibody titers fol...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.05.22273450
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22271928

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22271928: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">As the glucose oxidase (GOx)-conjugated (see Supporting Information) monoclonal anti-6-FAM antibody (SAB4600050-125UL, Merck, Germany) will now only bind to the 6-FAM label on the 5’ end of uncleaved reRNA, the signal obtained in the amperometric readout is highly specific and inversely proportional to the target concentration within the sample solution. β-lactam Detection: Functionalization of the immobilization area is accomplished by incubation with penicillin binding protein 3 (PBP-337; 250 µg ml−1 in PBS (10 mM; pH 7.4), expressed via in-house production) for 1 hour, followed by 30 minutes of blocking with biotin-free casein (85R-108, Fitzgerald, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-6-FAM</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>SAB4600050-125UL</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>penicillin binding protein 3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>casein ( 85R-108</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The protein concentration is determined by use of the Bradford method (Bio-Rad laboratories, USA) with bovine serum albumin (Carl Roth, Germany) as standard and the concentration of the pure protein is determined by analyzing the SDS gels with ImageJ.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImageJ</div><div>suggested: (ImageJ, RRID:SCR_003070)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Clinical Samples and RNA-Extraction: Patient samples were provided by the Medical Center – University of Freiburg and lysed in the Alinity Lysis Solution (09N20-001, Abbott, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Abbott</div><div>suggested: (Abbott, RRID:SCR_010477)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22271928
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.06.487306

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.06.487306: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After binding, samples were washed twice in sort buffer and incubated with a 1:100 dilution of α-Myc-FITC (Abcam, #Ab1263) and α-His-PE (Abcam, #Ab72467) antibody at room temperature for 10 minutes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>α-His-PE ( Abcam , #Ab72467 )</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 1 hour at 4 °C, cells were washed twice in sort buffer and stained with α-His-PE antibody (1:100).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>α-His-PE</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 293T cells expressing scFv on the cell surface were detached with trypsin-EDTA (Thermo Fisher Scientific) and washed twice in prechilled sort buffer (1% FCS, 25 mM HEPES-KOH pH 7.9, 1 mM EDTA in PBS).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T</div><div>suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">An expression vector for the secretion and purification of His-tagged proteins from mammalian cells was generated by insertion of DNA encoding an IGK leader and 8xHis tag into pCS2-MT+.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCS2-MT+</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A DNA fragment encoding the SARS-CoV-2 RBD (aa 319-591) was amplified from pCAGGS-SARS-CoV-2-Spike vector (a kind gift from Keith Grehan) and cloned in frame with the N-terminal IGK leader sequence and C-terminal 8xHis tag using NheI and XhoI sites.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCAGGS-SARS-CoV-2-Spike</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The round 3 enriched ultralong scFv library was transferred from pBovShow into this lentiviral vector and lentiviruses were generated by transient transfection of 293T cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pBovShow</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The next day, 4 μg Lenti-BovShow-IRES-PuroR, 4 μg of pCMVR8.74 packaging vector (Addgene plasmid #22036) and 2 μg of pMD2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCMVR8.74</div><div>suggested: RRID:Addgene_22036)</div></div><div style="margin-bottom:8px"><div>pMD2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">G coat protein vector (Addgene plasmid #12259; both gifts from Didier Trono) were mixed with PEI at a 1:3 molar ratio and added to the 10 cm2 dish.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>#12259</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudotype Neutralisation assays: Pseudotyped lentiviral particles were generated by transfecting 3 × 106 293T cells in a 10 cm2 dish with a lentivirus backbone plasmid encoding a luciferase reporter gene (BEI: NR-52516 pHAGE-CMV-Luc2-IRES-ZsGreen-W), a plasmid encoding either the SARS-CoV Spike (pCAGGS-SARS-CoV-Spike_Urbani), SARS-CoV-2 Spike (BEI: NR-52514) or VSV glycoprotein (VSV-G; pMD2.G) and the packaging vectors HDM-Hgpm2 (BEI: NR-52517), HDM-tat1b (BEI: NR-52518) and pRC-CMV-Rev1b (BEI: NR-52519).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHAGE-CMV-Luc2-IRES-ZsGreen-W</div><div>suggested: RRID:Addgene_164432)</div></div><div style="margin-bottom:8px"><div>pCAGGS-SARS-CoV-Spike_Urbani</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pMD2 . G</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pRC-CMV-Rev1b</div><div>suggested: RRID:Addgene_164443)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">293T cells were transfected with either B9-WT or B9-Mut plasmid DNA and cell-surface expressed scFvs were tested for binding to purified SARS-CoV RBD (200 nM) using the standard staining protocol.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>B9-Mut</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The raw HDX-MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset: PXD032965.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PRIDE</div><div>suggested: (Pride-asap, RRID:SCR_012052)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Disruption of the B9-scFv knob domain: The sequence encoding B9-scFv was mutated in the BovShow cell surface expression vector; residues 123YNCRPAVWY131 of the B9-scFv knob domain (B9-WT) were replaced with the irrelevant amino acid sequence 123ETCYYGSGL131 by site-directed mutagenesis (B9-Mut) with Q5 polymerase (New England Bioloabs)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>New England Bioloabs</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The KD for interactions between cell surface scFvs and recombinant RBD proteins was estimated by non-linear analyses of the log(molarity)-response plots on GraphPad.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.04.06.487306
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.05.487240

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.487240: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.05.487240
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273058

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273058: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273058
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273361

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273361: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  A limitation of our model with rolling strains is that we only implement sterilizing immunity, as attenuating immunity poses some computational challenges. However, we can use the equivalence captured by Eq. 17 to find out what strains would have had similar effects using our second mechanism. A more general limitation is in assuming SIR equations throughout. More factors, both biological (incubation period, super-spreaders, etc.) and social (confinement, fear, social distancing, etc.), affect the empirical parameters from SARS-CoV-2 analyzed. Our charts should be taken as limit cases. It is noteworthy, however, that we can produce meaningful tools for a real, ongoing epidemic process—this should be furthered. Note also that most of these factors would slow viral spread compared to actual SIR processes. Thus, more accurate models should result in more lenient thresholds. The SARS-CoV-2 pandemic made explicit a very important limitation of SIR-like models: while they reveal overall trends and the existence of phenomena such as herd-immunity thresholds, they are useless to predict even the most salient aspects of a specific out-break (namely, its magnitude and duration) [10]. We explore our models with the same philosophy, avoiding specific predictions and seeking broad qualitative changes induced by cross-immunity. To overcome the problems of compartmental models, and allow us to apply them in more realistic situations, two strategies are being explored: (i) To produce more de...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273361
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273072

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273072: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">After that, we selected pregnant and postpartum women aged 10 to 55 years old with data regarding their CVD status.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Among the limitations of the study, we should consider that the completion of the notification system included information about the presence or absence of CVD in 39.58% of the notifications, with a high percentage of loss. The difficulty in population-based use was also portrayed by other researchers. In the USA, for instance, only 5.8% (7162) of 122653 cases reported to the CDC had information about health conditions (32). In addition, we found limitation on the type of CV, since the notification form does not allow etiological distinction and interpretation of access to ICU admission in Brazil. This is because only 15% of maternity hospitals in our country have adult ICU beds (33).
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273072
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273427

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273427: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: All recruited participants provided written informed consent.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Inclusion criteria: >18 years of age; confirmed diagnosis of COPD (GOLD 2020)(7); a severe COPD exacerbation in the previous 12 months and/or chronic hypercapnic respiratory failure or sleep disordered breathing meeting established criteria for home NIV/CPAP treatment; personal or close contact with daily smartphone, tablet or desktop computer internet access to a web browser; able to give informed consent.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GOLD</div><div>suggested: (GOLD, RRID:SCR_000188)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses were performed using R Studio version 4.0.5 and GraphPad Prism version 9.3.1, with significance assessed at the 0.05 level.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Whilst the lack of a randomised control arm is an important caveat, the control cohort derivation with an index date and outcome follow-up time period matched to RECEIVER participants reduces potential bias from seasonality and COVID-19 pandemic impacts on COPD event rates. Conclusions from this study have to be tempered by residual biases and confounders, including incomplete clinical information available for the control cohort and reduced integrity of matching for the control:DYNAMIC-SCOT comparison. Reduced event rates were seen in the control cohort across COVID-19 pandemic, this is in line with other investigations and suggests that this cohort is representative(26,27). The increased time to first events in the survival analyses and reduced median admission rates in the intervention cohorts provide a reassuring safety signal and encouraging hypothesis-generating utility data. The admission and community exacerbation event rates in the intervention cohorts provide further safety data: they are reduced when compared with historical NHS GG&C data, and similar to recent published data. It is therefore unlikely that reduced admission events in the intervention cohorts relate to delays from inappropriate community management, or that the intervention leads to unsupervised overuse of corticosteroid/antibiotic courses. The reduced median occupied bed day rate profiles in the intervention cohorts are particularly encouraging. COPD is estimated to consume €48.4 billion annually i...
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04240353</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">RECEIVER: Digital Service Model for Chronic Obstructive Pulm…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273427
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.05.22273169

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.22273169: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Broad ethnic groups were used: White, Asian, Black, Mixed and Other.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>White</div><div>suggested: RRID:MMRRC_037613-MU)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations: SARS-CoV-2 infections were identified based on a registered positive test. There was limited community testing availability during the first wave of infections and access to lateral flow tests were not available until late 2020 (6th November in Liverpool only, 3rd December rest of region). These issues may lead to missed infections that would not be reported in our data resulting in under-counts for previous positive tests. Not all individuals may get tested, nor register their test, leading to undercounts of infections in our measures. We attempted to account for some of these issues by restricting analyses to individuals who had registered a negative test in the month before due to established inequalities in testing uptake (29). The impact of this can be seen by comparing the models to analyses for all residents (e.g., Table 2 and Appendix Table C). We also report significant inequalities in who reported negative tests across our exposure variables (Appendix Table A) which may bias underlying associations. The range of bias we are unable to observe shows how difficult it is to investigate these phenomena using routine data, so our results should not be over-interpreted. Our analyses are descriptive and exploratory. We could not investigate the mechanisms that may underlie the associations we report (e.g., the processes that explain why social inequalities changed over time). We also are unable to account for all potential confounders or explanatory factors (e....
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.05.22273169
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273181

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273181: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethical considerations: This research is supported by the Ethics Committee from Universidad Tecnologica de Pereira (Comité de Bioética de la Universidad Tecnologica de Pereira), who gave the ethical approval (# 52-28062).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sample size calculation and sampling strategy: We calculated sample size with an expected frequency of 50%, an acceptable error of 5%, and a design effect of 1 for a population survey, of a minimum sample size of 384 participants.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses were conducted on IBM SPSS Statistics for Mac, Version 26.0.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Another limitation is the absence of data in regard to doses quantification and biomarkers of endocannabinoid response in individuals consuming cannabis having SARS-CoV2 positive or suspected infection, in order to compare effects among different populations, dosing quantification, doses-response relation, biological and sociodemographic characteristics. These considerations could be taken into account for future research under more rigorous experimental protocols. Despite our survey limitations, we can consider a reasonable amount of evidence pointing at the phytocannabinoids possible mechanisms to prevent contagion or attenuate symptoms severity. The SARS-CoV-2 initial contagion enters the host through spike proteins (SP) having a high affinity with angiotensin-converting-enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2). Both proteins are expressed in multiple tissues, especially in lung, urogenital and gastrointestinal tissue, and participate in the fusion of the virus envelope with the the target cells membranes through an endocytosis mechanism. Inside the cell, the mRNA virus is released, completing the transcription and translation process of the viral structures through the ribosome, packaged in the Golgi apparatus, and infecting the contiguous cells by exocytosis 12. Cytokine release syndrome is triggered by internalization of ACE2 and activation of angiotensin 2, which in turns activates the expression of KB nuclear factor, increasing proinflammatory cyt...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273181
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.04.487020

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.487020: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">When necessary, conversion of gene names to UniProt identifiers, or vice versa, was performed using BioMart [28].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BioMart</div><div>suggested: (biomaRt, RRID:SCR_019214)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">These networks were compiled as CSV files and loaded into the Cytoscape platform, version 3.8.2 [30].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Cytoscape</div><div>suggested: (Cytoscape, RRID:SCR_003032)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.04.487020
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273425

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273425: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Study design and patient population: This a case-control retrospective study in a New York City Health + Hospital acute care facility in the South Bronx, approved by the Institutional Review Board [IRB # 21-007].</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">The median age was 63 years with 56.1% being male and predominant Latinx (74.1%) followed by African-Americans (18.0%).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis was conducted using IBM SPSS Statistics 27 (IBM Corp., Armonk, NY, USA) software. Results: Of the 584 patients hospitalized with COVID-19 pneumonia from July 1, 2020, to Feb 20, 2021, 175/584 (29.9%) patients requiring 5 or more liters of supplemental O2 were screened for the study.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study had several limitations; firstly, this retrospective observational study included two groups of hospitalized COVID-19 pneumonia patients from two different timeframes (July-Dec 2020 and Jan-Feb 20, 2021). Though these groups had a similar distribution in demographic, baseline characteristics, and burden of the disease, we accept that there were confounders including “variants of concern” and mortality differences due to comparatively lesser burden of disease in the July-Dec timeframe. The study is also limited by sample size and generalizability. There was no standard length of therapy for the baricitinib-treated group and ranged from 3 to 10 days. The decision to stop baricitinib was at the discretion of the treating physician based on the patient’s clinical improvement. Thirdly we had two patients still hospitalized on mechanical ventilation, without a clear outcome, when the data was analyzed. Fourthly, the inherent limitations of retrospective studies, especially lack randomization, cannot be ignored, though we believe our encouraging results contribute to the therapeutic options for hospitalized severe COVID-19 patients till further robust data/evidence is available. Lastly, the lack of benefit in patients requiring mechanical ventilation could be due to the smaller sample size.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273425
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.03.22273268

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.22273268: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethics approval: The Institutional Review Board of the Clinical Research and Genome Research Committee at Yamanashi Central Hospital approved this study and the use of an opt-out consent method (Approval No. C2019-30).<br>Consent: Ethics approval: The Institutional Review Board of the Clinical Research and Genome Research Committee at Yamanashi Central Hospital approved this study and the use of an opt-out consent method (Approval No. C2019-30).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">WGS analysis was performed as previously described [21-23].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>WGS</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  There are, however, several limitations. TaqMan assays do not always accurately determine the sublineages in some situations. WGS analysis may be necessary when the characteristic mutations of newly-emerging strains or sublineages remain under investigation. It should also be noted that if mutations occur at the TaqMan probe or primer locations, the PCR amplification efficiency will be reduced and the signal will be attenuated, which may make interpretation difficult (Figure 3B). Our study showed that the TaqMan assay can be used to specifically detect Omicron viruses and classify subvariants. By applying this method to SARS-CoV-2-positive specimens, it is possible to analyze multiple specimens rapidly. Although accumulated data are still needed [8, 11, 14, 34], BA.1 and BA.2 show different susceptibilities to antibody and antiviral therapy. Rapid classification of Omicron sublineages may be clinically critical in providing appropriate treatment to patients with COVID-19.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.03.22273268
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.05.22273167

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.22273167: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Single-cell proliferation scores: Single-cell proliferation scores were calculated using a previously described approach58, which is based on the average normalised expression levels of a pre-selected set of 11 mRNA features related to cell cycle (AURKB, HMGB2, HMMR, MCM4, MKI67, PCLAF, PCNA, TK1, TOP2A, TYMS, and UBE2C), subtracted by the aggregated expression of a control set of 50 randomly selected mRNA features.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">This led to a significant reduction in the number of CD56br cells analysed and a concomitant reduction in statistical power to identify IL-2-induced alterations.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Red blood cells were then lysed (BD FACS Lysing solution) and immunostained samples were acquired on a BD Fortessa (BD Biosciences) flow cytometer with FACSDiva software (BD Biosciences) and analysed using FlowJo (Tree Star, Inc.).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FACSDiva</div><div>suggested: (BD FACSDiva Software, RRID:SCR_001456)</div></div><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Validation of Day 55 signature in the COMBAT dataset: To confirm the differential expression of Day 55 signature genes after COVID-19 infection, we applied DESeq2 to pseudo-bulk RNAseq data from the COMBAT dataset, comparing 13 community COVID-19 patients with 10 healthy controls.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>DESeq2</div><div>suggested: (DESeq, RRID:SCR_000154)</div></div><div style="margin-bottom:8px"><div>COMBAT</div><div>suggested: (ComBat, RRID:SCR_010974)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT02265809</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Adaptive Study of IL-2 Dose Frequency on Regulatory T Cells …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">ISRCTN40319192</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.05.22273167
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22271935

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22271935: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
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medrxiv.org/cgi/content/10.1101/2022.04.04.22271935
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https://biorxiv.org/cgi/content/10.1101/2022.04.05.487060

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.487060: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">Aminoadamantane and aminoadamantane nitrate drugs: Aminoadamantane nitrate compounds (blindly coded NMT2, NMT3, NMT5-NMT9, and NMT5-Met (metabolite, sans nitro group) were synthesized by and obtained from EuMentis Therapeutics, Inc. (Newton, MA), and have been described previously6–9, 33.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After incubation with secondary antibodies (IR-dye 680LT-conjugated goat anti-mouse [1:20,000; Li-Cor, 926-68020] or IR-dye 800CW-conjugated goat anti-rabbit [1:15,000; Li-Cor, 926-32211]), membranes were scanned with an Odyssey infrared imaging system (Li-Cor)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mouse</div><div>suggested: (LI-COR Biosciences Cat# 926-68020, RRID:AB_10706161)</div></div><div style="margin-bottom:8px"><div>anti-rabbit</div><div>suggested: (Santa Cruz Biotechnology Cat# sc-53804, RRID:AB_783976)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immunoprecipitants were eluted and subjected to immunoblotting with anti-ACE2 antibody (1:1000, Cell Signaling, #15983) and anti-SARS-CoV-2 Spike protein antibody (1:2000, Abcam, ab275759)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2 Spike protein</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Primary antibodies and dilutions were as follows: Mouse anti-TNFα (5 µg/ml, Abcam, #ab1793) and rabbit anti-macrophage inflammatory protein 1α (MIP-1α)/CCL3+CCL3L1 (1:250</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-TNFα</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-macrophage inflammatory protein 1α ( MIP-1α)/CCL3+CCL3L1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 30 min, all cells were collected and subjected to biotin switch-assay and immunoblotting with anti-ACE2 antibody to assess the levels of SNO-ACE2 and total input ACE2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-ACE2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>total input ACE2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cell lines: HEK293T (System Biosciences, LV900A-1) and HEK293-Spike cells (SARS-CoV-2 Spike (D614)-expressing 293 cells [293-SARS2-S cells, InvivoGen]) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with GlutaMAX™ (DMEM, high glucose, GlutaMAX™ Supplement, Life Technologies, 10566016) supplemented with 10% fetal bovine serum (FBS; Sigma, F7524), 100 IU/ml, and 100 µg/ml penicillin-streptomycin (Thermo Fisher Scientific, 10378016) at 37 °C in a 5% CO2 incubator.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>HEK293-Spike</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>293</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 virus generation: Monkey Vero E6 cells were plated in a T225 flask with complete DMEM containing 10% FBS, 1×PenStrep, 2 mM L-glutamine and incubated for overnight at 37 °C in a humified atmosphere of 5% CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HeLa-ACE2 cells were seeded in the assay-ready plates at 1.6×103 cells/well in assay medium, and plates were incubated for 24 h at 37 ℃ with 5% CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HeLa-ACE2</div><div>suggested: JCRB Cat# JCRB1845, RRID:CVCL_B3LW)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Homogenized lungs were titrated 1:10 over 6 steps and layered over Vero cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">. Monkey Vero E6 cells (ATCC CRL-1586) were maintained in complete DMEM (Corning, 15-013-CV) containing 10% FBS, 1×PenStrep (Corning 20-002-CL), 2 mM L-glutamine (Corning, 25-005-CL) at 37 °C in a 5% CO2 incubator. Plasmids: hACE2 was a gift from Hyeryun Choe (Addgene plasmid #1786; http://n2t.net/addgene:1786 ; RRID:Addgene_1786)46.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div></div><div>detected: RRID:Addgene_1786)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The C262A, C498A, C261/498A mutant ACE2 constructs were generated using the QuikChange Lightning Multi Site-Directed Mutagenesis Kit (Agilent Technologies, 210514) according to the manufacturer’s protocol. pGBW-m4252984 (SARS-CoV-2 E [envelope]) was a gift from Ginkgo Bioworks (Addgene plasmid #153898; http://n2t.net/addgene:153898; RRID:Addgene_153898).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div></div><div>detected: RRID:Addgene_153898)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">MLV-gag/pol, MLV-CMV-Luciferase, SARS-CoV-2, and VSV-G plasmids were a gift from David Nemazee</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>VSV-G</div><div>suggested: RRID:Addgene_138479)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Expression and purification of human ACE2 protein: The N-terminal peptidase domain of human ACE2 (residues 19 to 615, GenBank: BAB40370.1) was cloned into phCMV3 vector and fused with C-terminal His-tag.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>phCMV3</div><div>suggested: RRID:Addgene_173431)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In brief, HEK293T cells were transiently co-transfected with MLV-gag/pol, MLV-CMV-Luciferase plasmid, and SARS- CoV-2 Spike (D614) or VSV-G plasmid.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MLV-CMV-Luciferase</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For transient expression in HEK293T cells, we used a transfection reagent (Fugene® HD, Promega) to co-transfect plasmids containing cDNAs for SARS-CoV-2 E protein (pGBW-m4133502, Addgene) and green fluorescent protein (GFP) at a ratio of 1:0.1 (0.5:0.05 µg/well, respectively).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pGBW-m4133502</div><div>suggested: RRID:Addgene_153565)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Maximum intensity projection of images was generated, and fluorescence intensity was analyzed with ImageJ software (https://imagej.nih.gov/ij/download.html) as previously described50.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImageJ</div><div>suggested: (ImageJ, RRID:SCR_003070)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Molecular dynamics (MD) simulations were performed on the Frontera supercomputer at the Texas Advanced Supercomputing Center (TACC) using NAMD 2.1461 and CHARMM36m all-atom additive force fields62–64.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NAMD</div><div>suggested: (NAMD, RRID:SCR_014894)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Molecular Devices) with a 10× objective, and total live cells per well quantified in the acquired images using the Live Dead Application Module (MetaXpress).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MetaXpress</div><div>suggested: (MetaXpress, RRID:SCR_016654)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses were performed using GraphPad Prism software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.04.05.487060
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.04.486920

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.486920: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">flurochrome conjugated FACS anti mouse antibodies-CD16/32, CD4, CD8, CD19 (BD, USA), TMB substrate (BD, USA), HRP streptavidin (BioLegend, Switzerland), HRP Goat anti-mouse IgG antibody (BioLegend, Switzerland)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti mouse antibodies-CD16/32 , CD4</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD8</div><div>suggested: (BioLegend Cat# 391503, RRID:AB_2721611)</div></div><div style="margin-bottom:8px"><div>CD19</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-mouse IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The sera was stored at 0 C and later was used for antibody titer: IgG, IgG1, IgG2a. 2.2.3 Spleen and splenocyte isolation: Mice were sacrificed with light ether anesthesia.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgG1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgG2a . 2.2.3 Spleen</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The cells were then stained with 5μl of PE-antiCD4, FITC-A antiCD8 and FITC-A antiCD19 flurochrome tagged antibodies for 45 min at 4°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PE-antiCD4</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>FITC-A</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>antiCD8</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>antiCD19</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, IFN-gamma, TNF-alpha and IL-6 coating antibody was diluted in bicarbonate-carbonate buffer and coated on ELISA plate for overnight at 4°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IFN-gamma , TNF-alpha</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IL-6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">2.2 Methodology: 2.2.1 Immunization: 4-6 weeks female BALB/c mice purchased from RCC Laboratories India Private Limited were grouped as antigen alone (1μg/dose), MF59 either in combination with antigen alone or in combination with MPL-A and CpG ODN at varying concentration of 10, 20 and 30μg.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BALB/c</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The pellets so collected were resuspended in sheath fluid and cell population was quantified using BD FACSsuit software [8].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BD FACSsuit</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.04.04.486920
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22271489

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22271489: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethical Approval and Consent to Participate: The study received ethical clearances from two bodies: Kenya Medical Research Institute: Scientific and Ethical Review Unit (SERU) KEMRI/SERU/CGHR/05/05/4038: and Jaramogi Oginga Odinga Teaching and Referral Hospital (JOOTRH) Ethical Review Board (ERB) IERC/2030/2020.<br>Consent: Written consent was obtained from all participants before the process of data collection.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The four additional non-essential but preferred criteria include: high scores on SafeCare, preferably actively using M-TIBA, preferably participating/interested in Medical Credit Fund loan program and participating in PharmAccess MomCare program.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PharmAccess MomCare</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22271489
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273026

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273026: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IACUC: The study was reviewed and approved by Institutional Ethical Committee (# EC/08/20/1711) 2.2 Assay protocol: Blood samples were collected on three time points i.e., day-1 of admission, day-3 and day-5 or on the day of discharge if discharged before 5 days.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">2.3 Statistical analysis: Statistical analysis was performed using the SPSS version 17.0 program for windows (SPSS Inc., Chicago, IL, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Another technical limitation was that the ELISA kit used in the study though can detect antibodies against human uPAR1 isoform (full length and DIIDIII fragment), most of the alternate isoforms of human uPAR can go undetected. Different isoforms of suPAR may be induced by the diverse variants of SARS-CoV-2. Therefore, we intend further studying the presence of different uPAR isoforms, which will be able to shed important insights in COVID-19 pathogenesis.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04590794</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">SuPAR in Adult Patients With Covid-19</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273026
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273356

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273356: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study has many methodological limitations which we are well aware of. The main limitation is the retrospective design. Physicians were asked to provide data about patients taken care of during an emergency situation, when each of them volunteered with the overarching goal to care for patients in need and save lives. For this reason, collected data include only essential information to get an overall picture of COVID-19 patients’ clinical profile and outcomes. Much more information is needed however to describe in detail the clinical course of COVID-19 and its response to drug treatments, such as: time to recovery, drug doses and time of administration, the nature, duration and outcomes of any post-recovery sequelae, reasons for hospitalization and treatments received in hospital, etc. In addition, we lack any kind of control group, therefore results could be compared only and very cautiously with whole population official Italian data referring to about the same time periods and concerning COVID-19 lethality, but not directly compared according to age range and sex, or for different outcomes, e.g. admission to hospital. Finally, a small sample of doctors (10) took part in this first study, and nevertheless they were able to collect data about nearly 400 patients, which represents so far the largest sample of COVID-19 patients thoroughly investigated in Italy. All the participating doctors included only consecutive patients thus minimizing any possible selection bias. In c...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273356
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.03.22273370

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.22273370: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: The data is collected on a physical field sheet that is transferred to the lab after collection.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The 96-well plate is transferred to the Bio-Rad QX200 Droplet Reader which is prepared for analysis by using the Bio-Rad QuantaSoft software package version 1.7.4.0917.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>QuantaSoft</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.03.22273370
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273148

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273148: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In our simulations, we rely on the PRCC Matlab codes presented in [42].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Matlab</div><div>suggested: (MATLAB, RRID:SCR_001622)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22273148
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.05.487114

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.487114: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All the SARS-CoV-2 genomic sequences were collected in a month-wise manner (based on the sample collection month) from the Virus Pathogen Resource (ViPR) database [18].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ViPR</div><div>suggested: (vipR, RRID:SCR_010685)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We created an empty matrix with 30000 columns and 55759 rows using the NumPy module of Python.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NumPy</div><div>suggested: (NumPy, RRID:SCR_008633)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To make the visualization more effective, we represent the dendrogram with a heatmap using the pdist and squareform method of scipy library.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>scipy</div><div>suggested: (SciPy, RRID:SCR_008058)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All these analyses were performed in python.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Functional impacts of mutations: To investigate the effect of mutation on protein function, we used the widely popular PredictSNP web server [22] available at https://loschmidt.chemi.muni.cz/predictsnp/.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PredictSNP</div><div>suggested: (PredictSNP, RRID:SCR_006327)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">This web tool is composed of six different predictors, PhD-SNP, MAPP, SNAP, PolyPhen-1,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SNAP</div><div>suggested: (SNAP, RRID:SCR_007936)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SIFT and PolyPhen-2 to predict whether mutation is deleterious or neutral.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SIFT</div><div>suggested: (SIFT, RRID:SCR_012813)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PhD-SNP, MAPP, SNAP, PolyPhen-1,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PhD-SNP</div><div>suggested: (PhD-SNP, RRID:SCR_010782)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, SIFT and PolyPhen-2 apply support vector machine, physicochemical characteristics and protein sequence alignment score, neural network approach, expert set of empirical rules, protein sequence alignment score and naïve Bayes respectively [22].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PolyPhen-2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In addition to its own ΔΔG prediction, DynaMut also predicts ΔΔG using NMA based ENCoM (Elastic network contact model) [24] and, other structure-based predictors like mCSM [25], SDM [26] and DUET [27].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>mCSM</div><div>suggested: (mCSM, RRID:SCR_010776)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To calculate the nLMI of WT and MT proteins, we employed Python-based correlationplus 0.2.1 tool [33].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Python-based</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.04.05.487114
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273429

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273429: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: 11 Study isolates are collected in viral transport media and frozen following collection.<br>IRB: The study was approved by both the BU Charles River Campus Institutional Review Board and the BU Medical Campus Institutional Review Board.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">First, the presence of SARS-CoV-2 viral nucleic acid in the sample is determined by SARS-CoV-2 CDC N1 RT-PCR and second, 200 microliters of sample are incubated with Caco2 cells for 4 days.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Caco2</div><div>suggested: CLS Cat# 300137/p1665_CaCo-2, RRID:CVCL_0025)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Participants are asked to upload a photograph of the test strip at the time it is read into our REDCap database (version 12.1.1, Vanderbilt University), where study staff then interpret the results.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>REDCap</div><div>suggested: (REDCap, RRID:SCR_003445)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Finally, for the antigen RDT sub-study, we calculated the sensitivity and specificity of the Abbott BinaxNow compared to culture positivity at days 4 through 6 from diagnosis and plotted Ct values by day from diagnosis and RDT result.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Abbott</div><div>suggested: (Abbott, RRID:SCR_010477)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273429
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.05.487103

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.05.487103: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phylogenetic analyses: Genome sequences of reference SARS-CoV-2 strains (collected from GISAID and NCBI) belonging to different clades/variants circulating worldwide as well as representative strains from the study were aligned by multiple alignment program MAFFT version 7.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MAFFT</div><div>suggested: (MAFFT, RRID:SCR_011811)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phylogenetic analysis was done using Molecular Evolutionary Genetics Analysis (MEGA) version XI by maximum-likelihood method using the best fit statistical model general time reversal (GTR) with 1000 bootstrap replicates.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MEGA</div><div>suggested: (Mega BLAST, RRID:SCR_011920)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Further, we have refined the PatchDock output using the FireDock (https://bioinfo3d.cs.tau.ac.il/FireDock/) web server where the global energy value was depicted [22].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PatchDock</div><div>suggested: (PatchDock, RRID:SCR_017589)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.04.05.487103
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.04.487083

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.487083: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Human specimens: This study was approved by the Colorado State University Institutional Review Board under protocol number 20-10057H.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were washed and a secondary anti-human IgG-horseradish peroxidase conjugated secondary antibody was added.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG-horseradish</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, diluted sera were mixed with virus, incubated for one hour at 37°C, added to a Vero cell monolayer, incubated an additional hour at 37°C, then overlaid with tragacanth media and incubated for two days.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.04.487083
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.03.22273360

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.22273360: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The study was approved by the Colorado Multiple Institutional Review Board with a waiver of informed consent.<br>Consent: The study was approved by the Colorado Multiple Institutional Review Board with a waiver of informed consent.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">When mAb treated patients were missing a SARS-CoV-2 positive date (70.5%), we randomly imputed missing test dates from the distribution of observed time between SARS-CoV-2 to mAb administration.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations: This study has several limitations. The setting was a single health system and geographically limited to one US state with relatively low racial and ethnic minority representation, though it serves both urban and rural populations through academic and community hospitals. Even though we used statewide data for mortality and vaccination status, hospitalizations were collected only within one single health system. If mAb-untreated patients were less likely to be seen in this health system, hence more likely to be hospitalized elsewhere, this may bias our results toward the null. We also relied on EHR data, including manual chart reviews, which may have missing or inaccurate information about the presence of chronic conditions.[23] These factors might have limited our ability to detect the impact of sotrovimab treatment. We only collected 28-day hospitalization and mortality data, and therefore we do not know whether sotrovimab effectiveness extends to a longer period after SARS-CoV-2 infection. However, our prior study would suggest that 28-day and 90-day data are similar with respect to hospitalization and mortality endpoints.[7] In this study, propensity scoring achieved excellent matching between mAb-treated and mAb-untreated patient groups across multiple variables, but unmeasured confounders may remain. Our EHR data does not contain information on SARS-CoV-2 variants at the patient level. However, during Colorado’s Delta phase more than 99% of sequenced SARS-C...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.03.22273360
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22272960

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22272960: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22272960
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273344

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273344: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethical consideration: Ethical clearance was obtained from Saint Paul’s Millennium Medical College institutional review board (IRB).<br>Consent: Then, the chief executive director and the clinical director were communicated about the purpose of the study, and permission was obtained on behalf of patients to access the data.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Cases were selected consecutively, and two respective controls next to the sampled case were included randomly with replacement after confining all death records in their order of medical record number (MRN).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sample size and recruitment methods: The sample size was estimated using the double population proportion formula by the statcalc program of Epi info software, considering unmatched case-control study assumptions.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then, it was exported to SPSS software version 25 for analysis.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  This study has certain limitations. First, it would be nice to run a stratified analysis for each type of DM and differentiate among newly versus known diabetic patients, which is not the case in our study. It did not enable us to see the possible variation in the mortality and factors affecting it among the two groups (newly diagnosed and chronic DM). Second, the retrospective nature of the study would delimit the strength of evidence drawn from the study since data were not collected primarily for research purposes.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273344
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.04.486994

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.486994: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The mouse anti-Flag (M2, Sigma-Aldrich), and mouse anti-GAPDH (G8140, US Biological, Salem MA) antibodies were used in this study.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-GAPDH</div><div>suggested: (US Biological Cat# G8140-01L, RRID:AB_2278712)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 3 weeks of selection, expanded clones were examined for the expression of Flag-tagged nsp12 (RdRp) by western blot using anti-Flag antibody.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Flag</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Establishment of the Stable cell lines: Permissive HEK293 cells were transfected with RdRp-luciferase reporter and pcDNA3.1.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293</div><div>suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 24h, cells were selected using 250ug/mL G418 (for 293/RdRp cell lines) or 250ug/mL G418 and 25ug/mL hygromycin (for 293/RdRp-nsp5,7,8,12-Flag cell lines).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293/RdRp</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>293/RdRp-nsp5,7,8,12-Flag</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For relative viral genome quantification post infection and compound treatment, control or USA-WA1/2020 virus was added onto the Vero E6 cells plated in a 24-well plate (100,000 cells per well) for 2h (37 °C and 5% CO2).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Establishment of the Stable cell lines: Permissive HEK293 cells were transfected with RdRp-luciferase reporter and pcDNA3.1.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1</div><div>suggested: RRID:Addgene_79663)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The input samples and the IP samples were resuspended in 45μL of SDS-PAGE loading buffer and denatured at 95°C for 5 min, resolved by SDS-PAGE and western blotted onto a 0.45 μM nitrocellulose membrane using standard protocols (Bio-Rad Laboratories, Hercules, CA, United States).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Bio-Rad Laboratories</div><div>suggested: (Bio-Rad Laboratories, RRID:SCR_008426)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The absolute half-maximal inhibitory concentrations (IC50) of dasabuvir for SARS-CoV-2 USA-WA1/2020 and B.1.617.2 were calculated, based on the amounts of residual virus in the supernatant at each concentration, using the Graphpad Prism™. 2.8. Plaque Assay: Vero E6 cells (100,000 cells/well) in 1mL medium were seeded in a 24-well culture plate for 2h (37 °C and 5% CO2).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Graphpad</div><div>suggested: (GraphPad, RRID:SCR_000306)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses were performed using Prism 8.0 software (GraphPad Inc.).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Prism</div><div>suggested: (PRISM, RRID:SCR_005375)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.04.04.486994
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273117

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273117: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  We acknowledge study limitations. Baseline measures (at/or before testing) were subject to recall bias because they were not taken at the time of acute infection. We were unable to assess whether symptoms waxed and waned between testing and questionnaire. The CLoCk study response rate (13.4%)4 is typical of surveys of this type;33 additionally, our participants are largely representative of the target population as a whole.4 Nevertheless, the possibility of selection bias in both directions (CYP more likely to participate if they have persistent symptoms, or less likely to participate if too unwell) among respondents cannot be ruled out. Furthermore, as the background epidemiological situation in relation to SARS-COV-2 infection prevalence changes, there is a need to reassess possible differences in our model’s predictive value over time. Finally, caution is required for predictions based on data extrapolation/situations where there are only a very small number of observations for different predictor combinations. To our knowledge, no other study has explicitly aimed to develop a risk prediction model for experiencing impairing physical symptoms several months after SARS-COV-2 testing. Moreover, the majority of previous studies lack a SARS-CoV-2 test-negative comparison group and so distinguishing long-term symptoms predicted by SARS-CoV-2 infection from background rates or pandemic-related effects remains a challenge.5 More recent studies include control groups and, thus, br...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.01.22273117
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273330

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273330: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study had some strengths and limitations. Amongst the strengths we highlight the use of a nation-wide surveillance system to monitor SARS-CoV-2 infections which can capture dynamics of COVID-19 transmission at the municipal level, allowing for evaluation of vaccination status and clinical follow-up of all suspected, confirmed, and negative COVID-19 cases in Mexico within the SISVER registry. This allowed us to evaluate three relevant outcomes for VE, including SARS-CoV-2 infection, and COVID-19 related hospitalization and death at a national level27. Furthermore, by evaluating a national vaccination campaign which incorporated multiple vaccines we were able to assess the feasibility of incorporating multiple vaccines simultaneously to maximize vaccination coverage, which will also be helpful when evaluating policies to implement heterologous schemes for vaccine boosters in the future. Finally, by incorporating a time-varying component to the vaccination status, we were able to capture shifts in exposure risks through the follow-up time to allow for more precise estimates of vaccine effectiveness for all evaluated outcomes. We would also like to acknowledge some limitations which should be considered to adequately interpret our results. First, the SISVER dataset is a sentinel surveillance system, which is designed to evaluate high-risk symptomatic cases which are assessed and tested for COVID-1931; because of its design, SISVER primarily identifies cases with moderate to s...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273330
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273314

1
1. sciscore 08 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273314: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The protocol was approved by the medical ethics committees of all participating centres, and written informed consent was obtained from all patients.<br>Consent: The protocol was approved by the medical ethics committees of all participating centres, and written informed consent was obtained from all patients.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Study design and participants: The COVID-Compromise trial was a randomised, controlled, double-blind, multicentre, phase 3 trial to evaluate the effects of COVIG in severely immunocompromised patients hospitalised with COVID-19.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">All investigators, research staff, and participants were blinded to the allocated treatment until day 28, but unblinding was possible before day 28 when the primary endpoint was reached.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">With a power of 90% and a two-sided alpha of 5% and a single pre-planned efficacy interim analysis, a sample size of 86 participants was required.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273314
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22272997

1
1. sciscore 07 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22272997: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22272997
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273042

1
1. sciscore 07 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273042: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22273042
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273372

1
1. sciscore 07 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273372: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">A validated machine learning model facilitates efficient identification of randomized trials (21).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">Key methods included description of the randomization process and allocation concealment, blinding of patients and healthcare providers, extent of and handling of missing outcome data, blinding of outcome assessors and adjudicators, and prespecification of outcomes and analyses.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">We did not perform a sample size calculation since we included all eligible trial reports identified through our living SRNMAS up to August 3rd, 2021.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Eligible preprint and peer reviewed articles report trials that randomize patients with suspected, probable, or confirmed COVID-19 to drug treatments, antiviral antibodies and cellular therapies, placebo, or standard care or trials that randomize healthy participants exposed or unexposed to COVID-19 to prophylactic drugs, standard care, or placebo.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antiviral</div><div>suggested: (Antibodies-Online Cat# ABIN753133, RRID:AB_11206991)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To assess risk of bias, reviewers, following training and calibration exercises, use a revision of the Cochrane tool for assessing risk of bias in randomized trials (RoB 2.0) (22) (Supplement 3).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Cochrane tool</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengths and limitations: The strengths of this study include the comprehensive search for, and inclusion of preprint and published COVID-19 trial reports and rigorous data collection. The generalizability of our results is, however, limited to COVID-19. Journals have expedited the publication of COVID-19 research and have been publishing more prolifically on COVID-19 than in other areas, which may reduce opportunity for revisions between preprints and their subsequent publications and may mean time to and predictors of publication may be different than in other research areas. Although the WHO COVID-19 database is a comprehensive source of published and preprint literature, it does not include all preprint servers—though preprint servers not covered by our search address other subjects and are unlikely to include COVID-19 trials. It is likely that preprint reports of trials that are subsequently published in journals represent the most rigorous or transparently reported preprints and that they are not representative of all trial preprints. To assess preprint trustworthiness, we compared reporting of key aspects of the methods and results between preprint and published trial reports. We acknowledge, however, that published trial reports may still contain errors and that posting trial reports as preprints may allow more errors to be identified prior to final publication. We report on the number of publications and preprints that were retracted. Preprints, however, may be less...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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medrxiv.org/cgi/content/10.1101/2022.04.04.22273372
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.04.486975

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.486975: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IACUC: The protocol was approved by the Georgia State University Institutional Animal Care and Use Committee (Protocol number A20044).<br>Euthanasia Agents: In independent experi-ments, mice were inoculated with PBS (Mock) or SARS-CoV-2 intranasally, and on days 3 and 5-7 after infection, animals were anesthetized using isoflurane and perfused with cold PBS.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Roughly equal numbers of male and female mice were used.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To titrate the infectious virus, tissue homogenates were 10-fold serially diluted with DMEM and applied to monolayered Vero E6 cells for 1 hour.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: RRID:CVCL_XD71)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Hemizygous K18-hACE2 mice (2B6.Cg-Tg (K18-ACE2)2Prlmn/J) were obtained from The Jackson Laboratory.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>K18-hACE2</div><div>suggested: RRID:IMSR_GPT:T037657)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Eight-week-old hemizygous K18-ACE2 mice were inoculated intranasally with PBS (mock) or 104 plaque-forming units (PFU) of SARS-CoV-2 as described previously [8,21,22].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>K18-ACE2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Infectious virus titration by plaque assays: Tissues harvested from virus-inoculated animals were weighed and homogenized in a bullet blender (Next Advance, Averill Park, NY, USA) using stainless steel or zirconium beads, followed by centrifugation and titration.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Tissues</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical Analysis: GraphPad Prism 8.0 was used to perform a Kaplan Meier log-rank test to compare survival curves.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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Visit annotations in context

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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.04.486975
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22272975

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22272975: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: All study subjects gave written informed consent prior to inclusion in the study.<br>IRB: The study was approved by the Clinical Ethics Committee of the Flinders Medical Centre using de-identified diagnostic sera (approval number 39.034)</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Proteomic profiling serum anti-PF4 antibodies: As denoted in the proteomics workflow (Figure 1A)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-PF4</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, bead-purified anti-PF4 antibody fraction and unbound fractions using ELISAs coated with individual PF4, SARS-CoV-2 spike S1 and S2 proteins (the Native Antigen Company, UK) at 4 μg/ml., purified anti-PF4 IgGs were then separated by SDS-PAGE; heavy- and light-chain bands excised for in-gel digestion with trypsin and chymotrypsin, respectively; and analysis of peptides performed in a state-of-the-art Thermo Orbitrap Fusion Lumos Tribrid mass spectrometer with peptide de novo sequencing and IMGT database matching performed by Peaks Studio XPro as detailed previously 15 with modifications.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-PF4 IgGs</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22272975
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273384

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273384: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The ethics committee of the medical faculty of the University of Duisburg-Essen approved the analysis of data for the improvement of diagnostic procedures (20-9512-BO).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 Assay (Abbott, Wiesbaden, Germany), Abbott RealTime SARS-CoV-2 assay (Abbott, Wiesbaden, Germany)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Abbott</div><div>suggested: (Abbott, RRID:SCR_010477)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">3, SPSS Inc., Chicago, IL, USA) and GraphPad Prism 6.0 (GraphPad, CA, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  This analysis has some limitations. We have no data on patient symptoms (including severity and time of onset) and some of the cases may have been diagnosed before as SARS-CoV-2 positive, prior to admittance. However, our data provide a valuable insight on the dynamic of viral shedding of SARS-CoV-2. To date, more than 5 billion COVID-19 tests have been performed worldwide since the beginning of the pandemic 1. The gold standard for SARS-CoV-2 diagnostics is the real-time PCR 11. It requires specialized equipment and personnel, is expensive and due to rapid increase in its use shortages in reagents have been observed. In an effort to reduce PCR testing and thus preserve resources, rapid SARS-CoV-2 tests have been recommended as an alternative in many but not all cases 2,5. Notwithstanding the concerted effort to reduce PCR testing, it has been our experience that testing in ours and other hospitals is more rigorous and less uniform in different departments than official national recommendations (see Introduction). A negative PCR result is more often than not necessary to release a patient from isolation, health care personnel can resume their duties with a negative or low positive (Ct>30) PCR result. Adapting the testing PCR strategy according to previous Ct values could be a way to save laboratory and personnel resources. It could be also used to manage hospital resources (personnel, bed capacity) more efficiently.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273384
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22272731

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22272731: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

Annotators

sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22272731
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.03.22273355

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.22273355: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Renal function was calculated by estimating glomerular filtration rate (GFR) by using Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation.22 2.2 Ethics: The study was approved by the Institutional Review Board at the VACHS.<br>Consent: Written informed consent was obtained from each participant.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">2.3 Evaluation of anti-SARS-CoV-2 neutralizing antibodies: Sera were tested for neutralization activity against SARS-CoV-2 using a single cycle infectivity assay with Spike-pseudotyped virus particles as described previously.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">These pseudotyped particles were titered on 293T-hACE2 cells seeded in 96 well plates.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T-hACE2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Curve-fitting using GraphPad PRISM was employed to calculate the neutralization titer half-maximal inhibitory concentration (IC-50 value) for each sample at each time-point.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>PRISM</div><div>suggested: (PRISM, RRID:SCR_005375)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">2.5 Visualizations: All univariate association figures were created using the Python package seaborn.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  This study has some important limitations. Our sample size is relatively small, and similar clinical correlations in larger samples may better inform vaccine responses based upon select clinical variables. We evaluated the neutralizing antibody titers over a six month time period after completion of the primary vaccine series. Evaluation beyond that time point in individuals who did not receive the booster dose may reveal further associations between clinical variables and duration of response. Similarly, we defined strength of the response based on the highest level of IC-50 obtained by each individual. Since the time-points when we collected samples were predetermined, it is possible that the true peak response occurs before or after the 1 month time-point. While this may affect the fold-change values, it will likely not alter the correlation of strength of response with clinical factors. Another limitation of our study is that we excluded subjects from statistical analysis if they had known history of COVID-19 before vaccination. The number of these subjects in our study was too small (13) to conduct multiple regression analysis. Further investigation of clinical factors that associate with vaccine responses in individuals with prior SARS-CoV-2 infection would be valuable, especially when compared with those who were not previously infected. Lastly, this work does not include memory B-cell and memory T-cell responses and how those correlate to clinical factors and IC-50 va...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.03.22273355
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22272848

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22272848: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Study Approval: All secretion samples were obtained under the auspices of research protocols approved the Stanford Institutional Review Board (IRB) (Stanford IRB approval #28205, #53685, #55650, #37232, and #43805).<br>Consent: Samples were collected after written informed consent from patients or their surrogates prior to inclusion in the study.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Histology quantification: 150 500 pixel x 500 pixel regions of interest (ROIs) were randomly sampled from each tissue section imaged with the Aperio (Leica) AT2 Digital Pathology whole slide scanner.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Rabbit anti-versican antibody, clone EPR12277 (ab177480; Abcam) and rabbit anti-TSG-6 antibody (ab204049; Abcam) were used at 1:50 dilution.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-versican</div><div>suggested: (Abcam Cat# ab177480, RRID:AB_2827732)</div></div><div style="margin-bottom:8px"><div>anti-TSG-6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For figure 3 and supplemental figures, most of the lung tissue samples from healthy, COVID-19 ARDS, and non-COVID-19 ARDS groups were obtained in collaboration with clinical partners at University of Texas Health Science Center at Houston (HSC-MS-15-1049 and HSC-MS-08-0354) and Houston Methodist Hospital (Pro00003392).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HSC-MS-15-1049</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>HSC-MS-08-0354</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Slides were scanned in bright-field at a 20× objective and the digital images imported for analysis using the Aperio Imagescope v12.4.3.5008 viewing software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Imagescope</div><div>suggested: (ImageScope, RRID:SCR_014311)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The RGB image was deconvolved into its hematoxylin and DAB components using the algorithm from (77), implemented in the rgb2hed function in the scikit-image Python package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  These studies have several limitations. Most notable is the small numbers of cases and samples of secretions involved. These findings need to be confirmed in larger, multi-center studies involving individuals with diverse backgrounds and case presentations. The underlying mechanisms that lead to increased HA would also benefit from further research to identify the causative cell types and signalling pathways. In addition, data in SARS-CoV-2 animal models would enable improved understanding of the contribution of HA to pathogenesis in this disease. Finally, to safely acquire the rheology data, the COVID-19 samples were heat treated to render the samples non-infectious. In control CF samples, this same heat treatment was found to decrease the modulus (Supplemental Figure 4A), presumably due to the denaturation of biopolymers in the sample. Since we observed that higher modulus samples had larger responses to enzymatic treatment, the true effect of enzymatic treatment on COVID-19 lung secretion may be larger than that reported here using heat-treated samples. Future studies should further evaluate a range of enzymatic treatment dosages and durations to assess the rheological effects on non-heat-treated COVID-19 lung secretions. Additionally, the necessity of using induction to collect healthy sputum is a limitation. These studies may inform the development of much needed therapeutics for patients with COVID-19. Indeed, a study of oral hymecromone as a potential tool for HA inhib...
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04359654</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Nebulised Dornase Alfa for Treatment of COVID-19</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04541979</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Aerosoliserat DNase for Treatment of Respiratory Failure in …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT02780752</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Study of Oral Hymecromone and Hyaluronan Synthesis</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22272848
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.04.22273385

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.04.22273385: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data: We use data from the publicly-available United States multiple cause of death files, from the National Vital Statistics System division of the National Center for Health Statistics (https://www.cdc.gov/nchs/data_access/vitalstatsonline.htm#Mortality_Multiple), and yearly population estimates compiled by the Surveillance, Epidemiology, and End Results Program (https://seer.cancer.gov/popdata/download.html).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>End Results Program</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The code, and all harmonized input and output data pertaining to our analysis, is hosted both on Zenodo (a general-purpose open-access repository developed under the European OpenAIRE program and operated by CERN) at https://zenodo.org/record/6402403, and on GitHub https://github.com/jmaburto/ex_USA_racial-ethnic_differences.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Zenodo</div><div>suggested: (ZENODO, RRID:SCR_004129)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.04.22273385
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.03.22272610

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.22272610: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Participants gave written informed consent.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengths and Limitations: This is the largest longitudinal study to-date of cardiac impairment in Long COVID with detailed biochemical and imaging characterisation of multi-organ function starting in April 2020. We included healthy, age-matched controls. All MRI was non-contrast. We recruited a real-world cohort at lower risk of COVID-19 severity and mortality. Unlike other studies(10), our approach offers quick, scalable assessment using standard MRI scanners. There are limitations. First, our CMR protocol excluded gadolinium contrast due to concerns regarding COVID-19-related renal complications, relying on native non-invasive T1 mapping to characterise myocardial inflammation, validated for acute myocarditis(31). Second, we did not have follow-up scans on individuals without impairment at baseline. Third, we did not have pre-COVID cardiac or multi-organ imaging available in participants. Third, our study population was not ethnically diverse, and COVID-19 has disproportionately affected non-white individuals. Conclusion: CMR shows that cardiac impairment persists in Long Covid in some individuals up to 12 months after first symptoms. Cardiac impairment is associated with acute COVID-19 hospitalisation and male gender, but subtypes of disease (based on symptoms, examination, and investigations) are yet to be established. Therapeutic options and effective clinical pathways require urgent clinical trials.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04369807</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Mapping Organ Health Following COVID-19 Disease Due to SARS-…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.03.22272610
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.03.486854

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.486854: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: Data collection, structure determination, and refinement: The X-ray diffraction data were collected at the beamlines BL18U (RBD-Fab2303) and BL02U (Fab2212) of the Shanghai Synchrotron Research Facility.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Authentication: Immunofluorescence imaging and analysis: For viral nucleocapsid detection in Vero-TMPRSS2 cells by immunofluorescence, cells were washed twice with PBS x1 and fixed in 4% formaldehyde for 30 min at RT.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The plates were then washed 3 times with washing buffer before adding secondary anti-IgG (Jackson ImmmunoResearch) antibody conjugated to horseradish peroxidase (HRP) diluted 1:5000 in blocking buffer, and incubation for 1 h at RT.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-IgG</div><div>suggested: (Vector Laboratories Cat# FI-5000, RRID:AB_2336128)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Monolayers were observed for at least 4 days for appearance of CPE and then fixed as above and stained with antibody against SARS-CoV-2 Nucleocapsid.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibody against SARS-CoV-2 Nucleocapsid.</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Fixed cells were washed with PBS x1 and permeabilized for immunofluorescence using BD Cytofix/Cytoperm according to the manufacturer’s protocol for fixed cells, and then stained for SARS-CoV-2 with a primary nucleocapsid antibody (GeneTex GTX135357) and a secondary anti-rabbit AF647 antibody (ThermoFisher A20185), The nuclei were counterstained with Sytox Green.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-rabbit AF647</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Expression and purification of soluble RBD, spike and antibodies for crystallization: SARS-CoV-2 RBD (residues Arg319 to Lys529) was expressed by using the Bac-to-Bac Baculovirus System (Invitrogen)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Lys529</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Supernatant containing S2P was collected four days after transfection, S2P was affinity purified by anti-Flag antibody beads and was eluted by 0.1 mg/mL 3×Flag peptide in 20 mM HEPES at pH 7.6 and 150 mM NaCl.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Flag</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK-293 cells stably expressing hACE2 were seeded into 0.1% gelatin-coated 96-well plates (Greiner) at an initial density of 0.75 × 105 cells per well.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK-293</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Virus titers were validated using a combination of fluorescent focus assay and tissue culture infectious dose (TCID)50 assays on Vero-TMPRSS2 and Calu-3 (ATCC) monolayers.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Calu-3</div><div>suggested: KCLB Cat# 30055, RRID:CVCL_0609)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For TCID50 assays, Vero-TMPRSS2 or Calu3 cells were infected as above and 100µL DMEM or MEM with 2% FBS was subsequently added per well.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Calu3</div><div>suggested: RRID:CVCL_EQ19)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immunofluorescence imaging and analysis: For viral nucleocapsid detection in Vero-TMPRSS2 cells by immunofluorescence, cells were washed twice with PBS x1 and fixed in 4% formaldehyde for 30 min at RT.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero-TMPRSS2</div><div>suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The S2P or S6P pCMV plasmids were used to transiently transfect HEK293F cells with polyethylenimine (PEI) (Polysciences, #24765).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293F</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Expression and purification of soluble RBD, spike and antibodies for crystallization: SARS-CoV-2 RBD (residues Arg319 to Lys529) was expressed by using the Bac-to-Bac Baculovirus System (Invitrogen)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2 RBD</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data collection, structure determination, and refinement: The X-ray diffraction data were collected at the beamlines BL18U (RBD-Fab2303) and BL02U (Fab2212) of the Shanghai Synchrotron Research Facility.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RBD-Fab2303</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody inhibition of hACE2 binding to cell-expressed spike: Expi293F cells were transfected with pcDNA 3.1 containing SΔC19 of wild type, Alpha, Beta, or Delta variants, using the ExpiFectamine 293 Transfection Kit (Thermo Fisher).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA 3.1</div><div>suggested: RRID:Addgene_20407)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudo-particle preparation and neutralization assays: SARS-CoV-2-spike pseudo-particles were obtained by co-transfecting Expi293F cells with pCMV delta R8.2, pLenti-GFP (Genecopoeia), and pcDNA 3.1 SΔC19 (Thermo Fisher) at a ratio of 1:2:1, respectively, according to the manufacturer’s instructions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCMV</div><div>suggested: RRID:Addgene_16459)</div></div><div style="margin-bottom:8px"><div>pLenti-GFP</div><div>suggested: RRID:Addgene_172394)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">RBD containing the gp67 signal peptide and a C-terminal 6×His tag was inserted into pFastBac1 to form the plasmid pFastBac1-RBD.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pFastBac1</div><div>suggested: RRID:Addgene_1956)</div></div><div style="margin-bottom:8px"><div>pFastBac1-RBD</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Fixed cells were washed with PBS x1 and permeabilized for immunofluorescence using BD Cytofix/Cytoperm according to the manufacturer’s protocol for fixed cells, and then stained for SARS-CoV-2 with a primary nucleocapsid antibody (GeneTex GTX135357) and a secondary anti-rabbit AF647 antibody (ThermoFisher A20185), The nuclei were counterstained with Sytox Green.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BD Cytofix/Cytoperm</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data were logged from the Incucyte analysis modules and graphed with GraphPad Prism 8.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SerialEM was used for the data collection.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SerialEM</div><div>suggested: (SerialEM, RRID:SCR_017293)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The CTF parameters of the micrographs were determined by using the program Gctf with local defocus variations taken into consideration59.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Gctf</div><div>suggested: (GCTF, RRID:SCR_016500)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">90569 particles were picked by Gautomatch and then were subjected to 2D classifications with RELION 3.0.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RELION</div><div>suggested: (RELION, RRID:SCR_016274)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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Visit annotations in context

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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.03.486854
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.03.486830

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.486830: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: COVIDITY study is a prospective observational serial sampling study of whole blood to observe the evolution of SARS-CoV-2 infection to characterize the host response to infection over time in peripheral blood (ethics approval obtained from the Health Research Authority, South Central Oxford C Research Ethics Committee).<br>Consent: Samples from patients with moderate COVID-19 admitted to hospitals in London (Hammersmith Hospital, Charing Cross Hospital, Saint Mary’s Hospital) and eligible to participate in the MATIS trial61 provided consent (ethics approval by the Health Research Authority,</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The antibodies used in the stainings were the following: CD14 (61D3, eBioscience), CD3 (UCHT1, BD), CD19 (HIB19, BD), CD1c (L161, Biolegend),</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD14</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD19</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD1c</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>L161</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The antibodies used for intracellular staining were the following: H3K27Ac, H3K9Me2, H3K4Me3, H3K27Me3 (all from Cell Signaling Technology), TNF (Mab11, Biolegen) and IL-10 (JES3-907, Thermo Fisher Scientific)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>H3K4Me3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>H3K27Me3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Mab11</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IL-10 ( JES3-907</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Intracellular staining of puromycin was performed using the anti-puromycin monoclonal antibody (1:600 dilution, clone R4743L-E8) for 45 minutes at 4 ºC.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-puromycin</div><div>suggested: (Rafael Jose ArgÃ¼ello - Dendritic cell laboratory, Centre dÂ´Immunology de Marseille Luminy Cat# R474, RRID:AB_2827926)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Generation of virus stocks: SARS-CoV-2 virus (SARS-CoV-2/England/IC19/2020 isolate, kindly provided by Wendy S Barclay) was expanded in Vero-E6 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero-E6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Titration of virus stocks: For SARS-CoV-2 titration, samples were serially diluted in OptiPRO SFM, 2X GlutaMAX (1:10) and added to Vero cell monolayers for 1 hour at 37 °C, 5% CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For CCCoV titration, viral supernatants were serially diluted in DMEM, non essential amino acids (1:10) and added to MRC-5 (229E strain),</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MRC-5</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">BSC-1 (OC43 strain) or LLCMK2 (NL63 strain) cell monolayers for 1 hour at 37 °C, 5% CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BSC-1</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Samples were run on a Fortessa instrument (BD Biosciences) and analyzed using FlowJo v.10.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, reads were aligned to the reference genome (GRCh38.99) using STAR v2.7.366 in the two-pass mode (ENCODE recommended parameters) and gene expression was quantified using featureCounts67.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>STAR</div><div>suggested: (STAR, RRID:SCR_004463)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mapping statistics and quality control metrics from FastQC and RNA-SeQC68 indicated high data quality for all samples with no outliers detected.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FastQC</div><div>suggested: (FastQC, RRID:SCR_014583)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Principal component analysis (PCA) with the prcomp function was used to explore the relationship between samples, after the filtered gene counts were transformed using a regularized log transformation from the DESeq270 package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>DESeq270</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Differential gene expression analysis was carried out using DESeq2, comparing unstimulated monocytes from COVID-19 patients (n=10) to unstimulated monocytes from healthy controls (HC) (n=6), and SARS-CoV-2-stimulated monocytes from COVID-19 patients (n=14) to stimulated monocytes from HC (n=12).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>DESeq2</div><div>suggested: (DESeq, RRID:SCR_000154)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pheatmap package was used to draw heatmaps illustrating variation in gene expression across samples.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Pheatmap</div><div>suggested: (pheatmap, RRID:SCR_016418)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We tested for enrichment of this gene set in the COVID-19 versus healthy contrasts using the geneSetTest function and barcodeplot functions from limma.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>limma</div><div>suggested: (LIMMA, RRID:SCR_010943)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cultures were subsequently stained with CD3 (UCHT1, BD Biosciences), CD20 (H1, BD Biosciences), CD14 (M5E2, Biolegend), CD16 (B73.1, BD Biosciences), phospho-IRF3 (Ser 396, Bioss), phospho-NFkB p65 (Ser 529, BD Biosciences) in PBS for 1 hour at room temperature, washed with PBS and resuspended in 250 µl PBS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BD Biosciences</div><div>suggested: (BD Biosciences, RRID:SCR_013311)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.03.486830
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22272714

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22272714: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: Sample Collection and Processing: Blood samples were collected into serum separation tubes (SST(tm), BD) and acid–citrate–dextrose tubes (ACD, BD).<br>IRB: Significance was set as *p <.05; **p <.01; ***p <.001; ****p <.0001. Ethics: RECOVER protocols were approved by the Research Ethics Board (REB) at the CHU Sainte-Justine (CHUSJ) under study MP-21-2021-3035 and in each of the five participating centers in the Province of Québec.<br>Consent: Written informed consent was obtained from all participants during the recruitment period, and ongoing consent was reviewed at each subsequent visit.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Participants who were symptomatic during infection (n=26) were randomly selected from the rest of the RECOVER cohort based on their serostatus at enrollment after being matched with participants from the asymptomatic group for sex, age, time since infection and time between infection and vaccination.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Laboratory.23 Absence of previous infection to SARS-CoV-2 was confirmed in the naïve cohort by performing an ELISA detecting specific IgG antibodies for the Nucleoprotein (anti-N) of SARS-CoV-2 and the anti-RBD ELISA before vaccination.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-N</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-RBD</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The residual infectivity of those mixtures was assessed in quadruplicate wells of African green monkey kidney E6 cell line (Vero ATCC® CRL-1586™)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: ATCC Cat# CRL-1586, RRID:CVCL_0574)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FlowJo software, version 10.7.1, was used to perform all data analysis.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistics: All statistical tests were performed using Prism 9, version 9.2.0 (2021 GraphPad Software, LLC) and data were displayed as mean ± SEM. Wilcoxon-Mann-Whitney or Kruskal-Wallis tests were used to evaluate statistical significance between groups for variables that did not follow a normal distribution.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations: Results of this study were obtained from a cohort of primarily middle-aged Caucasian females infected with SARS-CoV-2 eight months before vaccination. It remains to be evaluated if a shorter time between infection and vaccination will lead to similar results. Our study is also limited by a relatively small sample size of participants who did not experience symptoms during their initial infection. It will be essential to validate our findings in a larger population of subjects, as immune responses to SARS-CoV-2 are known to be highly heterogeneous. Furthermore, the protection induced by booster doses against VOCs in previously infected individuals remains to be evaluated. This study did not assess the impact of other approved adenovirus or mRNA vaccines against SARS-CoV-249,50, as primary series or boosters, as well as natural infection with emerging SARS-CoV-2 VOCs, as most of the cohort was infected at the beginning of 2020.51 Finally, the immunity score may underestimate the quality of the immune memory generated in recovered individuals since it is limited to three of the most standardized assays to interrogate immune response to SARS-CoV-2. Detailed functional, transcriptomic and repertoire analyses will be essential to fully grasp the immune memory differences between individuals who experienced symptoms or not following infection.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22272714
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.02.486748

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.02.486748: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After blocking, bone marrow cells were stained with CD3 Monoclonal Antibody (UCHT1), PE-Cyanine7, eBioscience™ (25-0038-42) 1:100 for 20 minutes at 4 °C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD3</div><div>suggested: (Thermo Fisher Scientific Cat# 25-0038-42, RRID:AB_1582253)</div></div><div style="margin-bottom:8px"><div>UCHT1</div><div>suggested: (Thermo Fisher Scientific Cat# 25-0038-42, RRID:AB_1582253)</div></div><div style="margin-bottom:8px"><div>25-0038-42</div><div>suggested: (Thermo Fisher Scientific Cat# 25-0038-42, RRID:AB_1582253)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Optimizing Archetypes and Cell Assignments: The objective function for kernel archetype analysis involves optimizing the non-convex product AB, and thus has many local minima.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>AB</div><div>suggested: RRID:BDSC_203)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SVD for scATAC-seq: We used the ArchR package23 for preprocessing of sc-ATAC data.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ArchR</div><div>suggested: (ArchR, RRID:SCR_020982)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Peak calling: Peak calling was performed using ArchR23.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ArchR23</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SVD was used as input to cluster the data using phenograph and visualize using umaps.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>phenograph</div><div>suggested: (Phenograph, RRID:SCR_016919)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Metacell raw counts for different datasets were determined as described in the “Metacell identification” section.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Metacell</div><div>suggested: (Metacell, RRID:SCR_017013)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We then computed a second aggregated gene expression using the single-cell groups from ATAC modality instead of the RNA modality.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ATAC</div><div>suggested: (Atac, RRID:SCR_015980)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Metacells methods comparison: Baran et. al. MetaCell: MetaCell9 approach uses a non-parametric graph algorithm to partition scRNA-seq data into distinct metacells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MetaCell9</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The “c7: immunologic signature” gene sets from Molecular Signature Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/index.jsp) was used.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>http://software.broadinstitute.org/gsea/msigdb/index.jsp</div><div>suggested: (Molecular Signatures Database, RRID:SCR_016863)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.02.486748
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.01.486788

1
1. sciscore 06 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.486788: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Authentication: Fluorescent staining of human tonsil: Multiplex immunolabeling on FFPE human tonsil sections was performed by sequential IF staining on COMET™ using the FFeX technology previously described by Lunaphore Technologies13, 20.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">DNA oligos and antibody-derived DNA tags: DNA oligos used were all synthesized by Integrated DNA Technologies with HPLC purification.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibody-derived DNA</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody-derived DNA tags for membrane proteins were purchased from Biolegend and listed in Table S5.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Antibody-derived DNA tags</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The product was purified with 1.6X SPRI beads and then quantified with QuBit and BioAnalyzer.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BioAnalyzer</div><div>suggested: (BioAnalyzer 2100, RRID:SCR_019715)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data preprocessing: For cDNAs derived from mRNAs, the raw fastq file of Read 2 containing the UMI, barcode A and barcode B regions, were first reformatted into the standard input format required by ST pipeline v1.7.2 21 using customized python script.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Using recommended ST pipeline parameters, the read 1 was STAR mapped to either the mouse genome (GRCm38) or the human genome (GRCh38).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>STAR</div><div>suggested: (STAR, RRID:SCR_004463)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All the heatmap was plotted using ggplot2. scRNA-seq and spatial data integration: The cell types of skin biopsy section were annotated through integration analysis using the matched scRNA-seq data as the reference.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ggplot2</div><div>suggested: (ggplot2, RRID:SCR_014601)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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Annotators

sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.01.486788
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273111

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273111: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses: Data processing and analyses were conducted using SAS version 9.4 (SAS Institute, Cary, NC).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SAS Institute</div><div>suggested: (Statistical Analysis System, RRID:SCR_008567)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  When using our results to inform prioritization of services, or to develop clinical prediction tools, we must consider these limitations so that other at-risk patients do not fall through the cracks. Finally, to provide insights on shared predictors of mortality in the context of a novel, emerging pathogen, we purposefully restricted the study period of SARS-CoV-2 to exclude hospitalizations of patients vaccinated against SARS-CoV-2, or those with SARS-CoV-2 variants. Future work would benefit from comparisons of predictors of mortality among patients hospitalized with influenza, RSV or SARS-CoV-2 variants and/or breakthrough infections to determine whether shared and divergent trends remain. Our results add to the growing literature base comparing similarities and differences in clinical disease progression of patients hospitalized with influenza and SARS-CoV-2 [42–44], and have three important implications for clinical care and health systems. First, shared predictors of mortality could be used to identify, target, and prioritize hospitalized patients who are at greatest risk of death for prevention (e.g. vaccines), testing (e.g. rapid tests) and therapeutics (e.g. antivirals). Second, the underlying prevalence of shared predictors in a given geography could help prepare health systems for, and efficiently allocate health resources during, times of peak respiratory infection transmission. Finally, differences in observed predictors of mortality across the three viruses sign...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273111
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.02.22273333

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.02.22273333: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Written informed consent was obtained from all study participants.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody titers are expressed as arbitrary units (AU)/ml, except for anti-WT IgG, which are expressed in the WHO-standard binding antibody units (BAU)/ml.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-WT IgG</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, heat-inactivated serum was 3-fold serially diluted, mixed with virus, incubated for 1 hour and finally added, in duplicates, to confluent Vero E6 cells in 96-well plates.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PCR, whole genome sequencing (WGS) and virus isolation was performed as previously described [19].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>WGS</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mann-Whitney U test was performed for comparisons of antibody titers between groups, peak Ct levels and number of positive days between groups, using GraphPad Prism version 9.2.0 (GraphPad Software, San Diego, California, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Further, post booster antibody titers were similar in participants with and without subsequent breakthrough infection, exemplifying limitations of vaccine induced antibody titres as a marker of protection against omicron breakthrough infection. Although identification of SARS-CoV-2 RNA through qPCR is not equivalent to the detection of infectious virus, low Ct values have repeatedly been shown to correspond to viable virus in cell cultures for both omicron [11 ,13] and other SARS-CoV-2 variants [27 ,28]. Consequently, Ct values are often used as a proxy of viral load. Fall et al., reported presence of infectious omicron virus in samples obtained up to eight days after symptom onset, and that the presence of infectious omicron virus was similar in non vaccinated, vaccinated and boosted individuals, implying that vaccine has little effect on viral load once infected [11]. In line with this, we here demonstrate high viral RNA levels up to nine days after first qPCR positive sample, including after symptom resolution, in the majority of omicron breakthrough infections occurring shortly after a vaccine booster dose. Together, this suggests that recently vaccinated omicron-infected individuals may transmit the virus for a longer time period than the five days quarantine from symptom onset recommended by current guidelines [29]. This is of particular importance in vulnerable environments such as healthcare settings. Our data are furthermore in line with a recent report demonstrating...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.02.22273333
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273239

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273239: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Starting with a randomly selected 1,000,000 samples, 997,140 were retained having passed missingness.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">These splits improve statistical power where the logistic regressions (LR) predict cases.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273239
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273214

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273214: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Study eligibility criteria were population-based studies describing the prevalence of anti-SARS-CoV-2 (IgG and/or IgM) serum antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2 (IgG</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our estimates of case ascertainment should be considered in the context of several limitations. While death counts are a more accurate indicator of disease burden [15], the number of deaths attributable to COVID-19 may have been underestimated, especially during the first months of the pandemic, affecting our model estimates [16]. Further, IFR values are subject to considerable change due to factors that affect severe outcomes such as increasing vaccination coverage and emerging new variants in the population. Specifically, we note that all IFR values were obtained from seroprevalence studies conducted before vaccination. Nonetheless, our estimates are consistent with serological data from Japan, with model’s mean estimates considerably overlapping the 95% confidence intervals reported in the studies. Effective vaccination strategies to achieve herd immunity and non-pharmaceutical control measures, coupled with robust surveillance systems, are needed to restrain the spread of SARS-2-CoV variants in the country. Sustainable and feasible long-term control of COVID-19 requires continuous review and understanding of the severity of the ongoing pandemic. Our method to estimate the true underlying cases could be a fundamental component to strengthen these population health control and surveillance measures.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.01.22273214
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.03.486864

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.486864: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IACUC: The protocols were approved by the Institutional Animal Care and Use Committee of National University Corporation Hokkaido University (approval ID: 20-0060).<br>IRB: All protocols involving specimens from human subjects recruited at Kyoto University and Kuramochi Clinic Interpark were reviewed and approved by the Institutional Review Boards of Kyoto University (approval ID: G1309) and Kuramochi Clinic Interpark (approval ID: G2021-004).<br>Consent: All human subjects provided written informed consent.<br>Euthanasia Agents: Sera of infected hamsters were collected at 16 days postinfection (d.p.i.) using cardiac puncture under anesthesia with isoflurane and stored at −80°C until use.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">, range: 29-56, 18% male) and sixteen vaccinees four weeks after their second mRNA-1273 (Moderna) vaccine (average age: 27, range: 20-47, 38% male)</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">We then selected 12 genomes and randomly selected 100 genomes that met criteria 1 and 2.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For protein detection, the following antibodies were used: mouse anti-SARS-CoV-2 S monoclonal antibody (clone 1A9, GeneTex, Cat# GTX632604, 1:10,000)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">mouse anti-HIV-1 p24 monoclonal antibody (183-H12-5C, obtained from the HIV Reagent Program, NIH, Cat# ARP-3537, 1:2,000), rabbit anti-beta actin (ACTB) monoclonal antibody (clone 13E5, Cell Signalling, Cat# 4970, 1:5,000)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-HIV-1</div><div>suggested: (NIH HIV Reagent Program Cat# 3537, RRID:AB_2832923)</div></div><div style="margin-bottom:8px"><div>anti-beta actin</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>ACTB</div><div>suggested: (Cell Signaling Technology Cat# 4970, RRID:AB_2223172)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, mouse anti-tubulin (TUBA) monoclonal antibody (clone DM1A, Sigma-Aldrich, Cat# T9026, 1:10,000)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-tubulin ( TUBA</div><div>suggested: (Antibodies-Online Cat# ABIN387720, RRID:AB_10763362)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, horseradish peroxidase (HRP)-conjugated horse anti-mouse IgG antibody (Cell Signaling, Cat# 7076S, 1:2,000)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mouse IgG</div><div>suggested: (Cell Signaling Technology Cat# 7076, RRID:AB_330924)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HRP-conjugated donkey anti-rabbit IgG polyclonal antibody (Jackson ImmunoResearch, Cat# 711-035-152, 1:10,000) and HRP-conjugated donkey anti-mouse IgG polyclonal antibody (Jackson ImmunoResearch, Cat# 715-035-150, 1:10,000).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HRP-conjugated donkey anti-mouse IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To measure the surface expression level of S protein, effector cells were stained with rabbit anti-SARS-CoV-2 S S1/S2 polyclonal antibody (Thermo Fisher Scientific, Cat# PA5-112048, 1:100)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2 S</div><div>suggested: (Bio X Cell Cat# BE0357, RRID:AB_2894776)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Normal rabbit IgG (SouthernBiotech, Cat# 0111-01, 1:100) was used as negative controls, and APC-conjugated goat anti-rabbit IgG polyclonal antibody (Jackson ImmunoResearch, Cat# 111-136-144, 1:50) was used as a secondary antibody.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-rabbit IgG</div><div>suggested: (Jackson ImmunoResearch Labs Cat# 111-136-144, RRID:AB_2337987)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cell culture: HEK293T cells (a human embryonic kidney cell line; ATCC, CRL-3216)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, HEK293 cells (a human embryonic kidney cell line; ATCC CRL-1573), and HOS-ACE2/TMPRSS2 cells, HOS cells stably expressing human ACE2 and TMPRSS2 (Ferreira et al., 2021; Ozono et al., 2021) were maintained in DMEM (high glucose) (Sigma-Aldrich, Cat# 6429-500ML) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (PS).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>HOS-ACE2/TMPRSS2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK293-C34 cells, IFNAR1 KO HEK293 cells expressing human ACE2 and TMPRSS2 by doxycycline treatment (Torii et al., 2021), were maintained in Dulbecco’s modified Eagle’s medium (high glucose) (Sigma-Aldrich, Cat# R8758-500ML) containing 10% FBS, 10 μg/ml blasticidin (InvivoGen, Cat# ant-bl-1) and 1% PS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293-C34</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">VeroE6/TMPRSS2 cells (VeroE6 cells stably expressing human TMPRSS2; JCRB1819) (Matsuyama et al., 2020) were maintained in DMEM (low glucose) (Wako, Cat# 041-29775) containing 10% FBS, G418 (1 mg/ml; Nacalai Tesque, Cat# G8168-10ML) and 1% PS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>VeroE6</div><div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK293-ACE2 cells and HEK293-ACE2/TMPRSS2 cells were transfected with pDSP1-7 (400ng).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293-ACE2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>HEK293-ACE2/TMPRSS2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 1 d before infection, VeroE6/TMPRSS2 cells (10,000 cells) were seeded into a 96-well plate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>VeroE6/TMPRSS2</div><div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The resulting PCR fragment was digested with KpnI and NotI and inserted into the corresponding site of the pCAGGS vector (Niwa et al., 1991).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCAGGS</div><div>suggested: RRID:Addgene_127347)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To prepare effector cells, HEK293 cells were cotransfected with the S expression plasmids (400 ng) and pDSP8-11 (400 ng) using TransIT-LT1 (Takara, Cat# MIR2300).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pDSP8-11</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To prepare target cells, HEK293 cells were cotransfected with pC-ACE2 (200 ng) and pDSP1-7 (400 ng)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pC-ACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Target HEK293 cells in selected wells were cotransfected with pC-TMPRSS2 (40 ng) in addition to the plasmids above.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pC-TMPRSS2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK293-ACE2 cells and HEK293-ACE2/TMPRSS2 cells were transfected with pDSP1-7 (400ng).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pDSP1-7</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">An enhanced yeast display platform for SARS-CoV-2 S RBD [wild-type (B.1.1), residues 336-528] yeast surface expression was established using Saccharomyces cerevisiae EBY100 strain and pJYDC1 plasmid (Addgene, Cat# 162458) as previously described (Dejnirattisai et al., 2022; Kimura et al., 2022; Motozono et al., 2021; Yamasoba et al., 2022; Zahradnik et al., 2021).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pJYDC1</div><div>suggested: RRID:Addgene_162458)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sequencing reads were trimmed using fastp v0.21.0 (Chen et al., 2018) and subsequently mapped to the viral genome sequences of a lineage A isolate (strain WK-521; GISAID ID: EPI_ISL_408667) (Matsuyama et al., 2020) using BWA-MEM v0.7.17 (Li and Durbin, 2009).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BWA-MEM</div><div>suggested: (Sniffles, RRID:SCR_017619)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Variant calling, filtering, and annotation were performed using SAMtools v1.9 (Li et al., 2009) and snpEff v5.0e (Cingolani et al., 2012).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SAMtools</div><div>suggested: (SAMTOOLS, RRID:SCR_002105)</div></div><div style="margin-bottom:8px"><div>snpEff</div><div>suggested: (SnpEff, RRID:SCR_005191)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The 48 Omicron genomes with two outgroup genomes EPI_ISL_402125 (strain Wuhan-Hu-1, B lineage) and EPI_ISL_406862 (B.1 lineage; one of the earliest sequences carrying the S D614G mutation) were aligned using FFT-NS-1 in MAFFT suite v7.407 (Katoh and Standley, 2013).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MAFFT</div><div>suggested: (MAFFT, RRID:SCR_011811)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">BEAST v1.10.4 (Suchard et al., 2018) was used to construct a timetree under an exponential growth coalescent model using a strict molecular clock.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BEAST</div><div>suggested: (BEAST, RRID:SCR_010228)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/) was used to show the tree.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FigTree</div><div>suggested: (FigTree, RRID:SCR_008515)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To further determine the population history of the Omicron genomes, we generated a Bayesian skyline plot using the same model (2 × 108 chain length for MCMC) and summarized the results using Tracer v1.7.1 (Rambaut et al., 2018)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Tracer</div><div>suggested: (Tracer, RRID:SCR_019121)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">mouse anti-HIV-1 p24 monoclonal antibody (183-H12-5C, obtained from the HIV Reagent Program, NIH, Cat# ARP-3537, 1:2,000), rabbit anti-beta actin (ACTB) monoclonal antibody (clone 13E5, Cell Signalling, Cat# 4970, 1:5,000)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HIV Reagent Program</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">(LI-COR Biosciences) or Fiji software v2.2.0 (ImageJ).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Fiji</div><div>suggested: (Fiji, RRID:SCR_002285)</div></div><div style="margin-bottom:8px"><div>ImageJ</div><div>suggested: (ImageJ, RRID:SCR_003070)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Surface expression level of S protein was measured using FACS Canto II (BD Biosciences) and the data were analyzed using FlowJo software v10.7.1 (BD Biosciences).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Nucleotide sequences were determined by a DNA sequencing service (Fasmac), and the sequence data were analyzed by Sequencher v5.1 software (Gene Codes Corporation).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Sequencher</div><div>suggested: (Sequencher, RRID:SCR_001528)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Information on the unexpected mutations detected is summarized in Table S4, and the raw data are deposited in Gene Expression Omnibus (accession number: GSE196649 and xxxx).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Gene Expression Omnibus</div><div>suggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The stained cells were washed with tap water and dried, and the size of plaques was measured using Adobe Photoshop 2021 v22.4.1 (Adobe)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Adobe Photoshop</div><div>suggested: (Adobe Photoshop, RRID:SCR_014199)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The assay of each serum was performed in triplicate, and the 50% neutralization titer (NT50) was calculated using Prism 9 (GraphPad Software)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Protein structure: All protein structural analyses were performed using the PyMOL molecular graphics system v2.5.0 (Schrödinger).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PyMOL</div><div>suggested: (PyMOL, RRID:SCR_000305)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The background binding subtracted fluorescent signal was fitted to a standard noncooperative Hill equation by nonlinear least-squares regression using Python v3.7 (https://www.python.org) as previously described (Zahradnik et al., 2021).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div><div style="margin-bottom:8px"><div>https://www.python.org</div><div>suggested: (CVXOPT - Python Software for Convex Optimization, RRID:SCR_002918)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations of the study: Here, we showed the importance of the S375F mutation to the virological properties of Omicron; however, the following issues remain unclear. First, although we showed that the S375F mutation determines the virological features of Omicron S, it remains unclear which mutations in Omicron S determine the pronounced immune resistance of Omicron S. Second, in addition to the Omicron BA.1 variant that we focused on this study, another recently emerged Omicron lineage, BA.2, also bears the S375F mutation. However, we have recently shown that the fusogenicity of BA.2 S is significantly higher than that of BA.1 S (Yamasoba et al., 2022). Together with the results shown in this study, these observations suggest that BA.2 S acquired certain compensatory mutation(s) that increased fusion efficacy. Further investigations will be needed to unveil the full evolutionary history of the Omicron lineage. Furthermore, the question of why the acquisition of the S375F mutation caused explosive spread despite reducing infectivity in tissue culture, S cleavage efficacy and fusogenicity also needs to be elucidated in detail by further studies.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.04.03.486864
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273257

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273257: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: 2.1 Common 4CE Data collection by HS: As previously described[16], each participating HS were responsible for and obtained ethics approval, as needed, from the appropriate ethics committee at their institution.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Medications administered were collected at the class level (as per the ATC standard nomenclature[22], e-Appendix 1).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ATC</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  A limitation of relying on billing codes to identify comorbidities is the challenge of accurately distinguishing comorbidities from complications. In our analysis, comorbidities were considered as those diagnoses from billing codes assigned up to one year before and up to 90 days after the admission. This approach is more sensitive, but it can lead to considering complications as comorbidities. It is particularly true for peptic ulcer disease or paralysis which was identified as a comorbidity associated with ARDS but which is also known to be a common complication of mechanical ventilation[28,29] or prolonged ICU admission. We perform a complementary univariable analysis on the sub population who had previous hospital visits and considering only the ICD code related to those previous visits as comorbidities (one year and – 14 days before the admission). In this univariable analysis presented in e-Table 2, ARDS was associated with the presence of peptic ulcer disease or paralysis in a previous hospitalization, which explained our choice to keep both in the main multivariable analysis that means considering them as comorbidities. “Paralysis” regroups is related a large diversity of diagnoses. including encephalitis, myelitis and encephalomyelitis, hereditary ataxia, cerebral palsy, hemiplegia and hemiparesis, paraplegia (paraparesis) and quadriplegia (quadriparesis), and other paralytic syndromes (e-Appendix 2); but a common co-occurrence is reduced lung capacity which could co...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273257
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273101

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273101: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  As currently implemented, our method suffers from a number of limitations that risk biasing the results. Several of the key parameters in our model, especially the estimates of PCR positivity over time from infection, generation interval distributions, are fixed and based on estimates derived from wildtype virus in a particular cohort of healthcare workers and may well be incorrect for other circulating variants or populations. Furthermore, generation times have been shown to change over time due to behavioural changes and epidemiological dynamics, which would affect our reproduction number estimates (Champredon & Dushoff, 2015; Hart et al., 2021; Park et al., 2021). PCR detection probabilities as a function of time since infection were based on independent normal distributions, whereas in reality they are likely to be correlated over time. We modelled the growth of infections as a stationary Gaussian process, whereas in reality variation over time has changed between periods of stability and rapid change due to changes in contact behaviour in response to the epidemic. Lastly, we assumed that antibody waning was exponential, and ignored any consequences of multiple rounds of vaccination or infection apart from converting those without detectable antibodies to having detectable antibodies. Future directions of this work should help address some of these limitations, for example by including more detail on antibody levels, or by including antibody measurements that may be able ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22273101
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273190

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273190: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our model has of course limitations. An important one is that we are not able to recognize that a strict full-containment would be effective (even if it is difficult to implement and to get a population to accept), as shown during the first wave of SARS-Cov-2 epidemic in China. This is because the proportion of immunized persons in our model is assumed to be stable and identical in all three strata. In particular, we do not capture in our model that the proportion of immunized persons in an infected household will increase rapidly in the event of a full-containment, so that there will be no one left to infect, thus stopping the epidemics. This will also apply to a lesser extend in a semi-containment [33,34]. We are currently investigating ways to extend our model in this respect, to take into account the fact that herd immunity is reached more quickly in households than in the general population. Other limitations of our model include the following. We are not able to assess the role of border controls to limit the circulation of virus variants. As mentioned in the Methods section, we ignored the important stratum of the homes for the elderly, while we did not consider the specific situation of children. A model with more than three strata might be preferable, although this would imply a larger number of parameters to estimate. In the end, our model is probably too simple. Note that the use of more sophisticated models (SEIR compartmental models or others) provided similar re...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273190
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.27.22271628

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.27.22271628: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Boundary shapefile of counties downloaded from TIGER/Line database (https://www.census.gov).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>https://www.census.gov</div><div>suggested: (U.S. Census Bureau, RRID:SCR_011587)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  The development and implementation of spatially-informed prediction models suffer from several limitations. Our models did not include mitigation measures or vaccine coverage, due in part to inconsistencies in implementation and data availability. The end date for the nationwide phase analysis, March 31, was before vaccine availability was opened to the general public in most states, but differences in vaccine uptake to that point represent a potential confounder. Early case numbers were heavily influenced by low test availability, leading to significant missing data. However, our analyses found similar features predicted case dynamics throughout the pandemic, suggesting that the effect of this missing data may be minimal. Finally, TMand Louvain clustering generate highly overlapping feature sets that may be specific to the breadth of data included. Thus, while spatial analysis provides a powerful predictive tool, the precise effect of each feature or set of features is likely to be context-specific. In conclusion, we show that spatial features account for the majority of variation in COVID-19 case and death dynamics across the US. Predictive modeling based on combinations of spatial features can identify counties at greatest risk for COVID-19 spread and can be used to direct aggressive mitigation strategies and limited resource pools to these areas. Finally, we show that topic modeling provides a new approach to dimensional reduction in epidemiologic data and may be of value...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.27.22271628
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273203

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273203: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: All participants gave informed consent, and the study was approved by the ethics committee of the University of Occupational and Environmental Health, Japan (approval number: R2-079 and R3-006).<br>IRB: All participants gave informed consent, and the study was approved by the ethics committee of the University of Occupational and Environmental Health, Japan (approval number: R2-079 and R3-006).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All analyses were conducted using Stata (Stata Statistical Software: Release 16; StataCorp LLC, College Station, TX, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>StataCorp</div><div>suggested: (Stata, RRID:SCR_012763)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  This study had several limitations. First, the survey was conducted via the internet, so generalizations should be made with caution. However, we attempted to reduce any bias by using cluster sampling with stratification by sex, region, and job type. Second, the study was likely affected by recall bias. The earlier vaccination was completed, the more time had elapsed by the time of the survey, which may have caused recall bias. Third, the timing of the follow-up survey might have affected the responses to the question of vaccination status in the last month, December. If a person received their second vaccine dose in the last week of December (after filling out the follow-up survey), they may have answered “unvaccinated” when asked about their vaccination status in the follow-up survey. However, the impact of this situation was likely small because second-dose vaccination was nearly complete in both the community and workplace programs by the end of November, and less than 1% of the respondents received their second vaccine dose in December.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273203
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22272552

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22272552: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: The donors provided informed consent and their samples were collected under an approved IRB protocol ([1149706-4] Diagnostic QC and Pre-Clinical Sample Collection Project: Ballad Health System Institutional Review Board (IRB #00003204), Johnson City, TN, USA).<br>IRB: The donors provided informed consent and their samples were collected under an approved IRB protocol ([1149706-4] Diagnostic QC and Pre-Clinical Sample Collection Project: Ballad Health System Institutional Review Board (IRB #00003204), Johnson City, TN, USA).<br>Field Sample Permit: These studies were conducted in compliance with all applicable regulatory guidelines.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">There were 10 female and 5 male donors, and all were white/Caucasian.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">CLIA and ELISA Assays: The samples in the seroconversion panels were tested for the presence of anti-SARS-CoV-2 antibodies using chemiluminescent immunoassays (</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Neutralizing Antibody Determination: Cell line: HEK293T cells (presumably of female origin) overexpressing wild-type human ACE-2 (Integral Molecular, USA) were used as target for SARS-CoV-2 spike expressing pseudovirus infection.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: RRID:CVCL_HA71)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then 2 × 104 HEK293T/hACE2 cells treated with DEAE-Dextran (Sigma-Aldrich, St. Louis, MO, USA) were added.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T/hACE2</div><div>suggested: RRID:CVCL_A7UK)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudovirus generation: Pseudoviruses (HIV reporter) expressing the SARS-CoV-2 S protein and luciferase were constructed using the defective HIV plasmid, pNL4-3.Luc.R-.E-.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pNL4-3.Luc.R-</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The plasmid was obtained from the NIH AIDS Reagent Program. [17] Expi293F cells were transfected using ExpiFectamine293 Reagent (Thermo Fisher Scientific, Waltham, MA, USA) with pNL4-3.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pNL4-3</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The results were normalized and the ID50 (the reciprocal dilution inhibiting 50% of the infection) was calculated by plotting the log of plasma dilution versus response and fitting to a 4-parameter equation in Prism 8.4.3 (GraphPad Software, San Diego, CA, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Prism</div><div>suggested: (PRISM, RRID:SCR_005375)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.28.22272552
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https://medrxiv.org/cgi/content/10.1101/2022.03.26.22272727

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.22272727: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  These benefits need to be weighed against the limitations of rapid antigen tests, including lower sensitivity among asymptomatic individuals and those with low viral load.8,9 Our finding indicating that distribution of tests several months prior to a surge in SARS-CoV-2 cases was still associated with a reduction in community transmission suggests that recipients of this intervention were responsible owners of a personal supply of rapid antigen tests. These findings, taken together with recent reports that rapid antigen tests’ performance remain consistent across variants, underscore the continued utility of rapid antigen tests.9 With emerging reports of the BA.2 variant causing a surge in cases across the globe and in the United States, these findings hold particular importance for the public health of the country.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.26.22272727
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273107

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273107: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">Screening was performed by at least two independent reviewers (AJM, NM, JPV-C, VS, JEF) who were blind to the other reviewer’s assessment.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">First, four databases – MEDLINE, Embase, Web of Science and Scopus, were explored to identify relevant investigations published between 1 December 2019 and 26 July 2021.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MEDLINE</div><div>suggested: (MEDLINE, RRID:SCR_002185)</div></div><div style="margin-bottom:8px"><div>Embase</div><div>suggested: (EMBASE, RRID:SCR_001650)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Second, using the same search terms and dates, we screened unpublished investigations made available on the medRxiv and bioRxiv preprint servers.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>bioRxiv</div><div>suggested: (bioRxiv, RRID:SCR_003933)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  We conducted a robust and thorough assessment of the methodological quality of investigations using a bespoke quality assessment tool for HHTIs which allowed for a more targeted critical appraisal and better understanding of strengths and limitations of HHTIs.(16) We only included investigations with a low or moderate risk of bias in our primary meta-analysis (n = 62) and subsequently only those aligned with the objectives of the WHO Unity Studies HHTI protocol. It also allowed us to carefully consider the appropriateness of pooling data across investigations that were conducted in different resource settings and environments, using different protocols and with differing internal and external validity. The use of a bespoke tool for methodological quality assessment does not guarantee that the intricacies of HHTI designs are fully captured, particularly where insufficient details are reported. We acknowledge that tailoring of the HHTI protocol according to cultural norms (e.g., household definition), capacity (e.g., laboratory testing, degree of follow up) and context (e.g., PHSM, local incidence, quarantine practices) may be required, increasing the true variance observed across investigations. As a result, unclear reporting may have inflated the heterogeneity in our review due to inappropriate inclusion or exclusion of some investigations. Of the 76 investigations that reported a hSAR, 13 were assessed to be at high risk of bias and subsequently excluded from the primary ana...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.04.01.22273107
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.02.22273341

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.02.22273341: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations of the current analysis include the possibility of COVID-19 deaths that occurred in 2020 among whom COVID-19 went undiagnosed, as well as the possibility of racial/ethnic misclassification of COVID-19 deaths on official death certificates. A 2016 CDC study estimated a race misclassification rate of 3% on death certificates for Asians [40]. The same report, however, estimated race misclassification for AIAN’s to be 40%, which has been a long-standing and persistent problem [41–48]. Asian subgroup misclassification on death certificates among Asian decedents is also a potential limitation, but its current extent is unclear. Moreover, the current analysis is based on COVID-19 deaths that occurred in 2020, at the tail end of which the U.S. vaccination campaign began (December 14) [49]. As such, racial/ethnic patterns in mortality outcomes observed in the current analysis may not necessarily reflect patterns that unfolded during later stages of the COVID-19 pandemic in 2021 and 2022 when COVID-19 vaccines became widely available and when the more transmissible and virulent Alpha, Delta, and Omicron SARS-CoV-2 variants emerged and successively usurped previously dominant variants. All mortality rates presented in the current analysis also contain the caveat that the denominators used to calculate them are based on population projections derived from a national survey, namely the CPS ASEC, which in fact experienced significant operational challenges in 2020 as a result o...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.02.22273341
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.02.486853

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.02.486853: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethics: Ethics approval was obtained from the Institutional Animal Ethics Committee (IAEC) (ref. no. RCB/ IAEC/2021/093), and Institutional Biosafety Committee (<br>IACUC: Ethics: Ethics approval was obtained from the Institutional Animal Ethics Committee (IAEC) (ref. no. RCB/ IAEC/2021/093), and Institutional Biosafety Committee (</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Male hamsters of 8 weeks old were infected with one-time SARS CoV-2 via nasal route inoculation using 1×105 plaque-forming units (PFU).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Contamination: The Vero E6 cell line was validated for free of mycoplasma contamination.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The lysate samples were further processed for SDS-PAGE followed by immunoblotting using primary antibodies against pAkt-Ser473, Akt, pAkt1-Thr308, Akt1, HIF1α, HIF2α, β-Actin (Cell Signalling, USA), as described in our work (15).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pAkt-Ser473 , Akt , pAkt1-Thr308</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Akt1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>HIF1α</div><div>suggested: (ABclonal Cat# A17906, RRID:AB_2861751)</div></div><div style="margin-bottom:8px"><div>HIF2α</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>β-Actin</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The plates were incubated at room temperature (RT) for 1 h and then washed three times with washing buffer (PBS + 0.1 % tween 20) and incubated with HRP conjugated antihamster IgG antibody at 1:10,000 dilution for another 1 h and washed four times with the washing buffer and incubated further with 100 μl of TMB substrate (Thermo Fisher Scientific), The reaction stopped with 1N H2SO4 solution.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HRP conjugated antihamster IgG</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS CoV-2 infection in Vero and U937 cells: Monkey kidney epithelial cell line Vero E6 (0.1×106 cells/well) was infected with P-3 Wuhan SARS CoV-2 (world reference # USA-WA-1/2020, as mentioned in our earlier work (15) at 0.01 MOI for 1 hr in Dulbecco’s Modified Eagle Medium (DMEM) with 2% FBS, supplemented with 1% non-essential amino acids.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Confocal microscopy: Vero E6, U937 cells or U937/PHD2-KD cells from above experiment were fixed in 4% paraformaldehyde for 20 min at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>U937</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Experiments using BALB/c mouse strain (RRID: IMSR_JAX_000651) and Syrian golden hamster (available form ICMR-National Institute of Nutrition, Hyderabad, India) were conducted within the guidelines of IAEC in the Biosafety level 3 (BSL3) facility of the institute.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BALB/c</div><div>detected: (IMSR Cat# JAX_000651, RRID:IMSR_JAX:000651)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The lysate samples were further processed for SDS-PAGE followed by immunoblotting using primary antibodies against pAkt-Ser473, Akt, pAkt1-Thr308, Akt1, HIF1α, HIF2α, β-Actin (Cell Signalling, USA), as described in our work (15).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pAkt1-Thr308</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Imaging was performed using Z-stacks at 0.25 μm per slice by sequential scanning and Image J Fiji software was used to obtain maximum intensity projection images.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Image J</div><div>suggested: (ImageJ, RRID:SCR_003070)</div></div><div style="margin-bottom:8px"><div>Fiji</div><div>suggested: (Fiji, RRID:SCR_002285)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells were then washed and acquired on BD FACS Verse and were analyzed with FlowJo software (Tree Star, USA)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Graph Pad Prism version 8.0 software was used for data analysis and P-values.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Graph Pad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.02.486853
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273143

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273143: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The trial protocol was approved by the Institutional Review Board (IRB) of each participating hospital and was performed in accordance with the International Council for Harmonization Good Clinical Practice guidelines.<br>Consent: Written informed consent was obtained from all participants.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Study design and participants: This phase 1/2, randomized, placebo-controlled, observer-blinded, dose-escalating trial was conducted at 14 centers in South Korea</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  The limitations of this study include the small sample size, especially for older adults, and short follow-up period. Nevertheless, the sample size provides a meaningful initial assessment of the frequency and intensity of the solicited AEs. As of January 31, 2022 (6 months post-vaccination), no AESI nor SAE related to vaccine have been reported. In conclusion, GBP510 adjuvanted with AS03 was well-tolerated with an acceptable safety profile, and highly immunogenic. The phase 1/2 trial has been extended to the homologous booster study, which assess the impact of a third dose (25μg GBP510 adjuvanted with AS03) on the durability and cross-protection. Based on the results of this phase 1/2 trial, a phase 3, randomized, observer-blind trial is underway to compare the immunogenicity and safety of 25 μg GBP510 adjuvanted with AS03 to ChAdOx1 in adults 18 years of age and older (initiated August 30, 2021). In addition, a Phase 2, heterologous GBP510 adjuvanted with AS03 booster trial began on January 6, 2022, to assess the merits of this immune-focused antigen as a universal booster to already licensed CoV-2 vaccines.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04750343</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Safety and Immunogenicity Study of SARS-CoV-2 Nanoparticle V…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273143
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.27.22271988

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.27.22271988: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: The protocol and patient consent forms were approved by the ethics committees or institutional review boards at all participating institutions (appendix p 1).<br>IRB: The protocol and patient consent forms were approved by the ethics committees or institutional review boards at all participating institutions (appendix p 1).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Study design: The study comprised a double-blind phase (up to 14 days) in which they were randomised to receive camostat mesilate or placebo, and a 2-week follow-up period after the last dose of the study drug.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">(appendix p 2 [sample size calculation]).</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Changes in viral load, antibody responses (IgG and IgM), and safety outcomes were analysed descriptively in terms of the number and percentage of patients or summary statistics, as appropriate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgM</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 infection must have been tested using a standard method at the time the study was conducted (e.g., reverse transcriptase-polymerase chain reaction [RT-PCR] test, loop-mediated isothermal amplification [LAMP] test, or antigen test).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>LAMP</div><div>suggested: (LAMP, RRID:SCR_001740)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SAS version 9.4 (SAS Institute, Cary, NC, USA) was used for all statistical analyses.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SAS Institute</div><div>suggested: (Statistical Analysis System, RRID:SCR_008567)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  A limitation of this study is that the improvement of the ordinal scale of severity could not be evaluated correctly because most patients were hospitalised for daily viral testing regardless of the presence or absence of symptoms and were hence classified as grade 3. Another possible limitation is that the effects of camostat mesilate against SARS-CoV-2 were evaluated using nasopharyngeal and nasal swab samples in the majority of patients. However, the appropriateness of an index of upper airway viral load in asymptomatic to moderate cases remains questionable. It is considered that the epidemic strain at the time was a D614G strain, but no data on the type of strain were collected for this study. Efficacy against currently circulating variants is unknown. There are some strengths of this study that should be mentioned. In particular, this was a double-blind, randomised, placebo-controlled study with robust randomisation as demonstrated by the high similarity of both groups. In addition, this study used a dose that was four to eight times higher than the clinical doses in Japan used for the acute symptoms of chronic pancreatitis and postoperative reflux oesophagitis based on the preclinical and early clinical evidence. Furthermore, the efficacy of camostat mesilate was assessed using multiple clinically relevant endpoints, including local and central laboratory tests for SARS-CoV-2 infection and viral load. Although the study results were negative, there were several lessons...
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04657497</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Study of FOY-305 in Patients With SARS-Cov-2 Infection (CO…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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medrxiv.org/cgi/content/10.1101/2022.03.27.22271988
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.03.22273353

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.03.22273353: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Strategy of literature search for meta-analysis: A systemic literature search of studies published in English was performed in PubMed, Embase, Google Scholar and Cochrane Library up to October 1, 2021 using the key words ‘metformin or biguanides’, ‘SARS-CoV2 or COVID-19’ and ‘mortality’.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PubMed</div><div>suggested: (PubMed, RRID:SCR_004846)</div></div><div style="margin-bottom:8px"><div>Embase</div><div>suggested: (EMBASE, RRID:SCR_001650)</div></div><div style="margin-bottom:8px"><div>Google Scholar</div><div>suggested: (Google Scholar, RRID:SCR_008878)</div></div><div style="margin-bottom:8px"><div>Cochrane Library</div><div>suggested: (Cochrane Library, RRID:SCR_013000)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Several limitations are present in our study. First, owing to lack of randomized clinical trials, all studies included for analysis were retrospective studies. Although efforts were made to balance and control for potential confounding factors by multiple variable adjustments and propensity score matching, due to the inherent nature of retrospective observational studies, residual confounders are likely to exist and could not be balanced. Therefore, even meta-analysis of studies with adjusted ORs o HRs could be misleading. Second, the size of the retrospective studies that were included in the meta-analysis varied considerably, resulting in moderate-to-high heterogeneity. Third, there were few studies investigating inpatient metformin use and in-hospital mortality. More studies are needed to perform a robust meta-analysis for inpatient metformin therapy and in-hospital mortality in patient with diabetes hospitalized for COVD-19. In conclusion, our findings demonstrate that there is a significant reduction of in-hospital mortality with outpatient or inpatient metformin therapy in patients with type 2 diabetes mellitus hospitalized for COVID-19 in the unadjusted analysis, but this mortality benefit does not retain after adjustments for confounding bias. Therefore, further randomized clinical trials are needed to provide clinical evidence regarding metformin therapy and in-hospital mortality in patient with diabetes hospitalized for COVD-19.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.04.03.22273353
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22272957

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22272957: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The model was developed in Microsoft Excel using Visual Basic for Applications (Microsoft Corp; Redmond, Washington).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Microsoft Excel</div><div>suggested: (Microsoft Excel, RRID:SCR_016137)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">1, 2020 in the Premier Healthcare COVID-19 Database.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Premier Healthcare</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  As with all predictive modeling exercises, there are limitations to the study. Firstly, there is high uncertainty regarding the VE against emerging variants. Additionally, VE may increase as manufacturers tailor the vaccine to improve protection against new strains. Regardless of the variant, studies have shown higher VE for mRNA-1273 compared to BNT162b2, and therefore this relationship was maintained in our hypothetical VE profiles in the model for both primary and booster vaccinations. The base case analysis results assume VE similar to that estimated against an omicron-like variant. To address the uncertainty surrounding VE, different scenarios were tested. Assuming a high initial VE still resulted in the same trends as the base case; 100% mRNA-1273 boosters decreased, and 100% BNT162b2 boosters increased outpatient visits, hospitalization and deaths, compared to the booster mix. Assuming a low initial VE with double the monthly rate of waning compared to the base case also maintained the same trends as the base case. With lower overall effectiveness for all vaccines the number of cases and associated resource use is higher in all booster mix scenarios. The incidence of COVID-19 had to be projected over the upcoming year and is highly uncertain. Still, scenarios where a high incidence rate and low incidence rate were tested did not change the overall model results, with 100% mRNA-1273 boosters resulting in less outpatient visits, hospitalizations and costs compared to the...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22272957
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22272858

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22272858: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: We obtained written and informed consent into off-label use for vaccine doses four and five from all patients.<br>IRB: The institutional ethics committee of Charité – Universitätsmedizin Berlin approved this retrospective analysis (ethics votum EA1/030/22).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Conversely, any positive SARS-CoV-2 RNA PCR, positive anti-SARS-CoV-2-N-protein antibodies, positive anti-SARS-CoV-2 Ig or administration of monoclonal anti-SARS-CoV-2-S-protein antibody therapy before the serological sample lead to exclusion of the respective following serological data.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2-N-protein</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-SARS-CoV-2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-SARS-CoV-2-S-protein</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Due to the study’s retrospective design, methodological limitations arise. However, the applied selection criteria for sample data account for the risk of selection bias. In a large number of patients at our institution, repeated serological measurements were not performed thus resulting in exclusion of singular samples. Hence, limiting the comparison of Ig levels between intervals to paired data samples decreased the size of the dataset but also reduces the risk selection bias due to singular samples that might not have been followed-up due to confounding reasons. Despite the limitations our analysis provides the first data of different assays and time course of the serological response in a large number of KTR.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22272858
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22271678

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22271678: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Fundación Jiménez Díaz Biobank, ref. PIC087-20; Clinical Research Ethics Committee Hospital Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca Biobank, ref.<br>Consent: Wherever possible, patients provided written or verbal informed consent to participate.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Subjects: This study included 1136 male patients from the STOP_Coronavirus cohort who were infected with SARS-CoV-2 as confirmed by positive PCR.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PCA was performed using Plink software, version 1.9 (12).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Plink</div><div>suggested: (PLINK, RRID:SCR_001757)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.25.22271678
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273020

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273020: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22273020
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https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273174

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273174: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Drug use was identified via RxNorm codes for dupilumab (1876376) and the lab value for C-reactive protein (9063). 1:1 matching was performed for age and sex.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RxNorm</div><div>suggested: (RxNorm, RRID:SCR_006645)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  However, there are limitations due to non-randomized groups resulting in sampling biases, difficulty defining temporal boundaries, and not being able to infer causational relationships. The N3C database used allowed for well-defined patient outcomes and temporal windows, however small sampling size may limit the statistical power through this method. Supportive analysis by TriNetX allowed for larger cohort of dupilumab (+) cases, but was limited to lower matching criteria and at a 1:1 ratio. Utilization of both datasets, then, provides two analyses which supported our hypothesis. Identification of dupilumab as a being associated with reduction in death due to COVID-19 may implicate this drug as a potential therapeutic option for patients. Future, large-scale clinical trial of dupilumab use during COVID-19 will be important for understanding the impact this drug may have on protecting patients from severe outcomes. Author contributions: AD wrote the manuscript. AD, IM, JL, and RB assisted with data analysis. All authors contributed to discussion regarding conceptualization and design of the reported studies. Authorship was determined using ICMJE recommendations. Attribution: This research was possible because of the patients whose information is included within the data and the organizations and scientists who have contributed to the on-going development of this community resource https://doi.org/10.1093/jamia/ocaa196.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273174
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22269942

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22269942: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: All patients who received tocilizumab, netakimab, or baricitinib provided written informed consent.<br>IRB: The study was approved by the local ethical committee of the City Clinical Hospital No.52. Procedures: All patients received SOC treatment at the time of hospital admission according to the corresponding COVID-19 Russian guidelines 2020 (Interim guidelines for the prevention, diagnosis and treatment of novel coronavirus infection (COVID-19).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT03447704</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">International Multicenter Comparative Randomized Placebo-con…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT03598751</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Clinical Study of Efficacy and Safety of BCD-085 (Monoclonal…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04356937</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Efficacy of Tocilizumab on Patients With COVID-19</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04320615</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Study to Evaluate the Safety and Efficacy of Tocilizumab i…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04381936</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomised Evaluation of COVID-19 Therapy</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04421027</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Study of Baricitinib (LY3009104) in Participants With COVI…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT03390101</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">An International Multicenter, Randomized, Double-blind, Plac…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT05302947</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">COVID-19 Study at the Russian Clinical and Research Center o…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22269942
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.01.486726

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.486726: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.01.486726
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.01.486719

1
1. sciscore 05 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.486719: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">B cells were incubated for 30 min at 4°C with biotinylated tri-S and DyLight 650-coupled RBD, washed once with 1% FBS-PBS (FACS buffer), and incubated for 30 min at 4°C with a cocktail of mouse anti-human antibodies: CD19 Alexa 700 (HIB19, BD Biosciences, San Jose,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human antibodies: CD19</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The cTfh antibody panel included: CD3 BV605 (SK7), CD4 PE-CF594 (RPA-T4), CD185/CXCR5 AF-488 (RF8B2), CD183/CXCR3 PE-Cy™5 (1C6/CXCR3), CD196/CCR6 PE-Cy™7 (11A9), CD197/CCR7 AF647 (3D12) (BD Biosciences), CD279/PD1 BV421 (EH12.2H7, BioLegend), and CD278/ICOS PE (ISA-3, Thermo Fisher Scientific).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD3</div><div>suggested: (SouthernBiotech Cat# 9515-31, RRID:AB_2796843)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The purified parental IgG1 antibody versions of benchmarked mAbs [REGN10933, REGN10987 (Hansen et al., 2020), CB6 (Shi et al., 2020), LY-CoV555 (Jones et al., 2021), CT-P59 (Kim et al., 2021), COV2-2196, COV2-2130 (Zost et al., 2020b), ADG-2 (Garrett Rappazzo et al., 2021) and S309 (Pinto et al., 2020)] were prepared as described above after cloning of synthetic DNA fragments (GeneArt, Thermo Fisher Scientific) coding for the immunoglobulin variable domains.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgG1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CB6</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>LY-CoV555</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>S309</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Comparative ELISA binding of Cv2.1169 IgG1 and IgA1 antibodies was performed at a concentration of 70 nM, and 7 consecutive dilutions in PBS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgA1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To quantify blood-circulating human Cv2.1169 IgA1 and IgG1 in treated K18-hACE2 mice and golden hamsters, high-binding 96-well ELISA plates (Costar, Corning) were coated overnight with 250 ng/well of purified goat anti-human IgA or IgG antibody (Jackson ImmunoResearch, 0.8 µg/ml final).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>purified goat anti-human IgA</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgG antibody</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After washings, the plates were revealed by incubation for 1 h with goat HRP-conjugated anti-mice IgG, anti-golden hamster IgG, anti-human IgG or anti-human IgA antibodies (Jackson ImmunoReseach, 0.8 µg/ml final) and by adding 100 µl of HRP chromogenic substrate (ABTS solution, Euromedex) after washing steps.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mice IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-golden hamster IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-human IgA</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEp-2 IFA assay: Recombinant SARS-CoV-2 S-specific and control IgG antibodies (mGO53 and ED38) at 100 µg/ml were analyzed by indirect immuno-fluorescence assay (IFA) on HEp-2 cells sections (ANA HEp-2 AeskuSlides®, Aesku.Diagnostics, Wendelsheim, Germany) using the kit’s controls and FITC-conjugated anti-human IgG antibodies as the tracer according to the manufacturer’ instructions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>control IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>ED38</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Membranes were inserted into a Miniblot apparatus (Immunetics) and then incubated with human mAbs (at a concentration of 1 µg/ml) and mouse anti-Hisx6 antibody (1 µg/ml, BD Biosciences) in PBS-T 5% dry milk in each channel for 2 h.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Hisx6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Microarrays were blocked for 1 h in blocking solution (Thermo Fisher), washed and incubated for 1h30 with IgG antibodies at 2.5 µg/ml as previously described (Grzelak et al., 2020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibodies (Cv2.1169, Cv2.1353, Cv2.3194, Cv2.3235 and Cv2.5213) and ACE2 ectodomain were covalently coupled to CM5 sensor chips (Biacore) using amino-coupling kit (Biacore) according to the manufacturer’s procedure.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody-dependent cellular phagocytosis (ADCP) assay: PBMC were isolated from healthy donors’ blood (Etablissement Français du Sang) using Ficoll Plaque Plus (GE Healthcare)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Antibody-dependent cellular phagocytosis ( ADCP</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phagocytic scores were calculated by dividing the fluorescence signals (% FITC-positive cells x geometric MFI FITC-positive cells) given by anti-SARS-CoV-2 spike antibodies by the one of the negative control antibody mGO53.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody-dependent cellular cytotoxicity (ADCC) assay: The ADCC activity of anti-SARS-CoV2 S IgG antibodies was determined using the ADCC Reporter Bioassay (Promega) as previously described (Dufloo et al., 2021).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV2 S IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 5×104 Raji-Spike cells were co-cultured with 5×104 Jurkat-CD16-NFAT-rLuc cells in presence or absence of SARS-CoV2 S-specific or control mGO53 IgG antibody at 10 µg/ml or 50 µg/ml and 10 consecutive 1:2 dilutions in PBS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>control mGO53 IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Crystallization and structure determinations: The Fab of anti-SARS-CoV-2 S antibody CR3022 (Ter Meulen et al., 2006), served as a crystallization chaperone molecule, and was produced and purified as described above (section with heading Single B-cell FACS sorting and expression-cloning of antibodies) (Koide, 2009).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2 S</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Six or 22 h post-inoculation, mice received an intraperitoneal (i.p.) injection of 5, 10, 20 or 40 mg/kg of Cv2.1169 IgG or IgA antibody, and of mGO53 control IgG or IgA antibody.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgA</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Four or 24 h post-intranasal inoculation, hamsters received an intraperitoneal (i.p.) injection of 10 or 5 mg/kg of Cv2.1169 IgG or IgA antibody, as well as the mGO53 control antibody or PBS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>mGO53</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Viruses were amplified by one or two passages in Vero E6 cell cultures and titrated.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: RRID:CVCL_XD71)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Drosophila S2 cells were stably co-transfected with pT350 and pCoPuro (for puromycin selection) plasmids.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>S2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEp-2 IFA assay: Recombinant SARS-CoV-2 S-specific and control IgG antibodies (mGO53 and ED38) at 100 µg/ml were analyzed by indirect immuno-fluorescence assay (IFA) on HEp-2 cells sections (ANA HEp-2 AeskuSlides®, Aesku.Diagnostics, Wendelsheim, Germany) using the kit’s controls and FITC-conjugated anti-human IgG antibodies as the tracer according to the manufacturer’ instructions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEp-2</div><div>suggested: CLS Cat# 300397/p694_Hep-2, RRID:CVCL_1906)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 5×104 Raji-Spike cells were co-cultured with 5×104 Jurkat-CD16-NFAT-rLuc cells in presence or absence of SARS-CoV2 S-specific or control mGO53 IgG antibody at 10 µg/ml or 50 µg/ml and 10 consecutive 1:2 dilutions in PBS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Jurkat-CD16-NFAT-rLuc</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 5×104 Raji-Spike cells were cultivated in the presence of 50% normal or heat-inactivated human serum, and with or without IgG antibodies (at 10 µg/ml or 50 µg/ml and 10 consecutive 1:2 dilutions in PBS).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Raji-Spike</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The supernatants were titrated on Vero-E6 cells by classical plaque assays using semisolid overlays (Avicel, RC581-NFDR080I, DuPont) and expressed and PFU/100 mg of tissue (Baer and Kehn-Hall, 2014).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero-E6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 infection and treatment in K18-hACE2 mice: B6.Cg-Tg(K18-ACE2)2Prlmn/J mice (stock #034860) were imported from The Jackson Laboratory (Bar Harbor, ME, USA) and bred at the Institut Pasteur under strict SPF conditions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>B6.Cg-Tg(K18-ACE2)2Prlmn/J</div><div>suggested: RRID:IMSR_JAX:034860)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Expression and purification of viral proteins: Codon-optimized nucleotide fragments encoding stabilized versions of SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43-CoV, HKU1-CoV, 229E-CoV, NL63-CoV (2P) and BA.1 spike (HexaPro) (S) ectodomains, and SARS-CoV-2 S2 domain, followed by a foldon trimerization motif and C-terminal tags (Hisx8-tag, Strep-tag, and AviTag) were synthesized and cloned into pcDNA3.1/Zeo(+) expression vector (Thermo Fisher Scientific).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1/Zeo(+</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For crystallographic experiments, a codon-optimized nucleotide fragment encoding the SARS-CoV-2 RBD protein (residues 331-528), followed by an enterokinase cleavage site and a C-terminal double strep-tag was cloned into a modified pMT/BiP expression vector (pT350, Invitrogen)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pMT/BiP</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Drosophila S2 cells were stably co-transfected with pT350 and pCoPuro (for puromycin selection) plasmids.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pT350</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pCoPuro</div><div>suggested: RRID:Addgene_17533)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For Cryo-EM experiments, a codon-optimized nucleotide fragment encoding the SARS-CoV-2 spike (S) protein (residues 1-1208) was cloned with its endogenous signal peptide in pcDNA3.1(+) vector, and expressed as a stabilized trimeric prefusion construct with six proline substitutions (F817P, A892P, A899P, A942P, K986P, V987P), along with a GSAS substitution at the furin cleavage site (residues 682–685), followed by a Foldon trimerization motif (Hsieh et al., 2020), and C-terminal tags (Hisx8-tag, Strep-tag and AviTag).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1 ( + )</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The dimeric form of Cv2.1169 IgA1 was produced by co-transfection of Freestyle™ 293-F cells with a human J chain pcDNA™3.1/Zeo(+) vector as previously described (Lorin and Mouquet, 2015)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA™3.1/Zeo(+</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To evaluate spike cross-reactivity, Freestyle™ 293-F were transfected with pUNO1-Spike-dfur expression vectors (Spike and SpikeV1 to V11 plasmids, Invivogen) (1.2 µg plasmid DNA per 106 cells) using PEI-precipitation method.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pUNO1-Spike-dfur</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 S-Fuse neutralization assay: S-Fuse cells (U2OS-ACE2 GFP1-10 or GFP 11 cells) were mixed (ratio 1:1) and plated at a density of 8 × 103 per well in a μClear 96-well plate (Greiner Bio-One) as previously described (Buchrieser et al., 2020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GFP1-10</div><div>suggested: RRID:Addgene_68715)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cv2.1169 were also cloned into human Igγ1NA, Igγ1LALA [N297A and L234A/L235A mutations introduced by Site-Directed Mutagenesis (QuickChange, Agilent Technologies)], Igα1 and Fab-Igα1-expressing vectors (Lorin and Mouquet,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Agilent Technologies</div><div>suggested: (Agilent Technologies, RRID:SCR_013575)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Flow cytometry binding assays: SARS-CoV-2 specificity validation of cloned human IgG antibodies was performed using the S-Flow assay as previously described (Grzelak et al., 2020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2</div><div>suggested: (Active Motif Cat# 91351, RRID:AB_2847848)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data were acquired using a CytoFLEX flow cytometer (Beckman Coulter), and analyzed using FlowJo software (v10.7.1; FlowJo LLC).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEp-2 sections were examined using the fluorescence microscope Axio Imager 2 (Zeiss, Jena, Germany), and pictures were taken at magnification x 40 with 5000 ms-acquisition using ZEN imaging software (Zen 2.0 blue version, Zeiss) at the Imagopole platform (Institut Pasteur)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Zen</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For each antibody, Z-scores were calculated using ProtoArray® Prospector software (v5.2.3, Thermo Fisher Scientific), and deviation (σ) to the diagonal, and polyreactivity index (PI) values were calculated as previously described (Planchais et al., 2019).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ProtoArray® Prospector</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The evaluation kinetic parameters of the studied interactions were performed by using BIAevaluation version 4.1.1 Software (Biacore).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BIAevaluation</div><div>suggested: (BIAevaluation Software, RRID:SCR_015936)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">IC50 values were calculated using Prism software (v.9.3.1,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Prism</div><div>suggested: (PRISM, RRID:SCR_005375)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The final models were built by combining real space model building in Coot (Emsley et al., 2010) with reciprocal space refinement with phenix.refine.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Coot</div><div>suggested: (Coot, RRID:SCR_014222)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The final models were validated with Molprobity (Williams et al., 2018).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Molprobity</div><div>suggested: (MolProbity, RRID:SCR_014226)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Superpositions and figures were rendered using Pymol and UCSF Chimera (Pettersen et al., 2004)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Pymol</div><div>suggested: (PyMOL, RRID:SCR_000305)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">CryoSPARC blob picker was used for automated particle picking and the resulting particles used to obtain initial 2D references, which were then used to auto-pick the micrographs.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CryoSPARC</div><div>suggested: (cryoSPARC, RRID:SCR_016501)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Volcano plot comparing gene features (n=206 parameters) of tri-S+ B cells and normal memory B-cells (mB) was also performed using GraphPad Prism software (v.8.4,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Circos plot linking antibody sequences with at least 75% identity within their CDRH3 was performed using online software at http://mkweb.bcgsc.ca/circos.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Circos</div><div>suggested: (Circos, RRID:SCR_011798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">GraphPad Prism Inc.)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Principal component analysis (PCA) was performed using the prcomp() function in R Studio Server (v1.4.1103)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>R Studio Server</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04325646</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sero-epidemiological Study of the SARS-CoV-2 Virus Responsib…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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biorxiv.org/cgi/content/10.1101/2022.04.01.486719
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.31.486561

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.486561: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For 2-51, DH1055, 4A8, S1M11, S2E12, C144, 2-43 and S309 the heavy and light chain were cloned into a single IgG1 expression vector to express a fully human IgG1 antibody.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>C144</div><div>suggested: (Leinco Technologies Cat# C144, RRID:AB_2828501)</div></div><div style="margin-bottom:8px"><div>human IgG1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">BioLayer Interferometry (BLI): The antibodies were immobilized on anti-hIgG (AHC) sensors (FortéBio cat#18-5060) in 1x kinetics buffer (FortéBio cat#18-1092) in 96-well black flat bottom polypylene microplates (FortéBio cat#3694).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-hIgG (AHC</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK293 cells were transfected with full-length S, human ACE2, human TMPRSS2 and GFP.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293</div><div>suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All proteins were expressed from pcDNA2004 plasmids using Trans-IT transfection reagent according to the manufacturer’s instructions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA2004</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The primer pairs used in SNAP were designed for generating libraries from first- or second-strand cDNA produced from viral isolates or clinical specimens enabling successful SARS-CoV-2 library preparation from samples with low viral titers.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SNAP</div><div>suggested: (SNAP, RRID:SCR_007936)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The Swift Biosciences SARS-CoV2 Version 2.0 kit (Catalog # CovG1 V2-96) has been optimized to achieve additional genome coverage on the Illumina sequencing platforms.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Swift Biosciences</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cryo-EM image processing: Dose-fractioned movies were gain-corrected, and beam-induced motion correction using MotionCor2(37) with the dose-weighting option.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MotionCor2</div><div>suggested: (MotionCor2, RRID:SCR_016499)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The Spike particles were automatically picked from the dose-weighted, motion corrected average images using Relion 3.0(38).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Relion</div><div>suggested: (RELION, RRID:SCR_016274)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The geometry parameters of the final models were validated in COOT and using MolProbity(45)and EMRinger(46).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>COOT</div><div>suggested: (Coot, RRID:SCR_014222)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Figures were produced using PyMOL (The PyMOL Molecular Graphics System) and Chimera.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PyMOL</div><div>suggested: (PyMOL, RRID:SCR_000305)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">When purified proteins were analyzed using SEC-MALS, μMALS detectors were inline and data was analyzed using Astra 7.3 software package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Astra</div><div>suggested: (ASTRA, RRID:SCR_016255)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04505722</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Study of Ad26.COV2.S for the Prevention of SARS-CoV-2-Medi…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.03.31.486561
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273296

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273296: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: We treated data collection time as a continuous variable giving the number 1 for studies that were conducted in December 2020, the number 2 for studies that were conducted in January 2020, etc.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">The population of interest was pregnant women and the outcome was the COVID-19 vaccination uptake.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We searched PubMed, Medline, Scopus, ProQuest, Web of Science, CINAHL, and a pre-print service (medRxiv) from inception to March 23, 2022.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PubMed</div><div>suggested: (PubMed, RRID:SCR_004846)</div></div><div style="margin-bottom:8px"><div>Medline</div><div>suggested: (MEDLINE, RRID:SCR_002185)</div></div><div style="margin-bottom:8px"><div>ProQuest</div><div>suggested: (ProQuest, RRID:SCR_006093)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations: Our review and meta-analysis is subject to some limitations. Data taken from databases may not provide the most up-to-date evidence regarding COVID-19 vaccination uptake among pregnant women due to publication process. This limitation is of particular importance in the present review, as the data on vaccination of pregnant women are constantly increasing. Moreover, data collection time among studies ranged from December 2020 to October 2021, while evidence regarding safety and efficacy of COVID-19 vaccines in pregnant women is increasing significantly on an ongoing basis. Thus, we should interpret the results of this review with care since they may not directly predict future behavior of pregnant women. Additionally, we could not generalize our results since the number of relevant studies included in this review is low and these studies were conducted only in five countries. Only five studies examined the factors that affect pregnant women decision to take a COVID-19 vaccine. Moreover, these studies investigated mainly demographic factors, e.g. age, ethnicity, race, etc. Τhere is a large gap in the literature on the factors influencing the decision of pregnant women to be vaccinated against the COVID-19. For instance, psychological factors and social media variables that could affect women’ attitudes towards COVID-19 vaccination uptake are not investigated so far. Regarding meta-analysis, we applied a random effects model and we performed subgroup and meta-regres...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.04.01.22273296
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273305

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273305: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The study was approved by the UCL Research Ethics Committee [12467/005] and all participants gave written informed consent.<br>Consent: The study was approved by the UCL Research Ethics Committee [12467/005] and all participants gave written informed consent.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">These included gender (women vs men), ethnicity (white vs ethnic minorities), age groups (age 18-29, 30-45, 46-59, 60+), education (up to GCSE levels, A-levels or equivalent, and university degree or above), income (<£16,000, £16,000-29,000, £30,000-59,000, £60-89,000, ≥£90,000 per annum), employment status (employed non-key worker, employed key worker, other), area of living (city, town, rural), living situation (living alone, living with adults only, living with children), number of close friends (0 to 10+) and usual social contacts (twice a month or less, once or twice a week, three times a week or more), self-reported diagnosis of any long-term physical health condition or any disability (yes vs no), and self-reported diagnosis of any long-term mental health condition (yes vs no).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Authentication: 29 To compare mental health growth trajectories between the two matched groups, data were analysed using growth curve models.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">As sensitivity analyses, (i) we reran the analyses using alternative matching methods, namely one-to-many nearest neighbour matching and kernel matching; (ii) we excluded anyone who said they were ‘unsure’ if they had long Covid; and (iii) we explored further people’s understanding of the term ‘long Covid’.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Covid’</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.04.01.22273305
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273193

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273193: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IACUC: This study was approved by the ethical committee for research of Federal University of Mato Grosso do Sul (CAAE: 43289221.5.0000.0021) The study population was adults (aged ≥18 years) residing in Brazil, and who underwent SARS-CoV-2 RT-PCR or rapid antigen testing associated with symptomatic illness13 during the study period.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">After identification of each case, we randomly chose one control from the set of all eligible matching controls, allowing for replacement of controls between cases.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Some limitations should be acknowledged. The data available for this study was collected as part of Brazil’s passive surveillance efforts for Covid-19, so important covariates may be missing or incomplete. The distribution of RT-PCR tests and antigen tests, which have significantly different sensitivity, changed over the course of the study period, which could have led to a decrease in estimated VE during the Omicron period through misclassification. However, a sensitivity analysis restricted to RT-PCR tests produced similar results. In addition, the test-negative controls may have been different during the Omicron and Delta periods, which could explain some of the difference in VE estimates. In particular, a higher proportion of controls were hospitalized or died during the Delta period (Table 1), implying either that other pathogens with severe outcomes were circulating during that period, or that less testing was being done in the outpatient setting during the Delta period. Finally, differences in effectiveness and waning patterns by age could be driven by other factors, including occupational exposure (e.g., health care workers) and personal risk mitigation behavior. Overall, we found that primary vaccination with two doses of the CoronaVac vaccine provided 50-60% effectiveness against severe Covid-19 outcomes during the Omicron epidemic in Brazil, although effectiveness against symptomatic disease was close to zero. While a homologous booster afforded little additional p...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273193
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273242

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273242: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: This study received non-research determination by the University of Massachusetts Chan Medical School Institutional Review Board.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengths and Limitations: This report offers a unique look into COVID-19 test reporting behaviors of nearly fifteen thousand digital assistant users throughout the United States. However, there are limitations to this data. The number of digital assistant users is quite small compared to all intervention participants, and with the current data, we are unable to assess the demographics or socioeconomic status of digital assistant users, nor how digital assistant users compare to non-users. Conclusion: Three-quarters of those who used the digital assistant for testing reported their results to the DoH, indicating that app-based reporting may be an effective way to increase reporting of rapid tests for COVID-19. However, the relatively low voluntary uptake of the digital assistant indicates that user-centered strategies may be necessary to maximize digital assistant usage.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273242
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273262

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273262: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273262
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273208

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273208: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  While it is an extensive collection of EHR data, various limitations exist in using this dataset to determine SARS-CoV-2 and COVID-19-related risks for the global population. For example, we observed a greater prevalence of NF1 patients in the N3C as compared to population prevalence estimates, indicating that this dataset may not represent the general population due to its specific data acquisition protocols. As with any multi-site combination of EHR data, there may also be site-related differences in clinical measures due to variations in clinical practice and medical record documentation. Any biases affecting analyses of care patterns or outcomes due to geographical, regional, cultural, or other differences between institutions remained unassessed due to anonymized coding of the N3C data contributing institutions in the de-identified dataset. Furthermore, clinical coding of patients with NF1, NF2, SWN or other rare diseases may be incomplete in EHRs, i.e. the codes used to define the study cohorts (Supplemental Tables 1-9) within N3C could have missed disease-positive patients without appropriately recorded diagnostic codes. Lastly, the SARS-CoV-2 testing rate, diagnosis and treatment of COVID-19, access to clinical care in various sites and various disease populations may vary significantly. Additionally, there are various considerations specific to the data deposited in the N3C data enclave. Due to N3C’s phenotype acquisition design, the patients included in the Data Enc...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273208
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273274

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273274: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273274
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.31.486548

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.486548: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: All participants provided written informed consent before participation in the study and the study was conducted in accordance with Good Clinical Practice.<br>IRB: The study was performed in compliance with all relevant ethical regulations and the protocol (DRO-1006) for studies with human participants was approved by the Institutional Review Board of the Rockefeller University.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were washed 6 times with washing buffer and then incubated with anti-human IgG, IgM or IgA secondary antibody conjugated to horseradish peroxidase (HRP) (Jackson ImmunoResearch 109-036-088, 109-035-129, and Sigma A0295) in blocking buffer at a 1:5,000 dilution (IgM and IgG) or 1:3,000 dilution (IgA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: (Jackson ImmunoResearch Labs Cat# 109-036-088, RRID:AB_2337594)</div></div><div style="margin-bottom:8px"><div>IgA</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The half-maximal neutralization titers for plasma (NT50) or half-maximal and 90% inhibitory concentrations for monoclonal antibodies (IC50 and IC90) were determined using four-parameter nonlinear regression (least squares regression method without weighting; constraints: top=1, bottom=0) (GraphPad Prism).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IC90</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The enriched B cells were incubated in Flourescence-Activated Cell-sorting (FACS) buffer (1× PBS, 2% FCS, 1 mM ethylenediaminetetraacetic acid (EDTA)) with the following anti-human antibodies (all at 1:200 dilution): anti-CD20-PECy7 (BD Biosciences, 335793), anti-CD3-APC-eFluro780 (Invitrogen, 47-0037-41), anti-CD8-APC-eFluor780 (Invitrogen, 47-0086-42), anti-CD16-APC-eFluor780 (Invitrogen, 47-0168-41), anti-CD14-APC-eFluor780 (Invitrogen, 47-0149-42), as well as Zombie NIR (BioLegend, 423105) and fluorophore-labeled Wuhan-Hu-1 RBD, NTD, and ovalbumin (Ova) for 30 min on ice.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD20-PECy7</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD3-APC-eFluro780</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD8-APC-eFluor780</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD16-APC-eFluor780</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD14-APC-eFluor780</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For B cell phenotype analysis, in addition to above antibodies, B cells were also stained with following anti-human antibodies (all at 1:200 dilution): anti-IgD-BV650 (BD, 740594), anti-CD27-BV786 (BD biosciences, 563327), anti-CD19-BV605 (Biolegend, 302244), anti-CD71-PerCP-Cy5.5 (Biolegend, 334114), anti-IgG-PECF594 (BD, 562538), anti-IgM-AF700 (Biolegend, 314538), anti-IgA-Viogreen (Miltenyi Biotec, 130-113-481)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human</div><div>suggested: (Abnova Cat# H00007360-A01, RRID:AB_563327)</div></div><div style="margin-bottom:8px"><div>anti-IgD-BV650</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD27-BV786</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD19-BV605</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD71-PerCP-Cy5.5</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-IgM-AF700 ( Biolegend , 314538) , anti-IgA-Viogreen ( Miltenyi Biotec , 130-113-481)</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The frequency distributions of human V genes in anti-SARS-CoV-2 antibodies from this study was compared to 131,284,220 IgH and IgL sequences generated by (50) and downloaded from cAb-Rep (51), a database of human shared BCR clonotypes available at https://cab-rep.c2b2.columbia.edu/.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 293T (CRL-11268) cells were obtained from ATCC, and the cells were transfected with pNL4-3 DEnv-nanoluc and pSARS-CoV-2-SΔ19.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T</div><div>suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 293T (CRL-11268) cells were obtained from ATCC, and the cells were transfected with pNL4-3 DEnv-nanoluc and pSARS-CoV-2-SΔ19.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pNL4-3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pSARS-CoV-2-SΔ19</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The average of its signal was used for normalization of all the other values on the same plate with Excel software before calculating the area under the curve using Prism V9.1 (GraphPad).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Excel</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Prism</div><div>suggested: (PRISM, RRID:SCR_005375)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For monoclonal antibodies, the ELISA half-maximal concentration (EC50) was determined using four-parameter nonlinear regression (GraphPad Prism V9.1).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">3,000 units/ml RNasin Ribonuclease Inhibitors (Promega, N2615)) per well using a FACS Aria III and FACSDiva software (Becton Dickinson) for acquisition and FlowJo for analysis.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FACSDiva</div><div>suggested: (BD FACSDiva Software, RRID:SCR_001456)</div></div><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For B cell phenotype analysis, in addition to above antibodies, B cells were also stained with following anti-human antibodies (all at 1:200 dilution): anti-IgD-BV650 (BD, 740594), anti-CD27-BV786 (BD biosciences, 563327), anti-CD19-BV605 (Biolegend, 302244), anti-CD71-PerCP-Cy5.5 (Biolegend, 334114), anti-IgG-PECF594 (BD, 562538), anti-IgM-AF700 (Biolegend, 314538), anti-IgA-Viogreen (Miltenyi Biotec, 130-113-481)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Biolegend , 314538) , anti-IgA-Viogreen ( Miltenyi Biotec</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Miltenyi</div><div>suggested: (Miltenyi Biotec, RRID:SCR_008984)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sequence analysis was performed using MacVector.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MacVector</div><div>suggested: (MacVector, RRID:SCR_015700)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">: Figures arranged in Adobe Illustrator 2022.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Adobe Illustrator</div><div>suggested: (Adobe Illustrator, RRID:SCR_010279)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.31.486548
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https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273299

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273299: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.04.01.22273299
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https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273267

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273267: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study relies on a number of potentially important assumptions, approximations and limitations. First, we chose the daily deaths as the dataset to fit to the model, inferring it from cumulative confirmed deaths, as opposed to using other data such as cases, which have been associated with known and considerably larger biases. However, while the deaths are likely a more reliable measure of the pandemic than cases they are far from perfect. Different states and countries use different criteria when registering deaths (for example, some report only confirmed deaths while others report both probable and confirmed deaths) and have different delays in reporting. Additionally, the reported numbers have been shown to be lower than the true toll of the pandemic (see e.g [33, 34, 46–49]). Our age-stratified compartmental model treats each population separately and ignores travel and importation of cases from other locations. While both global and local travel were significantly disrupted in 2020, they were responsible for the initial spread of COVID-19, and continue to play a role during latter periods. In this work, we ignored the initial introduction of cases to a location and focused on the dynamics of the virus following its introduction to a population. Also, we assumed the same quality of care over time at all locations. In practical terms, in the model, we assume that the probability of death from COVID-19 depended only on age during this period prior to wide spread vaccinati...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.31.22273267
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https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273281

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273281: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Other studies where VE estimates after 3 doses were over 90% have included older cohorts or have used physician manual review of medical notes to confirm the presence of severe COVID-19 symptoms.(13, 14) We only identified one study that had stratified by period after a booster dose – Thompson et al found VE of 91% in the first 2 months following a third dose and 78%>= 4 months after the third dose – this is similar to our findings in 18 to 64 year olds with some of the outcomes, though generally more waning than that we observed in 65+ year olds.(14) Limitations and advantages of the test negative case control design have been previously described.(8, 18, 20) One of the biggest limitations of this specific study is that in relies on hospital coded data which may have coding errors or not have interventions coded when they were used (e.g. oxygen use). A study where data are collected prospectively on cases using reporting forms or detailed case note review could avoid this misclassification bias, but is much more challenging to do with sufficiently large numbers.(21) One potential limitation for the TNCC design when looking at severe disease in controls is test sensitivity when a large proportion of those tested are truly positive. This, however, is more likely to affect Delta than Omicron analyses (as Delta is more severe) and is one of the reasons, along with study power, that in past analyses we have chosen to use all symptomatic pillar 2 controls for hospitalised COVID-19...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.04.01.22273281
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https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273316

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273316: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In this early stage of approximately exponential growth in the number of cumulative case, C(t), where C′(t) ≈ rC(t), we can estimate r by using cumulative cases at two points in time C(t1) and C(t2), where r = log (C(t1)/C(t2)) /(t1 − t2) and t1 > t2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>t1 − t2</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  We note there are several limitations with the current study. In our model it is assumed that vaccination makes the recipient immune (e.g., there are no breakthrough cases). A logical future direction would include waning immunity and booster shots. Another option would be to include vaccinated sub-populations with decreased transmission rates and shorter convalescence times. As differing variants have become dominant (e.g., delta, omicron), the parameters would need to be altered to reflect increased transmission rates and, perhaps, shortened infectious duration. We also assumed 100% compliance with interventions, meaning that every member of the community wears well-fitting masks at all times when they are indoors. Overall, our model exhibits results consistent with current public health messaging. Our model predicts that, despite increasing vaccination rates, it remains important to continue to socially distance and wear masks to reduce transmission. Whether these results will hold for more recent variants, such as delta and omicron, remains to be seen.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.04.01.22273316
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273236

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273236: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARI: A case is defined as SARI if the symptoms begin within the past ten days with fever (measured≥ 38□) and respiratory infection (cough) necessitating hospitalization9. 2 Study Protocol: An electronic search of PubMed/MEDLINE, Scopus and Google Scholar was carried out for all the articles published between January 2020 and December 2021 concerning the impact of the COVID-19 pandemic on Influenza surveillance.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Google Scholar</div><div>suggested: (Google Scholar, RRID:SCR_008878)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The forest plots were constructed using metaprop package in STATA.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>STATA</div><div>suggested: (Stata, RRID:SCR_012763)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations: Even though we limited the review to articles in English, very few studies were excluded for that reason. We could not include studies from Asia and South America because of incomplete data of cases tested in 2019, even after contacting the corresponding authors. Another limitation was the inaccuracy in the catchment population for hospital-based and non-sentinel surveillances. Due to a lack of studies enrolling all age groups from Japan, one hospital-based study among paediatric cases had to be included for the quantitative synthesis.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273236
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273059

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273059: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Participants who provided their consent were included in the study.<br>IRB: Ethics approval for the research was obtained from the Institutional Ethics Committee of the Public Health Foundation of India (Reference # TRC-IEC-342.1/17).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Despite the novel findings presented in this paper, a few study limitations are worth considering. All interviews were audio-recorded thus participants’ non-verbal cues could not be captured, which could have enriched descriptions of experiences and situations in the study. Due to snowball sampling the number of participants at state, district, and village levels were not equal. Thus, there could be reporting bias by the participants due to their difference in the level of engagement with programme implementation. In context to the impact of COVID-19 on adolescent health and development issues, we have captured the perspective of various stakeholders other than PEs. As indicated by the stakeholder, there was a limited impact so we did not explore these issues further by gender, socio-economic status, marital status, etc. We could not include adolescents who are part of RKSK in this study, thus the beneficiary perspective is missing. Finally, our study was limited to a few participants from two states, limiting our findings’ generalizability. All the above limitations will be considered while conducting an ongoing larger study with a bigger set of participants in the same study sites.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22273059
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.04.01.486695

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.486695: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Materials are available from the authors under a material transfer agreement with BioNTech.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BioNTech</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04380701</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Trial Investigating the Safety and Effects of Four BNT162 …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04949490</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Trial Investigating the Safety and Effects of One or Two A…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.04.01.486695
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273252

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273252: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations of our analysis include recruitment from vaccination centres, which may attract more health-conscious individuals, the selection of whom could lead to an underestimate of the true seroprevalence (Supplementary Table 1). Further, the history of COVID-19 infection was based on self-reporting which is less reliable than laboratory confirmed diagnosis.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.04.01.22273252
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.04.01.22273291

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.04.01.22273291: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Follow the Helsinki Declaration as revised in 2013,we analyzed 44 patients in the intensive isolation ward of Xiaogan Central Hospital, with an average age of 53 years, 27 males and 15 females.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.04.01.22273291
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273272

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273272: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273272
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273027

1
1. sciscore 04 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273027: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Authentication: This tool consists of seven validated items to measure symptoms of Generalized Anxiety Disorder on a 4-point Likert scale.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengths and weaknesses: The large sample size is a strength of this study. Among the 9,035 individuals included in the study, 3,883 had contracted COVID-19. The second strength is the temporal resolution, as we had both baseline survey and eight monthly follow-up surveys covering the second and third epidemic waves as well as the start of vaccination in Sweden. Our study also has limitations. On the one hand, as participation was open to all, our sample is not representative of the general Swedish population. For example, 81% of the participants were women and there was a relatively low proportion of younger people. Selection bias due to the method of recruitment could therefore not be excluded. For instance, it has been shown that people recruited through social media campaigns had higher levels of anxiety and depression, compared with people recruited by invitation, in the Omtanke2020 study (Lovik et al., 2021). To consider these limitations, we adjusted in all analyses for sex, age, and recruitment type. The modification of the PC-PTSD-5 scale to make it specific for the pandemic is another concern as it included three items on thinking and dreaming about COVID-19. As a result, this scale might have evaluated the post-traumatic stress of being in a pandemic rather than contracting the disease. We therefore referred to this outcome as COVID-19-related distress throughout this paper. Finally, the low correlation noted between stress and other mental health measures may be ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22273027
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486373

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486373: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Multiple sequence alignment for S gene (spike protein) of the SARS-CoV-2 variants, whose nucleotide sequences of each variant were obtained from NCBI, was analyzed by Clustal W program [18].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Clustal W</div><div>suggested: (An Extended and Parallel version of Clustal, RRID:SCR_008620)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then FastTree [19] with default parameters provided phylogenetic tree and evolutionary distances between each mutant.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FastTree</div><div>suggested: (FastTree, RRID:SCR_015501)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.30.486373
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273226

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273226: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: 2.1 Blood collection: Nine mL of blood is drawn in heparin tubes from five healthy volunteers under informed consent and 14 COVID-19 patients admitted at the Intensive Care Unit (ICU) at the Frankfurt University Hospital, seven of which with supported ventilation and six receiving extracorporeal membrane oxygenation (ECMO) (Online Supplementary Table S1).<br>IRB: The study is performed according to the Declaration of Helsinki and under the approval of the Fraunhofer Institute for Translational Medicine and Pharmacology ethics committee (reference #20-643, #20-982).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">2.4 Flow analysis: Velocity, lateral cell position in the y-direction, and projection area of each cell are determined using a customized python script.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Additional analyses, including untargeted analyses and Fish score calculation via MS/MS, are calculated against the ChemSpider database with Compound Discoverer 2.0 (Thermo Fisher, Bremen, Germany). 2.7 Proteomics: Proteomics analyses are performed via filter aided sample preparation (FASP) digestion and nano UHPLC-MS/MS identification (TIMS TOF Pro 2 Single Cell Proteomics, Bruker Daltonics, Bremen, Germany), as previously described (24).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ChemSpider</div><div>suggested: (ChemSpider, RRID:SCR_006360)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">2.8 Statistical analyses: Graphical representations and statistical analyses by T-test, repeated measures ANOVA or Kruskal-Wallis test are performed with GraphPad Prism (GraphPad Software, Inc, La Jolla, CA)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, MATLAB (MathWorks, Natick, MA), and MetaboAnalyst 5.0.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MATLAB</div><div>suggested: (MATLAB, RRID:SCR_001622)</div></div><div style="margin-bottom:8px"><div>MetaboAnalyst</div><div>suggested: (MetaboAnalyst, RRID:SCR_015539)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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medrxiv.org/cgi/content/10.1101/2022.03.31.22273226
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.31.486531

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.486531: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The study was approved by the Hadassah Medical Center (#0296-20-HMO) and the Sheba Medical Center (#2832-15-SMC) Institutional Review Boards.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The following primary antibodies were used: α-E-Cadherin (Mouse monoclonal, 1:100, Abcam, ab1416; for the detection of epithelial cells), α-SARS-CoV-2 Nucleocapsid (Rabbit monoclonal, 1:500, Abcam, ab271180).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>α-E-Cadherin</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>α-SARS-CoV-2 Nucleocapsid</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The following secondary antibodies were used: Donkey anti-Mouse IgG pre-adsorbed, Alexa Fluor® 568 (1:250, Abcam, Cat# ab175700), Goat anti-Rabbit IgG Highly Cross-Adsorbed Alexa Fluor Plus 647 (1:250, Thermo Fisher Scientific, Cat# A32733).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Mouse IgG</div><div>suggested: (DSHB Cat# LEP100 IgG, RRID:AB_528124)</div></div><div style="margin-bottom:8px"><div>anti-Rabbit IgG</div><div>suggested: (Biorbyt Cat# orb14385, RRID:AB_10735740)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells and viruses: Simian kidney Vero E6 (ATCC CRL-1586), Calu-3 (ATCC HTB-55), Madin-Darby Canine Kidney (MDCK, ATCC CCL-34™) cells and H1299-ACE2 overexpressed cells (kindly provided by Dr. Alex Sigal)1 were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Biological Industries, Beit Haemek, Israel), supplemented with 10% fetal bovine serum, 2 mM L-Glutamine, 10 IU/ml Penicillin, and 10 μg/ml streptomycin (Biological Industries, Beit Haemek, Israel).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>E6</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Calu-3</div><div>suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Influenza virus A(H1N1) pdm09 (NIBRG-121xp, Cat# 09/268; obtained from NIBSC, UK) was propagated in MDCK cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MDCK</div><div>suggested: CLS Cat# 602280/p823_MDCK_(NBL-2, RRID:CVCL_0422)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The virus titers of cleared infected cells- and tissue supernatants were determined by a standard plaque assay on H1299-ACE2 cells (SARS-CoV-2) or MDCK cells (influenza virus).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>H1299-ACE2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Whole-mount tissues were visualized using a Nikon A1R confocal microscope and were analyzed using NIS Elements software (Nikon).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NIS Elements</div><div>suggested: (NIS-Elements, RRID:SCR_014329)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis: All data, presented as means ± standard errors of the mean (SEM), were analyzed using paired, two-tailed t test in GraphPad Prism 9 software (GraphPad Software Inc., San Diego CA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study has several limitations. Native respiratory tissues in organ culture are relatively short-lived (up to 7 days in culture). Thus, our ex vivo infection models mirror early events of infection and do not address the late phase of viral transmission or the combined effects of the local and systemic immune responses. Nonetheless, our studies recapitulate SARS-CoV-2 infection and innate immune response within the authentic multicellular complexity of both the upper and the lower human respiratory tract, containing tissue-specific compositions of cell types, including immune cells, and extracellular matrix. To date, we are not aware of studies that have examined the distinctive innate tissue responses to Omicron as related to its altered replication phenotype in the lower respiratory tract. Such data are critical to better understand and address the evolution of SARS-CoV-2 into a less virulent human-tropic virus. In summary, our studies in native human nasal and lung tissues infected ex vivo reveal a significantly enhanced interferon response to Omicron, compared to precedent SARS-CoV-2 VOC. The findings imply that the early induction of antiviral ISG, which was most prominent in lung tissues, could play a part in the restricted replication and pathology of Omicron in the lungs. They provide insights for the attenuated pathogenicity of Omicron, and for further studies of pathways involved in the enhanced mucosal innate immune responses to this newly evolving variant.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.03.31.486531
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273238

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273238: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273238
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272927

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272927: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Other: According to Danish law, studies based entirely on registry data do not require approval from an ethics review board 6.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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medrxiv.org/cgi/content/10.1101/2022.03.25.22272927
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273218

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273218: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Sequencing prioritizing a new variant may have led to the overestimations, and is the limitation of our real-time prediction using sequence databases. An explicit inclusion of submission delays for each variant in the model may solve this problem for real-time predictions. Use of data sources without variant prioritization, such as results of PCR tests, can also solve this problem. Our model assumes that there was no difference between the generation times of both variants with a mean value of 4.64 days [17]. However, Hart et al. estimated the generation time of Delta (4.7 days) to be shorter than that of Alpha (5.5 days) [21]. To allow differences between generation times of variants, it is necessary to extend the model to also estimate the relative generation times of the variant w.r.t. that of the baseline variant [22].
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273218
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273222

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273222: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">First, we reduce inter-municipality mobility as reported by Google [34] in the four phases of the first wave in the Netherlands.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Google</div><div>suggested: (Google, RRID:SCR_017097)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Another limitation is that mobility in our framework is quantified based on mobile phone signal data that only provide anonymized movements between pairs of locations. As such, the data do not provide identifiers to link multiple movements into one itinerary, which means that in our analysis, agent movements are somewhat shorter on average than in reality, but agents also visit more different locations than in reality. We further assume that agent movements vary randomly day-by-day, whereas in reality commuting means that an agent would repeatedly travel to the same location. However, the impact of this simplifying assumption is limited as, at the start of an epidemic, the distribution of movement over agents is of relatively low importance, especially in the case of a relatively small and highly connected country as the Netherlands. This is in contrast to situations towards the tail of an epidemic or in larger geographies (e.g., Brazil [24, 25] and India [26]), where the transmission potential of “high-mobility corridors” can eventually dry up as a result of rising immunity among high-mobility individuals. Finally, we adopted data on national patterns in mobility (Google mobility), meaning that it was not possible to account for changes in mobility by geography or demographic group. The geographical aspects could be addressed by using longitudinal mobile phone signal data or individual-level self-reported data via mobile phone apps [27–29]. This would require that such data ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/content/10.1101/2022.03.31.22273222v1
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https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273230

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273230: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Posterior samples of the parameters are generated using Hamiltonian Monte Carlo (HMC) (Hoffman and Gelman, 2014) in Stan (Carpenter et al., 2017) using PyStan (v.2.19.0.0: https://mc-stan.org/users/interfaces/pystan).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PyStan</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Correlation analysis: Spearman’s rank-order correlation coefficient (rs) was calculated for delays between symptom-onset-to-confirmation, -hospitalisation and -death as well as hospitalisation-to-death for each state, using the scipy.stats ‘spearmanr’ function (scipy version 1.7.3).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>scipy</div><div>suggested: (SciPy, RRID:SCR_008058)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  While our results provide a rigorous underpinning and insight into delay distributions and impact of these on epidemiological parameters estimation, we acknowledge several limitations. The Global.health database which contains line lists that our distributions have been estimated from, though extensive, contains typing errors, and the degree to which these bias our estimates are unknown. Our data ingestion pipeline is mostly automated and only occasionally are we able to manually verify the accuracy of the data. Further, when comparing line list data between and within countries we note disparities in notification systems and differences in case definitions. Further work should evaluate the demographic biases in these data and how that may affect transmission dynamics (longer delays for less severe cases in younger age groups may impact transmission substantially). Lastly, there is a low testing rate for the countries analysed (Hasell et al., 2020) and heterogeneities in testing rates in both time and space (Vandenberg et al., 2021) which can influence the results for both cases and rt. Future epidemiological work is needed to compare parameters estimated from case data, death data and excess death data across different settings (Gostic et al., 2020) and more intensive monitoring and/or the use of alternative data sources such as genomic data (Inward, Faria and Parag, 2022) is needed to improve the reliability of estimations. Few countries report highly detailed epidemiologic...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.31.22273230
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https://medrxiv.org/cgi/content/10.1101/2022.03.27.22273007

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.27.22273007: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Search strategy: A comprehensive search of major electronic databases (PubMed and Google Scholar) was conducted on February 10, 2022, to locate all publications.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PubMed</div><div>suggested: (PubMed, RRID:SCR_004846)</div></div><div style="margin-bottom:8px"><div>Google Scholar</div><div>suggested: (Google Scholar, RRID:SCR_008878)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Microsoft Excel spreadsheets were used to collect the necessary information from the extracted data.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Microsoft Excel</div><div>suggested: (Microsoft Excel, RRID:SCR_016137)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272732

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272732: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immunohistochemistry and RNAscope (SARS-CoV-2): Immunohistochemistry was performed on a Leica Bond-RX autostainer (Leica Biosystems, US) with antibody targeting SARS-CoV-2 spike protein (Abcam, ab272504) at 2 μg·mL−1</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2 spike protein ( Abcam ,</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In this study the main factor of interest is disease with the main contrasts investigated as COVID19 vs control, pH1N1 vs control and COVID19 vs pH1N1 Gene set enrichment analysis: Gene sets from the Molecular Signatures Database49 (MsigDB, v7.2)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Gene set enrichment analysis: Gene</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Hallmarks, C2 (curated gene sets) and C5 (gene ontology terms) categories and KEGG pathways gene sets were obtained using the getMisgdb and appendKEGG functions from the msigdb R package (v1.1.5)49</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>KEGG</div><div>suggested: (KEGG, RRID:SCR_012773)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Gene set enrichment analysis (GSEA) were performed using fry from the limma package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Gene set enrichment analysis</div><div>suggested: (Gene Set Enrichment Analysis, RRID:SCR_003199)</div></div><div style="margin-bottom:8px"><div>limma</div><div>suggested: (LIMMA, RRID:SCR_010943)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.24.22272732
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https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272599

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272599: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The trial was reviewed and approved by the Erasme Hospital Ethics Committee (P2021/251) and the Federal Agency for Medicines and Health Products (EudraCT: 2021-002088-23A).<br>Consent: At the baseline visit, participants provided informed consent before having blood drawn and being vaccinated.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Study design: REDU-VAC is a participant-blinded, randomised, phase 4, multicentre, non-inferiority study investigating safety, reactogenicity and immunogenicity of a fractional dose of the mRNA COVID-19 vaccine BNT162b2 (Pfizer-BioNTech).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">To ensure participant blinding to the vaccine dose, randomisation lists were kept out of sight, vaccines were prepared, and syringes were filled beforehand.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">Statistical analysis: The sample size was calculated assuming a true difference of geometric means of the primary outcome on the log10 scale being 0 between the reduced and the full dose, and a standard deviation of GMT on the log10 scale being 0.27 (17).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 anti-receptor binding domain (RBD) specific IgG concentrations were measured by ELISA (reported as Binding Antibody Units [BAU]/mL) on days 0/21/49 and month 6.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2 anti-receptor binding domain (RBD</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 Specific Binding Antibodies: Enzyme-linked immunosorbent assay: Binding antibodies at baseline and after vaccination were assessed using an enzyme-linked immunosorbent assay (ELISA) for the quantitative detection of IgG-class antibodies to RBD (Receptor Binding Domain, Wuhan strain) (Wantai SARS-CoV-2 IgG ELISA (Quantitative); CE-marked; WS-1396; Beijing Wantai Biological Pharmacy Enterprise Co., Ltd, China).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgG-class</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Next, plates were incubated (37°C, 30 min) with horseradish peroxidase (HRP)-conjugated anti-human IgG antibodies and washed five times before adding a TMB and urea peroxide solution for 15 min (37°C, dark).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Multiplex Immunoassay (Luminex): Antibody responses at baseline were tested with an in house multiplex immunoassay (MIA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MIA</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In this test, IgG antibodies to SARS-CoV-2 antigens RBD, S1, S2 and N (Wuhan strain) were measured simultaneously in one assay run.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>SARS-CoV-2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 Neutralizing Antibodies: Serial dilutions of heat-inactivated serum (1/50-1/25600 in EMEM supplemented with 2mM L-glutamine, 100U/ml - 100μg/ml of Penicillin-Streptomycin and 2% fetal bovine serum) were incubated during 1h (37°C, 7% CO2) with 3xTCID100 of a wild type Wuhan strain (2019-nCoV-Italy-INMI1, reference 008V-03893), the B.1.617.2 Delta variant (83DJ-1) and the BA.1 Omicron variant of SARS-CoV-2, in parallel.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>83DJ-1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were then coated with human IFN-γ antibody (15 µg/ml) overnight at 4°C, washed and blocked with 200µl of Roswell Park Memorial Institute (RPMI) containing 10% fetal bovine serum (FBS) for at least two hours.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IFN-γ</div><div>suggested: (MABTECH Cat# 3420-2APT, RRID:AB_2877719)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After incubation, the plates were washed and incubated with the human biotinylated IFN-γ detection antibody (1µg/ml) for 2 hours, washed and the streptavidin–Horseradish Peroxidase (streptavidin-HRP) diluted at 1/750 in PBS-0,5% FBS was added for one hour.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>streptavidin-HRP</div><div>suggested: (Cell Signaling Technology Cat# 3999, RRID:AB_10830897)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Flow cytometry: Cells were stimulated in 96-well round-bottom plates with 1 × 106 PBMCs in RPMI 1640 medium (Lonza, Basel, Switzerland) supplemented with 10% heat-inactivated FBS (Sigma-Aldrich, Kawasaki, Japan), penicillin/streptomycin, amino acids and PepMix SARS-CoV-2 spike glycoprotein peptide pools (SUB1-SUB2, JPT, Berlin, Germany) in the presence of 1µg/mL purified anti-CD28 antibody (clone CD28.2, BD Biosciences, New Jersey, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD28</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After stimulation, Live/Dead fixable red stain (ThermoFisher, Massachusetts, USA) was used to exclude dead cells and the staining of surface antigens was carried out for 20 min with the following fluorochrome-conjugated antibodies: CD3 BV711 (UCHT-1; BD), anti-CD8 PeCy7 (RPA-T8; BD), CD4 HV450 (RPA-T4; BD).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD8</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD4</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sample-virus mixtures and virus/cell controls were added to Vero cells (18.000 cells/well) in a 96-well plate and incubated for five days (37°C, 7% CO2).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Net OD values were converted to arbitrary IgG units per ml by interpolation from a point-by-point plot fitted with the standard concentrations and net OD values (correlation coefficient R2≥0.9801), using GraphPad Prism version 9.0.0 for Windows (GraphPad Software, San Diego, California USA) and exported to Microsoft Excel.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>Microsoft Excel</div><div>suggested: (Microsoft Excel, RRID:SCR_016137)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Samples were acquired on a BD LSRFortessa flow cytometer and analyzed with FlowJo v9.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  This study has several limitations, the first being the relatively limited sample size. A larger number of participants would have resulted in smaller confidence intervals around the GMRs, which might have impacted the conclusions on non-inferiority. Although males were underrepresented in this study, we do not believe this is a major limitation as immune responses to COVID-19 mRNA vaccination in healthy, younger subjects are only minimally gender-dependent and importantly, there is no basis to assume that fractional dosing would affect immune responses differently between males and females (24–26). Secondly, the small proportion of previously infected participants in our study population (17/144, 12%) does not allow for a separate sensitivity analysis in this group. With record high COVID-19 incidences worldwide, the proportion of the population who experienced a past infection is rapidly growing, making analyses including previously infected people ever more relevant. In addition, breakthrough infections were not actively monitored by regular molecular testing. Therefore, we may have missed asymptomatic infections, which are not reported by the study participants. Thirdly, while protection from infection or disease has been convincingly correlated with titres of binding and neutralizing antibodies, as discussed previously, it is not possible to determine with certainty that the moderately lower titres observed in our study will translate to equally moderately lower efficacy...
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04852861</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Enrolling by invitation</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">COVID-19: Safety and Immunogenicity of a Reduced Dose of the…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.25.22272599
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.31.22273221

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.31.22273221: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Written informed consent was obtained from all participants.<br>IRB: The trial was reviewed and approved by the Medical research Ethics Committees United Nieuwegein (MEC-U, reference 20.125).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">We justified the sample size by calculating that 556 PLWH receiving mRNA vaccines would be sufficient to detect a serological response rate of 90% or lower compared to a hypothetical 95% response rate in controls with >80% power.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We defined a hyporesponse as 50-300 BAU/mL and non-response as <50 BAU/mL, based on previous studies which showed correlation of antibody concentration of 300 BAU/mL with a neutralising capacity of 1:40.[9, 22] In the subgroup, anti-spike SARS-CoV-2 specific T-cell response, and antibody response 21 days after the first vaccine dose were evaluated.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-spike SARS-CoV-2 specific T-cell response,</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data were analysed using IBM SPSS Statistics 25, R (v. 4.1.2), and GraphPad Prism 8.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Flow cytometry data were analysed using FlowJo software version 10.8.1.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.31.22273221
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272956

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272956: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  In this study, we have used mathematical modeling to demonstrate the strengths and limitations of a layered mitigation strategy in limiting in-school transmission while keeping schools open. We examined the impact of risk mitigation measures (masking, ionizers, ventilation, filtration) on limiting spread within a classroom when an infected person is present. Our findings underscore the critical importance of layered mitigation strategies in limiting in-school transmission. With that said, all of the examined measures can be readily defeated by sufficiently high viral loads, a biological change that has already been observed during the pandemic (for example between the Wuhan strain and the Delta variant). This is a crucial point: minimal effective measures for the disease as it is at present may have an increased risk of failure in the face of new variants of SARS-CoV-2. Our findings also indicate that the risk of transmission in schools may be hard to predict in certain settings (such as in the turbulent airflow patterns of a well-ventilated room). As a corollary, our work points to the central importance of relying on measures to limit the likelihood of having an infected person in the classroom: testing and isolation, limiting class sizes, and targeted closures when community transmission is high. The ongoing COVID-19 pandemic shows no signs of permitting a return to pre-pandemic life, with high rates of transmission leading to rapid viral evolution. The course of the pande...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.25.22272956
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486313

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486313: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Membranes were first incubated with the primary antibody (Anti-Glutathione antibody [D8], ab19534,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Anti-Glutathione</div><div>suggested: (Abcam Cat# ab19534, RRID:AB_880243)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">; Mouse anti DDDDK-Tag (FLAG-tag) mAb, AE005, ABclonal) in 5% BSA TBST for 16 h at 4 °C, washed with TBST three times, then incubated with the secondary antibody (HRP-labeled Goat Anti-Mouse IgG(H+L), A0216, Beyotime) in 5% BSA TBST (1 h, 25 °C), and washed with TBST three times.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti DDDDK-Tag (FLAG-tag</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Anti-Mouse IgG(H+L)</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In the present study, HEK293T cells were seeded in 12-well plates overnight.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For bacterial expression, the cDNA encoded the SARS-CoV-2 PLpro with E. coli codon optimization was ordered from GenScript and cloned into the pET15b expression vector with an N-terminal 6 × His-SUMO2 fusion tag.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pET15b</div><div>suggested: RRID:Addgene_129689)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For transfection of mammalian cell, the cDNA encoded the SARS-CoV-2 PLpro with mammalian codon optimization was also ordered from GenScript and cloned into the pcDNA 3.1 with an C-terminal FLAG tag.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA 3.1</div><div>suggested: RRID:Addgene_20407)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The sequence of pcDNA3-PL-flipGFP-T2A-mCherry was designed based on plasmid pcDNA3-TEV-flipGFP-T2A-mCherry (Addgene catalog NO.124429) where TEV cleave site was replaced by SARS-CoV-2 PLpro cleavage site (LRGGAPTK), and ordered from GenScript.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3-PL-flipGFP-T2A-mCherry</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pcDNA3-TEV-flipGFP-T2A-mCherry</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The resulting kobs values were then plotted versus compound concentrations ([C]), then kinact and Ki or Ka values were calculated according to the equation: kobs = kinact × ([C]/([C] + Ki or Ka)) using GraphPad Prism.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.03.30.486313
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486499

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486499: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Contamination: The absence of mycoplasma contamination was validated regularly with a PCR-based method (ATCC, Universal Mycoplasma Detection Kit, 30-1012K).</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To detect infection, plates were incubated overnight at 4 ⁰C with a rabbit anti-N protein monoclonal antibody (SioBiological 40143-R004) diluted 1:20,000.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-N protein</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were washed and treated with an AF488-conjugated goat anti-rabbit secondary antibody for 2 h at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-rabbit</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Infection efficiency, defined as GFP-positive cells divided by total nuclei, was calculated for each image using a CellProfiler pipeline.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CellProfiler</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT05166876</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Brequinar Combined With Dipyridamole in Patients With Mild t…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.03.30.486499
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486409

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486409: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Serum specimens: The research protocol regarding the use of human serum specimens was reviewed and approved by the University of Texas Medical Branch (UTMB) Institutional Review Board (IRB number 20-0070).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Afterwards, the serum-virus mixtures were loaded onto the pre-seeded Vero E6 cell monolayer in 96-well plates.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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biorxiv.org/cgi/content/10.1101/2022.03.30.486409
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486461

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486461: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Virus titers were determined by TCID50 titration on VeroE6 cells according to the Spearman-Kärber method.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>VeroE6</div><div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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biorxiv.org/cgi/content/10.1101/2022.03.30.486461
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486418

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486418: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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biorxiv.org/cgi/content/10.1101/2022.03.30.486418
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273206

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273206: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The trial was approved by the Ethics Committee (CPP Ile-de-France-III, approval #20.03.06.51744), and is sponsored by the Institut national de la santé et de la recherche médicale (Inserm, France); it was conducted in accordance with the Declaration of Helsinki.<br>Consent: Written informed consent was obtained from all included participants (or their legal representatives if unable to consent).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Women of childbearing potential must agree to use at least one primary form of contraception for the duration of the study.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Study design: DisCoVeRy is a phase 3, open-label, adaptive, multicentre, randomised, controlled, superiority trial for evaluating the efficacy and safety of repurposed drugs in adults hospitalised for COVID-19 (1).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">Virological methods: Systematic determination of the normalized viral load blinded to treatment arm was performed on NPS specimens by RNA extraction on the EMAG® platform (bioMerieux, Marcy-l’Étoile, France) following manufacturer’s instructions.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sample size calculation: The sample size was determined assuming the following scenario under SoC for each item of the ordinal scale at day 15: 1, 42%; 2, 38%; 3, 8%; 4, 7%; 5, 2%; 6, 1%; 7, 2%.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All analyses were performed using SAS v9.4 (SAS Institute, Cary, NC, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SAS Institute</div><div>suggested: (Statistical Analysis System, RRID:SCR_008567)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  The trial has some limitations. It was open, and not placebo-controlled. Indeed, several treatments were concomitantly evaluated at the beginning of the trial, and blinding was thus impossible due to the different modes of administration (intravenous, subcutaneous or oral) of the different treatment arms. This might have introduced bias in the follow up and management of patients, and in the evaluation of endpoints whose assessment contains elements of subjectivity: decision to begin corticosteroids in patients management or to begin mechanical ventilation might have been influenced by the knowledge of the treatment arm, even unconsciously. This risk of bias is however mitigated for the viral load, which was analysed blindly from treatment arm. Next, viral load assessment was not available for 18% of participants (nearly half at baseline). However, the proportions of participants with available viral loads at each sampling time were similar in both experimental groups, suggesting that NP sampling was not guided by the allocated treatment. Finally, plasma concentrations of the prodrug remdesivir and GS-441524 were assessed in only 10% of participants and the concentrations of its intracellular active metabolite were not measured. Although the trial was not designed as a pharmacokinetic study, it provides currently lacking data on remdesivir exposure in patients hospitalised with COVID-19.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04315948</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Trial of Treatments for COVID-19 in Hospitalized Adults</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273206
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486345

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486345: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The study was approved by the Institutional Review Board of the University of Florida.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Isolated genomic DNA was quantified by NanoDrop™ One/OneC</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NanoDrop™</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Quality Control: PLINK (v1.9) [20] was used for quality control and logistic analysis of the data.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PLINK</div><div>suggested: (PLINK, RRID:SCR_001757)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The data were phased using Eagle version 2.4 and imputed using Minimac4.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Eagle</div><div>suggested: (Eagle, RRID:SCR_017262)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Full-length amino acid sequences of structural proteins from SARS-CoV-2 whole-genome proteome (SnapGene, EPI_ISL_7196120_B.1.1.529, EPI_ISL_7196121_B.1.1.529) were used to infer all possible potentially relevant peptides (9mers for class I and 15mers for class II).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SnapGene</div><div>suggested: (SnapGene, RRID:SCR_015052)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The peptide in the template structure was mutated in COOT, too.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>COOT</div><div>suggested: (Coot, RRID:SCR_014222)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The geometry of the result complexes was regularized in PHENIX.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PHENIX</div><div>suggested: (Phenix, RRID:SCR_014224)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis: The association between the allele frequency of each HLA gene and cases and mortality were assessed by linear regression in GraphPad Prism (v9.3.1).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

biorxiv.org/cgi/content/10.1101/2022.03.30.486345
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273021

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273021: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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medrxiv.org/cgi/content/10.1101/2022.03.28.22273021
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https://medrxiv.org/cgi/content/10.1101/2022.03.26.22272973

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.22272973: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.26.22272973
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https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273010

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273010: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">(Illumina Inc.)], mapping was carried out using the bwa-mem2 tool (v2.2.1; https://github.com/bwa-mem2/bwa-mem2) on the Wuhan-Hu-1 isolate genome (GenBank accession no. NC_045512.2) before cleaning with the SAMtools program (v. 1.13; https://www.htslib.org/) (Danecek et al., 2021).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SAMtools</div><div>suggested: (SAMTOOLS, RRID:SCR_002105)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Variant calling was performed using FreeBayes (v1.3.5; https://github.com/freebayes/freebayes) (Garrison et al., 2012), and consensus genomes were built with the Bcftools program (v1.13; https://samtools.github.io/bcftools/bcftools.html).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FreeBayes</div><div>suggested: (FreeBayes, RRID:SCR_010761)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phylogenetic analyses were performed the MEGA X software (v10.2.5; https://www.megasoftware.net/) (Kumar et al., 2018) following sequence alignment with MAFFT (https://mafft.cbrc.jp/alignment/server/)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MEGA X</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>MAFFT</div><div>suggested: (MAFFT, RRID:SCR_011811)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">(Katoh et al., 2002), and trees were visualized with MEGA X.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MEGA</div><div>suggested: (Mega BLAST, RRID:SCR_011920)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The 10 genomes the most similar to these sequences among genomes of the Omicron 21L/BA.2 and 21K/BA.1 variants of the sequence database of our institute were selected by a BLAST search (Altschul et al., 1990) then incorporated in the phylogenies together with the sequence of the Wuhan-Hu-1 isolate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BLAST</div><div>suggested: (BLASTX, RRID:SCR_001653)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Genome sequences obtained and analyzed here were deposited in the NCBI GenBank nucleotide sequence database (https://www.ncbi.nlm.nih.gov/genbank/) (Sayers et al., 2022) (</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NCBI GenBank</div><div>suggested: (NCBI GenBank via FTP, RRID:SCR_010535)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.28.22273010
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273040

1
1. sciscore 03 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273040: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The burden tests were performed by pooling variants in three different variant sets (called masks): “pLoF” which included loss of functions as defined by high impact variants in the Ensembl database20 (i.e. transcript ablation, splice acceptor variant, splice donor variant, stop gained, frameshift variant, stop lost, start lost, transcript amplification), “coding5” which included all variants in pLoF as well as moderate impact indels and any missense variants that was predicted to be deleterious based on all of the in-silico pathogenicity prediction scores used, and “coding1” which included all variants in coding5 as well as all missense variants that were predicted to be deleterious in at least one of the in-silico pathogenicity prediction scores used.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLoF</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The burden tests were performed by pooling variants in three different variant sets (called masks): “pLoF” which included loss of functions as defined by high impact variants in the Ensembl database20 (i.e. transcript ablation, splice acceptor variant, splice donor variant, stop gained, frameshift variant, stop lost, start lost, transcript amplification), “coding5” which included all variants in pLoF as well as moderate impact indels and any missense variants that was predicted to be deleterious based on all of the in-silico pathogenicity prediction scores used, and “coding1” which included all variants in coding5 as well as all missense variants that were predicted to be deleterious in at least one of the in-silico pathogenicity prediction scores used.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Ensembl</div><div>suggested: (Ensembl, RRID:SCR_002344)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For in-silico prediction, we used the following five tools: SIFT47, LRT48, MutationTaster49, PolyPhen250 with the HDIV database, and PolyPhen2 with the HVAR database.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PolyPhen2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Summary statistics were then meta-analyzed using a fixed effect model within each ancestry and using a DerSimonian-Laird random effect model across ancestries with the Metal package51 and its random effect extension52.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Metal</div><div>suggested: (METAL, RRID:SCR_002013)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study had limitations. First, even if this is one of the world’s largest consortia using sequencing technologies for the study of rare variants, we remain limited by a relatively small sample size. For example, in a recent analyses of UK Biobank exomes, many of the phenotypes for which multiple genes were found using burden tests had a much higher number of cases than in our analyses (e.g. blonde hair colour, with 48,595 cases)19. Further, rare variant signals were commonly found in regions enriched in common variants found in GWASs. The fact that ABO and NSF were the only genes from the COVID-19 HGI GWAS that were also identified in our burden test (albeit using a more liberal significance threshold), also suggests a lack of statistical power. Similarly, GenOMICC, a cohort of similar size, was also unable to find rare variant associations using burden tests11. However, their analysis methods were different from ours, making further comparisons difficult. Nevertheless, this provides clear guidance that smaller studies looking at the effect of rare variants across the genome are at considerable risk of finding both false positive and false negative associations. Second, many cohorts used population controls, which may have decreased statistical power given that some controls may have been misclassified. However, given that COVID-19 critical illness remains a rare phenomenon43, our severe disease phenotype results are unlikely to be strongly affected by this. Further, the u...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22273040
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273041

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273041: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">26 Detailed information on all parameters is included in the Excel supplementary file.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Excel</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengths and limitations: To the best of our knowledge, our study is the first to perform a VOI analysis for the treatment of COVID-19 patients. Whereas trials and meta-analyses often conclude further research is needed7, and where current guidelines are based on statistical significance in clinical evidence, VOI results are based on both uncertainty as well as the potential consequences of making decisions with and without further evidence. Our paper expands the potential impact of drug approval by investigating not only drug efficacy and effectiveness, but also the overall net benefits. Considering the unprecedented rollout of clinical trials investigating potential treatments for COVID-19, objective research prioritization seems paramount.3,5 Our model can be updated with further evidence from trials and (cumulative) meta-analyses as they become available to continuously evaluate the optimal overall strategy as the pandemic evolves. Input parameters were based on best-available evidence. Some parameters, such as the quality of life of COVID-19 patients in 5 years and the costs of research, had to be estimated based on previous studies considering other diseases. Where necessary, we chose conservative approaches to our model parameters and settings. For example, treatment effects were only applied for reported trial duration and not extrapolated beyond and wide distributions were chosen to represent large uncertainty. Additionally, we calculated the net value for the US po...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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medrxiv.org/cgi/content/10.1101/2022.03.29.22273041
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.26.22272613

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.22272613: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Ethical permission: The study started after obtaining ethical permission from the Institute Ethics Committee.<br>IRB: Ethical permission: The study started after obtaining ethical permission from the Institute Ethics Committee.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sample size: The sample size estimation was based on the major primary outcome of the study i.e. vaccine effectiveness.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Many of the post-approval studies have had these limitations. The maximum vaccine protection observed after excluding the participants who received any dose during the second wave (pure vaccinated vs unvaccinated cohort analysis performed in Strategy C), was close to 17%. Interestingly, ‘1’ dose recipients showed a higher rate of SARS-CoV-2 infection compared to the unvaccinated. The time to occurrence of COVID-19 in “1” dose recipients was significantly shorter, as corroborated from the findings of the Kaplan-Meier analysis. The high risk of acquisition of disease in ‘1’ dose vaccinated individuals persisted even after adjusting for potential confounders in the Cox proportional hazard model. Compared to the unvaccinated, “1” dose recipients were nearly at 1.6-times higher risk of developing COVID-19. Increased COVID-19 occurrence rate after the first dose has been observed in some other studies and has been linked to the underlying high-risk group of the participants enrolled as well as to the vaccination centers being super-spreading sites of infection.5,6 However, since majority of the observed COVID-19 infections in our study were breakthrough, a direct immunomodulatory action of COVID-19 vaccines should also be investigated as a potential cause of suboptimal vaccine protection and increased propensity towards COVID-19. Some evidence in this regard is provided by a detailed Chinese study on post-vaccination immune modulation.15 Among other factors, young individuals <40 y...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.26.22272613
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22272716

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22272716: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Ct values were exported and analyzed in Microsoft Excel.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Microsoft Excel</div><div>suggested: (Microsoft Excel, RRID:SCR_016137)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Reads that fully contain the desired amplicon sequence were extracted with the bedtools (v2.30.0) intersect tool.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>bedtools</div><div>suggested: (BEDTools, RRID:SCR_006646)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Next, a consensus sequence was generated by first generating a pileup with the samtools mpileup tool using default settings and then generating a consensus with ivar (v1.3.1) using the parameters ‘-q 20 -t 0 -m 20’.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>samtools</div><div>suggested: (SAMTOOLS, RRID:SCR_002105)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Samples were kept frozen at -70°C until total nucleic extraction was performed using 200 µL elute and Applied Biosystems™ MagMAX™</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Applied Biosystems™</div><div>suggested: (Applied Biosystems, RRID:SCR_005039)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22272716
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273044

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273044: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Study approvals were obtained from the Columbia University Irving Medical Center Institutional Review Board (<br>Consent: The requirement for obtaining written informed consent was waived by the IRB.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical Analyses: Histogram plots were used to visualize the distribution of COVID-19 cases and admissions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Statistical Analyses</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations: Our study has several limitations. Cases of COVID-19 included in this analysis are likely to be undercounted from the first wave. All cases admitted with positive tests during this period would be included. Still, testing capacity was limited at the time resulting in tests being prioritized for patients with high clinical suspicion of COVID-19 or underlying comorbidities. Detection of incidental COVID-19 likely increased in the second wave when routine testing was widely available. Information bias in the EHR resulted in inadequate information to accurately characterize patients with co-morbid conditions. RT-PCR Ct data were also missing in a differential way that could have biased findings in either direction. The inclusion of patients admitted to our institution may also not wholly reflect NYC-wide cases since some individuals likely decided to avoid presentation to the hospital, especially during the first pandemic wave. In addition, it is possible that pre-existing immunity had a differential impact on infections and severe illness during the second wave. Our conclusions are limited to hospitalized patients. Extrapolating to the general population can increase the likelihood of Berkson’s bias in identifying spurious correlations not present outside the hospital setting. Our estimates of hospital capacity are based on COVID-19 admissions due to difficulties accurately estimating total hospital admissions from our database. Patients admitted with COVID-19, howe...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.29.22273044
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https://biorxiv.org/cgi/content/10.1101/2022.03.30.486403

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486403: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Ethics statement: The study was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional<br>IRB: The protocol was approved by the Ethics Committee of CHUM (protocol #19.381, approved on 25 March 2020).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ORF8 protein was probed with sheep anti-ORF8 antibody (dilution 1:1000, MRC Pure Reagents, Cat. DA088) for 16 hours at 4oC, followed by incubation with donkey anti-sheep HRP (horseradish peroxidase)-conjugated secondary antibody (1:2000, Invitrogen, Cat. AP184P) for 1 hour at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-ORF8</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-sheep HRP</div><div>suggested: (Millipore Cat# AP184P, RRID:AB_92611)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then, the anti-CD14-V450 (dilution 1:100, BD, Cat. 561390), anti-CD16-PE-Cy7 (dilution 1:100, BD, Cat. 560716) and anti-CD56-PE (dilution 1:100, BD, Cat. 556647) antibodies were added for 1 hour incubation on ice.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD14-V450</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD16-PE-Cy7</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD56-PE</div><div>suggested: (Beckman Coulter Cat# A07788, RRID:AB_2636814)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ORF8 Production: Three million HEK293T cells were seeded on 100 mm petri dishes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The data were analyzed with FlowJo.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses: Statistics were analyzed using GraphPad Prism version 8.0.2 (GraphPad, San Diego, CA, (USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.03.30.486403
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486377

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486377: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The study protocols were approved by the Cantonal Ethics Committee of Ticino, Switzerland (CE-TI-3428, 2018-02166; CE-TI-3687, 2020-01572).<br>Consent: All blood donors provided written informed consent for participation in the study.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Female hamsters of 6-8 weeks old were anesthetized with ketamine/xylazine/atropine and inoculated intranasally with 50 µl containing 1×104 TCID50 SARS-CoV-2 gamma variant (day 0).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">Tissue sections (5 μm) were analyzed after staining with hematoxylin and eosin and scored blindly for lung damage by an expert pathologist.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were washed 4 × in TBST and 30 μl of anti-human (Invitrogen) horseradish peroxidase-conjugated antibodies diluted 1:5,000 was added to each well and incubated at 37°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After washing, secondary antibody goat anti-human IgG (H+L) DyLight680 (0.2 µg/ml) was incubated for 45 min at room temperature before reading on Innopsys InnoScan 710-IR Microarray Scanner. Generation of recombinant ACE2-mFc: Residues 18-615 of human ACE2 (UniProtKB - Q9BYF1) were synthesized by Genscript and cloned into pINFUSE-mIgG2b-Fc2 expression plasmid (InvivoGen)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>ACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 2 h, infected cells were washed four times with DMEM before adding medium supplemented with anti-VSV-G antibody (I1- mouse hybridoma supernatant diluted 1 to 25, from CRL-2700, ATCC).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-VSV-G</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Recombinant protein was produced by transient transfection of Expi293 cells and purified using HiTrap Protein A column.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Expi293</div><div>suggested: RRID:CVCL_D615)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cell lines and media culture: 293T and A549 cells were cultured in high glucose DMEM (Gibco, catalog no. 61965-026) supplemented with 10% FBS, 1% (vol/vol)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HuH-7 cell line was obtained from JCRB Cell Bank and cultured in DMEM (Gibco, catalog no. 31885-023) supplemented with 10% FBS, 1% (vol/vol)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HuH-7</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Vero-TMPRSS2 cells were cultured in DMEM (Gibco, catalog no. 11995-040) supplemented with 10% FBS (VWR, catalog no. 97068-085) and PenStrep (Gibco, catalog no. 15140-122) (35).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero-TMPRSS2</div><div>suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The lentivirus-containing pellet was resuspended in 100 μl media and was used to transduce 293T or A549 cell lines.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549</div><div>suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">293T-ACE2, 293T-S, A549-ACE2 and A549-S cell lines were selected using 10 μg/ml puromycin (InvivoGen, catalog no. ant-pr-1) 4 days post-transduction.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549-S</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">293T-ACE2-TMPRSS2-GFP cell line was generated from 293T-ACE2 cells by subsequent transduction of pLVX-EF1a-TMPRSS2-IRES-ZsGreen1-containing lentivral prep and sorted using BD FACSAria III.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T-ACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A549-ACE2-TMPRSS2 and Huh7-TMPRSS2 stable cell lines were generated using commercial lentivirus (Addgene, catalog no. 154982-LV) and selected using 10 μg/ml blasticidin (InvivoGen</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Huh7-TMPRSS2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To produce NL63 VSV virus, HEK-293 cells were transfected with a pcDNA3.1 expression vector encoding full-length S harboring a truncation of the 20 C-terminal residues to improve membrane transport.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK-293</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For NL63 S pseudotyped virus neutralization assay, Vero E6-TMPRSS2 cells maintained in DMEM supplemented with 10% FBS and 1% PenStrep, were seeded into white 96-well plates at 45,000 cells/well and cultured overnight at 37°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6-TMPRSS2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Inhibition of cell-to-cell fusion: For testing inhibition of spike-mediated cell–cell fusion, A549-S and A549-ACE2-TMPRSS2 cells were stained with CFSE (Thermo Fisher, catalog no. C1157) and CellTrace™ Far Red (Thermo Fisher, catalog no. C34572), respectively, according to manufacturer’s instruction.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549-ACE2-TMPRSS2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The titer of the virus stock was determined by end-point dilution on Vero-E6 cells by the Reed and Muench method (76)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero-E6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To quantify infectious SARS-CoV-2 particles, endpoint titrations were performed on confluent Vero E6 cells in 96- well plates.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Transient expression and monoclonal antibody staining of HCoV S-expressing 293 cells: For transient expression of HCoV spike proteins, 293T cells were co-transfected, with plasmid encoding ZsGreen (Bei Resources, catalog no. NR-52516) and corresponding HCoV spike proteins: SARS-CoV-2 Wuhan-Hu-1 S (catalog no. NR-52514) from Bei Resources; MERS-CoV S (VG40069-G-N)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2 Wuhan-Hu-1 S</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 S PentaPro gene, codon optimized for mammalian expression, was synthesized by GeneScript and cloned into pcDNA3.1 (-) expression vector.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1 ( - )</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Generation of overexpression cell lines: pLVX-puro-ACE2 transfer plasmid was kindly provided by Manfred Kopf (ETH Zurich).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLVX-puro-ACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">pLVX-EF1a-TMPRSS2-IRES-ZsGreen1 transfer plasmid was generated from the reference pWPI-IRES-Bla-Ak-TMPRSS2 plasmid (Addgene, catalog no. 154982).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLVX-EF1a-TMPRSS2-IRES-ZsGreen1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pWPI-IRES-Bla-Ak-TMPRSS2</div><div>suggested: RRID:Addgene_154982)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">pLVX-puro-spike transfer plasmid was generated from reference pHDM-SARS-CoV-2 spike (BEI resources, catalog no. NR-52514)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLVX-puro-spike</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 293T cells at 70-80% confluency in T75 flask were co-transfected with transfer plasmids encoding genes of interest (ACE2, TMPRSS2 or SARS-CoV-2 S) and packaging plasmid psPax2 and envelope plasmid pMD.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>psPax2</div><div>suggested: RRID:Addgene_12260)</div></div><div style="margin-bottom:8px"><div>pMD</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 293T cells were co-transfected with a lentiviral backbone encoding luciferase reporter (pHAGE-CMV-Luc2-IRES-ZsGreen-W (Bei Resources, catalog no. NR-52516), HIV-based packaging plasmids (Tat, Gag-Pol and Rev) (Bei Resources, catalog no. NR-52518, NR-52517 and NR-52519) and various spike expression plasmids using PEI in Optimem.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHAGE-CMV-Luc2-IRES-ZsGreen-W</div><div>suggested: RRID:Addgene_164432)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To produce NL63 VSV virus, HEK-293 cells were transfected with a pcDNA3.1 expression vector encoding full-length S harboring a truncation of the 20 C-terminal residues to improve membrane transport.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1</div><div>suggested: RRID:Addgene_79663)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, NL63 S (VG40604-UT) from SinoBiological; SARS-CoV S (VG40150-G-N) from SinoBiological that was cloned into pHDM expression plasmid with 19 amino-acid C-terminal truncation (85), using PEI in Optimem as above.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHDM</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were immediately read at 450 nm on a BioTek plate reader and data plotted and fit in Prism 9 (GraphPad) using nonlinear regression sigmoidal, 4PL, X is the concentration to determine EC50 values from curve fits.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">First, the sequences were annotated using IgBlast version 1.16 (65) and IMGT as reference sequences (66).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgBlast</div><div>suggested: (IgBLAST, RRID:SCR_002873)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data was processed using GraphPad Prism v9.0.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Nine fields per well were imaged and were subsequently processed with Metaxpress and Powecore softwares.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Metaxpress</div><div>suggested: (MetaXpress, RRID:SCR_016654)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The variant was subjected to sequencing on a MinION platform (Oxford Nanopore) directly from the nasopharyngeal swabs; passage 2 virus on Vero E6 cells was used for the study described here.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MinION</div><div>suggested: (MinION, RRID:SCR_017985)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Initial phases were obtained by molecular replacement in Phaser (81) on the CCP4 suite, using crystal structures of Fabs as search models.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CCP4</div><div>suggested: (CCP4, RRID:SCR_007255)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Several subsequent rounds of model building and refinement were performed using Coot (82), Refmac5 (83) and Buster (84) to arrive to the final model for each complex.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Coot</div><div>suggested: (Coot, RRID:SCR_014222)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells were then washed and analyzed by flow cytometry using BD Symphony and FlowJo.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.30.486377
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https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273029

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273029: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Empirically, we draw on material from the COVID-19 Contact (CoCo) Study, a multi-method study carried out at Hannover Medical School.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CoCo</div><div>suggested: (CoCo, RRID:SCR_010947)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations: Our study reveals important gaps in HCW protection and health workforce governance. However, it has several limitations, which have been described in relation to the clinical part of the study (48,49). To summarise the major arguments: data on anti-SARS-CoV-2 IgG is only partially representative for Hannover Medical School and we do not know the source of infection in anti-SARS-CoV-2 IgG-positive HCWs (49). More specifically related to our selected survey data, the respondents might be biased; employees who are more concerned about their health and a COVID-19 infection might have been more interested in the study than those who do not care about potential health risks. We also do not know how the experience of an organisational environment characterised by low infection rates intersects with the individual sphere, and how different sources of information impact in individual perceptions. Further research and qualitative methodology would be necessary to provide in-depth information. Finally, the lessons that can be learned from an ‘optimal-case scenario’ in relation to individual perceptions and institutional/organisational conditions of HCW protection are generally limited and must be viewed with caution, because cross-country comparative data and in-depth organisational comparison are lacking. Our results may help to highlight the need for, and benefit of more comprehensive research and policy investigation into mental health of HCWs.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22273029
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273085

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273085: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We measured race/ethnicity using a single-race variable and a Hispanic variable, focusing on the following groups: Asian or Pacific Islander, non-Hispanic Black, Hispanic, and non-Hispanic White.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>non-Hispanic White</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.29.22273085
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273077

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273077: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethics: This study was approved by Yale Human Research Protection Program Institutional Review Board (IRB Protocol ID 2000028924).<br>Consent: Informed consent was obtained from all enrolled vaccinated HCWs.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sampling Variants of Concern (Fig. 1b): We randomly sampled 50 genome sequences per Variant of Concern (Alpha, Beta, Gamma, Delta, Lambda, Mu, Omicron) based on GISAID accession numbers using a random sampler implemented in R v.4.0.2.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Contamination: The cell line has been tested negative for contamination with mycoplasma.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, 300 µl of serial fold virus dilutions were used to infect Vero E6 cells in MEM supplemented NaHCO3, 4% FBS 0.6% Avicel RC-581.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Calu-3 cells were cultured in Eagle’s minimal essential medium (EMEM) with 10% FBS and 1% Penicillin/Streptomycin.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Calu-3</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To generate the viral stock of gamma used to test replication competence, 107 Vero-E6 cells overexpressing ACE2 and TMPRSS2 were infected with SARS-CoV-2 Isolate hCoV-19/Japan/TY7-503/2021 (BEI Resources #NR-54982) at an MOI of approximately 0.02.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero-E6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Ethics: This study was approved by Yale Human Research Protection Program Institutional Review Board (IRB Protocol ID 2000028924).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Yale Human Research Protection Program</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We visualized the plots using Prism v.9.3.1.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Prism</div><div>suggested: (PRISM, RRID:SCR_005375)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Table 5), we aligned our genome sequences with MAFFT using MN908947.3 as the reference.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MAFFT</div><div>suggested: (MAFFT, RRID:SCR_011811)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We performed phylogeographic reconstruction implemented in BEAST v1.10.5 using an asymmetric CTMC model for discrete state reconstructions and running for 1 million states 32.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BEAST</div><div>suggested: (BEAST, RRID:SCR_010228)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We tabulated sustained introductions per regional sink in Python v.3.8.3.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Reference based genome assembly pipelines, such as iVar40 used in this example, align reads to a reference genome using BWA41 to call variants and determine the most common nucleotide at any given position.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BWA41</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">An intermediate .bam file is produced and can be visualized in common GUI software, such as Geneious.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Geneious</div><div>suggested: (Geneious, RRID:SCR_010519)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Demographic information was aggregated through a systematic review and the clinical data were collected using REDCap.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>REDCap</div><div>suggested: (REDCap, RRID:SCR_003445)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study was not without limitations. The analysis presented above is retrospective and therefore not explicitly actionable. Rather, our intention was to examine genomic and clinical correlates of variant fitness that may inform the response to future variants. The data we have presented should be carefully interpreted. The experimental assays were performed in vitro, and therefore may not directly reflect biological dynamics in vivo. However, our objective was to compare specific characteristics in individual variants, which may be accomplished in vitro. Genomic frequencies should be interpreted with caution due to large fluctuations in the percentage of cases sequenced by week in each location. For this reason, long-term trends are more reliable than short-term trends. Lastly, the phylogeographic analyses presented comprised substantially downsampled data, potentially biasing our findings. In particular, characterizing patterns of sustained introductions should be interpreted with understanding. That is, the relative number of introductions across regions should be considered rather than the absolute number. This challenge is in part due to the retrospective nature of our study. Downsampling is less likely to be needed when a more recently emerged variant is the subject of analysis. Here, we present a multidisciplinary analysis of Mu, an immune evasive VOC that exhibited limited global spread. As new SARS-CoV-2 lineages emerge, their mutation profiles provide preliminary d...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273146

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273146: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We implemented both distributions in Python to assess loss of transmissibility due to fatal COVID-19 outcomes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The likelihood of fatal outcome over time is represented by a log-logistic distribution in the Scipy stats module with scale 31.18, shape 6.80, and loc parameter –14.51 according to Bai et al 43.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Scipy</div><div>suggested: (SciPy, RRID:SCR_008058)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our work has several key limitations. The model linking reinfection frequency, IFR and death toll is not age stratified, so it does not account for greater vaccine uptake in older populations. As a result, the model may overstate the death tolls, as risk of death is strongly age-dependent in COVID-19 89. Offsetting this limitation is the finding that the benefit of vaccinal immunity appears to be age-dependent 90, and so the higher vaccine uptake in older populations may be undermined by a lower level of vaccinal efficacy over time. Additionally, the model does not account for evolution-mediated vaccine resistance or waning of vaccinal immunity and thus assumes vaccines retain their high efficacy over the simulation interval. This is likely to be an optimistic assumption and will also have the impact of mitigating death tolls. Our work does not explicitly model vaccines or boosters-a full exploration of the impact of vaccines on viral evolution is outside the scope of this work but explored by us elsewhere (manuscript in preparation). Similarly, the interplay between the kinetics of antibody decay and population heterogeneity in the rate of waning of natural and vaccinal immunity will impact the level of protection that vaccines provide, and a full treatment of these effects is outside the scope of this work but described in a different work by us (manuscript in preparation). As is true of all SEIR-type models, ours assumes homogenous population mixing and thereby overestimat...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.29.22273146
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272952

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272952: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.25.22272952
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273175

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273175: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Informed consent was obtained from the residents, or their relatives when the residents did not have full capacity to sign legal documents.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Detection of past infection relied on anti-Spike (S) and anti-Nucleocapsid (N) antibodies for pre-vaccination sera, and only on anti-N antibodies for post-vaccination sera.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Spike (S)</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-Nucleocapsid (N)</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-N</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, this assay uses 293T cells stably expressing the Spike (S) protein (293T-S cells) and 293T control cells as control to detect anti-Spike antibodies by flow cytometry [20].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Spike</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, this assay uses 293T cells stably expressing the Spike (S) protein (293T-S cells) and 293T control cells as control to detect anti-Spike antibodies by flow cytometry [20].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T</div><div>suggested: RRID:CVCL_LC70)</div></div><div style="margin-bottom:8px"><div>293T-S</div><div>suggested: RRID:CVCL_LC70)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Viral stock were produced on Vero E6 cells, titrated on Vero E6 or S-Fuse cells and sequenced to confirm viral lineages (GISAID accession ID: EPI_ISL_2029113 and EPI_ISL_7413964 for Delta and Omicron isolates, respectively).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The assay is standardized with WHO international reference sera (20/136 and 20/130) and cross-validated with two commercially available ELISA (Abbott 147 and Beckmann 56) to allow calculation of BAU/mL [22].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Abbott</div><div>suggested: (Abbott, RRID:SCR_010477)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">This assay uses U2OS-ACE2 GFP1-10 and GFP 11 reporter cells, also termed S-Fuse cells, that become GFP+ upon infection with SARS-CoV-2 [23,24].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2</div><div>suggested: (Active Motif Cat# 91351, RRID:AB_2847848)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study has limitations. First, the small sample size limits our statistical power and precludes analysis of the characteristics that may further impact vaccine efficacy, such as gender, prexisting conditions or ongoing medications. Second, we did not have access to nasopharyngeal swabs to measure antibody levels at the site of viral entry and replication. We were thus unable to link breakthrough infections to local levels of antibodies, which might represent a better correlate of protection. Further studies are needed to determine the contribution of mucosal immunity on the acquisition of SARS-CoV-2 and the severity of COVID-19. Lastly, we only tested BA.1, the initial Omicron clade, which was circulating in France at the time of the investigation and was responsible of the breaktrough infections that occurred in the nursing homes of the study. It will be worth examining the neutralization activity of the sera against other Omicron sub-lineages, such as BA.2, at the next blood sampling of the same cohort participants. This study confirmed the importance of receiving at least three antigenic exposures to the Spike protein for achieving satisfactory neutralizing antibody levels against Omicron. Protection against Omicron was increased in those who had been previously infected in addition to the three doses, suggesting that a fourth antigenic exposure may be useful in this elderly population to prevent infection with a variant known for its high escape immunity properties.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04644159</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Longitudinal Follow-up of a Population Cohort in a French Ci…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273175
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272837

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272837: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: Ethics: This study was approved (EK Nr: 1064/2021) by the Institutional Review Board (IRB) of the Office of Research Oversight/Regulatory Affairs, Medical University of Innsbruck, Austria, which is responsible for all human research studies conducted in the State of Tyrol (Austria).<br>IRB: Ethics: This study was approved (EK Nr: 1064/2021) by the Institutional Review Board (IRB) of the Office of Research Oversight/Regulatory Affairs, Medical University of Innsbruck, Austria, which is responsible for all human research studies conducted in the State of Tyrol (Austria).<br>Consent: Study population, study design and recruitment: A total of 57 patients infected with Omicron, 34 with no history of prior vaccination and 23 patients who had received 2-3 doses of the BNT162b2 vaccine (Table S1), were recruited for the study under informed consent.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody assay: End-point binding IgG antibody titers to various SARS-CoV-2–derived antigens were measured using the Meso Scale Discovery (MSD) platform.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>End-point binding IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were coated with the specific antigen on spots in the 96 well plate and the bound antibodies in the samples (1:50000 dilution) were then detected by anti-human IgG antibodies conjugated with the MSD SULPHO-TAG which is then read on the MSD instrument which measures the light emitted from the tag.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ACE2 binding inhibition (Neutralization) ELISA: The V-PLEX COVID-19 ACE2 Neutralization kit (Meso Scale Discovery, Panel 23 (ACE2) Kit, K15570U) was used to quantitatively measure antibodies that block the binding of ACE2 to its cognate ligands (SARS-CoV-2 and variant spike subdomains).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ACE2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The raw data were subjected to QC analyses using the FastQC tool (version 0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FastQC</div><div>suggested: (FastQC, RRID:SCR_014583)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">mRNA-seq read quality control was done using Trimmomatic11 (version 0.36) and STAR RNA-seq12 (version STAR 2.5.4a) using 150 bp paired-end mode was used to align the reads (hg19).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>STAR</div><div>suggested: (STAR, RRID:SCR_004463)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HTSeq13 (version 0.9.1) was to retrieve the raw counts and subsequently, Bioconductor package DESeq214 in R (https://www.R-project.org/) was used to normalize the counts across samples and perform differential expression gene analysis.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Bioconductor</div><div>suggested: (Bioconductor, RRID:SCR_006442)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Quantification and statistical analysis: Differential expression gene (DEG) identification used Bioconductor package DESeq2 in R.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>DESeq2</div><div>suggested: (DESeq, RRID:SCR_000154)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">P-values of antibody between two groups were calculated using one-tailed Wilcoxon rank t-test on GraphPad Prism software (version 9.0.0).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.24.22272837
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.29.486331

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.486331: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mpro nucleotide sequences were obtained using BLASTN alignment (26) to the reference SARS-CoV-2 genome (NC_045512.2, isolate Wuhan-hu-1) (</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BLASTN</div><div>suggested: (BLASTN, RRID:SCR_001598)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Each subset of genomes was then aligned to the reference genome (Wuhan-hu-1) using MAFFT (30) (with –6mer pair flag for rapid alignment of large numbers of closely related viral genomes).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MAFFT</div><div>suggested: (MAFFT, RRID:SCR_011811)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Overall nucleotide diversity was inferred using MEGA X (31).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MEGA</div><div>suggested: (Mega BLAST, RRID:SCR_011920)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Runs were compared for convergence and the resulting dN/dS determined using RStudio (version 1.1.383).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RStudio</div><div>suggested: (RStudio, RRID:SCR_000432)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Another caveat of using GISAID datasets is that only consensus genome sequences are available. Potential emerging resistant mutations usually have low frequency (minor allele) within viral quasi-species and will not be uncovered from assembled genomic contigs. The presence of artifacts in assembled sequencing data is also expected due to inevitable errors in the sequencing process. While GISAID has implemented internal checks to flag potential errors in submitted assemblies, this does not eliminate the potential risk of misinterpreting artifacts as mutations. Nonetheless, the vast number of sequences available for analysis (>7 million SARS-CoV-2 genomes as of January 14, 2022) proved valuable in providing a comprehensive picture of the mutational landscape of Mpro. At present, SARS-CoV-2 continues to represent a global health threat as new variants emerge. It is essential to continue tracking Mpro mutations in global viral isolates, especially since nirmatrelvir, the active protease inhibitor in Paxlovid, is expected to become a widely accessible COVID-19 treatment option. However, at present, nirmatrelvir has yet to be deployed on a mass scale. Following FDA approval of remdesivir, its widespread usage in hospitals for the first year and a half of the COVID-19 pandemic has permitted analyses of known resistance mutations in viral isolates under remdesivir selection (57). Therefore, as more sampled viral isolates undergo nirmatrelvir selection, and as more sequences become av...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.03.29.486331
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273165

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273165: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Where significant changes were found, sensitivity analyses were carried out by assuming that every participant who had not returned their journal had experienced scores for every cycle with the same distribution as the pre-vaccine cycle scores recorded by those who did return their journals: the distribution was produced by randomly selecting a score from the pre-vaccine cycle data distribution for each missing value.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Analysis was carried out and graphs generated using Graphpad Prism 9.0.0.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Graphpad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  However, there are also a number of important weaknesses. Because the cohort is small, we may not have been able to detect real effects of vaccination on menstrual flow, or real relationships between menstrual and non-menstrual side effects. Some bias is also likely to have been introduced because it is unlikely that the participants who did not return their sheets did so at random, although we did attempt to account for this with a sensitivity analysis. Some bias is also likely to be introduced because “expected date of period” and “menstrual flow” are at least partially subjective, so there is the potential for participant’s expectations of how vaccination will impact their periods to impact their reports. In conclusion, in this small, prospectively-recruited cohort, we found that both the first and second doses of the COVID-19 vaccine were associated with a small delay to the subsequent period. This delay was not reported in interdose and post-vaccination cycles, suggesting that any changes are temporary. We were unable to detect changes to menstrual flow. These findings are reassuring, but work in larger prospectively-recruited cohorts is needed to more accurately determine how vaccination affects menstrual parameters.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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Visit annotations in context

Annotators

sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273165
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273068

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273068: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The study protocol was reviewed and approved by the Mount Sinai Hospital Institutional Review Board (IRB-20-03374).<br>Consent: All participants provided written informed consent.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sex (female, male), age (<40 years, 40+ years), and baseline titer (<1:800, ≥1:800) were included as covariates in the model, along with a random intercept for participant ID to account for repeated measures.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sex (female, male), age (<40 years, 40+ years), and baseline titer (<1:800, ≥1:800) were included as covariates in the model, along with a random intercept for participant ID to account for repeated measures.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The data of 813 distinct study visits from these 137 seropositive participants provide the basis for the modeling SARS-CoV-2 spike-binding IgG antibody durability.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2 spike-binding IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were washed three times with PBS-T and 50 μl/well of anti-human IgG (Fab-specific) horseradish peroxidase antibody (produced in goat; Sigma, A0293) diluted to 1:3,000 in PBS-T, 1% milk powder, were added to each well.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: (Sigma-Aldrich Cat# A0293, RRID:AB_257875)</div></div><div style="margin-bottom:8px"><div>A0293</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Endpoint titers, expressed as the last dilution before the signal dropped below an OD490nm of 0.15, were calculated in excel and data was plotted using GraphPad Prism 9.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  This analysis did, however, also have a few limitations. First, since we started enrollment during the first wave, a good portion of participants were unable to get molecular tests at the time of infection and we relied on retrospective reports of clinical signs and symptoms suggestive of COVID-19 for illness onset date. As such, recall bias in reported illness onset is a possibility. However, we anticipate that this exerted only a minor impact on our conclusions given the relatively homogenous exposures of participants who are all health care workers. Second, with healthcare worker vaccination beginning in December 2020 we were unable to effectively assess how circulating variants of concern may affect one’s risk of re-infection following natural infection. The increase in vaccinated participants (excluded from this analysis), while fortunate, also resulted in a smaller sample size at the end of the follow-up period extending into August 2021. In conclusion, our study shows that SARS-CoV-2 infection provides strong protection from reinfection and this protection may be associated with the presence of spike binding antibodies. In addition, it suggests that antibody levels induced by infection with ancestral SARS-CoV-2 variants are relatively stable over time and that the rate of seroreversion is low when measuring SARS-CoV-2 spike binding IgG antibodies.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

Annotators

sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22273068
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.30.486356

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.486356: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The BioJupies generator online server (https://maayanlab.cloud/biojupies/) was used for RNA-seq raw data analysis [1].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BioJupies</div><div>suggested: (BioJupies, RRID:SCR_016346)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Functional enrichment analysis: We utilized Enrichr [3] with Fisher’s exact test to conduct the functional enrichment analysis with the combined DEGs.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Enrichr</div><div>suggested: (Enrichr, RRID:SCR_001575)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In Enrichr analysis, we combined the signaling pathways from two libraries, including KEGG and Reactome, to create a single route.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>KEGG</div><div>suggested: (KEGG, RRID:SCR_012773)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Protein-protein interaction network analysis: The shared DEGs’ protein-protein interaction (PPI) was analyzed using the STRING database [4].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>STRING</div><div>suggested: (STRING, RRID:SCR_005223)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We applied different local- and global-based methods using the cytoHubba plugin [5] in Cytoscape v3.8.2 [6] to determine potential hubs proteins within the PPI network.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>cytoHubba</div><div>suggested: (cytoHubba, RRID:SCR_017677)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Finally, the protein networks were analyzed through Cytoscape v3.8.2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Cytoscape</div><div>suggested: (Cytoscape, RRID:SCR_003032)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Using the shared DEGs, we constructed the protein-drug interaction (PDI) network through the NetworkAnalyst v3.0 web server [7] in conjunction with the DrugBank v5.0 database (https://go.drugbank.com/docs/drugbank_v5.0.xsd).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NetworkAnalyst</div><div>suggested: (NetworkAnalyst, RRID:SCR_016909)</div></div><div style="margin-bottom:8px"><div>DrugBank</div><div>suggested: (DrugBank, RRID:SCR_002700)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

Annotators

sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.03.30.486356
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.29.486190

1
1. sciscore 02 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.486190: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethics statement: This research has been determined to be exempt by the Institutional Review Board of the Boston University Medical Center since it does not meet the definition of human subjects research, since all human samples were collected in an anonymous fashion and no identifiable private information was collected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Contamination: All cell lines are routinely tested for mycoplasma contamination and confirmed negative.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For CD169 blocking experiments, primary MDMs from 3 different donors were pre-incubated with 20 μg/ml anti-CD169 antibody (HSn 7D2, Novus Biologicals) or IgG1k (P3.6.2.8.1, eBioscience) for 30 min at 4°C prior to infection.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD169</div><div>suggested: (Thermo Fisher Scientific Cat# MA1-16891, RRID:AB_568734)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">This is followed by secondary staining for 30 min at 4°C with APC-conjugated mouse anti-His antibody (BioLegend, #362605, 1:50) or isotype control.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-His</div><div>suggested: (BioLegend Cat# 362605, RRID:AB_2715818)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The cells were incubated overnight at 4°C with a rabbit antibody directed against the SARS-CoV nucleocapsid protein (Rockland; 1:1000 dilution in 5% goat serum), which cross-reacts with the SARS-CoV-2 nucleocapsid protein, as previously described (99).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV nucleocapsid protein</div><div>suggested: (Creative Diagnostics Cat# DMAB8869, RRID:AB_2392503)</div></div><div style="margin-bottom:8px"><div>SARS-CoV-2 nucleocapsid protein</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The cells were washed four times in PBS and incubated with goat anti-rabbit antibody conjugated with AlexaFluor594 for 1 hour at room temperature (Invitrogen; 1:200 dilution in blocking reagent). 4’,6-diamidino-2-phenylindole (DAPI; Sigma-Aldrich) was used at 200 ng/ml for nuclei staining.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-rabbit</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For dsRNA staining (61), anti-dsRNA (Pan-Enterovirus Reagent, clone 9D5, Light Diagnostics, Millipore) antibody was used 1:2 overnight and anti-mouse-AF488 (Invitrogen) 1:200 dilution as secondary antibody with DAPI.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-dsRNA ( Pan-Enterovirus Reagent , clone 9D5 , Light Diagnostics , Millipore )</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-dsRNA ( Pan-Enterovirus Reagent ,</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-mouse-AF488</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Flow cytometry: To examine cell surface expression of CD169 or ACE2 in transduced THP1 or primary MDMs, approximately 0.5x106 cells were harvested with CellStripper (Corning), stained with Zombie-NIR (BioLegend, #423105, 1:250) followed by staining for 30 min at 4°C with the following antibodies; Alexa647-conjugated mouse anti-CD169 antibody (BioLegend, #346006, 1:50), Alexa647-conjugated</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ACE2</div><div>suggested: (Enzo Life Sciences Cat# BML-SA445, RRID:AB_2273641)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">mouse anti-ACE2 antibody (R&D systems, 1:200), or unconjugated goat anti-ACE2 polyclonal antibody (R&D systems, #AF933, 1:200) followed by Alexa488-conjugated chicken anti-goat antibody (Invitrogen, #A-21467, 1:100).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-goat</div><div>suggested: (Molecular Probes Cat# A-21467, RRID:AB_141893)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immunoblot Analysis: To assess expression of endogenous or transduced proteins, cell lysates containing 30- 40 µg total protein were separated by SDS-PAGE, transferred to nitrocellulose membranes and the membranes were probed with the following antibodies: mouse anti- TMPRSS2 (Santa Cruz, #515727, 1:1000), mouse anti-Cathepsin-L (Santa Cruz, #32320, 1:1000), goat anti-ACE-2 (R&D systems, #AF933, 1;1000), rabbit anti-STING (Cell Signaling, #13647, 1:1000), rabbit anti-MAVS (Thermo Fisher, #PA5-17256, 1:1000), mouse anti-RIG-I (AdipoGen, #20B-0009, 1:1000)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti- TMPRSS2 ( Santa Cruz , #515727</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-Cathepsin-L ( Santa Cruz , #32320</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-ACE-2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-STING ( Cell Signaling , #13647</div><div>suggested: (Cell Signaling Technology Cat# 13647, RRID:AB_2732796)</div></div><div style="margin-bottom:8px"><div>anti-MAVS</div><div>suggested: (Thermo Fisher Scientific Cat# PA5-17256, RRID:AB_10979584)</div></div><div style="margin-bottom:8px"><div>anti-RIG-I ( AdipoGen , #20B-0009</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Specific staining was visualized with secondary antibodies, goat anti-mouse-IgG-DyLight 680 (Thermo Scientific, #35518, 1:20000), goat anti-rabbit-IgG-DyLight 800 (Thermo Scientific, #SA5-35571, 1:20000), or a donkey anti-goat-IgG-IR-Dye 800 (Licor, #926-32214, 1:20000).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mouse-IgG-DyLight 680</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-rabbit-IgG-DyLight</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>#SA5-35571</div><div>suggested: (Thermo Fisher Scientific Cat# SA5-35571, RRID:AB_2556775)</div></div><div style="margin-bottom:8px"><div>anti-goat-IgG-IR-Dye</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">THP1 cells (ATCC) were maintained in RPMI/1640 (Gibco) containing 10% FBS and 1% pen/strep (50)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>THP1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To generate HEK293T/ACE2+, THP1/ACE2+ and THP1/CD169+/ACE2+ cells, HEK293T, THP1 or THP1/CD169 cells were transduced with pLenti-ACE2-IRES-puro lentivector and cultured in puromycin-containing media (2 μg/ml).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>THP1/CD169</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 titer was determined in Vero E6 cells by tissue culture infectious dose 50 (TCID50) assay using the Spearman Kärber algorithm.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Infection: For RNA analysis, 1x106 cells (THPI/PMA, MDMs, HEK293T) were seeded in 12-well plates.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">S binding: To evaluate SARS-CoV-2 S binding to various THP1 monocytes expressing different surface receptors, approximately 0.25x106 cells from parental THP1 or those expressing wt CD169, mutant CD169 (R116A), ACE2, or both wt CD169 and ACE2 were incubated for 30 min at 4 °C with 2 μg of spike glycoprotein (stabilized) from Wuhan-Hu-1 SARS- CoV-2 containing a C-terminal Histidine Tag, recombinant from HEK293F cells (BEI resources, #NR-52397).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293F</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For ACE2 cloning, the NotI-XhoI fragment from pLenti-ACE2- IRES-puro was inserted into the LV-3’LTR backbone.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLenti-ACE2- IRES-puro</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For cloning CD169 into LV-3’LTR vector, a BglII-AgeI fragment from LNC-CD169 was inserted into LV-3’LTR vector.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>LV-3’LTR</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HIV-1 packaging plasmid psPAX2 and VSV-G expression constructs have been previously described (39).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>psPAX2</div><div>suggested: RRID:Addgene_12260)</div></div><div style="margin-bottom:8px"><div>VSV-G</div><div>suggested: RRID:Addgene_138479)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All lentiviral vectors (pLKO.1) expressing shRNAs used for knockdown of host proteins were purchased from Sigma</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLKO.1</div><div>suggested: RRID:Addgene_13425)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data analysis was performed using FlowJo software (FlowJo).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">63x oil immersion objective; numerical aperture 1.4) controlled by Metamorph image acquisition software (Molecular Devices, San Jose, CA)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Metamorph</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistics: All the statistical analysis was performed using GraphPad Prism 9.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.29.486190
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https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273120

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273120: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All analyses were performed using SAS statistical software version 9.4 (SAS Institute Inc.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SAS statistical</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>SAS Institute</div><div>suggested: (Statistical Analysis System, RRID:SCR_008567)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  The study has several limitations. First, given the fluidity of the COVID-19 pandemic and the time it took each of the three countries to get there, external factors such as variants, holiday season, etc., could have affected the degree of implementation. For example, Nigeria reached 10,000 cases in May 2020 while Rwanda reached that point in January 2021. The state of the pandemic and global guidance had changed significantly in between that time. There are also specific limitations in the OxCGRT dataset itself. The dataset does not measure implementation or compliance, nor does it provide subnational measures for almost all countries apart from adding a flag denoting whether the restriction was national or subnational (25). Thus, our nation-focused analysis may miss some variation of policies implemented at the sub-national level. Additionally, our sample size of KIIs is relatively small, therefore there may be other diverse opinions about what worked and what did not during NPI implementation, that were not captured here. During pandemics, apart from effective vaccine strategies, NPIs are one of the most important tools that individuals and communities can utilize to limit disease spread and reduce deaths. In addition, the timing of NPI implementation is crucial. Delayed implementation of NPIs will lead to unchecked proliferation of disease in the community and overwhelm health systems (4,8,39). However, in addition to timing, the success of NPIs depends critically on the ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a protocol registration statement.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22273120
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273151

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273151: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethical considerations: Ethical clearance was obtained from the ethical review committee of Oda Bultum University and an official letter was submitted to the West Hararghe educational office.<br>Field Sample Permit: Permission to conduct the research among students in the school was obtained from the school principal.<br>Consent: After the purpose and the importance of the study were clearly explained, verbal informed consent was obtained from each participant and the information collected from each respondent was kept with complete confidentiality.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">There are about 50 public secondary schools in the West hararghe zone and there are about 54,260 students were enrolled in schools while as female 19737 (36.37%) and male 34523 (63.63%) students in 2021/2022 (West Hararghe Education bureau office September 02, 2021).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">All randomly Selected Secondary school students who were enrolled in the 2021 /2022 academic year found west Hararghe zone during the study period were the study population.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data was entered into Epi-data version 3.1 and then exported to SPSS version 26 software for analysis.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengthen and limitations: The main strength of this study was being that the first study identified the extent of adolescent substance use during the COVID-19 pandemic in Ethiopia. However, there were some limitations in this study. First, some specifics of substance use attributes (e.g., history of use disorder, detailed categories, procurement sources, and adverse health effects) were not captured, thus requiring further research. Secondly, the study could not employ qualitative data, so it might not address more associated factors. Despite limitations, this study sheds important light on substance use trends and correlates among adolescents during the COVID-19 pandemic
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22273151
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.30.22273186

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.30.22273186: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Collection of samples from patients with acute dengue infection: Real time PCR for the four DENVs were carried out in 297 blood sample of patients with clinically suspected to have an acute dengue infection, following informed consent.<br>IRB: Ethics approval for the study was obtained from the Ethics Review Committee, University of Sri Jayewardenepura and the administrative clearance was obtained from the Ministry of Health, Sri Lanka.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis: Statistical analysis was carried out using the GraphPad Prism (Version 9.3.1) and non-parametric statistical tests were used.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.30.22273186
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.27.22273000

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.27.22273000: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: The study was approved by the Central Ethical Committee of Hungary (OGYÉI/10296-1/2022 and IV/1722-1/2022/EKU) and followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines (17).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Nevertheless, our study has some limitations. The proportion of undetected cases might have been high and could have increased during the wave dominated by the Omicron variant. Therefore, we refrained from analyzing registered infections. We made an exemption when we estimated the impact of double booster and single booster vaccination, because we wanted to see how much the effect size is different in the case of SARS-CoV-2 infection and Covid-19 related mortality. Although the infection rates might be underestimated, we assume that the ascertainment bias was not likely to significantly affect the relative rates, as the proportion of unregistered cases among all cases was not likely to substantially differ in the two compared groups. We studied the effect of vaccination by age, and adjusted for age when studying total populations, but an important limitation of our study is that we could not adjust for other potential confounders, most importantly for chronic diseases. As chronic diseases represent an indication for early vaccination as well as booster vaccination, and are closely related to mortality, this confounding may have influenced our results to a certain extent. However, as booster and second booster vaccinations were especially recommended for elderly people with chronic diseases, our estimates are conservative. Our study is one of the very few demonstrating the benefit of second booster vaccination. Despite declining effectiveness against symptomatic disease caused...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.27.22273000
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.28.22273033

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.22273033: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: All participants gave written, voluntary and informed consent.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  There are limitations to both approaches. The recipients of communication must regard the message as relevant; this is a drawback of the one-way approach because without knowing their audience experts’ communication may be too detailed and detached from public’s values (9). The drawback of communication interventions informed by audience analysis only is the omission of topics not emphasised by the target group. Pandemic health risk communication also needs to provide people with information that they do not realise they need to protect themselves and others. Communication created based on audience analysis, without expert opinions may fail to fill knowledge gaps (4). There is no one-size-fits-all to the communication of health risk during a pandemic. There will always be unintended effects on some audience members. Both audience analysis and interdisciplinary collaboration among experts in medicine, public health, science, and communication may facilitate the creation of engaging messages with intended outcomes (4). 4.4 Limitations: This study uses a normative expert study approach to collect multi-professional domain-specific knowledge (25). Analytical generalisations made on a theoretical level can inform frameworks for inter-professional pandemic health risk communication and public health emergencies (51). This study holds strong information power due to the quality of the interview dialogue (52), and the inclusion of participants with relevant experiences with the pheno...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.28.22273033
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272954

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272954: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethics: Keele University’s Research Ethics Committee granted ethical approval for this study (reference: PS-200129).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">The predictive strength of each model was calculated as the Tjur coefficient of discrimination;21 this statistic can take values between 0 and 1, with higher values indicating greater predictive power.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.25.22272954
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273086

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273086: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  However, some limitations of register-based data should be considered when interpreting the results. Data in these registries are not collected for the purpose of this study, and therefore the focus on level of detail, error checking and precision in the available data is not guided by the current study, as would be the case for independent data gathering. For instance, while vaccines administered as part of the Norwegian vaccination program should be in our dataset, it is not unlikely that some have received vaccines outside Norway and not reported them to the Norwegian register (SYSVAK). While limitations in register-based data are important caveats – our cohort study encompassing the whole Norwegian adult population indicates that vaccine effectiveness against severe disease is high among vaccinated individuals. Our estimates remain qualitatively the same for protection against infection and severe disease when splitting by age groups, indicating that the confounding effect of factors that are relatively constant within age-groups introduce little bias in our adjusted models. Appropriate prioritisation and planning of vaccine campaigns is integral for combating COVID-19 and is only possible with updated knowledge on vaccine effectiveness of realistic vaccination regimens achieved in large populations. For our study the overall protection (i.e. a weighted mean of vaccine effectiveness over time) increase through the initial period with a peak of right below 60% on the 21st ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22273086
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.29.22273093

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.22273093: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: Ethics: Ethical approval for studies on the risk of severe disease by SARS-CoV-2 variant based on data from the national preparedness registry for COVID-19 was granted by Regional Committees for Medical Research Ethics - South East Norway, reference number 249509.<br>IRB: Ethics: Ethical approval for studies on the risk of severe disease by SARS-CoV-2 variant based on data from the national preparedness registry for COVID-19 was granted by Regional Committees for Medical Research Ethics - South East Norway, reference number 249509.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">From August 2021 there has been a general recommendation that all pregnant women in the second or third trimester get vaccinated.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  An important limitation with severity studies based on reported COVID-19 cases is that undiagnosed cases will affect reported outcome proportions, while systematic differences in undiagnosed cases between groups may affect comparisons. In our study, this is particularly relevant for the comparison of the Alpha wave to other variant waves. The testing strategy was enhanced after the Alpha wave, thus a higher proportion of asymptomatic and mild cases may have been diagnosed among school-age children and adolescents in the Delta and Omicron waves. Also, the small number of outcomes must be considered, which restricted further exploration of our results. Given the low incidence of severe outcomes among child and adolescent COVID-19 cases, which may be further reduced through vaccination (20, 31, 34, 36), analyses of pooled data from several countries or meta-analyses could provide more precise estimates that can better elucidate differences in the risk of these outcomes between VOC in younger age groups. Further, we have based the analysis on variant waves, not cases with known data. However, in models for all COVID-19 cases reported in Norway, results based on these waves were consistent with analyses based on cases with known variant in periods when one variant was superseding another (see supplement A, section 4). Finally, we analysed an Omicron wave when the sublineage BA.1 was the dominant circulating variant. Further studies are still needed to establish differences in dise...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.29.22273093
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272948

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272948: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethics approval: The EPICOV study received approval from an ethics committee (Comité de Protection des Personnes Sud Méditerranée III 2020-A01191-38) and from France’s National Data Protection Agency (Commission Nationale Informatique et Libertés, CNIL, MLD/MFI/AR205138).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Several characteristics were measured at study baseline: sex (female vs. male), age (25-30 vs. 18-24 years), urbanicity (rural area, <100 000 residents, ≥100 000 residents, Paris and suburbs), lone living (yes vs. no), having children (yes vs. no), and presence of a chronic disease (yes vs. no, the most frequent diseases reported were asthma - 4.6%, physical disability - 1.1%, gastro-intestinal disorder - 0.9%, musculo-skeletal disorder - 0.9%, respiratory disorder - 0.6%, diabetes - 0.5%).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">As previously described, participants (≥ 15 years of age, residing in mainland France or three out of five overseas territories) were randomly selected from the national tax database (FIDELI).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations and strengths: Our study has limitations which need to be acknowledged prior to interpreting the data. First, the EPICOV study started in the Spring of 2020 and we have only retrospective data on participants’ history of pre-existing mental health problems. Nevertheless, we were able to exclude from the statistical analyses participants who had the most severe forms of psychopathology. While future studies should examine prospective changes in mental health among cohorts of young people followed since prior to the COVID-19 pandemic, our results do not appear to be due to pre-existing severe mental health difficulties. Second, the EPICOV cohort suffered attrition, with participants belonging to socioeconomically disadvantaged groups least likely to participate over the long term (17). This lead us to conduct repeated measures analyses, which make it possible to maximize the use of information provided by study participants and limit possible biases due to attrition. Moreover, our statistical analyses are weighted to render the study sample representative of young adults in France. Third, in the EPICOV cohort, depression was ascertained with the PHQ-9 questionnaire, which is self-reported. While clinical diagnoses may yield a more accurate picture of severe depression, the PHQ-9 has satisfactory validity vs. clinical diagnosis (18) and we specifically studied a level of symptoms consistent with moderate to severe depression. Our study also has strengths which we wou...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.25.22272948
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.26.22272979

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.22272979: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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medrxiv.org/cgi/content/10.1101/2022.03.26.22272979
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.29.486282

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.486282: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IACUC: Animals: All experiments were performed on adult male C57BL/6J mice (3-6 months) following the ethical guidelines of NIH guidelines for animal research and approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Iowa.<br>Euthanasia Agents: (RT-qPCR): A separate group of mice was decapitated under an isoflurane chamber to collect brains for RT-qPCR experiments.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Animals: All experiments were performed on adult male C57BL/6J mice (3-6 months) following the ethical guidelines of NIH guidelines for animal research and approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Iowa.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">Images were analyzed by trained researchers blind to experimental conditions for expression parameters in ImageJ (Fiji) software as described previously (Sagarkar et al., 2021).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Further, the membranes were incubated overnight with antibodies specific to ACE2, TMPRSS2, and β-actin (Table 2) at 4°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ACE2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>TMPRSS2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>β-actin ( Table 2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Animals: All experiments were performed on adult male C57BL/6J mice (3-6 months) following the ethical guidelines of NIH guidelines for animal research and approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Iowa.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>C57BL/6J</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immuno-colocalization was analyzed by measuring the percentage of co-localization area pixels by total immunoreactive area pixels after setting color thresholding parameters in ImageJ (Fiji) software (Sagarkar et al., 2021).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImageJ</div><div>suggested: (ImageJ, RRID:SCR_003070)</div></div><div style="margin-bottom:8px"><div>Fiji</div><div>suggested: (Fiji, RRID:SCR_002285)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data and statistical analysis: The statistical analysis was performed using GraphPad Prism v.9 (CA, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.29.486282
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https://biorxiv.org/cgi/content/10.1101/2022.03.28.486152

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.486152: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: NIAID), National Institutes of Health protocol VRC 200 (NCT00067054) in compliance with the NIH Institutional Review Board (IRB) approved protocol and procedures.<br>Consent: All subjects met protocol eligibility criteria and agreed to participate in the study by signing the NIH IRB approved informed consent.<br>Field Sample Permit: Research studies with these samples were conducted by protecting the rights and privacy of the study participants.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Diluted antibody samples were applied and incubated 1 hr at 37°C followed by 6 washes with PBS-T; plates were the incubated with HRP-conjugated anti-human IgG (Jackson ImmunoResearch) diluted 1:10,000 in B3T buffer for 1 h at 37°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Directly conjugated antibodies purchased from BD Biosciences include CD19 PE-Cy5 (Clone HIB19; cat. 302210), CD14 BB660 (Clone M0P9; cat. 624925), CD3 BUV395 (Clone UCHT1; cat. 563546), CD4 BV480 (Clone SK3; cat. 566104), CD8a BUV805 (Clone SK1; cat. 612889), CD45RA BUV496 (Clone H100; cat. 750258)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD14</div><div>suggested: (BD Biosciences Cat# 750381, RRID:AB_2874552)</div></div><div style="margin-bottom:8px"><div>CD3</div><div>suggested: (BD Biosciences Cat# 563546, RRID:AB_2744387)</div></div><div style="margin-bottom:8px"><div>CD4</div><div>suggested: (BD Biosciences Cat# 566104, RRID:AB_2739506)</div></div><div style="margin-bottom:8px"><div>CD8a</div><div>suggested: (Abcam Cat# ab34397, RRID:AB_2291359)</div></div><div style="margin-bottom:8px"><div>CD45RA</div><div>suggested: (BD Biosciences Cat# 750258, RRID:AB_2874456)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibodies from Biolegend include CD16 BV570 (Clone 3G8; cat. 302036), CD56 BV750 (Clone 5.1H11; cat. 362556), CCR7 BV605 (Clone G043H7; cat. 353244) and CD69 APC-Fire750 (Clone FN50; cat. 310946)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD56</div><div>suggested: (DSHB Cat# 5.1H11, RRID:AB_531857)</div></div><div style="margin-bottom:8px"><div>CCR7</div><div>suggested: (GenWay Biotech Inc. Cat# GWB-EA1DA7, RRID:AB_10269678)</div></div><div style="margin-bottom:8px"><div>CD69</div><div>suggested: (BioLegend Cat# 310946, RRID:AB_2616709)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Anti-histidine antibody was immobilized on Series S Sensor Chip CM5 (Cytiva) through primary amine coupling using a His capture kit (Cytiva).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Anti-histidine</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Human IgG monoclonal antibodies (mAb) used for these analyses include: B1-182, CB6, A20-29.1, A19-46.1, LY-COV555, A19-61.1, S309, A23-97.1, A19-30.1, A23-80.1, and CR3022.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A19-61.1</div><div>suggested: (ABclonal Cat# A19611, RRID:AB_2862699)</div></div><div style="margin-bottom:8px"><div>A23-80.1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CR3022</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The antibodies used in the staining cocktail were: CD8-BV510 (Biolegend, clone RPA-T8, cat# 301048), CD56-BV510 (Biolegend, clone HCD56, cat# 318340), CD14-BV510 (Biolegend, clone M5E2, cat# 301842), CD16-BUV496 (BD Biosciences, clone 3G8, cat# 612944), CD3-APC-Cy7 (BD Biosciences, clone SP34-2, cat# 557757), CD19-PECy7</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD8-BV510</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD56-BV510</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD14-BV510</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD3-APC-Cy7</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Samples sorted for 10x Genomics single-cell RNAseq were individually labelled with an oligonucleotide-linked hashing antibody (Totalseq-C, Biolegend) in addition to the staining cocktail and sorted into a single tube according to the gating strategy shown in Fig.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Totalseq-C</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Human IgG monoclonal antibodies (mAb) used for these analyses include: B1-182, CB6, A20-29.1, A19-46.1, LY-COV555, A19-61.1, S309, A23-97.1, A19-30.1, A23-80.1, and CR3022.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>B1-182</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data were acquired on a modified BD FACSymphony and analyzed using FlowJo software (version 10.7.1).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Results are reported as percent competition and statistical analysis was performed using unpaired, two-tailed t-test (Graphpad Prism v.8.3.1).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Graphpad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The resulting sequences were annotated using SONAR v4.2 (81) in single-cell mode.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SONAR</div><div>suggested: (Edgerton Digital Collections, RRID:SCR_005962)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  LIMITATIONS OF THE STUDY: Our study is limited by sampling of paired heavy and light chain sequences from fewer than 1,000 SARS-CoV-2-specific B cells across 13 individuals. This scale is small in comparison to bulk IG sequencing studies (32, 61) and even a few single-cell studies (58, 60, 75). We are also limited in our ability to make functional repertoire comparisons due to varied sorting strategies and differences in functional assays used to assess isolated mAbs. Moreover, our cohort was sampled only at a single time point early in convalescence and included only one individual with high serum neutralization titers. It will be important to verify that our findings extend to later time points when the antibody repertoire has matured. In addition, further studies are needed to examine the response elicited by more recent SARS-CoV-2 variants such as Delta and Omicron.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT00067054</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Apheresis and Specimen Collection Procedures to Obtain Plasm…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

Annotators

sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.03.28.486152
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.29.482838

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.482838: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Proteins with more than 60% identity across the whole length of the antigen sequences used to generate the HPA antibody were selected.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HPA</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Secondary antibodies goat anti□mouse Alexa Fluor 555 (A21424), goat anti□rabbit Alexa Fluor 488 (A11034), and goat anti□chicken Alexa Fluor 647 (A21449), were diluted to 2.5 µg/ml in PBS containing 4% FBS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti□rabbit</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti□chicken</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Primary antibodies generated at the HPA were diluted to 2 µg/ml, commercial Sigma-1 R antibody to 3 µg/ml (MAB1076, R&D systems) chicken Calreticulin (Abcam, ab2908) to 1 µg/ml and mouse SARS-CoV-2 Spike monoclonal antibody (GTX632604 GeneTex) to 1 µg/ml.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Calreticulin ( Abcam ,</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Secondary antibodies goat anti□mouse Alexa Fluor 555 (A21424), goat anti□rabbit Alexa Fluor 488 (A11034), and goat anti□chicken Alexa Fluor 647 (A21449), were diluted to 2.5 µg/ml in PBS containing 4% BSA.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti□mouse</div><div>suggested: (C. Birchmeier - Max Delbruck Center for Molecular Medicine, Berlin, Germany Cat# Guinea pig anti-mouse Tlx3 polyclonal antibody, RRID:AB_2532145)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cell culture and virus infection: Vero E6 cell line was grown at 37°C in a 5% CO2 condition in Dulbecco’ modified Eagle’s medium (DMEM) containing 10% FBS (Gibco).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody selection: Validated antibodies from the HPA project were blasted against the Chlorocebus sabaeus sequence from Ensembl.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Ensembl</div><div>suggested: (Ensembl, RRID:SCR_002344)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Generation of virus and host protein interaction network: Viral bait - host protein and host protein-protein interaction network was visualized with Cytoscape (63).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Cytoscape</div><div>suggested: (Cytoscape, RRID:SCR_003032)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Human protein - protein interactions were derived from String database (64)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>String</div><div>suggested: (STRING, RRID:SCR_005223)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, KEGG database (</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>KEGG</div><div>suggested: (KEGG, RRID:SCR_012773)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, Reactome database (66), WikiPathways and Human Phenotype Ontology.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>WikiPathways</div><div>suggested: (WikiPathways, RRID:SCR_002134)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data was plotted using Graphpad Prism software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Graphpad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  A limitation of this study is that results are based on data from the non-human cell line Vero E6, originating from the African green monkey. This cell line is known for its dampened innate immune response and permissiveness to SARS-CoV-2, which makes it a feasible but a limiting virology model (62). When comparing subcellular localization of the hits from the host-response screen between non-infected Vero E6 cells and the immunofluorescence data on human cell lines as previously generated within the HPA, 80% of the patterns overlap between the species (data publicly available at www.proteinatlas.org). Looking at staining similarities across all proteins (n=546) stained in Vero E6 in addition to human cell lines within the HPA, 75% show overlap in subcellular localization. Due to the inter-species similarities, we speculate that host proteome landscape responses to SARS-CoV-2 infection in a partially similar manner in human cell lines. In this work we performed targeted phenotyping of disease relevant proteins as a funnel to guide target selection for drug repurposing or discovery. Further, we suggest that “targeted phenotyping” can be used to prioritize host targets for novel drugs, in this case for the treatment of COVID-19. Our approach can be applied as a stand-alone filter or as an integrated layer in multi-omics study for the selection of relevant host responses in infectious diseases. Given that the approach is easily scalable and transferable for infectious agents or ...
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04890509</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">A Study of Bemcentinib for the Treatment of COVID-19 in Hosp…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.29.482838
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https://biorxiv.org/cgi/content/10.1101/2022.03.29.486173

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.486173: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IACUC: Ethics statement: Animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) of the National Vaccine and Serum Institute (NVSI) and conducted under Chinese animal use guidelines.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Rat immunization: To test the immunogenicity of mos-tri-RBD, 10 Wistar rats with half male and half female (purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd., China) were immunized intramuscularly by two doses, three weeks apart, of mos-tri-RBD (10 μg per dose) mixed with 300μg aluminum hydroxide adjuvant.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After washing three times with PBST, the plate was incubated with HRP-conjugated goat anti-mouse IgG antibody at 37°C for one hour.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mouse IgG</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The homo-tri-RBD used in this study was stably expressed by CHO cells and purified following the similar processes described above.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CHO</div><div>suggested: CLS Cat# 603479/p746_CHO, RRID:CVCL_0213)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The constructed plasmids encoding the S protein of SARS-CoV-2 variants were transfected into HEK293T cells, which were simultaneously infected with G*ΔG-VSV.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: RRID:CVCL_HA71)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Subsequently, 100 µL trypsin-treated HuH-7 cells with the density of 2×105 per mL were added into the well of the plates, and incubated at 37 °C and 5% CO2 for 20 ∼ 24 hours.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HuH-7</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After incubation, Vero cell suspension with a density of 2×105 per mL was added into the mixture.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To evaluate the immune efficacy of mos-tri-RBD as a booster dose, a total of 30 Wistar rats, half male and half female, were intramuscularly primed with a dose (4μg/dose) of the inactivated vaccine BBIBP-CorV.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Wistar</div><div>suggested: RRID:RGD_150520162)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After adding signal peptide and Kozak sequences to N terminus, the construct was cloned into the PTT5 plasmid vector via the Hin dIII and Not I restriction sites.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PTT5</div><div>suggested: RRID:Addgene_52326)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In short, the gene sequences of the S protein of SARS-CoV-2 variants were codon-optimized and synthesized, which were then cloned into pcDNA3.1 plasmid vector.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1</div><div>suggested: RRID:Addgene_79663)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SPR assay: Surface plasmon resonance (SPR) assay was performed to quantify the binding avidity of the recombinant mos-tri-RBD to the receptor hACE2 using BIAcore 8K (GE Healthcare) with NTA chips.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BIAcore</div><div>suggested: (Biacore T100 System, RRID:SCR_019679)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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biorxiv.org/cgi/content/10.1101/2022.03.29.486173
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https://biorxiv.org/cgi/content/10.1101/2022.03.29.486253

1
1. sciscore 01 Apr 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.29.486253: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

biorxiv.org/cgi/content/10.1101/2022.03.29.486253
Mar 2022
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.24.485633

1
1. sciscore 31 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.485633: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The infectious titer of the P1 virus was quantified by fluorescent focus assay on Vero E6 cells (Figure S1b).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: RRID:CVCL_XD71)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04368728</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Study to Describe the Safety, Tolerability, Immunogenicity, …</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.03.24.485633
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.26.484261

1
1. sciscore 31 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.484261: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Serum samples: All participants gave informed consent before taking part in the study.<br>IRB: Samples from Bergen were from studies approved by the Northern and Western Norway Regional Ethical Committees (approval numbers 218629, 118664).<br>Field Sample Permit: All studies were approved by the Norwegian Regional Ethical Committee (reference numbers: 200631, 127798, 2021/8504, 135924, 204104).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The SARS-CoV-2 virus Human 2019-nCoV strain 2019-nCoV/Italy-InMI1 (008V-03893) from the European Virus Archive (EVA) was detected in Vero E6 cell cultures by ELISA using a mAb against SARS-CoV-2 nucleocapsid (40143-R004, SinoBiological) and HRP-conjugated goat anti-rabbit IgG-Fc mAb (SSA003, SinoBiological).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mixtures were transferred to 96-well plates seeded with Vero cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Expression and hapten-conjugation of recombinant ACE2: cDNA encoding a truncated human ACE2 fused to human albumin was sub-cloned into pFUSE2ss-CLIg-hk (InvivoGen).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pFUSE2ss-CLIg-hk</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The secreted fusion protein was purified on a CaptureSelect™ human albumin affinity matrix (Life Technologies), and protein eluted by adding 20 mM Tris and 2.0 M MgCl2, pH 7.0 before up-concentration using Amicon®</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Amicon®</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Further analysis was performed in Microsoft Excel.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Microsoft Excel</div><div>suggested: (Microsoft Excel, RRID:SCR_016137)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To visualize results as colored dot plots, we exported data from Excel to WinList 3D.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Excel</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Optical density (OD) was measured at 450/620 nm using the Synergy H1 Hybrid Multi-Mode Reader with the Gen5 2.00 (version 2.00.18) software (BioTek Instruments Inc., Winooski, VT, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Gen5</div><div>suggested: (Gen5, RRID:SCR_017317)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  The present study has limitations. First, we only measured serum neutralization of SARS-CoV-2wt. Further studies are needed to determine exact predictive values of Multi-IgG-RBD-ACE2 for protection against each VOC. Second, RBD-ACE2 interaction assays do not measure neutralizing antibodies binding outside of the RBD or factors that promote infectivity, such as virus replication rates. This may explain why the results shown in Fig. 3c did not recapitulate published differences in neutralizing titers for Delta and SARS-CoV-2wt (Fig. 3c) 37,40. The implication is that neutralization assays are still needed to establish if titers for new variants correlate with anti-RBD-wt levels 3. Finally, the arrays used for large-scale analysis of early vaccine responses shown in Fig. 8, did not contain RBD from Omicron. Reanalysis is necessary to determine if Omicron-neutralizing antibodies appear early, or first after many months of affinity maturation as suggested in a recent review 20. The results may have implications for establishing optimal dose intervals. In conclusion, we show that anti-RBDwt titers in post-vaccine sera are broadly predictive for levels of neutralizing antibodies to VOCs. Our results also demonstrate the feasibility and utility of Multi-IgG-ACE2-RBD in large-scale immunomonitoring.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.26.484261
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.26.485922

1
1. sciscore 31 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.485922: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: Human subject study and biosafety approvals for blood draws: All research activities with human blood specimens of pre-COVID-19, sero-negative (healthy) donors and convalescent COVID-19 patients were implemented under NIH guidelines for human subject studies and the protocols approved by the Northwestern University Institutional Review Board (STU00205299) as well as the Institutional Biosafety Committee for COVID-19 research.<br>IRB: Human subject study and biosafety approvals for blood draws: All research activities with human blood specimens of pre-COVID-19, sero-negative (healthy) donors and convalescent COVID-19 patients were implemented under NIH guidelines for human subject studies and the protocols approved by the Northwestern University Institutional Review Board (STU00205299) as well as the Institutional Biosafety Committee for COVID-19 research.<br>Consent: For collecting human blood specimens, patients and donors were recruited at Northwestern Memorial Hospital based on their availability and willingness to consent and participate in the research.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Results were normalized to the CR3022 antibody with known affinity to the receptor binding domain of SARS-CoV2 (Creative Biolabs, MRO-1214LC)(29, 52).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CR3022</div><div>suggested: (Imported from the IEDB Cat# CR3022, RRID:AB_2848080)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells were stained for surface antigens using fluorescence-conjugated monoclonal Abs specific to human CD45, CD3, CD4, CD127 and CD25 antibodies for Treg identification and sorting as well as CD45, CD3, CD64, CD14 and CD16 for monocyte characterization and sorting.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD45</div><div>suggested: (RayBiotech Cat# CS-11-0019, RRID:AB_1227882)</div></div><div style="margin-bottom:8px"><div>CD4</div><div>suggested: (BD Biosciences Cat# 560249, RRID:AB_1645496)</div></div><div style="margin-bottom:8px"><div>CD127</div><div>suggested: (BD Biosciences Cat# 560249, RRID:AB_1645496)</div></div><div style="margin-bottom:8px"><div>CD25</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD64</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD14</div><div>suggested: (BioLegend Cat# 348805, RRID:AB_2889063)</div></div><div style="margin-bottom:8px"><div>CD16</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Neutralization assays with 10 μL or 80 μL of plasma were performed using HEK293 cells with stable expression of human ACE2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293</div><div>suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">0.5 μL RBD-647 was then pre-incubated with PBS as a control or 80 μL patient-derived plasma for 45 minutes on ice, after which it was combined with 106 HEK/ACE2 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK/ACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The levels of RBD-647 binding to HEK293/ACE2 cells were then assessed BD FACSAria Cell Sorter and analyzed using FlowJo v10software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293/ACE2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The levels of RBD-647 binding to HEK293/ACE2 cells were then assessed BD FACSAria Cell Sorter and analyzed using FlowJo v10software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Quality control of the libraries was performed using an Invitrogen Qubit DNA high sensitivity kit (ThermoFisher Scientific, Q32851) and Agilent Bioanalyzer high sensitivity DNA kit (Agilent, 5067-4626).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Agilent Bioanalyzer</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">scRNA-seq data acquisition and analysis: Data from scRNA-seq was demultiplexed and mapped to hg38 (refdata-gex-GRCh38-2020-A) using Cell Ranger software version 4.0.0 (10x genomics).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Cell Ranger</div><div>suggested: (Cell Ranger , RRID:SCR_017344)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.26.485922
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https://biorxiv.org/cgi/content/10.1101/2022.03.25.485826

1
1. sciscore 31 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.485826: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.25.485826
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.25.485875

1
1. sciscore 31 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.485875: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.<br>IACUC: K18-hACE2 mice: The Institutional Animal Care and Use Committee at Rocky Mountain Laboratories provided animal study approvals, which were conducted in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility, following the basic principles and guidelines in the Guide for the Care and Use of Laboratory Animals eighth edition, the Animal Welfare Act, U.S. Department of Agriculture, and the U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Male and female macaques per group were balanced.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">All slides were examined by a board-certified veterinary anatomic pathologist who was blinded to study group allocations.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Contamination: Mycoplasma testing is performed at monthly intervals, and no mycoplasma was detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Raw Illumina sequencing data for the antibody-escape mapping experiments are available on the NCBI Short Read Archive (SRA) at BioProject PRJNA770094, BioSample SAMN26315988.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibody-escape</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Half-maximal inhibitory dilutions (ID50 values) were derived using 4-parameter nonlinear regression in AntibodyDatabase (87).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>AntibodyDatabase ( 87</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The libraries were washed and secondarily labeled for 1 hour with 1:100 fluorescein isothiocyanate-conjugated anti-MYC antibody (Immunology Consultants Lab, CYMC-45F) to label for RBD expression and 1:200 Alexa Fluor-647-conjugated goat anti-human-IgG Fc-gamma (Jackson ImmunoResearch 109-135-098) to label for bound NHP antibodies or Alexa Fluor-647-conjugated goat anti-mouse-IgG Fc-gamma (Jackson ImmunoResearch 115-605-008) to label for bound mouse antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-MYC</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-human-IgG Fc-gamma</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-mouse-IgG Fc-gamma</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">/, version 0.8.10) to process Illumina sequences into counts of each barcoded RBD variant in each pre-selection and antibody-escape population.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibody-escape population.</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells and virus for K18-hACE2 mouse studies: Virus propagation was performed in VeroE6 cells in DMEM containing 2% FBS, 1 mM L-glutamine, penicillin (50 U/mL), and streptomycin (50 μg/mL (DMEM2).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>VeroE6</div><div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The TCID50 assay was conducted by addition of 10-fold graded dilutions of samples to Vero/TMPRSS2 cell monolayers.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero/TMPRSS2</div><div>suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mosaic-8b RBD-mi3 and homotypic SARS-2 RBD-mi3 were compared by negative-stain EM.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Mosaic-8b RBD-mi3</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">K18-hACE2 mice: The Institutional Animal Care and Use Committee at Rocky Mountain Laboratories provided animal study approvals, which were conducted in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility, following the basic principles and guidelines in the Guide for the Care and Use of Laboratory Animals eighth edition, the Animal Welfare Act, U.S. Department of Agriculture, and the U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>K18-hACE2</div><div>suggested: RRID:IMSR_GPT:T037657)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immunizations of mosaic-8b or homotypic SARS-2 Beta (5 µg each based on RBD content, 11.4 µg of total RBD-mi3) in 100 µL of 50% v/v AddaVaxTM adjuvant (InvivoGen) were done using intramuscular (IM) injections of 7-8-week-old female BALB/c mice (Envigo) (8 animals per cohort).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BALB/c</div><div>suggested: RRID:IMSR_ORNL:BALB/cRl)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Preparation of RBD-mi3 nanoparticles: SpyCatcher003-mi3 nanoparticles (78) were expressed in BL21 (DE3)-RIPL E coli (Agilent) transformed with the pET28a His6-SpyCatcher003-mi3 gene (Addgene) as described (34, 84).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pET28a</div><div>suggested: RRID:Addgene_139598)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Raw Illumina sequencing data for the antibody-escape mapping experiments are available on the NCBI Short Read Archive (SRA) at BioProject PRJNA770094, BioSample SAMN26315988.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NCBI Short Read Archive</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Curves were plotted and analyzed to obtain midpoint titers (EC50 values) using Graphpad Prism 9.3.1 (Graphpad Softwatre, San Diego, CA) assuming a one-site binding model with a Hill coefficient.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Graphpad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>Graphpad</div><div>suggested: (GraphPad, RRID:SCR_000306)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Raw sequencing data are available on the NCBI SRA under BioProject PRJNA770094, BioSample SAMN26315988.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BioProject</div><div>suggested: (NCBI BioProject, RRID:SCR_004801)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.25.485875
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https://biorxiv.org/cgi/content/10.1101/2022.03.23.485512

1
1. sciscore 30 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.23.485512: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The cultures for Corona 229E-infected Huh7 cells and Influenza A-infected MDCK cells were prepared as described in et al.51, and Crisci et al.52, respectively.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Huh7</div><div>suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Adenovirus-infected HeLa cells were prepared as described in Jogler et al.56, vaccinia-infected BHK-21 cells were prepared as described in Earl et al.57, polio-infected HeLa cells were prepared as described in et al.58.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HeLa</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>BHK-21</div><div>suggested: ATCC Cat# CRL-6281, RRID:CVCL_1914)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Influenza-infected MDCK cells (see Supplementary Fig. 9) were prepared as described by Kim et al.59 and the images were captured with a Synentec CellaVista35 at 20x.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MDCK</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Bootstrapping on the knowledge acquired from those models allowed the AVIA models to converge faster and at a higher accuracy 64.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>AVIA</div><div>suggested: (AVIA, RRID:SCR_005172)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.23.485512
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https://biorxiv.org/cgi/content/10.1101/2022.03.28.486075

1
1. sciscore 30 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.28.486075: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Animals with sex- and age-matched littermates were randomly included in experiments.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">Animal experiments were carried out in a blinded fashion whenever feasible.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">For the number of animals needed to achieve statistically significant results, we conducted an a priori power analysis.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For assays examining the avid binding of dimeric sACE22-IgG1 and monoclonal antibodies, cells were resuspended in PBS-BSA containing 1:150 polyclonal chicken anti-MYC-FITC (Immunology Consultants Laboratory) and 1:300 anti-human IgG-APC (clone HP6017, BioLegend).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-MYC-FITC (Immunology Consultants Laboratory)</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-human IgG-APC</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HeLa-hACE2-11 (a stable human ACE2 HeLa clone) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) high glucose (4500 mg/l) with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C, 5% CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HeLa clone</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Calu-3 (ATCC HTB-55) cells were grown in Modified Eagle’s Medium high glucose (4500 mg/l) with 10% FBS, 4 mM L-Glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C with 5% CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Calu-3</div><div>suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Monoclonal antibodies, sACE2-8his proteins, and RBD-8his were expressed in Expi293F cells transfected using Expifectamine (Thermo Fisher) according to the manufacturer’s instructions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Expi293F</div><div>suggested: RRID:CVCL_D615)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Virus titers were quantitated by a plaque forming assay using Vero E6 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: RRID:CVCL_XD71)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudovirions were created following a polyethylenimine (PEI)-based transient co-transfection on 293T cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T</div><div>suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudovirus Inhibition Assay: HeLa-hACE2-11 cells were seeded (5×103 cells/well) onto white-bottomed 96-well tissue culture plates (100 μL/well) and incubated for 16 h, 37 °C, 5% CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HeLa-hACE2-11</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HeLa-hACE2-11 (a stable human ACE2 HeLa clone) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) high glucose (4500 mg/l) with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C, 5% CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HeLa-hACE2-11</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Hemizygous K18-hACE2 mice (strain 034860: B6.Cg-Tg(K18-ACE2)2Prlmn/J) were purchased from The Jackson Laboratory.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>K18-hACE2</div><div>suggested: RRID:IMSR_GPT:T037657)</div></div><div style="margin-bottom:8px"><div>B6.Cg-Tg(K18-ACE2)2Prlmn/J</div><div>suggested: RRID:IMSR_JAX:034860)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plasmids for sACE22-IgG1 (Addgene #154104), sACE22.v2.4-IgG1 (#154106), sACE2(18-615)-8his (#149268), sACE2(18-615).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>sACE22-IgG1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mutations for the CDY14 decoy receptor were introduced into the wild type sACE2 plasmids using extension overlap PCR and confirmed by Sanger sequencing.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>sACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">S Binding Assay: Human codon-optimized genes encoding N-terminal myc-tagged S proteins of BA.1 and BA.2 omicron were synthesized (Integrated DNA Technologies) and cloned into the NheI-XhoI sites of pcDNA3.1(+) (Invitrogen).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1(+)</div><div>suggested: RRID:Addgene_129020)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudovirion Production: Pseudoviruses were created using plasmids for SARS-CoV-2 Omicron B.1.1.529 (BA.1) S and HIV-1 proviral vector pNL4-3.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pNL4-3</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Images were taken by Aperio ImageScope 12.4.3 and analyzed by Zen software (Zeiss).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImageScope</div><div>suggested: (ImageScope, RRID:SCR_014311)</div></div><div style="margin-bottom:8px"><div>Zen</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">IC50 values were determined by fitting dose-response curves with four-parameter logistic regression in GraphPad Prism 8 software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04335136</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Completed</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Recombinant Human Angiotensin-converting Enzyme 2 (rhACE2) a…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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URL

biorxiv.org/cgi/content/10.1101/2022.03.28.486075
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.27.485958

1
1. sciscore 30 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.27.485958: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IACUC: All animal studies were approved in accordance with the Weizmann Institute’s Animal Care and Use Committee (IACUC) guidelines and regulations (approval number 00580120-3).<br>Euthanasia Agents: The mice were measured under general isoflurane inhalation anesthesia (5% induction, 1% maintenance) up to four hours after EVs injection using a gradient echo Fast Low Angle Shot (FLASH) with the following parameters: TR = 300 ms; TE = 2 ms; resolution of 0.23×0.23×0.7 mm3.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After overnight blocking in 5% milk in TBST, specific antibodies were applied to the membranes for 1 h to detect markers: CD81 (B-II, Santa Cruz, USA); c-myc (9E10, Santa Cruz, USA) (all 1:500); and beta-actin (C4, Santa Cruz, USA) (1:1000).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD81 (B-II, Santa Cruz, USA)</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>c-myc</div><div>suggested: (Covance Cat# MMS-150P-1000, RRID:AB_291322)</div></div><div style="margin-bottom:8px"><div>9E10</div><div>suggested: (Covance Cat# MMS-150R-500, RRID:AB_291327)</div></div><div style="margin-bottom:8px"><div>beta-actin</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>C4</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HRP-conjugated anti-mouse secondary HRP goat anti-mouse IgG antibody (#4053, Biolegend, USA) (1:5000 in TBST) was applied for 1 h before imaging using enhanced chemiluminescence substrate EZ-ECL Kit (Biological industries, catalog no. 20-500-120).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mouse</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-mouse IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The expression of ACE2 protein in cells was also confirmed by Western blot analysis, as described above, using a rabbit monoclonal ACE2 antibody (ab239924; 1:1000; Abcam, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ACE2</div><div>suggested: (Abcam Cat# ab239924, RRID:AB_2861381)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then the cells were detached from wells by PBS and incubated with ACE2 primary antibody (ab239924; 1:1000; Abcam, USA) for 1 hour on ice, washed with PBS and then incubated with anti-rabbit fluorescently-conjugated secondary antibody (Alexa Fluor 647 nm) for 1 hour on ice.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-rabbit fluorescently-conjugated secondary</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The stably expressing ACE2 HEK293T cell line was kindly obtained from the lab of Dr. Ron Diskin (Weizmann Institute of Science) and kept under puromycin antibiotics (0.5 μg/ml, Invitrogen, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: RRID:CVCL_HA71)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK-pAGDisplay-RBD stable cell line generation: The pAGDisplay-based plasmids expressing RBD (1 ug of DNA) were transfected in a 60 mm culture dish with 80% confluent HEK293 cells by a JetPrime transfection reagent (Polyplus, France) according to the manufacturer’s protocol.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293</div><div>suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Binding assays and affinity curve determination using cell-display: The HEK-pAGDisplay-RBD stable cells grown to 80% confluency were gently detached by Accutase (1/2 solution in PBS, 3 min, Sigma Aldrich cat.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK-pAGDisplay-RBD</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Colony PCR and sequencing were used for analysis and verification. pAGDisplay vector construction: pDisplay Mammalian Expression vector was purchased from Invitrogen (V66020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pAGDisplay</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The pAGDisplay vector backbone was assembled by combining a pET28b fragment bearing KanR and origin of replication, a pLVX vector fragment bearing WPRE, PuroR, and IRES sequences, and a pDisplay CMV promoter with a PDGFRβ expression cassette by a restriction-free three-component assembly 58.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLVX</div><div>suggested: RRID:Addgene_174088)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Protein production, purifications, and labeling procedures: The designed ALFA-tag binding nanobody (DnbALFA) and its mNeonGreen fusion were expressed by using expression plasmid pET28bdSUMO 62 and E.coli BL21(DE3) cells as described previously 60.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pET28bdSUMO</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Soluble his-tagged peptidase domain of ACE2 protein (Q18 – S740), inserted in pHLsec plasmid, was expressed in an Expi293F cell system with an ExpiFectamine 293 Transfection Kit (ThermoFisher, USA) according to the manufacturer’s protocol and purified as described previously 45.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHLsec</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK-pAGDisplay-RBD stable cell line generation: The pAGDisplay-based plasmids expressing RBD (1 ug of DNA) were transfected in a 60 mm culture dish with 80% confluent HEK293 cells by a JetPrime transfection reagent (Polyplus, France) according to the manufacturer’s protocol.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pAGDisplay-based</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mean FL-4 fluorescence signal values of RBD+ cells, subtracted by RFnano and the nonspecific signal of the RBD-population, were used to determine the KD of binding constants using a non-cooperative Hill equation and a nonlinear least-squares regression using Python 3.7 45.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Python</div><div>suggested: (IPython, RRID:SCR_001658)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The fluorescence signal (APC filter) of cells was measured by a FACS machine (LRS-II) and analyzed by the FlowJo software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">MR images were analyzed by the ImageJ software or by a custom-made script written in MATLAB (MathWorks, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MATLAB</div><div>suggested: (MATLAB, RRID:SCR_001622)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After tuning and matching to the1H frequency, shimming of the magnetic field, and B0 correction, the tumor area was measured with the following parameters: both axial and coronal images were acquired; T2 and T2* maps were reconstructed in the Paravision software; and were followed by analysis in the ImageJ software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImageJ</div><div>suggested: (ImageJ, RRID:SCR_003070)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis was performed using GraphPad Prism 8.0 software (GraphPad Software Inc., USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
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biorxiv.org/cgi/content/10.1101/2022.03.27.485958
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https://biorxiv.org/cgi/content/10.1101/2022.03.25.485832

1
1. sciscore 30 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.485832: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: Animals: Animal research was conducted at the United States Army Medical Research Institute of Infectious Diseases (USAMRIID).<br>IACUC: Ethics statement: These experiments and procedures were reviewed and approved by the United States Army Medical Research Institute for Infectious Diseases Institutional Animal Care and Use Committee (IACUC).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Genders were mixed male and female, and all animals were SARS-CoV-2 naïve at the outset of the study.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Contamination: R4719 was determined to have no detectable mycoplasma, endotoxin or adventitious agents based on the assays and techniques used.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Serum binding and ACE-2 inhibitory antibody assessment: SARS-CoV-2-specific binding IgG antibody responses were measured using MULTI-SPOT® 96-well plates, V-PLEX SARS-CoV-2 Panel 7 Kit (Meso Scale Discovery (MSD), Rockville, MD).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2-specific binding IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">MSD SULFO-TAG™ conjugated anti-IgG antibody was added to each well.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Stimulations consisted of two pools of peptides spanning the S protein of SARS-CoV-2 or SARS-CoV-1 (1 µg/mL, JPT, PM-WCPV-S and PM-CVHSA-S respectively) in the presence of Brefeldin A (0.65 µL/mL, GolgiPlug™, BD Cytofix/Cytoperm Kit, Cat. 555028), co-stimulatory antibodies anti-CD28 (BD Biosciences Cat.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-1 (1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Following stimulation, cells were stained serially with LIVE/DEAD Fixable Blue Dead Cell Stain (ThermoFisher #L23105) and a cocktail of fluorescent-labeled antibodies (BD Biosciences unless otherwise indicated) to cell surface markers CD4-PE-Cy5.5 (S3.5, ThermoFisher #MHCD0418, Lot 2118390 and 2247858), CD8-BV570 (RPA-T8, BioLegend #301038, Lot B281322), CD45RA BUV395 (5H9, #552888, Lot 154382 and 259854), CD28 BUV737 (CD28.2, #612815, Lot 0113886), CCR7-BV650 (GO43H7, # 353234, Lot B297645 and B316676) and HLA-DR-BV480 (G46-6, # 566113, Lot 0055314).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD8-BV570</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>RPA-T8</div><div>suggested: (BD Biosciences Cat# 563795, RRID:AB_2722501)</div></div><div style="margin-bottom:8px"><div>CD45RA</div><div>suggested: (BD Biosciences Cat# 552888, RRID:AB_394517)</div></div><div style="margin-bottom:8px"><div>CD28</div><div>suggested: (BD Biosciences Cat# 612815, RRID:AB_2870140)</div></div><div style="margin-bottom:8px"><div>CCR7-BV650</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>B316676</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>G46-6</div><div>suggested: (BD Biosciences Cat# 566113, RRID:AB_2739515)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Infectivity and neutralization titers were determined using ACE2-expressing HEK293 target cells (Integral Molecular, Philadelphia, PA) in a semi-automated assay format using robotic liquid handling (Biomek NXp Beckman Coulter, Brea, CA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293</div><div>suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, biotinylated SARS-CoV-2 Spike trimer (Hexapro) was incubated with red streptavidin-fluorescent beads (Molecular Probes, Eugene, OR) for 2h at 37°C. 10 μl of a 100-fold dilution of beads–protein was incubated 2h at 37°C with 100μl 900-fold diluted plasma samples before addition of THP-1 cells (25,000 cells per well; Millipore Sigma, Burlington, MA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>THP-1</div><div>suggested: CLS Cat# 300356/p804_THP-1, RRID:CVCL_0006)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">293F-Spike-S2-WT cells were incubated with 10-fold diluted heat-inactivated (56°C for 30 min) plasma samples for 30 min at 37°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293F-Spike-S2-WT</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 pseudovirions (PSV) were produced by co-transfection of HEK293T/17 cells with a SARS-CoV-2 S plasmid (pcDNA3.4), derived from the Wuhan-Hu-1 genome sequence (GenBank accession number: MN908947.3) and an HIV-1 (pNL4-3.Luc.R-E-, NIH HIV Reagent Program, Catalog number 3418).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.4</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pNL4-3.Luc.R-E-</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, SARS-CoV-2 Spike-expressing 293 FreeStyle (293F) cells were generated by transfection with linearized plasmid (pcDNA3.1) encoding codon-optimized full-length SARS-CoV-2 Spike protein matching the amino acid sequence of the IL-CDC-IL1/2020 isolate (GenBank ACC# MN988713).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1</div><div>suggested: RRID:Addgene_79663)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Reduced data in the NSS files was extracted into Microsoft Excel workbooks using Notocord-derived formula add-ins, and the 30-minute (min) averages were calculated for each parameter for each subject.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Microsoft Excel</div><div>suggested: (Microsoft Excel, RRID:SCR_016137)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Assay equivalency was established by participation in the SARS-CoV-2 Neutralizing Assay Concordance Survey (SNACS) run by the Virology Quality Assurance Program and External Quality Assurance Program Oversite Laboratory (EQAPOL) at the Duke Human Vaccine Institute, sponsored through programs supported by the National Institute of Allergy and Infectious Diseases, Division of AIDS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Quality Assurance Program</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Quality Assurance Program Oversite Laboratory</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sample staining was measured on a FACSymphony(tm) A5 SORP (Becton Dickenson) and data was analyzed using FlowJo v.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Display of multicomponent distributions were performed with SPICE v6.0 (NIH, Bethesda, MD).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPICE</div><div>suggested: (SPICE, RRID:SCR_016603)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04784767</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Active, not recruiting</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">SARS-COV-2-Spike-Ferritin-Nanoparticle (SpFN) Vaccine With A…</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.25.485832
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.26.485903

1
1. sciscore 30 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.485903: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data source and group stratification: The source data for this study was generated within the framework of COV-IRT consortium (www.cov-irt.org) and deposited at the Short Read Archive (SRA) database with the project reference PRJNA671371, corresponding to a previously published study [26].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Short Read Archive</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Analysis of RNAseq data: Raw Illumina sequence reads obtained by a pair-end sequencing strategy, were filtered, and trimmed with Trimmomatic software [34].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Trimmomatic</div><div>suggested: (Trimmomatic, RRID:SCR_011848)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Filtered sequence reads were dual-aligned with the reference SARS-CoV-2 genome from Wuhan (strain reference MN908947.3) and the human genome (genome build GRCh38 and GENCODE v33) using the STAR aligner [35].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GENCODE</div><div>suggested: (GENCODE, RRID:SCR_014966)</div></div><div style="margin-bottom:8px"><div>STAR</div><div>suggested: (STAR, RRID:SCR_004463)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data was normalized using the variance-stabilizing transform (vst) in the DESeq2 package [</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>DESeq2</div><div>suggested: (DESeq, RRID:SCR_000154)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In addition to the classical GO-term enrichment analysis, the redundant ontology terms were filtered by REVIGO software [41].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>REVIGO</div><div>suggested: (REViGO, RRID:SCR_005825)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Graphical analysis and representation of lncRNA-centered regulatory networks was performed by NAViGaTOR software [43]</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NAViGaTOR</div><div>suggested: (TMA Navigator, RRID:SCR_005599)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.26.485903
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.26.22272984

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.22272984: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Informed consent for the use of anonymized CT values or samples obtained in routine clinical diagnostics was not obtained and is not required, and is in accordance with the study permit obtained by the Swedish Ethical Review Authority (Dnr 2020-01945 and 2022-01139-02, Etikprövningsmyndigheten).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">For the purpose and analyses of the current study, sample identities were anonymised, and IDs were replaced by a randomized code (i.e., those listed in supplementary tables).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In the parallel genotyping of 133 SARS-CoV-2-positive samples, performed using Thermo Fisher TaqMan SARS-CoV-2 Mutation Panel Assay (according to the manufacturers instructions) and our SARS-CoV-2 N1/RP/SBA1 assay, all Omicron samples were of the BA.1 lineage as demonstrated by WGS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Thermo Fisher TaqMan</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>WGS</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 One-Step RT-PCR Kit, RdRp and N Genes, IVD (NZYTech) was performed according to the manufacturer’s instructions (Version 13/2021, December 2021).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NZYTech</div><div>suggested: (NZYTech, RRID:SCR_016772)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sequencing data analysis: Raw data was quality trimmed using fastp10 v0.20.0 and de novo assembled using MEGAHIT11 v1.2.9 [--min-contig-len 5000]</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MEGAHIT11</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Disjoint contigs were scaffolded against the SARS-CoV-2 reference genome [ASM985889v3] using RagTag12 v2.1.0 and SARS-CoV-2 lineage was assigned using pangolin13 v3.1.20 [lineages version 2022-02-28].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RagTag12</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Alignment statistics was obtained using Minimap214 v2.24-r1122 [-ax sr Sars_cov_2.ASM985889v3.dna_sm.toplevel.fa.gz] and samtools15 v1.10 [stats] [coverage].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Minimap214</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>samtools15</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.26.22272984
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.24.485649

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.485649: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The R1 and R2 were then assembled using pRESTO, The Repertoire Sequencing Toolkit (15).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pRESTO</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FastQC was performed on read 1 (R1) and read 2 (R2) separately.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FastQC</div><div>suggested: (FastQC, RRID:SCR_014583)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The assembled reads were subjected to trimming using quality Phred score 20 as cutoff.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Phred</div><div>suggested: (Phred, RRID:SCR_001017)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The quality trimmed reads were further processed using IgBLAST (17).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgBLAST</div><div>suggested: (IgBLAST, RRID:SCR_002873)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">R package circlize (20) was used to create chord diagram for visualizing V-J usage frequencies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>circlize</div><div>suggested: (circlize, RRID:SCR_002141)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To assess the closeness of the repertoire across samples, Jaccard distance was calculated using vegan package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>vegan</div><div>suggested: (vegan, RRID:SCR_011950)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.24.485649
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https://biorxiv.org/cgi/content/10.1101/2022.03.23.485576

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.23.485576: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Expression of different coronavirus E proteins, the SARS-CoV-2 S, and SARS-CoV S protein were confirmed by transfection with the Turbofect transfection reagent (ThermoFisher) followed by radiolabeling and immunoprecipitation analysis using a mouse monoclonal antibody directed against the HA-tag (Thermo-Fisher, #26183) or an antibody against SARS-CoV Spike protein (Sino Biologicals, #40590-T62).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibody against SARS-CoV Spike protein</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The cultures were then incubated at 4C overnight with an and a rabbit monoclonal antibody against either Golgin-97 (Abcam, #ab84340) or Calnexin (Cell Signaling Technology, #2679).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Calnexin (Cell Signaling Technology, #2679</div><div>suggested: (Cell Signaling Technology Cat# 2679, RRID:AB_2228381)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The cells were washed in PBS, incubated with a secondary goat anti-rabbit antibody conjugated to AlexaFluor™-488 (Invitrogen, A11008) for 1 h at room temperature, washed, and reacted with rabbit anti-mouse conjugated to AlexaFluor™- 594 (Invitrogen, A11062) for 1 h.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-rabbit</div><div>suggested: (Thermo Fisher Scientific Cat# A-11008, RRID:AB_143165)</div></div><div style="margin-bottom:8px"><div>anti-mouse</div><div>suggested: (Innovative Research Cat# A11062, RRID:AB_1500656)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Expression of E was detected using an HA-tag antibody (Invitrogen).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HA-tag</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Aliquots of cells from the same co-transfections were also analyzed for protein expression by immunoblots using antibodies directed against the HA-tag (E proteins, SARS-CoV-2 S protein, and Vpu), the SARS-Cov-1 S protein, or against GFP to monitor SARS-CoV-2 N-GFP expression.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2 S protein,</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>GFP</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The lysates were transferred to new tubes and BST-2 (using an anti-BST-2 antibody), the E proteins (all having a C-terminal HA-tag), and SARS-CoV and SARS-CoV-2 S proteins, and N-GFP proteins, or GAPDH (to equalize loading) immunoprecipitated using appropriate antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-BST-2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>GAPDH</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immunofluorescence studies: To examine the intracellular localization of the SARS-CoV-2 E protein, COS-7 cells grown on 13 mm cover slips were transfected with either the empty pcDNA3.1(+) vector or one expressing the SARS-CoV-2 E protein using Turbofect transfection reagent (ThermoFisher).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>COS-7</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">At 48 h post-transfection (pt), the culture medium was collected, clarified by low-speed centrifugation, and the supernatants analyzed for infectious virus by titration on TZM-bl cells (29, 30, 91–95).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>TZM-bl</div><div>suggested: RRID:CVCL_B478)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Levels of infectious virus were determined by preparing a series of 10-fold dilutions of the culture supernatant followed by inoculation of Vero cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero</div><div>suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">At 24 h, equal levels of HIV-1ΔEnv-/VSV-G pseudotyped virus (M.O.I. of 0.1) were used to infect HEK293 cells for 48h.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plasmids with the entire HIV-1 NL4-3 genome (pNL4-3) and pNL4-3Δvpu were obtained from the NIH AIDS Reagent Branch.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pNL4-3Δvpu</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK293 cells were co-transfected with empty pcDNA3.1(+) or the vector expressing E proteins and pNL4-3.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pNL4-3</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK293 cells were transfected with either the empty pcDNA3.1(+) vector or one expressing SARS-CoV-2 E protein.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1(+)</div><div>suggested: RRID:Addgene_129020)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Analysis of the phosphorylation of eIF-2α: To determine if the expression of the E protein of SARS-CoV-2 resulted in phosphorylation of eIF2α, HEK293 cells seeded in 6-well plates were either left untransfected or transfected with 1 μg of pUC19 or of a SARS-CoV-2 E-expressing plasmid.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pUC19</div><div>suggested: RRID:Addgene_50005)</div></div><div style="margin-bottom:8px"><div>SARS-CoV-2 E-expressing</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK293 cells were co-transfected with either empty pcDNA3.1(+) vector and pcDNA3.1(+) expressing the human BST-2 protein, or pcDNA3.1(+) expressing each of the proteins described above and BST-2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1</div><div>suggested: RRID:Addgene_79663)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plasmids expressing the SARS-CoV and SARS-CoV-2 S proteins were purchased from Sino Biologicals (catalog # VG40150-G-N; VG40589-CY).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Sino Biologicals</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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URL

biorxiv.org/cgi/content/10.1101/2022.03.23.485576
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.24.485591

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.485591: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibodies used in this study include: IRF3, phospho-IRF3, IRF7, phsopho-STAT1 (Cell signalling technology), IRF1 (BD Transduction Laboratories), GAPDH (Santa Cruze Biotechnology), 229E N protein (Ingenasa), OC43 N protein (Milipore), SARS-CoV-2 N protein (Sino Biological).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IRF3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>phospho-IRF3, IRF7</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>phsopho-STAT1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IRF1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>GAPDH</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells, viruses, and reagents: Human lung fibroblast cell line MRC5, human lung cancer cell line H1299, human lung cancer cell line Calu-3, mouse fibroblast cell line L929, human coronaviruses HCoV-OC43 and HCoV-229E were obtained from the American Type Culture Collection (ATCC; Manassas, VA, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MRC5</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>H1299</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Calu-3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>HCoV-229E</div><div>suggested: JCRB Cat# JCRB1838, RRID:CVCL_B3M4)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">VSV was amplified and titrated by plaque assay using L929 cells as described previously (47).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>L929</div><div>suggested: ECACC Cat# 86032004, RRID:CVCL_4238)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The SARS-CoV-2 isolate (UT-NCGM02/Human/2020/Tokyo) (49) was propagated in VeroE6-TMPRSS2 cells in DMEM containing 5% heat-inactivated FBS at 37 °C in 5 % CO2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>VeroE6-TMPRSS2</div><div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">pcDNA3-IRF3 was purchased from Addgene.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3-IRF3</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For overexpression of IRFs, cells in 24-well plates (4×104 cells/well) were transfected with control pcDNA3, pcDNA-IRF1, pcDNA-IRF3 or pcDNA-IRF7 using Lipofectamine 3000 Transfection Reagent (Life Technologies) and 24 hours later challenged with or without 229E or OC43.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3</div><div>suggested: RRID:Addgene_15475)</div></div><div style="margin-bottom:8px"><div>pcDNA-IRF1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pcDNA-IRF3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pcDNA-IRF7</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis: Two-way ANOVA followed by Sidak’s post hoc test was performed using GraphPad Prism 6.0 software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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URL

biorxiv.org/cgi/content/10.1101/2022.03.24.485591
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272768

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272768: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: This study was conducted in accordance with the declaration of Helsinki and with the approval of the Ethics Committee of the Charité (EA 1/144/927 13, EA2/066/20 and EA1/317/20) and the Charité - BIH COVID-19 research board.<br>Consent: Autopsy consent was obtained from the families of the patients.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The following antibodies were used for staining: anti-Collagen I-PE, anti-Collagen IV-FITC</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Collagen I-PE, anti-Collagen IV-FITC</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-Collagen</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We used following antibodies and dilutions for staining: Sytox-AF488 (1:40.000, Thermo Fisher), ER-TR7-AF546 (1st 1:200/2nd 1:100, Santa Cruz Biotechnology) or near-infrared (NIR) CD3-iFluor790 (1:50</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ER-TR7-AF546</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>1st</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD3-iFluor790</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The ImageCycler is a robotic microscopic system with 3 main components:(1) an inverted widefield (epi)fluorescence microscope Leica DM IRE2 equipped with a CMOS camera and a motor-controlled XY-stage, (2) CAVRO XL3000 Pipette/Diluter</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImageCycler</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Images were then normalized in Fiji, where a rolling ball algorithm was used for background estimation, edges were removed (accounting for the maximum allowed shift during the autofocus procedure) and fluorescence intensities were scaled to the full intensity range (16 bit => 216).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Fiji</div><div>suggested: (Fiji, RRID:SCR_002285)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cell segmentation and single-cell feature extraction: Segmentation was performed in a two-step process as previously described 17, a signal-classification step using Ilastik 1.3.2 62 and an object-recognition step using CellProfiler 3.1.8 63.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Ilastik</div><div>suggested: (Ilastik, RRID:SCR_015246)</div></div><div style="margin-bottom:8px"><div>CellProfiler</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Seurat package 4.0.0 64 was used in R (R Core Team (2021, 2021) (https://www.R-project.org/) to perform mean centering and scaling, followed by principal component analysis (PCA), and reduced the dimensions of the data to the top 11 principal components in the lung and 10 principal components in the lung dLNs.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Seurat</div><div>suggested: (SEURAT, RRID:SCR_007322)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Frames around the capture area on the Visium slide were aligned manually and spots covering the tissue were manually selected based on the immunofluorescence staining, using Loupe Browser 5.1.0 software (10x Genomics).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Loupe Browser</div><div>suggested: (Loupe Browser, RRID:SCR_018555)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Image processing: We separately acquired 16-bit grayscale TIFF images for each channel by light sheet microscopy with the ImSpector software (LaVision Biotec)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImSpector</div><div>suggested: (Imspector, RRID:SCR_018863)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Tiff stacks were converted (ImarisConverterx64) into Imaris files (.ims) and stitched by Imaris Stitcher.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Imaris</div><div>suggested: (Imaris, RRID:SCR_007370)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Quantification and statistical analysis: Statistical analysis was performed with GraphPad Prism® 9.2.0 (Graph Pad Software, LA Jolla, CA, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism®</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Despite the non-negligible limitations of post-mortem studies, we think the mechanisms described here might also help to shed light into the pathophysiology of the Long-COVID syndrome. By combining advanced microscopy approaches coupled to single-cell computational analysis with ST techniques in autopsy tissues, we delineated the fibrovascular niche, as a site where a dysregulated immune response leads to tissue repurposing in prolonged COVID-19 disease. In line with the idea that endothelial dysfunction is a key pathogenic mechanism in COVID-19 13,14 and that endothelial cells are major participants in and regulators of inflammatory reactions 34, we identify EndMT as a mechanism driving fibrosis. When activated endothelial cells undergo EndMT, they are transcriptionally reprogrammed, their tight cellular junctions are disrupted and they turn into fibroblast-like cells. Consequently, they lose the expression of cell adhesion proteins, such as CD31, while mesenchyme-specific factors, including α-SMA, are upregulated 35. All these features are evident in our samples (Fig. 2A-C, Fig. 3A-C, Fig. S4C). In addition, we find that fibroblasts in COVID-19 lung fibrovascular niches express the chemokine receptor CCR8 (Fig. 3C). Its ligand, CCL18, has previously been linked to pulmonary inflammation and fibrosis 36 and it is the biomarker most consistently associated with negative outcomes in IPF 37. It was previously reported to be enriched in SARS-CoV-2 RNA+ myeloid cells in the lungs...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.24.22272768
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https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272871

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272871: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Field Sample Permit: Ethics: Samples used in this study were collected as part of an approved ongoing surveillance conducted by the NRC of HCL.<br>IRB: This study was approved by the ethics committee of the Hospices Civils de Lyon (HCL), Lyon, France and registered on the HCL database of RIPHN studies (AGORA N°41).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sample selection: The samples sequenced at the National Reference Center (NRC) of Respiratory Viruses of Hospices Civils de Lyon (HCL) selected for this study were i) samples from systematic sequencing of hospitalized patients in the Lyon area (university hospital of Lyon, HCL) and from HCL health care workers; ii) samples from random sequencing performed during the weekly Flash survey conducted by the EMERGEN consortium (French consortium for the genomic surveillance of emerging pathogens).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Following interim biosafety guidelines established by WHO, NPS were inoculated on confluent Vero E6 TMPRSS2 cells with DMEM supplemented with 2% penicillin– streptomycin, 1% L-glutamine, 2% G418 and 2% inactivated fetal bovine serum.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6 TMPRSS2</div><div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mapped reads were processed to remove duplicates tagged by picard, then realigned by abra2 to improve indel detection sensitivity and finally clipped with samtools ampliconclip to remove read ends containing primer sequences.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>samtools</div><div>suggested: (SAMTOOLS, RRID:SCR_002105)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your code and data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  This study has several limitations. First, the follow-up duration for the assessment of BA.1 /BA.2 co-infection is short, and as BA.2 detection is still increasing in France, the prevalence of BA.1 /BA.2 co-infection may be underestimated. In addition, ICU admission and vaccination status information was lacking for some Flash cases, limiting the clinical characterization of co-infected patients. Finally, additional sequencing methods were not tested, such as metagenomics or hybrid capture which are less prone to amplification-bias toward specific lineages 7. However, these techniques have lower sensitivity and lower throughput and were therefore not suitable as first-line sequencing methods in our laboratory 20. In conclusion, our findings emphasize the importance of using appropriate experimental and bioinformatic methods for the comprehensive identification of SARS-CoV-2 co-infections. Although these events are rare, SARS-CoV-2 co-infections need to be properly identified as they can lead to the emergence of new variants after a recombination event.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.24.22272871
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.23.22270017

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.23.22270017: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: All patients provided written and informed consent into off-label use for vaccine doses four and five.<br>IRB: The ethics committee of Charité – Universitätsmedizin Berlin approved this study (EA1/030/22).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We used an anti-SARS-CoV-2 enzyme-linked immunosorbent assays (ELISA) for the detection of IgG antibodies against the S1 domain of the SARS-CoV-2 spike (S) protein in serum according to the instructions of the manufacturer (Anti-SARS-CoV-2-ELISA (IgG),</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Anti-SARS-CoV-2-ELISA ( IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Comparison of mycophenolic acid (MPA) dose adjustment regimens: Due to the important role of MPA with regard to the response to immunization, different approaches for MPA dose adjustment before fourth SARS-CoV-2 immunization were followed at our institution according to the patients’ individual risk factors such as previous rejection episodes, anti-HLA antibodies, previous response to SARS-CoV-2 immunization, and based on the physicians’ and patients’ shared-decision making.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-HLA</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations arise from the study’s retrospective design. While serological measurements were routinely performed at our institution, there was a considerable number of vaccinations that were not preceded or followed by serological measurements (Figure 1). Consequently, a patient-based approach was discarded in favor of a vaccination-based evaluation, introducing a risk of selection bias. However, our approach allows to account for the incompleteness of the data and to optimize the number of examinable vaccinations. Intraindividual changes of titers between or after vaccinations were not represented with this approach, whereas protection after vaccination will evolve and might effectively decrease over time. With regard to the effects of MPA dose adjustment around the fourth vaccination, the retrospective assignment to treatment groups limits the validity of the results because groups were not fully matched and confounding factors could have influenced the group assignment. Nevertheless, comparison of the major potential influencing factors was provided to account for these risks. Finally, while this study focuses on vaccine-induced humoral response as correlate of protection from disease, there are other contributors to immunity such as T cell response that may influence the degree of protection. In conclusion, repeated vaccination against SARS-CoV-2 of up to five times effectively induces humoral serological response in kidney transplant recipients. Serological response can ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.23.22270017
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272926

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272926: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethics: Following initial approval by the UK Health Research Authority, all participating sites obtained approval from their national/local institutional review boards<br>Consent: The need for individual patient informed consent was waived.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Aggregated, standardized data were uploaded using the REDCap online platform (S2 File).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>REDCap</div><div>suggested: (REDCap, RRID:SCR_003445)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengths and limitations: Our study presents multinational data enabling the comparison between infection prevention measures, national SARS-CoV-2 prevalenceand the impact on acute illness and injuries in children between European countries. Most participating sites were tertiary institutions, with dedicated pediatric emergency medicine teams, with potential implications for the generalisability of our findings. At present, no standardized data extraction system for pediatric urgent and emergency care exists between European countries; and the EPISODES study is the first to navigate the difficulties of dealing with different data systems, data availabilityand varying coding practices. Hence, also limited by the time restrictions caused by the COVID-19 pandemic, some sites were not able to provide data for all domains, and two sites (NL002, HUN002) were only able to provide data for part of the study duration. Limitations of electronic health records to describe patients’ diagnoses are well known. [71] Participating study sites had unique coding systems, and we urged all study teams to be consistent in transforming local data to fit the study clinical report form. Although most diagnoses linked to SARS-CoV-2 in children were included in the pre-defined clinical report form, other diagnoses might be of interest in future studies. Of note, coding for children with Multi Inflammatory Syndrome in Children (MIS-C) proved unreliable, with no unique diagnostic codes available for th...
  
  Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Identifier</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Status</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Title</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">ISRCTN91495258</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NA</td></tr></table>
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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Visit annotations in context

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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.25.22272926
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.21.22272700

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.21.22272700: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
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  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.21.22272700
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.23.485575

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.23.485575: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To detect hACE2, cells were washed twice in PBS and incubated 1 hour at 4°C with primary goat antibody anti-human ACE2 protein (R&D AF933) (1:100).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human ACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibodies: Immunoblotting were performed by using the following antibodies: rabbit anti-M 1:1000 (100-401-A55, Rockland TEBU-BIO);rabbit anti-N 1:3000 (200-401-A50,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-M</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-N</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">anti-GAPDH antibody coupled to HRP 1:25000 (G9295, Sigma).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-GAPDH</div><div>suggested: (Sigma-Aldrich Cat# G9295, RRID:AB_1078992)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For immuno-spotting, rabbit anti-Spike neutralizing Antibody 1:100 (40592-R001, Sino Biological), mouse anti-CD81 1:100 (sc7637, 1.3.3.22, Santa Cruz)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Spike</div><div>suggested: (Sino Biological Cat# 40592-R001, RRID:AB_2857936)</div></div><div style="margin-bottom:8px"><div>anti-CD81</div><div>suggested: (Santa Cruz Biotechnology Cat# sc-7637, RRID:AB_627190)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells and culture conditions: The HEK293T human embryonic kidney cell line were obtained from ECACC (Sigma-Aldrich, Germany) and maintained in cultured in Dulbecco’s modified essential medium (DMEM, Gibco) supplemented with 10% heat inactivated fetal calf serum (FCS, Thermo Fisher, USA), 50 U/mL of penicillin (Ozyme, France), 50 μg/mL of streptomycin (Ozyme,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The human pulmonary alveolar A549-hACE2 and A549-hACE2mScarlet stable cell lines were engineered using 2 different lentiviral vectors.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549-hACE2mScarlet</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For A549-hACE2-mScarlet, A549 were transduced with VSVg pseudotypes particules derived from lentiviral vector expressing mScarlet red fluorescent protein from Olivier Schwartz laboratory at Institut Pasteur (Paris, France) to express the human receptor hACE2mScarlet.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549-hACE2-mScarlet</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Transduction efficiency was assessed by monitoring mScarlet expression (Maximum Excitation 569nm/Maximum Emission 594nm) using flow cytometry in comparison with A549 cells (Supplemental Figure 1B).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Human pulmonary A549-hACE2 cells were harvested live in cold PBS 1x (after 24h in culture on glass coverslip).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549-hACE2</div><div>suggested: RRID:CVCL_A5KB)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The GFP and mEOS2 tags were amplified by PCR from peGFP and pmEOS2 using Pfu Polymerase (M7741, Promega), dNTP mix (10297018, Thermo Scientific) and primers designed to carry NheI and KpnI restriction sites (Sigma Aldrich).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pmEOS2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PCR amplified inserts were added at the N-terminus of N protein in pcDNA3.1+ plasmid, and purified with the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1+</div><div>suggested: RRID:Addgene_117272)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Each band intensity on the immunoblot were quantified using ImagJ software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImagJ</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Fluorescence intensity fluctuations traces (at least 120) were recorded for 10s and correlated immediately with the built-in Zen software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Zen</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PALM acquisitions were analyzed using the ThunderSTORM plugin in Fiji [23].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Fiji</div><div>suggested: (Fiji, RRID:SCR_002285)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">13 Images corresponding to 250-300 fluorescent VLPs were analyzed by ImageJ/Fiji software and ComDet Plugin was used for quantifiying the number of fluorescent VLPs and the double GFP/mCherry colocalization.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImageJ/Fiji</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses: Statistical analyses were performed using Origin 8.5 and Graph Pad prism software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Origin</div><div>suggested: (Origin, RRID:SCR_014212)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">GraphPad: GraphPad was used for performing graphs.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

biorxiv.org/cgi/content/10.1101/2022.03.23.485575
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.23.22272167

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.23.22272167: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Data: After institutional review board approval of respective institutions, we extracted date of diagnosis for Crohn’s Disease (CD) (n=349) and Ulcerative Colitis (UC) (n=145) patients presenting in pediatric GI clinic diagnosed 2016-2021 from electronic health records (EHRs).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Gender was a free entry field, and only male and female patients were present in the data; 44.0% were female and 56.0% were male.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To show seasonal patterns in diagnoses, we plotted total cases by month with loess regression and 95% confidence intervals using ggplot2 stratified by pandemic versus pre-pandemic diagnosis.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ggplot2</div><div>suggested: (ggplot2, RRID:SCR_014601)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study has several limitations. IBD does not present with consistent patterns, resulting in wide variability in data. The 4-6 month lag between the city’s peak infection rate and CD is more consistent with a SARS-nCoV2 infection pathogenesis than with delayed presentation from cases during the lockdown period. Our data does not include all pediatric gastroenterology groups in NYC, which may create effects due to variations in patient choice of providers. Our study suggests a risk that large increases of SARS-nCoV2 infection in pediatric patients may drive increases in IBD diagnoses, in particular CD. Given recent widespread infection during the omicron wave, this study highlights the necessity of follow-up investigation of changes in incidence using existing data infrastructure.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.23.22272167
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.26.22272766

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.22272766: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Following prior publications [14–18], IgG antibodies against spike protein (SP-IgG) or total Ig antibodies against nucleocapsid protein (NP-total Ig) were measured using the commercial chemiluminescent enzyme immunoassay (AIA-CL SARS-CoV-2 SP-IgG and NP-total Ig antibody detection reagents, Tosoh, Japan) to assess prior infection (NP-total Ig) or vaccination against SARS-CoV-2 (SP-IgG or NP-total Ig).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Ig</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>NP-total Ig</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>SARS-CoV-2 (SP-IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>NP-total Ig).</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  However, the present study has several limitations. First, the cross-sectional nature of the study limits the ability to investigate causality between measured variables. However, given the growing evidence regarding the effectiveness of vaccination on the immunity against and risk of contracting COVID-19, our findings provide an accurate description of the humoral immunity against variants, including assessments of the emerging variants such as Omicron BA.1 and BA.2. Second, the assay used to assess the positivity of the neutralization antibodies was qualitative. That is, we could only evaluate the presence or absence of the neutralization antibodies at a certain threshold, equivalent to the neutralizing titer of 51 or more in the HIV-based pseudovirus method [15]. However, our findings are consisitent with published studies using the quantitative assessments of the neutralization antibodies[23, 24]. Third, the response rate of our study was approximately 21%, which is not sufficiently high. However, to adjust the differences in age and sex distribution between our study and the overall population of Yokohama City, weighted prevalence rates were estimated and the results were almost identical. Lastly, our study provides evidence regarding a certain period of time in Yokohama City, Japan, and the generalizability may be limited. However, because the vaccination has been similarly provided to the nationwide population in Japan and the vaccination rates in Japan are similar to ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.26.22272766
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.23.22272771

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.23.22272771: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethics approval was granted by the local ethics committees in Erlangen (Az. 340_21B) and Munich (Az. 26/21 and Az.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Study design and participants: The study is a follow-up analysis of 473 homologously or heterologously vaccinated participants that were previously only assessed for the production of antibodies using sVNT5.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>sVNT5</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody avidity: Binding strength of the SARS-Cov-2 IgG antibodies was determined by adaptation of the commercial IgG agile SARS-CoV-2 ELISA (Virion/Serion, Germany) using ammonium thiocyanate (NH4SCN) (Roth, Germany) as previously described16,54,55.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-Cov-2 IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Serum samples were measured using the IgG agile SARS-CoV-2 ELISA and diluted to 100 U/mL according to the standard curve provided by the manufacturer to exclude an influence of variable antibody concentrations.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>ELISA</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">As a primary antibody, the SinoBiological anti-SARS-CoV-2-N T62 antibody (40143-T62) was used.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2-N T62</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Goat anti-rabbit IgG2a-HRP antibody (EMD Millipore / order number 12-348) with 1% FCS-PBS was diluted to 1:4000 ratio.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Goat anti-rabbit IgG2a-HRP antibody</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-rabbit IgG2a-HRP</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FACS-based analysis of anti-S binding antibodies: A modified version of our previously published serological assay was used, in which HEK 293T cells either stably expressing the spike protein from the original Wuhan strain or transiently expressing the spike protein of B.1.167.2 or B1.1.529, respectively, were used as target cells56.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-S</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To quantify antigen-specific antibodies, 5×105 HEK 293T cells were incubated with serum samples diluted in 100 µl FACS-PBS (PBS with 0.5% BSA and 1 mM sodium azide) for 20 minutes at 4°C to bind to spike protein on the surface.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antigen-specific</div><div>suggested: (Miltenyi Biotec Cat# 130-092-105, RRID:AB_615062)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After washing with 200 µl buffer, bound S-specific antibodies were detected with anti-human IgG-AF647 (4°C, 30 min incubation; clone HP6017, Biolegend, Cat #409320).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG-AF647</div><div>suggested: (SouthernBiotech Cat# 2040-31, RRID:AB_2795651)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The median fluorescence intensity (MFI) correlates with the level of bound antibodies56.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibodies56</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ELISPOT plates (Millipore) were coated with anti-human IFN-γ monoclonal antibody (clone 1-DIK, Mabtech) at 0.5 µg/well overnight at 4°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IFN-γ</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After the stimulation period, the plates were washed and 80 µL of anti-human IFN-γ (FITC)/anti-human IL-2 (Hapten2) detection antibody solution was added for 2h at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Hapten2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After one hour of preincubation, the inoculum was transferred to the pre-seeded VeroE6 cells for another one-hour incubation at 37°C before the inoculum was replaced by supplemented DMEM.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>VeroE6</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FACS-based analysis of anti-S binding antibodies: A modified version of our previously published serological assay was used, in which HEK 293T cells either stably expressing the spike protein from the original Wuhan strain or transiently expressing the spike protein of B.1.167.2 or B1.1.529, respectively, were used as target cells56.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK 293T</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For the assessment of pseudotype neutralization, HEK293T-ACE2 cells were seeded at 2×104 cells/well in a 96well flat bottom plate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T-ACE2</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To produce pseudotyped reporter particles, HEK293T cells were transfected with the SIV-based self-inactivating vector encoding luciferase (pGAE-LucW), the SIV-based packaging plasmid (pAdSIV3), and the respective spike variant-encoding plasmid as described previously58.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pGAE-LucW</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The inhibition curve of each sample was analyzed by statistical analysis software Graph Pad Prism (GraphPad Software, USA), and 50% inhibitory concentration (IC50) was determined using non-linear regression.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Graph Pad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After further washing, samples were measured on an AttuneNxt (ThermoFisher) and analyzed using FlowJo software (Tree Star Inc.)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The reciprocal serum ID50 was determined with Prism GraphPad 9 (San Diego, California, USA) by application of the Sigmoidal 4PL function.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Isolation and cultivation of peripheral blood mononuclear cell (PBMC): PBMCs were isolated from citrate peripheral blood of vaccinated individuals by density gradient centrifugation using Biocoll® separating solution, density 1.077 g/ml (Bio&Sell) and frozen in heat-inactivated FCS + 10% DMSO (Sigma-Aldrich) for liquid nitrogen storage.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Biocoll®</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis and graphical presentation: Statistics as well as figures were created with PRISM GraphPad 9.3.1.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PRISM GraphPad</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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medrxiv.org/cgi/content/10.1101/2022.03.23.22272771
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.26.22272977

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.26.22272977: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">The study participants were then divided into gender, male, n=36, and female, n=32.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Trim galore, a wrapper around Cutadapt version 3.7 and FastQC was used for the adapter trimming and to do further quality assessment of the raw file (15).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Cutadapt</div><div>suggested: (cutadapt, RRID:SCR_011841)</div></div><div style="margin-bottom:8px"><div>FastQC</div><div>suggested: (FastQC, RRID:SCR_014583)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The STAR, the splice aware genome aligner was used to align adapter-trimmed single-end reads to the human reference genome [hg38] (16).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>STAR</div><div>suggested: (STAR, RRID:SCR_004463)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The alignment post-processing was then conducted using the Picard tool (https://broadinstitute.github.io/picard/) with the “Picard markDuplicates” command to mark duplicate reads.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Picard</div><div>suggested: (Picard, RRID:SCR_006525)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Finally, the overall quality of the alignment and the data, in general, were assessed using MultiQC software (18).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MultiQC</div><div>suggested: (MultiQC, RRID:SCR_014982)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The reported variants were then annotated to study their effects in proteins and genes using the Variant Effect Predictor (VEP) tool (19), using “homo_sapiens” as the target organism.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Variant Effect Predictor</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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URL

medrxiv.org/cgi/content/10.1101/2022.03.26.22272977
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272915

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272915: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study does, however, have some limitations. Firstly, we only include cases with sequenced genomes, and thus our sample predominantly includes cases with lower Ct, because these cases are more likely to have been sequenced. This is likely to be particularly important when the Ct distribution of infections differs between variants. Additionally, this limits us to the set of individuals who have been tested by PCR, likely to represent hospitalised patients more than those in the community. Also, our sample size was not large enough to adjust for all the factors we would have liked to (e.g. fitting a dose by vaccine brand interaction, given that different brands are known to provide differential protection against different variants[7,15,16]). There have been a series of other studies investigating each of the comparisons in our study individually. For Alpha versus previous variants, most previous studies have also estimated an increase in severity over extant diversity. A wide variety of end points have been used, 28-day mortality, hospitalisation, and an ordinal scale based around supplemental oxygen[17-27]. Our estimates are consistent with the majority of these studies. Our sample is smaller than was used in some of these studies, but we benefit from much higher resolution clinical data, and being able to control for comorbidities. When considering the Delta variant, two UK community analyses found that Delta (or an S-gene proxy) infections were associated with a higher r...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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sciscore

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medrxiv.org/cgi/content/10.1101/2022.03.24.22272915
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.23.485570

1
1. sciscore 29 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.23.485570: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Enteroids were incubated with primary antibodies (Table 4) overnight at 4°C with agitation, then washed three times with PBS and incubated with secondary antibodies (Table 4) and phalloidin (F-actin detection) (1:100) (Invitrogen) for 1 hr at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>F-actin detection</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 24 hr incubation at 37°C 5% CO2, MA104 cells (1 x 105 cells/well) were added to transfected BSR-T7 cells and co-cultured for 4 days in FBS-free DMEM supplemented with 0.5μg/mL porcine pancreatic trypsin type IX (Sigma-Aldrich)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BSR-T7</div><div>suggested: CCLV Cat# CCLV-RIE 0583, RRID:CVCL_RW96)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plasmid construction: pT7 plasmids used for reverse genetics of SA11 RV were kindly provided by Takeshi Kobayashi [42] through the Addgene plasmid repository against IDs #89162-72.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pT7</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The constructs were synthesised by Invitrogen GeneArt on either pMK-RQ (kanamycin resistance), pMA-RQ or pMA-T (ampicillin resistance) vectors.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pMK-RQ</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pMA-RQ</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pMA-T</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">RF strain NSP3 constructs RBM, T2A-RBM, RBD and T2A-RBD were ordered as gene blocks from Invitrogen GeneArt and cloned into pT7-NSP2SA11 expression plasmid (Addgene #89169) after the NSP2 ORF was removed using SmaI and SalI restriction enzymes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pT7-NSP2SA11</div><div>suggested: RRID:Addgene_89169)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">At 70% confluency, monolayers of BSR-T7 cells in 6-well plates were co-transfected with 11 plasmids corresponding to each RV genome segment (2.5μg for plasmids encoding NSP2 and NSP5; 0.8μg for the remaining plasmids) and plasmids encoding two vaccinia virus capping enzyme subunits (pCAG-D1R and pCAG-D12L −0.8μg each) using 16μL Lipofectamine 2000 (Invitrogen) per transfection reaction in a total volume of 200μL of Opti-MEM (Gibco).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCAG-D1R</div><div>suggested: RRID:Addgene_89160)</div></div><div style="margin-bottom:8px"><div>pCAG-D12L</div><div>suggested: RRID:Addgene_89161)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The panels of viruses were titred by plaque assays, and the presence of mutations in the target gene segments was confirmed by RT-PCR and Sanger sequencing (GATC Biotech or Genewiz, Germany) as described below.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Genewiz</div><div>suggested: (GENEWIZ, RRID:SCR_003177)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Quantification was performed by densitometry of scanned gel images using Image J.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Image J</div><div>suggested: (ImageJ, RRID:SCR_003070)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The optical density (OD) was measured at 405nm using Cytation™ 3 Cell Imaging Multi-Mode Reader (Agilent) and data was analysed using BioTek Gen5 software (Agilent).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Gen5</div><div>suggested: (Gen5, RRID:SCR_017317)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Images were analysed using the Zen Black software and processed using Photoshop v23.1.1.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Zen Black</div><div>suggested: (Black Zen software, RRID:SCR_018163)</div></div><div style="margin-bottom:8px"><div>Photoshop</div><div>suggested: (Adobe Photoshop, RRID:SCR_014199)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis: GraphPad Prism v9 was used for all statistical analyses.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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biorxiv.org/cgi/content/10.1101/2022.03.23.485570
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272863

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272863: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  19 In summary, the equitable distribution of vaccines in the population at greatest risk should be prioritized and its distribution worldwide before proposing the vaccination of CYP. 20 Among the limitations of the study, particularly its lack of global representativity related with a convenience selection of the participant countries, it is worth mentioning that the fast and variable Sars-CoV-2 pandemic dynamics press to have variable and quick measures; the epidemiologic definitions have changed over time, as well as data collection, the number and specificity of tests that are carried out, and other variables. After the caveat referred above, the results of the research, in terms of severity and mortality, confirm that regardless of the level of development and access to vaccines, the SARS-CoV-2 affections to the CYP are similar in the countries analyzed, confirming that this population presents fewer negative results compared to the rest of age range populations. As a summary, the results of the present study reinforce the idea of the urgent need to prioritize globally and equitably vaccine distribution in the population at greatest risk, and to apply the precautionary principle in the CYP before deciding to massively vaccinate it.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.24.22272863
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.25.485748

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.485748: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: This study’s ethics approval was approved by the China-Japan Friendship Hospital review boards, and each participant signed informed consent.<br>Consent: This study’s ethics approval was approved by the China-Japan Friendship Hospital review boards, and each participant signed informed consent.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Mass spectrometry data processing: The Ms data of QIV cohort and COVID-19 (1) male cohort(DDA MS data) is performed label-free quantitative comparisons.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Missing values were assumed to be biased toward low abundance proteins that were below the MS detection limit, referred to as “missing not at random”, an assumption that is frequently made in proteomics studies12,13.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Base peak chromatograms were inspected visually in Xcalibur Qual Brower version 4.0.27.19(Thermo Fisher Scientific).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Xcalibur Qual Brower</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">RAW files were processed by MaxQuant version 1.6.17.0 (http://www.maxquant.org) using default parameters unless otherwise specified5–7.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MaxQuant</div><div>suggested: (MaxQuant, RRID:SCR_014485)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data processing was using Perseus version 1.6.14.0 (</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Perseus</div><div>suggested: (Perseus, RRID:SCR_015753)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To generate a spectral library, ten DDA raw files were first searched by Proteome Discoverer (version 2.1; Thermo Scientific) with SEQUEST HT against the Uniprot human sequence database (November 27, 2020; 196,211 sequences).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Proteome Discoverer</div><div>suggested: (Proteome Discoverer, RRID:SCR_014477)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The differential proteins were analyzed by Gene Ontology (GO) based on biological processes(BP), cellular components(CC), and molecular functions(MF) using DAVID18, and biological process from WebGestalt (</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>WebGestalt</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">(http://www.webgestalt.org).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>http://www.webgestalt.org</div><div>suggested: (WebGestalt: WEB-based GEne SeT AnaLysis Toolkit, RRID:SCR_006786)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Protein interaction network analysis was performed using the STRING database (https://string-db.org/cgi/input.pl) and visualized by Cytoscape (V.3.7.1)19 and OmicsBean work-bench (http://www.omicsbean.cn).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>STRING</div><div>suggested: (STRING, RRID:SCR_005223)</div></div><div style="margin-bottom:8px"><div>Cytoscape</div><div>suggested: (Cytoscape, RRID:SCR_003032)</div></div><div style="margin-bottom:8px"><div>http://www.omicsbean.cn</div><div>suggested: (OmicsBean, RRID:SCR_016322)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.03.25.485748
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.25.485815

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.485815: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethical statement: Human experimental work was conducted according to Human Research Ethics Committees.<br>Consent: All participants provided written informed consent prior to the study.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Assessment of the immunogenicity of the r3CL-pro, the rRBD and the chimeric r3CLpro-RBD: Seven weeks-old male and female CD1 outbred mice were used to assess the immunogenicity of the recombinantly-produced proteins according to the schedule shown in Figure 2.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 1 h incubation at RT, and washing five times with PBST, the secondary antibody HRP anti-Human IgG (Fc specific) (Sigma-Aldrich) was added (1:15,000), and the plates incubated for 1 h at RT.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Human IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After washing five times with PBST, the secondary antibody HRP goat to mouse-anti-IgG (ThermoFisher Scientific) was added (1:10,000), and the plates incubated for 1 h at RT.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>mouse-anti-IgG</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Assessment of the immunogenicity of the r3CL-pro, the rRBD and the chimeric r3CLpro-RBD: Seven weeks-old male and female CD1 outbred mice were used to assess the immunogenicity of the recombinantly-produced proteins according to the schedule shown in Figure 2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD1</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Recombinant protein production in Escherichia coli cells and purification: Sequences encoding the 3CL-pro and RBD proteins were codon optimized for expression in Escherichia coli and cloned into the pET-28a(+) vector (Genscript Biotech).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pET-28a(+ )</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

biorxiv.org/cgi/content/10.1101/2022.03.25.485815
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272878

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272878: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Participation in this study was voluntary and written informed consents were obtained.<br>IRB: The study was approved by the Research Ethics Board of St.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Limitations: There were several possible limitations in this study. At the vaccination sites in Chuo City, only residents of the Chuo City were eligible for vaccination. The characteristics of the participants include a high percentage of those with a university or graduate school education and a high level of health literacy. According to the national census in Japan [29], the national average of those with a university or graduate school education was 19.9%, while the participants in this study was 66.7%. The mean HLS-14 score in the national survey conducted by Suga (2013) was 50.3[17], while that of the participants in this study was 55.7, suggesting the possibility of selection bias and a higher level of health awareness than people in general. Therefore, most participants have had the thought of recommending vaccination. Furthermore, since only Comirnaty™ was provided at the vaccination site in this study, comments from people who had taken other vaccines were not available. Although the side effects reported for each vaccine were different, the incidence rate of side effects did not differ significantly for any COVID-19 vaccines, so the influence on the results of this study was considered to be minimal[26]. Elderly people and those under 20 years of age were not enrolled in this study. Enrollment in the study did not begin until August 2021, and many elderly people had already been vaccinated, so it was difficult to recruit them. Those under 20 years of age were also ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.24.22272878
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https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272899

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272899: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: [13] Ethical approval for the study was obtained from the ALSPAC Ethics and Law Committee and the Local Research Ethics Committees.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Sample: Data were from the Avon Longitudinal Study of Parents and Children (ALSPAC) an ongoing longitudinal population-based cohort study that recruited pregnant women residing in Avon (South-West of England) with expected delivery dates between 1st April 1991 and 31st December 1992. [11, 12] The cohort consists of 14,901 children, now young adults (ages 27-29).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.24.22272899
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https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272942

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272942: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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medrxiv.org/cgi/content/10.1101/2022.03.25.22272942
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.18.22272356

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.18.22272356: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: Ethical and institutional approval: Specimens were analyzed under a protocol approved by the Gundersen Health System Institutional Review Board (#2-20-03-008; PI: Kenny) to perform next-generation sequencing on remnant specimens after completion of diagnostic testing.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All statistical analysis was performed using the SAS software suite, version 9.4 (SAS Foundation, Cary NC).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SAS</div><div>suggested: (SASqPCR, RRID:SCR_003056)</div></div></td></tr></table>
  Results from OddPub: Thank you for sharing your data.
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Moreover, intra-facility mitigation efforts would have been insufficient in face of inadequacies in infection control practices taking place during transportation, commingling of patients outside the facility, vaccine uptake among persons in the ESRD patients’ close orbit, and practical limitations imposed on facilities unable to meet all elements of existing guidelines (such as cohorting, segregating, and distancing dialysis patients in markedly resource-limited settings). With no additional cases identified after the first round of testing, our facility demonstrated the effectiveness of a pod with a separate entrance to control the spread of this strain within the facility (Table 3E). All staff entering the area used full respiratory protection with a PAPR or N95 mask. The team also reengaged the facilities team to assess facility air exchange. Collectively, these variables should be reviewed on an ongoing basis during facility quality assurance and performance improvement meetings. Individual behaviors outside the facility during shared transport (by either patients or staff) or pre-/post-treatment socializing were likely of higher prospective risk compared to those risks existing within the facility, and presumably contributed to the size of the cluster, albeit largely outside the control of facility management. This outbreak occurred several months after widespread availability of SARS-CoV-2 vaccines, by which time rates of new vaccinations had substantially slowed. Evid...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.18.22272356
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272864

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272864: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  We have limitations in this analysis. Although the analysis was constructed to ensure a temporal relationship between the independent variables and dependent variable by a week, it is hard to conclude a causal relationship yet. We used daily statistics based on testing and were thus unable to analyze the number of quarantined people per case directly, which is an important element of the tracing-testing-isolation and quarantine policy. This may underestimate the impact of tracing-testing-isolation and quarantine when tests are conveniently done decoupled with trace and quarantine. Additionally, we conducted the analysis on a national level. So, the heterogeneity between states in the COVID-19 prevention and control policies and practices is not taken into account in this analysis. The emergence of new variants, waning vaccination effectivity, and continued breakthrough infections are possible contributing factors to the persistent effectiveness of mobility restrictions and testing. The emergence of highly contagious variant viruses, such as the Delta and Omicron continue to threaten the health system15,16. Also, studies show that the effect of currently available vaccinations wane over time, both in serology-based laboratory studies and in empirical studies17,18. Studies have also reported breakthrough infections that occur among fully vaccinated population (those who have completed their 2nd dose)19. In the presence of such circumstances, high vaccination rates alone do not ...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.24.22272864
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272950

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272950: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">The Avon Longitudinal Study of Parents and Children (ALSPAC) is an ongoing population-based study that recruited pregnant women residing in Avon in the south west of England with expected delivery dates between 1st April 1991 and 31st December 1992.14-16 The cohort consists of mothers and their partners (G0) associated with 15,454 pregnancies, resulting in 15,589 foetuses (G1) of which 14,901 were alive at 1 year of age.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Study data were collected and managed using REDCap electronic data capture tools hosted at the University of Bristol.20 Measures of Routine: Participants were asked whether they kept a similar routine (e.g. bedtime, mealtimes) to how things were before the official lockdown was announced on 23rd March 2020, with response options “no, not at all”, “yes, a bit”, “yes, a lot” and, “yes, completely”.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>REDCap</div><div>suggested: (REDCap, RRID:SCR_003445)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Strengths and Limitations: This is a novel study looking at the effect of Covid-19 pandemic on younger children, using longitudinal pre- and during-pandemic data from the ALSPAC cohort. Although this provides a good size sample, the population in the sample is limited in ethnic diversity and geographical spread, which may limit the generalisability of our results to other populations. The cross-sectional nature of this work means that, although we have described an association between keeping routine and fewer behavioural and emotional difficulties in children, we are unable to determine the direction of causality, i.e. we cannot conclude that keeping to routine leads to lower emotional and behavioural difficulties, since it is also possible that children having fewer emotional and behavioural difficulties makes it easier to follow a routine. Other possible explanations for these results are that like all cohort studies, ALSPAC has incomplete recruitment and loss to follow-up; the current recruitment at a relatively young age and the focus of analyses in cross-generational effects are more specific to ALSPAG-G2.16 Furthermore, whilst we have attempted to adjust for factors that may confound the relationship between routine and emotional and behavioural difficulties, it is possible that residual confounding from unmeasured variables may affect this apparent relationship. The association between routine and lower parental anxiety is cross-sectional, so we do not know whether ro...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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URL

medrxiv.org/cgi/content/10.1101/2022.03.25.22272950
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.25.22272946

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.25.22272946: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  
  NIH rigor criteria are not applicable to paper type.
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our use of the infectious contact ratio bypasses this problem of interference, with the caveat that there is autocorrelation between successive estimated contact ratios due to the smoothing described in Kamiya et al [14]. Nonetheless, we also found in that study that the bias was small and unlikely to have a substantive effect on our results. In estimating the effect of mask-wearing on the infectious contact ratio, we have not adjusted for all potential sources of confounding. For example, other actions to mitigate the spread of the virus may also have been changing at the same time as mask wearing, and may be partly responsible for the effect we attribute to wearing masks. Behavioural survey data from the Irish Department of Health and NISRA indicate that many of the relevant behaviours that could bias the effect remained fairly constant throughout (for example hand washing, which was high from early during the period considered), or increased to a smaller extent than mask-wearing (eg self-reported social distancing) [29] [30]. When we included other NPI variables in the regression model, counterfactual predictions were little changed, but confidence intervals were inflated; this could be due to co-linearity. It is possible that early adopters of mask wearing were those who were at higher risk of severe COVID-19, so that the observed effect of mask wearing reflects the patterns of uptake in the population, and cannot be interpreted as the effect of adoption by a random propo...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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medrxiv.org/cgi/content/10.1101/2022.03.25.22272946
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272919

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272919: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">IRB: 30 Analyses were conducted in R version 4.0.3. Ethics: We received ethics approval for this study from the Research Ethics Board at the University of Toronto (#00031358).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  Our study also had a few limitations. First, we did not consider time since vaccination in our analysis. In a recent study in the United States, time since vaccination was not shown to significantly impact SARS-CoV-2 vaccine effectiveness estimates against hospitalization in this population.11 We were unable to assess two dose effectiveness against hospitalization specifically among cases ages 5-11 years due to few hospitalizations among two-dose vaccinated individuals. The availability of testing, and the propensity to get tested may have differed between vaccinated and unvaccinated individuals, and the reporting of comorbidities may have been more common among hospitalized SARS-CoV-2 cases. Finally, there may be misclassification because we used time as proxy for infecting variant among adolescents in our evaluation of effect measure modification. With the continued emergence of variants that may further decrease SARS-CoV-2 vaccine effectiveness against infection, it is vital to consider how effective these vaccines are at preventing severe outcomes.34 Given that two dose vaccine effectiveness against hospitalization following infection is approximately 63% in adolescents, and may be lower in youth ages 5-11 years, it is important to continue non-pharmaceutical interventions to prevent infection risk in these populations. Given that SARS-CoV-2 is primarily an airborne infection, this study supports the continued use of high-quality masks, increased ventilation, and accessib...
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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medrxiv.org/cgi/content/10.1101/2022.03.24.22272919
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272904

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272904: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  
  No key resources detected.
  
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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medrxiv.org/cgi/content/10.1101/2022.03.24.22272904
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22272884

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22272884: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consent: Informed written consent was obtained from all patients at admission to the hospital.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The analysis was performed using SPSS, version 25 (IBM, Armonk, NY, USA) [16] The association of various characteristics with mortality was analyzed.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SPSS</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
  The limitations of this study are that we did not include patients from other hospitals for comparative analysis. Furthermore, we did not include the response to various treatments, and lastly, the patient’s social characteristics, such as local residence, occupation, and income, were not included in this analysis. Further research is needed to develop a comprehensive scoring system for COVID-19. The system for scoring should be practical and straightforward to predict the disease severity and the management steps for COVID-19. Both prospective and retrospective analyses from the global north and the global south are needed to identify the critical factors in managing this disease.
  
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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sciscore

URL

medrxiv.org/cgi/content/10.1101/2022.03.24.22272884
www.medrxiv.org www.medrxiv.org

https://medrxiv.org/cgi/content/10.1101/2022.03.24.22271703

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.22271703: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Types of studies: randomized trials, non-randomized trials, observational studies, and modelling studies on the effects of travel-related control measures affecting human travel during the COVID-19 pandemic Search methods for identification of studies: We adapted the search strategies from Burns 2021, by excluding terms not-related to COVID- 19 (such as MERS, H1N1, SARS01).</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We searched Scopus, Pubmed, the Cochrane COVID-19 WHO COVID-19 Global Literature on Coronavirus disease, MedRXiv and BioRXiv.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Pubmed</div><div>suggested: (PubMed, RRID:SCR_004846)</div></div><div style="margin-bottom:8px"><div>BioRXiv</div><div>suggested: (bioRxiv, RRID:SCR_003933)</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
  Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
  </footer>
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medrxiv.org/cgi/content/10.1101/2022.03.24.22271703
www.biorxiv.org www.biorxiv.org

https://biorxiv.org/cgi/content/10.1101/2022.03.24.485734

1
1. sciscore 28 Mar 2022
  
  in SciScore
  
  SciScore for 10.1101/2022.03.24.485734: (What is this?)
  
  Please note, not all rigor criteria are appropriate for all manuscripts.
  
  Table 1: Rigor
  <table><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Ethics</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>
  Table 2: Resources
  <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells and Viruses: The A549 cells (human lung adenocarcinoma), Caco-2 (human colorectal adenocarcinoma), HEK-293 (human embryonic kidney epithelial cells), and Vero E6 (normal monkey kidney epithelial cells) were obtained through ATCC.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Caco-2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>HEK-293</div><div>suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)</div></div><div style="margin-bottom:8px"><div>Vero E6</div><div>suggested: RRID:CVCL_XD71)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">At 48 h after transfection, the supernatant from the cultures was collected, filtered through a 0.45-μm-pore-size filter, and used to infect Vero-E6 cells, as described before (115, 116).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero-E6</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Recombinant DNA</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HEK-293 cells were seeded in a 60 mm dish at 60% confluence and were co-transfected with the pLenti-mCherry-FLAG-γ134.5 plasmid described above, the Gag-Pol-expressing plasmid, and the vesicular stomatitis virus G (VSV-G)-expressing plasmid at a ratio of 7:7:1 (5 μg total amount of DNA) using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLenti-mCherry-FLAG-γ134.5</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>VSV-G)-expressing</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The genes were expressed in the pcDNA3.1 (+) vector.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1 (+)</div><div>suggested: RRID:Addgene_80020)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The pcDNA3.1 (+)-N-eGFP-N plasmid, expressing N from SARS-CoV-2, was obtained from GenScript Biotech (Catalog # MC_0101137).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA3.1 (+)-N-eGFP-N</div><div>suggested: None</div></div></td></tr></table>
  Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
  
  Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
  Results from TrialIdentifier: No clinical trial numbers were referenced.
  
  Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
  
  Results from JetFighter: We did not find any issues relating to colormaps.
  
  Results from rtransparent:
  
  No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
  No funding statement was detected.
  No protocol registration statement was detected.
  
  Results from scite Reference Check: We found no unreliable references.
  
  <footer>
  About SciScore
  SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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