35,428 Matching Annotations
  1. Sep 2021
  2. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.18.460895
    1
    1. sciscore 21 Sep 2021

      SciScore for 10.1101/2021.09.18.460895: (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: Biosafety: All aspects of this study were approved by the Institutional Animal Care and Use and Institutional Biosafety Committee of Center for Discovery and Innovation of Hackensack University Medical Centre (IACUC 282) and adhere to the National Research Council 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">Both male and female mice (N=16) were intraperitoneally (i.p.) infected with 103 trypomastigotes at 6 weeks 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">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">Adiponectin-specific mouse monoclonal antibody (#ab22554, Abcam), AdipoR1-specific rabbit polyclonal antibody (#ab70362, Abcam), AdipoR2-specific rabbit polyclonal antibody (#ABT12, Sigma-Aldrich), PPARα-specific rabbit polyclonal antibody (#PA1-822A, Thermo Fisher Scientific), PPARγ-specific rabbit polyclonal antibody (#2492, Cell Signaling Technology), pAMPK-specific rabbit monoclonal antibody (#2535S, Cell Signaling Technology), Cytochrome C-specific rabbit monoclonal antibody (#4280S, Cell Signaling Technology), Superoxide dismutase 1-specific mouse monoclonal antibody (#4266S, Cell Signaling Technology), Hexokinase 2-specific rabbit monoclonal antibody (#2867S, Cell Signaling Technology), β1 adrenergic receptor-specific rabbit polyclonal antibody (#12271S, Cell Signaling Technology), F4/80-specific rat monoclonal antibody (#NB 600-404, Novus Biologicals), TNFα-specific rabbit polyclonal antibody (#ab6671, Abcam), pHSL (Ser563)-specific rabbit monoclonal antibody(#4139, Cell Signaling Technology), ATGL-specific rabbit monoclonal antibody(#30A4, Cell Signaling Technology, Perilipin-specific rabbit monoclonal antibody (#D1D8, Cell Signaling Technology), IFNγ-specific rabbit monoclonal antibody (#EPR1108, Abcam), CD4-specific rabbit polyclonal antibody (#NBP1-19371, Novus biologicals), CD8-specific rabbit polyclonal antibody(#NBP2-29475, Novus biologicals), T-cadherin-specific rabbit polyclonal antibody (#ABT121, Millipore), FABP4-specific rabbit monoclonal antibody (#3544, Cell Signaling Technology), IL6-specific mouse monoclonal antibody (#66146-1-lg, Proteintech), IL10-specific rabbit polyclonal antibody (#20850-1-AP, Proteintech), BNIP3-specific rabbit monoclonal antibody (#44060, Cell Signaling Technology), Caspase 3-specific rabbit polyclonal antibody (#9662, Cell Signaling Technology) were used as primary antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibody(#4139</div><div>suggested: (Cell Signaling Technology Cat# 3544, RRID:AB_2278257)</div></div><div style="margin-bottom:8px"><div>antibody(#30A4, Cell Signaling Technology, Perilipin-specific</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD4-specific</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CD8-specific</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>antibody(#NBP2-29475</div><div>suggested: (Novus Cat# NBP1-44060, RRID:AB_2212858)</div></div><div style="margin-bottom:8px"><div>IL10-specific</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>antibody (#9662, Cell Signaling Technology)</div><div>suggested: (Cell Signaling Technology Cat# 9662, RRID:AB_331439)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Horseradish peroxidase (HRP)-conjugated anti-mouse immunoglobulin (#7076, Cell Signaling Technology) or HRP-conjugated anti-rabbit immunoglobulin (#7074, Cell Signaling Technology) antibody was used to detect specific protein bands (as shown in the figure legends) using a chemiluminescence system.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mouse immunoglobulin (#7076, Cell Signaling Technology)</div><div>suggested: (Cell Signaling Technology Cat# 7076, RRID:AB_330924)</div></div><div style="margin-bottom:8px"><div>anti-rabbit immunoglobulin (#7074, Cell Signaling Technology)</div><div>suggested: (Cell Signaling Technology Cat# 7074, RRID:AB_2099233)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">β-actin-specific rabbit monoclonal antibody (#4970S, Cell Signaling Technology) or Guanosine nucleotide dissociation inhibitor (GDI) (#71-0300, Invitrogen) were used as protein loading controls.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>β-actin-specific rabbit monoclonal antibody (#4970S, Cell Signaling Technology)</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>rabbit monoclonal antibody (#4970S, Cell Signaling Technology)</div><div>suggested: (Cell Signaling Technology Cat# 4970, RRID:AB_2223172)</div></div><div style="margin-bottom:8px"><div>antibody</div><div>suggested: (Cell Signaling Technology Cat# 4970, RRID:AB_2223172)</div></div><div style="margin-bottom:8px"><div>Guanosine nucleotide dissociation inhibitor (GDI</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">The Brazil strain of T. cruzi was maintained by passage in C3H/HeJ mice (Jackson Laboratories, Bar Harbor, ME).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>C3H/HeJ</div><div>suggested: RRID:IMSR_JAX:000659)</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">Adiponectin-specific mouse monoclonal antibody (#ab22554, Abcam), AdipoR1-specific rabbit polyclonal antibody (#ab70362, Abcam), AdipoR2-specific rabbit polyclonal antibody (#ABT12, Sigma-Aldrich), PPARα-specific rabbit polyclonal antibody (#PA1-822A, Thermo Fisher Scientific), PPARγ-specific rabbit polyclonal antibody (#2492, Cell Signaling Technology), pAMPK-specific rabbit monoclonal antibody (#2535S, Cell Signaling Technology), Cytochrome C-specific rabbit monoclonal antibody (#4280S, Cell Signaling Technology), Superoxide dismutase 1-specific mouse monoclonal antibody (#4266S, Cell Signaling Technology), Hexokinase 2-specific rabbit monoclonal antibody (#2867S, Cell Signaling Technology), β1 adrenergic receptor-specific rabbit polyclonal antibody (#12271S, Cell Signaling Technology), F4/80-specific rat monoclonal antibody (#NB 600-404, Novus Biologicals), TNFα-specific rabbit polyclonal antibody (#ab6671, Abcam), pHSL (Ser563)-specific rabbit monoclonal antibody(#4139, Cell Signaling Technology), ATGL-specific rabbit monoclonal antibody(#30A4, Cell Signaling Technology, Perilipin-specific rabbit monoclonal antibody (#D1D8, Cell Signaling Technology), IFNγ-specific rabbit monoclonal antibody (#EPR1108, Abcam), CD4-specific rabbit polyclonal antibody (#NBP1-19371, Novus biologicals), CD8-specific rabbit polyclonal antibody(#NBP2-29475, Novus biologicals), T-cadherin-specific rabbit polyclonal antibody (#ABT121, Millipore), FABP4-specific rabbit monoclonal antibody (#3544, Cell Signaling Technology), IL6-specific mouse monoclonal antibody (#66146-1-lg, Proteintech), IL10-specific rabbit polyclonal antibody (#20850-1-AP, Proteintech), BNIP3-specific rabbit monoclonal antibody (#44060, Cell Signaling Technology), Caspase 3-specific rabbit polyclonal antibody (#9662, Cell Signaling Technology) were used as primary antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Cell Signaling Technology</div><div>suggested: (Cell Signaling Technology, RRID:SCR_004431)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data were pooled, and statistical analysis was performed using a Student’s t-test (Microsoft Excel) as appropriate and significance differences were determined as p values between < 0.05 and <0.001 as appropriate.</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.

      </footer>

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    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.18.460895
  3. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.17.460613
    1
    1. sciscore 21 Sep 2021

      SciScore for 10.1101/2021.09.17.460613: (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 virus was purified by phagocytosis, reproduced in Vero-E6 cells, and stored in -80 °C for future use.</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.

      </footer>

    Visit annotations in context

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.17.460613
  4. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.16.460724
    1
    1. sciscore 21 Sep 2021

      SciScore for 10.1101/2021.09.16.460724: (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: The study was approved by Institute Animal Ethics committee.<br>IACUC: The study was performed according to the guidelines of Committee for the Purpose of Control and Supervision of Experiments on Animals, Government of India. mAb (ZRC3308-A7 and ZRC3308-B10) generation: The codon optimized, light and heavy chain genes of ZRC3308-A7 (CAS RN: 2640223-84-1) and ZRC3308-B10 (CAS RN: 2640224-48-0) were cloned in dual assembly eukaryotic expression vector, DGV-GS, with Glutamine synthase selection marker (DGV-GS).<br>Euthanasia Agents: Four animals each of the prophylactic and therapeutic study group were sacrificed by overdose of isoflurane anesthesia on 3, 5 and 7 DPI and necropsy was performed to collect nasal wash, nasal turbinates, lungs and blood samples.</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">Pharmacokinetic study in hamsters: A total of 18 female hamsters, aged 11-12 weeks were divided into four groups according to the dose of the cocktail i.e., 50 mg/kg (25 mg/kg of ZRC3308-A7 + 25 mg/kg of ZRC-3308-B10), 5 mg/kg (2.5 mg/kg of ZRC3308-A7 + 2.5 mg/kg of ZRC3308-B10), 1.0 mg/kg (0.5 mg/kg of ZRC3308-A7 + 0.5 mg/kg of ZRC3308-B10), and placebo consisting of 5 animals each except for the placebo which consisted of only 3 animals.</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">The lesions were blindly scored based on the vascular changes, bronchial lesions, alveolar pathological changes like septal thickening, pneumocyte hyperplasia, consolidation, edematous changes and inflammatory cell infiltration.</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 was accomplished using 1/1000 diluted peroxidase conjugated sheep anti-C1q polyclonal antibody (Abcam, UK).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-C1q</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ELISA based detection of mAb levels in serum: Two separate ELISA methods were used to detect ZRC3308-A7 and ZRC3308-B10 antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ZRC3308-B10</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Detection was accomplished using 1/100,000 diluted peroxidase conjugated goat anti-human lambda light chain secondary antibody for ZRC3308-A7 (Novus Biologics, USA) and 1/135,000 diluted Goat anti-Human kappa light chain secondary antibody for ZRC3308-B10 (Novus Biologics, USA) to specifically detect the two antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human lambda light chain</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-Human kappa light chain</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The groups were high (50mg/kg), medium (5 mg/kg), low (1mg/kg) dose of mAb cocktail, an IgG1 isotype antibody (Trastuzumab @ 50 mg/kg) control and a placebo control.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>an IgG1</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 ACE2 expressing cells (1.0×104 per well) were seeded in a flat tissue culture plate.</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">Vero E6 cells (1.0×106 per well) were seeded to 24-well plates in maintenance medium for 24 hrs 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>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">GraphPad Prism 8, Inc., San Diego, CA, USA).</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">Statistical analysis: Graphpad Prism version 8.4.3 software was used for data analysis of the experimental challenge study.</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:
      However, the 6-hour therapeutic group had limitation of small sample size. The interim results of the phase 1-3 clinical trials (ClinicalTrials.gov number: NCT04425629) of the mAb REGN-COV2 in patients with early infection showed a reduced SARS-CoV-2 RNA level in nasopharyngeal swab samples following mAb administration19. Similar results were reported in case of bamlanivimab (LY-CoV555) treatment in patients with a median of 4 days after symptom onset20. Anti-SARS-CoV-2 mAbs which received EUA like bamlanivimab plus etesevimab and casirivimab plus imdevimab have also not been shown to be beneficial in hospitalized patients with severe COVID-19 and these products warns of worst clinical outcomes in such patients14,15. We also observed severe pneumonic changes in the group infected with a high inoculum dose treated with mAb 24 hours post infection. But the similar changes were not observed in the prophylactic and therapeutic groups exposed with a lower virus dose. Rapid induction of pneumonic changes in hamster model is a limitation in the therapeutic evaluation in the present study. The trials have also shown low clinical benefits with LY-CoV555 treatment in hospitalized COVID-19 patients25. In the present study, we have characterized ZRC 3308 mAb cocktail for COVID 19 treatment, which was found to be cross neutralizing and a promising candidate for the prophylactic use and for therapy in early cases which have not progressed to severe disease.

      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">NCT04425629</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">Safety, Tolerability, and Efficacy of Anti-Spike (S) SARS-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.
      • 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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.16.460724
  5. dhdebates.gc.cuny.edu dhdebates.gc.cuny.edu
    “49. Messy Data and Faulty Tools | Joanna Swafford” in “Debates in the Digital Humanities 2016” on Debates in the DH Manifold
    1
    1. sg1484 20 Sep 2021
      interrogating the tool’s methodology or code,

      Are lit. scholars just assuming coders know what they're doing because it's a cross-discipline thing and they don't know how to peer review the tool itself?

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    URL

    dhdebates.gc.cuny.edu/read/untitled/section/7e0afe14-e266-4359-aa4a-5dff02735e8b
  6. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.14.21263541
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.14.21263541: (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 study was approved by the Institutional Review Boards at Hospital Clínico Universidad de Chile and at the Faculty of Medicine, Universidad de Chile (Protocol ID.<br>Consent: All patients and healthy controls were required to understand the study and sign an informed consent.<br>Field Sample Permit: Sample processing and cell isolation: Whole blood for flow cytometry analysis was collected in EDTA-coated vacutainers, and all blood samples were processed the same day as 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><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">Next, 100 µl per well of HRP-conjugated anti-human IgG (HRP Donkey anti-human IgG Clone: Poly24109) or anti-human IgA (Goat Anti-Human IgA alpha chain (HRP) ABCAM ab97215) secondary antibody diluted 1:10,000 in 0.1% TPB was added and incubated for 1 hour at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: (BioLegend Cat# 410902, RRID:AB_2686937)</div></div><div style="margin-bottom:8px"><div>anti-human IgA</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Anti-Human IgA alpha chain ( HRP</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The following antibodies were used on a dilution 1/100: CD4 FITC (OKT4); CD138 PE (DL-101); CD56 PerCP/Cy5.5 (HCD56);</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CD56</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Additional antibodies used on a 1/200 dilution were: CD3 PE/Dazzle 594 (UCHT1); CD45 PE/Cy7 (HI30); HLA-DR BV785 (L243); CD45RA BV650 (HI100); IgD FITC (IA6-2).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BV785</div><div>suggested: (BioLegend Cat# 307642, RRID:AB_2563461)</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">EH12.2H7); CD11b FITC (ICRF44); PD-L1 PE (29E.2A3); CD19 PE/Dazzle 594 (HIB19); CD86 BV650 (IT2.2); CD64 BV711 (10.1);</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PD-L1</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 clinical data was stored using REDCap (Research Electronic Data Capture) software(29).</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">Unsupervised flow cytometry analysis of CD45+ cells in PBMC samples was done using Uniform Manifold Approximation Projection (UMAP) along with the FlowSOM automated clustering tool of FlowJo Software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowSOM</div><div>suggested: (FlowSOM, RRID:SCR_016899)</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">Statistical analysis: Statistical analyses were performed using Prism 8 software (GraphPad).</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.
      • 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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.14.21263541
  7. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.14.21263505
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.14.21263505: (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: This study was approved by Imperial College Research Ethics Committee (ICREC) (Ref: 20IC6188).<br>Consent: Informed written and verbal consent was obtained from 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">Women were also asked whether they felt it was important to have their baby vaccinated during the pandemic.</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:
      Consistent with the findings by Bell et al., we also observed that women from ethnic minorities were more likely to report physical limitations and feeling unsafe when accessing vaccines for their children during the pandemic (18). Different factors affect ethnic minorities living the UK having lower vaccine uptake including access barriers and vaccine confidence (27, 28). However, during COVID-19 the increased risk to ethnic-minority populations has been well publicised (29) and ethnic-minority pregnant women are also more likely to admitted to hospital with COVID-19 (30). Ethnic-minority women may have therefore been more nervous about attending healthcare settings for pregnancy vaccines. We found that more women were vaccinated at hospital antenatal settings during COVID-19 compared to previous pregnancies which supports previous work that antenatal hospital vaccine clinics play a key role in delivering pregnancy vaccines (15) and only 7.5% of women reported a hospital vaccine appointment being changed. Further evaluation of the impact of antenatally delivered vaccines on uptake, including during COVID-19 is required (14, 31). We also found that where women received pregnancy vaccines varied geographically across the UK nations and regionally. This could reflect variation in pre-existing maternal vaccine service provision prior to the pandemic, changes to services in response to the pandemic or transport variation. Mcquaid et al found that the impact of COVID-19 on routine...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.14.21263505
  8. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.14.21263603
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.14.21263603: (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 participants provided written informed consent and all study protocols were approved by the Cedars-Sinai Medical Center institutional</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">Coupling efficiency was confirmed by incubation of 625 beads from each coupled region with a phycoerythrin-conjugated anti-6×□HisTag antibody (Abcam, Cambridge, UK) at a concentration of 10 μg/mL for 45 min shaking at 900 rpm and room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-6×□HisTag</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The bound AABs were detected by addition of R-phycoerythrin-labelled goat anti-human IgG detection antibody (Ab) (5□µg/ml, Dianova, Hamburg, Germany) for 1 hr at RT, after several PBS washes.</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><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">Other antigens were produced in-house using E.coli SCS1 carrying plasmid pSE111, which contains an N-terminally located hexa-histidine-tag.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pSE111</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">For all HCW participants, EDTA plasma specimens were transported within 1 hour of phlebotomy to the Cedars-Sinai Department of Pathology and Laboratory Medicine and underwent serology testing using the Abbott Diagnostics SARS-CoV-2 IgG chemiluminescent microparticle immunoassay (Abbott Diagnostics, Abbott Park, Illinois) against the nucleocapsid (N) antigen of the SARS-CoV-2 virus (12, 13).</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">Statistical analyses: Data processing and analysis were performed using R v3.5.1 and KNIME 2.12 (https://www.knime.org/) (21, 22).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>KNIME</div><div>suggested: (Knime, RRID:SCR_006164)</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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.14.21263603
  9. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.14.21263567
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.14.21263567: (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: Legal basis for data collection and ethics approval: In England and Wales routine anonymised data from medical records was collected without the need for consent under regulation 3 (4) of the Health Service (Control of Patient Information) Regulations 2002.<br>IRB: Ethical approval was given by the South Central–Oxford C Research Ethics Committee in England (reference 13/SC/0149) and the Scotland A Research Ethics Committee (reference 20/SS/0028).</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 collection: Data were collected from healthcare records onto case report forms through a secure online database, REDCap (Research Electronic Data Capture, Vanderbilt University, hosted by the University of Oxford, UK).</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">We used R (R Core Team version 3.6.3, Vienna, Austria) for statistical analyses, with packages including tidyverse, finalfit lubridate, UpSetR and ggplot2.</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:
      Accepting the limitations above, we provide evidence suggesting the emergence of the alpha variant did not lead to more severe disease in CYP in the UK. With the Delta variant now dominating in the UK, our study serves an exemplar of both the strengths and limitations of large hospital-based studies in informing immediate public health approaches to emerging new variants. The key strength of our study is in providing a granularity of individual patient data which allows us to look in detail at clinical presentations and outcomes, identify important sources of bias, and provide comprehensive data over time. The key limitation is that this nuanced approach takes time to perform and is outpaced by the rapid evolution of this pandemic. As a result, initial incomplete data is by necessity used to inform policy, while more accurate information may only be gained in retrospect. We urge other paediatric cohort studies to develop processes to define and record asymptomatic and incidental SARS-CoV-2 infection and differentiate this in analyses from COVID-19 disease. In addition, this study raises the possibility of as yet unidentified risk factors for critical care in CYP without comorbidities. As new variants of SARS-CoV-2 emerge, there is no guarantee that the generally mild disease observed in CYP to date will continue to predominate. Paediatricians and epidemiologists must remain vigilant in monitoring patterns of SARS-Cov-2 infection in CYP and develop more efficient systems to in...

      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">ISRCTN66726260</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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.14.21263567
  10. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.14.460411
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.14.460411: (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

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.14.460411
  11. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.15.21263613
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.15.21263613: (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:
      However, this dataset has three important limitations. Firstly, the NICE COVID-19 dataset does not contain information on comorbidities. When interpreting our results, it is important to consider that groups with increased risk of severe COVID-19 were prioritized for vaccination in early 2021. The relatively low VE of Spikevax (Moderna) might be related to the use of specifically this vaccine for patient groups at medically high risk for severe COVID-19, such as immunocompromised patients. In this group, the chance of vaccine breakthrough infection requiring hospitalization is relatively high (12-14). Other studies have not found a lower VE against severe COVID-19 for the Spikevax vaccine in the general population. Puranik et al. found a Spikevax VE against hospitalization of 81% in the US in July 2021, and a Canadian study found a single-dose Spikevax VE against hospitalization with Delta of 96% (6, 15). Secondly, the NICE COVID-19 registry includes all hospitalized patients with a positive SARS-CoV-2 test, also when the indication for hospitalization was not COVID-19, when patients test positive by routine screening at admission. This might bias our VE estimates if vaccination impacts the likelihood of being admitted with SARS-CoV-2 rather than because of SARS-CoV-2. Such misclassification of COVID-19 hospitalizations could be more likely for vaccinated patients as their risk of severe COVID-19 is greatly reduced resulting in underestimation of the VE. On the other hand unv...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.15.21263613
  12. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.14.21263545
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.14.21263545: (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">Under Healthcare Access and Quality, we included the percentage of population with health insurance coverage (Table B27001).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Under Healthcare</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We use the MatchIt package84 with the nearest neighbor method and Mahalanobis distance measure to perform the matching.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MatchIt</div><div>suggested: None</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:
      We note the inherent limitations of studying digital engagement using digitally obtained data: This and other studies with online data can inadvertently exclude those who leave no or very little digital footprint3. Our information sources provide signals about levels of activity, but we cannot study details of changes in types of access if there is no engagement. Our analysis is also limited to the footprint of Bing as one of several search engines used for online information access, and Bing’s user population may not be fully representative of the United States population. Our study carefully controls for internet access, as measured by the census, during the analysis such that any observed effects cannot be explained by differences in population internet access. Our approach combines search log data with socioeconomic and environmental variables that are routinely captured through census tracks to examine the influence of such census variables on potentially a diverse array of different topic areas of digital engagement at population scales. Our observed changes can only be attributed to ZIP code levels and not individuals because individual-level SDoH factors are not available and to preserve anonymity. Like any retrospective observational study, the potential for unobserved or uncontrolled confounding prevents us from making causal claims. However, we adjusted for observed confounding through a matching-based and difference-in-difference based methodology (Methods). Our 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.

      </footer>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.14.21263545
  13. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.17.460782
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.17.460782: (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">Detection was achieved using horseradish peroxidase-conjugate secondary antibody anti-rabbit and anti-mouse (Bio Rad #1706516, #1706515) and visualized with ECL (Cytiva RPN2232).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mouse</div><div>suggested: (Bio-Rad Cat# 170-6516, RRID:AB_11125547)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibodies: The primary antibodies used in this study are: rabbit anti-SARS-CoV-2 Spike S1 Subunit (Sino Biological, 40150-T62)</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">Secondary antibody used are: horseradish peroxidase-conjugate anti-rabbit and anti-mouse (Bio Rad #1706516, #1706515).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-rabbit</div><div>suggested: (Bio-Rad Cat# 170-6515, RRID:AB_11125142)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After washing, AP-conjugated goat anti-rat IgG antibody (SIGMA A8438) or AP-conjugated goat anti-rabbit IgG antibody (SIGMA A8025) was added, and the plates were further incubated for 1 hour at RT.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-rat IgG</div><div>suggested: (Sigma-Aldrich Cat# A8438, RRID:AB_258391)</div></div><div style="margin-bottom:8px"><div>anti-rabbit IgG</div><div>suggested: (Sigma-Aldrich Cat# A8025, RRID:AB_258372)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FACS: Vero E6 cells were incubated with RBD protein (0.45 μg/mL, final concentration) followed by incubation with human anti-RBD antibody (primary antibody) (40150-D003, Sino Biological) and goat anti-human IgG AF488-conjugated antibody (secondary antibody) (A-11013, Thermo Fisher Scientific)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-RBD</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: (Molecular Probes Cat# A-11013, RRID:AB_141360)</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">Hi-5 cells (BTI-TN-5B1-4) (Gibco #B85502) were cultured in Express Five™ SFM (Serum-Free Media) medium (Gibco #B85502 Expression Systems) at a cell density of 0.5 x 106 cells/mL and infected with recombinant virus.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Hi-5</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FACS: Vero E6 cells were incubated with RBD protein (0.45 μg/mL, final concentration) followed by incubation with human anti-RBD antibody (primary antibody) (40150-D003, Sino Biological) and goat anti-human IgG AF488-conjugated antibody (secondary antibody) (A-11013, Thermo Fisher Scientific)</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">After a wash step in 1× kinetic buffer for 120 s, the ACE2-Fc-captured biosensor tips were then submerged for 300 s in wells containing different concentrations of antigen (RBD E. coli, insect, and HEK-293) to evaluate association curves, followed by 900 s of dissociation time in kinetic buffer.</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><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">RBD protein production in E. coli: The SARS-CoV-2 Spike Receptor Binding Domain sequence (aa 319-541, Uniprot ID P0DTC2) was cloned with a C-terminal 6x-His tag into a pET-21a(+) plasmid. E. coli BL21 Star™ (DE3) (genotype: F−ompT hsdSB (rB−, mB−) galdcmrne131) competent cells, and E. coli Lemo21 (DE3) (genotype: fhuA2 [lon] ompT gal (λ DE3) [dcm] ΔhsdS/ pLemo(CamR)) competent cells were transformed with 100 ng of plasmid of interest.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pET-21a(+</div><div>suggested: RRID:Addgene_12669)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">RBD protein production in insect cells: The SARS-CoV-2 Spike Receptor Binding Domain sequence (aa 319-541, Uniprot ID P0DTC2) was cloned into a pFAST-bac1 plasmid downstream of the gp64 signal sequence to promote secretion, along with a C-terminal 8x-His tag for affinity purification.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pFAST-bac1</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">Raw data were analyzed using the Biopharma Finder 2.1 software from ThermoFisher Scientific.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Biopharma Finder</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 high costs (resources), the time-consuming production, the requirement of specific equipment, and access to dedicated facilities could be a limitation for many laboratories or for the industrial production. By contrast, the bacterial-derived RBD offers a low production cost, a broader availability, and easy handling as main advantages, which make it more accessible. However, limitations in the quality of the produced sample include the absence of glycosylation that partially affects protein stability and efficiency, the presence of heterogeneous folded populations, and the relative low production yields which may result in a final product not eligible for some clinical and medical applications. Overall, all the recombinantly produced RBDs represent valuable tools for research purposes against the pandemic. Recently, expression and purification strategies described in this article have been also proved to be successful in the production of mutants of RBD corresponding to the variants of concern.

      Results from TrialIdentifier: No clinical trial numbers were referenced.

      Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.17.460782
  14. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.17.460745
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.17.460745: (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 Ethics Review Committee for Animal Experimentation approved all experimental protocols used in the present study (Protocol Number: A2020MED-18).<br>Euthanasia Agents: Bioluminescent imaging: The hamsters were sacrificed by isoflurane and cervical dislocation 24 h after infection.</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">Hamster models: Male 6-to 10-week-old hamsters were purchased from Japan SLC Inc. (Shizuoka, Japan).</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 expression plasmid for the truncated S protein of SARS-CoV-2 and pCAG-SARS-CoV-2 S (Wuhan) was provided by Dr. Shuetsu Fukushi, National Institute of Infectious Diseases, Japan.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCAG-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">Pseudotyped VSVs bearing envelope (G) (VSV-G) were also generated.</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><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">Differences between low and high SARS-CoV-2pv concentrations were examined for statistical significance using an unpaired Student’s t-test with GraphPad Prism version 8.4.3 (GraphPad Software, 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: 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: Please consider improving the rainbow (“jet”) colormap(s) used on page 20. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

      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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.17.460745
  15. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263535
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.13.21263535: (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 this study’s limitations. As with all observational studies, confounding variables may affect interpretation of results. In particular, data for months 5 and 6 primarily reflect patients who received their doses vaccine early (e.g. January and February of 2021) with a moderately higher proportion of BNT162b2/Pfizer vaccine recipients, and these patients may be frailer at baseline. In addition, we did not correlate antibody titers with breakthrough infection, an issue which remains complex and controversial. In conclusion, immunity to SARS-CoV-2 vaccines, as indicated by SAb-IgG titers, wanes over time in maintenance dialysis patients without a prior history of COVID-19. In the setting of SARS-CoV-2 variants of concern, the impact of waning titers on breakthrough infections needs to be monitored closely. The current CDC recommendation to provide a third vaccine dose based on clinical assessment for immune compromise is an important consideration for the maintenance dialysis population. A large proportion of maintenance dialysis patients have suboptimal response to the currently recommended vaccine regimens. Therefore, additional doses of vaccine should be considered for this vulnerable population, whether routinely or, with further investigation, potentially guided by protective correlates such as antibody response.

      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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263535
  16. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21262609
    1
    1. sciscore 20 Sep 2021

      SciScore for 10.1101/2021.09.09.21262609: (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:
      In order to keep the model as generic and as simple as possible in a context of limited data, we made several assumptions and limitations that should be highlighted. First, we assumed homogeneous mixing within the HCW and patient populations. Regarding HCWs, the risks of exposure are most probably profession-dependent. Similarly, small clusters of contacts may exist within the patient population. The homogeneous mixing assumption may have led us to overestimate the risk of epidemic spread. Second, we estimated transmission rates using data from an outbreak observed in a specific ward and those estimates were then used to characterize all other wards. In doing so, we assumed the same contact patterns n all wards. Third, given that visits were strictly prohibited during the first pandemic wave, we did not account for contamination of patients and HCWs by visitors. In further analyses, this assumption should be relaxed to avoid underestimating the epidemic risk. Also, it would be of interest to account for vaccination in both patient and HCW populations in the model. Vaccine roll-out in LTCFs and hospitals surely plays an important role in further mitigating the spread of infection. Moreover, testing strategies based on network structure could be designed so as to make better use of testing resources in the hospital setting. Following the end of the first lockdown on 11 May 2020, the hospital has been implementing contact tracing to break chains of transmission. Resulting contac...

      Results from TrialIdentifier: No clinical trial numbers were referenced.

      Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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/10.1101/2021.09.09.21262609
  17. www.djangoproject.com www.djangoproject.com
    FAQ: Django's Trademark Licensing Agreement | Django
    2
    1. mrchrisadams 20 Sep 2021
      ... I'm not happy with the way an event/group handled my code of conduct complaint? The first line for reporting any code of conduct violation should always be the event or group organizers themselves. However, if you've done this, and you're not happy with the response you've received, contact the DSF by email: foundation@djangoproject.com and the DSF will investigate and respond. In the extreme case, this response may be to revoke the group/events license to use the Django name

      A potential escalation path for events and conferences when the denial and delay response talks come out

    2. mrchrisadams 20 Sep 2021
      You must also adopt a code of conduct (the Ada initiative draft is a good starting point, but you can choose another code if you wish), and agree to run your event in the spirit of the Django Community code of conduct.

      This is good example of trademark law being used to enforce norms around codes of conducts

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    djangoproject.com/trademarks/faq/
  18. highgrowthengineering.substack.com highgrowthengineering.substack.com
    Writing maintainable code at speed 🏎
    1
    1. bradleyess 20 Sep 2021
      In this example, we have two systems, worked on by two teams:A newly created fraud detection system, that is being written by the Fraud Detection team. They’re tasked with spotting fraudulent payments and preventing them, whilst providing a good experience to genuine customers. They’ve been told that they should launch as soon as they are ready — every day that they don’t, the business loses more money.An existing billing system, owned by the Payments team. This service will call out to the fraud detection system to determine whether it should accept the payment. They already have the ability to reject payments.Even though we have to build at speed, how can we avoid coupling the two teams and systems unnecessarily? Here’s how I’d approach the problem.Fraud detection teamOn the first day, define the types of decisions that you’ll return as part of your interface. Accept and reject seem like sensible places to start: we can make changes later on. Then, create your new ‘fraud detection service’. To start with, it will allow every transaction that it is passed. a.image2.image-link.image2-230-1418 { padding-bottom: 16.22002820874471%; padding-bottom: min(16.22002820874471%, 230px); width: 100%; height: 0; } a.image2.image-link.image2-230-1418 img { max-width: 1418px; max-height: 230px; } Payments teamOn the second day, integrate with the new fraud detection service by calling it. For safety purposes, ignore any decision that isn’t accepting the payment, and alert the Fraud Detection team when this is the case. a.image2.image-link.image2-1110-1456 { padding-bottom: 76.23626373626374%; padding-bottom: min(76.23626373626374%, 1110px); width: 100%; height: 0; } a.image2.image-link.image2-1110-1456 img { max-width: 1456px; max-height: 1110px; } With trivial amounts of work, we’ve now got the foundations in place. The Fraud Detection team can get to work on building a great system to predict fraud with the data they’re being passed, knowing that there’s no possible way that their system can reject any live payments.Let’s fast-forward a little. The Fraud Detection team now has a promising model for predicting fraud. They’re ready to launch an experiment where they’ll send a percentage of payments to the new system and start rejecting payments. They send a pull request to the Payments team, removing the ‘safety code’ that was added — they now want the ability to reject payments. a.image2.image-link.image2-479-1456 { padding-bottom: 32.89835164835165%; padding-bottom: min(32.89835164835165%, 479px); width: 100%; height: 0; } a.image2.image-link.image2-479-1456 img { max-width: 1456px; max-height: 479px; } They roll out their change, but with the experiment switched off. The system is still accepting all payments. a.image2.image-link.image2-368-1408 { padding-bottom: 26.136363636363637%; padding-bottom: min(26.136363636363637%, 368px); width: 100%; height: 0; } a.image2.image-link.image2-368-1408 img { max-width: 1408px; max-height: 368px; } Later on in the week, they launch their experiment. They’re now stopping fraud. 🎉This example highlights a few important themes:Going quick doesn’t always mean trading off maintainability. Nothing in this example is crufty.Synchronisation between teams can kill speed. If you must synchronise, it’s best to synchronise against interfaces, early on. This is a ‘formal’ way of specifying how your systems will interact with each other. Once you’ve put the foundations in place, teams can work independently of each other against these interfaces.Smaller changes are generally safer changes. At each stage, we didn’t change much, but ensured that it was safe.

      Working together between teams isn't an inherently bad thing, perhaps even an inevitability.

      The great architects and software engineers collaborate upfront on agreed upon interfaces, hiding any technical debt or cruft behind their interface and allowing the dependent teams to develop their features without being blocked.

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    highgrowthengineering.substack.com/p/writing-maintainable-code-at-speed
  19. forums.linuxmint.com forums.linuxmint.com
    Linux 20 - No micro and headphone sound - Linux Mint Forums
    1
    1. R4M 19 Sep 2021
      Okay, let's try something different: Code: Select allsudo tee /etc/modprobe.d/blacklist-realtek.conf <<<'blacklist snd_hda_codec_realtek' Run that in the terminal then shut down for a few minutes. Don't simply reboot.

      Après avoir désactivé le fastboot de windows 10, permet de corriger les problème de son innexplicables avec les casques

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    forums.linuxmint.com/viewtopic.php
  20. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.16.460663
    1
    1. sciscore 19 Sep 2021

      SciScore for 10.1101/2021.09.16.460663: (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 were adults and were enrolled in the study after providing 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">All individuals were between 18 and 70 years old (36±11, female:male ratio=3.2) (Extended Table I)</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 human, mouse and hamster antigen-specific antibodies: Plates were coated overnight with 0.4 μg/well of either N, RBD, S recombinant proteins, or alternatively 104 PFU/well of UV-inactivated SARS-CoV-2, and blocked for 2 hours with PBS containing 2% bovine serum albumin (PBS-2% BSA) at 37°C.</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></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Serum were serially diluted and the bronchoalveolar lavage (BALF) samples tested at 1:1 dilution in PBS-2% BSA and incubated for 1 hour at 37°C, and then incubated with anti-human IgG-HRP antibody (Fapon), anti-hamster IgG-HRP or anti-mouse total IgG, IgG1, IgG2c conjugated with streptavidin-HRP (Southern Biotech).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG-HRP</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-hamster IgG-HRP</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-mouse total IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgG1 , IgG2c</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 20 hours of culture, the plates were washed and incubated with biotinylated antibody anti-IFN-γ (XMG1.2 – BD).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-IFN-γ</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The secondary antibody Alexa Fluor 594 anti-mouse IgG (ThermoFisher) was added and the nucleus was stained with DAPI (ThermoFisher).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>The secondary antibody Alexa Fluor 594 anti-mouse IgG</div><div>suggested: None</div></div><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">Immunofluorescence assays: A 16-well chamber slide (ThermoFisher) was coated with 104 Vero E6 cells/well and incubated overnight with SARS-CoV-2 in a multiplicity of infection (M.O.I) of 10.</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">Mice, hamsters, virus and ethics statement: Female C57BL/6 mice, 6-10 weeks old, were purchased from the Center for Laboratory Animal Facilities of the Federal University of Minas Gerais (CEBIO-UFMG)</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">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">Competent E. coli Star™ (DE3) were transformed with the pET24 vector with N or the RBD sequences and E. coli pRARE with the pET24_with SpiN.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pET24</div><div>suggested: RRID:Addgene_73142)</div></div><div style="margin-bottom:8px"><div>pRARE</div><div>suggested: RRID:Addgene_84650)</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 sequences were translated in silico using the standard genetic code and multiple aligned together with N or S proteins of Lineage B (Wuhan – EPI_ISL_402123) by the Kalign tool 46 with parameters 8.52 “gap extension penalty”, 54.90 “gap open penalty” and 4.42 “gap terminal penalty”.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Kalign</div><div>suggested: (Kalign, RRID:SCR_011810)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immunization, challenge and histopathology: Hamsters and C57BL/6 or hACE2 mice received two administrations at 21 days apart, containing 10 μg of RBD, N or SpiN adjuvanted with 50 μg of Hiltonol® (Poly ICLC, supplied by Oncovir, Washington, D.C.) 39,40, or with AddaVax™ (oil-in-water emulsion similar to MF59) in a volume of 1:1 AddaVax™:Antigen 50.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>AddaVax™</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Images were processed with the software ImageJ version 2.1 for Mac.</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">Data were analyzed using FlowJo v10.5.3 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">Statistical analysis: Statistical analysis was conducted using GraphPad Prism 6.0 for Mac (GraphPad 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.

      <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/10.1101/2021.09.16.460663
  21. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263511
    1
    1. sciscore 19 Sep 2021

      SciScore for 10.1101/2021.09.13.21263511: (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">The final set of features used for modeling is as below: Modelling: We used logistic regression, decision tree and random forest from the scikit-learn [6]5 library and the extreme gradient boosting algorithm from the XGBoost [7] library.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>scikit-learn</div><div>suggested: (scikit-learn, RRID:SCR_002577)</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 some limitations for generalization of these models, which need further validations with dataset from other states of India. Despite this, the study’s model has the potential to predict the patients at high risk and thus, consequently initiating preventive care or aiding in early detection of mucormycosis infection. Moreover, including a dataset for a longer time span would enable more accurate results with a larger dataset. Future studies could include predicting the number of days after discharge, when a patient has a possibility of developing mucormycosis.

      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/10.1101/2021.09.13.21263511
  22. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263194
    1
    1. sciscore 19 Sep 2021

      SciScore for 10.1101/2021.09.07.21263194: (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">Each study was analyzed for the following variables: NCT identifier, recruitment, randomization strategy, type of control arm, baseline patient status, median neutralizing antibody (nAb) titer in both recipients (before CCP transfusion) and CCP units, type of viral neutralization test (VNT), primary endpoint, signals of efficacy, and reasons for failure At the same date, the ClinicalTrials.gov database was searched for CCP RCTs worldwide having as status “completed”, “active, not yet recruiting” or “recruiting”.</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">On September 7, 2021, we searched PubMed (which is also indexing the medrXiv prepublishing server) for clinical trials of CCP in COVID19, focusing on RCTs and PSM studies only.</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></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">NCT04359810</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">Plasma Therapy of COVID-19 in Severely Ill Patients</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04338360</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Approved for marketing</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Expanded Access to Convalescent Plasma for the Treatment of …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04361253</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Terminated</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Evaluation of SARS-CoV-2 (COVID-19) Antibody-containing Plas…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04421404</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">Effects of COVID-19 Convalescent Plasma (CCP) on Coronavirus…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04397757</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 Convalescent Plasma for the Treatment of Hospitaliz…</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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21263194
  23. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263371
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263371: (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: 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">NCT04738331</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">Analysing the French COVID-19 Epidemic Using a National 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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263371
  24. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263497
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263497: (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:
      This study has some limitations. The data used contained several missing values that were omitted before performing the Cox PH model. We did not apply any missing value technique to impute them. Some essential variables including hand washing facilities, smokers prevalence, hospital patients per million, poverty rate, etc. have not been considered in the analysis due to data deficiency.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263497
  25. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263473
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263473: (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 Institutional Ethics Committee of the Yamagata University Faculty of Medicine approved this study (approval number; 2021-130, approval date: June 29, 2021).<br>Consent: The opt-out method was used to obtain informed consent, which is available on our website.</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 questionnaire was designed using the free web-based Google Forms software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Google Forms</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses were performed using JMP version 11.0 software (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:
      There are several limitations to our study. The first limitation is that the survey was an internet-based questionnaire, and symptoms and allergy history were self-reported. Particularly, it is unclear whether the diagnosis of allergic diseases is correct. Secondly, not many subjects had a history of anaphylaxis or adverse reactions to vaccinations; thus, the statistical reliability of the study may not be high. Thirdly, it is possible that some of the staff did not receive the vaccine because of a history of allergy. Therefore, it is possible that some people with a history of allergies may not have participated in this study. It is expected that large-scale and detailed data on adverse reactions to COVID-19 vaccination will be accumulated in the future, and the advantages and disadvantages of vaccination, especially for people with a history of allergy, will be verified. In conclusion, although the tolerance of BNT162b2 was worse in individuals with allergies than those without, no serious adverse reactions such as anaphylaxis or death were observed. For those who are hesitant about COVID-19 vaccination because of allergy, data from a large adverse reaction study can be expected to be very helpful. We hope that the results of this study will be used to successfully complete the vaccination.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263473
  26. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263437
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263437: (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 design and consent forms for all procedures (project identification code: 2019–0423) were approved by the Ethics Committee for Human Participants at the Niigata University School of Medicine (Niigata, Japan) and complied with the Helsinki Declaration of 1964, as revised in 2013. 2.2 Fluorometric measurement of platelet polyphosphate using DAPI: After storage at 4 °C for 24 h, the fixed platelets were centrifuged at 578 × g for 5 min, and the supernatants were carefully aspirated as much as possible.</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 female groups (initial dose=36.3±15.0, second dose=36.3±12.3) were significantly younger in average than the male groups (initial dose=56.8±8.8, second dose=56.0±7.8) in both cases.</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 Mann-Whitney U test was performed to compare the two groups (SigmaPlot 13.0; Systat Software, Inc., San Jose, CA, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SigmaPlot</div><div>suggested: (SigmaPlot, RRID:SCR_003210)</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:
      4.5 Limitations: In Japan, the vaccination of medical staff is strictly controlled and scheduled. In addition, our limited capacity to handle samples made it difficult to secure sufficient donor numbers. As a result, we could not expand the sample size to what we originally calculated. Thus, further investigation is needed to reach a definitive conclusion; however, the present findings regarding gender and age differences seem to essentially be consistent with the previous reports of antibody formation36-38 and, as a pilot study, are worth further investigation.

      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/10.1101/2021.09.13.21263437
  27. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263543
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263543: (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">All analyses have been done using statsmodels package in Python (42).</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: 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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263543
  28. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263348
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.09.21263348: (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 study was reviewed and approved by the Institutional Review Board of the Icahn School of Medicine at Mount Sinai (HS#13-00981).<br>Field Sample Permit: SARS-CoV-2 specimen collection and testing: Upper respiratory tract (e.g., nasopharyngeal, anterior nares) and saliva specimens collected for SARS-CoV-2 testing underwent diagnostic testing in the MSHS Clinical Microbiology Laboratory (CML), which is certified under Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a and meets requirements to perform high-complexity tests.</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: SARS-CoV-2 sequencing, assembly and phylogenetic analyses: SARS-CoV-2 viral RNA underwent reverse transcription, PCR amplification and next-generation sequencing followed by genome assembly and lineage assignment using a phylogenetic-based nomenclature as described by Rambaut et al. 27 using the PANGOLIN tool, version 2021-04-28 28 as previously described 25,26.</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 Multiple Alignment using Fast Fourier Transform (MAFFT) platform 29,30 which is publicly available for use online (https://mafft.cbrc.jp/alignment/server/add_fragments.html?frommanualnov6) was used to align each file.</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">Mismatches by position in PBS regions of forward/reverse primer and probe sequences were manually counted on Microsoft Excel v16.48.</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">Statistical analyses: For statistical comparison of fraction of PBS with mismatches in genomes with detected targets versus those with dropout targets, normality was assessed by D’Agostino and Pearson test (GraphPad Prism 9.1.0), which indicated that all distributions were non-parametric; thus, a Mann-Whitney test (two-tailed) was performed (GraphPad).</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">Display Items: All figures are original and were generated using the GraphPad Prism software 9.1.0, R software package ggplot2, NCBI Multiple Sequence Alignment Viewer v.</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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">1.17.0 (https://www.ncbi.nlm.nih.gov/tools/msaviewer/), and finished in Adobe Illustrator 2021 (v.25.2.1).</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: 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 number of studies have described substitutions in the ORF1ab, S, E, and N genes that may interfere with specific RT-PCR targets 1,5,9,11,12,14–16,18, but these studies have inherent limitations. Several are in silico analyses that do not reflect diagnostic performance in the clinical setting 1,5,16,18, whereas others do not definitively demonstrate target dropout due to substitutions as they utilize platforms for which primer/probe sequence information is not publicly available 9,11,14,15. In addition, the later studies are based on assays that interrogate up to 3 diagnostic targets, and are limited by the number and diversity of viral sequences surveyed over finite timeframes, some prior to the emergence and expansion of VOCs. In the current study, we describe a robust evaluation of the impact of PBS mismatches on Agena MassARRAY® SARS-CoV-2 Panel target results for over 1,200 specimens over a five-month time period that corresponds with the rapid emergence of viral VOIs/VOCs (December 2020 through April 2021). This large dataset enabled direct correlation of detection of each of five different Agena diagnostic viral targets with genomic sequence data Additionally, by using publicly available primer/probe sequences to map lineage-specific substitutions, we were able to further evaluate the impact of mismatches on target results and to demonstrate an association between variation in SARS-CoV-2 PBSs and target dropout. Our analysis revealed that several mutations result in N...

      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/10.1101/2021.09.09.21263348
  29. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263214
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263214: (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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263214
  30. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21262182
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21262182: (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: Institutional Review Board (IRB): This was an IRB-approved HIPPA/PHIPPA compliant study.<br>Consent: The need for 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

      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 authors themselves raise this as a limitation of their study. Data from the Center for Disease Control (CDC) also report a lower incidence than that in our study. Using myocarditis cases reported to VAERS with onset within 7 days after dose 2 of an mRNA vaccine, crude reporting rates (i.e., using confirmed and unconfirmed cases) per million second dose recipients were calculated using national COVID-19 vaccine administration data as of June 11, 2021. The highest reporting rates were among males aged 12-17 years and those aged 18-24 years (62.8 and 50.5 reported myocarditis cases per million second doses of mRNA COVID-19 vaccine administered, respectively). We were not able to break down the denominator of all vaccinations in the Ottawa area by age. Therefore, although our patients were largely in the vulnerable 18-30 age category, our denominator included the full adult age spectrum. As such it is possible that the numbers, we quote are an underestimate of incidence for the 18-30 age group itself. In support of this, is the initial report from Israel of a 1 in 3000 to 1 in 6000 incidence of myocarditis following vaccination in young adults(9). Most reports have emphasized mild illness and brief in-hospital stay – and this was our experience also. However, one of the larger cohorts to date described the need for heart failure treatment in 40% of its myocarditis patients (despite an absence of prior heart failure episodes) and intensive care in 10%(14). That report also dem...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21262182
  31. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21262360
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21262360: (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: We detected the following sentences addressing limitations in the study:
      Statement of principal findings: Strengths and limitations: Strengths of this study are the elimination of calendar time effects by the matched case-control design, the comprehensive linkage to e-health records and the focus on severe cases as main outcome measure. Hospitalised cases may include some test-positive individuals whose admission or continued stay in hospital was for another underlying diagnosis: this in turn may lead to underestimation of vaccine efficacy against COVID-19, especially in risk groups with comorbidities. Such misclassification is less likely to occur with the narrow definition of severe COVID-19 used in the REACT-SCOT study. Even in this large cohort, the numbers of severe cases in some CEV subgroups are too small for vaccine efficacy against severe disease to be estimated accurately within these subgroups. Another limitation is that as most immunosuppressants and drugs for cancer are prescribed only in hospital and where prescribing records are not held in electronic form, we cannot study the relation of risk to different classes of immunosuppressant drugs. The national shielding list does not hold information about drug therapy or diagnoses other than the seven broad categories listed as CEV. Relation to other studies: A recent report based on primary care data examined vaccine efficacy against symptomatic COVID-19 for which a medical consultation was recorded (8). For those who had been advised to shield, the efficacy after two doses of any vacci...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21262360
  32. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263414
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263414: (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: The study was approved by the Uganda Virus Research Institute’s Research Ethics Committee (Ref.<br>Field Sample Permit: GC/127/20/08/785), registered, and cleared by the Uganda National Council for Science and Technology (UNCST) (registration number HS878ES).<br>Consent: Written informed consent was obtained from participants before blood specimens and other data were 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></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">Therefore, any sample that was solely IgM positive by CoronaChek™ was retested by the Abbott ARCHITECT AdviseDx SARS-CoV-2 IgM chemiluminescent microparticle immunoassay (CMIA) (Abbott, Chicago, IL).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CoronaChek™</div><div>suggested: None</div></div><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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263414
  33. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263365
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263365: (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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263365
  34. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263432
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263432: (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 and evolutionary Analysis: The complete genome sequences of 90 SARS-CoV-2 obtained were aligned using MAFFT version 7 (https://mafft.cbrc.jp/alignment/server/) against the Wuhan-Hu-1 reference genome (Accession number: NC_0455122), with all parameters set at default (Katoh et al., 2019; Kuraku et al., 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">Based on the whole genome sequences, a maximum likelihood tree was constructed using MEGA X with 50 bootstraps resampling to ascertain the common antecedent among each strain (Tingting et al., 2020).</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></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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263432
  35. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.15.459215
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.15.459215: (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">Sequence analyses and phylogenetic reconstruction: All sequences were aligned against the reference genome (EPI_ISL_402125) using the default settings in ClustalW [21].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ClustalW</div><div>suggested: (ClustalW, RRID:SCR_017277)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phylogenies were constructed using IQ-TREE 2.1.2 [22].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IQ-TREE</div><div>suggested: (IQ-TREE, RRID:SCR_017254)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The ancestor sequences of SARS-CoV-2 and RaTG13 were reconstructed using codeml implemented in PAML 4 [26] under the free ratio model.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PAML</div><div>suggested: (PAML, RRID:SCR_014932)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">An array of selection detection methods implemented in HyPhy was applied to detect whether the lineage leading to minks has experienced adaptive evolution [27].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HyPhy</div><div>suggested: (HyPhy, RRID:SCR_016162)</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

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.15.459215
  36. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.14.460338
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.14.460338: (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: Blood samples were collected after obtaining signed informed consent in accordance with institutionally approved IRB protocols.</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 incubation, plates were washed three times and incubated for 30 minutes at room temperature with cross-absorbed goat anti-human IgG-horseradish peroxidase (HRP)-conjugated secondary antibody (ThermoFisher Scientific; A18811) diluted to a 1:2500 dilution in ELISA wash buffer.</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">For this assay, 293T cells are transfected with SARS-CoV-2 spike expression vector and co-cultured with either a FcγR2a, or FcγR3a, CD4+ Jurkat reporter cell line, which expresses firefly luciferase upon FcγR activation.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Jurkat</div><div>suggested: TKG Cat# TKG 0209, RRID:CVCL_0065)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To quantify background (i.e., IgG activation-independent) luciferase production, reporter cells were co-cultured with the spike-expressing 293T cells in the absence of any IgG.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T</div><div>suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)</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">Lithium heparin-coated tubes were used for blood collection and plasma was isolated using Ficoll-Hypaque (GE Healthcare; 17-1440-03) in accordance with manufacturer’s instructions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GE Healthcare</div><div>suggested: (GE Healthcare, RRID:SCR_000004)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Polyclonal IgG was isolated from 200μl of donor plasma using a protein A/G spin column kit, followed by desalting using Zeba spin columns according to manufacturer’s instructions (ThermoFisher Scientific; 89892)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ThermoFisher Scientific</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The optical density at 450 nm (OD450) was measured using a BioTek Powerwave HT plate reader using Gen5 software.</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">The data were quantified using Flow Jo software (Tree Star, Inc).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Flow Jo</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 analysis: Statistical and data analyses were performed using GraphPad Prism 8.4.3, R 4.0.4, and R Studio 1.4.1103.</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">Graphs were generated in Prism and R Studio and statistical differences between two groups were calculated by Mann-Whitney U-test.</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">Scatter plots, bar graphs, heatmaps, and polar plots were visualized with ggplot2 (v3.3.3 R Studio).</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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The completed data were scaled to unit variance using FactoMineR (v2.4 R studio).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FactoMineR</div><div>suggested: (FactoMineR, RRID:SCR_014602)</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:
      One caveat to the previous studies that found FcγR activity to be critical for effective humoral immunity is that all of those studies were conducted with neutralizing IgG. Therefore, we cannot rule out that FcγR activation in the absence of a neutralizing response does not contribute to severe COVID-19 pathogenesis, as may be the case with individuals with anti-S2’FP dominant IgG profiles. Therefore, it will be important to dissect how IgG-targeting of neutralizing and non-neutralizing epitopes influences the relationship between FcγR activation and disease outcomes. Additionally, it will be important to examine the contribution of FcγR activation to systemic inflammation and control of virus replication in animal models that faithfully mimic human FcγR-signaling effects. In conclusion, the data presented here demonstrate that immunological history—particularly antibody repertoire from seasonal betacoronaviruses—predicts and potentially determines COVID-19 disease severity. Specifically, an anti-HR2-dominant Ab profile represents an efficient protective recall response, an anti-S2’FP dominant Ab profile suggests a deleterious inefficient recall response, and a predominantly anti-RBD profile likely reflects a protective de novo response. These data become particularly important in assessing epitope-targeting early in disease, which could allow earlier interventions with treatments like monoclonal Ab therapies, preventing progression to ARDS. Additionally, assessing the humora...

      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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.14.460338
  37. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.15.460543
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.15.460543: (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">MCSG1, MCSG2, MCSG3, and MCSG4 (Anatrace), Index (Hampton Research) and Wizard 1&2 (Jena Bioscience) screens were used at 16 °C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MCSG1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For the PLpro-C111S/Ub2-K48R,D77 complex (11 mg/ml), crystals appeared in MCSG-2 F11 and were improved in hanging drops with a protein-to-matrix ratio of 2:1 in 0.2 M di-sodium tartrate, 15 % (w/v) PEG3350 after seeding with 1/10 volume of PLpro-C111S/Ub2-K48R,D77 microcrystals.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MCSG-2 F11</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">All cross-linking reactions were quenched with 172 mM (4 times excess) Ammonium Bicarbonate (AB) for 30 minutes at 37 °C while shaking at 350 rpm.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>AB</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">Human ISG15 gene was also synthesised and cloned directly into pMCSG53 vector.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pMCSG53</div><div>suggested: RRID:Addgene_167255)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Unlabeled Ub variants were expressed in BL12(DE3) E.coli cells containing a helper pJY2 plasmid and purified as described elsewhere27.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pJY2</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">PALMIST and GUSSI software is freely available for academic users on UTSW MBR core’s website (https://www.utsouthwestern.edu/labs/mbr/software/).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GUSSI</div><div>suggested: (GUSSI, RRID:SCR_014962)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Intensities were converted to structure factor amplitudes in the truncate program33 from the CCP4 package34.</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 rounds of manual adjustments of structure models using COOT39 and refinements with REFMAC program38 from CCP4 suite34 were done.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>REFMAC</div><div>suggested: (Refmac, RRID:SCR_014225)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The stereochemistry of the structure was validated with PHENIX suite40 incorporating MOLPROBITY41 tools.</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">The data were processed using Topspin (Bruker) and analyzed using Sparky 3.19042.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Sparky</div><div>suggested: (Sparky , RRID:SCR_014228)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Selection of common interface residues was carried out in PyMOL 2.4.1.</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">These simulations were performed using BioHPC computing cluster at UT Southwestern Medical Center.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BioHPC</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The plots were made using GraphPad Prism 8 and mapped onto the protease structure using PyMOL 2.4.1.</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 relax protocol and Flex_ΔΔG used Rosetta v3.13 and v3.12, respectively.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Rosetta</div><div>suggested: (Rosetta, RRID:SCR_015701)</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:
      The original structure of PLproCoV-1 bound to K48-linked Ub2 revealed both Ubs bound to the protease through binding sites present in both proximal and distal Ubs with minor caveats of the linkage not being hydrolysable and the C-terminal tail covalently linked to the protease. There remains no structure of the ISG15 bound to PLproCoV-1 suggesting that the dramatically reduced affinity must impact binding both proximal and distal binding UBL domains of ISG15. Our new structure of PLproCoV-2 bound to human ISG15 as well as the previously determined structure of PLproCoV-2 bound to mISG15 reveal a dual UBL domain recognition binding mode despite surprising sequence variation between the mouse and human forms of ISG15, in particular the substrate binding interface (Fig. 1b). Our in silico alanine scan of the interfaces uncovered which residues may play central roles in stabilizing the ISG15 binding mode for PLproCoV-2 and implicated V66 as being important for stabilizing the distal UBL domain of ISG15. Furthermore, our evolutionary analysis of SARS-CoV-2 variants highlights sequence variation at key sites suggesting the PLpro variants exist that may have altered substrate specificity with unknown disease outcomes. Impact of PLpro sequence drift on substrate specificity: Much of the focus on understanding how sequence variation impacts pathogenicity, infectivity and virulence of SARS-CoV-2 has been centered on sequence changes in surface proteins such as the receptor-binding doma...

      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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.15.460543
  38. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263292
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263292: (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: Protocols in this study were reviewed and approved by the National Institutes of Health (NIH) Central Intramural Institutional Review Board (IRB).<br>Consent: All participants provided written informed consent prior to any study procedures in accordance with the Declaration of Helsinki.</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">Cells were washed twice with the FLICA kit wash buffer and then incubated with LIVE/DEAD Fixable AQUA Dead Cells Stain (Thermo Fisher, USA) for 15 min at RT, followed by extracellular staining in PBS + 1% BSA with the following fluorochrome-conjugated antibodies for monocyte phenotyping: anti-CD14 BV605 (Clone:M5E2)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD14</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells were fixed and permeabilized with Cytofix/Cytoperm (BD Biosciences, USA) overnight at 4°C and stained for 1h at RT for intracellular ASC, with anti-ASC/TMS1 AF647 antibody from Novus Biologicals, Littleton, CO.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-ASC/TMS1 AF647</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Flow Cytometry: PBMCs were stained with the following list of fluorescently labeled antibodies against cell surface markers subsequently detected by flow cytometry: anti- CD14 BV605 (Clone:M5E2), anti-CD16 PE-Cy7/BV711 (Clone:3G8), and anti- CD3 PE (Clone:HIT3a) from BioLegend; anti-CD20 e450 (Clone:2H7)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD16 PE-Cy7/BV711</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti- CD3</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD20</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">GFP fluorescence was detected by staining cells with Alexa Fluor 647 anti- GFP antibody at 1:200 (Biolegend).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GFP</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">To determine viral titers by TCID50 assay, cells were harvested, lysed by freeze/thawing and plated in triplicate onto Vero E6 cells using 10-fold serial dilutions.</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">All compensation and gating analyses were performed using FlowJo 10.5.3 (TreeStar, Ashland, OR, 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">Statistical Analyses: Statistical analyses were performed using non-parametric Mann-Whitney or Kruskal-Wallis test in GraphPad Prism 8.0.1 software (GraphPad, 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:
      The limitations of the current study include lack of critically ill ventilated ICU patients (as participants had to be able to provide consent), lack of multiple longitudinal sampling and small sample size. Nevertheless, our findings collectively corroborate the hypothesis that early exposure of alveolar macrophages and endothelial cells to SARS-CoV-2 may induce oxidative stress dysregulation and aberrant cytokine secretion. This initial cell priming event may contribute to the enhanced recruitment to the site of infection of pre-activated circulating monocytes pre-committed to inflammasome activation and aberrant oxidative stress response, resulting in exacerbation of tissue immunopathology and ultimately organ failure. In this context, recent advances in targeting ROS by administration of glutathione or glutathione precursors (N-acetyl-cysteine, NAC), as well as IL-1 signaling by administrating Anakinra, a IL-1 Receptor antagonist (IL-1Ra), have been reported to prevent inflammation and/or worse clinical outcome in COVID-19 patients (Cauchois et al., 2020; Cavalli et al., 2020; Horowitz et al., 2020; Huet et al., 2020; Ibrahim et al., 2020; Kyriazopoulou et al., 2021a; Kyriazopoulou et al., 2021b). Thus, our findings suggest that early treatment with antioxidants and IL-1 signaling inhibitors may represent potential therapeutic intervention for COVID-19 by preventing deleterious effects downstream of the inflammasome pathway and consequently tissue immunopathology and that ...

      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">NCT04401436</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">COVID-19 Associated Lymphopenia Pathogenesis Study in Blood</td></tr></table>

      Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263292
  39. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263430
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.13.21263430: (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 Human subject collection: The samples were collected between March 2020 and February 2021; all subjects enrolled in this research responded voluntarily to an informed consent formulary previously approved by the Ethics Committee of Colombian National Health Institute<br>IRB: 2.1 Human subject collection: The samples were collected between March 2020 and February 2021; all subjects enrolled in this research responded voluntarily to an informed consent formulary previously approved by the Ethics Committee of Colombian National Health Institute</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">Additionally, SARS-CoV2 IgG anti-Nucleocapsid antibodies detection on the Allinity ci series (Abbott, Chicago,IL, USA) was done as screening, where relative light units (RLU) >1.4 were interpreted as positive.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Nucleocapsid</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">This study was conducted in compliance with ethical principles of the Declaration of Helsinki and to the conditions provided by the Ministry of Health - Colombia. 2.2 Cells: African green monkey kidney Vero E6 cells (ATCC CRL-1586™) were used to propagate the SARS-CoV-2 isolates and the neutralization assays.</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 sequence dataset was aligned using the MAFFT software v7 (26,27).</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">Additionally, SARS-CoV2 IgG anti-Nucleocapsid antibodies detection on the Allinity ci series (Abbott, Chicago,IL, USA) was done as screening, where relative light units (RLU) >1.4 were interpreted as positive.</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">The data were analyzed in GraphPad Prism (v9.0.2).</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:
      A limitation of this study is the small number of convalescent samples tested, and the absence of samples from vaccinated individuals, future work with more subjects, including vaccinated individuals will help to determine the clinical impact of this mutation, as well as its role in the effectiveness of currently approved vaccine strategies.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263430
  40. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.14.460394
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.14.460394: (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: CCP recipients and clinical parameters: This study was approved by the University of Wisconsin Institutional Review Board.<br>Consent: Cases met all criteria for enrollment under the Mayo Clinic Expanded Access Protocol (IND # 20-003312) (EAP) and gave written, informed consent for CCP transfusion and 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><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">Rhesus Anti-SARS CoV Spike monoclonal antibody (NHP Reagent Resource)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Anti-SARS</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">anti-Dengue monoclonal antibody, and 6 negative control plasma samples were added to each plate for validation.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Dengue</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Area under the curve (AUC) was calculated (Graphpad Prism) as a measure of the anti-S antibody titers.</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">Anti-SARS-CoV2 Ig assay (CoV2T) (Ortho Clinical Diagnostics, Markham, Ontario): This assay is an automated assay that uses a two stage immunometric technique to identify anti-SARS-CoV2 Spike protein antibodies (IgG and IgM).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV2 Spike protein antibodies ( IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgM</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A cut-off threshold value was defined to determine a reactive sample and the signal to cut-off value (S/CO) was used as a quantitative measure of anti-spike antibodies.</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><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Architect Anti-SARS-CoV2 IgG assay (Abbott Laboratories, Chicago, IL): This assay is an automated, two-step immunoassay for the detection of IgG antibodies to SARS-CoV2 nucleocapsid proteins.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Anti-SARS-CoV2 IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>SARS-CoV2 nucleocapsid proteins .</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibodies are captured on antigen coated paramagnetic microparticles and then detected by incubation with an acridinium-conjugated anti-human IgG.</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">Although neither of these assays are used clinically as a quantitative test for the purposes of this study both the S/CO and the Index were considered to be reflective of the amount of anti-SARS-CoV2 antibodies in each sample.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV2</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">. 293T cells were transduced with retroviral particles carrying a pQCXIP vector encoding the gene for the human ACE2 protein, then selected and maintained in D10 supplemented with 1µg/ml Puromycin.</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">The 293T-ACE2 cells were transduced with retroviral particles carrying pQCXIH vector encoding the gene for FcαR and selected in D10 supplemented with 100μg/ml Hygromycin B and 1μg/ml Puromycin.</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">Expression of FcαR and ACE2 in 293T-ACE2-FcαR cells were confirmed by flow cytometry.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T-ACE2-FcαR</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">The 293T-ACE2 cells were transduced with retroviral particles carrying pQCXIH vector encoding the gene for FcαR and selected in D10 supplemented with 100μg/ml Hygromycin B and 1μg/ml Puromycin.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pQCXIH</div><div>suggested: RRID:Addgene_37104)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Separately, the 293T-ACE2 cells were transduced with retroviral particles carrying pQCXIP vector encoding the gene for FcγRII.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pQCXIP</div><div>suggested: RRID:Addgene_15714)</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">Area under the curve (AUC) was calculated (Graphpad Prism) as a measure of the anti-S antibody titers.</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">Architect Anti-SARS-CoV2 IgG assay (Abbott Laboratories, Chicago, IL): This assay is an automated, two-step immunoassay for the detection of IgG antibodies to SARS-CoV2 nucleocapsid proteins.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Abbott Laboratories</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All statistical analysis was done using the GraphPad Prism software (GraphPad Software, Inc La Jolla, CA).</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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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/10.1101/2021.09.14.460394
  41. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.15.459697
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.15.459697: (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 top 10 models were then selected and the models of M homodimers were obtained using two symmetric docking approaches, SymDock and Galaxy 4-6.</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">We then placed the M-dimer model into the experimental EM density map of the ORF3a dimer (EMD-22139 11) using Phenix 15 and relied on the EM map to further refine the structure in ISOLDE 16, a package for UCSF Chimera X molecular visualization program 17.</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">All CG-MD simulations were performed using the GROMACS package (versions 2019) and the Martini 3 force field.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GROMACS</div><div>suggested: (GROMACS, RRID:SCR_014565)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Results were plotted using Python 3.9 55 and Bokeh library 56</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">A Sankey diagram of connected components was plotted in MATLAB 57 using visualization module of PisCES algorithm 58. 10.</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">We used the Mercator projection, which is a cylindrical projection that preserves local directions and shapes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Mercator</div><div>suggested: (Mercator, RRID:SCR_014493)</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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    biorxiv.org/cgi/content/10.1101/2021.09.15.459697
  42. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.15.460487
    1
    1. sciscore 18 Sep 2021

      SciScore for 10.1101/2021.09.15.460487: (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: All animal studies were conducted in compliance with local, state, and federal regulations and were approved by Bioqual and City of Hope Institutional Animal Care and Use Committees (IACUC).<br>IACUC: All animal studies were conducted in compliance with local, state, and federal regulations and were approved by Bioqual and City of Hope Institutional Animal Care and Use Committees (IACUC).<br>Consent: Subjects gave 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">Thirty 6-8 weeks old Syrian hamsters were randomly assigned to the groups, with 3 females and 3 males in each group.</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">Thirty 6-8 weeks old Syrian hamsters were randomly assigned to the groups, with 3 females and 3 males in each group.</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">Board certified pathologists were blinded to the vaccine groups and mock controls were used as a comparator.</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, anti-Hamster IgG HRP secondary antibodies measuring total IgG(H+L), IgG1, or IgG2/IgG3 (Southern Biotech 6061-05, 1940-05, 1935-05) were diluted 1:1000 in blocking buffer and added to the plates.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-Hamster IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>total IgG(H+L</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgG1</div><div>suggested: (SouthernBiotech Cat# 1940-05, RRID:AB_2795558)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Goat anti-Monkey IgG (H+L) secondary antibody (ThermoFisher PA1-84631) was diluted 1:10,000.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Goat anti-Monkey IgG</div><div>suggested: (Thermo Fisher Scientific Cat# PA1-84631, RRID:AB_933605)</div></div><div style="margin-bottom:8px"><div>anti-Monkey IgG</div><div>suggested: (Thermo Fisher Scientific Cat# PA1-84631, RRID:AB_933605)</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 stock was produced by infecting Vero E6-hACE2 cells (BEI Resources NR-53726) at low MOI with deposited passage 3 virus and resulted in a titer of 1.99×106 TCID50/ml.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero E6-hACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The stock was generated using Vero-E6 cells infected with seed stock virus obtained from Kenneth Plante at UTMB (lot # TVP 23156).</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">Vero E6 cells (ATCC, CRL-1586) were seeded in 24-well plates at 175,000 cells/well in DMEM/ 10% FBS/Gentamicin.</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">The mixture was added to 5×106 HEK293T/17 cells (ATCC CRL11268) seeded the day before in 10 cm dishes and the cells were incubated for 72h at 37°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T/17</div><div>suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">: Vero TMPRSS2 cells (Vaccine Research Center-NIAID) were plated at 25,000 cells/well in DMEM/10% FBS/Gentamicin.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Vero TMPRSS2</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">PV production: SARS-CoV-2 PV was produced using a plasmid lentiviral system based on pALD-gag-pol, pALD-rev, and pALD-GFP (Aldevron)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pALD-rev</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pALD-GFP</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plasmid pALD-GFP was modified to express Firefly luciferase (pALD-Fluc)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pALD-Fluc</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plasmid pCMV3-S (Sino Biological VG40589-UT) was used and modified to express SARS-CoV-2 Wuhan-Hu-1 S with D614G modification.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCMV3-S</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Customized gene sequences cloned into pTwist-CMV-BetaGlobin (Twist Biosciences) were used to express SARS-CoV-2 VOC-specific S variants (Table S1).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pTwist-CMV-BetaGlobin</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 titers that gave 50% neutralization (NT50) were calculated by determining the linear slope of the graph plotting NT versus serum dilution by using the next higher and lower NT using Office Excel (v2019)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Office Excel</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 Prism 8 (GraphPad, v8.3.0).</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: 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">NCT04639466</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">A Synthetic MVA-based SARS-CoV-2 Vaccine, COH04S1, for the P…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04977024</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">SARS-CoV-2 Vaccine (COH04S1) Versus Emergency Use Authorizat…</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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  43. o-date.github.io o-date.github.io
    The Open Digital Archaeology Textbook Environment
    1
    1. sambhullar2001 17 Sep 2021
      By manipulating the code that produces these images in both random and patterned ways, we manipulate the meaning of the image and the way in which these images communicate information to the viewer.

      That is interesting in essence... however are machines able to give the same emotion to certain archaeological finds that humans can. In essence can they link the arbitrary together? I suppose computation can be a good data collector/organizer, however, I still have my reservations for it against doing the ENTIRETY of the archaeological process.

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  44. sakai.duke.edu sakai.duke.edu
    Time, Work-Discipline, and Industrial Capitalism
    1
    1. chrisaldrich 17 Sep 2021
      n the extraordinary Law Book of the Crowley Iron Works. Here, at the very birth of the large-scale unit in manufacturing industry, the old autocrat, Crowley, found it necessary to design an entire civil and penal code, running to more than Ioo,ooo words, to govern and regulate his refractory labour-force.

      A historical precursor to the company-town. One wonders if this was used as a model by Hershey, Pullman, Levittown(s), etc.?

      Levittown Hershey Pullman company towns power capitalism
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  45. jrnold.github.io jrnold.github.io
    14 Strings | R for Data Science Solutions
    3
    1. learner11 17 Sep 2021
      (123) 456-7890

      I don't get this match when passing the respective code to the console.

    2. learner11 17 Sep 2021
      (123) 456-7890

      I don't get this match when passing the respective code to the console.

    3. learner11 17 Sep 2021
      (123) 456-7890

      I don't get this match when passing the respective code to the console. Any ideas why? What does the s* do?

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  46. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.14.460408
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.14.460408: (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">Cells were then incubated for 2 h at room temperature with primary anti-SARS-CoV-2 N protein rabbit polyclonal antibody (kind gift from Dr. Adolfo Garcia-Sastre), followed by three PBS washes and 1 h incubation with Alexa Fluor 488-conjugated anti-rabbit secondary antibody (A-11008, ThermoFisher) diluted in 3% BSA.</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-rabbit</div><div>suggested: (Molecular Probes Cat# A-11008, RRID:AB_143165)</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">Differential expression analysis of transcriptomic data on SARS-CoV-2 infection: Several RNA-sequencing datasets of SARS-CoV-2-infected and matched control samples were obtained as follows: Vero E6 cells (Riva et al. 2020; from the GEO database, dataset ID GSE153940), A549 cells with exogenous ACE2 (A549ACE2; Blanco-Melo et al. 2020; from GEO, GSE147507), nasopharyngeal swab samples from human COVID-19 patients (Butler et al. 2020 and Lieberman et al. 2020, from the Supplementary Materials of the respective publications), single-cell data of nasopharyngeal and bronchial samples from COVID-19 patients (Chua et al. 2020; from FigShare https://doi.org/10.6084/m9.figshare.12436517), and single-cell data of bronchoalveolar lavage fluid from COVID-19 patients (Liao et al. 2020; obtained following instructions in https://github.com/zhangzlab/covid_balf).</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">For the Vero E6 and A549ACE2 data, we performed differential expression (DE) analysis of virus-infected vs control samples with the DESeq2 R package (Love et al. 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><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Calculation of weighted DE score: Each of 140 candidates have the same or different significant DE genes from six different transcriptomic datasets - in vitro Vero E6 (Riva et al. 2020), in vitro A549ACE2 cells (Blanco-Melo et al. 2020), two in vivo Bulk Swab datasets (Butler et al. 2020 and Lieberman et al. 2020) and two in vivo single-cell RNA-seq datasets (Chua et al. 2020 and Liao et al. 2020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>A549ACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Targeted siRNA screen: Screen: To evaluate the effect of the 26 predicted targets on viral replication and cell viability, a targeted siRNA screen was conducted using human Caco-2 cells (ATCC)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Caco-2</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">Differential expression analysis of transcriptomic data on SARS-CoV-2 infection: Several RNA-sequencing datasets of SARS-CoV-2-infected and matched control samples were obtained as follows: Vero E6 cells (Riva et al. 2020; from the GEO database, dataset ID GSE153940), A549 cells with exogenous ACE2 (A549ACE2; Blanco-Melo et al. 2020; from GEO, GSE147507), nasopharyngeal swab samples from human COVID-19 patients (Butler et al. 2020 and Lieberman et al. 2020, from the Supplementary Materials of the respective publications), single-cell data of nasopharyngeal and bronchial samples from COVID-19 patients (Chua et al. 2020; from FigShare https://doi.org/10.6084/m9.figshare.12436517), and single-cell data of bronchoalveolar lavage fluid from COVID-19 patients (Liao et al. 2020; obtained following instructions in https://github.com/zhangzlab/covid_balf).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FigShare</div><div>suggested: (FigShare, RRID:SCR_004328)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For the Vero E6 and A549ACE2 data, we performed differential expression (DE) analysis of virus-infected vs control samples with the DESeq2 R package (Love et al. 2014).</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">Annotation of the final SL-based candidate target gene list: The predicted targets (140 candidates) were mapped to known drugs (clinically approved and experimental/ investigational) that target (i.e. inhibit) them using drug target annotation from DrugBank (Wishart et al. 2018).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><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 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: 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">NCT04518735</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">Evolution of COVID-19 in Anticoagulated or Antiaggregated Pa…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04844658</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">Covid-19, Hospitalized, PatIents, Nasafytol</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04578158</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">Trial to Study the Adjuvant Benefits of Quercetin Phytosome …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04377789</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">Effect of Quercetin on Prophylaxis and Treatment of 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.

      </footer>

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    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.14.460408
  47. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.11.21263428
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.11.21263428: (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 Review and IRB Approval: Our study protocol (Protocol Number 21-026) was reviewed and approved by the Institutional Review Board of Providence College on January 15, 2021.<br>Consent: An informed consent statement was included in the survey instrument to welcome respondents who had clicked on the anonymous survey link provided by Qualtrics.</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: All statistical analyses were conducted using Statistical Package for the Social Sciences (SPSS) version 27.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Statistical Package for the Social Sciences</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div><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 has several limitations. As we already noted above, the use of an open-access online survey may result in sampling bias so we cannot generalize our findings to the entire Filipino population (Wyatt, 2000; Eysenbach & Wyatt, 2002). It is notable that young people aged 18-30 years, who make up around 28% of the population of the Philippines (https://www.populationpyramid.net/philippines/), constitute 52.4% of our respondents. Unexpectedly, however, senior citizens aged 61-89 years of age, who constitute 8% of the country’s population are also over-represented with 11.8% of the respondents. Furthermore, the responses were based on self-report and may be subject to self-reporting bias and a tendency to report socially desirable responses especially in a strongly collectivist society like the Philippines. One final limitation of our study is the bias associated with the assessment of acceptance and WTP for a hypothetical COVID-19 vaccine before any concrete vaccines actually exist (Schmidt & Bijmolt, 2019). We therefore intend to undertake a follow-up survey once the vaccine rollout in the country has stabilized. Nonetheless, despite these shortcomings, we believe that our findings will provide insights to support the vaccine rollout of the COVID-19 vaccines in the Philippines by helping public health authorities to understand vaccine demand and vaccine hesitancy in the country. Indeed, based on these findings, we inaugurated the UST-CoVAX public awareness campaign that ...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.11.21263428
  48. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263448
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263448: (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>

    Visit annotations in context

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    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263448
  49. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263291
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263291: (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 mean ages of the COVID-19 and non-Covid-19 control groups are 77.5 (SD 12.9) and 83.9 (SD 8.9) respectively (ns); each group has 9 females and 11 males.</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 computed soft-thresholding power (β), using the pickSoftThreshold function.</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">Sequencing libraries were prepared with 100 ng of total RNA using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina, Inc. cat # 20040529) following the manufacturer’s protocol.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Ribo-Zero Plus</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After sequencing, FASTQs files were aligned to the Human Reference Genome HG38 using STAR 105, and summarized at the gene level with HTSeq.</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><div style="margin-bottom:8px"><div>HTSeq</div><div>suggested: (HTSeq, RRID:SCR_005514)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Quality controls were conducted using MultiQC software 106 and Principal Component Analysis (PCA).</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">Differential gene expression was calculated between the COVID-19 samples and the controls using DEseq2, adjusting for age at death, sex, brain tissue source (Banner or Mayo Clinic) and neuropathologically-determined presence or absence of a diagnostic level of a major neurodegenerative disease.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>DEseq2</div><div>suggested: (DESeq2, RRID:SCR_015687)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pathway analysis was conducted on the DEGs using a hypergeometric statistic referencing the REACTOME database as implemented in the clusterProfiler R package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>REACTOME</div><div>suggested: (Reactome, RRID:SCR_003485)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The eigengenes were compared by module between COVID-19 positive and controls using a linear model as implemented in limma, adjusting the p-values for multiple testing by accounting for the number of modules using the FDR method.</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">Finally, the top hub genes in the coexpression modules were identified using the function chooseTopHubInEachModule as implemented in the WGCNA package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>WGCNA</div><div>suggested: (Weighted Gene Co-expression Network Analysis, RRID:SCR_003302)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pathway analysis was conducted using the genes significantly correlated with pseudotime by means of the clusterProfiler R package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>clusterProfiler</div><div>suggested: (clusterProfiler, RRID:SCR_016884)</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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263291
  50. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263386
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263386: (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">In the present study 30 random samples were taken from the whole period.</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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263386
  51. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263158
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263158: (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 project was approved by the Monash University Human Research Ethics Committee (#ID: 24449).<br>Consent: The first page of the survey described the study, its purpose, and advised readers that continuing to the next page would be an indicator of consent to participate 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">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 used STATA SE/v16.</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 to our study include that this the survey was only available in English, which is likely to have reduced representation of ethnic groups. Internet access was required, which may account for the increased representation of those in the least disadvantaged quintile. Furthermore, since we rely on self-reported behaviour, there is the risk of a social desirability bias, with participants potentially over-reporting socially desirable traits in their responses and the voluntary nature of the survey makes it prone to a selection bias. (9, 42) There is a paucity of studies on what influences people to consider taking the vaccine in Australia in 2021, where access to the SARS-CoV-2 vaccines is increasing, but still limited by age and occupation at the time of the survey. Since this survey, the rapid emergence of the highly transmissibility Delta variant, the major challenges of large scale, extended lockdowns escalating the imperative for rapid vaccination, and highlighting the importance of work in this field. Behavioural research such as the iCARE study can inform policymakers in understanding the public’s knowledge, attitudes, perceptions and beliefs towards the SARS-CoV-2 vaccine, which in turn drive their behaviours including vaccination and can aid with targeting public health messages. (21)

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263158
  52. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263486
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.13.21263486: (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 separately for their participation in the screening and, if applicable, when they participated in the qualitative interview.<br>IRB: The ethical review board at the Medical Faculty, Heidelberg University, Germany approved this study (S-141/2021).</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, our study also has limitations. First, only parents and students who had decided to voluntarily participate in the overarching screening program could be recruited for interviews; critical voices therefore might be underrepresented in the data on parents and their children. Additionally, as RDTs for SARS-CoV-2 have been introduced in Germany on a large scale in recent months, generalizability of our results to other countries where RDTs were less present in the public discourse might be limited. RDT-based screening is an acceptable and easily scalable intervention to decrease risk of transmissions at schools and facilitate face-to-face teaching amidst a pandemic. Policymakers should ensure comprehensive capacity building for testing, fit-for-purpose training materials for all age levels and train-the-trainer programs to enable scale up of universal screening. Furthermore, consistent communication on regulations and readily available support networks (hotlines via phone or email) can reduce burden for school staff and families.

      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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263486
  53. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.11.21262855
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.11.21262855: (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: 2.2 Search strategy: We systematically searched databases including Medline (via PubMed), Web of Science, World Health Organization (WHO) COVID-19 database, and China National Knowledge Infrastructure (CNKI), from their inception to 23 July 2021 to find out original studies related to the safety, immunogenicity, and efficacy of COVID-19 vaccine in children or adolescents.</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">2.4 Data extraction: The following data was extracted from the original studies: 1) basic information: publication date, country, study design, name of vaccine; 2) participants information: age, sample size, female/male number; and 3) outcome information: safety, immunogenicity, and efficacy of COVID-19.</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 study design was limited to primary studies, including randomized clinical trials (RCTs), non-RCTs or observational studies.</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 addition, the Cochrane Handbook for Systematic Reviews of Interventions was followed to develop this systematic review [14].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Cochrane Handbook</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">2.2 Search strategy: We systematically searched databases including Medline (via PubMed), Web of Science, World Health Organization (WHO) COVID-19 database, and China National Knowledge Infrastructure (CNKI), from their inception to 23 July 2021 to find out original studies related to the safety, immunogenicity, and efficacy of COVID-19 vaccine in children or adolescents.</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></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We first developed a search strategy for Medline after several attempts, and the search strategies for the other databases were then adapted from Medline.</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></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We also searched Google Scholar and reference lists of identified articles to avoid missing important literature.</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">We used Endnote 20.0.1 in the whole screening process.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Endnote</div><div>suggested: (EndNote, RRID:SCR_014001)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The meta-analyses are planned to be performed in RevMan 5.4.1 (The Cochrane Collaboration, 2020.) and Stata/SE 15.1 (Copyright 1985-2017 StataCorp LLC) software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RevMan</div><div>suggested: (RevMan, RRID:SCR_003581)</div></div><div style="margin-bottom:8px"><div>Cochrane Collaboration</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>StataCorp</div><div>suggested: (Stata, RRID:SCR_012763)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Microsoft Excel 16.51 (2019) was used for data processing and analysis.</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">Adobe Illustrator will be used to map ongoing clinical trials of COVID-19 vaccine in children or adolescents worldwide.</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: 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 showed that some vaccines have now been developed in pediatric populations with associated RCTs and proven protective efficacy and safety, however, these two studies both have limitations on small sample size and lack of long-term safety and immunogenicity data, for example, myocarditis and pericarditis should be closely monitored. Most cases of myocarditis and pericarditis associated with the COVID-19 vaccine were mild and mostly in males. According to Washington State Department of Health data on immunization, Schauer et al. [26] estimated a possible incidence of 0.008% in adolescents 16-17 years of age and 0.01% in those 12 through 15 years of age following the second dose. Another population to consider for vaccination of children and adolescents is multisystemic inflammatory syndrome (MIS). In April 2020, children with presentations similar to incomplete Kawasaki disease (KD) or toxic shock syndrome were documented in reports from the UK [31]. Since then, such children have been reported in other parts of the world [32-34]. This is termed multisystemic inflammatory syndrome in children (MIS-C). Study showed that the pooled proportions of MIS-C in Hispanic and Black cases were 34.6% (95% CI, 28.3–40.9) and 31.5% (95% CI, 24.8–38.1), respectively [35]. The overall mortality of MIS-C is approximately 1–2% [36]. Our review did not involve the children with MIS-C. Therefore, it is unclear whether children with SARS-CoV-2 infection complicated by multisystemic inflam...

      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">NCT04816643</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 Evaluate the Safety, Tolerability, and Immunogenici…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04796896</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">A Study to Evaluate Safety and Effectiveness of mRNA-1273 CO…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04299724</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">Safety and Immunity of Covid-19 aAPC Vaccine</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04276896</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">Immunity and Safety of Covid-19 Synthetic Minigene Vaccine</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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.11.21262855
  54. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.11.21263211
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.11.21263211: (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 study include the small size of the population and the short follow-up period. Larger studies with longer follow up and comparison between biologics with different mechanisms of action are necessary to establish the efficacy of the vaccine in these patients.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.11.21263211
  55. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263332
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.10.21263332: (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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263332
  56. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263084
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.10.21263084: (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">Study population: The National Immunization Program (NIP) provided an anonymized dataset containing individual-level data on vaccination and the occurrence of Severe Acute Respiratory Illness (SARI).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>National Immunization Program</div><div>suggested: (Centers for Disease Control and Prevention, RRID:SCR_012976)</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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263084
  57. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263487
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.13.21263487: (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">Laboratory testing: SARS-CoV-2 antibody levels were measured on venous or capillary blood samples using an ELISA detecting anti-trimeric spike IgG developed by the University of Oxford36,38.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-trimeric spike IgG</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We used linear generalized additive models (GAMs) to model anti-spike IgG antibody measurements after the first and second dose.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-spike IgG</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">After this, it used a commercialised CE-marked version of the assay, the Thermo Fisher OmniPATH 384 Combi SARS-CoV-2 IgG ELISA (Thermo Fisher Scientific), with the same antigen and colorimetric detection.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Thermo Fisher OmniPATH</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Combined nose and throat swabs were tested by PCR assays using the Thermo Fisher TaqPath SARS-CoV-2 assay at high-throughput national ‘Lighthouse’ laboratories in Glasgow and Milton Keynes (up until 8 February 2021).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Thermo Fisher TaqPath</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PCR outputs were analysed using UgenTec FastFinder 3.300.5, with an assay-specific algorithm and decision mechanism that allows conversion of amplification assay raw data into test results with minimal manual intervention.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>UgenTec FastFinder</div><div>suggested: None</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:
      Study limitations include insufficient data to include two mRNA-1273 Moderna vaccine doses in analyses. We measured anti-spike IgG antibody using a single assay, with the upper limit of quantification approached by a reasonable number of measurements (n=4189, 5.9%) in the few weeks following second BNT162b2 vaccination, potentially leading to under-estimating peak levels and over-estimating half-lives in those with the highest responses, e.g. younger age groups. As antibody responses were calibrated to a monoclonal antibody they can be compared with other studies. Neutralising antibodies and T-cell responses were not measured, but neutralisation titres were strongly correlated with anti-spike IgG titres (Figure S9). We are not currently powered to assess correlates of protection, the relationship between antibody levels and vaccine effectiveness, which requires further investigation. In summary, the second ChAdOx1 or BNT162b2 dose significantly boosts anti-spike IgG levels, and dosing interval has a limited impact on antibody response. This supports reducing the dosing interval to 8 weeks to increase protection against the widespread Delta variant; for BNT162b2, this could probably be reduced further to 3-weeks in those who have not yet received their second dose (predominantly ≤40 years). Older individuals, males, and those with long-term health conditions have substantially faster antibody declines with BNT162b2 but not ChAdOX1. Protection based on current positivity thresh...

      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">ISRCTN21086382</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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    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263487
  58. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.14.460265
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.14.460265: (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">SNORD126 knockdown: HepG2 cells were cultured in complete Eagle’s Minimum Essential Medium (EMEM from Wisent) and passaged twice a week, according to ATCC guidelines.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HepG2</div><div>suggested: CLS Cat# 300198/p2277_Hep-G2, RRID:CVCL_0027)</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">High-throughput RNA-RNA interaction analysis: The high-throughput RNA-RNA interaction datasets from PARIS (SRR2814761, SRR2814762, SRR2814763, SRR2814764 and SRR2814765), LIGR-seq (SRR3361013 and SRR3361017) and SPLASH (SRR3404924, SRR3404925, SRR3404936 and SRR3404937) were obtained from the short read archive SRA (https://www.ncbi.nlm.nih.gov/sra) using fastq-dump from the SRA toolkit (v2.8.2).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>https://www.ncbi.nlm.nih.gov/sra</div><div>suggested: (NCBI Sequence Read Archive (SRA, RRID:SCR_004891)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PCR duplicates were removed from LIGR-seq datasets using the script readCollpase.pl from the icSHAPE pipeline and the reads were trimmed using Trimmomatic version 0.35 with the following options : HEADCROP:5 ILLUMINACLIP:TruSeq3-SE.fa:2:30:4 TRAILING:20 MINLEN:25.</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">All the samples were analyzed using the PARIS pipeline as described in sections 3.7 and 3.8 from (Lu et al. 2018).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PARIS</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The RNA duplexes were assigned to genes using the annotation file described in (Boivin et al. 2018) to which missing rRNA annotations from RefSeq were added.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RefSeq</div><div>suggested: (RefSeq, RRID:SCR_003496)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Interactions from snoRNABase and from the literature that were shorter than 13 nucleotides were padded by adding their flanking sequence to respect the length threshold.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>snoRNABase</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">(Fig 2E) Building the model: The model used is a gradient boosting classifier from scikit-learn (v0.21.3) (Pedregosa et al. 2011).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>scikit-learn</div><div>suggested: (scikit-learn, RRID:SCR_002577)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The gene ontology enrichment analysis of the predicted targets was done using g:Profiler (Raudvere et al. 2019).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>g:Profiler</div><div>suggested: (G:Profiler, RRID:SCR_006809)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The number of overlaps between the predicted interactions and the eCLIP regions was computed using BEDTools intersect -s.</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">RNA-seq analysis: The resulting base calls were converted to fastq files using bcl2fastq v2.20 (Illumina) with the following options: --minimum-trimmed-read-length 13, --mask-short-adapter- reads 13, --no-lane-splitting.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>bcl2fastq</div><div>suggested: (bcl2fastq , RRID:SCR_015058)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The sequence quality was assessed using FastQC v0.11.5 (Andrews) before and after the trimming.</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 trimmed sequences were aligned to the human genome (hg38) using STAR v2.6.1a (Dobin et al. 2013) with the options --outFilterScoreMinOverLread 0.3, -- outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, -- winAnchorMultimapNmax 10, --alignEndsProtrude 5 ConcordantPair.</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">Only primary alignments were kept using samtools view -F 256 (v1.5) (Li et al. 2009).</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">The gene quantification was done using CoCo correct_count -s 2 -p (v0.2.5p1) (Deschamps- Francoeur et al. 2019).</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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">DESeq2 (Love et al. 2014) was used for the differential expression analysis.</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">The alternative splicing analysis was done using MAJIQ v2.2 and VOILA with the option --threshold 0.1 (Vaquero-Garcia et al. 2016).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MAJIQ</div><div>suggested: (MAJIQ, RRID:SCR_016706)</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: Please consider improving the rainbow (“jet”) colormap(s) used on page 50. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

      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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.14.460265
  59. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263463
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263463: (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 Scientific Research Ethics Committee of Birzeit University and by Beit-Jala 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">Data was applied and presented upon the IBM Statistical Package for the Social Sciences version 22.0.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Statistical Package for the Social Sciences</div><div>suggested: (SPSS, RRID:SCR_002865)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">(SPSS).</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 research has some limitations: first, it is a cross-sectional study holding obstacles restricting the potential bias and difficulty proofing the relation between the exposure and the outcome. Other, it is a single-centre, and its results could vary in another setting. Comprehensively, those conclusions present data supporting a conservative antibiotic administration for severely unwell COVID-19 infected patients. Our examination regarding the impacts of employing antifungals to manage COVID-19 patients can work as a successful reference for future COVID-19 therapy.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263463
  60. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263456
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263456: (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: Information on the purpose and design of the study was provided at the beginning of the on-line questionnaire, and HCWs provided informed consent to participate anonymously in the study.<br>IRB: The Ethics Committee of Department of Nursing, National and Kapodistrian University of Athens approved the study protocol (reference number; 370, 02-09-2021).</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">We subsequently decided to substantially increase the sample size to minimize random error.</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">IBM SPSS Statistics for Windows, Version 21.0.</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:
      Our findings should be interpreted in the context of several limitations. Given the convenience sample, the on-line data collection, and the unknown response rate, the extent to which our findings can be generalized to other parents is unknown. For instance, parents with limited internet access were less likely to participate in our study. There may have been an information bias in our study since vaccine uptake was self-reported and some parents may have falsely reported that they vaccinated their children. However, the fact that the questionnaire was completed anonymously may have reduced this bias. Moreover, we have explored several factors that may influence parents’ decision to vaccinate their children, but clearly there are other factors that can be studied such as psychological factors, mass media variables, impact of fake news, etc. Finally, our sample included mainly mothers with a high level of education. Thus, further studies with representative samples are critically needed to draw safer conclusions.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263456
  61. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263072
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.10.21263072: (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: All samples collected were anonymized using an alpha-numeric identification code, and the study was approved by the Local Ethics Committee.<br>Field Sample Permit: The conserving solution contained in the saliva collection tubes was provided by Biofarma Srl and it is protected by intellectual property.</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 performed by STATA 16 statistical software and statistical significance was set at p < 0.05.</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:
      Saliva samples can sometimes be difficult to handle with existing RNA extraction methods and equipment and the heterogeneity of saliva specimen can represent limitations, but there are several advantages (14, 31, 32, 36). Actually, saliva sample collection is non-invasive and can be easily performed by the individual themselves and this could reduce the risk of transmission to the sample takers (13, 14, 17). In our study, a high-concentrate saline solution was employed to collect saliva samples. The ionic strength of the solution acts as denaturing agent and destroys all protein and muco-protein’s structure, interfering on the interaction between the virus and the host cell. This observation represents an additional key aspect in mitigate the risk of infection during sample collection and allows to bypass the absence of dedicate spaces for the safe conduction of laboratory activity. In this work, the combination of the saliva self-collection procedure with the inhibiting property of Bsawb solution, could be considered an advancement to facilitate COVID-19 diagnostics. Furthermore, saliva collection facilitates sampling of children or disabled and this can increase the acceptance to routine testing practices performed at repeated intervals among high-risk populations. This modality of sample collection is easy and non-invasive, so it may be performed by non-healthcare professionals or individuals themselves who are properly instructed (13, 14, 16, 35). Overall, recent 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.

      </footer>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263072
  62. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21262527
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.10.21262527: (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 committees of the IDIAPJGol Foundation (ref. 20/067) and IGTP Health Institute (ref.</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: Sample size calculation for healthy and infected cohorts can be found in the supplementary protocol.</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 analysis reported in this work includes only participants with SARS-CoV-2 antibodies.</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></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Participants with positive anti-N serology or/and RT-PCR were also tested for antibodies against the spike (S) subunit of SARS-CoV-2 by means of an enzyme immunoassay (ELISA) for the quantitative determination of IgG class antibodies using DECOV1901.</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>DECOV1901</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:
      Semi-quantitative tests have some limitations, especially at the upper threshold, where further dilutions may be necessary. The limited availability of quantitative in vitro diagnostic techniques at the beginning of the pandemic necessitated the use of semi-quantitative techniques. Also, given the rapid development of diagnostic tests and the lack of information on them, we had to conduct an ELISA evaluation study prior to this work. In May 2020, when the study began, the techniques for measuring antibodies to SARS-CoV-2 were qualitative or semi-quantitative, so once the WHO international standard for quantification of IgG(S) antibodies was established we retrospectively analyzed a measurement of IgG spike S1 using a quantitative technique. The follow-up of IgG(S) levels stopped as participants were vaccinated, while the IgM(N) and IgG(N) continued. Key questions remain unanswered, such as whether these models kinetics will be valid in vaccinated individuals; if the kinetics and duration of anti-S antibodies are similar in natural infection and vaccination; and whether previously infected and uninfected patients will show the same kinetics after vaccination. Epidemiological modelling studies, including long-term immune monitoring, will be crucial in the case of SARS CoV-2 but also to evaluate the interactions with other coronaviruses for accurate predictions in the case of other viral coinfections (e.g. flu, other coronavirus, HIV-1) 22, 23 To conclude, we monitored three ant...

      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">NCT04885478</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">Professional's Health in Epidemiological Crisis 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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21262527
  63. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263372
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.10.21263372: (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:
      An implementation method is a more complicated operation, indicated by the scaled-up involvement of Hatzola in the UK coronavirus vaccine programme, and involves the following key considerations: Strengths and limitations: UK data has consistently suggested that ethnic and religious minorities are less likely to accept the new COVID-19 vaccinations.2 This study interviewed a wide range of people, including public health professionals, community representatives and intended beneficiaries to examine opportunities to promote high coverage levels. We recognise that some stakeholders involved in delivering the coronavirus vaccination programme were unable to be recruited. Further work should consider how collaborative organisations perceive the feasibility of localised vaccination services as outlined above.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263372
  64. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263383
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.10.21263383: (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">Model simulations were performed in Python 3.6.3 [49], while analyses were in R 3.6.1 [50].</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: 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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263383
  65. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21263476
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.13.21263476: (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: 9 This study was conducted in accordance with the guidelines of the Declaration of Helsinki and was approved by the Ethics Committee of the University of Occupational and Environmental Health, Japan (reference No. R2-079 and R3-006).<br>Consent: In addition, informed consent was obtained via a form on the internet.</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:
      This study has several limitations. First, because this was an Internet-based study, and it is uncertain whether the results are generalizable. However, we selected participants by occupation, region, and prefecture based on infection incidence to minimize bias among the participants. Second, company policies on COVID-19 identified in this study were based on participant reports; it is possible that some participants were unaware of their company’s policies. In conclusion, we showed that the absence of a company policy requesting that employees refrain from attending work while sick is significantly associated with increased attendance while experiencing fever or cold symptoms. We also showed that individuals with an unstable socioeconomic status and lower level of support from their supervisors and coworkers are more likely to attend work while sick. In the future, it is crucial to encourage more companies to establish policies that request employees to refrain from attending work while sick and to support those with unstable socioeconomic status.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21263476
  66. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263453
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263453: (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">Subsequently, we evaluated the consensus files for quality using Nextclade tool v1.5.2 (https://clades.nextstrain.org), those with more than 1% of ambiguities “Ns” had the FASTQ files imported into Geneious Prime 2021 for trimming and assembling using a customized workflow employing BBDuk and BBMap tools (v38.84) and the NC_045512.2 RefSeq as a template with carefully visually inspection.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BBMap</div><div>suggested: (BBmap, RRID:SCR_016965)</div></div><div style="margin-bottom:8px"><div>RefSeq</div><div>suggested: (RefSeq, RRID:SCR_003496)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sequences were aligned using MAFFT v7.475 (28) and then subjected to maximum-likelihood (ML) phylogenetic analysis using IQ-TREE v2.1.2 (29) under the general time-reversible (GTR) model of nucleotide substitution with a gamma-distributed rate variation among sites, four rate categories (G4), a proportion of invariable sites (I) and empirical base frequencies (F) nucleotide substitution model, as selected by the ModelFinder application (30).</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><div style="margin-bottom:8px"><div>IQ-TREE</div><div>suggested: (IQ-TREE, RRID:SCR_017254)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The temporal signal of the P.1 and P.1+ sequences was assessed from the ML tree by performing a regression analysis of the root-to-tip divergence against sampling time using TempEst (31).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>TempEst</div><div>suggested: (TempEst, RRID:SCR_017304)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">1.3 to P.1.8 plus P.1+Δ144 sampled in Brazil using the Bayesian Markov Chain Monte Carlo (MCMC) approach implemented in BEAST 1.10.4 (32) with BEAGLE library v3 (33) to improve computational time.</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><div style="margin-bottom:8px"><div>BEAGLE</div><div>suggested: (BEAGLE, RRID:SCR_001789)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">MCMC was run sufficiently long to ensure convergence (effective sample size [ESS] > 200) in all parameters estimates as assessed in TRACER v1.7 (37).</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">The maximum clade credibility (MCC) tree was summarized with TreeAnnotator v1.10 and visualized using FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>TreeAnnotator</div><div>suggested: (BEAST2, RRID:SCR_017307)</div></div><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">Graphics and statistical analyses were performed using GraphPad v9.02</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.

      </footer>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263453
  67. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263373
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263373: (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: All studies were approved by the Institutional Review Board of FAH-SYSU and written consent was obtained from all participants.<br>Consent: All studies were approved by the Institutional Review Board of FAH-SYSU and written consent was obtained from all participants.<br>Field Sample Permit: Cell isolation: Blood samples were collected into the heparinized tubes and processed right after sample 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">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 incubated with IFN-γ detection antibody (1μg/ml, MabTech, #3420-6-250), followed by Avidin-HRP (1μg/ml, Vector, #A-2004-5) and visualized using the ACE substrate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>#A-2004-5</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">, Tocris, #4536/10) and IL-2 (20 ng/ml, PeproTech, #200-02-10) for 3 days to secrete a detectable amount of antibody28, 29.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IL-2</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>antibody28</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">anti-CD69-Super Bright 436, anti-CD134 (OX40)-BV605 and anti-CD137-(4-1BB)-PE antibodies for antigen-specific T cell analysis.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD134</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD137-</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>4-1BB)-PE</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">As for phenotype analysis of SARS-CoV-2-specific T cells, cells were further labeled with anti-CCR7-APC/cy7, anti-CD45RA-BV650, anti-CXCR5-BV711 and anti-PD-1-PE/cy7 antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CCR7-APC/cy7</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD45RA-BV650</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CXCR5-BV711</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-PD-1-PE/cy7</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells were washed with PBS and then stained with the following antibody cocktail: anti-CD3-Pacific Blue™, anti-CD19-PE-CY7, anti-CD27-AF700, anti-IgD-FITC, anti-CD38-BV650, anti-IgM-BV605, anti-IgG-AF647, anti-IgA-PE all from BioLegend at 1:100 dilution.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD3-Pacific</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD19-PE-CY7</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-CD27-AF700</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-IgD-FITC</div><div>suggested: (Miltenyi Biotec Cat# 130-099-633, RRID:AB_2659770)</div></div><div style="margin-bottom:8px"><div>anti-CD38-BV650</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-IgM-BV605</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-IgG-AF647</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-IgA-PE</div><div>suggested: (Miltenyi Biotec Cat# 130-093-128, RRID:AB_1036158)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Plates were washed 3 times by PBST, processed to 100 μl/well goat HRP conjugated anti-human IgG antibody (2040-05, SouthernBiotech) at 1:3000 dilution in PBST for staining in 30 minutes at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: (SouthernBiotech Cat# 2040-05, RRID:AB_2795644)</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</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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    URL

    medrxiv.org/content/10.1101/2021.09.12.21263373v1
  68. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263451
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.12.21263451: (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.

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    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263451
  69. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263333
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.10.21263333: (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 for the SARS-CoV-2-related study, based on the WHO First Few Hundred protocol, was approved by the Medical-Ethical Review Committee of University Medical Center Utrecht (NL13529.041.06).<br>Consent: Written informed consent was received from all participants and/or from parents/guardians of minor participants (<16 years old).</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">Subsequently, plates were washed and incubated for 1 hour with 1 μg/mL anti-human IFN-γ detection biotinylated-antibody (7-B6-1, Mabtech) in PBS-0.05% casein (Sigma).</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><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">Statistics: Statistical analyses were performed using Prism V7.0 (GraphPad).</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.

      </footer>

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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263333
  70. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.08.27.457922
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.08.27.457922: (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: UK Biobank research has approval from the North West Multicenter Research Ethical Committee.<br>Consent: All participants provided written informed consent for 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">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">SAS version 9.4 TS1M5 (SAS Institute Inc.</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:
      Several limitations are notable when interpreting the results. First, UK Biobank is a volunteer cohort, and participants are likely healthier than the general population, which may limit the effect of sleep on BAs in our analysis as their AAs are expected to be lower than the general population theoretically. Furthermore, the measurement bias of air pollution must be noted. The air pollution data we used were mostly only a single measurement of the annual average outdoor air pollution level in 2010 since home addresses of the participants are unavailable during follow-up. Because the initial assessment visit of UK Biobank was from 2006 to 2010, we were unable to determine the lag or short-term (<1 month) effects of air pollution on both sleep and BAs. Also, as most individuals spend a large amount of time indoors, individual exposure to all forms of air pollution may differ from that indicated by the ambient outdoor levels we used. Additionally, self-reported sleep data was used in our analyses, misclassification of sleep behaviors was therefore inevitable. However, such bias may attenuate our findings toward the null and underestimate the effects we observed. Meanwhile, our sleep index dichotomized six sleep behaviors for simplicity but did not include all sleep behaviors or take the changes of sleep behaviors before and after the survey into consideration, which may cause residual bias to some extents. Last, participants in this study were mostly of European descent, which ...

      Results from TrialIdentifier: No clinical trial numbers were referenced.

      Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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

    URL

    biorxiv.org/cgi/content/10.1101/2021.08.27.457922
  71. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.03.21263105
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.03.21263105: (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.</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 participants and sample collection: The study participants were enrolled in the ACTIV-2/AIDS Clinical Trials Group (ACTG) A5401 phase 2 randomized, placebo-controlled trial of bamlanivimab 7000mg and 700mg mAb therapy.</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">IgG was detected by incubation with MSD SULFO-TAG anti-IgG antibody.</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><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 quantitative Laboratory Developed Test (LDT) was developed utilizing open mode functionality on m2000sp/rt (Abbott, Chicago, IL) by using EUA Abbott SARS-CoV-2 qualitative reagents30.</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">Raw sequence data were analyzed using PASeq v1.4 (https://www.paseq.org).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PASeq</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, data were quality filtered using Trimmomatic (v0.30), using a Q25/5 bp sliding window and a 70 bp minimum length.</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 reads were then merged with pear v0.9.6 aligned to the reference sequence using Bowtie2 v2.1.0)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pear</div><div>suggested: (PEAR, RRID:SCR_003776)</div></div><div style="margin-bottom:8px"><div>Bowtie2</div><div>suggested: (Bowtie 2, RRID:SCR_016368)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All statistical analyses were performed in GraphPad Prism (Version 9.1.1)</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: We detected the following sentences addressing limitations in the study:
      One limitation to this study is that bamlanivimab is no longer used clinically as a single agent. These results, though, provide important proof of principle for the role that drug resistance may have on virologic and clinical efficacy of SARS-CoV-2 antiviral therapies. These lessons have implications for the development of novel COVID-19 antiviral therapies and have continued relevance for other clinically-approved single agent monoclonal antibody treatments29 and for combination therapies where one agent may be ineffective due to circulating variants13. Another limitation of this study is the limited sample size of this phase 2 study, especially in the bamlanivimab 7000mg cohort. While treatment-emergent mutations were not found in ACTIV-2 participants receiving the higher 7000mg dose of bamlanivimab, they were frequently detected in the larger BLAZE-1 phase 2 trial of the 7000mg dose7. One difference between these studies was the longer duration since symptom onset for the ACTIV-2 participants, who enrolled a median of 6 days since symptom onset versus 4 days for the BLAZE-1 participants. This likely led to higher pretreatment viral loads, which we found to be a risk factor for resistance emergence. Unfortunately, baseline viral loads could not be compared between studies as the BLAZE-1 study did not use a quantitative SARS-CoV-2 viral load assay. These disparate results highlight the importance of incorporating quantitative viral load testing and resistance testing for CO...

      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">NCT04518410</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">ACTIV-2: A Study for Outpatients 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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    medrxiv.org/cgi/content/10.1101/2021.09.03.21263105
  72. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.13.460111
    1
    1. sciscore 17 Sep 2021

      SciScore for 10.1101/2021.09.13.460111: (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: Mouse studies and in vivo infections: All mouse studies were performed at the University of North Carolina (Animal Welfare Assurance #A3410-01) using protocols (#20-059) approved by the University of North Carolina Institutional Animal Care and Use 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">For Matute-Bello scoring samples were blinded and three random fields of lung tissue were chosen and scored for the following: (A) neutrophils in alveolar space (none = 0, 1–5 cells = 1, > 5 cells = 2), (B) neutrophils in interstitial space (none = 0, 1–5 cells = 1, > 5 cells = 2), (C) hyaline membranes (none = 0, one membrane = 1, > 1 membrane = 2), (D) Proteinaceous debris in air spaces (none = 0, one instance = 1, > 1 instance = 2), (E) alveolar septal thickening (< 2Å~ mock thickness = 0, 2–4Å~ mock thickness = 1, > 4Å~ mock thickness = 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">For Matute-Bello scoring samples were blinded and three random fields of lung tissue were chosen and scored for the following: (A) neutrophils in alveolar space (none = 0, 1–5 cells = 1, > 5 cells = 2), (B) neutrophils in interstitial space (none = 0, 1–5 cells = 1, > 5 cells = 2), (C) hyaline membranes (none = 0, one membrane = 1, > 1 membrane = 2), (D) Proteinaceous debris in air spaces (none = 0, one instance = 1, > 1 instance = 2), (E) alveolar septal thickening (< 2Å~ mock thickness = 0, 2–4Å~ mock thickness = 1, > 4Å~ mock thickness = 2).</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">For virus titration by plaque assay, the caudal lobe of the right lung was homogenized in PBS, and the resulting homogenate was serial-diluted and inoculated onto confluent monolayers of Vero E6 cells, followed by agarose overlay.</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">In vitro assays for antiviral activity: A549-hACE2 cells were plated at a density of 20,000 cells/well/100 μl in black-walled clear-bottom 96-well plates 24 hrs prior to infection.</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">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">Even groups (n=10, or less as indicated) of 10-week-old female BALB/c mice (Envigo; #047) were used in all in vivo efficacy studies.</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">Data was fit using a four-parameter non-linear regression analysis 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: We detected the following sentences addressing limitations in the study:
      Because of this caveat associated with our mouse model, the time in which to intervene with a direct acting antiviral and sufficiently improve outcomes is curtailed in mice as compared to humans. Our recent study with RDV exemplifies this where we found the degree of therapeutic benefit in mice infected with SARS-CoV-2 MA10 was dependent on the time of initiation (17). Here, we show that oral administration with GS-621763 prevents body weight loss, loss of pulmonary function, severe lung pathology and virus replication when administered at 12 and 24 hrs after infection. While we observed improvement in some metrics with RDV initiated at 24 hr in our prior studies (17), GS-621763 therapy initiated at a similar time comparatively improved all metrics assessed. Thus, herein we provide proof-of-concept preclinical data that the orally bioavailable ester analog of RDV GS-621763 can exert potent antiviral effects in vivo during an ongoing SARS-CoV-2 infection. Lastly, we show that GS-621763 therapy provides similar levels of protection from SARS-CoV-2 pathogenesis as MPV, an oral nucleoside analog prodrug effective against SARS-CoV-2 in mice that is currently in human clinical trials. Future directions are focused on extending these studies to evaluate the efficacy of combinations of antivirals in our models of SARS-CoV-2 pathogenesis and in other models that can evaluate the blockade of transmission such as hamster and ferret. In summary, we provide preclinical data 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.

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    biorxiv.org/cgi/content/10.1101/2021.09.13.460111
  73. runestone.academy runestone.academy
    8.13. Exercises — Foundations of Python Programming
    1
    1. wcwou 16 Sep 2021
      Write code that asks the user to input a year and output True if it’s a leap year, or False otherwise. Use if statements.

      Rewrite: you are provided with a list years of integers; create another list is_leap_year of boolean variables telling whether the corresponding integers in years are leap years or not. You don't need to ask the user for input.

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    runestone.academy/runestone/books/published/fopp/Conditionals/Exercises.html
  74. docs.neurodata.io docs.neurodata.io
    6.4. Estimating Parameters in Network Models via Spectral Methods — Hands-on Network Machine Learning with Scikit-Learn and Graspologic
    1
    1. aloftus2 16 Sep 2021
      l = RDPGEstimator(loops=False) # number of latent dimensions is not known model.fit(A) Phat = model.p_mat_

      i'd make a "d_hat" variable somewhere in this code

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    docs.neurodata.io/graph-stats-book/representations/ch6/estimating-parameters_spectral.html
  75. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.04.21262932
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.04.21262932: (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: Saliva and Faecal samples were collected from all confirmed COVID-19 patients whose pharyngeal swab sample already taken tested positive for SARS-CoV 2 by qualitative RT-PCR and consented to be part of this case study through a signed consent form that was read and administered to them.<br>IRB: 3.9 Ethical Consideration: Ethical clearance was sought or obtained from the Komfo Anokye Teaching Hospital (KATH) Institutional Review Board (KATH-IRB) through the Research and Development (R&D) Unit of 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

      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/10.1101/2021.09.04.21262932
  76. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263140
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263140: (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 aspects: The study was submitted and approved by Ethics Committee of Faculty of Medicine (Universidade Federal Fluminense) and Prontobaby Group, under number 4.100.232 dated from June 20, 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></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 statistical analysis: The two periods were analysed regarding the following variables: Total number of admitted patients (with all diseases), total number of admitted patients with confirmed COVID-19 and number of deaths A descriptive analysis was performed using 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></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 research was conducted in two reference pediatric hospitals of Rio de Janeiro which could be considered a limitation of the study, but considering that hospitals received patients from all neighborhood of the city, the results could reflect the true dynamics of virus circulation in the city. The second limitation is disponibility of different vaccines, with different rates of effectiveness and unknown effects for long-term protection against Delta variant, which was the most one prevalent in Rio de Janeiro at the moment of the current research.

      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/10.1101/2021.09.09.21263140
  77. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.14.460211
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.14.460211: (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 measurements were smoothened by 5 points through the adjacent-averaging method in Origin 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">OPLS 2005 forcefield in Desmond simulation package (v2018.4) 29 and GROMOS54A7 forcefield, utilizing the in-house cluster facility, simulation of the complex was achieved in Gromacs v5.1.2 30.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Gromacs</div><div>suggested: (GROMACS, RRID:SCR_014565)</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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    biorxiv.org/cgi/content/10.1101/2021.09.14.460211
  78. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263049
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263049: (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">The laboratory was blinded to the clinical status of the donors but not to HIV-1 infection status.</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">WHO anti SARS-CoV-2 immunoglobulin International Standard (IS) sample: In December 2020, the WHO released a well-characterized international standard for the purpose of improving comparability of results among different assays in different laboratories and reducing interlaboratory variability of anti-SARS-CoV-2 antibody assays.</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</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The intended use of the International Standard is for the calibration and harmonization of serological assays detecting anti-SARS-CoV-2 neutralizing antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV-2 neutralizing antibodies.</div><div>suggested: (Creative Diagnostics Cat# CABT-CS064, RRID:AB_2891088)</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">Transfection mixtures were added to pre-seeded HEK 293T/17 cells in T-75 flasks containing 12 ml of growth medium and incubated for 16-20 h at 37°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK 293T/17</div><div>suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">293T/ACE2-MF cells were detached from T75 culture flasks using TrypLE Select Enzyme solution, suspended in growth medium (100,000 cells/ml) and immediately added to all wells (10,000 cells in 100 µL of growth medium per well).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293T/ACE2-MF</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudovirus stock was produced in HEK 293 cells via a calcium phosphate transfection using a combination of spike plasmid (pCXAS-SARS-CoV-2-D614G) and lentiviral backbone plasmid (F-lucP.CNDOΔU3)</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><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">Pseudovirions were produced in HEK293T/17 cells (ATCC cat. no. CRL-11268) by transfection using Fugene 6 (Promega Cat#E2692) and a combination of spike plasmid, lentiviral backbone plasmid (pCMV ΔR8.2) and firefly Luc reporter gene plasmid (pHR’ CMV Luc)36 in a 1:17:17 ratio in Opti-MEM (Life Technologies).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCMV ΔR8.2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A codon-optimized version of the full-length spike gene of the Wuhan-1 SARS-CoV-2 strain (MN908947.3) (GenScript) was cloned into the Monogram proprietary env expression vector, pCXAS-PXMX, for use in the assay.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCXAS-PXMX</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudovirus stock was produced in HEK 293 cells via a calcium phosphate transfection using a combination of spike plasmid (pCXAS-SARS-CoV-2-D614G) and lentiviral backbone plasmid (F-lucP.CNDOΔU3)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCXAS-SARS-CoV-2-D614G</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">All mutations were confirmed by full-length spike gene sequencing by Sanger Sequencing, using Sequencher and SnapGene for sequence analyses.</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><div style="margin-bottom:8px"><div>SnapGene</div><div>suggested: (SnapGene, RRID:SCR_015052)</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 several limitations of this study. First, for evaluating the performance of the calibration approaches, we only considered a limited number of samples from trials of the mRNA-1273 vaccine. This potentially limits our ability to generalize findings from the calibration study to other COVID-19 vaccine platforms. We plan to assay a subset of samples from phase 3 trials of other COVID-19 vaccines to further validate the calibration approaches when those data become available. Second, to develop the calibration algorithms, both labs must have their assays performed on a common pool of independent samples that are expected to cover a similar dynamic range as the readouts requiring calibration. Access to such a common pool may be challenging for many labs. In that case, Approach 1 might be the most feasible option as long as the WHO IS sample is available in sufficient quantity. Third, for all three approaches, we focused the calibration only for titers above the lower limit of detection (LLoD) of the reference assays. Methods that account for calibration of responses below the LLoD, especially in the context of two assays having different LLoDs, are currently under development. Fourth, this study only concerns data from two specific labs measuring nAbs. Further validation is needed to investigate the performance of the three approaches applied to the calibration of other assays and/or immune responses. Although the described calibration approaches are only applied to the ...

      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">NCT04283461</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 2019-nCoV Vaccine (mRNA-1…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04470427</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 to Evaluate Efficacy, Safety, and Immunogenicity of …</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04403880</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">Characterizing SARS-CoV-2-specific Immunity in Individuals W…</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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263049
  79. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21262710
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.10.21262710: (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.<br>IRB: (Project code RC 5.17.01) and by National Ethics Committee of INMI IRCCS Lazzaro Spallanzani (Opinion No. 403 of the 2020/2021 Trial Registry).</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 cut-off to determine AO was 94 cm in men and 80 cm in women [8, 12].</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">Serological testing for SARS-CoV-2 glycoprotein-specific anti-spike (S) IgG was performed using LIAISON® assay, which measures IgG neutralizing antibodies against the Trimeric complex (IgG-TrimericS), which includes the receptor-binding-domain (RBD) and N-terminal-domain (NTD) sites from the three S1 subunits.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-spike (S) IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>N-terminal-domain (NTD</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">All statistical analyses were done with 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:
      Limitations of our study include lack of measurement of virus-specific T-cell. Anti-N antibodies were assessed only once to determine a prior SARS-CoV-2 infection. In addition, we did not evaluate pro-inflammatory markers of inflammation. Hence, our findings highlight the need to extend the duration of serological monitoring of antibody levels in infection-naïve individuals with AO, a higher risk population category in terms of possible weaker antibody response.

      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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21262710
  80. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263410
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.10.21263410: (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 ethics and research committees of Instituto Nacional de Medicina Genómica (CEI/1479/20 and CEI 2020/21).</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">We ran all tests with Thermo Fisher’s ABI QuantStudio 5 or QuantStudio 7 real-time thermal cyclers.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Thermo Fisher’s</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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263410
  81. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263251
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263251: (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 local ethics committee of CHUSJ and performed in the respect of the Helsinki declaration.<br>Consent: As such, the study was considered by the ethical committee as exempt from the need to take specific written informed consent from the patients enrolled.</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 was performed using SPSS from 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:
      This study has several limitations. Its retrospective and non-interventional nature limited the availability of follow-up samples with pre-established time-points. The lack of asymptomatic COVID19-positive patients precluded additional comparisons. Additionally, the COVID-19-negative individuals presented with heterogeneous clinical manifestations. Nevertheless, the large and well-defined cohort allowed the confirmation that COVID-19 causes more marked decreases in serum iron and increases in serum ferritin than other pathologies. More importantly, our data consolidate low serum iron, low transferrin, and high IL-6 as important predictors of disease severity in 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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263251
  82. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.03.21262691
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.03.21262691: (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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.03.21262691
  83. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263342
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263342: (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:
      4.1 Limitations: Vaccination policies in the three regions may have biased the results towards a higher numbers of adverse events reports myocarditis and pericarditis from younger vaccinees compared with older vaccinees. In each of these regions, younger people were more likely to have received mRNA vaccines, which may have contributed to higher reporting rates of myocarditis and pericarditis in younger vaccinees. The frequency of reported events per age group was presented as a crude number, and reporting rates could only be calculated as an overall estimate rather than stratified by age; based on the data available for vaccinations administered, it was not possible to determine the proportion of all vaccinees per age group who reported an event of myocarditis or pericarditis. This is very important, because it is likely that the reporting rate of myocarditis and pericarditis with mRNA COVID-19 vaccines will be higher in young people and even higher in young men if the reporting rates are stratified by age and sex. The regulatory authorities and Marketing Authorisations Holders (MAHs) need to follow up reports of these conditions with reporters to obtain as much information and make this information available publicly. Myocarditis and pericarditis following mfRNA COVID-19 vaccines is an area which requires further research. The data sources for this study were spontaneous reporting systems of the UK, US, and EEA. All spontaneous reporting systems have well-known 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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263342
  84. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21261607
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.07.21261607: (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 informed consent.<br>IRB: The study was approved by the Research Ethics Committee of the Community of Aragon (C.I. PI21/155 and COL21/000) and all patients 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">We conducted a case-control study in women diagnosed with COVID-19 during pregnancy with and without gestational hypertensive disorders.</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 perform an analysis of SARS-CoV-2 RNA levels in placental tissue and SARS-CoV-2 antibodies in umbilical cord.</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></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The SARS-CoV-2 IgG assay is designed to detect IgG antibodies to the nucleocapsid protein of SARS-CoV-2. (IgG; SARS-CoV-2 IgG Assay, Abbott Laboratories Ireland, Dublin, Ireland) and IgM+IgA antibodies (IgM+IgA; COVID-19 VIRCLIA IgM+IgA, Vircell Microbiologists, Granada, Spain).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>detect IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>SARS-CoV-2. (IgG; SARS-CoV-2 IgG Assay, Abbott Laboratories Ireland, Dublin, Ireland)</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgM+IgA antibodies (IgM+IgA; COVID-19 VIRCLIA IgM+IgA, Vircell Microbiologists, Granada, Spain)</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 SARS-CoV-2 IgG assay is designed to detect IgG antibodies to the nucleocapsid protein of SARS-CoV-2. (IgG; SARS-CoV-2 IgG Assay, Abbott Laboratories Ireland, Dublin, Ireland) and IgM+IgA antibodies (IgM+IgA; COVID-19 VIRCLIA IgM+IgA, Vircell Microbiologists, Granada, Spain).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Abbott Laboratories</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis was performed using SPSS 22.0.</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:
      The main limitation of our study is the small sample size. Further studies with a large number of patients are required to confirm the association between high SARS-CoV-2 viral load in placenta tissue and the development of HDP. Moreover, our hospital’s protocols changed as the pandemic progressed. Therefore, different methodologies have been used for viral RNA detection. As not all tests proved to be equally sensitive and specific, the use of distinct tests may have caused a discrepancy with studies published previously [13, 16, 22]. In addition, we do not have sequencing data from nasopharyngeal maternal swabs available, but all pregnant women were diagnosed before the alpha (B.1.1.7 UK) variant and delta (B.1.617.2 India) were routinely detected in our area. A final limitation to address is the fact that for each placenta we tested only a single sample. As SARS-CoV2 is not necessarily homogenously present (or absent) throughout the placenta, the identification of samples as positive or negative should be interpreted in this context. Among the strengths of the study, we highlight the inclusion of women who tested positive for SARS-CoV-2 in each of the three trimesters of pregnancy. We demonstrate a higher viral load in placental tissue in the case group than in the control group and a higher frequency of infected placentas. Besides, as SARS-CoV-2 RT-PCR test carried out at the time of birth showed all mothers tested negative, we could rule out the possibility of acute mater...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21261607
  85. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263359
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263359: (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">To inform our choice of distribution for each input variable, we gathered data from the literature on human-bat contacts, human SARSr-CoV seroprevalence, and human SARS antibody duration (see the Supplemental Material for details).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>human SARS</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:
      Limitations of AOH maps70 include the potential inaccuracy of the IUCN species ranges71, habitat suitability assignments, and elevation limits. Additionally, the map of terrestrial habitat types we used in our analyses72,73 did not include caves, an important habitat type for many bat species. We used carbonate rock outcrop data as a proxy for cave distribution and this could be ground-truthed. Our analytical framework provides a strategy that has potential for improving preparedness for emerging diseases and pandemic risk. It has produced maps that can be used to conduct more cost-effective field surveys for viral discovery programs, and estimates of spillover rates that can guide targeted human surveillance to identify clusters of cases of a new CoV infection earlier and help prevent spread. It may also give vital guidance for efforts to identify the reservoir hosts of the SARS-CoV-2 progenitor, and the sites of COVID origins or first emergence34. Our analysis pipeline and framework are based on open-source code and can therefore serve as a resource to update and modify spillover risk maps and estimates as new data become available. These could include serological surveys in people using new diagnostic assays that can detect virus-specific neutralizing antibodies to differentiate COVID-19 variants, vaccine strains, and different clades of bat SARSr-CoVs74, or data from ethnographic surveys that identify changes in bat-to-human contact as habitats are increasingly modified 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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263359
  86. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.13.21262971
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.13.21262971: (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 Institutional Ethics Committee (IEC) at All India Institute of Medical Sciences, Rishikesh (CTRI/2020/06/025593).<br>Consent: Consent was obtained electronically after the participants read the online information sheet regarding the nature and implications of 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">There was no randomization since the decision for drug prophylaxis and dosing was taken by the participants themselves as per available Government guideline and other literatures.</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:
      None of the participants on follow up showed any abnormity in electrocardiogram and fundus examination This study had few limitations. Firstly, the design of the study was a cohort study, just observing the participants taking HCQs or not. The sample size in the intervention arm was very small and we cannot exclude the possibility of a modest prophylactic effect that remained undetected. Moreover, the frequency of exposure to COVID-19 was not quantified and the drug concentrations were not monitored. The cohort comprised mostly of young and healthy healthcare workers. Therefore, the results cannot be generalised for the more vulnerable sections of the population. The study was conducted at a single centre in the North India and therefore, may not be representative of disease prevalence and exposure in other regions. The design of the study was such that the participants got themselves tested as per the clinical need only and as a result, 66 % of the total participants were never tested during the study period. Hence, asymptomatic COVID-19 infections were not accounted for. Drugs like ivermectin and antiretroviral agents have also been tried and tested for the prevention of COVID-19, but head-to-head trials have been lacking. Of these, ivermectin received governmental approval for mass distribution in various states in India.(20) However, as per the available evidence, none of these agents should be used for chemo-prophylaxis outside the context of a clinical trial.(21,22) Eve...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.13.21262971
  87. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.04.21262414
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.04.21262414: (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: Specimens were shipped from collection sites and stored frozen at Vitalant Research Institute (VRI) until panel assembly and frozen distribution.</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">Uniquely blinded identical panels were distributed to experienced testing laboratories to determine performance characteristics including sensitivity, specificity, repeatability, dilutional performance, and durability of reactivity over time.</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: All statistical analyses were performed using the R statistical programming language (v. 4.0.4, [6]) and using various packages, including the binom package for confidence intervals on proportions [7], the glm2 package [8] for regression analysis and the ggplot2 package [9] for plotting.</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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In the case of the Bio-Rad BioPlex assay (Bio-Rad, Hercules, CA), on-board dilutions were conducted by the testing lab and used to estimate reactivity in specimens where initial results were above the assay’s limit of quantitation.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BioPlex</div><div>suggested: (BioPlex, RRID:SCR_016144)</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 Wantai assay has been widely used in serosurveillance globally [25-27]; while this demonstrated lower specificity and reproducibility than the best performing assays, it performs adequately for serosurveillance with accounting for those limitations. Several other assays, including the Abbott IgG anti-N and EUROIMMUN IgG anti-S assays, have been employed in large-scale serosurveillance, but require adjustments for rapid waning and seroreversion to estimate cumulative incidence or attack rates, especially over longer periods and multiple epidemic waves. This study provides critical data that can be applied to adjust for waning in other studies. This study has several limitations. Asymptomatic cases are underrepresented in the panel as CCP donors qualify based on recovery from symptomatic infection, potentially resulting in overestimation of sensitivity. The assessment of durability of bAb detection is based on CCP donations from donors whose continued qualification required ongoing Ortho VITROS Total Ig anti-S1 reactivity. Although these CCP donors do not have documented dates of NAT-positivity, symptom onset or resolution, the first donations were generally within 1-2 months of symptom resolution [5]. To address these limitations we developed approaches to adequately characterize sensitivity and durability of reactivity. The number of specimens included in the dilutional series subpanels are not sufficient for robust assessment of endpoint dilutional sensitivity. This stud...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.04.21262414
  88. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.13.460185
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.13.460185: (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, there are limitations in our work. Many other physical and pathological factors impact the inflammation status of the lungs of patients with SARS-CoV-2 infections. For example, the genomic RNA sensor system triggers the innate immune reaction, stimulates the translation of other proteins from the genome or subgenome of the virus, and may thereby increase lung injury. Consequently, appropriated animal models can be employed for the determination of ORF7 in vivo in the future. Additionally, the effect of ORF7 on the microenvironment of the lung should not be considered alone. Instead, there should be a systematic examination of the impact of all factors and their interactions on lung inflammation.

      Results from TrialIdentifier: No clinical trial numbers were referenced.

      Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.13.460185
  89. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.13.460191
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.13.460191: (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: Animal studies were conducted in compliance with all relevant local, state, and federal regulations and were approved by the Bioqual Institutional Animal Care and Use Committee (IACUC).<br>IACUC: Animal studies were conducted in compliance with all relevant local, state, and federal regulations and were approved by the Bioqual 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">Animals, virus stocks, and study design: 21 outbred Indian-origin adult male and female rhesus macaques (Macaca mulatta) ages 6-14 years old were randomly allocated to groups.</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, virus stocks, and study design: 21 outbred Indian-origin adult male and female rhesus macaques (Macaca mulatta) ages 6-14 years old were randomly allocated to groups.</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 immunologic and virologic studies were performed blinded.</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">ELISPOT plates were coated with mouse anti-human IFN-γ monoclonal antibody from BD Pharmigen at 5 µg/well and incubated 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><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 WA1/2020 (USA-WA1/2020; BEI Resources; NR-5228) challenge stock was grown in VeroE6 cells and deep sequenced as described previously (33).</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">Briefly, the packaging plasmid psPAX2 (AIDS Resource and Reagent Program), luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene), and spike protein expressing pcDNA3.1-SARS CoV-2 SΔCT of variants were co-transfected into HEK293T cells by lipofectamine 2000 (ThermoFisher).</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 mixture was incubated at 37°C for 1 h before adding to HEK293T-hACE2 cells.</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">Briefly, the packaging plasmid psPAX2 (AIDS Resource and Reagent Program), luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene), and spike protein expressing pcDNA3.1-SARS CoV-2 SΔCT of variants were co-transfected into HEK293T cells by lipofectamine 2000 (ThermoFisher).</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>pLenti-CMV</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pcDNA3.1-SARS</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The gene fragment was subsequently cloned into a pcDNA3.1+ expression plasmid using restriction site cloning (Integrated DNA Technologies).</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">Statistical analyses: Comparisons of virologic and immunologic data was performed using GraphPad Prism 8.4.2 (GraphPad 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><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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    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.13.460191
  90. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.13.460163
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.13.460163: (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: The authenticity of Vero E6 cells was verified through STR profiling by ATCC.<br>Contamination: The cells were tested negative for 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">The full-length viral RNA transcripts were electroporated into 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><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 analyses were performed by Graphpad Prism 9 for all experiments as detailed in legends to individual figures.</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:
      One limitation of this study is the potential for mutations to alter neutralization by affecting spike function rather than antigenicity (e.g., mutation P681R that improves viral replication through enhanced spike processing), despite the variant viruses exhibiting specific infectivities similar to that of the original USA-WA1/2020 virus on Vero E6 cells. Another limitation is that the study focuses only on the effect of spike glycoprotein mutations on neutralization in cell culture. Mutations outside the spike gene may also alter viral replication and/or host immune response. The susceptibility of Delta, Delta plus, Lambda, and other variants to BNT162b2-elicited neutralization indicates that antigenic change does not yet appear to be the major mechanism of increased Delta variant pathogenicity or spread. This finding suggests that changing the strain of the spike glycoprotein encoded by the vaccine may not be the most effective response to the emergence and spread of the Delta variant. Nevertheless, Pfizer and BioNTech are preparing for the possibility that a strain change may someday be necessary by testing prototype, antigenically updated vaccines. The data in this paper support the ongoing BNT162b2 mass immunization strategy to control the variants and to minimize the emergence of new variants. Increasing the vaccination rate in the population, together with implementing public health measures, remains the primary means to end 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.

      </footer>

    Visit annotations in context

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.13.460163
  91. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.14.460275
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.14.460275: (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 protocols were reviewed and approved by the University of Kentucky Institutional Animal Care and Use Committee and adhere to the guidelines of the National Institutes of Health.</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">Primary isolates of lung ATII cells: Alveolar type II (ATII) cells were isolated from male mice as described previously.(27) Briefly, lungs were removed and digested in dispase, the resulting cell suspension was filtered, and ATII cells were separated by differential adherence to culture plates coated with exclusion antibodies.(28, 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><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">3T3-L1 adipocytes: Murine 3T3-L1 cells were obtained from ATCC (CL-173) and maintained in DMEM containing fetal bovine serum (FBS, 10%).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>3T3-L1</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: To define sex differences in mRNA abundance of ACE2 and associated cell machinery, male and female Ldlr-/- mice (2 months of age; n = 4 mice/group/sex) were obtained from the Jackson Laboratory.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Ldlr-/-</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">ReliOn), 3-isobutyl-1-methylxanthine (0.5 mM, Catalog I6879, Sigma-Aldrich), dexamethasone (1.0 μM, Catalog# 194561, MP Bio), and rosiglitazone (2 μM; Catolog# 194561, Sigma-Aldrich) for three days.</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">Data were analyzed and graphed using GraphPad Prism 9.0.2 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

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.14.460275
  92. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263347
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263347: (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">Here, the Countries/ Territories with missing entries were omitted, and 98 countries randomly fitted to top variable indices of correlation coefficient for unbiased cause-effect relationships.</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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263347
  93. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.14.459961
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.14.459961: (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: All experiments involving SARS-CoV-2 or its derivatives were performed in Biosafety Level 3 (BSL-3) facilities at the Medical University of Vienna and performed after approval by the institutional review board of the Austrian Ministry of Sciences (BMBWF-2020-0.253.770) and in accordance with the directives of the EU.</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: Filter samples were analyzed for levels of APN01 using high performance liquid chromatography (HPLC) with UV wavelength detection according to a validated method.</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">After one-hour incubation at 37°C, the dilutions were transferred to wells containing Vero E6 target cells (MOI 0.001).</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">Activity of APN01 in a mouse model of SARS-CoV-2 infection: Ten-week-old BALB/c mice (Charles River) received daily intranasal treatments with 100 µg APN01 or the respective dilution of vehicle in endotoxin-free PBS (Gibco).</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">Blank well readings were subtracted from sample dilution readings, and nonlinear regression to derive EC50 values was performed through a 4-parameter logistic equation by GraphPad Prism v.</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:
      A limitation of our toxicology results is that only a single species of experimental animals is included. Additional confidence in the results could be generated by including non-human primates in the analysis. Of note, mice also did not show any signs of pathologies when they received APN01 or mouse soluble ACE2 into their respiratory system for 5 day efficacy studies. Moreover, the prior experience in clinical administration of APN01 in severe COVID-19 patients via the i.v. route, without serious adverse events (manuscript in preparation), supports moving ahead with Phase I testing using a conservative dose escalation strategy. A starting clinical dose of ¼ the maximum feasible concentration for 15 minutes provides an estimated 100-fold safety margin assuming 100% aerosol deposition when compared to the NO(A)EL observed in dogs. Escalation to twice per day and then increasing concentrations of ½ to the maximum feasible concentration is the anticipated design. A Phase I trial for safety and tolerability of aerosolized APN01 in healthy volunteers is currently underway (NCT number pending) which will be followed by Phase II trials in individuals infected with SARS-CoV-2. The latter trials will use viral clearance as the primary endpoint with severe disease and hospitalization as secondary endpoints. In summary, our study demonstrates both the potent preclinical activity of locally administered APN01 in a mouse model of COVID-19 as well as the feasibility and excellent safety p...

      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><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04647695</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">IFN-beta 1b and Remdesivir for COVID19</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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.14.459961
  94. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.03.21262757
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.03.21262757: (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">The definition for asymptomatic and symptomatic SARS-CoV-2 cases Suspected COVID-19 case: Individuals who have any one of the epidemiological histories, and meet any two of the clinical manifestations; if there is no clear epidemiological history, meet any 2 of the clinical manifestations, and the SARS-CoV-2-specific IgM antibody is positive; or meets 3 of the clinical manifestations.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2-specific IgM</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 IgG antibody turns from negative to positive or the IgG antibody titer in the recovery phase is 4 times or more higher than that in the acute phase.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2-specific IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgG</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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.03.21262757
  95. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263341
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263341: (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 calculations were carried out using SPSS V26.</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:
      Despite these limitations, group sizes were sufficient to enable comparisons (although not to the level of specific ethnic groups) and, while not providing population-level prevalence data, the sample does enable, for the first time, identification of risk factors to inform future practice and policy. Bereaved people reported worse experiences in relation to hospital and care home deaths than deaths at home or hospice, as in pre-pandemic studies25-28. In the first ten weeks of the pandemic in the UK, deaths in care homes increased by 220%, and home and hospital deaths by 77% and 90%, respectively, while hospice deaths fell by 20%29. The increase in home deaths was sustained30 and hospices shifted their resources to the community31. Our findings suggest that despite the rise in home deaths during the pandemic, they were associated with better experiences of end-of-life care than deaths in other settings, indicating that primary and community care services were successful in supporting home deaths, particularly in light of the additional pressures on services32. The finding that COVID-19 deaths were associated with poorer end-of-life and early bereavement experiences lends some support to the hypothesis that the pandemic will increase levels of prolonged grief disorder and other longer-term poor bereavement outcomes. Among the COVID-19 bereaved, such outcomes might be explained by the higher likelihood of poor end-of-life care experiences when a death is unexpected as well as t...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263341
  96. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263296
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.08.21263296: (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">Seroprevalence survey (i.e., serosurvey) in the context of SARS-CoV-2 are large-scale studies aimed at estimating the true prevalence of SARS-CoV-2 (i.e., the cumulative percent infected over a period of time) within the target population utilizing serology testing for IgG or IgM antibody presence (18) scaled to the level of a geographic location (e.g., nationwide, statewide, citywide, or districtwide), a community, or a smaller group.</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><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">IFR[text word] OR infection*[text word] OR CFR[text word] OR case*[text word] OR transmission*[text word] OR mortalit*[text word] OR mortality[mesh] OR fatalit*[text word] OR lethalit*[text word] OR death*[text word] OR burden[text word] OR underreporting[text word] OR “under-reporting”[text word] OR seroprevalence[text word] OR serosurvey[text word] OR serology[text word] OR serology[mesh] OR seroconversion[text word] OR seroconversion[mesh] OR “serosurveillance”[text word] OR Seroepidemiologic studies[mesh] OR seroepid*[text word] OR seropositiv*[text word] OR antibod*[text word] OR antibodies[mesh] OR surveillance[text word] OR SIR[text word] OR SEIR[text word] OR “susceptible-exposed-infected-removed”[text word] OR “susceptible-infected-removed”[text word] (1 AND 2 AND 3) Embase (Elsevier) Date searched: 7/3/2021 Number of results: 1,119 Date filter: 2020 to 2021 Other filters applied: Embase only and not Medline (as Medline is included in PubMed) 1. covid-19:ti,ab,kw OR COVID19:ti,ab,kw OR SARS-CoV-2:ti,ab,kw OR SARS-CoV2:ti,ab,kw OR “severe acute respiratory syndrome coronavirus 2”:ti,ab,kw OR 2019-nCoV:ti,ab,kw OR 2019nCoV:ti,ab,kw OR coronavirus:ti,ab,kw OR ‘Coronavirinae’/exp OR ‘coronavirus disease 2019’/exp 2. india:ti,ab,kw OR ‘india’/exp OR indian:ti,ab,kw OR pakistan:ti,ab,kw OR pakistani:ti,ab,kw OR ‘pakistan’/exp OR bangladesh:ti,ab,kw OR bangladeshi:ti,ab,kw OR ‘bangladesh’/de OR nepal:ti,ab,kw OR ‘nepal’/de OR “sri lanka”:ti,ab,kw OR “sri lankan”:ti</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>covid-19:ti</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">To identify relevant papers, we searched four databases: PubMed, Embase, Global Index Medicus, and isearch for preprints (encompassing bioRxiv, medRxiv, and SSRN).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Embase</div><div>suggested: (EMBASE, RRID:SCR_001650)</div></div><div style="margin-bottom:8px"><div>bioRxiv</div><div>suggested: (bioRxiv, RRID:SCR_003933)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">IFR[text word] OR infection*[text word] OR CFR[text word] OR case*[text word] OR transmission*[text word] OR mortalit*[text word] OR mortality[mesh] OR fatalit*[text word] OR lethalit*[text word] OR death*[text word] OR burden[text word] OR underreporting[text word] OR “under-reporting”[text word] OR seroprevalence[text word] OR serosurvey[text word] OR serology[text word] OR serology[mesh] OR seroconversion[text word] OR seroconversion[mesh] OR “serosurveillance”[text word] OR Seroepidemiologic studies[mesh] OR seroepid*[text word] OR seropositiv*[text word] OR antibod*[text word] OR antibodies[mesh] OR surveillance[text word] OR SIR[text word] OR SEIR[text word] OR “susceptible-exposed-infected-removed”[text word] OR “susceptible-infected-removed”[text word] (1 AND 2 AND 3) Embase (Elsevier) Date searched: 7/3/2021 Number of results: 1,119 Date filter: 2020 to 2021 Other filters applied: Embase only and not Medline (as Medline is included in PubMed) 1. covid-19:ti,ab,kw OR COVID19:ti,ab,kw OR SARS-CoV-2:ti,ab,kw OR SARS-CoV2:ti,ab,kw OR “severe acute respiratory syndrome coronavirus 2”:ti,ab,kw OR 2019-nCoV:ti,ab,kw OR 2019nCoV:ti,ab,kw OR coronavirus:ti,ab,kw OR ‘Coronavirinae’/exp OR ‘coronavirus disease 2019’/exp 2. india:ti,ab,kw OR ‘india’/exp OR indian:ti,ab,kw OR pakistan:ti,ab,kw OR pakistani:ti,ab,kw OR ‘pakistan’/exp OR bangladesh:ti,ab,kw OR bangladeshi:ti,ab,kw OR ‘bangladesh’/de OR nepal:ti,ab,kw OR ‘nepal’/de OR “sri lanka”:ti,ab,kw OR “sri lankan”:ti</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>PubMed</div><div>suggested: (PubMed, RRID:SCR_004846)</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 leads us to the limitations of the meta-analysis presented herein. Limitations of Meta-analysis: We were not able to incorporate Bangladesh, Nepal, Pakistan, nor Sri Lanka in the meta-analysis presented in this paper as no eligible studies were available for these countries (aside from Pakistan, which had 2 included seroprevalence surveys), as previously discussed in the Results section. There were insufficient age-as well as sex-disaggregated IFRs for India (and for the neighboring countries) to examine heterogeneity in IFR estimates by either demographic. Furthermore, although age and sex-disaggregated seroprevalence estimates were extracted from the included studies, disaggregated deaths and cases by these demographics are not available for India nor for its states, cities, nor districts, at the time of this review. Additionally, there were insufficient data on excess deaths for select states (e.g., Jammu and Kashmir and Puducherry) that precluded our ability to compute IFR2 for studies encompassed in these states and, as such, we were unable to include these studies in the meta-analysis for the regional IFR2. Additionally, we caution that several of the included studies in the quantitative synthesis are in the process of being peer-reviewed, and so multiple underlying datapoints have not yet been verified. Lastly, we note that global studies that examine India along with multiple other countries (as part of a country level global analysis) but do not explicitly refer...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.08.21263296
  97. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21262725
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.07.21262725: (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: Research Subjects: Blood was collected from 67 volunteers with informed consent, who had been previously infected with SARS-CoV-2 corona virus or been vaccinated against the virus or been unexposed.</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">Qualitative Detection of anti-SARS-CoV2 Antibodies in Human Serum: Anti-SARS-CoV2 antibodies in human serum or in a drop of full blood were detected by a two-step incubation antigen sandwich ELISA using the RBD of the S1 protein of the SARS-CoV2 virus.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV2</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 vectors were transfected into Flip-InTM-Chinese hamster ovary (CHO) cells (Life Technologies) using the Lipofectamine 2000 Reagent (Invitrogen, #11668-019), together with the plasmid pOG44, providing site-directed recombination.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Flip-InTM-Chinese hamster ovary ( CHO )</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 RBD-His and NP-Strep: The various CHO-spike-RBD-His cells and CHO-spike-NP-Strep cells were grown in suspension in ProCHO5, 4 mM L-glutamine and 600 µg/ml Hygromycin B in flasks to submaximal density at 37°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>CHO-spike-NP-Strep</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">Life Technologies) by adding the signal sequence METPAQLLFLLLLWLPDTTG at the beginning and cloned into the plasmid vector pcDNA5/FRT via BamHI and XhoI.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA5/FRT</div><div>suggested: RRID:Addgene_31983)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The resulting vectors were called pcDNA5/CoV-RBD-His and pcDNA5/CoV-NP-Strep, respectively, and allow for expression and secretion of RBD-His or NP-Strep into the culture medium of mammalian cells under the control of the human cytomegalovirus (CMV) immediate-early enhancer/promoter.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pcDNA5/CoV-RBD-His</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pcDNA5/CoV-NP-Strep</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The vectors were transfected into Flip-InTM-Chinese hamster ovary (CHO) cells (Life Technologies) using the Lipofectamine 2000 Reagent (Invitrogen, #11668-019), together with the plasmid pOG44, providing site-directed recombination.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pOG44</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">Then, IC50 values minus blank values were calculated for each sample using results from all dilutions with SigmaPlot v14.5.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SigmaPlot</div><div>suggested: (SigmaPlot, RRID:SCR_003210)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical Analysis: Statistical analysis was performed using SPSS software version 26.</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: 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21262725
  98. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.12.21263447
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.12.21263447: (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 authors assert that all procedures contributing to this work comply with the ethical standards of the relevant national and institutional committees on human experimentation and with the Helsinki Declaration of 1975, as revised in 2008.<br>Consent: Written informed consent was obtained from all study subjects.</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">All genotyped participants of the PsyCourse Study with a diagnosis from the psychotic-to-affective spectrum as well as controls (n=1346, age [mean±SD] 47.75±13.81, 47.39% female) or for whom an extraversion score was available (n= 1190) were included in the analysis.</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">DNA samples of PsyCourse participants were genotyped on the Illumina Infinium PsychArray, and imputed using the 1000 Genomes project dataset as reference panel (for details, see(23)).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>1000 Genomes</div><div>suggested: (1000 Genomes Project and AWS, RRID:SCR_008801)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PRS scoring and association testing using linear or ordinal regressions were implemented in PLINK (version 1.9) and R (version 4.0.3).</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: We detected the following sentences addressing limitations in the study:
      An additional limitation lies in the fact that no direct risk assessment was possible for the individuals with individual-level data on major psychiatric disorders and personality traits since no COVID-19 phenotypes were available. Lastly, we are unable to fully exclude sample overlap especially on the side of the controls used in the included GWAS. However, LDSC results should be robust to both of these overlaps(18). Hypothetically, it is possible that—for example—only a small subset of common genetic risk factors in a given pathway relevant to major psychiatric disorders or personality traits is associated with COVID-19 susceptibility. Although we cannot fully exclude all such effects, our data suggest that non-genetic factors play important roles in the interplay between personality traits and COVID-19. A direct genetic overlap is unlikely to contribute to the increased, but yet-unexplained COVID-19 risk seen in individuals with a psychiatric diagnosis prior to SARS-CoV-2 infection(4) but a shared genetic risk could still be mediated by intermediate phenotypes such as, for example, lower socio-economic status or educational attainment in those with severe psychotic disorders. As a consequence, an even greater focus should be placed on psychosocial interventions, ensuring the best treatment for individuals with severe psychiatric disorders as well as targeted measures of prevention and psychoeducation for individuals with personality determinants that place them at an incre...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.12.21263447
  99. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.03.21262841
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.03.21262841: (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 approved by the local Research Ethics Committee and written informed consent was waived.<br>Consent: This study was approved by the local Research Ethics Committee and written 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">Positive α-sma cells were evaluated in ten different, randomly selected high-power fields of the lungs.</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">Histological evaluation was performed by specialized pulmonary pathologists (MLB, VLC, ATF) blinded to clinical history.</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">Immunohistochemistry for anti-alpha smooth muscle actin (α-SMA) (Abcam, ab5694) and anti-SARS-CoV-2 polyclonal antibody, developed by our group for in situ detection of SARS-CoV-2, were performed in paraffin-embedded sections of 3-μm thickness, following our lab protocol10.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-alpha smooth muscle actin (α-SMA)</div><div>suggested: None</div></div><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">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 performed with SPSS v.</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: 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.03.21262841
  100. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263139
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263139: (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">Estimating time-varying, severity-specific assay sensitivities: To estimate time-varying, severity-specific assay sensitivities, we used longitudinal antibody response data collected from a cohort of participants with PCR-confirmed SARS-CoV-2 through the University of California, San Francisco-based Long term Impact of Infection with Novel Coronavirus (LIINC) natural history study (NCT04357821).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>NCT04357821</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">We used the R statistical software (version 3.5.3), EpiNow2 R package (version 1.2.1), and the Stan programming language (versions 2.19.3 and 2.21.2) for all analyses.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>EpiNow2</div><div>suggested: None</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:
      There are a number of caveats associated with this analysis. The accuracy of this approach hinges on the accuracy of symptom onset curves reconstructed from the selected reported time series. This limitation is not unique to seroprevalence estimation; accurate estimates of downstream metrics such as the time-varying reproduction number similarly rely on the robustness of these data streams over time (32,47). Estimation will also be sensitive to the data type chosen; for example, hospitalizations and deaths are generally more robust to temporal trends in under-ascertainment than cases, but this may be context-specific. A key consideration here is the small sample size for asymptomatically infected individuals, who potentially comprise a majority of all SARS-CoV-2 infections (48,49). While the distinction between asymptomatic versus minimally symptomatic may be difficult to define, it is imperative to better understand the magnitude and kinetics of antibody responses in this group of individuals to better understand the extent of bias in seroprevalence estimates. The decision to model asymptomatic individuals as their own severity group or aggregated with the other non-hospitalized individuals has a major effect on overall adjusted seropositivity. Our framework accounts for differences in assay sensitivity by disease severity and time, but does not explicitly incorporate other potentially important sources of variation, such as age and sex (16,50,51). Lastly, our focus has been...

      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">NCT04357821</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">Combinatorial Therapy to Induce an HIV Remission</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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263139
  101. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21262911
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.07.21262911: (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 ethics and research committees of the Instituto Nacional de Medicina Genómica (CEI/1479/20 and CEI 2020/21).<br>Field Sample Permit: Effective reproduction number estimation for variants B.1.1.222 and B.1.1.519: We grouped all sequenced samples based on the epidemiological week as the date of sample collection.<br>Consent: Verbal consent and identification were the first steps when calling each subject included in the final analysis.</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">Sequencing was performed on the MinION platform, and the final library (15 ng) was loaded onto the flow cell R.9 according to the manufacturer’s instructions.</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">A final consensus FASTA file was generated by first marking positions not covered by at least 20 reads from either group as low coverage and building a pre-consensus FASTA with BCFtools consensus, which was subsequently aligned against the reference sequence using muscle (v.3.8.1551).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BCFtools</div><div>suggested: (SAMtools/BCFtools, RRID:SCR_005227)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phylogenetic Analysis: The sequences were aligned with MAFFT (version 7.475) using the FFT-NS-2 algorithm20,21.</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">A maximum-likelihood phylogeny was calculated with FastTree (version 2.1.11) compiled with the double precision tag using a generalized time-reversible model (GTR)22,23.</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.

      </footer>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21262911
  102. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.03.21262611
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.03.21262611: (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">For instance, in the case of a gene belonging to an autosome with 2 common variants (named A and B), 3 combinations are possible (A, B, and AB), and (consequently) 3 Boolean features were defined both for the AD and AR model.</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">Library enrichment was tested by qPCR, and the size distribution and concentration were determined using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).</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">Variant calling was performed according to the GATK4[24] best practice guidelines, using BWA [25] for mapping and ANNOVAR [26] for annotating.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BWA</div><div>suggested: (BWA, RRID:SCR_010910)</div></div><div style="margin-bottom:8px"><div>ANNOVAR</div><div>suggested: (ANNOVAR, RRID:SCR_012821)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Finally, annotation was performed using Variant Effect Predictor (VEP, version 101).</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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Variants were genotyped with the GATK GenotypeGVCFs tool v4.1.8.1.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GATK</div><div>suggested: (GATK, RRID:SCR_001876)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Therefore, the genetic ancestry of the patients was estimated using a random forest classifier trained on samples from the 1000 genomes project and using as input features the first 20 principal components computed from the common variants by PLINK [27].</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">ABS(meanβ)∗count∗F Pathway enrichment analysis was made using the GSEA-preranked module (v. 7.2.4) of the Genepattern platform [26], on several pathway categories (BIOCARTA,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Genepattern</div><div>suggested: (GenePattern, RRID:SCR_003201)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">KEGG, REACTOME, GOBP, HALLMARKS, C7 and C8), limiting the size of genesets to the 10-300 range and performing 10,000 permutations.</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">The networks showing similarity of significant pathways were built using the EnrichmentMap algorithm [30] in the Cytoscape suite (v. 3.8.2) [31–32].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>EnrichmentMap</div><div>suggested: (EnrichmentMap, RRID:SCR_016052)</div></div><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.

      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/10.1101/2021.09.03.21262611
  103. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263355
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.09.21263355: (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/10.1101/2021.09.09.21263355
  104. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263196
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.07.21263196: (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">Here, 97 Countries/ Territories randomly fitted to top variable indices of correlation coefficient for unbiased cause-effect relationships (Table 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">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/10.1101/2021.09.07.21263196
  105. www.mghassany.com www.mghassany.com
    2 Multiple Linear Regression | Machine Learning
    1
    1. axelboumendil 16 Sep 2021
      r fontawesome::fa(“r-project,” fill =“steelblue”)’s

      r code has not been compiled or recognized

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    mghassany.com/MLcourse/multiple-linear-regression.html
  106. www.sciencedirect.com www.sciencedirect.com
    Physical restraint mouse models to assess immune responses under stress with or without habituation
    2
    1. scibot 16 Sep 2021
      Strain code: 028

      DOI: 10.1016/j.xpro.2021.100838

      Resource: (IMSR Cat# CRL_028,RRID:IMSR_CRL:028)

      Curator: @Naa003

      SciCrunch record: RRID:IMSR_CRL:028

      What is this?
      RRIDCUR:Missing RRID:IMSR_CRL:028
    2. scibot 16 Sep 2021
      Strain code: 027

      DOI: 10.1016/j.xpro.2021.100838

      Resource: (IMSR Cat# CRL_027,RRID:IMSR_CRL:027)

      Curator: @Naa003

      SciCrunch record: RRID:IMSR_CRL:027

      What is this?
      RRID:IMSR_CRL:027 RRIDCUR:Missing
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    sciencedirect.com/science/article/pii/S266616672100544X
  107. dl-acm-org.revproxy.brown.edu dl-acm-org.revproxy.brown.edu
    Bush - As We May Think.pdf
    2
    1. kcobey 16 Sep 2021
      Thereafter, at any time, when one of these items is inview, the other can be instantly recalled merely by tappinga button below the corresponding code space.

      It's interesting that this is seen as a core feature of the memex-- even THE core feature. There's a clear importance placed as association as a driving force of innovation, and it really begs the question-- what other parts of the internet have become "core features"? How else has connectivity permeated the space, outside the link? At its core, are we still mainly working with this link structure? I think so.

    2. lgelfond 14 Sep 2021
      At the bot-tom of each there are a numberof blank code spaces, and apointer is set to indicate one ofthese on each item. The usertaps a single key, and the itemsare permanently joined. In eachcode space appears the codeword. Out of view, but also inthe code space, is inserted a setof dots for photocell viewing;and on each item these dots bytheir positions designate theindex number of the other item.

      I'm curious how new this thinking was—I remember when we talked in class about the founder-myth and how most of these inventions built on top of one another, but the way it is presented here suggests Bush essentially invented the concept of the link as a way of navigating through material (which seems doubtful). Regardless, working through all of these ideas with hypothetical inventions that make them work I think is fascinating.

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    dl-acm-org.revproxy.brown.edu/doi/pdf/10.1145/227181.227186
  108. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.13.459777
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.13.459777: (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.
      • 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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    biorxiv.org/cgi/content/10.1101/2021.09.13.459777
  109. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.10.459410
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.10.459410: (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: Upon sorting, the cells were tested negative for mycoplasma.</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 and reagents: Mouse anti-Spike and anti-GAPDH were purchased from Genetex and Rabbit anti-N from Sino Biological (Clinisciences).</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><div style="margin-bottom:8px"><div>anti-GAPDH</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">The mouse anti-dsRNA antibody (J2) was from Jena Bioscience and rabbit anti-Calnexin from Elabscience.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-dsRNA</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-Calnexin</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 and primary cells: Huh7.5.1 (Zhong et al., 2005), Vero E6 (ECACC #85020206), Caco2, and HEK 293T cells were cultured in DMEM GlutaMAX (Thermo Fisher Scientific) supplemented with 10% fetal calf serum and penicillin-streptomycin (500 μg/ml; GIBCO).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Caco2</div><div>suggested: None</div></div><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">Vials of the Vero E6 N-Ruby3 stable cell line were conserved in liquid nitrogen in 10% DMSO.</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><div style="margin-bottom:8px"><div>N-Ruby3</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Infections of 50 000 cells were performed at MOI 2 for HCoV-229E-Renilla (as measured on Huh7.5.1 cells) and infection efficiency was analyzed one day later by measuring Renilla activity (Renilla Luciferase Assay System,</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Huh7.5.1</div><div>suggested: RRID:CVCL_E049)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ZIKV was amplified in Vero cells for 72 h in DMEM GlutaMAX (Gibco) supplemented with 2% fetal bovine serum (FBS; Dominique Dutscher), 10 mM HEPES (Thermo Fisher Scientific) and 1X penicillin-streptomycin (Gibco).</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">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">Bajar et al, Sci Rep, 2016), N was firstly amplified by PCR from the plasmid pLVX-EF1alpha-SARS-CoV-2-N-2xStrep-IRES-Puro (addgene#141391) using the sense primer 5’ TTGCGGCCGCGCCACCATGAGCGATAACG-3’ (NotI site underlined) and the antisense primer 5’-CGCCTGAGTAGAATCGGCT-3 (overlapped region underlined).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLVX-EF1alpha-SARS-CoV-2-N-2xStrep-IRES-Puro</div><div>suggested: RRID:Addgene_141391)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The resulting PCR product was ligated into the digested NotI and BamHI lentiviral plasmid pHAGE IRES puro.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHAGE IRES puro</div><div>suggested: RRID:Addgene_122202)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The resulting plasmid pHAGE N-mRuby3 IRES puro is available on Addgene (#170466).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHAGE N-mRuby3</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In parallel, a pHAGE N-mNeonGreen IRES puro was also generated (Addgene #170467).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHAGE N-mNeonGreen IRES</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Generation of stable cell line: HEK 293T cells were transfected with pxPAX2, VSV-G and pHAGE N-mRuby3 IRES puro using JetPrime</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHAGE N-mRuby3 IRES puro</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">Live cell imaging: Image acquisition was performed on an AxioObserver.Z1 inverted microscope (Zeiss) mounted with a CSU-X1 spinning disk head (Yokogawa), a back-illuminated EMCCD camera (Evolve, Photometrics) and a ×100, 1.4 NA oil objective (Zeiss) controlled by MetaMoprh.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MetaMoprh</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Images were processed using Fiji (ImageJ software version 1.51h) and quantitative analyses were performed using Bitplane Imaris x64 version 9.2.</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><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">The mean and standard deviation (SD) of the mean were plotted using GraphPad Prism version 7.04.</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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    biorxiv.org/cgi/content/10.1101/2021.09.10.459410
  110. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.11.459879
    1
    1. sciscore 16 Sep 2021

      SciScore for 10.1101/2021.09.11.459879: (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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    biorxiv.org/cgi/content/10.1101/2021.09.11.459879
  111. www.biorxiv.org www.biorxiv.org
    Global cellular response to chemical perturbation of PLK4 activity and abnormal centrosome number
    1
    1. EMBOpress 15 Sep 2021

      Note: This rebuttal was posted by the corresponding author to Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons

      Reply to the reviewers

      1. General Statements [optional]

      We thank the reviewers for their critical review of our manuscript. We are excited to see that the reviewers agree that we have presented high-quality data that advances the centrosome field and is worthy of publication following revision. The authors also agree with the reviewers that the data presentation requires improvement, that some experiments require additional replicates with robust statistical analyses and that a model or summary would help clarify the differences between previously published results and ours. We will address all these concerns in the revised version of our manuscript. The reviewer comments in their entirety can be found below in italic followed by our response in bold.

      Considering that the manuscript was very well received we believe it makes a strong candidate for publication in eLife. In terms of editors at eLife, we believe that Anna Akhmanova and Jeremy Reiter would be very well suited to handle this manuscript.

      We hope that you will concur with us that the revision plan detailed below adequately addresses the reviewers’ comments.

      2. Description of the planned revisions

      Reviewer 1, Major points

        • Previous data suggested that an important role of TRIM37 was to limit accumulation of CEP192 levels, yet here CEP192 levels appeared unchanged in TRIM37 knockout cells that stably express wild-type or RING domain mutant TRIM37. However, in agreement with previous work, transient expression of TRIM37 reduced CEP192 levels along with those of other PCM and centriole components in an E3-dependent manner. These data are rather confusing in light of the literature, and the current report does not really deal with these discrepancies but to me they suggest that high levels of TRIM37 can target multiple centrosome components for degradation, but this may be an experimental artefact.* We agree that acutely overexpressed TRIM37 results in decreased CEP192 levels and is consistent with published results. We also provide evidence that CEP192 levels are not correspondingly increased in the absence of TRIM37, nor are they decreased in a cell line that stably overexpresses FLAG-BirA TRIM37. This suggests that the decreased CEP192 (and PCNT and CEP120) after acute overexpression of TRIM37 might be short-lived or a consequence of overexpression. We will discuss this possibility more clearly in the revised mansucript. In addition, we will perform Western blots for TRIM37 in wild type cells, cells stably expressing FLAG-BirA TRIM37 and cells induced to express TRIM37-3xFLAG to more directly compare the amount of TRIM37 present in these cell lines.
      • The choice of cells for particular experiments is not always stated or explained. For instance, in Figure 3A: Trim37 KO pool used while in Figure 3B TRIM37 single KO. These are then combined with both transient and stable expression of TRIM37 mutants.*

      We apologize for this and will clarify the choice of cell lines in the results section. Importantly, because some of our results challenge previously published reports, we performed critical experiments using multiple cell lines. For example, we show that centrinone B-induced growth arrest is independent of TRIM37 E3 ligase activity using a single RPE-1 TRIM37-/- clone, an RPE-1 TRIM37-/- pool and an A375 TRIM37-/- pool. We feel this is a highlight of our work and this new data will be included in the revised version of the manuscript and will be emphasized.

      • Two different concentrations (200 nM and 500 nM) of centrinone were used to compare responses of too many or no centrosomes in RPE1 and A375 . While these concentrations result in centrosome amplification (200 nM) and loss (500 nM) in RPE1 cells, the phenotypes seem much less clear-cut in A375 cells. At 200nM 70% of cells have 0 or 1 centrioles (~35% each category) and only about 15% have centrosome amplification, whereas centrosome amplification occurs in 30% of RPE1 with 0-1 centrioles seen in fewer than 10% (Figure 4 - figure supplement 1H). Hence the different outcomes of centrinone treatment makes conclusions about cell-type specific responses difficult. This difference may be due to differences in drug uptake/efflux, PLK4 activity or in expression of other components of these pathways. In fact, 167nM centrinone B in A375 cells would have been a much closer match to the 200nM treatment of RPE-1. These points should be discussed as they impact the conclusions.*

      The reviewer rightly points out that the response to centrinone appears to differ between cell types, as shown previously (Meitinger et al., 2020 and Yeow et al., 2020), and that this difference may impact our conclusions. Although we don’t think that the major conclusions drawn will change, we will discuss these caveats within the results and discussion of the manuscript.

      • I find the different outcomes of stable versus acute expression of TRIM37 ligase mutant confusing. Here, stable expression of TRIM37 ligase mutant increases mitotic length compared to that of TRIM37 wild-type, which contradicts a recent report by (Meitinger et al. 2021). What could be the potential reason for these differences? *

      It is unclear why we obtain results that differ from Meitinger et al. We are using similar cell lines (RPE-1 hTert vs. RPE-1 hTert Cas9) with similar TRIM37 constructs (TRIM37-3xFLAG) that are induced in similar ways (both are doxycycline inducible but using different systems). For our experiment, we used a single TRIM37 KO clone. As an independent validation, we will repeat this experiment using our TRIM37 KO pools in both RPE-1 and A375 cells and discuss these results and implications.

      What could be the mechanism for TRIM37 action in regulating spindle assembly/mitotic duration and cell proliferation upon centrosome loss? How do those acentrosomal MTOCs form that decrease mitotic duration and promote proliferation?

      These are insightful questions that we feel lie at the heart of TRIM37 function. Current models posit that in the absence of TRIM37, PLK4 condensates form and are required to nucleate ectoptic accumulations of PCM components (ex. CEP192) that facilitate mitosis (Meitinger et al. 2020). A number of our findings are not consistent with this model. First, PLK4 is detected in the Cenpas/condensates only using a single antibody (Wong et al., 2015) (two other antibodies have been reported to be used (Sillibourne et al., 2010, Moyer et al., 2015) and we have used another (Millipore MABC544 clone 6H5) - none of these three detect PLK4 at the condensates). Additionally, the PLK4 signal observed is not sensitive to PLK4 siRNA (Balestraet al. 2021, Figure 4 – figure supplement 1I). In our manuscript we also provide evidence that overexpressed PLK4-3xFLAG cannot be detected (using PLK4 or FLAG antibodies) at these strucures. Moreover, our experiments using TRIM37 mutants show that Cenpas formation and ectopic PCM assembly are mechanistically distinct; Cenpas are not resolved after expression of TRIM37 C18R, yet ectopic PCM structures are suppressed (Figure 5E and G). Our data do, however, suggest that the ability to form ectopic PCM structures is inversely correlated to growth arrest activity (i.e. cells that form ectopic PCM fail to arrest). How these structures form and how they affect growth arrest are still critical, open questions. We will discuss these possibilities further in the revised manuscript.

      Do the authors find a difference in the % of cells expressing TRIM37 mutants upon stable or acute expression? This part needs a better summary, and again a table would help. I also wonder about protein expression levels; wild-type FB-TRIM37 seems to be expressed at much lower levels than the mutants in Figure 5B.

      The differences in overall abundance are not due to heterogenous expression within the population. The TRIM37 mutants are expressed in all cells after stable and acute expression. We will provide quantification of immunofluorescence images and statistics to show this. TRIM37 mediates its own degradation in an E3-dependent manner (Meitinger et al. 2021, Figure 3f). Our results are consistent with this as the TRIM37 C18R and TRIM37 __DRING mutants have a higher overall abundance compared to TRIM37 or TRIM37 D__505-709. These experiments are ongoing and we will discuss this further in the revised manuscript and provide a summary table.

      • Other means of centrosome depletion (Cenpj, SAS6 etc) would have been useful to include in the manuscript in support of E3 ligase dependent and independent roles of TRIM37. It is not essential to perform these experiment but if data are available, including these would improve the paper. *

      We will generate new data using a double TRIM37 KO, SASS6 KO line to address TRIM37 ligase-dependent and -independent functions.

      • The authors show that TRIM37 regulates PLK4 phosphorylation and that this modification could only be observed in HEK293T and not in RPE1. Why would there be a difference between HEK293 and RPE1?*

      We will address this by surveying a panel of cell lines to determine if there any cell type dependent differences in TRIM37 modification. Any potential differences will be addressed in the discussion.

      • Statistical analysis for graphs should be included. Figure 5 is ok but graphs in Figures 3, 4, 6, 7 would benefit.*

      This point is well taken. In the revised manuscript, we will ensure that all experiments are performed in biological triplicate and that proper statistical analyses are included to support our conclusions.

      • The authors characterise TRIM37 localisation. They detect it at centrosomes (as shown by Yeow et al 2021) and more specifically at the PCM, but apparently the signal is not present in all cells. They should also provide a quantification of the % of cells with centrosomal TRIM37 signal and compare this to cells expressing Flag-tagged Trim37. The specificity of the antibody signal using TRIM37-/- should be confirmed. *

      We will perform immunofluorescence experiments using wild type and TRIM37-/- cells to demonstrate the specificity of the antibody signal. We will also provide a more detailed analysis regarding TRIM37 localization noting 1) the number of cells with centrosomal TRIM37 2) cell cycle correlation with centrosomal TRIM37 and 3) a comparison with FLAG-BirA tagged TRIM37.

      Reviewer 1, Minor points

      1.Page 3: "A recent screen for mediators of supernumerary centrosome-induced arrest identified PIDDosome/p53 and placed the distal appendage protein ANKRD26 within this pathway [31]". It appears that the reference for Burigotto et al. is missing.

      This reference will be inserted.

      2.Page 6: The authors state that: TP53BP1, USP28 and CDKN1A are also suppressors in the Nutlin-3a screen and suggest that they act in a general p53 pathway. However Meitinger et al (2016) showed that depletion of TP53BP1 or USP28 did not affect the upregulation of p53 and p21 upon Mdm2 inhibition.

      Our data is consistent with previous reports that TP53BP1 and USP28 are required for cell arrest after Nutlin-3a treatment (Cuella-Martin R et al. 2016). We will discuss possible explanations for the results observed by Meitinger et al.

      3.Page 9: "First, we performed live cell imaging to measure mitotic length in cells grown in centrinone". For consistency the authors should say centrinone B here as wellI

      We will change the text to indicate using centrinone B.

      4.Page 9: "Cells lacking TRIM37 suppressed the growth arrest from 150 to 500 nM centrinone B in RPE-1 and 167 to 500 nM in A375 cells". The growth data for the A375 cells seem to be missing from the figures.

      We refer to Figure 4D and Figure 4 – figure supplement 1G that contain the RPE-1 and A375 growth data, respectively. We will modify the text to more clearly refer to the data.

      5.Page 10: "Our results confirmed that PLK4 and TRIM37 form a complex in RPE-1 cells (Figure 3G)" It appears the authors referred to the wrong figure, it should be Figure 4B.

      Our apologies. The correct figure reference will be used.

      6.Figure 1C: The nuclear p53 signal is not apparent with 500 nM centrinone B in the exemplary cells. Did the authors use thresholding to quantify p53/p21 positive cells?

      The p53 staining in centrinone-treated cells is somewhat variable. To quantify the data, we used automated image analysis and set a cut off based on p53 intensity in DMSO-treated cells to indicate p53-positive cells. To improve the figure we will repeat the experiment and use a lower magnification image to show a more representative field of cells stained for p53. The quantification pipeline will be better explained in the methods section.

      7.Figure 4D and Figure 4 - Figure supplement 1G: The graph is misleading and should not be presented as a continuous line.

      We are sorry that the reviewer finds the graph misleading. We will change the way this data is presented to make it easier to understand and to facilitate indicating statistical differences. Instead of a scatter plot of all the data, we will present the data as individual boxplots at each centrinone B concentration with statistical differences indicated. We hope this will address any confusion regarding these data.

      8.Figure 5A and C: A direct and statistical comparison mitotic timing upon expression different Trim37 mutants to wildtype and trim37-/- cells is missing

      In Figure 5A we compare RPE-1 WT to TRIM37-/- at each centrinone B concentration and within each line we compare each centrinone B concentration to DMSO. Perhaps we do not understand the reviewer’s concern here, but we do not think any comparisons are missing from this panel. In Figure 5C, we compare the mitotic lengths between cell lines expressing TRIM37 WT or TRIM37 C18R since we focus on the requirement for the E3 ligase activity of TRIM37. For this experiment we did not include a wild-type control, but we will perform statistical analyses between control cells expressing FLAG-BirA and those expressing FB-TRIM37 WT or FB-TRIM37 C18R. We hope this addresses this concern.

      9.Figure 6B: A loading control/Ponceau staining is missing as well as the quantification of protein levels

      This experiment will be repeated for proper quantification and we will include a loading control for our representative results.

      10.Figure 6D: It is unclear if the centrosomal signal intensity was quantified in interphase or mitotic cells

      The centrosomal signal was quantified in mitotic cells only. This results and figure legend will be updated to more clearly indicate this.

      11.Figure 7C: A loading control/Ponceau staining is missing

      The experiment will be repeated and a sample will be taken prior to immunoprecipitation to indicate the input amounts for each sample.

      12.Figure 2 - figure supplement 2F and G: It would help if the authors could highlight the cell line, e.g. RPE-1 (F) or A375 (G) in the venn diagrams.

      In Figure 2 – figure supplement 2G we highlight the genes found in RPE-1 and A375 screens only in the overlap of the Venn diagram using font colour. We will colour code the hits from each cell line in panels (F) and (G). We thank the reviewer for this suggestion.

      13.Figure 4 - figure supplement 1E: it appears that the BirA antibody gives only an unspecific signal. It would be useful to show if the different TRIM37 variants are able to localise to the centrosomes. Furthermore it appears that centrosomes are missing in the C18R and 505-709 variants. It would be useful if the authors quantify centrosome numbers upon expression of different Trim37 variants as shown in Figure 4 - figure supplement 1. To make the identification of the cell easier it would help to include a DNA signal or indicate the outline of the cell.

      The anti-BirA antibody does give a slightly diffuse signal, although we disagree that it is unspecific considering that the BirA signal is only observed in cells expressing FLAG-BirA alone or BirA fusion proteins.

      We agree with this reviewer that we did not make any statements about the centrosomal localization of the TRIM37 mutants. We will re-analyze our images to quantify relative centrosomal localization of these proteins. The images as displayed in this Figure panel appear to be somewhat confusing to the reviewer. In terms of scale, only a small portion of the cell surrounding the centrosome is shown, therefore a nuclear or cell outline cannot be displayed on these images. In each image a centrosome is present, even in the C18R and 505-709 samples. We will show images of entire cells with insets to highlight the region surrounding the centrosome.

      14.The generation of stable and dox-inducible cell lines is missing in the material and methods

      We apologize for this omission. This information will be added.

      Reviewer 2, Major points

        • The centrosomal localization of endogenous TRIM37 should be validated by comparing control and knockout/knockdown cells.* We will perform these experiments as outlined in response to Reviewer 1, Major point 8.
      • Some of the quantifications are derived from only two experiments and in many cases no statistical testing was done. The authors should test the observed effects and add extra replicates to make the data more robust, where required. *

      We will ensure experiments are performed in biological triplicate and that appropriate statistical analyses are performed (see comment to Reviewer 1, Major point 7)

      • Fig. 5 supplements: panels showing effects on marker proteins in cells by IF lack quantification of the claimed effects. Without providing some type of quantifications for key findings, it is unclear how strong or penetrant the effects are.*

      Quantification and statistical testing will be performed for these experiments.

      Reviewer 2, Minor points

      I would suggest a final, summarizing schematic that illustrates the main findings in a cartoon/flow chart manner.

      We will improve the discussion of our main findings as well as provide a model/table of comparisons to improve the clarity of our manuscript.

        • Please revise incorrect abstract sentence: "We identify TRIM37 as a key mediator of growth arrest when PLK4 activity is partially or fully inhibited but is not required for growth arrest triggered by supernumerary centrosomes." __In our screens, we find that TRIM37 is required for growth arrest after treating cells with 200 and 500 nM centrinone B. Treatment of cells with 200 nM centrinone B causes centriole overduplication and our initial hypothesis was that centriole overduplication alone is inducing growth arrest. To test this in a parallel manner, we also overexpressed PLK4 to induce centriole overduplication. Surprisingly, but consistent with recently published results (Evans et al*., 2020), TRIM37 was not required for growth arrest after PLK4 overexpression. Thus, TRIM37 is required for growth arrest after 200 nM centrinone treatment, but not PLK4 overexpression, yet both of these conditions induce centriole overduplication. This concept will be highlighted, discussed and clarified in the text. We will change the abstract sentence to ‘We identify TRIM37 as a key mediator of growth arrest when PLK4 activity is partially or fully inhibited, but it is not required for growth arrest after PLK4 overexpression’__.

      Please also see similar comment to Reviewer 3, Major point 1.

      • In various figures and supplements showing centrosome and condensates/Cenpas, these are very difficult to distinguish due to their small size. I suggest to magnify regions of interest and/or add arrowheads in different colors marking the specific structures.*

      This comment is similar to Reviewer 1, Minor point 13. We will use coloured arrowheads to indicate different structures. Where possible, we will use magnified regions to improve clarity.

      • Fig. 2A: What is the purpose of the schematics on the right of panel A? The labels in the graph are unreadable and the network diagram without any labels is also not very useful. This could be removed. *

      The schematics on the right indicate a ‘generic analysis’ using the NGS sequencing data. We agree it is not essential and it will be removed.

      • Fig. 2B: The network presentation is not very easy to read. What are the functional groups/pathways here? The clusters should be labeled accordingly. What is the meaning of the different sizes of the circles? Maybe key interactions (e.g. TRIM37) could be indicated in a different color shade to highlight these? *

      In our figure we tried to highlight 1) the connectivity among screening conditions and 2) complexes that were identified by the screens. In our figure, each node (other than the six hub nodes that denote a screen condition) represents a hit from the screens. Thus, the nodes are connected by edges only to the screening conditions, not to each other. In this scenario, highlighting TRIM37 ‘interactions’ would only highlight the screening conditions for which TRIM37 was a hit (200 nM RPE-1, 500 nM RPE-1, 200 nM A375, 500 nM A375). We could try to overlay functional enrichment data on the graph, but this data is presented separately in Figure 2 – figure supplement A-D. The large circles represent hits found in previous screens and is indicated in the legend. Given the challenges of this figure we will modify it to improve its clarity.

      Reviewer 3, Major points

        • The presentation throughout the manuscript sometimes made it difficult to follow exactly what the authors meant when they referred to the various doses of Centrinone used in their experiments-often using the terms "low" or "high" without specifying exactly what they mean. In Figure 1A, for example, they present a growth inhibition curve using a log10 scale of Centrinone concentration, and they conclude that growth was inhibited "at concentrations above 150nM, with full inhibition observed at concentrations greater than 200nM". I presume this is just sloppy language, as it appears that growth is significantly inhibited at 150nM and full growth inhibition is achieved at 200nM. However, in Figure 4D, the authors show another growth inhibition curve (this time presented on a linear scale) where significant growth inhibition is seen well below 100nM and full inhibition appears to be achieved at ~125nM. The discrepancy between these experiments is not noted, nor any reason for it explained. We agree with the reviewers and apologize for using ‘low’ and ‘high’ as they are ambiguous. We will ensure that we refer specifically to each concentration of centrinone B used (ex. 50 nM, 150 nM etc.). The comparison between Figure 1A and Figure 4D is not straightforward. The experiments presented were performed approximately 6 years apart and in slightly different ways. As reviewer 3 indicates, Figure 1A is presented in a log scale; this makes it difficult for the reader to determine the exact concentrations of centrinone B used. For this panel, we used, 0 (DMSO), 10, 30, 75, 165, 200 and 500 nM centrinone B. For Figure 4D, we used 0, 50, 125, 150, 167, 200 and 500 nM. The only point that might be anomalous is 75 nM in Figure 1A. We do see approximately 25% inhibition using 50 nM centrinone B in Figure 4D, but no inhibition using 75 nM in Figure 1A. We can offer two explanations for this discrepancy. First, we noticed small deviations in the potency of centrinone B batches. Second, for Figure 1A, cells were assayed using a passaging assay where they are continuously plated, counted and re-seeded. Cells in Figure 4D were assayed using a clonogenic assay where cells are plated at low density and allowed to grow over the course of approximately two weeks. It is possible that a combination of these factors led to the highlighted discrepancy. We feel that the discrepancy is a minor one and we propose the following as a solution. We will present the growth data in Figure 1A as a scatter / box plot using only 200 and 500 nM centrinone B since these are the drug concentrations we use for the screen conditions and the key conclusions are derived only from these concentrations (i.e. both concentrations result in p53-dependent growth arrest where centrioles are overduplicated after 200 nM centrinone B, while centrioles are lost after treatment with 500 nM). We hope that this explanation and changes satisfy the reviewers.

      While discrepancies such as this may seem trivial, they make it hard to interpret some of the authors conclusions. For example, in their initial screen, the "low" dose of Centrinone (200nM) leads to centriole amplification and genes that block centriole duplication or PIDDosome function (which normally signals the presence of extra centrioles) are required for the growth arrest triggered by this concentration of the drug (Figure 1B). To me, this suggests that centriole amplification is required for this growth arrest at 200nM. However, when the authors test a more graded series of concentrations they conclude "excess centrioles might not be the trigger for this arrest at low Centrinone B concentrations". I assume they are using "low" here to indicate concentrations at or below 150nM (even though they use low to mean 200nM in their initial screen)? In the Discussion, they state that TRIM37 is "required for the growth arrest in response to partially or fully inhibited PLK4, but this activity was independent of the presence of excess centrioles". Again, it is not clear to which experiments they are referring when they talk about "partially" or "fully" inhibited PLK4, but, if this is correct, then why are genes required for centriole duplication and PIDDosome function identified in their initial screen as being required for the growth arrest at 200nM but not 500nM? Do they consider 200nM to be fully inhibiting PLK4? *

      We observed that cells arrested after treatment with either 200 or 500 nM centrinone B. Additionally, we observed centriole over-duplication after 200 nM but centriole loss at 500 nM. Our initial hypothesis was therefore that either centriole overduplication or loss resulted in growth arrest. Our subsequent results with TRIM37 caused us to question this simple interpretation. To determine if centriole overduplication caused by 200 nM centrinone B triggers growth arrest in this case, we induced centriole overduplication by overexpressing PLK4 and, surprisingly, TRIM37 was not required for growth arrest in these conditions, similar to that observed by __Evans et al., 2020. Thus, we have two conditions where centriole overduplication is observed where the growth arrest in only one condition is dependent on TRIM37. This is an important difference that we will better highlight in our revised manuscript. We will also present a better model and/or table outlining our most salient results. Briefly, it is thought that partially inhibited PLK4 blocks its own auto-phosphorylation and therefore blocks its degradation. The overall abundance of PLK4 therefore increases under these conditions and overduplication occurs. In our hands, we consider PLK4 to be partially inhibited in RPE-1 or A375 cells at any concentrations of centrinone B at 200 nM or lower.__

      Please also see similar comment to Reviewer 2, Minor point 1.

      Presumably it will only require textual changes to address this point, but it is hard to assess the broader significance of the paper until these points are clarified: is the main point of this paper that the cells response to Centrinone treatment is complicated and the role of TRIM37 equally so; or, is there a narrative that leads to a clear hypothesis that can explain these surprising findings?

      We don’t currently have a model that explains all the results we observe with TRIM37. We have data that is consistent with some previously published results and data that challenges some of these recent reports. The current model suggests that TRIM37 E3-dependent remodeling of CEP192 underlies its growth arrest activity after centriole loss. Importantly, we find that TRIM37 supports growth arrest in an E3-ligase-independent manner. We will discuss this further in our revised manuscript, as well as providing additional hypotheses based on our other observations of TRIM37 function.

      • It seems a striking omission that the authors show that p53 and p21 are induced by 200nM and 500nM Centrinone (Figure 1D), but they don't assay these proteins at any concentration lower than this. Perhaps they are saving this data for a subsequent manuscript, but the authors certainly seem to draw conclusions from several experiments they perform at concentrations below 200nM, so they should at least explain why they don't assay p53 and p21 status in these experiments. *

      We apologize for not including this data in the original version of the manuscript. It will be included in the revised version.

      Reviewer 3, Minor points

        • In the abstract the authors claim that the way in which altered centrosome numbers cause a p53-dependent growth arrest is evolutionarily conserved. This is misleading, as it implies that the loss and gain of centrosomes trigger the same arrest (which is probably not correct), and most of the data to date suggests that flies and worms (two popular models for centrosome research) do not have such a growth-arrest pathway.* This is a good point. We will modify this statement to indicate that p53-dependent arrest is confined to mammalian cells: “Altered centrosome numbers cause a p53-dependent growth arrest in both mouse and human cells through mechanisms that are still poorly defined”.

      Reviewer 3, comment in ‘significance’

      I could not discern, however, whether one could draw any broader conclusions than this, in part due to the presentation problems described above. Moreover, in the abstract the authors propose that altering PLK4 activity alone is sufficient to signal growth arrest. This would be an important conclusion, and I presume this refers to the very low dosage Centrinone experiments that trigger growth arrest without altering centrosome numbers and which does not require TRIM37? If so, this arrest is poorly characterised here and will be the subject of a future investigation, so it seems to strange to have this as a major conclusion in the abstract.

      We agree. As reviewer 3 points out, based on our findings we hypothesize that altered PLK4 activity could itself signal growth arrest. As this is not supported experimentally, we will remove it from the abstract and discuss this tantalizing possibility within the discussion.

      3. Description of the revisions that have already been incorporated in the transferred manuscript

      Please insert a point-by-point reply describing the revisions that were already carried out and included in the transferred manuscript. If no revisions have been carried out yet, please leave this section empty.

      Most of the experiments are currently ongoing and the preliminary results we have obtained discussed in the previous section. The revised manuscript will be modified to address each and every concern of the three reviewers as detailed above.

      4. Description of analyses that authors prefer not to carry out

      Please include a point-by-point response explaining why some of the requested data or additional analyses might not be necessary or cannot be provided within the scope of a revision. This can be due to time or resource limitations or in case of disagreement about the necessity of such additional data given the scope of the study. Please leave empty if not applicable.

      We will carry out all the experiments requested by the reviewers as detailed above.

      References

      Balestra FR et al., TRIM37 prevents formation of centriolar protein assemblies by regulating Centrobin. Elife. 2021 Jan 25

      Cuella-Martin R et al., 53BP1 Integrates DNA Repair and p53-Dependent Cell Fate Decisions via Distinct Mechanisms. Mol Cell. 2016 Oct 6;64(1):51-64

      Evans LT et al., ANKRD26 recruits PIDD1 to centriolar distal appendages to activate the PIDDosome following centrosome amplification. EMBO J. 2021 Feb 15;40(4)

      Meitinger F et al., TRIM37 controls cancer-specific vulnerability to PLK4 inhibition. Nature. 2020 Sep;585(7825):440-446

      Moyer TC et al., Binding of STIL to Plk4 activates kinase activity to promote centriole assembly. J Cell Biol. 2015 Jun 22;209(6):863-78

      Sillibourne JE et al.,Autophosphorylation of polo-like kinase 4 and its role in centriole duplication. Mol Biol Cell. 2010 Feb 15;21(4):547-61

      Wong YL et al., Cell biology. Reversible centriole depletion with an inhibitor of Polo-like kinase 4. Science. 2015 Jun 5;348(6239):1155-60

      Yeow ZY et al., Targeting TRIM37-driven centrosome dysfunction in 17q23-amplified breast cancer. Nature. 2020 Sep;585(7825):447-452

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    biorxiv.org/content/10.1101/2021.06.25.449796v1
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    Positional SHAP (PoSHAP) for Interpretation of Machine Learning Models Trained from Biological Sequences
    2
    1. EMBOpress 15 Sep 2021

      Note: This rebuttal was posted by the corresponding author to Review Commons. Content has not been altered except for formatting.

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      Reply to the reviewers

      Reviewer #1 (Evidence, reproducibility and clarity (Required)): In this paper, the authors use a previously published method SHAP for interpreting deep learning (DL) models (specifically LSTMs) that are trained for predicting physicochemical attributes of peptides (such as antigenicity and collisional cross section). The paper shows that it's capable of identifying some amino acid residues contributing to the prediction results of the DL models. Reviewer #1 (Significance (Required)):

      1. One main ideas of the paper is to use SHAP for determine the significant amino acids at each position (or pairs of AA at each position) contributing to the prediction. Some of the interpretation results are consistent with findings reported previously. This is very nice; however, most of these findings are statistical results such "XX is often present at the second position for the peptides with the positive outcome", which are relatively straightforward and may be derived by using some statistical methods without using DL models. We expect more complex patterns can be discovered in addition to these statistical observations.

      We thank the reviewers for these comments.

      First, to the point about discovering complex patterns, we note that one use of PoSHAP we discuss later in the paper is that PoSHAP enables interposition dependence analysis, which depends on interactions between residues and would not be reflected by summary statistics.

      Second, we agree it is important to show whether PoSHAP produces different residue importance maps than simple statistical summaries of amino acids in each group. The strongest binding peptides, or the highest mobility for the CCS model, were determined by taking only peptides that fall above a linear regression best fit of the ranked experimental values. Statistical summary heatmaps were created and then compared to those from PoSHAP revealing some similarities but also many differences. We added the following text and new figure to the results section to illustrate these points:

      “We wondered whether the patterns revealed by PoSHAP simply reflect the summary statistics for the high-binding or high-CCS subset of peptides. As expected, due to known differences in amino acid abundance across the proteome, the prevalence of amino acids was different across the training data and were also heterogeneous across positions (Figure 5A). To determine the subset of high CCS peptides, peptides were ordered in the training set by their CCS rank and then linear regression was performed to get the average trend line (Figure 5B). Any peptide above that trendline was defined as “high CCS”, and the frequency of amino acids at each position in this set was summarized using a heatmap (Figure 5C). Compared to the statistical amino acid frequencies, PoSHAP suggests a greater importance to arginine at both termini, the importance of tryptophan to increase CCS becomes apparent, and interior glutamic acid contributes less to high CCS than the frequencies would suggest (Figure 5D). The same analysis was repeated for MHC data (Supplementary Figures 9 and 10). This demonstrates that PoSHAP found non-linear relationships between the inputs and the outputs that are not present by simple correlation. “

      Figure 5: Amino acid summary statistics differ from PoSHAP values for the CCS data. (A) Amino acid counts as a function of position for training data. (B) Procedure for picking the ‘top peptides’ with the highest CCS. Linear regression was performed on the peptides ranked by their actual CCS value. Any peptide that fell above the trendline and overall mean were defined as ‘top peptides’. (C) Counts of amino acids for the top peptides were summarized in a heatmap. (D) Mean SHAP values across amino acids and positions from PoSHAP analysis.

      We also added the corresponding supplemental figures showing the same examples for the MAMU A001 model and human MHC models:

      Supplemental Figure 9: Amino acid summary statistics differ from PoSHAP values for the A001 MAMU MHC I data. (A) Amino acid counts as a function of position for training data. (B) Procedure for picking the ‘top peptides’ with the highest CCS. Linear regression was performed on the peptides ranked by their actual CCS value. Any peptide that fell above the trendline and overall mean were defined as ‘top peptides’. (C) Counts of amino acids for the top peptides were summarized in a heatmap. (D) Mean SHAP values across amino acids and positions from PoSHAP analysis. For the MAMU model, the amino acid frequencies of the input peptides show no obvious preference for amino acid position, but some amino acids are over-represented overall. The presence of the “end” token is more likely to be a high binder statistically (C), but the PoSHAP reveals that this end token is not the main determinant of binding (D).

      Supplemental Figure 10: Amino acid summary statistics differ from PoSHAP values for the human A1101 MHC I data. (A) Amino acid counts as a function of position for training data. The distribution of amino acids in this data. (B) Procedure for picking the ‘top peptides’ with the highest CCS. Linear regression was performed on the peptides ranked by their actual CCS value. Any peptide that fell above the trendline and overall mean were defined as ‘top peptides’. (C) Counts of amino acids for the top peptides were summarized in a heatmap. (D) Mean SHAP values across amino acids and positions from PoSHAP analysis. There are clear differences between the summary statistics of top peptides (C) and PoSHAP heatmap (D). For example, the end token is prominent in the summary statistics absent from the PoSHAP interpretation. Also, the preference for S/T/V at position two is tempered according to PoSHAP, but would be determined to be very important by the summary statistics.

      Although the interpreting results reported in the paper largely agree with previous reports, the paper did not explicitly model the frequency of different amino acid in the training data. For instance, if the amino acid 'A' happens to be over-represented in the positive samples of peptides in the training data, the DL model may consider it as to contribute to the positive prediction, which may not be not true. This issue might become more serious when pairs of amino acids are considered. The authors may want to analyze this potential issue in their results.

      We agree and understand the concern for the overrepresentation of amino acids that might skew the training of our models. To determine if this is an issue, as part of the response to the previous question, we looked at the amino acid counts for all peptides (Figure 5A, Supplemental Figures 9A and 10A). In general, the PoSHAP heatmaps (panel Ds in the same figures) look very different from the frequencies of amino acids (panel Cs in the figures), suggesting that amino acid frequencies have not caused any problem.

      Even on a balanced training dataset, the LSTM model to be interpreted may still contain arbitrary bias due to invertible overfitting, which the authors did not discuss. It will be more convincing by training multiple models using different hyper-parameters and optimization algorithms, and then see if similar interpretation results can be reached among most or all of these models.

      We assume the reviewer meant ‘inevitable overfitting’ instead of “invertible overfitting”? If so, the original manuscript did assess overfitting in Figure S4 based on the training and validation loss over training epochs.

      We think the reviewer makes a good point that different models might produce different interpretations, so we trained new models without optimization and with different hyperparameters and with a different optimizer (RMS prop). We see essentially the same PoSHAP interpretations. We added the following text to the results section along with these three new supplemental figures:

      “Given the dependence of the model interpretation results on the model used, the same model architecture trained with different parameters might result in different model interpretation. Given this, models for each of the three tasks mentioned here were retrained with different hyperparameters including the “RMS prop” optimizer. Each model produces similar or better prediction performance compared to the earlier version, and the model interpretation by PoSHAP was almost identical to the previous results in all three cases (Supplementary figures 12, 13, 14). This suggests that the model architecture drives the differences in interpretation, not the model training process.”

      Supplemental Figure 12. PoSHAP Analysis of Mamu A001 With Unoptimized Hyperparameters and RMSprop. A new model for the Mamu data was trained using the same architectures but with different hyperparameters and RMSprop as the optimization algorithm. Loss was plotted as mean squared error compared to the validation data. (A) Similar metrics for MSE, r, and p-values were obtained (B). Similar patterns are also observed for the PoSHAP heatmap of A001. (C) A dependence plot for A001 shows similar patterns to the Adam optimized model, including the positional dependence of proline at position two for high SHAP values of serine and threonine.

      Supplemental Figure 13. PoSHAP Analysis of A:11*01 With Unoptimized Hyperparameters and RMSprop. A new model for the A:11*01 data was trained using the same architectures but with different hyperparameters and RMSprop as the optimization algorithm. Loss was plotted as mean squared error compared to the validation data. (A) Similar metrics for MSE, r, and p-values were obtained (B). Similar patterns are also observed for the PoSHAP heatmap of A:11*01. (C) The SHAP ranges by position plot for A:11*01 shows similar patterns to the Adam optimized model, including the largest range of SHAP values at position two, nine, and ten.

      Supplemental Figure 14. PoSHAP Analysis of CCS With Unoptimized Hyperparameters and RMSprop. A new model for the CCS data was trained using the same architectures but with different hyperparameters and RMSprop as the optimization algorithm. Loss was plotted as mean squared error compared to the validation data. (A) Similar metrics for MSE, r, and p-values were obtained (B). Similar patterns are also observed for the PoSHAP heatmap of CCS. (C) Dependence analysis was performed on the dataset and the combined distance-interaction type bar plot shows similar relationships between the groupings, notably charge repulsion’s split.

      For the dependence analysis, it is not completely clear why the distance is used as the variable, while the relative position of the amino acid residue in the peptide is ignored. For example, if there is a strong interaction between the first and the last residues in the peptide, their distance changes depending on the peptide length. In figure 6, the authors showed strong interactions between amino acid that are 8-9 residues apart may suggest the peptide length actually plays a role here.

      We used distance because as the dependence analysis is a calculation of the difference in means between two distributions of SHAP values, dependent of the amino acid at another position. We believe that the distance between these interacting points is a natural choice and among the most informative metrics to explain these interactions. We agree with the reviewer that peptide length is important to the magnitude of the interactions between amino acids. We also recognize that there may be interactions between the peptide termini that could be obscured by the interactions of the longer peptides. To better explore this possibility, we performed the dependence analysis on each of the different peptide lengths separately (8, 9, or 10 here) to see if this is the case. Unfortunately, given the smaller size of these data subsets, we were unable to show significant differences in the interaction groupings. Though, interestingly enough, the significant interactions for the peptides of length eight only occurred between neighboring amino acids or the termini. This may suggest an interaction between termini that could be explored in the future.

      We added the following text and supplemental figure 11 to the results:

      “Finally, to try to ask if the absolute positions of amino acids in the peptide are relevant for the interaction, the data was split into 8, 9, or 10mers before analysis (Supplemental Figure 11). This revealed that there may be interactions between the termini, but this effect may be difficult to observe because there are significantly fewer 8mers and 9mers in the CCS dataset.”

      Supplemental Figure 11. SHAP Values of Collisional Cross Section by Peptide Length. The impact of peptide length on SHAP values was explored for the CCS data. The dataset was split into peptides of length 8, 9, and 10. All SHAP values were plotted as violin plots. The mean SHAP values were plotted in heatmaps by position and amino acid and standardized. Significant interactions by dependence analysis were plotted in bar charts by distance between interactions.

      To further support our decision to use distance as an interaction metric, we have also now included an additional box plot for Figure 7, demonstrating the interactions between each of the categories combined with distance. We have found that some of the bimodality of the interaction categories are explained by the distance at which they interact. Most strikingly is charge repulsion that decreases CCS when neighboring but increases CCS when the interaction is further.

      We added the following text and updated Figure 7 to the results section:

      “Additionally, there are interesting differences in the interactions of the amino acid among the significant set of interactions (Figure 76B). All significant interactions from the CCS data (Supplemental Table 3, adj. p-value Though it is evident that the mean of each interaction type corresponds to the expected impact those interactions would have on CCS, each of the interaction dependence plots are bimodal, with some interactions increasing CCS and some decreasing it. To dissect this observation further, we combined the two methods of splitting the data to see if the bimodality of interaction types would be resolved by distance (Figure 7C). Though definitive conclusions cannot be made for most categories, likely due to the ever decreasing sample size by splitting, of note is the difference between neighboring charge repulsion and non-neighboring charge repulsion. Neighboring charge repulsion seems to decrease CCS while distant charge repulsion increases CCS (see adjusted p-value from Tukey’s posthoc test in Figure 7D). When distant, charge repulsion makes intuitive sense as the amino acids are forced apart, linearizing the peptide and increasing the surface area. When neighboring, it is possible that the repulsion causes a kink in the linear peptide, decreasing the cross section. Overall, these analyses demonstrate that the models were able to learn fundamental chemical properties of the amino acids and through PoSHAP analysis we were able to uncover them.”*

      Figure 7. Dependence analysis of CCS model. (A) Significant (Bonferroni corr. P-value = charge repulsion, * = other, and δ = polar. For the distance analysis, interactions were grouped into three categories, neighboring (distance = 1), near (distance = 2, 3, 4, 5,6), and far (distance = 7, 8, 9). * indicates significance (ANOVA with Tukey’s post hoc test p-value

      Also, it would be better to show that how the result looks like when applying this method to peptides in the negative samples (e.g., the peptides that are not bound by MHC in the antigenicity prediction experiment). Will the interpreting results also be negative?

      We agree this is an interesting idea. We updated the supplemental figure showing PoSHAP of top peptide subsets to also show PoSHAP of bottom peptide subsets (supplemental figure 8). The results suggest that certain amino acid positions are detrimental to binding, for example D/E at various positions. We updated this section to add:

      “We also performed the same analysis with the eight peptides with the lowest binding predictions (Supplemental Figure 8). These PoSHAP heatmaps are primarily composed of negative SHAP values, suggesting that using this subset reveals amino acids at certain positions that are detrimental to MHC binding.”

      Supplemental Figure 8. Pooled PoSHAP for bottom and top predicted subsets of the data. The mean SHAP values for each amino acid at each position were calculated for the peptides with the bottom (A) or top (B) 0.013% predicted intensity (top 8 peptides) for the “A” Mamu alleles. Due to the small sample size, most of the amino acid positions have a value of zero. The positions with extreme values, however, illustrate important amino acids for prediction. Notably for A001 and A002, aspartic acid and glutamic acid contribute to low prediction along the peptide, suggesting charge may inhibit binding. For the top predictions, phenylalanine or leucine are important at the first position for both A001 and A008. A serine or threonine at position two is important for A001, A002, and A008. All alleles demonstrate the importance of a proline near the middle of the peptide.

      Finally, it will be interesting to see the interpreting results when the method is applied to the DL models on more challenging tasks such as the prediction of tandem mass spectra of peptides. The authors may want to discuss these applications.

      We agree it would be very interesting to apply this method to interpret predictions of tandem mass spectra. In this paper we already demonstrated PoSHAP on three different datasets with three different models, so we feel that adding a fourth model is out of the scope of this work. We do agree that we would like to explore this option in the future. We added this idea to the discussion section:

      “Altogether the advances described herein are likely to find widespread use for interpreting models trained from biological sequences, including models not covered here such as those to predict tandem mass spectra (reviewed in 33).”

      I am primarily interested in algorithmic and statistical problems in genomics and proteomics. We have develop deep learning models for predicting the full tandem mass spectrum of peptides, and am interested model interpretation methods to explain the fragmentation mechanism resulting in non-conventional fragment ions in tandem mass spectra of peptides. I review the paper in collaboration with my Ph.D students, who are developing deep learning models for computational mass spectrometry.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)): **Comments to the Authors** In this study, the authors developed a framework named PoSHAP for the interpretation of neural networks trained on biological sequences. The current manuscript can be stronger if the following issues can be clearly addressed.

      1. As interpreting model with SHAP is a vital part of this manuscript, it would be better to provide descriptions of the underlying principles of SHAP to enable the readers to understand the paper easily.

      We recognize that understanding the principles of SHAP is vital. To better explain SHAP, we have added the following text to the introduction:

      “SHAP is a perturbation-based explanation method where the contribution of an input is calculated by hiding that input and determining the effect on the output. SHAP expands this using the game theoretic approach of Shapely values that ensures the contributions of the inputs plus a calculated baseline sum to the predicted output.”

      It is emphasized in the manuscript that PoSHAP is introduced to interpret neural networks trained on biological sequences. However, it is not clear why the authors choose the Model Agnostic Kernel SHAP, which is based on Linear LIME. Although it can be used for any model, the performance of which may not be optimal. In this regards, perhaps Deep SHAP or Gradient SHAP is more appropriate, both of which are designed for deep learning networks [1]. It would be better to provide some additional experiments on Deep SHAP and this work will be more convincing if the same or similar contribution of each position on each peptide as that of Kernel SHAP. [1] Lundberg, S., and S. I. Lee. "A Unified Approach to Interpreting Model Predictions." Nips 2017.

      Our goal in using KernelExplainer was to demonstrate that PoSHAP was not dependent on model specific interpretation methods. However, we have realized that this intention may not have been clearly stated or demonstrated. To expand on this, we have included a new Figure 8, which shows PoSHAP analysis comparisons to other classes of machine learning models, all using Kernel Explainer. This result was interesting because it revealed that even though the XGboost model technically performed better at prediction (Figure 8A, reduced MSE and higher spearman rho), and produced a similar PoSHAP motif heatmap, the interpositional dependences from the perspective of distance (Figure 8C) or chemical interactions (Figure 8D) were substantially muted. This is also apparent with the other standard machine learning model ExtraTrees. This result shows that the choice of model architecture is important, and this direct comparison would not be possible if we used the DeepExplainer.

      We added the following text and figure to the manuscript:

      “ PoSHAP uses the SHAP KernelExplainer method, which is based on Local interpretable model-agnostic explanations (LIME). Using the general KernelExpplainer method enables direct comparison of interpretations produced by different models trained from the same data. To ask whether PoSHAP interpretation changes based on the model used, the CCS data was used to train XGboost or ExtraTrees models. Surprisingly, the XGboost model performed better than the LSTM model with regard to MSE and spearman rho between true and predicted values in the test set (Figure 8A). ExtraTrees was slightly worse than the other two models. The model interpretation heatmaps from PoSHAP were similar between the LSTM and XGboost, but the interpretation from the ExtraTrees model was missing the high average SHAP due to n-terminal histidine or arginine (Figure 8B). Even though XGboost produced a similar PoSHAP heatmap, the interpositional dependence with regard to distance (Figure 8C) and chemical interactions (Figure 8D) was muted. This shows that the choice of model is important for revealing amino acid interactions.”

      Figure 8. CCS PoSHAP of Various Machine Learning Models. PoSHAP analysis was performed on two additional machine learning models, Extra Trees and Extreme Gradient Boosting (XGB). Predictions were plotted against experimental values and the Mean Squared Error and r values are reported for each model (A). PoSHAP heatmaps were created for each model (B), illustrating an increase in model complexity as more sophisticated models are used. Dependence analysis was performed on each model and the significant interactions are plotted by distance (C) and by combined distance and interaction type (D).

      As described in the manuscript, "Correlations between true and predicted values were assessed by MSE, Spearman's rank correlation coefficient, and the correlation p-value." As an important indicator for evaluation, the exact p-values should be provided in the seven subgraphs in Figure 2, not p=0.0.

      We agree with the reviewer that reporting accurate p-values can assist in evaluation. We have updated the figures to reflect the p-values as far as we were able to determine them. Unfortunately, we are limited by the nature of the double data type in python and so reported that the p-value was less than the minimum value allowed by a double in six of the seven graphs. Additionally, the scales have been marked symmetrically as you mentioned in comment 4.

      It should be noted that the coordinate scales of Figure 2B and Figure 2C need to be marked symmetrically. And from Figure 2B, we can see that, the IC50 with smaller (0.8) values cannot be well predicted. Can the authors provide a detailed explanation about these results?

      We understand the reviewer’s concern with poor prediction of extreme values. Figure B represents the IC50 prediction for the A1101 human allele which was the smallest of the datasets we used for training. It only consists of 4,522 entries, around 1/10 of the data used for the Mamu alleles and CCS. Because of this, it is likely that there were not enough examples of datapoints at the extremes to reliably train the model to account for them. However, given the limited size of the dataset, we were surprised with the satisfactory predictions. More importantly, the purpose of our paper is model interpretation not model prediction accuracy, and this shows that even when predictions are not perfect, the model interpretation by PoSHAP can still be effective. We thank the reviewer for noticing this and added the following statement to the results:

      “Remarkably, this was achieved for A\11:01 using a total dataset of only 4,522 examples, which shows that PoSHAP can be effective with even less than 10,000 training examples. “*

      References are needed in some descriptions in the manuscript. For example, "one might train a network to take an input of peptide sequence and predict chromatographic retention time", "RNNs have found extensive application to natural language processing, and by extension as a similar type of data, predictions from biological sequences such as peptides or nucleic acids".

      We apologize for missing these references. We have now cited these statements and have added many additional references as part of our revision.

      The description of the adopted three models in the section "Model architecture" is a bit confusing. As described in this section, "The LSTM layer outputs a 50x128 dimensional matrix to a dropout layer where a proportion of values are randomly set to 0", "a second LSTM layer outputs a tensor with length 128 and a second dropout layer then randomly sets a proportion of values to 0". But as shown in the Supplemental Figure 3, the output size of the first LSTM was 10x128. Also, as shown in Table 1, the dropout rates were not 0. Therefore, the section should be adjusted for clear clarification.

      We apologize for the confusing wording. We meant that dropout layers randomly set values=0, not that the dropout proportion was 0. We reworded this part to read:

      “The LSTM layer outputs a 10x128 dimensional matrix to a dropout layer where a proportion of values are randomly “dropped”, or set to 0. For the MHC models, a second LSTM layer outputs a tensor with length 128 to a second dropout layer. Then in all models, a dense layer reduces the data dimensionality to 64. For the MHC models, the data is then passed through a leaky rectified linear unit (LeakyReLU) activation before a final dropout layer, present in all models.”

      Reviewer #2 (Significance (Required)): Pls refer to my comments provided as above.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)): **Summary:** The main goal of the work is to provide the interpretation of Deep Neural Networks (LSTM in the paper) trained on biological sequences. For this purpose authors used the framework introduced earlier - SHapley Additive exPlanations (SHAP), in particular - the slight adaptation of this method called positional SHAP (PoSHAP), because they are interested in the impact of each position of the input sequence to the model output. They demonstrate this on three regression tasks that predict peptide properties. **Major comments** The main contribution, highlighted in the paper: authors showed how PoSHAP discloses amino acid motifs that influence MHC I binding. Further they described how PoSHAP enables understanding of interpositional dependence of amino acids that result in high affinity predictions. Also they argued that this work also contributes to a method for accurate prediction of peptide-MHC I affinity using peptide array data enabled by novel application of a neural network that combines amino acid embedding and LSTM layers.

      There are some comments about the statements above: 1.Why was the LSTM model chosen? Recent publications showed the success of the Transformer model for biological sequences; however this direction was not covered in the related work overview. The architecture choice then should be better justified. Also the choice of LSTM for the biological sequences is not new and authors should better claim their statement about "novel application of a neural network that combines amino acid embedding and LSTM layers ". Where exactly is the novelty? Could the community use the pretrained embeddings for their purpose?

      The reviewer is correct that transformer models are highly effective for making predictions from biological sequences. In fact, many models do well, and there is no single correct choice of model for this task. Though there are many models to choose from, our models are sufficiently accurate. Importantly, the main contribution of our manuscript is not to train the most accurate models, but rather to demonstrate a strategy for positional model interpretation based on SHAP. Related to that point, please note our response to reviewer #2’s second comment that our approach uses the kernel explainer and can be applied to any model. However, we do agree that we neglected coverage of the transformer model in the introduction and have added a paragraph to the introduction covering some of the recent work in this area:

      “Many effective deep learning model architectures are available for making predictions from inputs of biological sequences, and there is currently no single correct choice. CNN models such as MHCflurry 2.0 (40) and LSTM models are effective at predicting MHC binding of peptides (41). Even simpler models, such as random forests, have been used to predict MHC binding (42,43). Prediction of other peptide properties like tandem mass spectra are often done with CNN or LSTM models (33). More recently, given the extraordinary performance of transformer models like BERT (44) and GPT-3 (45) for NLP, there is interest in transformer models for biological sequences (46).”

      We also want to be sure we do not overstate the novelty of our contributions. We have updated our discussion to better reflect the nature of our contributions. We reworded the statement quoted above to read:

      “Overall, the three modeling examples laid out herein serve as a tutorial for PoSHAP interpretation of almost any model trained from almost any biological sequence.”

      The attention mechanism itself provides the great opportunity to interpret the model predictions. In the introduction section authors made a statement that attention layers may limit the flexibility of model architecture when designing new models. Could they better explain this limit? Because recent state of the art models successfully work with long biological sequences and show better results then any other models (one example could be found here: https://openreview.net/pdf?id=YWtLZvLmud7). Authors should cover these limits more, that also related to the motivation of the LSTM choice.

      We added a paragraph to our introduction to expand on attention and its limitations:

      “Attention mechanisms have been successful in recapitulating experimentally defined binding motifs, but require that the model be constructed with attention layers. This may limit the flexibility of model architecture when designing new models. For example, attention mechanisms are specific to neural networks. Simpler models, such as random forests and XGboost, may also be more suitable for some applications, and these cannot utilize attention. Also, while attention mechanisms are currently very effective, there is always a possibility that new architectures will emerge that make interpretations using attention infeasible. Beyond this, attention is a metric of the model itself, while SHAP values are calculated on a per input basis. By looking at the model through the lens of the inputs, we can understand the model’s “reasoning” behind any peptide. Attention mechanisms also do not enable dissection of interpositional dependencies between amino acids. Thus, new methods for model agnostic interpretation are desirable.”

      Another statement was made about the PoSHAP - adaptation of the SHAP method. It is hard to follow through the explanation of this adaptation - it is not clear what exactly is this adaptation. For example, Kernel SHAP from the original paper computes feature importance, in this paper authors compute the impact of each position, that is basically also the feature importances. Thus authors should better explain the statement about PoSHAP novelty. Will it be possible to use PoSHAP for any other model trained for the same purpose? If yes, for better reproducibility, authors should provide the place where exactly in the repo is the code for this. Also mathematical notations are missing in the Positional SHAP (PoSHAP) section - it is better to explain the adaptation with them to increase the understanding of the section.

      We apologize for the ambiguous wording in the abstract stating that “PoSHAP adapts SHAP”. We have reworded this statement to “PoSHAP utilizes SHAP”. The novelty of this approach is taking the feature importance values calculated by SHAP and structuring them to include each position’s index to allow for the interpretation of biological sequences. As we demonstrate here, this allows for novel interpretations of previously published data and will enable model interpretation in future studies that learn from biological sequences. Although this is practically very simple, we are not yet aware of any examples in the literature that do this.

      The following two SHAP force plots demonstrate the difference between using SHAP as-is versus PoSHAP. There is a demonstrated need for such a framework, considering the dearth of biological sequence model interpretation using SHAP and the ambiguity within biological sequence SHAP interpretation. For example, Meier et al., Nature Communications, 2021 performed an analysis like our Figure S7C, which just shows the range of SHAP values per residue. Although we can learn something about which AAs are important based on the range of their SHAP values, SHAP as-is doesn’t reveal a motif. While our position indexing is a simple change, it enables all the rich, sequence dependent analysis we performed in this paper. We added the following text to the results section with this new supplementary figure:

      “PoSHAP utilizes the standard SHAP package but adapts the analysis by simply appending an index to each input and maintaining positional information after the kernelExplainer interpretation, which enables tracking of each input postion’s contribution to an output prediction (supplementary figure 5, showing force plot with and without index).”

      Supplemental Figure 5. SHAP Forceplots Demonstrating PoSHAP Indexing. Two forceplots were created with the SHAP forceplot method of the third peptide in the CCS testing set. (A) shows the plot with encoded inputs mapped to their amino acid. (B) shows the plot with the encoded inputs mapped to their amino acid and position. The addition of positional indexing removes the ambiguity of contributions, for example, glutamine having both a positive and a negative SHAP contribution to the prediction of the third peptide.

      We have updated the repository to include a tutorial that demonstrates PoSHAP on provided data and explains how to use PoSHAP with your own model and data.

      In the experimental section, authors first compare the results with previously known. For example, for the human MHC allele A*11:01 model PoSHAP analysis shows the similar results as was shown with another approach. Based on the provided explanation, it is not clear why PoSHAP is better than the previously published method. The advantage of the PoSHAP should be better explained.

      We agree with the reviewer that the benefits of our approach should be as clear as possible. The referenced section of the paper is to validate our approach compared to another model interpretation technique. We added a new third paragraph to the discussion section to clearly explain the benefits of PoSHAP:

      “There are several benefits of PoSHAP over competing methods. First, PoSHAP determines important residues despite biases in the frequencies of amino acids (Figure 5, Supplementary Figures 9 and 10). PoSHAP is also applicable to any model trained from sequential data (Figure 8), and enables dissection of interpositional dependencies (Figures 6 and 7). Finally, we include a clearly explained jupyter notebook on Github that will take any model and dataset and perform PoSHAP analysis.”

      In the experimental section, after the PoSHAP performance verification, hypothesis generation was introduced. However, it is not clear how many hypotheses were generated; how many of them were known before; what kind of other categories are inside these hypotheses (unknown, possible and potentially interesting, etc).

      We are unsure as to how to quantify the number of hypotheses generated by our approach. In a sense, the SHAP value of each amino acid at each position within a heatmap represents a hypothesis of the contribution of that amino acid to the metric being predicted. Each significant interaction listed in the first three supplemental tables represents a hypothesis of the interactions between two given amino acids at two positions. To make these into testable hypotheses requires some analysis, as we have discussed. i.e. the two binding motifs (L-T-P, F-S-P) of A001, or the distance-type interactions within the CCS.

      The README section in the GitHub repo is not easily understandable. An additional explanation for each step is required (e.g., links to the folders where the calculated SHAP values, the trained models, all splits and all-important benchmarks are).

      We have updated the README and repository to explain how to use PoSHAP, and explanations of each item in the repository.

      **Minor comments**

      1. The prior studies should be covered better (see Major comments).

      We apologize for not better covering prior studies. We have significantly expanded the introduction by adding two new paragraphs and at least 10 additional citations.

      The work consists of some typos, for example: "However, because many reports forgo model interpretation" - "t" is missed.

      We did intend to use the word “forgo” not “forget” in that sentence. We have checked again thoroughly for spelling and grammar mistakes.

      The hyperparameters table, hyperparameter search section should be moved to the supplemental material, that's technical details.

      We moved this table to the supplementary materials.

      Reviewer #3 (Significance (Required)): Interpretation of the model results is an important topic for biology. New findings here could lead to new interactions opening, new drugs development etc. That is relevant for the applied ML Researches and computational biologists. This paper aims to provide a way to do it. Because my field of interest and expertise lies in Machine Learning for healthcare, language modelling of biological sequences and Natural Language Processing, this work is of great interest to me. So I mostly evaluated ML methodology presented in the paper.

      PeerReviewed
    2. EMBOpress 15 Sep 2021

      Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons

      Referee #3

      Evidence, reproducibility and clarity

      Summary:

      The main goal of the work is to provide the interpretation of Deep Neural Networks (LSTM in the paper) trained on biological sequences. For this purpose authors used the framework introduced earlier - SHapley Additive exPlanations (SHAP), in particular - the slight adaptation of this method called positional SHAP (PoSHAP), because they are interested in the impact of each position of the input sequence to the model output. They demonstrate this on three regression tasks that predict peptide properties.

      Major comments

      The main contribution, highlighted in the paper: authors showed how PoSHAP discloses amino acid motifs that influence MHC I binding. Further they described how PoSHAP enables understanding of interpositional dependence of amino acids that result in high affinity predictions. Also they argued that this work also contributes to a method for accurate prediction of peptide-MHC I affinity using peptide array data enabled by novel application of a neural network that combines amino acid embedding and LSTM layers.

      There are some comments about the statements above:

      1.Why was the LSTM model chosen? Recent publications showed the success of the Transformer model for biological sequences, however this direction was not covered in the related work overview. The architecture choice then should be better justified. Also the choice of LSTM for the biological sequences is not new and authors should better claim their statement about "novel application of a neural network that combines amino acid embedding and LSTM layers ". Where exactly is the novelty? Could the community use the pretrained embeddings for their purpose?

      1. The attention mechanism itself provides the great opportunity to interpret the model predictions. In the introduction section authors made a statement that attention layers may limit the flexibility of model architecture when designing new models. Could they better explain this limit? Because recent state of the art models successfully work with long biological sequences and show better results then any other models (one example could be found here: https://openreview.net/pdf?id=YWtLZvLmud7). Authors should cover these limits more, that also related to the motivation of the LSTM choice.
      2. Another statement was made about the PoSHAP - adaptation of the SHAP method. It is hard to follow through the explanation of this adaptation - it is not clear what exactly is this adaptation. For example, Kernel SHAP from the original paper computes feature importance, in this paper authors compute the impact of each position, that is basically also the feature importances. Thus authors should better explain the statement about PoSHAP novelty. Will it be possible to use PoSHAP for any other model trained for the same purpose? If yes, for better reproducibility, authors should provide the place where exactly in the repo is the code for this. Also mathematical notations are missing in the Positional SHAP (PoSHAP) section - it is better to explain the adaptation with them to increase the understanding of the section.
      3. In the experimental section, authors first compare the results with previously known. For example, for the human MHC allele A*11:01 model PoSHAP analysis shows the similar results as was shown with another approach. Based on the provided explanation, it is not clear why PoSHAP is better than the previously published method. The advantage of the PoSHAP should be better explained.
      4. In the experimental section, after the PoSHAP performance verification, hypothesis generation was introduced. However, it is not clear how many hypotheses were generated; how many of them were known before; what kind of other categories are inside these hypotheses (unknown, possible and potentially interesting, etc).
      5. The README section in the GitHub repo is not easily understandable. An additional explanation for each step is required (e.g. links to the folders where the calculated SHAP values, the trained models, all splits and all important benchmarks are).

      Minor comments

      1. The prior studies should be covered better (see Major comments).
      2. The work consists of some typos, for example: "However, because many reports forgo model interpretation" - "t" is missed.
      3. The hyperparameters table, hyperparameter search section should be moved to the supplemental material, that's technical details.

      Significance

      Interpretation of the model results is an important topic for biology. New findings here could lead to new interactions opening, new drugs development etc. That is relevant for the applied ML Researches and computational biologists. This paper aims to provide a way to do it. Because my field of interest and expertise lies in Machine Learning for healthcare, language modelling of biological sequences and Natural Language Processing, this work is of great interest to me. So I mostly evaluated ML methodology presented in the paper.

      PeerReviewed
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    URL

    biorxiv.org/content/10.1101/2021.03.04.433939v2
  113. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263160
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263160: (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/10.1101/2021.09.06.21263160
  114. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263166
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263166: (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">8 This association was then examined separately for women and men.</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:
      This study has strengths and limitations. Patients were not randomized and the differences in mortality may be explained by factors other than the development of health services, clinical management, and scientific evidence. However, it should be noted that a randomized study investigating all these factors in different months would not be feasible. The observation of a large number of patients, all those discharged from 17 hospitals, the adjustment of statistical models for reported predictors of mortality,8 and the consistency of the results with the ones obtained in the sensitivity analysis, are strengths of this research. This study provides encouraging results for policy makers, hospital clinicians, and researchers to continue their work. However, more epidemiological studies in larger databases looking at trends of mortality in patients with different sociodemographic and clinical profile are required. The death rate of Covid-19 patients remains high and more studies to improve clinical outcomes are also necessary. Future research may address the safety and efficacy of innovative or repurposed interventions specifically in female patients.

      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/10.1101/2021.09.06.21263166
  115. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.13.460130
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.13.460130: (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">PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) [24], SNAP2 (https://rostlab.org/services/snap2web/) [25],</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><div style="margin-bottom:8px"><div>http://genetics.bwh.harvard.edu/pph2/</div><div>suggested: (PolyPhen: Polymorphism Phenotyping, RRID:SCR_013189)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mutation Assessor (http://mutationassessor.org/r3/) [26, 27], and Protein Analysis Through Evolutionary Relationships (PANTHER) coding SNP (cSNP) (http://www.pantherdb.org/tools/csnpScoreForm.jsp) [28] tools were used for the first analysis to determine the effects of the missense SNPs.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PANTHER</div><div>suggested: (PANTHER, RRID:SCR_004869)</div></div><div style="margin-bottom:8px"><div>http://www.pantherdb.org/tools/csnpScoreForm.jsp</div><div>suggested: (PANTHER Evolutionary analysis of coding SNPs, RRID:SCR_005145)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SIFT is a program that predicts the functional effect of an amino acid substitution in a particular protein.</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">The rsIDs of missense SNPs extracted from NCBI dbSNP were pasted into the SIFT4G predictions tool.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>dbSNP</div><div>suggested: (dbSNP, RRID:SCR_002338)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Amino acid FASTA sequences of IFITM1, IFITM2, and IFITM3 proteins were copied from UniProt (https://www.uniprot.org/) [31] and inserted into the PROVEAN Protein tool with substitutions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>https://www.uniprot.org/</div><div>suggested: (Universal Protein Resource, RRID:SCR_002380)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">PolyPhen-2 works similarly to PROVEAN.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PROVEAN</div><div>suggested: (PROVEAN, RRID:SCR_002182)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mutation Assessor and PANTHER cSNP tools estimate the effects of the substitutions in the evolutionary base.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Mutation Assessor</div><div>suggested: (UMD p53 Mutation Database, RRID:SCR_006720)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Homology modeling of wild and mutant Types of IFITM1, IFITM2, and IFITM3 proteins: Amino acid sequences (FASTA format) of wild-type protein products of IFITM1, IFITM2, and IFITM3 were obtained from UniProt [31].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>UniProt</div><div>suggested: (UniProtKB, RRID:SCR_004426)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">I-TASSER provides the Confidence (C)-score, estimated TM-score, and estimated RMSD value for each model it creates.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>I-TASSER</div><div>suggested: (I-TASSER, RRID:SCR_014627)</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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    URL

    biorxiv.org/cgi/content/10.1101/2021.09.13.460130
  116. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263026
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.09.21263026: (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">Identification of the clinically extremely vulnerable: In Scotland, people were formally recognised as clinically extremely vulnerable if their medical records showed they were in one of six categories: people with solid organ transplants, specific cancers, severe respiratory conditions, rare diseases, who were pregnant with significant heart disease, and who were on immunosuppression therapies 12.</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 include that the population covers a region that was somewhat less affected by coronavirus (COVID death rates at the end of the shielding period of 31st July 2020: 26 per 100,000 in Grampian compared to 47/100,000 in Scotland, 54/100,000 in Lothian and 63/100,000 in Greater Glasgow and Clyde30). An appropriate next step would be to scale these analyses across wider areas of Scotland and the UK. Rapid and reliable identification of the clinically vulnerable will continue to be important, and this analysis suggests two ways identification could be improved. First, sharing primary care records. In Scotland, primary care records are not shared nationally, limiting who could be identified as clinically extremely vulnerable to COVID and supported. Second, improving person-level sociodemographic data collection, including ethnicity. COVID hospital admissions and deaths have made it clear that sociodemographic characteristics affect clinical vulnerability to COVID. But in Scotland, ethnicity data are not well recorded, and the sociodemographic data available is for small areas rather than individuals. Neither ethnicity no socioeconomic data were not used to identify those who should shield. Collecting these data during healthcare visits and sharing them nationally could help improve care of the people who are clinically vulnerable. Healthcare changed dramatically for the clinically extremely vulnerable population during the pandemic. The increased reliance on emergency ca...

      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/10.1101/2021.09.09.21263026
  117. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263311
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263311: (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: Prior to study start, this study was approved and deemed exempt by the University of Pennsylvania Institutional Review Board (UPenn 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

      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 key limitation of our analysis is the reliance on EHR, which could introduce confounding if the level of completeness was disproportionally affected by ethnicity. Our findings corroborate the impact of COVID-19 in the elderly seen broadly. Patients over age 75 were at greatest risk for death and/or readmission. Improved strategies for post-discharge care of COVID-19 patients are needed to address the sustained vulnerability of these patients [23]. Passive data collection through routine electronic health records facilitates rapid research; however, the data are subject to a number of limitations. Records of comorbidities at hospital admission may be incomplete. Further, comorbidities diagnosed and treated outside the Penn health care system may not have been captured. Information regarding discharge destination (e.g. independent living or nursing home facility) was not available. Penn EHR may also have missed readmissions or deaths that occurred outside the Penn system. Linkage with federal and state registries will provide more complete data on survival, but these registries take time to be updated. Future work is needed to fully capture long-term outcomes of 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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    URL

    medrxiv.org/cgi/content/10.1101/2021.09.08.21263311
  118. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263057
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263057: (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: Ethical approval was received from the University of Melbourne Human Research Ethics Committee (study number 1954615.4).</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: We detected the following sentences addressing limitations in the study:
      Limitations of the study include the highly clonal nature of cases in Victoria at this time, with >95% of cases from the second wave being seeded for a single tm event. This limited the ability to resolve some transmission networks, particularly early in the outbreak, and may erroneously suggest single introductions of a cluster when there may have been multiple introductions from a genomic cluster from the community. This increases the importance of quality epidemiologic data to assist with interpretation of genomic data when performing these analyses. Our investigations were also limited by HCW and patient cases that were not able to be sequenced although numbers were relatively small, and the proportion of cases successfully sequenced was greater than most other jurisdictions. Similar processes could easily be applied to other healthcare systems where genomics is less commonly available; in particular, focussed sequencing of hospitalised cases and HCWs could achieve very similar results, albeit with a small chance of false-positive genomic links due to multiple introductions of the same genomic cluster from the community. The results from each facility have shown that there were multiple contributors to COVID-19 infections in HCWs in Victoria in 2020, and that while there were common factors contributing to transmission across different facilities, each outbreak was in fact a unique combination of contributors and had to be assessed individually. Through our experience wor...

      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/10.1101/2021.09.08.21263057
  119. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263331
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.09.21263331: (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 considerations: Written and informed consent for adults and assent and parental consent for minor participants was obtained.<br>IRB: The study was approved by the Institutional Ethics Committee, Maulana</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 samples were transported and processed at the Clinical Virology Lab, Institute of Liver & Biliary Sciences, New Delhi. Anti SARS CoV-2 IgG antibodies were detected by using the VITROS assay on VITROS 3600 instrument based on Chemiluminescent technology as per the kit literature [4].</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><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: the sociodemographic data of the participants collected through a brief interview schedule was entered in Microsoft Excel 2013 and merged with their antibody test results.</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">The data were analysed with IBM SPSS Version 25 (Armonk, NY:</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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">IBM Corp) and Stata 14 (StataCorp, 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: 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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263331
  120. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.13.460076
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.13.460076: (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: In vivo experiments and vaccination: Vaccination experiments have been performed according to ethical guidelines, under a protocol approved by the Grenoble Ethical Committee for Animal Experimentation and the French Ministry of Higher Education and Researcher (reference number: APAFIS#27765-2020102114206782 v2).</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">5-week-old female Balb/c mice were purchased from Janvier (Le Genestet St. Isle, France).</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">EXPI293 cells grown in EXPI293 expression medium were transiently transfected with the vector according to the manufacturer’s protocol (Thermo Fisher Scientific).</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">Briefly, gag/pol and luciferase plasmids were co-transfected with a SARS-CoV-2 spike plasmid with a C-term deletion of 18aa at 1/0,4/1 ratio on adherent HEK293T cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Before use, supernatants were tittered using HeLa ACE-2 cells to determine the appropriate dilution of pseudovirus necessary to obtain about 150 000 RLU per well in a 48 well-plate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HeLa ACE-2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Neutralization assay (mAb): Serial 3-fold dilutions starting from 1/10 dilution (serum), or 6µg/mL (known bNAbs) were let in contact with the pseudoviruses for 1h at 37°C in 96-w white plates (Greiner #675083), before addition of HeLa ACE2 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HeLa 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: 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">5-week-old female Balb/c mice were purchased from Janvier (Le Genestet St. Isle, France).</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">Synthetic DNA (Genscript) was cloned in the pACEBac1 using the restriction sites BamHI and HindIII.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pACEBac1</div><div>suggested: RRID:Addgene_109156)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">RBD purification: The following reagent was produced under HHSN272201400008C and obtained through BEI Resources, NIAID, NIH: Vector pCAGGS Containing the SARS-Related Coronavirus 2, Wuhan-Hu-1 Spike Glycoprotein Receptor Binding Domain (RBD), NR-52309.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCAGGS</div><div>suggested: RRID:Addgene_18926)</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">Automated data collection was performed with SerialEM, acquiring one image per hole, in counting mode.</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">Image processing and cryo-EM structure refinement: Movie drift correction was performed with Motioncor2 37 using frames from 2 to 40.</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">CTF determination was performed with Relion 3.1.2 (Scheres 2012).</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">Statistical analyses: For ELISA and neutralization assays, IC50 were deduced from crude data after normalization using GraphPad Prism “log(inhibitor) vs normalized response” function.</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/10.1101/2021.09.13.460076
  121. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263154
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263154: (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: Using standardised methodology (population-based, random stratified sampling) 11 cross-sectional studies were conducted with data collection during April 23-29, April 30 – May 6, May 22-31, June 11-22, August 6-25, September 21 – October 3, November 11-19, November 26 – December 6, December 11-20 in 2020, and January 7-18, January 21 – February 2 in 2021.</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">Using standardised methodology (population-based, random stratified sampling) 11 cross-sectional studies were conducted with data collection during April 23-29, April 30 – May 6, May 22-31, June 11-22, August 6-25, September 21 – October 3, November 11-19, November 26 – December 6, December 11-20 in 2020, and January 7-18, January 21 – February 2 in 2021.</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 several limitations. The degree to which the study is representative of the larger population is influenced by the low response rate and potential selective factors associated with responses. To minimise non-response bias, the prevalence estimates were weighted (age, gender, and region) to ensure representativeness of the source population. Yet, there could be other factors for which we did not have detailed information about population distributions which are also associated with testing positive for SARS-CoV-2. The number of people testing SARS-CoV-2 RNA positive in the cross-sectional studies is low leading to relatively large uncertainty around estimates. We see the long period of observation and population-based nationwide study design as strengths of our work. Interpretation of changes in SARS-CoV-2 incidence and positivity rates originating from case notification or clinical cases is likely to be confounded by substantial changes in testing practice over time. Our study is based on a series of cross-sectional studies with a standardised methodology, and is thereby very unlikely to be influenced by the testing practice. As this evaluation is based upon observing a single population over time, we speculate that selection bias or unmeasured confounders would operate rather uniformly over the period of observation, though presenting a less threatening trend of SARS-CoV-2 prevalence and analysis of factors associated with SARS-CoV-2 positivity.

      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">ISRCTN10182320</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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.06.21263154
  122. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263266
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.09.21263266: (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 evaluation of the collected findings within the scope of the study was carried out with the consent of the patients and completely anonymised.</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">Sample collection and testing methods: To obtain material for testing, the sterile foam swab supplied with the ID NOW™ COVID-19 test (Abbott, Chicago, USA) was used to collect anterior nasal specimens from patients arriving in the ambulance whilst in a prone position.</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">After extraction and completely anonymised processing of the data, further statistical evaluations were carried out using SPSS v23 software.</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: 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

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263266
  123. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263228
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263228: (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 all new lineages have been generated and all nodes assigned a lineage, a global multinomial logistic regression is performed, using the Python package sklearn.linear_model, yielding estimates for the relative growth rates of all lineages.</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: 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: Please consider improving the rainbow (“jet”) colormap(s) used on page 26. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21263228
  124. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263315
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.09.21263315: (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: [14] Rights and ethics: The study was approved by the local ethics committee for health research of Caen university hospital (ID 2293) on March 24th 2021.</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">As selecting a single set of controls could have led to an incorrect measurement of association due to random variations of ORs, we used a bootstrap method to perform 1,000 random samplings of controls, with replacement.</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">Participants: Healthcare personnel (medical and paramedical professionals, as well as personnel from laboratories, hospital pharmacies and administration) working in health establishments (hospitals, clinics, rehabilitation and recuperation care facilities and establishments specializing in psychiatry), nursing homes and establishments for handicapped children and adults in Normandy, France, were invited to participate in the study.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Participants: Healthcare</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The analyses were performed in R version 4.1.1 (R Development Core Team).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>R Development Core</div><div>suggested: (R Project for Statistical Computing, RRID:SCR_001905)</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 presents some limitations. The questionnaire was filled in retrospectively by participants, and for respondents with history of COVID-19, the questions covered a short period of time before infection. HCWs were likely to not remember exactly what measures they applied during this period, although the infection was a noticeable event and had raised questions about its origin. This recall bias is unavoidable with studies based on questionnaires. Studies with a prospective measure of exposures and PPE use would help minimize this bias, observations of practices being more reliable than declarations, but are more difficult to conduct. Moreover, the use of an online questionnaire may have prevented certain profiles of caregivers from participating in the study. Another bias may result from an involuntary overestimation of PPE use by HCWs who declared a history of COVID-19 infection, explaining our results for PPE being a risk factor (namely respirators, face shields and protective goggles) during care of non COVID-19 positive patients. Another issue is that cases and controls who completed the questionnaire did so voluntarily. Therefore, respondents may not be fully representative of the general population of HCWs in France. Unfortunately, no estimation of the global response rate within HCWs in Normandy was able to be performed. The questionnaire was sent to health establishments’ management and then relayed to HCWs. There was no feedback as to how many HCWs had access...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263315
  125. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21262951
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.09.21262951: (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">The proportion of Ns in the ROI sequences was calculated with the alphabetfrequency function of the Biostrings package [12].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Biostrings</div><div>suggested: (Biostrings, RRID:SCR_016949)</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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21262951
  126. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263200
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263200: (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 ethics committee of the University Medical Center of Rostock.<br>Consent: It is filed under A 2020-0086 and 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">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 amounts of antibody:fluorophore-combinations were used: 0.25 µg CD127:APC/R700 (clone HIL-7R-M21), 1 µg CD147:BV421 (TRA-1-85), 0.5 µg CD45RO:BV480 (UCHL1, BD Biosciences, Franklin Lakes/NJ, United States), 1 µg CD11b:PerCP/Cy5.5 (ICRF44), 0.8 µg CD11c:BV785 (3.9), 0.56 µg CD14:BV510 (</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibody:fluorophore-combinations</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>UCHL1</div><div>suggested: (BioLegend Cat# 304233, RRID:AB_11219394)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After washing, PE-conjugated anti-human IgG/IgM detection antibodies were added to the samples followed by incubation for 1.5 h at room temperature and 600 rpm.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG/IgM</div><div>suggested: (MyBioSource Cat# MBS703131, RRID:AB_10887474)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">4.5 Cytokine analysis: For the determination of cytokine concentrations in plasma samples, the LEGENDplexTM Human Anti-Virus Response Panel (Biolegend) was used containing capture beads and detection antibodies for Interleukin (IL-)1β, IL-6, IL-8, IL-10, IL-12p70, Interferon (IFN)α</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IL-6</div><div>suggested: (Bio-Rad Cat# M60009RDPD, RRID:AB_2857368)</div></div><div style="margin-bottom:8px"><div>IL-8</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IL-10</div><div>suggested: (Bio-Rad Cat# M60009RDPD, RRID:AB_2857368)</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 detail, the kit provided unstimulated HeLa cells, HeLa cells stimulated with tumor necrosis factor (TNF)α/Calyculin A, MCF7 cells stimulated with insulin-like growth factor 1 and A431 cells stimulated with epidermal growth factor.</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>MCF7</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>A431</div><div>suggested: CLS Cat# 300112/p753_A-431, RRID:CVCL_0037)</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">Analysis of flow cytometry data was done using the FlowJo software version 10.7 (FlowJo, Ashland/OR, United States) with the manual gating strategy shown in supplemental Figure 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">Data acquisition was performed using the Cytek® Aurora (Cytek Biosciences). 4.6 Statistics: Data analysis and visualization were performed using R (version 3.5.1), InStat (GraphPad, San Diego/CA, United States) and SPSS (IBM, Armonk/NY, United States).</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>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: 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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 8, 38, 6 and 7. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21263200
  127. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.11.21263417
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.11.21263417: (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">The PCR run was analyzed with Bio-Rad CFX Manager software version 3.1 (Bio-Rad Laboratories).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Bio-Rad CFX Manager</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>CFX</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>Bio-Rad Laboratories</div><div>suggested: (Bio-Rad Laboratories, RRID:SCR_008426)</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 becomes more important in India since the development of a proper and integrated wastewater treatment system is far-fetched even in the urban areas considering the overall limitations. Therefore, the present study aimed to investigate the applicability of WBE in the prediction and monitoring of COVID-19 wave in a city level paradigm with a limited interconnected sewerage system. Despite the presence of disconnected and fragmented WWTPs, undergoing the treatment of only 60-70% of the total wastewater generated, the collection sites were selected such that they covered most of the total WWTPs installed in the city. A combination of small and medium decentralized WWTPs and large centralized treatment plants was selected to investigate in detail about the ability & feasibility of WBE to detect the upcoming COVID-19 active case load rise in advance. As mentioned in results section 3.1, it was observed that even with such a restricted coverage, the increase in positivity from various sites could be observed at least 14-20 days (at a total active case count of less than 50 per day) before a visible rise in newly detected active cases. Another important observation to be made in this case study that in contrast to Kumar et al., 2021 this study shows that if the sites are selected carefully it is possible to directly correlate the positivity rate of the sites to the upcoming wave in advance. As is the case in point where this study was able to predict the upcoming wave of COVID19...

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.11.21263417
  128. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21262027
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21262027: (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: Experiments on Cat and Dog sera: Serum samples were collected from cats and dogs belonging to owners who developed COVID-19-like symptoms and subsequently tested positive for SARS-CoV-2 infection by RT-qPCR.,<br>IRB: Samples and data collections were conducted according to the guidelines of the Declaration of Helsinki, and approved by the Ethics Committee Sciences et Santé Animale n°115 (protocol code COVIFEL approved on 1 September 2020, registered under SSA_2020_010).<br>Euthanasia Agents: Cells were then incubated for 72 h at 37 °C with 5% of CO2.<br>Consent: Ethical statement: All sera from the first cohort, and whole blood samples from the second cohort, were obtained from the Toulouse hospital, where all patients give, by default, their consent for any biological material left over to be used for research purposes after all the clinical tests requested by doctors have been duly completed.</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">All the positive samples of this cohort, as well as a set of randomly selected negatives, were submitted to a repeat of the assay, which showed excellent reproducibility.</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">After transferring the pictures to computer files, the hemagglutination tests were scored by three independent assessors, of which two were blinded.</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 Jurkat-S and Jurkat-R cell lines were both checked for the absence of mycoplasma contamination using the HEK blue hTLR2 kit (Invivogen, Toulouse, France) FACS staining: Before experiments, cells in the cultures of both Jurkat-S and Jurkat-R cell lines were counted, and sufficient numbers harvested to have a bit more than 105 cells of each per sample to be tested.</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">Reagents: Polyclonal anti-human and anti-mouse Igs secondary antibodies, all conjugated to Alexa-488, were from Jackson laboratories, and purchased from Ozyme (France)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-mouse Igs secondary</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">109-545-129; anti-mouse Ig-G: 115-545-003 Anti-cat IgG (F4262) and anti-dog IgG (F7884) secondary antibodies, both conjugated to FITC, were obtained from Sigma. Anti RBD monoclonal antibodies: FI3A (site 1) and FD-11A (site 3) (Huang et al. 2021); C121 (site 2) (Robbiani et al. 2020); CR3022 (site 4) (ter Meulen et al. 2006); EY6A (site 4) (Zhou et al. 2020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>109-545-129; anti-mouse Ig-G: 115-545-003 Anti-cat IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-dog IgG</div><div>suggested: (Sigma-Aldrich Cat# F7884, RRID:AB_259743)</div></div><div style="margin-bottom:8px"><div>F7884</div><div>suggested: (Sigma-Aldrich Cat# F7884, RRID:AB_259743)</div></div><div style="margin-bottom:8px"><div>Anti RBD</div><div>suggested: (BioLegend Cat# 944803, RRID:AB_2892509)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All those were obtained using antibody-expression plasmids, as previously described (Townsend et al. 2021).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antibody-expression</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For specific isotyping, i.e. for staining separately with either anti-IgG, -IgA or -IgM, as well as the pan-specific anti-Ig-GAM secondary antibody, we used double the quantities of cells and of serum or plasma for the primary step, and split the samples into 4 wells after the second wash, before proceeding to the subsequent steps as for the standard protocol.</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><div style="margin-bottom:8px"><div>anti-Ig-GAM</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Monoclonal anti-SARS-CoV CR3022 antibody (BEI Resources, NIAID, NIH) was used as a positive control.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-SARS-CoV CR3022</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">Lentiviral infectious supernatants were obtained after transient transfection of HEK cells with pLV-or pCDH-derived vectors, together with the packaging R8-2, and VSV-G plasmids.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The Jurkat-S and Jurkat-R cell lines were both checked for the absence of mycoplasma contamination using the HEK blue hTLR2 kit (Invivogen, Toulouse, France) FACS staining: Before experiments, cells in the cultures of both Jurkat-S and Jurkat-R cell lines were counted, and sufficient numbers harvested to have a bit more than 105 cells of each per sample to be tested.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Jurkat-R</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Each sample requires 2.105 jurkat cells, which is roughly the amount obtained with 0.5 ml of standard tissue culture medium, which costs around 50 €/L, i.e. 2.5 cts/sample.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>jurkat</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Experiments on mouse sera: Virus preparation and inactivation: SARS-CoV2 was grown on Vero E6 cells (ATCC) in DMEM (Dutscher) supplemented with 100 U/mL penicillin, 100 μg/ml streptomycin (Invitrogen), and 2% heat inactivated fetal bovine serum (Sigma).</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">Sero-neutralisation assay: Serum samples and controls were heat-inactivated at 56 °C for 30 min, serially diluted in DMEM starting at 1:10, mixed with an equal volume of SARS-CoV-2 stock (previously amplified and titrated on Vero-E6 cells and diluted in DMEM to contain 2000 TCID50/ml), incubated for 2 hours at 37 °C, and 100 µL transferred to tissue-culture 96 well plates plated with 12.000 Vero-E6 cells per well the day before the assay, in DMEM complemented with 10% of heat-inactivated fetal bovine serum and 1% of penicillin-streptomycin at 37 °C with 5% of CO2 (medium was removed before adding the virus-serum dilutions).</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">pLV-EF1a-SARS-CoV-2-S-IRES-Puro was created by cloning a codon-optimized version of the SARS-CoV-2 S gene (GenBank: QHD43416.1) into the pLV-EF1a-IRES-Puro backbone (Addgene plasmid # 85132 ; http://n2t.net/addgene:85132 ; RRID:Addgene_85132) using BamHI and EcoRI sites.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pLV-EF1a-SARS-CoV-2-S-IRES-Puro</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div></div><div>detected: RRID:Addgene_85132)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The lentiviral vector for the expression of mCherry was obtained by replacing the GFP sequence of GFP by that of mCherry in the pCDH-EF1α-MCS*-T2A-GFP plasmid (https://systembio.com/shop/pcdh-ef1α-mcs-t2a-gfp-cdna-single-promoter-cloning-and-expression-lentivector/</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCDH-EF1α-MCS*-T2A-GFP</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Lentiviral infectious supernatants were obtained after transient transfection of HEK cells with pLV-or pCDH-derived vectors, together with the packaging R8-2, and VSV-G plasmids.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCDH-derived</div><div>suggested: None</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">The Jurkat-R cells were obtained by successive transduction with the pCDH-GFP lentiviral vector described above, then with the empty pLV lentiviral vector, followed by selection with Puromycin at 10µg/mL.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pCDH-GFP</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pLV</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">Post-acquisition analysis of all the samples was performed using the Flowjo software (version 10.7.1) Cost of the Jurkat-S&R-flow test: The cost per sample of the Jurkat-S&R-flow test lies in large part with the price of the secondary antibodies used.</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:
      As alluded to in the introduction, one of the possible caveats of using a human cell line to express the S protein is that some blood samples will contain allo-reactive antibodies directed against that cell line, possibly as a consequence of a pregnancy, or past history of receiving a blood transfusion or organ transplant (Hickey et al. 2016; Karahan et al. 2020). The third column of Figure 1 shows examples of such samples containing marked levels of alloreactive antibodies, i.e. samples for which the J-R cells show significant levels of staining compared to the same cells labelled with just the secondary antibody. Based on our results collected on more than 350 clinical samples, we evaluate that ca. 30 % of samples will contain allo-reactive Abs that will result in levels of staining of Jurkat cells that are more than five-fold that of the signal obtained for the negative control (and 3-6 % more than ten-fold). Of note, we did not notice an increased frequency of allo-reactivity in samples from women compared to men, which suggests that allo-reactivity after pregnancy is not a major cause in the origin of those allo-reactions. A difficult question with all serological tests is that of where to set the threshold beyond which the specific signals detected can confidently be considered as positive, which will be directly linked to the balance between sensitivity and specificity of the assay. Based on the analyses of various cohorts of positive and negative samples (some of whic...

      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/content/10.1101/2021.09.06.21262027v3
  129. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21262986
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21262986: (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">The analysis will be carried out by a researcher blinded to the participants’ allocation through the program Stata SE 16.1 (2020; StataCorp.</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 calculation is based on the functional capacity results assessed by the 6-min walking test from the 2020 study by Kai Liu et al.(20).</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 will be carried out by a researcher blinded to the participants’ allocation through the program Stata SE 16.1 (2020; StataCorp.</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: 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/10.1101/2021.09.06.21262986
  130. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21262542
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.09.21262542: (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:
      Strengths and limitations: This is the first comprehensive study using a national dataset of all hospital admissions in England examining disruptions in a number of areas including routine, complex, emergency and elective procedures. Previous studies have been limited by examining disruptions in surgical care of people from single centres or regions and mainly related to cancers,14 patient experiences,15 and single routine or emergency procedures.16-18 Our study is limited to a particular range of surgical procedures because we wanted to see how the system had been able to cope with procedures of different types. However, these types do not serve as a classification system for two reasons. First, they overlap. For example, cancer operations are urgent because they are time critical. Second, they are hard to define or categorise in much the same way as a tree and a bush. Thus, our criteria simply illustrate features of different surgeries that act as barriers (e.g. complexity) or facilitators (e.g. degree of urgency) to access to surgery during an acute rise in hospital admissions. We think our findings show that when an operation is complex, not just technically but in terms of the pathway patients follow, then this acts as a barrier even if surgery is time-critical. This study does not seek to identify where on the patient pathway barriers occur databases. Implications: While reductions in surgery were attenuated in the second peak compared to the first peak, it would be unw...

      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/10.1101/2021.09.09.21262542
  131. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263223
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263223: (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: 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/10.1101/2021.09.07.21263223
  132. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.02.21263035
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.02.21263035: (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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    URL

    medrxiv.org/cgi/content/10.1101/2021.09.02.21263035
  133. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263276
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263276: (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">Due to the limited number of events, we only had power to run SCCS for Bell’s Palsy (Appendix table 2).[49] Any subgroups with less than 5 people were blinded and reported as <5, following information governance requirements.</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:
      Study strengths and limitations: The main strength of our study is the population-based method with data from the UK primary care system, which have great representativeness and complete capture of vaccinations among the UK population. In addition, the use of self-controlled case series study design took the advantage of within person comparison to reduce time-fixed confounding. We also further adjusted for age and seasonality to control for time-varying confounding. Our study has limitations. As we only included primary care data, diagnoses from inpatient settings may not be captured and the absolute risk may be underestimated. However, a previous study has showed that CPRD primary care data captures immune-mediated neurological disorders like GBS accurately, even without linking hospital data.[72] Within-database comparisons are recommended when comparing observed and expected rates due to database-level heterogeneity.[43] We used CPRD Aurum and CPRD GOLD. Although both contain UK primary care data, these data come from different electronic health record clinical systems and use different medical coding. However, one study showed that the two databases generated similar estimates.[73] We used code lists and algorithms for the identification of neuro-immune events previously published as part of a study on the background rates of COVID-19 AESI.[43] Mapping to the OMOP common data model also helped maximise comparability. The short follow-up time after vaccination may have le...

      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/10.1101/2021.09.08.21263276
  134. www.linkedin.com www.linkedin.com
    Why Are We Teaching Humans How To Code And Machines How To Learn? | LinkedIn
    1
    1. gyuri 15 Sep 2021
      Why Are We Teaching Humans How To Code And Machines How To Learn?

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    linkedin.com/pulse/why-we-teaching-humans-how-code-machines-learn-andres-colmenares/
  135. github.com github.com
    getify/You-Dont-Know-JS
    1
    1. billyangg 15 Sep 2021

      The passage is just an introduction to several basic concepts of programming.

      And we know the programming language JavaScript is quite useful in building web applications and it is often abbreviated JS. The passage also provides a list of resources that may help readers dig into these topics further.

      The first chapter taught you some basic concepts and the first thing we should know is code. The source code is a set of special instructions to tell the computer to perform tasks. Source codes are stored in a text file. We can modify the text by using the so-called IDE, which is like a text editor application. For convenience, developers could also type code into a developer console in a browser.

      The next thing we should know is statements. A group of words, numbers and operators that performs a specific task is a statement. Some characters are variables, which are used to hold values. Some values stand alone without being stored in a variable for example a number 10. Operators are used to performing actions, without them we cannot do arithmetic tasks. Expressions are small pieces of code, for example, we use variable a to store a value and this is a variable expression. If we do the multiplication that piece of code is a so-called arithmetic expression like "a * b".

      After we finish typing the code we wanna run this program. The source code we are familiar with can not directly be executed on computers, because computer do not understand. So we need a utility on the computer to transform our source code into a form that the computer can understand. That utility is called an interpreter or a compiler. If this process is done from top to bottom, line by line, every time the program is run, which is usually called interpreting the code. If the translation is done ahead of time, we call that compiling the code. As for the JS, the engine compiles the code on the fly and then immediately runs the compiled code.

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    github.com/getify/You-Dont-Know-JS/blob/1st-ed/up & going/ch1.md
  136. web.hypothes.is web.hypothes.is
    Annotating the law | Hypothes.is
    1
    1. Rajesh_Pachaiappan 15 Sep 2021
      Return to the Hypothesis sidebar and click on the image button in the text editor. The following bit of code will appear:

      .hypothesis-howto Annotate an image with surrounding text. Describe Image

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    URL

    web.hypothes.is/blog/using-social-annotation-to-improve-student-comprehension-and-engagement-in-condensed-summer-courses/
  137. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263188
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263188: (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 used the Python libraries google_streetview.</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: Thank you for sharing your code and data.

      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
      Future work should take under consideration the potential caveats of imbalanced data to improve the classification accuracy for the extreme risk label and other labels with fewer observations. Ongoing and future work includes the development of a classification model for the four outcome labels (i.e., moderate, high, very high and extreme COVID-19 risk). We will implement techniques that can potentiate the classification capacity of the neural networks, including ensemble models,11 novel loss functions not currently implemented in the Keras environment (e.g., squared earth mover’s distance-based loss function),12 and we may try other architectures (e.g., SqueezeNet13) with similar precision yet less computationally expensive. Strengths and limitations: In this preliminary work, we followed a pre-defined analytical protocol which included transfer learning leveraging on large and deep neural networks trained with millions of images (ImageNet). We still had to train the parameters of the output layer, for which we did not have a massive number of images. Future work could expand our analysis with information and images from more bus stops or other public spaces to train a more robust model. Ideally, these images should come from different cities. This information may be available in other countries. There are further limitations we must acknowledge. First, the images and labels were not synchronic; that is, the figures and the labels were not collected on the same date. This is...

      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/10.1101/2021.09.06.21263188
  138. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263100
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263100: (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 email provided instructions for participation in the study, including an alteration of consent and a study-specific passcode required for study registration.</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 included male and female.</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">23-24 To detect SARS-CoV-2, this study used the Aptima Panther SARS-CoV-2 Assay, which uses qualitative detection of RNA from SARS-CoV-2 isolated and purified nasopharyngeal, oropharyngeal and nasal swab specimens obtained from individuals who meet COVID-19 clinical and/or epidemiological criteria.25 Both the SARS-CoV-2 Antibody Assay and the Aptima Panther TMA SARS-CoV-2 Assay were approved for use under Emergency Use Authorization in US laboratories certified under the Clinical Laboratory Improvement Amendments of 1988.26 Prior to recruitment, this study obtained approval by the Institutional Review Board (#20-168E).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>#20-168E</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">Race/ethnicity included Hispanic; White, Non-Hispanic; Black, Non-Hispanic; Asian, Non-Hispanic; American Indian, Non-Hispanic; or Mixed-race, Non-Hispanic (those who identified as two or more races).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Hispanic; White</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 methods: Data management and analysis were performed by the study research team and conducted using SAS statistical software (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</div><div>suggested: (SASqPCR, RRID:SCR_003056)</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:
      Limitations: There are several limitations to this study. Most important, there was no viral testing done to participants’ blood samples, eliminating the ability to conclusively determine whether two SARS-CoV-2 test results in the same individual were due to true reinfection or recurrence. Second, abstracted data for this study did not include symptomatology; therefore, we cannot determine 1) reasons participants tested multiple times, 2) sickness severity of participants with positive SARS-CoV-2 test results, or 3) commonalities among individuals with positive results. This information could have contributed to the body of literature that correlates viral load with the ability to transmit the virus.27 Finally, because there is no universally accepted definition of reinfection, the study team used CDC retesting guidelines and some recently published guidance on proposed operational definitions of the terms to define reinfection and considered all subsequent positive test results to be recurrence. Implications: Overall, this study indicates that reinfection is possible but unlikely, and both reinfection and recurrence are more likely among high-exposure groups like clinical healthcare workers. Individuals in high-exposure groups should continue to abide by previous public health precautions, irrespective of policy easement. Widespread vaccination may be a solution to easing up on public health recommendations, but more long-term data is needed on vaccine efficacy, transmission...

      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/10.1101/2021.09.07.21263100
  139. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263031
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263031: (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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    URL

    medrxiv.org/cgi/content/10.1101/2021.09.06.21263031
  140. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263149
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263149: (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 approval: Written informed consent was obtained from all participants or their authorized substitute decision makers.<br>IRB: This study was approved by the University of British Columbia/Providence Health Care and Simon Fraser University Research Ethics Boards (protocol H20-03906).</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">Vaccine-induced antibody responses against SARS-CoV-2 were assessed three ways: (1) Commercial and in-house assays to detect binding antibodies targeting the spike receptor binding domain (RBD); (2) Angiotensin-converting enzyme 2 (ACE2) competition assays to detect receptor-blocking antibodies; and (3) Neutralization assays to detect antibodies that prevent virus infection of target cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Angiotensin-converting enzyme 2</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">Binding antibody assays: We examined total binding antibodies against the SARS-CoV-2 N and RBD in serum using the Elecsys Anti-SARS-CoV-2 assay (which detects anti-N antibodies generated following infection) and Anti-SARS-CoV-2 S assay (which quantifies total antibodies against RBD generated following infection or vaccination), respectively, on a Cobas e601 module analyzer (Roche Diagnostics).</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-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">Bound IgG was detected using PE-conjugated anti-human IgG secondary antibody (BioLegend) with results reported as arbitrary median fluorescence intensities (MFI).</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><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">Analyses were conducted using Prism v9.2.0 (GraphPad).</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: We detected the following sentences addressing limitations in the study:
      A limitation of our study is that precise immune correlates of protection for SARS-CoV-2 transmission and disease severity remain incompletely characterized 32, so the implications of our results as they relate to individual-level control of COVID-19 remain uncertain. The levels of immunity induced in older adults seen here following vaccination may be sufficient to prevent symptomatic infection or severe disease in many cases, so studies linking vaccine immunogenicity data to clinical outcomes specifically among older adults are needed. Due to the timing of the vaccine rollout in British Columbia, our sample size for the durability assessments was modest; however, the weaker responses observed among LTC residents were nevertheless statistically significant. Due to small numbers of participants who received Moderna, we were unable to assess differences in responses between mRNA vaccines 14,33. Overall, our results extend a growing body of evidence indicating that COVID-19 mRNA vaccines are less immunogenic in older compared to younger adults and reveal substantial waning of immunity across all ages in the first three months following receipt of two doses of vaccine. The combined effects of lower peak immunity and natural waning of vaccine-induced responses may leave older adults at continued risk of infection by SARS-CoV-2 or its variants.

      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/10.1101/2021.09.06.21263149
  141. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263385
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.10.21263385: (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 approved by the New England 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">Statistical analysis: To ensure balance between treatment groups in the absence of baseline randomization, and in addition to the 1:10 risk-set sampling by time, location, age, sex, and comorbidity score described above, we performed 1:4 propensity score (PS) matching with a caliper of ±0.01.</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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263385
  142. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263213
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263213: (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 Population: This was a retrospective study, approved by the UM Institutional Review Board, on multiple outcomes of COVID-19 patients and their associated risk factors.</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: First, as a small number of patients who transferred in from other institutions did not have medical history data, we had to remove them from analysis, though their impacts on our results were limited. Second, as this study was based exclusively on patients of Michigan Medicine, there may be biases in the patient mix, affecting the generalizability to more diverse populations or other geographic areas. On the other hand, these patients did offer an opportunity to study COVID-19 outcomes in a local region that had been severely impacted by the pandemic. Third, this was a retrospective study of an existing EMR database. As such, we are limited in our ability to draw causal interpretations from these results. In addition, due to the nature of EMR data, there is always the possibility for misclassification bias and/or inaccurate data entry. Lastly, future work, with longer follow-up, should focus on the residual impact of COVID-19 among recovered patients to elucidate the effect of lasting symptoms and acquired comorbidity burden on long-term quality of life and mortality.

      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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21263213
  143. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263222
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263222: (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: Inability to provide informed consent or to have an authorized relative or designated person provide informed consent, or to comply with the protocol requirements; 2.</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: ODYSSEY is a double-blinded Phase 3 study with a planned randomization of a total of 300 hospitalized severely ill COVID-19 patients (Clinicaltrials.gov: NCT04326426).</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">CXCL16 levels in plasma were determined with an enzyme□linked immunosorbent assay (ELISA) assay (Thermofisher ID: # EHCXCL16) performed on plasma collected at baseline in cases and in a set of healthy controls (assay range 2.74-2000 pg/mL).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Thermofisher ID</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">DNA sample size distributions are profiled by a Fragment Analyzer (Advanced Analytics) or BioAnalyzer (Agilent Technologies), to assess sample quality and integrity.</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">Whole genome sequencing (WGS) libraries were prepared using the Truseq DNA PCR-free Library Preparation Kit.</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">Paired-end 150 bp reads were aligned to the GRCh37 human reference (BWA-MEM v0.7.8) and processed with GATK best-practices workflow (GATK v3.4.0).</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><div style="margin-bottom:8px"><div>GATK</div><div>suggested: (GATK, RRID:SCR_001876)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All high quality variants obtained from GATK were annotated for functional effects (intronic, intergenic, splicing, nonsynonymous, stopgain and frameshifts) based on RefSeq transcripts using Annovar31.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RefSeq</div><div>suggested: (RefSeq, RRID:SCR_003496)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Additionally, Annovar was used to match general population frequencies from public databases (Exac, gnomAD, ESP6500, 1000g) and to prioritize rare, loss-of-function variants.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Annovar</div><div>suggested: (ANNOVAR, RRID:SCR_012821)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Linear models adjusted for PC, age and sex were conducted in PLINK.</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: 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">NCT04326426</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">ODYSSEY: A Study to Investigate the Efficacy of Tradipitant …</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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21263222
  144. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263248
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263248: (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">The latter expression followed from a mechanistic consideration of bond dissociation triggered by the competition between the BCR and the antibody for the antigen (39).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>antigen</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">If plasma cells died at the per capita rate δp, then the affinity-weighted cumulative plasma cell output would beIf the antibody production rate of plasma cells was β per generation (64), the instantaneous affinity-weighted antibody output would be βP(g), which given the clearance rate, δA, of circulating antibodies yielded the affinity-weighted cumulative antibody output asWe performed the simulations and analysed the results using programs written in MATLAB.</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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.08.21263248
  145. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263236
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263236: (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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    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21263236
  146. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263246
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263246: (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 informed consent document was presented before the questionnaires, and the consent was a requirement for participation.<br>IRB: The Ethics Committee at Rio de Janeiro State University approved all procedures (report #2.990.087). 2.2. Measures: We adopted three validated and normalized measures to ensure good quality of data; one instrument for each psychological dimension: psychological stress, depression, and anxiety.</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">Demographic information was collected through a simple one-page questionnaire containing: gender (male, female and non-specific), age (in years) and risk for COVID-19 (“Do you have any current disease that increases your risk for COVID-19 lethality?</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">Furthermore, differences in PSS-10, FDI, and STATI-S between data-collection (time), gender, risk (binary variable indicating whether individual has a pre-existing comorbidity that increased risk of COVID-19 fatality) and their interaction were evaluated using linear mixed effects models, where a random intercept was generated per participant.</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 present research had some limitations that are important to highlight. Limitations include the self-reported nature of the data, as participants filled out the questionnaire by filling out a 45-minute Google Form, which was used to analyze mental health outcomes. Further, participants were asked if they had an illness which increased fatality risk for COVID-19 and were given a few examples of such conditions (i.e., obesity, diabetes, high blood pressure and other cardiac and respiratory conditions). Therefore, outside of these categories given to participants, the answer to this question relies on their knowledge of comorbidities that increase fatality risk for COVID-19 and their perception to the risk. For example, an individual with Vitamin D deficiency may be unaware of their status and state that they do not have any condition that increases risk for COVID-19 lethality, even though this condition increases fatality risk for COVID-19 (World Health Organization, 2017).

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21263246
  147. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263173
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263173: (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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.06.21263173
  148. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263168
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263168: (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 Protocol: After obtaining approval from the institute ethics committee (IEC-450/02.07.2021), medical records of the COVID-19 positive patients that underwent surgical resection for mucormycosis at National Cancer Institute</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">[11] Statistical Analysis: Data pertaining to selected variables in the study were extracted from the records and entered into MS Excel software version 16.0</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MS Excel</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The data were summarized using the medians with interquartile ranges [25th – 75th] for continuous variables and numbers and =proportions (%) for categorical variables Data were statistically reviewed using IBM SPSS Version 24</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 has some limitations. First, the study had a retrospective nature and was based on the analysis of anaesthesia and hospital records. Second, all the patients were from a single center. Our study has one strength as this is the first of its kind study in anesthetic perspectives of COVID-19 associated mucormycosis that can be used as a platform for further studies on this topic.

      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/10.1101/2021.09.06.21263168
  149. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.11.459844
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.11.459844: (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">Gene nsp1 nsp2 nsp3 nsp4 nsp5 nsp6 nsp7 nsp8 nsp9 nsp10 RdRp nsp13 nsp14 nsp15 nsp16 S1 S2 ORF3a E M ORF6 ORF7a ORF7b ORF8 N ORF9b Evol rate 0.1 × 10−3 0.2 × 10−3 1.3 × 10−3 0.8 × 10−3 0.5 × 10−3 3.4 × 10−3 0.3 × 10−3 0.3 × 10−3 0.7 × 10−3 0.1 × 10−3 0.5 × 10−3 0.8 × 10−3 0.3 × 10−3 0.3 × 10−3 0.3 × 10−3 8.4 × 10−3 3.5 × 10−3 1.8 × 10−3 1.6 × 10−3 0.7 × 10−3 0.2 × 10−3 1.5 × 10−3 1.7 × 10−3 16.5 × 10−3 6.10 × 10−3 2.10 × 10−3 5 r 0.05 -0.10 0.30 0.28 -0.09 0.35 -0.42 0.04 0.06 -0.05 0.15 0.20 -0.03 0.15 -0.22 0.46 0.24 -0.06 0.03 0.29 0.01 0.43 0.22 0.19 0.21 0.27 p-value 0.43 0.89 0.09 0.06 0.84 0.01 1.00 0.44 0.30 0.81 0.26 0.15 0.69 0.23 0.96 <0.005 0.10 0.86 0.39 0.04 0.53 <0.005 0.05 0.19 0.22 0.05 to synonymous sites.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Gene nsp1 nsp2 nsp3 nsp4 nsp5 nsp6 nsp7 nsp8 nsp9 nsp10 RdRp nsp13 nsp14 nsp15 nsp16</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">Time-resolved phylogenies were inferred using Augur 12.0.0 [31], IQ-TREE 2.1.2 [32], and TreeTime 0.8.2 [33].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Augur</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IQ-TREE</div><div>suggested: (IQ-TREE, RRID:SCR_017254)</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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    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.11.459844
  150. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.11.459886
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.11.459886: (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">Collection of sequences: All RNA viruses having the host specificity to human and viruses belonging to Nidovirales order were identified from ViralZone Expasy(Viralzone) website and further validated using International Committee on Taxonomy of Viruses (ICTV)(Lefkowitz et al. 2018) website.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ViralZone Expasy(Viralzone</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The tree was visualized using Figtree v1.4.4(Rambaut</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">The sequences of Tobaniviridae family were used as the query and distant orthologs were searched in Refseq protein database with default settings.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Refseq</div><div>suggested: (RefSeq, RRID:SCR_003496)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Codon usage: The codon usage pattern of NSP12 and NSP14 ExoN in Tobaniviridae, Mesoniviridae and Coronaviridae was calculated using EMBOSS Cusp webserver(Rice et al. 2000) and visualized as a heatmap in RStudio.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>EMBOSS</div><div>suggested: (EMBOSS, RRID:SCR_008493)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The Euclidean distance between NSP12 and NSP14 ExoN was calculated using dist function in RStudio.</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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Structure modelling and validation: The structure of SARS-CoV2 NSP14 was modelled based on SARS-CoV NSP14 (PDB #5C8S) using I-TASSER web server(Zhang 2008).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>I-TASSER</div><div>suggested: (I-TASSER, RRID:SCR_014627)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Graphing, Advanced Computation and Exploration (GRACE) program, version 5.1.22 and MATLAB were used to construct graphs/plots.</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">The secondary structure prediction in the ZnF1 motif for Tobaniviridae, Mesoniviridae and Coronaviridae was done using Jpred tool(Cuff et al. 1998) in JALVIEW software(Waterhouse et al. 2009).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Jpred</div><div>suggested: (Jpred, RRID:SCR_016504)</div></div><div style="margin-bottom:8px"><div>JALVIEW</div><div>suggested: (Jalview, RRID:SCR_006459)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The number of residues in each protein coevolving with the active site, ZnF1 and ZnF2 motifs of NSP14_ExoN were calculated and plotted as a circos plot using Circos package v0.69-9.</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">This heatmap was also depicted in the structure of ZnF1 and ZnF2 motifs using Chimera software to map coevolving residues between ZnFs and core replication machinery.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Chimera</div><div>suggested: (Chimera, RRID:SCR_002959)</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

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.11.459886
  151. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.11.459891
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.11.459891: (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">At Spike protein position 657 in Table 1, there are 20 alignable viral proteins from coronaviruses most closely related to SARS-CoV-2, which are N at this position in 85% of the viruses, including SARS-CoV-2, and D at this position in 15% of the alignable betacoronaviruses.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2</div><div>suggested: (BioLegend Cat# 946101, RRID:AB_2892515)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The resulting database was used in the BLASTP (PMID 2231712) search for the homologs of C. elegans ER proteins.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BLASTP</div><div>suggested: (BLASTP, RRID:SCR_001010)</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

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.11.459891
  152. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.02.21262480
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.02.21262480: (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:
      An alternative definition of hospital-acquired infection reliant on the date of first positive swab would have its own limitations: patients could enter with symptoms and not test positive until more than a week into their stay for example.26 Due to the delay from infection to symptom onset, hospital-acquired transmission of SARS-CoV-2 may be missed under common definitions of hospital-acquired. We estimated that nearly 20% of symptomatic COVID-19 patients in hospitals in England in the first wave acquired their infection in hospital settings. Whilst this is likely to have contributed little to the overall number of infections in England, the vulnerability of the hospital community means that this is an important area for further focus. Increased awareness and testing, especially of patients on discharge, as is now commonly in place, is needed to prevent hospitals becoming vehicles for SARS-CoV-2 transmission.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.02.21262480
  153. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263027
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263027: (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 approved by the local Ethical Review Board (41/21) and conducted according to the Declaration of Helsinki.<br>Consent: Blood Plasma samples of patients with PIMS/MIS-C according were taken after written informed consent in the department of Pediatric Cardiology of the Saarland University Hospital (Homburg/Saar, Germany), the Department of Pediatrics, Klinikum Saarbrücken (Germany), the Department of Pediatric Rheumatology and Immunology of the University Children’s Hospital Muenster (Germany), the Department of Pediatrics, Hospital Sant Joan de</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">All patients with PIMS/MIS-C fulfilled the WHO criteria, in addition all patients were seropositive for antibodies against SARS-CoV-2 or had positive PCR, with the exception of one patient who had only reported contact to SARS-CoV2.</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>SARS-CoV2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ELISA for autoantibodies against PGRN, IL-1-Ra: The ELISA for autoantibodies was performed as previously described (19).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PGRN</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Recombinant IL-1-Ra at 40ng/mL (Biozol, #PPT-AF-2000-01RA) alone or with either anti-IL-1-Ra antibody at 5 µg/mL (antibodies-online#ABIN2856394), recombinant SLP-antibody at 5µg/mL (abcam, #ab191883), plasma diluted 1:20 of a patient with acute PIMS/MIS-C and high-titered IL-1-Ra-antibodies (PIMS-I), or plasma diluted 1:20 of the same patient 7 months after PIMS/MIS-C without anymore detectable IL-1-Ra-Abs were preincubated for 2h at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>#PPT-AF-2000-01RA</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-IL-1-Ra</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>antibodies-online#ABIN2856394</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 short, the antigens were obtained using the coding sequences of the GRN gene encoding PGRN, isoform 1 precursor of IL1RN were recombinantly expressed with a C-terminal FLAG-tag in HEK293 cells under the control of a cytomegalovirus promoter (pSFI).</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></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 relatively small number of cases included in the present study, due to the rarity of the disease, is a limitation. Nonetheless, these antibodies suggest to be pathogenetically relevant and should be further investigated in PIMS/MIS-C and other hyperinflammatory diseases.

      Results from TrialIdentifier: No clinical trial numbers were referenced.

      Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.08.21263027
  154. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263232
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263232: (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: Written informed consent was obtained from all study participants prior to study initiation.<br>IRB: The study was approved by the Ethics Committee at HCB (references HCB/2020/0336 and HCB/2021/0196).</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, population and setting: The baseline study population included 578 randomly selected HCW from HCB who delivered care and services directly or indirectly to patients.</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">Quantification of antibodies to SARS-CoV-2: We measured IgA, IgG and IgM antibody levels (median fluorescence intensity, MFI) to different SARS-CoV-2 antigens using previously developed assays based on the quantitative suspension array technology Luminex (Supplementary Information) [37, 41].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2: We measured IgA, IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>IgM</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibody avidity was determined as the percentage of IgA and IgG levels against RBD, S and S2 antigens measured incubating samples with a chaotropic agent (urea 4M, 30 min at room temperature) over the IgA and IgG levels measured in the same samples without chaotropic agent.</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><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 for each participant were collected and managed using REDCap version 8.8.2 hosted at ISGlobal through a standardized electronic questionnaire as previously described [36].</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: 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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.08.21263232
  155. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.06.21263151
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.06.21263151: (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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.06.21263151
  156. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21262922
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.10.21262922: (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 data mining process was done using ‘R’(https://www.r-project.org/) with the packages ‘vegan’, ‘forecast’, ‘dynamictreecut’ and ‘rnaturalearth’.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>https://www.r-project.org/</div><div>suggested: (R Project for Statistical Computing, RRID:SCR_001905)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 genome sequences were obtained by next-generation sequencing with various procedures since February 2020 until August 2021: (i) with the Illumina technology using the Nextera XT paired end strategy on MiSeq instruments (Illumina Inc., San Diego, CA, USA), as previously described (3); (ii) with the Illumina COVIDSeq protocol on a NovaSeq 6000 instrument (Illumina Inc.) since April 2021; or (iii) with Oxford Nanopore technology (ONT) on MinION or GridION instruments (Oxford Nanopore Technologies Ltd., Oxford, UK), as previously described (3)</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">Genome sequence analyses: Genome consensus sequences were generated by mapping on the SARS-CoV-2 genome GenBank accession no. NC_045512.2 (Wuhan-Hu-1 isolate) with the CLC Genomics workbench v.7 (with the following thresholds: 0.8 for coverage and 0.9 for similarity) (https://digitalinsights.qiagen.com/), as previously described (3), or the Minimap2 software (44).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Genome</div><div>suggested: (JGI Genome Portal, RRID:SCR_002383)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SAMtools was used for soft clipping of Artic primers (https://artic.network/), and to remove PCR duplicates (46)</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">Pairwise nucleotide distances between SARS-CoV-2 genomes were computed using the MEGA7 software v10.2.5 (https://www.megasoftware.net/).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>MEGA7</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 classification and naming system: Phylogeny reconstructions based on the SARS-CoV-2 genomes obtained in our laboratory were performed using the nextstrain/ncov tool (https://github.com/nextstrain/ncov) then visualised with Auspice (https://docs.nextstrain.org/projects/auspice/en/stable/) or FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/); the limitation of sampling per date of collection of respiratory specimens was desactivated.</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">Statistical analyses: Statistical tests were carried out using R 4.0.2 (https://cran.r-project.org/) and GraphPad software v5.01 (https://www.graphpad.com/).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>https://cran.r-project.org/</div><div>suggested: (CRAN, RRID:SCR_003005)</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 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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21262922
  157. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263264
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263264: (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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.08.21263264
  158. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263095
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263095: (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 collection: Samples for laboratory studies were obtained under informed consent from participants in an ongoing community based, SARS-CoV-2 testing, genomic surveillance, and vaccination program “Unidos en Salud”, which serves a predominantly Latino community in the Mission neighborhood in San Francisco, California [8,9].</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: Cells were verified to be free of mycoplasma contamination with the MycoAlert Mycoplasma detection kit (Lonza).</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">Pseudoviruses were titered on Huh7.5.1 cells overexpressing ACE2 and TMPRSS2 (gift of Andreas Puschnik) using GFP expression to measure the concentration of focus forming units (ffu) [13].</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Huh7.5.1</div><div>suggested: RRID:CVCL_E049)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudovirus neutralization experiments: Huh7.5.1-ACE2-TMPRSS2 cells were seeded in 96-well plates at a density of 7000 cells/well one day prior to pseudovirus inoculation.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Huh7.5.1-ACE2-TMPRSS2</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 analysis: Pseudovirus flow cytometry data was analyzed with FlowJo to determine the percentage of GFP-positive cells, indicating pseudovirus transduction.</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">Neutralization titers (NT50 and NT90) were calculated from eight-point response curves generated in GraphPad Prism 7 using four-parameter logistic regression.</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:
      A limitation of this study is the relatively small number of serum samples, however the shift in neutralization titer between D614G and variant pseudoviruses shows strong consistency between samples. These serology data leverage human exposures to an array of naturally occurring spike mutations, including those relevant to B.1.617.2, providing a real-world complement to previous animal studies investigating heterologous boosting or multivalent vaccination strategies [14,15]. Together, these results contribute additional evidence suggesting that heterologous boosting strategies may be an important and effective measure to address newly emergent variants with the potential to evade existing acquired immunity. Future studies investigating immune responses to additional emerging variants in vaccinated and unvaccinated individuals will contribute to identifying spike antigen versions that elicit broadly neutralizing antibody responses.

      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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.08.21263095
  159. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.11.459907
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.11.459907: (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">Mouse HLA affinity prediction: NetH2pan 4.0 [61,62] was used to predict mouse HLA affinity of CD8 epitopes using MHCI alleles of the most commonly used mouse strains to study COVID-19 vaccines: C57BL/6 and BALB/c rodents.</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><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">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 selected 28 epitopes from previous papers that had been found to be immunogenic in convalescent COVID-19 patients [27, 31-33] and 20 epitopes from ViPR with positive assay and 100% match with the SARS-CoV-2 N protein reference sequence.</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">Allergenicity prediction: AllerTop 2.0 [57,58] was used to predict allergenicity of 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">Instability index prediction: ProtParam [59] was used to predict the instability index [60] to determine whether an epitope was stable or unstable in vivo.</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></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The 3D structures of MHC molecules were downloaded from Protein Database Bank on RCSB.org and processed on PyMOL to remove the epitope.</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: 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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.11.459907
  160. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263265
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.08.21263265: (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

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.08.21263265
  161. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21263221
    1
    1. sciscore 15 Sep 2021

      SciScore for 10.1101/2021.09.07.21263221: (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 Institutional Review Committee of the Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka (approval memo number: SHNIBPS/Jan-14(09)).</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">Serological testing for antibodies to the RBD of the S1 subunit of the viral spike protein (IgG) was performed from the plasma samples using a commercially available Anti-SARS-CoV-2 ELISA kit as per instruction supplied by the manufacturer.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>viral spike protein (IgG</div><div>suggested: None</div></div><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">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 in Graphpad Prism 9.0.</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: We detected the following sentences addressing limitations in the study:
      One of the key limitations of our study is the small sample size which does not represent the larger population. That is our findings need to be carefully evaluated and tested further through more extensive research with larger samples. Overall, our observation and findings from other studies suggest COVID-19 vaccines are likely to provide long-term protection. Despite occurrences of breakthrough infections, it’s not worrisome yet as most breakthrough cases are mild even with the current aggressive delta variant prevalence all over the world. The World Health Organization has strongly protested against the decision of giving booster doses as there is a lack of evidence in support of such doses (20). The rise of breakthrough cases is worrying thus we can conduct more studies on them and try to identify who is getting more affected so that they can be prioritized for variant-specific booster dosages if strong evidence arises. As Saha et. al. mentioned the world is seeing vaccine apartheid where richer countries are experimenting with booster shots and the low-middle income countries in the Global South including Bangladesh are struggling to control the case and death numbers from COVID as they couldn’t provide a single shot of COVID vaccine to most of its people (21). We must not advise for booster shots unless stronger evidence arises and an equitable vaccine distribution is ensured throughout the world.

      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/10.1101/2021.09.07.21263221
  162. www.gao.gov www.gao.gov
    GAO-18-177, HOMELAND DEFENSE: Urgent Need for DOD and FAA to Address Risks and Improve Planning for Technology That Tracks Military Aircraft
    1
    1. helicoptersofdc 14 Sep 2021
      FAA and aviation groups have reported that with the proliferation of commercial and amateur receivers, the public can now track individual aircraft by receiving the aircraft’s ICAO address, squawk code, and altitude. In addition, these entities have reported that since aviation groups and hobbyists have connected the receivers, the networked receivers can calculate and identify the latitude and longitude of the aircraft they are tracking. In addition, according to these reports, some groups maintain aircraft information databases and receiver networks that can identify aircraft by ICAO address and can locate aircraft by comparing the time difference of arrival of Mode S signals between three or more receivers.20 Using data derived from this work, interested parties—including adversaries (for example, foreign intelligence entities, terrorists, and criminals)—can identify military aircraft by type and registration number, and can track the aircraft while in flight through Mode S fixed address broadcasts. Using this readily available public information, we were able to track various kinds of military aircraft that were equipped with Mode S transponders.

      Mode S triangulation

      helicoptersofdc
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    gao.gov/assets/gao-18-177.pdf
  163. www.theguardian.com www.theguardian.com
    Dead Sea scroll deciphered to reveal ancient calendar
    1
    1. chrisaldrich 14 Sep 2021
      “The scroll is written in code, but its actual content is simple and well-known, and there was no reason to conceal it,” they write in the Journal of Biblical Literature. “This practice is also found in many places outside the land of Israel, where leaders write in secret code even when discussing universally known matters, as a reflection of their status. The custom was intended to show that the author was familiar with the code, while others were not.”

      Ancient scribes sometimes wrote in code even though the topics at hand were well known as a means of showing their status.

      cryptography Dead Sea Scrolls status indicators power knowledge archaeology of knowledge
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    theguardian.com/books/2018/jan/26/dead-sea-scroll-deciphered-to-reveal-ancient-calendar
  164. Local file Local file
    Untitled document
    2
    1. waternew 14 Sep 2021
      解缠有各种定义[52,48,2,7,18]，但共同的目标是由线性子空间构成的潜在空间，每个空间控制一个变异因子。

      latent code 简单理解就是，为了更好的对数据进行分类或生成，需要对数据的特征进行表示，但是数据有很多特征，这些特征之间相互关联，耦合性较高，导致模型很难弄清楚它们之间的关联，使得学习效率低下，因此需要寻找到这些表面特征之下隐藏的深层次的关系，将这些关系进行解耦，得到的隐藏特征，即latent code。由 latent code组成的空间就是 latent space。

    2. waternew 14 Sep 2021
      图1.虽然传统的生成器[29]仅通过输入层提供潜在编码，但我们首先将输入映射到中间潜在空间W，然后在每一个卷积层通过自适应实例规范化（AdaIN）控制生成器。在评估非线性之前，在每次卷积之后添加高斯噪声。这里“A”代表学习的仿射变换，“B”将学习的每通道缩放因子应用于噪声输入。映射网络f由8个层组成，合成网络g由18层组成-每个分辨率两层（分辨率从）。使用单独的1×1卷积将最后一层的输出转换为RGB，类似于Karras等人[29]。

      ①AdaIN的作用？ 2017 年提出的风格迁移算法 AdaIN，出自论文《Arbitrary Style Transfer in Real-time with Adaptive Instance Normalization》。AdaIN 基于前向神经网络，作者提出了一种标准化方法 Adaptive Instance Normalization (AdaIN)，从而实现任意风格的迁移。 ②Mapping network Mapping network 要做的事就是对隐藏空间（latent space）进行解耦 ③latent code 简单理解就是，为了更好的对数据进行分类或生成，需要对数据的特征进行表示，但是数据有很多特征，这些特征之间相互关联，耦合性较高，导致模型很难弄清楚它们之间的关联，使得学习效率低下，因此需要寻找到这些表面特征之下隐藏的深层次的关系，将这些关系进行解耦，得到的隐藏特征，即latent code。由 latent code组成的空间就是 latent space。

    Annotators

  165. www.sciencedirect.com www.sciencedirect.com
    Single-dose intranasal vaccination elicits systemic and mucosal immunity against SARS-CoV-2
    1
    1. scibot 14 Sep 2021
      Strain Code: 028

      DOI: 10.1016/j.isci.2021.103037

      Resource: (IMSR Cat# CRL_028,RRID:IMSR_CRL:028)

      Curator: @Naa003

      SciCrunch record: RRID:IMSR_CRL:028

      What is this?
      RRID:IMSR_CRL:028 RRIDCUR:Missing
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    sciencedirect.com/science/article/pii/S2589004221010051
  166. www.sciencedirect.com www.sciencedirect.com
    Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH
    1
    1. scibot 14 Sep 2021
      code: 027

      DOI: 10.1016/j.crmeth.2021.100068

      Resource: (IMSR Cat# CRL_027,RRID:IMSR_CRL:027)

      Curator: @Naa003

      SciCrunch record: RRID:IMSR_CRL:027

      What is this?
      RRID:IMSR_CRL:027 RRIDCUR:Missing
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    sciencedirect.com/science/article/pii/S266723752100120X
  167. www.sanity.io www.sanity.io
    Why Typescript and Svelte are a match made in heaven
    2
    1. TylerRick 14 Sep 2021
      TypeScript is an extension of JavaScript. You can think of it as JavaScript with a few extra features. These features are largely focused on defining the type and shape of JavaScript objects. It requires that you be declarative about the code you're writing and have an understanding of the values your functions, variables, and objects are expecting.While it requires more code, TypeScript is a fantastic means of catching common JavaScript bugs while in development. And for just that reason, it's worth the extra characters.
      TypeScript good explanation answer the "why?"
    2. TylerRick 14 Sep 2021
      React, on the other hand, often requires a fair amount of boilerplate code, even for simple interactions.
      React disadvantages/drawbacks/cons verbose / noisy / too much boilerplate
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    sanity.io/guides/using-typescript-with-svelte
  168. github.com github.com
    Reimagining svelte2tsx · Issue #1077 · sveltejs/language-tools
    1
    1. TylerRick 14 Sep 2021
      Code that is needed to create the output and the output itself is hard to read because of all the workarounds we have to use, especially around shadowed variables and control flow
      hard to read (readability) transpiling
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    github.com/sveltejs/language-tools/issues/1077
  169. www.gitmemory.com www.gitmemory.com
    Svelte Language Tools broken - gitpod
    1
    1. TylerRick 14 Sep 2021
      Couldn't start client Svelte
      VS Code Svelte I have this problem too
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    gitmemory.com/issue/gitpod-io/gitpod/4034/824475213
  170. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263268
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.08.21263268: (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">After the launch of Texas CARES, an immunoassay for detection of antibodies to the SARS-CoV-2 spike protein (Roche S-test) became available and was added to the immunoassay for detection of antibodies to the SARS-CoV-2 nucleocapsid protein (Roche N-test), so that we are able to monitor the combined impact of prior infection and the COVID-19 vaccine.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>SARS-CoV-2 nucleocapsid 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: 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/10.1101/2021.09.08.21263268
  171. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263279
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.08.21263279: (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/content/10.1101/2021.09.08.21263279v3
  172. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.07.21261811
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.07.21261811: (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 approved by the Western Institutional Review Board (IRB).<br>Consent: All participants, parents/legal guardians, or legally authorized representatives 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">Participants were excluded if they (1) had a history of hypersensitivity to ciclesonide, (2) had taken an inhaled or intranasal corticosteroid within 14 days, (3) had taken oral corticosteroids within 90 days, (4) had participated in any other clinical trial or use of any investigational agent within 30 days, (5) had a history of cystic fibrosis, (6) has a history of idiopathic pulmonary fibrosis, (7) were receiving treatment with hydroxychloroquine/chloroquine, or (8) were pregnant.</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 was a phase III, multicenter, double-blinded, randomized placebo-controlled trial to assess the safety and efficacy of ciclesonide metered-dose inhaler (MDI) for the treatment of non-hospitalized patients with symptomatic COVID-19 infection.</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">Individual site personnel dispensed individual kits in order, blinded to the assignment.</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 final primary outcome, a sample size of approximately 232 patients (116 per arm) was required to achieve 90% power at α = 0.05.</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">NCT04377711</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 the Safety and Efficacy of Ciclesonide in the Tre…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04193878</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">ARrest RESpiraTory Failure From PNEUMONIA</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04330586</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 Trial of Ciclesonide in Adults With Mild-to-moderate COVID…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04331054</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Terminated</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Protective Role of Inhaled Steroids for Covid-19 Infection</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04331470</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">Evaluation of Efficacy of Levamisole and Formoterol+Budesoni…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04355637</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">Inhaled Corticosteroid Treatment of COVID19 Patients With Pn…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04356495</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 COVID-19 Outpatient Treatment in Individuals With R…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04381364</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">Inhalation of Ciclesonide for Patients With COVID-19: A Rand…</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04416399</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Terminated</td><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">STerOids in COVID-19 Study</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">ISRCTN86534580</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>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.07.21261811
  173. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.10.459749
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.10.459749: (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">4.1 Mice: All in vivo experiments were performed using (8-12 weeks old) wild-type (wt) female BALB/cOlaHsd mice purchased from Harlan.</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">SARS-CoV-2 strains were propagated in VERO E6 cells (ATCC—CRL 1586) in T175 Flasks using Dulbecco’s Modified Eagle’s - high glucose medium (DMEM) (Euroclone, Pero, Italy) supplemented with 2mM L-glutamine (Lonza, Milano, Italy), 100 units/mL penicillin-streptomycin (Lonza, Milano, Italy and 2% fetal bovine serum (FBS) (Euroclo, Pero, Italy).</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">4.1 Mice: All in vivo experiments were performed using (8-12 weeks old) wild-type (wt) female BALB/cOlaHsd mice purchased from Harlan.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BALB/cOlaHsd</div><div>suggested: RRID:MGI:5653315)</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 amino acid (a.a.) sequence of each RBD was inserted into a pTWIST-CMV-BetaGlobin-WPRE-Neo vector (Twist Bioscience, San Fransico, CA, USA)</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pTWIST-CMV-BetaGlobin-WPRE-Neo</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">4.18 Statistical analysis: Data were analyzed and presented as (mean ± SEM) using Student’s t-test or one-way ANOVA as mentioned in the figure legend, with 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

      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

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.10.459749
  174. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.09.459504
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.09.459504: (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 subjects: Mass General Brigham Institutional Review Board approved this study and protocol.</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">For the anti-S and anti-RBD antibody standard, the monoclonal antibody CR3022 was serially diluted 2 times from 0.5 μg/mL.</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><div style="margin-bottom:8px"><div>anti-RBD</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells were stained with Biolegend antibodies FITC anti-CD27 (356404), PE anti-CCR7 (353204), Percp</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-CD27</div><div>suggested: (BioLegend Cat# 356404, RRID:AB_2561788)</div></div><div style="margin-bottom:8px"><div>anti-CCR7</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 cell line (ATCC) was maintained in DMEM containing 10% FBS, 100 U/mL penicillin and 100 U/mL streptomycin (Gibco).</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">SARS-CoV-2 pseudovirus neutralization assay: 293T cells were co-transfected with pHDM vector expressing SARS-CoV-2 variants, pLenti CMV Puro LUC (w168-1), and psPAX2 (Addgene) with lipofetamine 3000.</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><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 be consistent with the pHDM-Wuhan-Hu-1-delta21 and pHDM-D614G-delta21 plasmids obtained from Addgene, the c-terminal 21 amino acid on all the variants were deleted (Crawford et al., 2020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHDM-Wuhan-Hu-1-delta21</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pHDM-D614G-delta21</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Binding signals were scored positive if OD405 values were above 5x PBS control on the same plate. mAb spike binding EC50 measurement: 293T cells were co-transfected with pHDM-Wuhan-Hu-1 and pMAX-GFP plasmids at a 4:1 ratio by lipofectamine 3000 (Thermo fisher).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHDM-Wuhan-Hu-1</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>pMAX-GFP</div><div>suggested: RRID:Addgene_16007)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">293T cell pool cotransfected with pHEF-VsVg and pMAX-GFP plasmids at a 4:1 ratio was used as a negative control.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHEF-VsVg</div><div>suggested: RRID:Addgene_22501)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">SARS-CoV-2 pseudovirus neutralization assay: 293T cells were co-transfected with pHDM vector expressing SARS-CoV-2 variants, pLenti CMV Puro LUC (w168-1), and psPAX2 (Addgene) with lipofetamine 3000.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pHDM</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>psPAX2</div><div>suggested: RRID:Addgene_12260)</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">After enrollment, clinical team identified one subject was not diagnosed by nasopharyngeal swab RT-PCR test, but by Quest Diagnostics antibody test and symptoms consistent with COVID-19 (Chen et al., 2020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Quest</div><div>suggested: (QUEST, RRID:SCR_005210)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Graphpad software generated standard curves for each plate by non-linear regression.</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">The EC50 for each S-binding mAb was reported as the concentration with 50% of maximal binding determined by non-linear regression 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.

      </footer>

    Visit annotations in context

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.09.459504
  175. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.10.21263376
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.10.21263376: (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 UK Medicines and Healthcare products Regulatory Agency (MHRA) and West Midlands Edgbaston Research Ethics Committee.<br>Consent: All participants provided written informed consent before enrolment.</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">Participants: Eligible participants included healthy adult males and non-pregnant and non-lactating females between 18 and 75 years 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">The sample size was flexible, based on the need for the study to adapt to accruing safety data.</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 previously published work, a physiologically based pharmacokinetic (PBPK) model was validated for nitazoxanide using Simbiology (MATLAB</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">, STATA version 16 and R version 4.0.2.</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:
      This is a limitation of all first-in-human healthy volunteer studies, within which it is always difficult to generate pharmacodynamic data. The median age and lack of medical comorbidities in this healthy volunteer cohort also differs from the main target population for early use of antivirals, although their use in post-exposure prophylaxis and to reduce isolation requirements in low-risk groups is also being considered. There is an urgent unmet need for safe and effective antiviral therapeutics in early-stage mild/moderate COVID-19. These are aimed at preventing progression of disease to hospitalisation and death, and possibly also reducing viral transmission in community settings. Re-purposing and dose escalation of nitazoxanide for COVID-19 is supported by in-vitro data, PBPK modelling and now robust safety and pharmacokinetic data at the 1500mg BD dose. This dose will provide the maximum potential to demonstrate antiviral activity of nitazoxanide in subsequent trials to provide a definitive outcome on the utility of this drug in COVID-19. Study Highlights: What is the current knowledge on the topic?: Nitazoxanide is an anti-parasitic medication licensed by the FDA at standard dosing (500mg BD) with an established safety profile. Antiviral activity has been demonstrated for numerous viruses with in vitro data demonstrating activity against SARS-CoV-2. No steady-state pharmacokinetic data are available at higher doses or in COVID-19 but PBPK modelling has indicated a 1500m...

      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">NCT04746183</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">AGILE (Early Phase Platform Trial for 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.

      </footer>

    Visit annotations in context

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.10.21263376
  176. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263284
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.08.21263284: (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: Study population, study design and recruitment: Sixteen COVID-19 recovered volunteers who were infected with SARS-CoV-2 and developed COVID-19 in the spring of 2020 and 14 SARS-CoV-2 naïve healthy volunteers and (Supplementary Table 1) were recruited for the study under informed consent.<br>Field Sample Permit: 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: 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).</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">Anti-S binding ELISA: Anti-SARS-CoV-2 S-Protein antibodies were measured using the Roche Elecsys Anti-SARS-CoV-2 S immunoassay on a Cobas e411 analyzer (Roche Diagnostics, Basel, Switzerland) as described somewhere else18.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Anti-S binding ELISA: Anti-SARS-CoV-2 S-Protein</div><div>suggested: None</div></div><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">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 Trimmomatic 19 (version 0.36) and STAR RNA-seq 20 (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>Trimmomatic</div><div>suggested: (Trimmomatic, RRID:SCR_011848)</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">HTSeq 21 (version 0.9.1) was to retrieve the raw counts and subsequently, Bioconductor package DESeq2 22 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>HTSeq</div><div>suggested: (HTSeq, RRID:SCR_005514)</div></div><div style="margin-bottom:8px"><div>Bioconductor</div><div>suggested: (Bioconductor, RRID:SCR_006442)</div></div><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">Additionally, the RUVSeq 23 package was applied to remove confounding factors.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>RUVSeq</div><div>suggested: (RUVSeq, RRID:SCR_006263)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The visualization was done using dplyr (https://CRAN.R-project.org/package=dplyr) and ggplot2 24.</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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">P-values of cytokines were calculated using two-stage linear step-up procedure of Benjamini, Krieger and Yekutieli 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: We detected the following sentences addressing limitations in the study:
      Limitations of this study: This elderly cohort previously infected with SARS-CoV-2 was from a narrowly defined geographically area and included only one gender (females). The infection occurred in the spring of 2020 and the viral strain had not been sequenced. The SARS-CoV-2 antigen-naïve population was from a narrowly defined geographically area. The study was confined to the BNT162b mRNA vaccine.

      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/10.1101/2021.09.08.21263284
  177. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.08.21263283
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.08.21263283: (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: Data analysis: We excluded locations representing fewer than 5000 people in their catchment population to reduce data variability, and locations which did not consent to data sharing.</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">Cts were called from raw fluorescence data using the Cy0 algorithm from the qpcR package (v1.4-1) in R (Guescini et al., 2008), and manually inspected for agreement with the raw traces in the native BioRad Maestro software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BioRad Maestro</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses and visualizations were performed in Python 3.8.</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: Thank you for sharing your code and data.

      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
      Our study has several limitations. First, wastewater SARS-CoV-2 concentrations are highly variable due to sampling, lab processing, and qPCR analysis. We attempted to reduce this challenge through normalization with a fecal virus with biological similarities to SARS-CoV-2 (Wu et al., 2020) and by optimizing our lab protocols (Methods). However, we still observed large spikes in wastewater concentrations in some locations which were not explained by changes in reported COVID-19 cases. These data challenges are common in the field of wastewater-based epidemiology, and our group and others are actively developing models to correct for variability and better interpret spikes. Second, the geographic comparisons between wastewater results and reported cases are not exact, as sampling location catchments may represent a subset or superset of the respective comparison counties (Table S1). However, we found no relationship between a catchment’s coverage of its comparison county and its correlation between wastewater and cases, indicating that these wastewater catchments were sufficient to identify broad and general trends in their associated communities (Fig S4). Alternative public health applications of wastewater-based epidemiology like building-level or manhole sampling may require more granular insight, in which geographies may need to be more precisely aligned. Third, wastewater data showed a range of correlation strengths with reported cases (Fig 1, Fig S3). In addition to techn...

      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/10.1101/2021.09.08.21263283
  178. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263351
    1
    1. sciscore 14 Sep 2021

      SciScore for 10.1101/2021.09.09.21263351: (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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    medrxiv.org/cgi/content/10.1101/2021.09.09.21263351
  179. docs.google.com docs.google.com
    Syllabus - Sacred Scripture
    1
    1. FreddyZhang 14 Sep 2021

      if we don't have our computer in us, can we use our phone to scan the QR code?

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    docs.google.com/presentation/d/e/2PACX-1vQYWmvmqS0tM4zL27VGgnMfEP6Pzebx92IxO5RNWwC2vazAcBEGJniRuv4lJ7bdfoj_Qi2XKGKluV16/pub
  180. betterprogramming.pub betterprogramming.pub
    The Right Usage of Aliases in Webpack and TypeScript
    1
    1. TylerRick 14 Sep 2021
      From my point of view, this approach will help you to write cleaner code. Also, it will help to maintain the project. For instance, moving a file from the current directory to another will cause fewer problems, because every file uses an absolute path instead of a relative one. Last but not least, it helps you during development.
      not: relative import paths webpack: resolve.alias advantages/merits/pros maintainability portability (computing)
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    betterprogramming.pub/the-right-usage-of-aliases-in-webpack-typescript-4418327f47fa
  181. blog.johnnyreilly.com blog.johnnyreilly.com
    Using TypeScript and webpack alias: goodbye relative paths | I CAN MAKE THIS WORK
    2
    1. TylerRick 14 Sep 2021
      The declarations you make in the tsconfig.json are re-stated in the webpack.config.js. Who wants to maintain two sets of code where one would do? Not me.
      avoid duplication TypeScript: tsconfig.json: compilerOptions.paths webpack: resolve.alias
    2. TylerRick 14 Sep 2021
      Let's not get over-excited. Actually, we're only part-way there; you can compile this code with the TypeScript compiler.... But is that enough?I bundle my TypeScript with ts-loader and webpack. If I try and use my new exciting import statement above with my build system then disappointment is in my future. webpack will be all like "import whuuuuuuuut?"You see, webpack doesn't know what we told the TypeScript compiler in the tsconfig.json.
      not enough to just have _; also need _ TypeScript: tsconfig.json webpack: resolve.alias TypeScript: tsconfig.json: compilerOptions.paths
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    blog.johnnyreilly.com/2018/08/21/typescript-webpack-alias-goodbye-relative-paths/
  182. github.com github.com
    resolve.alias not works · Issue #4160 · webpack/webpack
    1
    1. TylerRick 13 Sep 2021
      This is not dumb at all. It is exceedingly common to use aliases. It's not about being lazy, it's about writing portable code.
      portability (computing)
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    github.com/webpack/webpack/issues/4160
  183. github.com github.com
    sveltejs/svelte-loader
    1
    1. TylerRick 13 Sep 2021
      Webpack's resolve.mainFields option determines which fields in package.json are used to resolve identifiers. If you're using Svelte components installed from npm, you should specify this option so that your app can use the original component source code, rather than consuming the already-compiled version (which is less efficient).
      webpack: resolve.mainFields answer the "why?" good explanation svelte-loader
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    github.com/sveltejs/svelte-loader
  184. developer.mozilla.org developer.mozilla.org
    import
    1
    1. TylerRick 13 Sep 2021
      Import a module for its side effects only Import an entire module for side effects only, without importing anything. This runs the module's global code, but doesn't actually import any values.
      importing module for its side effects
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    developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Statements/import
  185. thoughtstorms.info thoughtstorms.info
    Untitled document
    1
    1. offray 13 Sep 2021
      Why shouldn't an IntegratedDevelopmentEnvironment be like Wiki?

      Efforts in that very sense are being done by the GToolkit

      wikis
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    thoughtstorms.info/view/ProgrammingWithAndInWiki
  186. Local file Local file
    The Kiss
    1
    1. ethanseow 13 Sep 2021
      Whenever she wore this dress I was unable toresist touching the fabric of the skirt. I found the notes evocative,mysterious, and if she let me, I traced my nger over the stitcheddots as if they represented a dierent code than that of music’s, likeBraille or Morse, a message that I might in time decipher.

      love from the mother is finally shown, she is trying to decipher it

    Annotators

  187. www.biorxiv.org www.biorxiv.org
    METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance
    2
    1. Public_Reviews 13 Sep 2021

      Evaluation Summary:

      This work examines how METTLL18-mediated RPL3 histidine methylation on 245 position regulates translation elongation and protects cells from cellular aggregation of Tyr-rich proteins. The study hints at the existence of a "ribosome code" and how posttranslational modification of ribosomal proteins could affect translation.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

      evaluationSummary
    2. Public_Reviews 13 Sep 2021

      Reviewer #3 (Public Review):

      In this article, Matsuura-Suzuki et al provided strong evidence that the mammalian protein METTL18 methylates a histidine residue in the ribosomal protein RPL3 using a combination of Click chemistry, quantitative mass spectrometry, and in vitro methylation assays. They showed that METTL18 was associated with early sucrose gradient fractions prior to the 40S peak on a polysome profile and interpreted that as evidence that RPL3 is modified early in the 60S subunit biogenesis pathway. They performed cryo-EM of ribosomes from a METTL18-knockout strain, and show that the methyl group on the histidine present in published cryo-EM data was missing in their new cryo-EM structure. The missing methyl group gave minor changes in the residue conformation, in keeping with the minor effects observed on translation. They performed ribosome profiling to determine what is being translated efficiently in cells with and without METTL18, and found decreased enrichment of Tyrosine codons in the A site of ribosomes from cells lacking METTL18. They further showed that longer ribosome footprints corresponding to sequences within ribosomes that have already bound to A-site tRNA contained less Tyrosine codons in the A site when lacking METTL18. This suggests methylation normally slows down elongation after tRNA loading but prior to EF-2 dissociation. They hypothesize that this decreased rate affects protein folding and follow up with fluorescence microscopy to show that EGFP aggregated more readily in cells lacking METTL18, suggesting that translation elongation slow down mediated by METTL18 leads to enhanced folding. Finally, they performed SILAC on aggregated proteins to confirm that more tyrosine was incorporated into protein aggregates from cells lacking METTL18.

      The article is interesting and uses a large number of different techniques to present evidence that histidine methylation of RPL3 leads to decreased elongation rates at Tyrosine codons, allowing time for effective protein folding. I agree with the interpretation of the results, although I do have minor concerns:

      1. The magnitude of each effect observed by ribosome profiling is very small, which is not unusual for ribosome modifications or methylation. Methylation seems to occur on all ribosomes in the cell since the modification is present in several cryo-EM structures. The authors suggest that the modification occurs during biogenesis prior to folding and being inaccessible to METTL18, so it is unlikely to be removed. For that reason, I do not think it is warranted to claim that this is an example of a ribosome code, or translation tuning. Those terms would indicate regulated modifications that come on and off of proteins, but the authors have not presented evidence that the activity is regulated (and don't really need to for this paper to be impactful).

      2. In Figure 4-supplement 1, it appears there are slightly more 80S less 60S in the METTL18 knockout with no change in 40S. It might be normal variability in this cell type, but quantitation of the peaks from 2 or more experiments is needed to make the claim that ribosome biogenesis is unaffected by METTL18 deletion. Likewise, the authors need to quantitate the area under the curve for 40S and 60S levels from several replicates and show an average -/+ error for figure 3, supplement 1 because that result is essential to claim that ribosome biogenesis is unaffected.

      3. The effect of methylation could be any step after accommodation of tRNA in the A site and before dissociation of EF-2, including peptidyl transfer. More evidence is needed for claiming strongly that methylation slows translocation specifically. This could be followed up in vitro in a new study.

      peerReview
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    biorxiv.org/content/10.1101/2021.07.29.454307v1
  188. docs.google.com docs.google.com
    Syllabus - Sacraments and the Church
    1
    1. mikefedor 13 Sep 2021

      The QR sign out code is a good way to keep track of the bathroom line as well as know where everyone is.

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    docs.google.com/presentation/d/e/2PACX-1vRwY0UWdYJtxs21Tx8ckJylggOC1uwlvB90KF4H24BV6bGTr3SgQswI--9caKUpu5vfOXVKYRXztAWa/pub
  189. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.10.459744
    1
    1. sciscore 13 Sep 2021

      SciScore for 10.1101/2021.09.10.459744: (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">ELISA experiments: 96-well ELISA plates were coated with 100μL of anti-ACE2 coating antibody (2μg/ml diluted in PBS pH 7.4) over night at room temperature.</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></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Following incubation for 1 hour at room temperature, plates were washed five times with washing buffer after which 100μL of anti-Histidine detection antibody (diluted 1/500 in blocking buffer) was added for another hour.</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><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">Surface Plasmon Resonance Analysis: Recombinant SARS-CoV-2 spike proteins (His-tagged) were purchased from Acro Biosystems Inc. (Newark, USA) or produced inhouse by overexpression of respective constructs in HEK293T cells followed by purification via nickel NTA chromatography and size exclusion chromatography.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Vero E6 cells were cultured in DMEM medium (Gibco, Gaithersburg, MD, USA or Thermofisher) containing 10% fetal bovine serum (FBS).</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 (HTB-55; American Type Culture Collection [ATCC], Manassas, VA, USA) were cultured in DMEM F12 Medium (ATCC) with 20% FBS.</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">Mutations in isolates used at the Karolinska are as follows (with Spike mutations indicated in bold): Preparation of recombinant human ACE2: Clinical grade recombinant human ACE2 (amino acids 18-740) was produced by the contract manufacturer Polymun Scientific (Klosterneuburg, Austria) from CHO cells according to GMP guidelines under serum free conditions and formulated as a physiologic aqueous solution, as described previously (Haschke et al</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><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">Using BiaEvaluation 4.1 software, kinetic analysis was carried out by applying a Langmuir 1:1 (apparent affinity) and a bivalent analyte binding algorithm, which separates first step binding (A + B = AB; affinity) from the second step binding (AB + B = AB2; avidity)</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">Using BiaEvaluation 4.1 software, kinetic analysis was carried out by applying a Langmuir 1:1 (apparent affinity) and a bivalent analyte binding algorithm, which separates first step binding (A + B = AB; affinity) from the second step binding (AB + B = AB2; avidity)</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">Half-maximal inhibitory concentration (IC50) and inhibitory concentration 90 (IC90) were calculated using GraphPad Prism Software (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></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Visualizations of RBDs and full-length Spike protein: Visualizations were rendered with pymol software (the PyMOL Molecular Graphics System, Version 2.4 Schrödinger, LLC), based on a model of the fully glycosylated Spike-ACE2 complex described in Capraz et al., (submitted for publication) and https://covid.molssi.org//models/#spike-protein-in-complex-with-human-ace2-ace2-spike-binding. Primers and Antibodies: The following tables lists the primers and Antibodies used in this study:</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: 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 this study: Our study used two different cell types and should be expanded using additional human cell types and also organoids. Moreover, to indeed make a claim on universality, additional variants should (and can) be tested using affinity/avidity measurements and neutralization assays.

      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

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.10.459744
  190. www.biorxiv.org www.biorxiv.org
    https://biorxiv.org/cgi/content/10.1101/2021.09.10.459786
    1
    1. sciscore 13 Sep 2021

      SciScore for 10.1101/2021.09.10.459786: (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">For fluorescent imaging, HEK293A cells (ATCC, USA) were maintained in Dulbecco’s Modified Eagle Medium (DMEM - Lonza, Switzerland) complemented with 10% fetal bovine serum (Biosera, France) and Penicillin/Streptomycin (100 U/ml and 100 μg/ml, respectively - Lonza, Switzerland).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293A</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Vero-E6 cells were seeded in a 96-well plate on the day before the experiments.</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">The D4H domain-coding sequence from this plasmid was subcloned into the pEYFP-C1 plasmid containing mVenus in place of EYFP, using BglII and BamHI restriction enzymes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pEYFP-C1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cytosolic Cerulean was expressed from a pEYFP-N1 plasmid where EYFP had been replaced with Cerulean.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>pEYFP-N1</div><div>suggested: RRID:Addgene_37202)</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">Virus infection-induced gene expression signatures: Microarray gene expression profiles of different virus-infected cell lines were downloaded from Gene Expression Omnibus (GEO) with accession numbers GSE28166 (H5N1), GSE37571 (Influenza), GSE33267 (SARS-CoV-1), GSE56677 and GSE45042 (MERS-CoV).</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">Preprocessing and differential expression (DE) analysis was performed by using R package limma (Ritchie et al. 2015).</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">Differential expression (DE) analysis was performed using R library DESeq2 (Love, Huber, and Anders 2014).</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">We matched LINCS-L1000 drugs with ChEMBL effective drug dataset (http://chembl.blogspot.com/2020/05/chembl27-sars-cov-2-release.html) using drug names and simplified molecular-input line-entry system (SMILES).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ChEMBL</div><div>suggested: (ChEMBL, RRID:SCR_014042)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">In addition, we used PROGENy pathway activity scores to weight the prior knowledge network and assist CARNIVAL in the discovery of optimal networks connecting the upstream perturbation (RIG-I like receptors) to the downstream targets (TFs).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PROGENy</div><div>suggested: (PROGENY, RRID:SCR_006647)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We performed ROC analysis using scikit-learn Python library to evaluate similarity-based and machine learning-based predictions.</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: 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>

    Visit annotations in context

    Annotators

    URL

    biorxiv.org/cgi/content/10.1101/2021.09.10.459786
  191. www.medrxiv.org www.medrxiv.org
    https://medrxiv.org/cgi/content/10.1101/2021.09.09.21263328
    1
    1. sciscore 13 Sep 2021

      SciScore for 10.1101/2021.09.09.21263328: (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 and survey instrument were approved by the Harvard T.H. Chan School of Public Health 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">To incentivize participation, small monetary incentives are provided to randomly selected users who complete the surveys.</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

    Annotators

    URL

    medrxiv.org/cgi/content/10.1101/2021.09.09.21263328