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    1. SciScore for 10.1101/2020.09.23.308239: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A derivative of the Broad repurposing library was used to incubate Caco-2 cells before infecting them with an isolate of SARS-CoV-2 (FFM-1 isolate, see 35).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Caco-2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pathway enrichment Associated pathways for subgraphs and significant targets were identified using the Enrichr 33 Python package.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Python</div> <div>suggested: (IPython, RRID:SCR_001658)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly, gene symbol lists were assembled from their respective subgraph or dataset and compared against multiple pathway gene set libraries including Reactome, KEGG, and WikiPathways.</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> <div style="margin-bottom:8px"> <div>KEGG</div> <div>suggested: (KEGG, RRID:SCR_012773)</div> </div> <div style="margin-bottom:8px"> <div>WikiPathways</div> <div>suggested: (WikiPathways, RRID:SCR_002134)</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201863: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">All affiliated with the University of Pennsylvania Perelman School of Medicine. # Patients were initially approached for consent after testing positive for SARS-CoV-2 by polymerase chain reaction (PCR).</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right: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></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Clinical data abstraction For inpatients, clinical data were abstracted from the electronic medical record into REDCap databases.</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">Flow Cytometric Analyses All analysis and visualization was performed in FlowJo (Treestar, version 10.6.2).</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.312355: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Finally, the best allele-epitope complexes were selected 94 based upon visual inspection and the PatchDock criteria, as well as they were compared 95 with their respective control peptides (co-crystal ligands of HLA-C*06:02 and HLA- 96 DRB1*01:01). 97 2.4.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>PatchDock</div> <div>suggested: (PatchDock, RRID:SCR_017589)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Structure prediction, refinement, and validation 115 PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred/) [38,39] and GalaxyWEB 116 (http://galaxy.seoklab.org/) [40,41] were utilized to predict the secondary and tertiary 117 structure, respectively, of the multi-epitope vaccine construct.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>http://bioinf.cs.ucl.ac.uk/psipred/</div> <div>suggested: (PSIPRED, RRID:SCR_010246)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The best model was refined 118 with GalaxyWEB [40,41] whereas its visualization was obtained from the VMD software 119 (Version 1.9.3) [32].</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GalaxyWEB</div> <div>suggested: (GalaxyWEB, RRID:SCR_018558)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The HLA allele genotypic frequencies 146 available on IEDB-AR were obtained from Allele Frequency Database (AFD) 147 (http://www.allelefrequencies.net/).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>http://www.allelefrequencies.net/</div> <div>suggested: (Allele Frequencies in Worldwide Populations, RRID:SCR_007259)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The results were shown on a world 151 map using Rstudio software (Version 3.5.3) [48].</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">213 The tertiary structure was subjected to refinement using the GalaxyRefine server.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GalaxyRefine</div> <div>suggested: (GalaxyRefine, RRID:SCR_018531)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">RMSD (0.292), MolProbity (2.364),</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MolProbity</div> <div>suggested: (MolProbity, RRID:SCR_014226)</div> </div> </td></tr></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:

      Discussion 257 Immunoinformatics represents a valuable tool whereby the limitations in the selection of 258 appropriate antigens and immunodominant epitopes may be overcome [17]. Previous in 259 silico-based reports have shown that the SARS-CoV-2 S glycoprotein contains potential 260 epitopes [8-11]. Therefore, researchers have recently attempted to design epitope-based 261 vaccine candidates against SARS-CoV-2 [10, 11]. Despite these relevant contributions, one 262 group only used T cell epitopes and did not include BC epitopes [10], which are 263 fundamental players in antiviral immune response [18]. The second work, on the other 264 hand, considered several viral membrane proteins, including the S glycoprotein, to 265 identified probable T and BC epitopes [11]. Although the predicted epitopes showed good 266 immunogenic potential, the vaccine does not target S glycoprotein RBM [11]. In the 267 present study, highly potential B and T cell epitopes from the SARS-CoV-2 glycoprotein 268 were predicted and the best selected to design a high-quality multi-epitope vaccine 269 candidate. Remarkably, this vaccine harbours 2 epitopes (E19 in Table 1 and E10 in Table 270 2) that could evoke immune responses against SARS-CoV-2 RBM—the main responsible 271 for virus entry into human cells [4,51], whereas 4 epitopes (E43, E44, E45, and E46 in 272 Table 1) may direct the immune attack against other regions of SARS-CoV-2 RBD. These 273 results are consistent with in vitro data that have d...


      Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><tr><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">NCT01609257</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">Norovirus Bivalent-Vaccine Efficacy Study</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.312298: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">Cell lines were tested negative for mycoplasma contamination.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Primary antibodies were detected by incubating membranes with 1:5000 dilution of HRP-conjugated (Southern Biotech) secondary anti-mouse and anti-rabbit antibodies for 1 h at room temperature.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-mouse</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-rabbit</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The following primary antibodies and their dilutions were used in this study: GAPDH (SCBT, sc-32233) at 1:1000, ACE2 (R&D Systems, AF933) at 1:1000, TMPRSS2 (Abcam, ab92323) at 1:1000.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GAPDH</div> <div>suggested: (Santa Cruz Biotechnology Cat# sc-32233, RRID:AB_627679)</div> </div> <div style="margin-bottom:8px"> <div>ACE2</div> <div>suggested: (LifeSpan Cat# LS-C347-1000, RRID:AB_1271963)</div> </div> <div style="margin-bottom:8px"> <div>TMPRSS2</div> <div>suggested: (Abcam Cat# ab92323, RRID:AB_10585592)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Vero cells (ATCC) and A549-ACE2 cells (gift from Olivier Schwartz) were cultured in DMEM (Gibco) supplemented penicillin/streptomycin (Gibco)</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>A549-ACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Lentivirus was produced in HEK293FT by co-transfection of cDNA containing lentiviral plasmid together with pCMV-dR8.2 dvpr (Addgene, #8455, gift from Bob Weinberg), pCMV-VSV-G (Addgene, #8454, gift from Bob Weinberg) and pAdVAntage (Promega) using FugeneHD (Promega).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HEK293FT</div> <div>suggested: ATCC Cat# PTA-5077, RRID:CVCL_6911)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Viral titers were determined by standard plaque assay using either Huh7.5.1 cells (OC43 and 229E) or Vero cells (SARS-CoV-2).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Vero</div> <div>suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Genome-wide CRISPR screens Huh7.5.1-Cas9 cells were generated by lentiviral transduction with lentiCas9-blast (Addgene, #52962, gift from Feng Zhang) and subsequently selected with blasticidin for days.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Huh7.5.1-Cas9</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To generate CRISPR KO libraries, a total of million Huh7.5.1-Cas9-blast or Huh7.5.1-Cas9-blast+ACE2-IRES-TMPRSS2-hygro cells were transduced with lentivirus of the human GeCKO v2 library (Addgene, #1000000049, gift from Feng Zhang) at a moi of 0.4 and subsequently selected using puromycin and expanded for 7 days.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Huh7.5.1-Cas9-blast</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>Huh7.5.1-Cas9-blast+ACE2-IRES-TMPRSS2-hygro</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cell viability assay Huh7.5.1 cells were treated with compounds at the same concentrations and durations as in infection assays.</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;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Non-linear curves were fitted with least squares regression using GraphPad Prism 8 and IC50 was determined for (a-c).</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">To generate CRISPR KO libraries, a total of million Huh7.5.1-Cas9-blast or Huh7.5.1-Cas9-blast+ACE2-IRES-TMPRSS2-hygro cells were transduced with lentivirus of the human GeCKO v2 library (Addgene, #1000000049, gift from Feng Zhang) at a moi of 0.4 and subsequently selected using puromycin and expanded for 7 days.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GeCKO</div> <div>suggested: (Gecko, RRID:SCR_009001)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The gene ontology enrichment of the individual screens was run on genes with MaGECK positive score <= 0.005 using the GO Biological Processes of the Molecular Signatures Database (MSigDB). .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GO Biological</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Of these, interconnected genes were visualized using Cytoscape (n=284).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Cytoscape</div> <div>suggested: (Cytoscape, RRID:SCR_003032)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data availability Raw sequencing data for CRISPR KO screens will be made available through the EMBL-EBI ArrayExpress (https://www.ebi.ac.uk/arrayexpress/).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>ArrayExpress</div> <div>suggested: (ArrayExpress, RRID:SCR_002964)</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.21.300913: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 reference genome isolate Wuhan-Hu-1 (GenBank, accession no. MN908947) was obtained from NCBI and used to guide the alignment, variant calling and consensus sequence generation in the protocol.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>NCBI</div> <div>suggested: (NCBI, RRID:SCR_006472)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The mappings were further sorted and indexed using samtools (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">First, we re-built the tree using the set of 4,039 genomes using the general time-reversible model as used by the NextStrain platform and allowing IQ-TREE (Minh et al., 2020) to automatically choose the precise model.</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">Visualizations Visualizations of phylogenetic trees were produced using custom scripts implemented in Python and R.</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.20202382: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.20189522: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">This study was approved by the National Health Commission of China and the institutional review board at Huoshenshan Hospital (HSSLL025).</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 data were analyzed with SPSS version 19.0 software (SPSS, Inc, Chicago, Illinois, 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:

      Our study has some limitations. Due to the retrospective study design, not all laboratory tests were done in all patients, including D-dimer and procalcitonin. Therefore, their role might be underestimated in predicting in-hospital death. Although we have adjusted for various variables that were associated with death in Cox regression analysis, there may be other potential confounders.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.307751: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">From May 11 to 22, 384 patients were contacted and 84 reported owning dogs and/or cats. 34 gave us their informed consent to sample their pets.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Three microsphere immunoassays (MIA) detected anti-SARS-CoV-2 IgGs produced in response to viral N, S1, or S2 proteins, and a retrovirus-based pseudoparticle assay detected SARS-CoV-2 neutralizing antibodies (Methods).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-SARS-CoV-2 IgGs</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Prepandemic (including non SARS-CoV2 coronaviruses positive) sera from France were used as negative controls, and anti-SARS-CoV-2 RBD antibody was used as positive control.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-SARS-CoV-2 RBD</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">10µg of three recombinant SARS-CoV-2 antigens (nucleoprotein, spike subunit 1 and spike subunit 2) were used to capture specific serum antibodies, whereas a recombinant human protein (O6-methylguanine DNA methyltransferase) was used as a control antigen in the assay.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>antigens (nucleoprotein, spike subunit 1</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>spike subunit 2</div> <div>suggested: (Thermo Fisher Scientific Cat# MA5-29983, RRID:AB_2785782)</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.20200196: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The model was constructed in Microsoft Excel using an Excel Visual Basic Macro to run the simulations.</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 analysis has several limitations. Firstly, the number of months ICU capacity is breached is influenced by the interplay between epidemic conditions and policy choices (which can affect ICU admission of other diseases).(19) As this will have different implications for costs and health outcomes in each scenario, it will be important to consider regional heterogeneity in epidemic conditions, health system capacity and willingness to pay in order to guide optimal treatment strategies. Second, we did not consider potential changes in the clinical course with disease progression nor change of distribution of disease severity among the patient population over time. Importantly, efficacy of remdesivir and dexamethasone in preventing mortality can be influenced by several factors – time of treatment initiation after symptom onset (20, 21), age (22), comorbidities(23), potential adverse events(24), and use of other medications(25, 26). As additional treatment options become available(27), it would also be important to collect more data on the duration of illness and its relationship to the outcome (both in terms of efficacy and safety)(24) and conduct more detailed analyses considering patient population characteristics, change of epidemic curves and local health system capacity, that can guide an optimal treatment strategy in a resource constrained setting. Third, our cost data does not include additional costs associated with adverse events management and also may not fully incor...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.20202150: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">CRIS has received approval as a data source for secondary analyses (Oxford Research Ethics Committee C, reference 18/SC/0372).</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</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:

      Considering other limitations, data for this manuscript were drawn from specific services of interest and do not reflect SLaM’s full activity; they were also combined by broad service categories and we did not seek to investigate within-service variation. Daily contact numbers were quantified from structured fields applied to case note entries and might reflect recording behaviour rather than activity levels (e.g. if multiple contacts were recorded within one entry); also, the dichotomy between face-to-face and non-face-to-face contact is a relatively crude one and does not reflect the quality or depth of assessments being recorded. Finally, statistical power was limited because of the short period evaluated, as well as being limited by lack of data on cause of death and applied to a heterogeneous sample of past and present service users. First author’s note, in the interests of transparency: the findings reported in this paper were submitted in manuscripts to BMJ Open, BJPsych Open, and BJPsych Bulletin, with the first submission on 21st April 2020 after a data extraction on 2nd April 2020 (daily deaths data were updated in a subsequent extraction for later submissions). The findings were adjudicated to be insufficiently informative by the first two journals and the manuscript was rejected by the third because of difficulties obtaining reviews. By the time final feedback was received (31st July 2020), the study was judged by the authors to be too out of date for further atte...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.311845: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 mapped individual sequences to the NCBI reference genome (NC_045512) using a codon-aware extension to the analyses/tree/master/codon-msa), translated mapped sequence to amino-acids and performed multiple protein sequence alignment with the ----auto settings function of MAFFT (version 7.453)43.</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">The multiple sequence alignment of SARS-CoV-2 genomes was aligned with the sequence of the coronavirus genome of the Rhinolophus affinis bat (RaTG13)19 and visually inspected and adjusted in MEGA X44,45.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MEGA</div> <div>suggested: (Mega BLAST, RRID:SCR_011920)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We noted that the earliest sample included in GISAID, (ID: EPI_ISL_402123), was collected on 24 December 2019, although the NCBI website lists its collection date as 23 December 2019 (GenBank ID: MT019529).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>NCBI</div> <div>suggested: (NCBI, RRID:SCR_006472)</div> </div> </td></tr></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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.308668: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Diffraction data were then reduced and scaled using the Aimless53 program from the CCP4 suite54; molecular replacement using PDB code 6WQF25 was then performed with Molrep54 from the CCP4 program suite.</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">The geometry of the final model was then carefully checked with Molprobity.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Molprobity</div> <div>suggested: (MolProbity, RRID:SCR_014226)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The joint X-ray/neutron refinement of ligand-free 3CL Mpro was performed using nCNS58,59 and the structure was manipulated in Coot.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Coot</div> <div>suggested: (Coot, RRID:SCR_014222)</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your data.


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.21.299776: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">CovaDOTS33 uses a set of synthetic schemes and available building blocks, to create covalent analogs of existing non-covalent ligands, but was only assessed retrospectively.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>CovaDOTS33</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Curating target structures from the PDB Using pymol scripts (The PyMOL Molecular Graphics System, Version 2.0.4 Schrödinger, LLC), we filtered only the structures that have a ligand in which one of its atoms is within 6 Å cysteine residue.</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">Computational optimisation of the Mpro inhibitor We used the RDKit reaction functionalities, as well as OpenBabel (http://openbabel.org/wiki/Main_Page) to prepare virtual libraries of analogs of compound 10.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>http://openbabel.org/wiki/Main_Page</div> <div>suggested: (Open Babel, RRID:SCR_014920)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Most combinations of these components were made by Enamine and tested as part of the CovidMoonshot effort47,67.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>CovidMoonshot</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:

      Despite the success of our protocol, several caveats remain. First is the fact that currently the protocol does not take into account the synthetic feasibility of the proposed designs. When selecting candidates for prospective evaluation, we found that some of the molecules required complicated synthesis. Incorporating into our pipeline a strategy such as DOTS33,48, other retrosynthesis algorithms49–51 or even the use of synthetic feasibility scores52–54, can significantly improve the quality of proposed candidates in the future. Another point for improvement is the relatively weak potency of our prospective designs in comparison to their parent compounds. One likely explanation for these lower affinities is the removal of non-covalent affinity elements which are not sufficiently compensated by the gains from covalent bond formation. For example, in compound 2 (derived from PDB: 4QTA) more than 350 Da of the original compound55 is removed (Supp. Fig. 2), resulting in three orders of magnitude loss in potency. However the remaining covalent fragment still shows significant inhibition of ERK2. Another example is compound 1, its parent compound (PDB: 4QP9) has an IC50 of 71 nM, however the propyl-pyrazole group we have omitted in order to accommodate the electrophile (Supp. Fig. 2) improved the parent reversible binder by more than 150-fold. Lastly the loss of a hydrogen bond between the Mpro backbone NH of Gly143 and the furanyl oxygen of ML188 (PDB: 3V3M), decreased potency, u...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.21.306720: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 up-regulated (log2 fold change >=2) genes in host transcriptional response to SARS-CoV-2 in three cell cultures: human A549 lung alveolar cells (102 genes)</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;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 create gene sets that are directly related to SARS-CoV-2 infection (COVID-19), we identified several relevant reports5,28,29 and captured gene sets available from these studies into the GeneWeaver environment.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GeneWeaver</div> <div>suggested: (Gene Weaver, RRID:SCR_003009)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Gene Set Comparison To identify genes that were shared by all five comorbidities or four out of five comorbidities, we used the GeneWeaver ‘Combine GeneSets’ tool.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GeneSets’</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Reactome Pathway Enrichment Analysis For pathway enrichment, we submitted the gene lists to the Reactome ‘Analyze Gene List’ enrichment tool (https://reactome.org/PathwayBrowser/#TOOL=AT) based on Reactome version 72.</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">We corrected for any symbols that were out of date and again used the Reactome Pathway analysis tool.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Reactome Pathway analysis tool</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">We searched the GeneWeaver Data repository for gene sets associated with these comorbidities and identified gene sets from MeSH and HPO that we used in our analyses (Table 1).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MeSH</div> <div>suggested: (MeSH, RRID:SCR_004750)</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.20202325: (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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.20202259: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">It was not a demand from the Scientific Ethics Committee of Sweden that webinars were done, instead Swedish participants received written information and they were given contact information for the study organizer, which they were told to use if they had any questions.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">More men than women participated in Denmark (75.5% men), while the opposite was the case among Swedish participants (32.9% men).</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 were tested for SARS-CoV-2 antibodies every second week for a period of 8 weeks from June 22, 2020 until August 10, 2020.</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 were tested for SARS-CoV2 antibodies every second week for a period of 8 weeks from June 22, 2020 until August 10, 2020.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <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">Finally, multivariable logistic regression models were applied to assess the association between job function, number of people contacts and the risk of being tested positive with SARSCoV-2 antibodies, respectively.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>SARSCoV-2</div> <div>suggested: None</div> </div> </td></tr></table>

      Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).


      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

      Limitations of the study is the self-reported nature of data. Participants had to perform the antibody tests themselves and report the results back to the study organizers. This may have caused misclassification of cases. However, if such bias exists it is likely to be random and therefore not affect study results. Moreover, the relatively low sensitivity of the test (82.58%) has potentially caused an underestimation of the seroprevalence. Testing participants multiple times may have reduced the level of underestimation. The potential underestimation was further reduced by additional testing of participants who tested positive for only one of the two SARS-CoV-2 antibodies IgM or IgG. Another limitation to the study is the number of participants. Since the seroprevalence is low, the statistically insignificant findings may be an artefact of reduced statistical power. Moreover, because of the low seroprevalence and because the infection rate has been low during the study period, we did not have statistical power to investigate the development of the seroprevalence across time or to test for interactions. Descriptive statistics presenting the distribution of seropositivity among study participants, seem to present a trend among Swedish employees showing that the more people contact an employee encounter during a workday, the higher the proportion of employees with a positive test. We do not observe a similar trend among Danish participants. However, this is likely to be explaine...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.312595: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Identification of Human Single-Domain Antibodies against SARS-CoV-2. 43.</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;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Pseudotyped particle production and neutralizing assay To generate retroviral pseudotyped particles, HEK293T cells were co-transfected 405 with the vectors expressing the various viral envelope glycoproteins, the murine leukemia virus core/packaging components (MLV Gag-Pol), and a retroviral transfect vector expressing the green fluorescence protein (GFP).</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">Fifty microliters of VeroE6-hACE2 cells (104 cells/well) were seeded in a 48-well 410 415 plate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>VeroE6-hACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 models were manually adjusted as guided by the 2Fo-Fc maps in Coot (48), and refined using Phenix (49).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Coot</div> <div>suggested: (Coot, RRID:SCR_014222)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Structures were visualized using PyMol (50).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>PyMol</div> <div>suggested: (PyMOL, RRID:SCR_000305)</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your data.


      Results from LimitationRecognizer: 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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.27.20202754: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Finally, we included 3 randomised trials evaluating remdesivir in addition to standard care versus standard care alone.</td></tr><tr"><td style="min-width:100px;margin-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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Description of the included studies The three trials identified were the Adaptive COVID-19 Treatment Trial (ACTT-1 [24]), the CAP-China remdesivir 2 [25] and SIMPLE 2 [26].</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>ACTT-1</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 the time of releasing this article, this repository included more than 66989 articles relevant to Coronavirus disease, coming from the following databases, trial registries, preprint servers and websites relevant to COVID-19: Epistemonikos database, Pubmed, EMBASE, ICTRP Search Portal, Clinicaltrials.gov, ISRCTN registry, Chinese Clinical Trial Registry, IRCT - Iranian Registry of Clinical Trials, EU Clinical Trials Register: Clinical trials for covid-19, NIPH Clinical Trials Search (Japan) - Japan Primary Registries Network (JPRN) (JapicCTI, JMACCT CTR, jRCT, UMIN CTR), UMIN-CTR - UMIN Clinical Trials Registry, JRCT - Japan Registry of Clinical Trials, JAPIC Clinical Trials Information, Clinical Research Information Service (CRiS), Republic of Korea, ANZCTR - Australian New Zealand Clinical Trials Registry, ReBec - Brazilian Clinical Trials Registry, CTRI - Clinical Trials Registry - India, DRKS - German Clinical Trials Register, LBCTR - Lebanese Clinical Trials Registry, TCTR - Thai Clinical Trials Registry, NTR - The Netherlands National Trial Register,PACTR - Pan African Clinical Trial Registry, REPEC - Peruvian Clinical Trial Registry,SLCTR - Sri Lanka Clinical Trials Registry, medRxiv Preprints, bioRxiv Preprints, SSRN Preprints, WHO COVID-19 database.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Pubmed</div> <div>suggested: (PubMed, RRID:SCR_004846)</div> </div> <div style="margin-bottom:8px"> <div>EMBASE</div> <div>suggested: (EMBASE, RRID:SCR_001650)</div> </div> <div style="margin-bottom:8px"> <div>bioRxiv</div> <div>suggested: (bioRxiv, RRID:SCR_003933)</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your code and data.


      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

      One of the limitations comes from the lack of precision of the result for the main outcomes. The early termination of the ACTT-1 trial can be seen as a missed opportunity in this regard [25]. In addition, all the trials concluded enrollment before the release of the RECOVERY trial which showed a mortality reduction with dexamethasone [27]. It is not clear if this factor would modify the effect, if any, of remdesivir. By now, clinicians and other decision makers are in a difficult position. The pressure to act is high, particularly after the the US Food and Drug Administration issued an emergency use authorisation of remdesivir for the treatment of COVID-19 [12]. We anticipate that the range of recommendations from different organisations should range between a suggestion against its use and a weak recommendation for its use in severe cases, especially in settings without resource constraints. There are at least 46 ongoing trials that we expect will provide data in the near future. Making sense of this information is not going to be an easy task. Systematic reviews are considered the gold standard to make sense of multiple trials addressing a similar scientific question, but the traditional model for conducting reviews has several limitations, including a high demand for time and resources [28] and a rapid obsolescence [29]. Amidst the COVID-19 crisis, researchers should make their best effort to answer the urgent needs of health decision makers yet without giving up scientifi...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201541: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Approval was obtained from the ethics committee of the Medical Faculty of the Otto- von-Guericke University Magdeburg.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</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 also limitations. Mouthwash with gargling was performed as a self- administered procedure and we observed some variation in adherence to the protocol regarding the duration and intensity of gargling, which may have influenced the results. Furthermore, we did not compare different RNA extraction methods, which may show a better performance with mouthwash specimens. There is a high likelihood of aerosol formation during gargling. Thus, mouthwash should be performed alone in a well-ventilated area. This may limit its use in patients to minimize exposure of health-care personel.In conclusion, SARS-CoV2 detection with mouthwash showed a low sensitivity compared to oro-nasopharyngeal swabs. Thus, we do not recommend mouthwash performing combined oro-nasopharyngeal swabs, especially in patients with no or mild symptoms. Transparency declaration JF reports personal fees from Biomérieux and the Medical Association of Saxony- Anhalt, outside the submitted work; WM, MD, IT, JB and AJK report no conflicts of interest. There was no specific funding for this study. Contribution AJK and IT designed the study; DM, JB, IT and AJK conducted the investigation; MW, BJ, and AJK edited, reviewed and interpreted the data; WM and AJK wrote the original draft and all authors approved the manuscript. Acknowledgement We thank the technical personnel of the Institute of Medical Microbiology and Hospital Hygiene and the Institute of Transfusion Medicine, Medical Faculty, Otto-von-Guericke U...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.20202457: (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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.27.20202556: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">1b) for the ratio RcI/T defined in Eq. 1. DAILY HINFECTEDêTESTL¥100 CUMULATIVE  INFECTED b) INFECTEDêTEST ¥ ÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚ Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï ÊÊ Ê Ê Ê Ê Ê Ê ÊÊÊ Ê Ê Ê Ê Ê Á Á Ú ÁÁÁÁ Á Ú Á Ú ÏÏ Ï ÚÚ Ú Ú ÚÚ Ï Ú Ï Ú ÚÚÚÚ ÚÚÚÚÚÚÚ Ï Ï Ï Á Ú ÚÚÚ ÚÚ Ú ÁÁÁÁÁ ÁÁ Á ÏÏÏ Ï Ï Ï ÚÚ Á Á Á ÁÁÁÁÁ ÁÁ Ï Ï Ï ÏÏÏÏÏ ÏÏ Ï Ï Ï Ï Ï Ï Á Figure 2: Daily behaviour of the cumulative # of infected persons: a) the 1st month case until 7th May (fully oliva points), 7-31th May (open pink circle); b) 1-22th June (open pink circle), 23-30th June (oliva full square), July (open green circle), August (full dark blue triangle), 12th September (open yellow circle).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>INFECTEDêTEST ¥ ÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚÚ Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï ÊÊ Ê Ê Ê Ê Ê Ê ÊÊÊ Ê Ê Ê Ê Ê Á Á Ú ÁÁÁÁ Á Ú Á Ú ÏÏ Ï ÚÚ Ú Ú ÚÚ Ï Ú Ï Ú ÚÚÚÚ ÚÚÚÚÚÚÚ Ï Ï Ï Á Ú ÚÚÚ ÚÚ Ú ÁÁÁÁÁ ÁÁ Á ÏÏÏ Ï Ï Ï ÚÚ Á Á Á ÁÁÁÁÁ ÁÁ Ï Ï Ï ÏÏÏÏÏ ÏÏ Ï Ï Ï Ï</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray"> OF DAYS FROM 01ê06ê2020 TO 12ê09ê2020  OF DAYS FROM 21ê03ê2020 TO 12ê09ê2020 b) ÚÚÚÚÚÚ ÚÚÚÚÚÚÚÚ ÚÚÚÚÚÚ Ú Ú Ú Ú ÚÚ ÚÚÚ Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Á 000 Ê  OF DAYS FROM 21ê03ê2020 TO 31ê05ê2020 a) 000 • Phases of the pandemic One can notice from the previous figures that there are two phases : – Small or Epidemic phase until 48 days (7th May). – Large or Pandemic Phase after 7th May.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>ÚÚÚÚÚÚ ÚÚÚÚÚÚÚÚ ÚÚÚÚÚÚ Ú Ú Ú Ú ÚÚ ÚÚÚ Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Á 000</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">CUMULATIVE  INFECTED a) (16) – Gaussian-like model [4]: ag = 14551.94 , bg = 109.22 , cg = −29.18 , (17) 000 000 000 ÚÚÚÚÚÚÚÚ ÚÚÚÚÚÚÚÚ ÚÚÚÚÚÚ Ú Ú Ú ÚÚÚ Ú Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï OF DAYS FROM 09ê05ê2020 TO 12ê09ê2020 From the previous parameters, one finds that the LPESG model finds a peak around b s × c s ≈ 126 days, while the Gaussian-like model finds a gaussian centered at days which are compatible.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>ÚÚÚÚÚÚ Ú Ú Ú ÚÚÚ Ú Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï Ï</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">12b) but after a low pass filter obtained using Matlab alogrithm which is expected to reduce the statistical (stochastic) variations of the data. 13 the predicted values of Reff as function of the number of days using the daily infected data (open red circles) given in Fig. 12.</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 have also shown that the COVID-19 in Madagascar can be split into three phases : the small phase until 43th days called epidemic where the peak is reached around the (15-28)th day, the transition background phase from 7th May to 15th June and the large phase (real pandemic) beyond 15th June where the peak is reached around the end of august 2020.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Madagascar</div> <div>suggested: (Madagascar, RRID:SCR_003274)</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.21.306357: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">References and notes 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 1. 3.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>279 280 281 282 283 284 285 286 287 288 289</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The expression vector was then stably transfected into GH-CHO (dhfr -/-) cell line and high expression clones were selected and adapted to SFM-4-CHO (Hyclone) serum free medium and ACE2-Fc was produced in a 15 L bioreactor as essentially as described for S-Trimer above.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>dhfr -/-</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 stepwise gene amplification with increasing concentrations (0.0–10 nM) of MTX (Sigma), clones producing the highest S-Trimer titer were adapted to SFM-4CHO serum-free medium (GE BioSciences).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GE BioSciences</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Receptor binding studies of S-Trimers to human ACE2-Fc The avidity of different S-Trimer binding to the SARS-CoV-2 receptor ACE2 were assessed by BioLayer Interferometry measurements on ForteBio Octet QKe (Pall, New York).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>BioLayer</div> <div>suggested: (Harvard Medical School Center for Macromolecular Interactions Core Facility, RRID:SCR_018270)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cryo-EM Image processing For MT S-Trimer protein, motion correction for cryo-EM images and contrast transfer function (CTF) estimation were performed using motioncorr2 (4) and CTFFIND4 (5) respectively. 574,832 particles were automatically picked from 534 images collected on grid without graphene oxide (GO) using Laplacian-ofGaussian in Relion 3.0.7 (6), and 1,029,938 particles was automatically picked from 1584 images collected on grid with GO.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Relion</div> <div>suggested: (RELION, RRID:SCR_016274)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The model was manually built in COOT (7) and real space refinement was performed in Phenix (8) using rotomer, Ramachandran and secondary structure restraints.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>COOT</div> <div>suggested: (Coot, RRID:SCR_014222)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">2.24 Clash score 7.53 C-beta outliers (%) 0.00 CC (mask) 0.84 MolProbity score 1.87</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MolProbity</div> <div>suggested: (MolProbity, RRID:SCR_014226)</div> </div> </td></tr></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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201616: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.308965: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 Sprotein-immobilized biosensors were immersed in 1:40 serum dilution solution with serum antibodies as the analyte and the association (120 s; 180-300) and dissociation (240 s; 300-540) steps were conducted to detect the kinetics of antibody-protein interaction.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>antibody-protein interaction.</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">** A dengue antibody, DEN3, was used as a control.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>DEN3</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">ELISA binding 96-well half-area plates (Corning cat. # 3690, Thermo Fisher Scientific) were coated overnight at 4°C with 2 ug/ml of mouse anti-His-tag antibody (Invitrogen cat. # MA121315-1MG, Thermo Fisher Scientific) in PBS.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-His-tag</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After the washes, a secondary antibody conjugated with alkaline phosphatase (AffiniPure goat anti-human IgG Fc fragment specific, Jackson ImmunoResearch Laboratories cat. # 109-055-008) diluted 1:1000 in 1% BSA/PBS-T, was added to each well.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>AffiniPure goat anti-human IgG Fc fragment specific</div> <div>suggested: (Jackson ImmunoResearch Labs Cat# 109-005-008, RRID:AB_2337534)</div> </div> <div style="margin-bottom:8px"> <div>anti-human IgG</div> <div>suggested: (Jackson ImmunoResearch Labs Cat# 109-055-008, RRID:AB_2337601)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A mixture of fluorescently labeled antibodies to cell surface markers was prepared, including antibodies specific for the T cell markers CD3(APC Cy7, BD Pharmingen #557757), CD4(APC-Cy7, Biolegend #317418) and CD8(APC-Cy7, BD Pharmingen</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>CD3</div> <div>suggested: (BD Biosciences Cat# 557757, RRID:AB_396863)</div> </div> <div style="margin-bottom:8px"> <div>CD4</div> <div>suggested: (BioLegend Cat# 317418, RRID:AB_571947)</div> </div> <div style="margin-bottom:8px"> <div>APC-Cy7</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>CD8</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">CELISA binding Binding of serum antibodies or mAbs to human coronavirus spike proteins expressed on HEK293T cell surface was determined by flow cytometry, as described previously 31.</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">HEK293T cells were transfected with plasmids encoding full-length coronavirus spikes including SARS-CoV-1, SARS-CoV-2, MERS-CoV, HCoV-HKU1, HCoV-OC43, HCoVNL63 and HCoV-229E.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HCoVNL63</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">. 293T cells were plated in advance overnight with DMEM medium +10% FBS + 1% Pen/Strep + 1% L-glutamine.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>293T</div> <div>suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Following the infection, HeLa-hACE2 cells were lysed using 1x luciferase lysis buffer (25mM Gly-Gly pH 7.8, 15mM MgSO4, 4mM EGTA, 1% Triton X-100)</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HeLa-hACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">20µL of the supernatant was transferred to a 384-well plate seeded with 2E3 HeLa-ACE2 cells and incubated for an additional 24 hours at 34°C.</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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HCoV-NL63 S (up to ~0.6% - range = ~0.04-0.6%) protein single positive and SARS-CoV-2/HCoV-HKU1 S (up to ~2.4% - range = ~0.02-2.4%) and SARS-CoV2/HCoV-NL63 S-protein (up to ~0.09% - range = ~0-0.09%) double positives.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HCoV-NL63 S</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 extend of biotinylation was evaluated by BioLayer Interferometry binding value using streptavidin biosensors.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>BioLayer</div> <div>suggested: (Harvard Medical School Center for Macromolecular Interactions Core Facility, RRID:SCR_018270)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After another two washes, stained cells were analyzed using flow cytometry (BD Lyrics cytometers), and the binding data were generated by calculating the percent (%) PE-positive cells for antigen binding using FlowJo 10 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">The absorbance was measured after 8, 20, and 30 minutes, and was recorded at an optical density of 405 nm (OD405) using a VersaMax microplate reader (Molecular Devices), where data were collected using SoftMax software version 5.4.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>SoftMax</div> <div>suggested: (SoftMax Pro Data Acquisition and Analysis Software, RRID:SCR_014240)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Gibson assembly products were finally transformed into competent E.coli cells and single colonies were picked for sequencing and analysis on IMGT V-Quest online tool (http://www.imgt.org) as well as downstream plasmid production for antibody expression.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>http://www.imgt.org</div> <div>suggested: (IMGT - the international ImMunoGeneTics information system, RRID:SCR_012780)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">10µL of human polyclonal sera diluted 1:500 in Perm/Wash Buffer (BD Biosciences)was added to the plate and incubated at RT for 2 hours.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>BD Biosciences)was</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The PFU/mL of the monocyte plate supernatant was calculated and graphed using Prism 8 software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Prism</div> <div>suggested: (PRISM, RRID:SCR_005375)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The Leginon software 37 was used to automate data collection on a FEI Tecnai Spirit (120keV), paired a FEI Eagle 4k x 4k camera.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Leginon</div> <div>suggested: (Leginon, RRID:SCR_016731)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">RELION 3.0 40 was used to generate the 2D class averages.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>RELION</div> <div>suggested: (RELION, RRID:SCR_016274)</div> </div> </td></tr></table>

      Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.313601: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Study design for animal infections Approval of the study protocol was obtained from the Colorado State University Institutional Animal Care and Use Committee (protocol 993).</td></tr><tr"><td style="min-width:100px;margin-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">Immunoreactions were visualized and blindly scored by a single pathologist.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Male Syrian hamsters (n=20, 10 weeks of age, obtained from Charles River Laboratory).</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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Assessing antibody binding to native spike protein: A vector encoding a full-length spike protein sequence encompassing residues 13-1273 of UniProtKB accession number P0DTC2, that was fused to green fluorescent protein (GFP) as a reporter (Sino Biologicals, Cat# VG40590ACG) was used to transiently transfect 293F cells using the FreeStyle™ 293F Expression System (ThermoFisher Scientific, cat# K90001).</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><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After 2 days, when a robust GFP signal was observed, aliquots of the transfected cells and untransfected 293F cells were washed in ice cold phosphatebuffered saline containing EDTA and 0.5% BSA, pH 7.4 (PBSM) then incubated in the presence of AvGn-B, isotype control antibody or ACE2-Fc for 45 mins with rotation at 4° C, washed 3 times in ice-cold PBSM and then bound antibody detected with goat anti-human kappa-A647 (SouthernBiotech, cat# 2060-31) After washing, cell-bound Alexa-657 was analyzed using an IntelliCyt® iQue Screener PLUS and ForeCyt Software (Sartorius).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>AvGn-B,</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-human kappa-A647</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibodies to SARS-CoV-2 nucleocapsid protein (mouse, 1:500), pancytokeratin, factor-VIII and ionized calcium binding adaptor molecule (IBA-1) (Leica Biosystems) or negative control slides primary antibody was replaced by a rabbit non-specific IgG isotype negative control antibody for 20 minutes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>SARS-CoV-2 nucleocapsid protein (mouse, 1:500), pancytokeratin, factor-VIII and ionized calcium binding adaptor molecule (IBA-1</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>non-specific IgG</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Results Isolation of an anti-SARS-CoV-2 RBD antibody clone that blocks receptor binding and can neutralize SARS-CoV-2 activity.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-SARS-CoV-2 RBD</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 2 days, when a robust GFP signal was observed, aliquots of the transfected cells and untransfected 293F cells were washed in ice cold phosphatebuffered saline containing EDTA and 0.5% BSA, pH 7.4 (PBSM) then incubated in the presence of AvGn-B, isotype control antibody or ACE2-Fc for 45 mins with rotation at 4° C, washed 3 times in ice-cold PBSM and then bound antibody detected with goat anti-human kappa-A647 (SouthernBiotech, cat# 2060-31) After washing, cell-bound Alexa-657 was analyzed using an IntelliCyt® iQue Screener PLUS and ForeCyt Software (Sartorius).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>293F</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Determining the viral neutralization activity of antibody clones in vitro Vero E6 cells were plated overnight in 96-well plates at 20,000 cells per well.</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;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 OD readings were plotted against concentration using Prism software (Graphpad CA) for curve fitting and determination of the apparent KD value.</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">Assessing antibody binding to native spike protein: A vector encoding a full-length spike protein sequence encompassing residues 13-1273 of UniProtKB accession number P0DTC2, that was fused to green fluorescent protein (GFP) as a reporter (Sino Biologicals, Cat# VG40590ACG) was used to transiently transfect 293F cells using the FreeStyle™ 293F Expression System (ThermoFisher Scientific, cat# K90001).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>UniProtKB</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">Male Syrian hamsters (n=20, 10 weeks of age, obtained from Charles River Laboratory).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Charles River Laboratory</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Co-localization and intensity measurements were obtained using the Count and Measure feature of cellSens.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>cellSens</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Curve fitting in A, B, D and E was performed using Prism software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Prism</div> <div>suggested: (PRISM, RRID:SCR_005375)</div> </div> </td></tr></table>

      Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: Please consider improving the rainbow (“jet”) colormap used on page 27. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.20201236: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201558: (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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20198986: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Mean age was 34.5 years and 48.0% were female patients.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 evaluations were performed with the software STATA16.0 (StataCorp, College Station, Texas).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>StataCorp</div> <div>suggested: (Stata, RRID:SCR_012763)</div> </div> </td></tr></table>

      Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).


      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

      Limitations The study has a number of limitations. It is based on secondary analysis of administrative claims data. Under- or overdocumentation of individual diagnoses cannot be ruled out. Furthermore, there are limitations with regard to external validity of the patient characteristics and reported incidences since the patient collective studied was composed exclusively of AOK-insured persons. Although the collective of AOK-insured persons accounts for more than one-third of hospital cases in Germany, there are certain differences versus the population of persons insured by other statutory sickness funds in terms of the age structure and comorbidity profile [10]. The reported case reduction is also influenced by changes of the AOK collective between the years. The number of insured persons slightly rose from 2019 to 2020, so that case reductions might be slightly underestimated. However, the differences between the years were less than 2% within each group.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.20201301: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Ethical consideration: The research protocol was reviewed and approved by the Institute Ethics Committee.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Majority of them were female (77.8%), married (55.3%), completed M.Sc. Ph.D. Job title Student Teaching staff/ Faculty Nursing Officer/Administrator Practice speciality Mental Health Nursing Non-Mental Health Nursing Current place of work Clinic/Hospital Educational Institute Community health facility Type of institute Central Govt State Govt Private NGO # α Mean±SD, Median (Q1, Q3) # 150 (22.2) 526 (77.8) 291 (43) 374 (55.3) 11 (1.6)</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Totally 685 responses were received and 676 forms were completed which were analyzed using SPSS software (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:

      Strengths & limitations: The main strengths of the present study were large sample size and inclusion of nurses and nursing students from all over India which may be representative of the country and hence increases the generalizability of the findings. The present study also included nurses who had experience of taking care of persons with COVID 19 positive (although less n=26) and documented their experiences which is very first of its kind in the Indian setting. Further, using open-ended questions in addition to standardized tools enhanced the richness of the data. The present study was not without certain limitations such as cross-sectional survey design. The findings should be interpreted cautiously as it does not provide cause and effect relationship rather provides the possibilities of the direction which needs to be studied in future. Further, the possibility of social desirability bias due to self-reported questionnaire could not be avoided. Despite the limitations, the present study provides important findings on psychological preparedness in an important section of health care professionals i.e. nurses and nursing students. Aspects of psychological preparedness studied here may help in planning further for pandemic management.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201350: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.307975: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">n°35RC20_9795_HARMONICOV, ClinicalTrials.gov Identifier: NCT04373200) and informed consent was obtained from patients 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">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">To generate input data for training CellCnn, sub-samples of 2000 cells, termed multi-cell inputs (MCIs), were chosen randomly from each sample independently.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Files were then uploaded to the Cytobank cloud-based platform (Cytobank, Inc.).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Cytobank</div> <div>suggested: (Cytobank, RRID:SCR_014043)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FlowSOM uses Self-Organizing Maps (SOMs) to partition cells into clusters based on their phenotype, and then builds a Minimal Spanning Tree (MST) to connect the nodes of the SOM, allowing the identification of metaclusters (i.e. group of clusters).</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> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cytometry data was explored with Kaluza Analysis Software (Beckman Coulter).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Kaluza</div> <div>suggested: (Kaluza, RRID:SCR_016182)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Hierarchical clustering and heatmaps were generated with R v3.6.3, using Rstudio v1.2.5033 and the pheatmap package.</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> <div style="margin-bottom:8px"> <div>pheatmap</div> <div>suggested: (pheatmap, RRID:SCR_016418)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis Statistical analyses were performed with Graphpad Prism 8.4.3.</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:

      Besides the low number of included patients, our study has some limitations. By focusing on severe patients with and without ARDS, we cannot make conclusions about phenotypic changes in mild and moderate diseases. Moreover, since the mass cytometry was conducted on PBMCs, we lack information on the neutrophil lineage, which appears affected in the COVID-19 (18). It would also be interesting to link these data with in situ data from lung tissue samples and bronchoalveolar lavages. However, our detailed analysis of circulating immune cells shows that immune monitoring of severe COVID-19 patients brings interesting prognostic biomarkers independently of their clinical classification in ARDSpos versus ARDSneg. Moreover, we demonstrated that at the biological level, COVID-19 associated ARDS is different from other causes of ARDS, and might benefit from personalized therapy in addition to standard ARDS management (18, 43). Materials and Methods Patients This study was performed in the infectious diseases department and intensive care unit (ICU) at Rennes University Hospital. The study design was approved by our ethic committee (CHU Rennes, n°35RC20_9795_HARMONICOV, ClinicalTrials.gov Identifier: NCT04373200) and informed consent was obtained from patients in accordance with the Declaration of Helsinki. Peripheral blood was collected in tubes containing lithium heparin from COVID-19negARDSpos, COVID19posARDSpos, and COVID-19posARDSneg patients. Peripheral blood samples were drawn at...


      Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><tr><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">NCT04373200</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">Human Ab Response & immunoMONItoring of COVID-19 Patients</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.27.20202465: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Fieldworker investigators were trained to explain the project, collect informed consent and carry out the interviews.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Nine age-groups ([0-15 years[, [15-20[, [20-25[, [20-25[, [25-35[, [35-45[, [45-55[, [55-65[, ≥65 years ) were used within males and females groups and for each age-sex subgroups, we applied an adjustment factor cijk, to have a final statistical weight wijk = (Mi/mi)*cijk , where i indexes municipalities, j indexes sex groups and k indexes age groups.</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 inherent in the study design. Our approach made it possible to obtain rapid estimates of the impact of the epidemic. However, convenience sampling may result in a lack of population representation if part of the general population has lower access to the laboratories and health centers participating in the study. In our study, we observed a significant under-representation of men and children under 15 years of age, and therefore performed a post-stratification adjustment. However, this may have led to large confidence intervals for some of parameter estimates. In addition, sample size calculation was determined to obtain a sufficient point estimate of territory-wide prevalence estimates but not to study risk factors of infection. A few municipalities with no laboratory or health centers were not represented. However, the municipalities represented by the laboratories and health centers involved in the study are home to 80% of the population, so that our estimates are likely a good reflection of the situation across the territory. We may underestimate infection levels if precarious populations are at higher risk of infection and have limited access to health facilities. Although specificity of the test used in our study is satisfactory according to our internal validation, we cannot rule out the possibility that a proportion of people infected at the beginning of the epidemic i.e. more than 3 months before our survey may have become seronegati...


      Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><tr><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">NCT04490850</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 Seroprevalence Study in French Guiana</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.23.309849: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">BHK-21 cells and Vero E6 cells were maintained in high-glucose Dulbecco's Modified Eagle Medium (DMEM) (Nacalai Tesque) containing 10% fetal bovine serum (FBS) (Sigma), 100 units/ml penicillin and 100 μg/ml streptomycin (P/S) (Sigma).</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">IFNAR1-deficient HEK293 cells, in which human ACE2 and TMPRSS2 are induced by tetracycline, were established and designated as HEK293-3P6C33 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HEK293-3P6C33</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then, this plasmid was co-transfected with a transposase-expression vector, pCMV-hyPBase (Yusa et al., 2011) (kindly provided from Welcome Trust Sanger Institute), into HEK293 cells, whose IFNAR1 had been knocked out using a CRISPR/Cas9 system.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HEK293</div> <div>suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Transfection The CPER products (25 μl out of a 50 μl reaction volume) were transfected into HEK293-3P6C33 cells or BHK-21 cells with Trans IT LT-1 (Mirus), following the manufacturer’s protocols.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>BHK-21</div> <div>suggested: ATCC Cat# CRL-6282, RRID:CVCL_1914)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">At 6 hours post-transfection, the culture supernatants of HEK293-3P6C33 cells were replaced with DMEM containing 2% FBS and doxycycline hydrochloride (1 μg/ml), and BHK-21 cells were overlaid by VeroE6/TMPRSS2 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>VeroE6/TMPRSS2</div> <div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div> </div> </td></tr></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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.21.305441: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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, MLV-gag/pol and MLV-CMV plasmids was co-transfected into HEK293T cells along with full-length or P384A SARS-CoV-2 spike plasmids using Lipofectamine 2000 to produce pseudoviruses competent for single-round infection.</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">For each well, 10,000 HeLa-hACE2 cells in 50 μl of media supplemented with μg/ml dextran were added to the antibody-virus mixture.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HeLa-hACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Structures were solved by molecular replacement using PHASER [43] with PDB 6W41 for CR3022 Fab [20] and PDB 2AJF for SARS-CoV RBD [44].</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>PHASER</div> <div>suggested: (Phaser, RRID:SCR_014219)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Iterative model building and refinement were carried out in COOT [45] and PHENIX [46], respectively.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>COOT</div> <div>suggested: (Coot, RRID:SCR_014222)</div> </div> <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">Ramachandran statistics were calculated using MolProbity [47].</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MolProbity</div> <div>suggested: (MolProbity, RRID:SCR_014226)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Micrographs were collected using Leginon [48] and images were transferred to Appion [49] for particle picking using a difference-of-Gaussians picker (DoG-picker) [50] and generation of particle stacks.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Leginon</div> <div>suggested: (Leginon, RRID:SCR_016731)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Select 3D classes were auto-refined on Relion and used for making figures using UCSF Chimera [52]</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">Micrographs were collected through Leginon software at a nominal defocus range of -0.4 µm to -1.6 µm and MotionCor2 was used for alignment and dose weighting of the frames [48, 53].</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 estimations were performed using GCTF and micrographs were selected using the Curate Exposures tool in CryoSPARC based on their CTF resolution estimates (cutoff 5 Å) for downstream particle picking, extraction and iterative rounds of 2D classification and selection [55].</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GCTF</div> <div>suggested: (GCTF, RRID:SCR_016500)</div> </div> <div style="margin-bottom:8px"> <div>CryoSPARC</div> <div>suggested: (cryoSPARC, RRID:SCR_016501)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Calculation of rotation angles Comparisons of subunit rotation angles among different structures were performed with a software ‘Superpose’ in the CCP4 package [56, 57].</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></table>

      Results from OddPub: Thank you for sharing your data.


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.27.20202168: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Anonymous XN-analyser raw data files were provided to Sysmex Europe collaborators for analysis using virtual analyser software, specifically to obtain reactive lymphocyte (RE-LYMPH), antibody-synthesising lymphocyte (AS-LYMPH) and reactive monocyte (RE-MONO) counts.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>antibody-synthesising lymphocyte (AS-LYMPH)</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">(MedCalc Software Ltd, Ostend, Belgium; https://www.medcalc.org; 2020) was used.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MedCalc</div> <div>suggested: (MedCalc, RRID:SCR_015044)</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 its retrospective nature, as data retrieved from hospital records were sometimes incomplete. Our study was performed at a time that COVID-19 was a new disease entity that constrained the health care in many of the participating centers which may have affected management decisions and therefore study outcome parameters. Data from out-patient settings including more mild cases, and from nursing homes that usually accommodate high risk patients, are needed. Furthermore, clinical data collection was limited, including comorbidity affecting COVID-19 susceptibility and ICU admission decisions, notably as the demand for ICU beds was greater than the availability at the time of our study. Importantly, the conditions of our fast-tracked ethics clearance to facilitate rapid study initiation, did not permit data collection. about bacterial superinfections and medication (antibiotics, corticosteroids), while these factors may affect outcome and haemocytometric parameters. Finally, our prognostic score includes Sysmex unique parameters. This is a limitation as the score is not universally applicable to all haematology analysers, although the concept is transferable (see Table S1 for parameters available on other manufacturer haematology platforms). However, it is the very ability to quantify blood cell activation, a reflection of the general immune response status of an individual, that has rendered our prognostic score (which incorporates cell activation para...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.313270: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 against nucleocapsid protein of anti-SARS-CoV-2 N protein (Genscript) and GAPDH of anti-GAPDH (Proteintech) were used at 1:3000 dilutions.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Antibodies against nucleocapsid protein of anti-SARS-CoV-2 N protein ( Genscript )</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>GAPDH</div> <div>suggested: (LifeSpan Cat# LS-C41945-3000, RRID:AB_1054935)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The second antibody of HRP-conjugated affinipure Goat anti-mouse IgG (H+L) was diluted at 1:20000.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-mouse IgG</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The primary antibodies are anti-OCT4 rabbit polyclonal antibody (Proteintech), anti-SSEA-4 antibody (STEMCELL Technologies), anti-Sox17 antibody (R&D System), anti-Brachyury antibody (Cell Signaling Technology) and ani-Nestin antibody (R&D System).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-OCT4</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-SSEA-4</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-Sox17</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-Brachyury antibody ( Cell Signaling Technology )</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>ani-Nestin</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 cell lines, coronavirus and key reagents Vero E6 cells were cultured in high-glucose-containing Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum.</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;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 analyzed using GraphPad Prism 8 software (GraphPad Software Inc.</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 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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.20202234: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">320 Ethical approval 321 322 323 This study was approved by the ethics committee associated with the Faculty of Medicine at The First Affiliated Hospital of Guangxi Medical University[2020(KY-E-06).].</td></tr><tr"><td style="min-width:100px;margin-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">Two attending 106 radiologists were invited to interpret all chest CT scans independently, and they were blinded 107 to the clinical information of each patient.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px 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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 data analyses were carried out using IBM Statistical Package 133 for the Social Sciences for Windows, version 25 (SPSS Inc., Chicago, Illinois), and graphs 134 were created using GraphPad Prism 7.0 software (GraphPad Software Inc., San Diego, CA, 135 USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>SPSS</div> <div>suggested: (SPSS, RRID:SCR_002865)</div> </div> <div style="margin-bottom:8px"> <div>GraphPad 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:

      289 The present study has some limitations. First, due to the limited number of cases, some 290 results need to be further validated with more patients. Second, the effect of antiviral agents and corticosteroidson COVID-19 needs further validation. Prospective studies should be 292 performed to get more accurate results. Third, because this was a retrospective analysis, the 293 time of CT imaging and nucleic acid test was not standardized and unified, t may have reduced 294 the accuracy of the result. More cases need to be analyzed to obtain more information. 295


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.314385: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Othocoronavirinae, family Coronaviridae, order Nidovirales, four genera, as alphacoronavirus (alpha-CoV), betacoronavirus (betaCoV), gammacoronavirus (gamma-CoV), and deltacoronavirus (delta-CoV) 5. Methodology: Gene sequences from gene bank: Total 562 complete genome sequences of the SARS-CoV-2 strains from the infected individuals are retrieved from the GISAID and NCBI database.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>NCBI</div> <div>suggested: (NCBI, RRID:SCR_006472)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Molecular visualization tool PyMOL (http://www.pymol.org/) was employed for visualization of 3D structures and its modifications.</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: Please consider improving the rainbow (“jet”) colormap used on page 14. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.285940: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">The medical ethics committee of the University Medical Center Groningen approved the study, and all subjects gave their written informed consent.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">The donors were 2 male and 2 female non-smoking healthy control volunteers (less than 2.5 packyears) with no history of respiratory disease aged 49-62.</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">All cells were mycoplasma negative and maintained at 37°C under 5% CO2.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 original stock was passaged twice in Vero E6 cells to obtain a working stock.</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">Cyt otoxicit ywas ca lcula tedu singthefol lo win gfor mu la: %=(−)(−) An tiv iralassa yin VeroE6and Cal u-3cellsVer oE 6ce lls wer es eeded atadensityof1.3x 105in1 2-wellpl atesand Calu -3 cellsweres eed edatadens ityo f2x 10 5in24-wellpl at es .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Calu-3</div> <div>suggested: BCRJ Cat# 0264, RRID:CVCL_0609)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 human lung epithelial cell line Calu-3 (ATCC HTB-55) was maintained in DMEM F-12 (Lonza, Switzerland) supplemented with 10% FBS, 1% Glutamax (Thermofisher), 1% non-essential amino acid (Thermofisher), penicillin (100 U/mL), and streptomycin (100 U/mL) (Gibco).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Thermofisher</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data was analyzed using Kaluza software (Beckman Coulter).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Kaluza</div> <div>suggested: (Kaluza, RRID:SCR_016182)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All data was analyzed in GraphPad Prism 8 software (La Jolla, CA, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GraphPad Prism</div> <div>suggested: (GraphPad Prism, RRID:SCR_002798)</div> </div> </td></tr></table>

      Results from OddPub: We did not detect 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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.312553: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Immunostaining was performed for SARS-CoV-2 nucleocapsid protein expression using the SARS-CoV-2 nucleocapsid antibody at 1:1000 dilution in blocking solution incubated for 30min.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>30min</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After washing primary antibody away, a secondary Alexa fluor 488 donkey anti-rabbit IgG(H+L) antibody(Thermo-Fisher) was used at 1:400 dilution in blocking solution and incubated for 30min.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-rabbit IgG(H+L</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>antibody(Thermo-Fisher</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Antibodies against cardiac troponin T (cTnT, Abcam ab8295; 1:100 mouse) and SARS-CoV-2 nucleocapsid were incubated with cells in blocking solution overnight at 4 °C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>cardiac troponin T ( cTnT , Abcam ab8295; 1:100 mouse )</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>cardiac troponin T ( cTnT ,</div> <div>suggested: (Antibodies-Online Cat# ABIN236605, RRID:AB_10764918)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Secondary antibodies were from Invitrogen: goat anti-mouse IgG AlexaFluor594 (A-11005) for J2 and goat anti-rabbit IgG AlexaFluor488 (A-11070) for nucleocapsid.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-mouse IgG</div> <div>suggested: (Molecular Probes Cat# A-11005, RRID:AB_141372)</div> </div> <div style="margin-bottom:8px"> <div>anti-rabbit IgG</div> <div>suggested: (Molecular Probes Cat# A-11070, RRID:AB_142134)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Primary Antibody Antibody species p-PKR (phospho-T446) [E120] rabbit PKR (D7F7) rabbit p-eif2α (S51) rabbit eif2α rabbit GAPDH (14C10) rabbit SARS-CoV-2 N rabbit MERS-CoV N mouse pSTAT1 (Tyr701)</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>phospho-T446</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>PKR</div> <div>suggested: (Cell Signaling Technology Cat# 12297, RRID:AB_2665515)</div> </div> <div style="margin-bottom:8px"> <div>p-eif2α</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>GAPDH</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>Tyr701</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">STAT1 mouse 1:1000 ACE2 rabbit MAVS rabbit V5 rabbit RNase L mouse 5% milk/TBST 1:1000 MDA5 rabbit 5% milk/TBST 1:1000 HRP linked HRP linked same as primary same as primary 1:1000 1:1000 1:1000 Santa Cruz (C136): SC-464 Cell Signaling Technology 4355S Cell Signaling Technology 24930S Cell Signaling Technology 13202S gift from Dr. Robert Silverman (Cleveland Clinic) Cell Signaling Technology 5321S Secondary Antibody goat anti-rabbit IgG goat anti-mouse IgG 1:3000 1:3000 Cell Signaling Technology 7074S Cell Signaling Technology 7076S Quantitative PCR (RT-qPCR).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>STAT1</div> <div>suggested: (Santa Cruz Biotechnology Cat# sc-464, RRID:AB_675899)</div> </div> <div style="margin-bottom:8px"> <div>ACE2</div> <div>suggested: (Cell Signaling Technology Cat# 4355, RRID:AB_2797606)</div> </div> <div style="margin-bottom:8px"> <div>V5</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>C136): SC-464 Cell Signaling Technology 4355S Cell Signaling Technology 24930S Cell Signaling Technology 13202S</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-rabbit IgG goat anti-mouse IgG</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-mouse</div> <div>suggested: (Cell Signaling Technology Cat# 7076, RRID:AB_330924)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Recombinant MERS-CoV and MERS-CoV-DNS4ab were described previously (Comar et al., 2019) and were propagated in Vero-CCL81 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Vero-CCL81</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Human HEK 293T cells were cultured in DMEM supplemented with 10% FBS and 1 mM sodium pyruvate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HEK 293T</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">iPSCs were maintained on Geltrex (Thermofisher Scientific)- Cells were passaged every 5-7 days using Stem-MACS Passaging Solution Differentiation of SV20 into cardiomyocytes (iCMs) was performed using Generation of A549ACE2 cells.</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">Supernatants harvested 48 hours primer 5′- post-transfection were used for transduction into A549 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>A549</div> <div>suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Briefly virus supernatant was 10-fold serial diluted and inoculum was absorbed on Vero cells for 1 hour at 37°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Vero</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A549, Calu-3, and iAT2 cells were lysed at indicated times post infection in RLT buffer and DNase- treated before total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Calu-3</div> <div>suggested: BCRJ Cat# 0264, RRID:CVCL_0609)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Images were processed using Fiji/Image J software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Fiji/Image J</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">RNA was harvested with buffer RLT (Qiagen RNeasy #74106) or Trizol-LS (Ambion) and analyzed on an RNA chip with an Agilent Bioanalyzer using the Agilent RNA 6000 Nano Kit and its prescribed protocol as we have described previously (Cat #: 5067-1511).</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">All statistical analyses and plotting of data were performed using GraphPad Prism software (GraphPad Software, Inc., 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 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: Please consider improving the rainbow (“jet”) colormap used on pages 50 and 51. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20197061: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</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. The purpose of the open letter was primarily to advocate for increased protection for HCWs, and thus the methodology was not designed to optimally probe HCW perspectives. The study may not be representative of all HCWs as the response rate was 12% at 48 hours and it did not capture all types of HCWs including a large sample of nurses, administrative or support staff. Occupational moral injury has not been well described in healthcare and deserves further research to better understand its root causes, preventative strategies and evidence based remediation. Response and non-response bias common to survey methodology may be operating and these findings require confirmation in studies from other jurisdictions. Finally, there was no ‘check’ to ensure that respondents were indeed HCWs, however the consistency of themes would argue otherwise. Constructive engagement with HCWs that also addresses their moral injury presents the challenge for healthcare leaders during this pandemic and beyond. This process should be seen as an opportunity to harness the resourcefulness of HCWs that many respondents felt had been sidelined, with the wealth of governance and operational experience among healthcare leaders, policy makers and government in order to fast track solutions. Achieving shared goals necessarily starts with better consultation and a dose of courage in all actors. Not doing so risks the contagion described in this report spreading throughout Aus...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.314070: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">All work using live SARS-COV-2 was performed in BSL4 using standard operating protocols approved by the Rocky Mountain Laboratories Institutional Biosafety Committee.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Syrian hamsters (Mesocricetus auratus), 6-8-weeks-of-age and >27-weeks-of- age, males and females, were purchased from Envigo.</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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 secondary antibody is an anti-rabbit IgG polymer from Vector Laboratories ImPress VR.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-rabbit IgG</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Vero E6 cells were maintained in DMEM (Sigma) supplemented with 10% fetal calf serum (Gibco), 1 mM L-glutamine (Gibco), 50 U/ml penicillin and 50 μg/ml streptomycin (Gibco).</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">293T and baby hamster kidney (BHK) were maintained in DMEM (Gibco) supplemented with fetal bovine serum, penicillin/streptomycin and L-glutamine. Plasmids.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>293T</div> <div>suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">BHK cells were transfected in 96-well format with 100 ng of host receptor plasmid, or no receptor and subsequently infected with spike-pseudotyped VSV particles as previously described (18).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>BHK</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 in Prism 8 (GraphPad).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GraphPad</div> <div>suggested: (GraphPad Prism, RRID:SCR_002798)</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your data.


      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

      Although, as with all animal models, there are some limitations exemplified by the lack of a systemic response to SARS-CoV-2 infection. The only mild disease manifestation and ability to quickly limit the infection make this model less suitable to study the mechanisms of severe COVID-19. However, the consistent and easily measured lung disease found in hamsters of all ages and sex make this a suitable infection model to evaluate SARS-CoV-2 countermeasure development.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20183459: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Participants gave consent for the use of their samples for this purpose.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Results Participant characteristics A total of 39 participants were included, of which 22 (56.4%) were female (Table 1).</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Two-hundred and nine matched venous and capillary blood samples were obtained from thirty nine participants and analysed using a COVID-19 IgG ELISA to detect antibodies against SARS-CoV-2.</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">Detection of SARS-CoV-2 antibodies in capillary and venous blood On the day following sample collection (day 1), the venous and capillary samples (refrigerated and stored at room temperate) were run in triplicate on the COVID-19 IgG ELISA (Omega Diagnostics Ltd, Littleport, Cambridgeshire, UK) according to manufacturer’s instructions; positive, cut-off, and negative controls were run in duplicate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>COVID-19 IgG</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analyses were performed using Prism (version 8, GraphPad, USA).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Prism</div> <div>suggested: (PRISM, RRID:SCR_005375)</div> </div> <div style="margin-bottom:8px"> <div>GraphPad</div> <div>suggested: (GraphPad Prism, RRID:SCR_002798)</div> </div> </td></tr></table>

      Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.310078: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">calling was implemented in DnaSP (Version 6.12.03) respectively and then visualized in Jalview (Version</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>DnaSP</div> <div>suggested: (DnaSP, RRID:SCR_003067)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phylogenetic analysis was with MEGA X software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MEGA X</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The genomes were initially aligned with MAUVE to check for large scale genomic changes including large deletions, gene inversion, and genome rearrangements.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MAUVE</div> <div>suggested: (Mauve, RRID:SCR_012852)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then, the sequences were re-aligned in MAFFT (Fig.1) to produce aligned sequences that were fed into DnaSP for SNP and haplotype analysis and subsequently into Jalview 2.11.1.0 for visualization and automatic determination of allelic frequency of SNPs.</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>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">Phylogenetic Analysis Maximum likelihood phylogenetic tree construction was implemented in MEGA X using sequences that had been aligned by MAFFT employing Tamura-Nei evolutionary model under assumption of uniform nucleotide substitution [21, 22].</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: Thank you for sharing your data.


      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

      A limitation of this study is the small sample size of eighteen genome sequences used in this study, which we consider too small for detection of all SARSCoV-2 SNPs in Nigeria. In subsequent studies, it will be of interest to see if distribution of SNPs and conserved regions identified in this study are peculiar to Nigerian SARS-CoV-2 or have complete overlap with genomes of SARS-CoV-2 found elsewhere. If there are regions of nonoverlap, any attempt to produce testing kits with high sensitivity for Nigeria’s COVID-19 cases should take note of the conserved regions and SNP distribution in the genomes of SARS-CoV-2 detected in this study. The frequency of SNPs observed in the Nigerian SARS-CoV-2 genome is higher than twice the frequency of SNPs in human genome which is generally taken to be 1 SNP per 1000 bps. The UTRs, especially 3’UTR, are mutation hot spots in Nigerian SARS-CoV-2 genome. This is expected because UTRs, unlike coding sequences, are generally under more relaxed or neutral selection pressure which allow mutations to accumulate at a higher rate in that region [25]. Relatively high SNP densities were also recorded in some of the coding regions of Nigerian SARS-CoV-2. An example is ORF 10 region with a SNP density of 8.55 SNPs/1000 nts. Although coronaviridae have proofreading capability due to their exonuclease activity during nucleotide replication, mutation rate of SARS-CoV-2 was estimated at ~6 × 10− 4 nucleotides/genome/year with the capacity to mutate during ...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.312165: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Ethics statement Animal experiments were approved by the Committee on the Ethics of Animal Care and Use of the Science and Technology Agency of Jiangsu Province.</td></tr><tr"><td style="min-width:100px;margin-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 pigs were randomly separated into three groups, housed in separate rooms, and fed the same artificial milk substitutes that meet the nutrient and energy recommendations of the National Research Council [NRC, 2012] at the animal facility of the Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Fifteen neonatal male pigs at birth were obtained from a TGEV-free farm in Nanjing without suckling.</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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Proteins were resolved in SDS-PAGE and detected as described (47) using the following antibodies: GAPDH (631402, Biolegend), rotavirus VP6 (rabbit polyclonal, ABclonal technology), and SARS-CoV-2 S2 (40592-T62, Sino Biological).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GAPDH</div> <div>suggested: (BioLegend Cat# 631402, RRID:AB_2107422)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Secondary antibodies were anti-rabbit (7074, Cell Signaling) or anti- mouse (7076, Cell Signaling) immunoglobulin G horseradish peroxidase-linked antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-rabbit ( 7074 , Cell Signaling )</div> <div>suggested: (Cell Signaling Technology Cat# 7074, RRID:AB_2099233)</div> </div> <div style="margin-bottom:8px"> <div>anti-</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Serum samples were collected from each pig at 24 and 48 hpi to detect specific anti-TGEV antibodies.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-TGEV</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For immunofluorescence analysis, samples were incubated with rabbit anti-TGEV-N antibody (1:500, DA0224, Shanghai YouLong Biotech) for 30 min at 37 ºC.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-TGEV-N</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">After three washes, samples were stained with Cy3-conjugated goat anti-rabbit secondary antibody (Beyotime) and DAPI (Invitrogen).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-rabbit</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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: Vero E6 cells (CRL-1586, ATCC) and Vero cells (CCL81, ATCC) were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, and 1 X Penicillin-Streptomycin- Glutamine.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Vero</div> <div>suggested: ATCC Cat# CCL-81, RRID:CVCL_0059)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Calu-3 cells (HTB-55, ATCC) and swine ST cells (CRL-1746, ATCC) were DMEM supplemented with 10% FBS and 1 X Penicillin-Streptomycin-Glutamine.</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">HEK293, HEK293-hACE2, and HEK293-hACE2-TMPRSS2 cells were cultured in complete DMEM containing G418 and/or blasticidin and used as previously described (11).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HEK293-hACE2-TMPRSS2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">MA104 and Vero E6-TMPRSS2 cells were cultured as before (42).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Vero E6-TMPRSS2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cell cytotoxicity assay The viability of Vero E6 and MA104 cells after drug treatment was determined using the Cell Counting Kit 8 (ab228554, Abcam).</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">HEK293 cells were treated with NTZ (10 μM), JIB-04 (3 μM), or transfected with low-molecular-weight poly(I:C) (100 ng/ml) for 24 hr.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HEK293</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">HSV-1 syn17+ strain was a gift from Ann Arvin at Stanford University.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>HSV-1 syn17+</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Image analysis was performed using ImageJ and customized R scripts.</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">Absorbance at 460nm was measured using Gen5 software and BioTek ELx800 Microplate Reader.</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">All siRNA used in this study were designed and synthesized by GenePharma (Shanghai, China) and their sequences of siRNAs are listed in Table S2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GenePharma</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Percentage of GFP positive cells and GFP intensity were determined by BD LSRFortessa™ X-20 cell analyzer and analyzed by FlowJo v10.6.2 (BD)</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">RNA sample quality was measured by both NanoDrop spectrophotometer (Thermo Fisher) and Bioanalyzer 2100 (Agilent).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>NanoDrop</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Differential gene expression analysis was performed using DESeq2.</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 RNA-seq raw and processed datasets were deposited onto NCBI Gene Expression Omnibus database (GSE156219)</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">2E, 2F, 3C, S3D, S3F, 4C, and 4D was calculated by Student's t test using Prism 8.4.3 (GraphPad).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GraphPad</div> <div>suggested: (GraphPad Prism, RRID:SCR_002798)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Non- linear regression (curve fit) was performed to calculate EC50 and CC50 values for Fig. 1B, 2A, and 2C using Prism 8.4.3.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Prism</div> <div>suggested: (PRISM, RRID:SCR_005375)</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your data.


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: We found the following clinical trial numbers in your paper:<br><table><tr><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">NCT04341493</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">Hydroxychloroquine vs Nitazoxanide in Patients With COVID-19</td></tr><tr><td style="min-width:95px; border-right:1px solid lightgray; border-bottom:1px solid lightgray">NCT04348409</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">Efficacy and Safety of Nitazoxanide for the Treatment of Hos...</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201582: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Materials and Methods Patients Patients admitted to our quaternary neonatal and infant intensive care unit (NICU) were included in this study, which was deemed exempt from oversight by the Children’s Hospital of Philadelphia Institutional Review Board.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.23.309294: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Group of BALB/c mice were infected intranasally with 2×104 PFU of MASCp6.</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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">S. H. Scheres, Processing of Structurally Heterogeneous Cryo-EM Data in RELION.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>RELION</div> <div>suggested: (RELION, RRID:SCR_016274)</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your data.


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.312769: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">All work with SARS-CoV-2 or icSARS-CoV-2-mNG was performed in a biosafety level facility with approval from the office of Environmental Health and Safety and the Institutional Animal Care and Use Committee at Yale University.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Only male mice were used due to availability.</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">All cell lines tested negative for Mycoplasma spp.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Huh7.5 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 10% heat-inactivated FBS and 1% Penicillin/Streptomycin.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Huh7.5</div> <div>suggested: RRID:CVCL_7927)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">50 µl of virus was diluted in 5 ml media and then added to 107 Vero-E6 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Vero-E6</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">From GSE147507 (14), we re-analyzed the raw count data from Calu-3 and A549-ACE2 cells, comparing SARS-CoV-2 infection to matched mock controls.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Calu-3</div> <div>suggested: BCRJ Cat# 0264, RRID:CVCL_0609)</div> </div> <div style="margin-bottom:8px"> <div>A549-ACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Spike Glycoprotein Gene, NR-52310, was produced under HHSN272201400008C and obtained through BEI Resources, NIAID, NIH. 293T cells were transfected with the pCAGGS vector expressing the SARS-CoV-2 spike glycoprotein and then incubated with replication-deficient VSV expressing Renilla luciferase for 1 hour at 37°C (27).</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;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">NSAID treatment does not affect Ace2 expression in mouse tissues (A-B) C57BL/6 mice were treated intraperitoneally with DMSO, 30 mg/kg ibuprofen, or 1 mg/kg meloxicam daily for 4 days.</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><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">( F) K18-hACE2 mice were infected intranasally with 1.2 × 106 PFU of SARS-CoV-2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>K18-hACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mice C57BL/6J and K18-hACE2 [B6.Cg-Tg(K18-ACE2)2Prlmn/J (17)] were purchased from Jackson Laboratory.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>K18-hACE2 [ B6.Cg-Tg(K18-ACE2)2Prlmn/J</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">C57BL/6J mice were anesthetized using 30% isoflurane and administered 30 mg/kg ibuprofen, 1 mg/kg meloxicam, or an equivalent amount of DMSO intraperitoneally in a volume of 10 ml/kg daily for days.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>C57BL/6J</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 performed differential expression analysis using the Wald test from DESeq2 (45), using a Benjamini-Hochberg adjusted p < 0.05 as the cutoff for statistical significance.</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">For visualization of Ptgs2 expression, the DESeq2- normalized counts were exported and plotted in 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><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Total cell numbers were quantified by Gen5 software for brightfield images.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Gen5</div> <div>suggested: (Gen5, RRID:SCR_017317)</div> </div> </td></tr></table>

      Results from OddPub: 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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.20200238: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 new set of differential equations corresponding to these three nodes are: (p2 (1 t1 ) + p3 (1 t2 ))xE (t) xU (t) @xU = µxU (t) 1 µc xU (t) @t De 1 Dr (p1 + p2 t1 + p3 t2 )(1 f ) xE (t) xP (t) @xP = µc xP (t) µ xP (t) @t De Dr f (p1 + p2 t1 + p3 t2 ) xE (t) µc xF (t) @xF 2 xF (t) = µ xF (t) @t De Dr 2 Due to identifiability issues, all the parameters described above cannot be estimated.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>p1 + p2 t1 + p3 t2 </div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>p1 + p2 t1 + p3 t2 ) xE</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">B u S0 De De (1 µ) M i0 As0 ◆B ✓ ◆ + R0 = ✓ 1 @ 1 µ+ µ + 1 µc + De 1 DR ✓ ✓ ◆◆ (1 f )p11 (1 f )(T0 (1 µ)Se0 ) t1 p12 t2 p13 + + ↵p De D (1 µ) M i0 As0 ✓ e ◆ (5) + 1 µ + µc + DR ✓ ✓ ◆◆ 1 0 f (T0 (1 µ)Se ) t1 p12 t2 p13 f p11 + + C De De (1 µ) M i0 As0 C ✓ ◆ A 1 µ + µc + DR Decoupling the effect of selection and misclassification on R0 : To provide some intuition about the effect of selection bias and misclassification on the value of R0 , we consider an example setting where we first compute the value of R0 from equation (5) with f = 0 (no misclassification, selection), f = 0.3 (misclassification+selection) using the same set of parameters.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>t1 p12 t2 p13 + + ↵p</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>t1 p12 t2 p13 f p11 +</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 run the algorithm for 100,000 iterations with a burn-in period of 100,000 using RStudio [18].</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>RStudio</div> <div>suggested: (RStudio, RRID:SCR_000432)</div> </div> </td></tr></table>

      Results from OddPub: 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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.308783: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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-VEGFR2 pY1175 was used to detect the activation of the pathway triggered by VEGF-A165 in the cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Anti-VEGFR2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Titer was determined to be approximately 1x107 PFU/mL as determined by median tissue culture infectious dose (TCID50) assay on Vero-E6-TMPRSS2 cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Vero-E6-TMPRSS2</div> <div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">450 Screening compounds for VSV-eGFP-SARS-CoV-2 inhibition African green monkey kidney (Vero)-E6-TMPRSS2 cells were plated at 15,000 cells per well in black/clear bottom 96 well tissue culture plates (Thermo Fisher Scientific 165305).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Vero)-E6-TMPRSS2</div> <div>suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">385 Docking of known NRP-1 targeting compounds Representatives of known compound series54-56, 58, 59, 61 were prepared for screening in LigPrep using the OPLS3e force field, neutral ionization, desalting, and tautomer generation.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>LigPrep</div> <div>suggested: (Ligprep, RRID:SCR_016746)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sum GFP fluorescence intensity, normalized to cell count by HCS CellMask Blue (Thermo #H32720), was measured and for each well and plotted with Prism 6 (GraphPad Software).</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 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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201889: (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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.21.305490: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">11a-b 11c-d 12a-b 12c-d 13a-b 13c-d 14a-b 14c-d 15a-b 15c-d 16a-b 16c-d 17a-b 17c-d 18a-b 18c-d 19a-b 19c-d RBD-ACE2 complex (6M0J) Final conformers of MD 1a-b RBD-ACE2 complex (6M0J) Final conformers of MD 2a-b RBD-ACE2 complex (6M0J) Final conformers of MD 3a-b RBD-ACE2 complex (6M0J) Final conformers of MD 4a-b RBD-ACE2 complex (6M0J) Final conformers of MD 5a-b RBD-ACE2 complex (6M0J) Final conformers of MD 6a-b RBD-ACE2 complex (6M0J) Final conformers of MD 7a-b RBD-ACE2 complex (6M0J) Final conformers of MD 8a-b RBD-ACE2 complex (6M0J) Final conformers of MD 9a-b RBD-ACE2 complex (6M0J) Final conformers of MD 10a-b RBD-ACE2 complex (6M0J) Final conformers of MD 11a-b RBD-ACE2 complex (6M0J) Final conformers of MD 12a-b RBD-ACE2 complex (6M0J) Final conformers of MD 13a-b RBD-ACE2 complex (6M0J) Final conformers of MD 14a-b RBD-ACE2 complex (6M0J) Final conformers of MD 15a-b RBD-ACE2 complex (6M0J) Final conformers of MD 16a-b RBD-ACE2 complex (6M0J) Final conformers of MD 17a-b RBD-ACE2 complex (6M0J) Final conformers of MD 18a-b RBD-ACE2 complex (6M0J) Final conformers of MD 19a-b WT SARS-CoV-2 WT SARS-CoV-2 K417A K417A K417E K417E E484A E484A E484K E484K Y489A Y489A N487A N487A F486A F486A Y505A Y505A Q453A Q453A T500A T500A Y449A Y449A Q493A Q493A Q498A Q498A N501A N501A L455A L455A F456A</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>11a-b 11c-d 12a-b 12c-d 13a-b 13c-d 14a-b 14c-d 15a-b 15c-d 16a-b 16c-d 17a-b 17c-d 18a-b 18c-d 19a-b 19c-d RBD-ACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A Y473A Y473A F486A/N487A F486A/N487A MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD Simulation Duration (ns) (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 20a-b 20c-d 21a-b 21c-d 22a-b 22c-d 23a-b 23c-d 24a-b 24c-d 25a-b 25c-d 26a-b 26c-d 27a-b 27c-d 28a-b 28c-d 29a-b 29c-d 30a-b 30c-d 31a-b 31c-d 32a-b 32c-d 33a-b 33c-d RBD-ACE2 complex (6M0J) Final conformers of MD 20a-b RBD-ACE2 complex (6M0J) Final conformers of MD 21a-b RBD-ACE2 complex (6M0J) Final conformers of MD 22a-b RBD-ACE2 complex (6M0J) Final conformers of MD 23a-b RBD-ACE2 complex (6M0J) Final conformers of MD 24a-b RBD-ACE2 complex (6M0J) Final conformers of MD 25a-b RBD-ACE2 complex (6M0J) Final conformers of MD 26a-b RBD-ACE2 complex (6M0J) Final conformers of MD 27a-b RBD-ACE2 complex (6M0J) Final conformers of MD 28a-b RBD-ACE2 complex (6M0J) Final conformers of MD 29a-b RBD-ACE2 complex (6M0J) Final conformers of MD 30a-b RBD-ACE2 complex (6M0J) Final conformers of MD 31a-b RBD-ACE2 complex (6M0J) Final conformers of MD 32a-b RBD-ACE2 complex (6M0J) Final conformers of MD 33a-b E484A/Y489A E484A/Y489A E484A/F486A E484A/F486A T500A/Y505A T500A/Y505A Y453A/K417E Y453A/K417E Q493A/Y453A Q493A/Y453A Q493A/K417E Q493A/K417E Y449A/Q498A Y449A/Q498A Y449A/Y505A Y449A/Y505A Q498A/T500A Q498A/T500A N501A/T500A N501A/T500A N501A/Q498A N501A/Q498A L455A/F456A L455A/F456A F456A/Y473A F456A/Y473A WT SARS-CoV WT SARS-CoV MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD MD SMD (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150 (a) 100, (b) 100 (c) 150, (d) 150</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>21a-b 21c-d 22a-b 22c-d 23a-b 23c-d 24a-b 24c-d 25a-b 25c-d 26a-b 26c-d 27a-b 27c-d 28a-b 28c-d 29a-b 29c-d 30a-b 30c-d 31a-b 31c-d 32a-b 32c-d 33a-b 33c-d RBD-ACE2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Single and double point mutants were generated using the Mutator Plugin in VMD (41).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Mutator Plugin</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">All MD simulations were performed in NAMD 2.13 (42) using the CHARMM36 (43) force field with a time step of 2 fs.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>NAMD</div> <div>suggested: (NAMD, RRID:SCR_014894)</div> </div> </td></tr></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 used on pages 13, 15 and 19. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.307637: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Method This experiment was approved by the Flinders University Social and Behavioral Research Ethics Committee.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Participants ranged from 18-78 years (M = 35.7, SD = 12.3), half were male (50.70%, female = 48.8%, non-binary = 0.4%; 0.2% did not answer) and most were Caucasian 59.9%.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 analyses using Null-Hypothesis Significance Tests (α = .05) in SPSS Version 25 and JASP for MacOS version 0.13.1 (39).</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: Thank you for sharing your data.


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20200774: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Random-effects high-vs-low metaanalysis followed by dose-response analysis using generalized least squares model in a two-stage random-effects meta-analysis were conducted.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">Search strategy Two independent investigators performed thorough literature searches, with discrepancies resolved by a third investigator in a blinded fashion.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px 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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">Consequently, a total of 35 studies with 14,502 patients were included in this systematic review, where 7918 patients were male (54.6%), and hypertension (4940 [34.1%]) as well as diabetes (4540 [31.3%]) were the most reported comorbidities (Appendix Table S4).</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Searches were conducted through PubMed,</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">Ovid EMBASE, CENTRAL,</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> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">0 (R Foundation for Statistical Computing, Vienna, Austria)16, and additional analyses with MetaXL software ver.5.3. ( EpiGear International, Queensland, Australia)17.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MetaXL</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20200329: (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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20194431: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">The research was approved according to the substantiated opinion number 4.086.949, by the Research Ethics Committee of São Pedro Psychiatric Hospital, Porto Alegre – RS.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 statistical analysis was carried out using the software IBM SPSS statistics v.20.0.</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:

      21,22 Study limitations The first limitation attributed to this study is related to the chosen sample, which was made by convenience. The non-probabilistic sample enabled a high response rate. However, the generalization of the results to the Brazilian population, in general, is not possible. External validity is limited to samples of the same profile. The inclusive criteria for people aged 18 or over have excluded the teenagers of the population, whose marijuana consumption may be higher, and whose alcohol consumption shows singular characteristics, related to parties and groups. This population portion may have changed the consumption behavior during the pandemic, but these changes were not ensured by this research. This age range may be addressed in future studies. This research may be influenced by memory bias, once the participants were requested to recall habits and behaviors to answer determined questions in the survey. Finally, the need to send a concise survey that is simple for the participant to complete led to the joint exploration of the psychoactive substances without any distinction between different types of substances. In other words, there were no questions that specified psychoactive drugs one by one and their respective frequencies of use and doses of consumption, before and after the start of the pandemic. Thus, the richness of the data related to the high increase or decrease in the consumption of some substances may have been missed, because the analyse...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.20201285: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">This study was approved by the IRB of the Chattogram General Hospital Ethics Committee and the patients gave oral consent regarding data collection and usage.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">R-script and GraphPad Prism version 7.04 was used to perform all of the statistical analyses and the figure plotting.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GraphPad Prism</div> <div>suggested: (GraphPad Prism, RRID:SCR_002798)</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your code.


      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

      Although the findings of this study were significant, limitations were also in order. Firstly, laboratory data collection to conduct a broad and extensive study was inevitably challenging as the laboratory results were not systematically collected. Secondly, the evaluated data was extracted retrospectively from patients’ medical files and not all laboratory tests were conducted on all patients. Thirdly, because of the study’s objective to identify the critical care needs of patients with the greatest severity of illness, the sample size is small. Therefore, more thorough assessment of comorbidities in larger samples of critical Bangladeshi patients with COVID-19 and future studies are required. Despite these limitations, this study represented the largest cohort of critically ill COVID-19 patients from Bangladesh reported to date.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.23.309948: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">Ethics Approval Ethical approval for this study was granted by the University of Glasgow School of Veterinary Medicine ethics committee (EA27/20).</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">The positive surveillance sample from cat 2 had been collected from a six-year-old female Siamese cat that presented with bilateral yellow ocular discharge as well as a serous nasal discharge.</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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 sodiumcitrate pressure cooking, the rabbit anti-nucleocapsid antibody (NovusBio, code: NB100-56683SS, dilution 1:100) and an AlexaFluor-488 secondary antibody (ThermoFisher, code: A-11034) as well as the ProLong™ Gold Antifade Mountant with DAPI (ThermoFisher, code: P36935) were used.</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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">As positive controls (for immunofluorescence and in situhybridisation), FFPE-Vero cell pellets experimentally infected with SARS CoV-2 were used and mock infected FFPE-Vero cells served as negative controls.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>FFPE-Vero</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Reads were quality filtered with TrimGalore (https://github.com/FelixKrueger/TrimGalore), aligned to the Wuhan-Hu-1 reference strain (GenBank accession MN908947.3) using BWA (13) followed by primer trimming and consensus calling with iVar (14).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>TrimGalore</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>BWA</div> <div>suggested: (BWA, RRID:SCR_010910)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A maximumlikelihood phylogenetic tree of all unique human SARS-CoV-2 sequences from the same county as cat 2 (n = 324), along with the cat 2 genome, the closest UK human sequence and the Wuhan-Hu-1 reference, was created using IQ-TREE (15) with the GTR substitution model (selected by IQ-Tree ModelFinder) and 1000 bootstraps.</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></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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.26.20202010: (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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.313510: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Scov2 A459 DPP4 Mock NHBE H129 36h H129 24h H129 mock Calu3 24h Calu3 mock Caco2 24h Caco2 mock DPP4 Mock A459 A ACE2 Infected MOCK ACE2 G ACE2 Scov2 NHBE Scov2 A459 Mock NHBE Mock A459 H129 36h H129 24h H129 mock Calu3 24h Calu3 mock Caco2 24h Caco2 mock F H TMPRSS2 TMPRSS2 Infected Scov2 NHBE Scov2 A459 Mock NHBE Mock A459 H129 36h H129 24h H129 mock Calu3 24h Calu3 mock Caco2 24h Caco2 mock MOCK Fig 3.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Caco2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A: IFN-beta expression in Calu-3 cells 12h post-infection; B: IFN-beta expression in Calu-3 cells 24h post-infection; C: IFN-beta expression in Calu-3 cells 48h post-infection; D: IFN-epsilon expression in Calu-3 cells 12h post-infection; E: IFN-epsilon expression in Calu-3 cells 24h post-infection; F: IFN-epsilon expression in Calu-3 cells 48h post-infection.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Calu-3</div> <div>suggested: BCRJ Cat# 0264, RRID:CVCL_0609)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">A: IFN-alpha-8 expression in Calu-3 cells; B: IFN-beta expression in Calu-3 cells; C: IFN-epsilon expression in Calu-3 cells; D: IFN-alpha-8 expression in Caco-2 cells; E: IFN-beta expression in Caco-2 cells; F: IFN-epsilon expression in Caco-2 cells.</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><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Samples composed of infected H1299 cell lines were excluded, due to the lack of differentially expressed genes.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>H1299</div> <div>suggested: NCI-DTP Cat# NCI-H1299, RRID:CVCL_0060)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Datasets were obtained from the Gene Expression Omnibus (GEO) repository, except for the proteomic dataset, which was obtained from the Proteomics Identification Database (PRIDE).</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> <div style="margin-bottom:8px"> <div>PRIDE</div> <div>suggested: (Pride-asap, RRID:SCR_012052)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Unless otherwise stated, significant differential expression (q<0.05) was calculated using the intersection between three algorithms, namely edgeR, DEseq2 and limma [26–28] (Robinson et al, 2010; Love et al, 2014; Ritchie et al, 2015), and with a minimum logFC of 0.5.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>edgeR</div> <div>suggested: (edgeR, RRID:SCR_012802)</div> </div> <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">The numbers were based on the intersection of three algorithms with logFC >0.5 and q<0.05, except for the proteome dataset where a single algorithm (DEseq2) and a logFC of 0.2 were selected.</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">KEGG Pathway KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION</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></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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201921: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">All participants supplied written consent and the experiments were approved by the IRBs of the Sheba, Hadassah, and Rambam Medical Centers</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201731: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Up to five control patients for each case were randomly sampled from the entire registered population of CPRD GOLD, matching on age, gender, index date and general practice.</td></tr><tr"><td style="min-width:100px;margin-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">Sex as a biological variable</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 weaknesses of the study This study drew on a large, longitudinal population-based data resource that enabled us to conduct a matched case-control analysis of risk factors for clinical COVID-19 diagnosis, as well as a cohort study of risk factors for COVID-19 mortality. As noted above, most cases were diagnosed clinically as suspected cases because of the limited capacity for testing in the early stage of the pandemic. General practice systems capture comprehensive data for all prescriptions issued by the general practice, so we can be confident that this exposure was accurately recorded. However, prescription utilisation may not be universal and nonadherence to prescribed medicines may be widespread. Data for covariates was not always completely recorded. Data on ethnicity were missing for almost half the sample as reported by others;25 an important limitation given the disproportionate impact COVID-19 has had on ethnic minority populations in the US and UK.14 30 31 COVID-19 susceptibility and severity have also been associated with measures of deprivation.14 Matching on practice may have accounted for differences in area-level deprivation to an extent, but deprivation based on participants’ home postcodes or individual-level deprivation measures might improve precision. It is known that observational studies on COVID-19 outcomes may be susceptible to collider bias.22 23 This can lead to spurious associations if both antihypertensive therapy and COVID-19 are ass...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.308338: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Following panning 492 individual clones of the second selection round were screened by standard Phage-ELISA procedures using a horseradish peroxidase-labeled anti-M13 monoclonal antibody (GE-Healthcare).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-M13</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For immunoblotting proteins were transferred on nitrocellulose membrane (Bio-Rad Laboratories) and detection was performed using anti- His primary antibody (Penta-His Antibody, #34660, Qiagen) followed by donkey-anti-mouse secondary antibody labeled with AlexaFluor647 (Invitrogen) using a Typhoon Trio scanner (GE-Healthcare, Freiburg, Germany; excitation 633 nm, emission filter settings 670 nm BP 30).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-</div> <div>suggested: (Aviva Systems Biology Cat# ARP34660_P050, RRID:AB_2044928)</div> </div> <div style="margin-bottom:8px"> <div>donkey-anti-mouse</div> <div>suggested: (Jackson ImmunoResearch Labs Cat# 715-065-151, RRID:AB_2340785)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 expression of SARS-CoV-2 proteins (RBD, stabilized homotrimeric Spike and S1 domain) Expi293 cells were applied in agreement to the protocol of Stadlbauer et al. [ 32].</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">( B) Neutralization potency of Nb-Set1 (NM1226, NM1228) in combination with Nb-Set2 (NM1230) was analyzed in Caco-2 cells using the SARS-CoV-2 strain icSARS-CoV-2-mNG.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Caco-2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 immunoblotting proteins were transferred on nitrocellulose membrane (Bio-Rad Laboratories) and detection was performed using anti- His primary antibody (Penta-His Antibody, #34660, Qiagen) followed by donkey-anti-mouse secondary antibody labeled with AlexaFluor647 (Invitrogen) using a Typhoon Trio scanner (GE-Healthcare, Freiburg, Germany; excitation 633 nm, emission filter settings 670 nm BP 30).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Bio-Rad Laboratories</div> <div>suggested: (Bio-Rad Laboratories, RRID:SCR_008426)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">By this means, global fits were obtained using the BLItzPro software and the global dissociation constant (KD) was calculated.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>BLItzPro</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The peptides were identified by exact mass and their fragment ion spectrum using protein database searches by Proteome Discoverer v2.1.0.81 (Thermo Fisher Scientific, Dreieich, Germany) and implemented SEQUEST HT search engine.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Proteome Discoverer</div> <div>suggested: (Proteome Discoverer, RRID:SCR_014477)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">For quantification of infection rates, images were taken with the Cytation3 (Biotek) and Hoechst+ and mNG+ cells were automatically counted by the Gen5 Software (Biotek).</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">Inhibitory concentration 50 (IC50) was calculated as the half- maximal inhibitory dose using 4-parameter nonlinear regression (GraphPad Prism).</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">Analyses and Statistics Graph preparation and statistical analysis was performed using the GraphPad Prism Software (Version 8.3.0).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GraphPad Prism</div> <div>suggested: (GraphPad Prism, RRID:SCR_002798)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Phylogenetic tree based on a ClustalW alignment of the CDR3 sequences is shown (lower panel).</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></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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.24.20201228: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid lightgray">This study was exempted by the IRB from informed consent requirement as a retrospective chart review study.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Randomization</td><td style="min-width:100px;border-bottom:1px solid lightgray">Model tuning was accomplished using 10000 random sets of hyperparameters for each of 4 model architectures (AdaBoost, Extra Trees, Gradient Boosting, Random Forest).</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Blinding</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Power Analysis</td><td style="min-width:100px;border-bottom:1px solid lightgray">This demonstrates that had viral clade been a dominant determinant of outcome the machine learning models would have had sufficient power to detect this effect.</td></tr><tr"><td style="min-width:100px;margin-right:1em; border-right: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></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Libraries were sequenced on MiSeq, NextSeq or NovaSeq instruments (Illumina) using 1x185, 1x75, or 1x100 runs respectively.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>MiSeq</div> <div>suggested: (A5-miseq, RRID:SCR_012148)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Raw reads and consensus sequences were deposited to NCBI SRA and Genbank respectively under BioProject PRJNA610428.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>BioProject</div> <div>suggested: (NCBI BioProject, RRID:SCR_004801)</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your data.


      Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

      This study has some unique strengths and weaknesses. Our data were derived from a single health-care system encompassing three hospitals in a major metropolitan area. By using a single medical system, we had access to substantial medical history on these subjects as well as reduced concern regarding the influence of hospital system on outcomes (i.e. we assume that decisions for hospitalization and quality of care of hospitalized patients will be more consistent in patients treated within a single system). Our system served as the primary site for COVID-19 testing particularly in March and April, 2020, which gave us access to a substantial number of patients with linked outcome data. However, our outcomes at present are limited to hospitalization and death. Use of hospitalization as outcome represents a useful dichotomous outcome that is a proxy for disease severity. However, the decision to admit may be influenced by factors other than the patient’s immediate status, and may be biased toward admission of patients with significant comorbidities, advanced age, or socio-economic considerations. It is conceivable that viral sequence variants might be associated with differential outcomes looking at more granular and direct disease features such as pulmonary radiologic outcomes or specific complications. The use of machine learning produced predictive models with excellent overall performance, particularly for predicting those patients who would not require hospitalization. Althou...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.20192443: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">25 Serological testing used enzyme-linked immunosorbent assay (ELISA) for anti-spike, anti-RBD, and anti-N IgG, IgM and IgA antibodies, as well as a functional assay for antibodies that block binding of RBD to an ACE2 fusion protein.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-spike, anti-RBD,</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-N IgG</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>IgA</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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.20.300574: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">Sex as a biological variable</td><td style="min-width:100px;border-bottom:1px solid lightgray">shRNA experiments in neurons were conducted in control NSB553 (male, 31 years old, European descent) and NSB2607 (male, 15 years old, European descent) hiPSCs (Hoffman et al., 2017); wildtype and shRNA intestinal cell experiments were conducted in 1383D6 (male, 36 years, Asian descent) (Takayama et al., 2017). hiPSC-NPC culture: hiPSC-NPCs were cultured in hNPC media (DMEM/F12 (Life Technologies #10565), 1x N-2 (Life Technologies #17502-048), 1x B-27-RA (Life Technologies #12587-010), 20 ng/mL FGF2 (Life Technologies)) on Matrigel (Corning, #354230). hiPSC-NPCs at full confluence (1-1.5x107 cells / well of a 6-well plate) were dissociated with Accutase (Innovative Cell Technologies) for 5 mins, spun down (5 mins X 1000g), resuspended and seeded onto Matrigel-coated plates at 3-5x106 cells / well.</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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 monoclonal anti-SARS-CoV-2 Nucleocapsid [1C7C7] protein (1:1000, a kind gift by Dr. T. Moran, Center for Therapeutic Antibody Discovery at the Icahn School of Medicine at Mount Sinai) and rabbit anti-ß-III-tubulin (Convence, PRB-435P, 1:2000) or goat anti-EpCAM, (R&D Biosystems #AF960, 1:500) overnight at 4°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-SARS-CoV-2 Nucleocapsid [1C7C7] protein</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-ß-III-tubulin</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>PRB-435P</div> <div>suggested: (Covance Cat# PRB-435P-100, RRID:AB_291637)</div> </div> <div style="margin-bottom:8px"> <div>anti-EpCAM</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Then slides were incubated with primary antibody (EpCAM, 1:50, R&D Biosystems #AF960; Villin, Abcam, ab130751, COV2-NP 1:100, ACE2 1:100) overnight.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>COV2-NP</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Slides were then incubated with corresponding anti-mouse, antirabbit, and anti-goat secondary antibodies (1:200, 2 hrs) and DAPI (1:2000, 10 mins) and mounted with ImmuMount.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-mouse, antirabbit,</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-goat</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Western blot analysis was performed using 100 µg of total protein using anti-ACE2 (Abcam/ab239924/EPR4435(2)), anti-CD147 (Abcam/ab666/MEM-M6/1), antiFURIN (Abcam/ab183495/EPR14674) or anti-b-ACTIN (Cell Signaling/#4970S/ 13E5) primary antibodies (1:5000, 1-hr) followed by autoradiographic detection using corresponding anti-mouse (Cell Signaling/#7076S) or anti-rabbit (Cell Signaling/#7074S) secondary antibodies conjugated with HRP (1:5000, 1-hr).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>anti-ACE2</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-CD147</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>antiFURIN</div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div>anti-b-ACTIN</div> <div>suggested: (MBL International Cat# PM053-7, RRID:AB_10697035)</div> </div> <div style="margin-bottom:8px"> <div>anti-mouse</div> <div>suggested: (Cell Signaling Technology Cat# 7076, RRID:AB_330924)</div> </div> <div style="margin-bottom:8px"> <div>anti-rabbit</div> <div>suggested: (Cell Signaling Technology Cat# 7074, RRID:AB_2099233)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 was propagated in Vero E6 cells in DMEM supplemented with 2% FBS, 4.5 g/L D-glucose, 4 mM L-glutamine, 10 mM Non-Essential Amino Acids, 1 mM Sodium Pyruvate and 10 mM HEPES.</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;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Reads were aligned to Mesocricetus auratus Ensembl MesAur1.0 using STAR aligner, and mappid using CustomDESeq2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>STAR</div> <div>suggested: (STAR, RRID:SCR_015899)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Differential expression analysis was performed using edgeR (v3.26.8) (Robinson et al., 2010), limma (v3.40.6) (Ritchie et al., 2015) and Glimma (v1.12.0) (Su et al., 2017) packages.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>edgeR</div> <div>suggested: (edgeR, RRID:SCR_012802)</div> </div> <div style="margin-bottom:8px"> <div>limma</div> <div>suggested: (LIMMA, RRID:SCR_010943)</div> </div> <div style="margin-bottom:8px"> <div>Glimma</div> <div>suggested: (Glimma, RRID:SCR_017389)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Enrichment analysis was performed using WebGestaltR (0.4.4) using custom neural gene sets of interest (Schrode et al., 2019) and interferon gene sets (Blanco-Melo et al., 2020).</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>WebGestaltR</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The images were quantified using the CellProfiler software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>CellProfiler</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Data analysis: Data from all phenotypic assays above were first organized in a Microsoft Excel spreadsheet and analyzed using GraphPad PRISM 8 software or R.</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> <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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.23.310565: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 metadata is cleaned to remove obvious typos, and to unify labels with the same meaning, e.g., "MinION" and "Nanopore MinION".</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">SNV Assignments SNVs and insertions/deletions (indels) at the nucleotide and amino acid level are determined by aligning each sequence to the WIV04 reference sequence (WIV04 is a high quality December, isolate that is 100% identical to the first publicly available SARS-CoV-2 genome reference Wuhan-Hu-1/NC_045512.2, excepting the sequences at the end of the genomes) using bowtie2.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>bowtie2</div> <div>suggested: None</div> </div> </td></tr></table>

      Results from OddPub: Thank you for sharing your code and data.


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201772: (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:

      The probabilistic model we developed represents a first step to link viral load to SARS-CoV-2 infectiousness, but it has limitations. First, the model used a Michaelis-Menten term to model the saturation effect for simplicity. The data we used to support this functional form were limited and other functional forms incorporating a saturation effect may also be able to explain the data. Second, the model makes several simplifying assumptions including assuming that all contacts are of the same duration and the parameter values in the model are the same across patients, whereas in reality, there may exist considerable heterogeneity (43, 58). Therefore, further model developments incorporating different aspects of heterogeneity in the transmission process (40, 58), rigorous parameter estimation from clinical and epidemiological data, and testing of alternative models are warranted. The viral load in the LRT is maintained at intermediate-to-high levels for a prolonged period of time (5, 16). In Ref. (5), multiple viral peaks in the LRT were observed in several patients. We tested different hypotheses to explain this observation by constructing mathematical models that include the immune responses, proliferation of target cells or spatial spread of virus in the lungs. The best model for explaining the data is the one that implicitly considers spatial spread of virus in the lungs. If virus can reach new physiological compartments, e.g. different regions of the lungs, then new target...


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We did not find any issues relating to the usage of bar graphs.


      Results from JetFighter: We did not find any issues relating to colormaps.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.22.308098: (What is this?)

      Please note, not all rigor criteria are appropriate for all manuscripts.

      Table 1: Rigor

      <table><tr"><td style="min-width:100px;margin-right:1em; border-right:1px solid lightgray; border-bottom:1px solid lightgray">Institutional Review Board Statement</td><td style="min-width:100px;border-bottom:1px solid 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">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">Cell Line Authentication</td><td style="min-width:100px;border-bottom:1px solid lightgray">not detected.</td></tr></table>

      Table 2: Resources

      <table><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 generate icSARS-CoV-2-mNG stocks, 200,000 Caco-2 cells were infected with 50 μl of virus stock in a 6-well plate, the supernatant was harvested 48 hpi, centrifuged, and stored at -80°C.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Caco-2</div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td 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 8.0 was used for statistical analyses and to generate graphs.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>GraphPad</div> <div>suggested: (GraphPad Prism, RRID:SCR_002798)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Other software used included Gen5 v.3.10.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>Gen5</div> <div>suggested: (Gen5, RRID:SCR_017317)</div> </div> </td></tr></table>

      Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).


      Results from LimitationRecognizer: 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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.21.307439: (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><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Quantobio Biotechnology Co., Ltd., China) before infecting hACE2-transfected 293T cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div>293T</div> <div>suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</td></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sequential data processing was carried out on RELION.</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">Manual model rebuilding was carried out using Coot39 and refined with PHENIX real-space refinement40.</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></table>

      Results from OddPub: Thank you for sharing your data.


      Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.


      Results from TrialIdentifier: No clinical trial numbers were referenced.


      Results from Barzooka: We 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: Please consider improving the rainbow (“jet”) colormap used on page 21. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

    1. SciScore for 10.1101/2020.09.25.20201996: (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.


      About SciScore

      SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.