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  1. SciScore for 10.1101/2021.07.15.21260285: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The UCSF Institutional Review Board (IRB) granted a waiver of consent under IRB protocol #17-24056.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    We also processed negative control samples (water and HeLa cell RNA) to account for background contamination.
    suggested: CLS Cat# 300194/p772_HeLa, RRID:CVCL_0030)
    Software and Algorithms
    Metagenomic analysis of respiratory viruses: Samples were processed through the IDSeq pipeline36,37, which performs reference based alignment at both the nucleotide and amino acid level against sequences in the National Center for Biotechnology Information (NCBI) nucleotide (NT) and non-redundant (NR) databases, respectively, followed by assembly of the reads matching each taxon detected.
    suggested: (IDseq, RRID:SCR_019038)
    Human gene expression quantification: Following demultiplexing, sequencing reads were pseudo-aligned with kallisto39 (v. 0.46.1; including bias correction) to an index consisting of all transcripts associated with human protein coding genes (ENSEMBL v.99), cytosolic and mitochondrial ribosomal RNA sequences, and the sequences of ERCC RNA standards.
    suggested: (Ensembl, RRID:SCR_002344)
    The design formula for the direct comparison between children and adults with SARS-CoV-2 was ∼log10(rpM) + age cohort, where age cohort was either “children” or “adults”.
    suggested: (BioLegend Cat# 944703, RRID:AB_2890874)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Our study has several limitations that should be kept in mind: 1) a larger sample size would have increased the generalizability of our findings; 2) we could not directly control for timing since onset of infection; 3) proteomic measurements may have provided additional insight but were not possible from the available swab specimens, which were collected into a virus inactivating agent; 4) our findings regarding tissue cellular composition require validation by single-cell sequencing; and lastly, 5) the majority of subjects with COVID-19 had mild disease at the time of sampling and did not require hospitalization. Results may have differed if specimens from a greater proportion of severely ill individuals had been available, however, this likely resulted in a more relevant comparison since few children develop severe disease. Taken together, our findings suggest children elicit a more robust pro-inflammatory and adaptive immune response to SARS-CoV-2 infection in the upper airway compared to adults but an overall comparable type I interferon response. Children, unlike adults, also display decreased proportions of ciliated cells, the primary targets of SARS-CoV-2, upon infection with the virus. These differences in the upper airway immune response and tissue composition may both contribute to the protection of children from severe disease in the lower respiratory tract. Further study is warranted to unravel why children are better protected specifically against SARS-CoV-2, or ...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

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

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

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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

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