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  1. SciScore for 10.1101/2022.01.20.22269491: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Study approval: This study (NCT00001230) was approved by the National Institute of Allergy and Infectious Diseases (NIAID) Institutional Review Board.
    Consent: Written informed consent was obtained from all participants.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    The cells were washed twice with Perm buffer (BioLegend) and resuspended with the intracellular antibody pool containing anti-CD69 (FITC), anti-CD154 (APC), anti-TNF-a (Alexa Fluor 700) and anti-IFN-y (BUV737) (Supplemental Table I) for 30 min at 4°C.
    anti-CD69
    suggested: (BD Biosciences Cat# 560739, RRID:AB_1727505)
    anti-CD154
    suggested: (Thermo Fisher Scientific Cat# 56-1548-42, RRID:AB_2848470)
    anti-TNF-a
    suggested: None
    anti-IFN-y ( BUV737 )
    suggested: None
    Software and Algorithms
    SentencesResources
    Finally, the cells were washed twice with Perm buffer and then acquired using the BD LSRFortessa flow cytometer (BD Biosciences) and FACSDiva software (BD Biosciences) for acquisition.
    FACSDiva
    suggested: (BD FACSDiva Software, RRID:SCR_001456)
    All analyses were performed using FlowJo v10.5.3
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    The remainder of the single cell RNA-Seq (scRNA) analysis was performed with Seurat v3.2.2 [37].
    Seurat
    suggested: (SEURAT, RRID:SCR_007322)
    Differential expression analysis was performed to identify cluster-specific markers and to compare the S and M cell populations using MAST [40], or “Model-based Analysis of Single-cell Transcriptomics”, whereas the cluster-specific canonical pathway enrichment profiles were generated using Ingenuity Pathway Analysis (IPA, Qiagen, Redwood City, CA, USA).
    MAST
    suggested: (MAST, RRID:SCR_016340)
    Ingenuity Pathway Analysis
    suggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)

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


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

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT00001230RecruitingHost Response to Infection and Treatment in Filarial Disease…


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


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


    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a protocol registration statement.

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


    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex 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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