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  1. SciScore for 10.1101/2022.01.07.475453: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: All procedures used in this study (sex and age matched) complied with federal guidelines and the institutional policies of the Yale School of Medicine Animal Care and Use Committee.
    Euthanasia Agents: Briefly, animals were anaesthetized using a mixture of ketamine (50 mg/kg) and xylazine (5 mg/kg), injected i.p. The rostral neck was shaved and disinfected.
    Consent: Isolation of patient plasma and cytokine/chemokine measurements: Patient plasma was collected with informed consent and IRB approval as previously described (Lucas et al., 2020).
    Sex as a biological variableMouse models: 6- to 12-week-old female CD1 and BALB/c mice were purchased from Charles River and Jackson Laboratory, respectively, and housed at Yale University.
    Randomizationnot detected.
    BlindingConfocal imaging and quantification: All cell counting was performed by experimenters blinded to experimental conditions on a Zeiss LSM700 or LSM800 scanning confocal microscope (Zeiss).
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Rabbit anti-SARS-CoV-2 nucleocapsid (1:250, GeneTex GTX135357), rabbit anti-IBA1 (1:1000, Wako Chemicals 019-19741), rat anti-CD68 (1:200, Abcam ab53444), rabbit anti-DCX (1:500, Abcam ab18723), rabbit anti-ASPA (1:250, EMD Millipore ABN1698), goat anti-PDGFRa (1:500; R&D Systems AF1062), mouse anti-CC1 (1:100; EMD Millipore OP80) were diluted in 1% normal donkey serum in 0.3% Triton X-100 in TBS and incubated overnight at 4°C (CC1 was incubated for 7 days at 4°C).
    anti-DCX
    suggested: (Abcam Cat# ab18723, RRID:AB_732011)
    Sections were then rinsed three times in 1X TBS and incubated in secondary antibody solution (Alexa 647 donkey anti-rabbit IgG, 1:500 (Jackson Immunoresearch); Alexa 488 donkey anti rat IgG, 1:500 (Jackson Immunoresearch); Alexa 594 donkey anti-rabbit IgG, 1:500 (Jackson Immunoresearch); Alexa 488 donkey anti goat IgG, 1:500 (Jackson Immunoresearch); Alexa 647 donkey anti-mouse IgG, 1:500 (Jackson Immunoresearch) in 1% blocking solution at room temperature protected from light for two hours.
    anti rat IgG
    suggested: None
    anti-rabbit IgG
    suggested: (Jackson ImmunoResearch Labs Cat# 711-545-152, RRID:AB_2313584)
    anti goat IgG
    suggested: None
    anti-mouse IgG
    suggested: (Jackson ImmunoResearch Labs Cat# 015-500-003, RRID:AB_2337222)
    Antibodies included IBA1 (Wako 019-19741) and CD68 (Thermo Fisher Scientific 14-0688-82).
    IBA1
    suggested: (FUJIFILM Wako Shibayagi Cat# 019-19741, RRID:AB_839504)
    CD68
    suggested: (Thermo Fisher Scientific Cat# 14-0688-82, RRID:AB_11151139)
    Antibody binding was visualized with 3,3′- diaminobenzidine (DAB; Vector Laboratories).
    DAB
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Generation of SARS-CoV-2 stocks: To generate SARS-CoV-2 viral stocks, Huh7.5 cells were inoculated with SARS-CoV-2 isolate USA-WA1/2020 (NR-52281; BEI Resources) to generate a P1 stock.
    Huh7.5
    suggested: RRID:CVCL_7927)
    Virus titer was determined by plaque assay using Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Experimental Models: Organisms/Strains
    SentencesResources
    Mouse models: 6- to 12-week-old female CD1 and BALB/c mice were purchased from Charles River and Jackson Laboratory, respectively, and housed at Yale University.
    BALB/c
    suggested: RRID:IMSR_ORNL:BALB/cRl)
    Software and Algorithms
    SentencesResources
    Images were taken at 20X magnification and analyzed using FIJI software.
    FIJI
    suggested: (Fiji, RRID:SCR_002285)
    The cingulum of the corpus callosum in each hemisphere was imaged with one 319.5 × 319.5 μm field and cells were quantified using the “Spots” function in Imaris image analysis software (Oxford Instruments).
    Imaris
    suggested: (Imaris, RRID:SCR_007370)
    g-ratios were measured by dividing the axonal diameter by the diameter of the entire fiber (diameter of axon/diameter of axon + myelin sheath) using ImageJ software.
    ImageJ
    suggested: (ImageJ, RRID:SCR_003070)
    All statistics were performed using Prism Software (Graphpad).
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)

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


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

    Results from TrialIdentifier: No clinical trial numbers were referenced.


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


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


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

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


    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex 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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  2. Published on bioRxiv

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