Mucociliary transport deficiency and disease progression in Syrian hamsters with SARS-CoV-2 infection

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1. Version published to 10.1172/jci.insight.163962

   Jan 10, 2023
2. 

   ScreenIT

   Jan 20, 2022

   SciScore for 10.1101/2022.01.16.476016: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Animal model and sample collection: All procedures involving animals and SARS-CoV-2 were approved by the Institutional Animal Care and the Use Committee (# 20232) and Institutional Biosafety Committee (# 10-262) at the University of Alabama at Birmingham (UAB).
   Sex as a biological variable	not detected.
   Randomization	Random effects included random intercept only.
   Blinding	Histological analysis: H&E stained trachea and lung slices were blinded and semiquantitatively scored by a board-certified veterinary anatomic pathologist following published criteria54.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Standard IHC process was …

   SciScore for 10.1101/2022.01.16.476016: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Animal model and sample collection: All procedures involving animals and SARS-CoV-2 were approved by the Institutional Animal Care and the Use Committee (# 20232) and Institutional Biosafety Committee (# 10-262) at the University of Alabama at Birmingham (UAB).
   Sex as a biological variable	not detected.
   Randomization	Random effects included random intercept only.
   Blinding	Histological analysis: H&E stained trachea and lung slices were blinded and semiquantitatively scored by a board-certified veterinary anatomic pathologist following published criteria54.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Standard IHC process was applied with antigen retrieval by 0.01 M sodium citrate buffer (pH 6), 1:30,000 dilution of anti-acetylated tubulin (cat. # T7451 from Sigma-Aldrich) and 1:500 dilution of goat anti-mouse IgG H&L secondary antibody conjugated with HRP (Abcam ab6789).	anti-acetylated tubulin suggested: (Sigma-Aldrich Cat# T7451, RRID:AB_609894) anti-mouse IgG suggested: (Abcam Cat# ab6789, RRID:AB_955439)
   Experimental Models: Cell Lines
   Sentences	Resources
   Briefly, virus was serially diluted and added to confluent Vero E6 cells grown on 6-well plates.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Airway surface liquid (ASL) depth, periciliary layer (PCL) height, cilia beat frequency (CBF), mucociliary transport (MCT) rate, and ciliation coverage (CC) on epithelial surfaces of tracheas were analyzed using ImageJ (NIH, Bethesda, MD) and MATLAB software (MathWorks, Natick, MA)57–60.	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   52 The CBF map was generated through a MATLAB script to visualize the location and frequency of active cilia across the epithelial cell surface and the proportion of pixels with active cilia quantified as previously described71.	MATLAB suggested: (MATLAB, RRID:SCR_001622)
   Statistical analysis: Data were analyzed using unpaired t-test, one-way or two-way analysis of variance (ANOVA) followed by recommended Tukey’s or Šídák’s multiple-comparison tests, descriptive statistics, and regression methods (both univariable regression and linear mixed models) in GraphPad Prism 9.2.0 (	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   GraphPad Software, Inc., La Jolla, CA)	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   ), SPSS Statistics (IBM, Armonk, NY), or SAS v9.4 (Cary, NC).	SPSS suggested: (SPSS, RRID:SCR_002865)

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   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).

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   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.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 29. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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   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.

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

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3. 

   Version published to 10.1101/2022.01.16.476016v1 on bioRxiv

   Jan 18, 2022