1. SciScore for 10.1101/2021.02.14.431177: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Autopsy and biopsy materials were obtained from the Pontificia Universidade Catolica do Parana PUCPR the National Commission for Research Ethics (CONEP) under ethics approval numbers 2020001792/30188020.7.1001.0020 and 2020001934/30822820.8.000.0020.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies: The following antibodies were used: mouse anti-ACE2 (Santa Cruz, sc-390851, IF1:200) goat anti-ACE2 (R&D systems, AF933, WB 1:1000), mouse anti-dsRNA (Millipore, MABE1134, IF1:100)
    suggested: (Santa Cruz Biotechnology Cat# sc-390851, RRID:AB_2861379)
    suggested: (Millipore Cat# MABE1134, RRID:AB_2819101)
    Experimental Models: Cell Lines
    Cell culture: Human umbilical vein endothelial cells (HUVECs), and human microvascular endothelial cells from lungs (HMVEC-L) purchased from Lonza (Cat# CC-2935, and CC-2527 respectively) were cultured until passage 8 in EGM-Plus or EGM-2MV medium, supplemented with singlequots (Lonza Cat# CC-5035, CC-3102)
    suggested: None
    Calu-3 cells purchased from ATCC (Cat# HTB-55) were maintained in MEM (Invitrogen), containing 10% (v/v) heat-inactivated foetal bovine serum (Cytiva), 100 U/ml penicillin and streptomycin (Life Technologies Australia), and grown in EGM-2MV for endothelial co-culture experiments.
    suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)
    Monocultures of HUVEC, HMVEC or Calu-3 cells were performed on 24 well cell culture inserts (Corning 6.5 mm Transwell, 0.4 µm polycarbonate membrane Cat#3413) coated with 5 µg/ml FN (Sigma).
    suggested: None
    Virus was grown on Vero cells and titred [38].
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
    Software and Algorithms
    Image analysis: Analysis of immunofluorescent images was performed using ImageJ version 2.0.0-rc-69/1.52n.
    suggested: (ImageJ, RRID:SCR_003070)
    Imaris (Bitplane) version 8 was used to create the XZ projection in Figure 4B’’.
    suggested: (Imaris, RRID:SCR_007370)
    Statistical analysis: All statistical analysis was performed using Graphpad Prism version 9.0.
    Graphpad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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 present study was subject to several limitations. Firstly, coagulation, thrombosis and induction of angiogenesis in the lungs of deceased COVID-19 patients has been described in addition to endothelial dysfunction [3]. This angiogenic response is thought to be predominantly mediated through intussusceptive angiogenesis, where a new blood vessel is formed by splitting of an existing vessel. This effect appears to be specific to COVID-19 patients, as lungs from decreased influenza patients do not display increased angiogenic features. Whether this is due to relative hypoxia in the lungs remains unclear, although elevated angiogenic growth factors such as VEGF-A and VEGF-C have been associated with COVID-19 [3, 39]. In this study we have not addressed the effect of SARS-CoV-2 exposure on the angiogenic capacity of endothelial cells in culture. Given the intimate association between inflammation, endothelial dysfunction and angiogenesis [40, 55], these are critical aspects of COVID-19 pathology that remain to be addressed in subsequent studies. An additional limitation of the present study is that, due to the reductionist nature of the in vitro systems used herein, we were unable to address the contribution of immune cells to endothelial cell dysfunction during SARS-CoV-2 infection. Multiple studies attribute the sustained inflammatory response directly to immune cells, wherein macrophage activation, monocyte NLRP3 inflammasome signalling, complement activation and extrusion ...

    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.

    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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