1. SciScore for 10.1101/2021.08.02.454730: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.


    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:
    Our model has limitations and should only be seen as a modest step of putting key elements of the innate immune system into a dynamic framework. In particular, we omit the anti-inflammatory cytokines secreted by the macrophages that reduce recruitment of macrophages in a previous model of innate immunity [55]. Extension of these next-level cells may reduce and extend the macrophage dynamics to the longer timescales where adaptive immunity also comes into play. The model could be extended further into the disease progression with more components in the immune systems including the role of CD8 T cells. A previous study about the motif comprised of the interactions between antigen and CD8 T cells also suggested that bistability would result from the interplay between antigen and the immune system [56]. It is also interesting to compare our model to the quite different and elaborate model of ref. [57] that follows a population of human cells by assuming that IFN-1 converts infected cells to resistant cells. In that model, the NK cells are the main cause of direct virus elimination, and the macrophages primarily act by inducing IFN-1 that in turn reduce virus proliferation. Despite the substantial differences, the model in ref. [57] contains the central motif of Fig. 2B, leading to similar predictions of increased macrophages activity associated with reduction of IFN-1 signaling. The heterogeneity of the viral kinetics has been discussed in other relevant models in contexts that i...

    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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