Elevated plasma levels of CXCL16 in severe COVID-19 patients

  1. Sandra P. Smieszek
  2. Vasilios M. Polymeropoulos
  3. Christos M. Polymeropoulos
  4. Bartlomiej P. Przychodzen
  5. Gunther Birznieks
  6. Mihael H. Polymeropoulos

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Abstract

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  1. Version published to 10.1016/j.cyto.2022.155810
  2. ScreenIT

    SciScore for 10.1101/2021.09.07.21263222: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Inability to provide informed consent or to have an authorized relative or designated person provide informed consent, or to comply with the protocol requirements; 2.
    Sex as a biological variablenot detected.
    RandomizationParticipants: ODYSSEY is a double-blinded Phase 3 study with a planned randomization of a total of 300 hospitalized severely ill COVID-19 patients (Clinicaltrials.gov: NCT04326426).
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    CXCL16 levels in plasma were determined with an enzyme□linked immunosorbent assay (ELISA) assay (Thermofisher ID: # EHCXCL16) performed on plasma collected at baseline in cases and in a set of healthy controls (assay range 2.74-2000 pg/mL).
    Thermofisher ID
    suggested: None
    DNA sample size distributions are profiled by a Fragment Analyzer (Advanced Analytics) or BioAnalyzer (Agilent Technologies), to assess sample quality and integrity.
    BioAnalyzer
    suggested: (BioAnalyzer 2100, RRID:SCR_019715)
    Whole genome sequencing (WGS) libraries were prepared using the Truseq DNA PCR-free Library Preparation Kit.
    WGS
    suggested: None
    Paired-end 150 bp reads were aligned to the GRCh37 human reference (BWA-MEM v0.7.8) and processed with GATK best-practices workflow (GATK v3.4.0).
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    GATK
    suggested: (GATK, RRID:SCR_001876)
    All high quality variants obtained from GATK were annotated for functional effects (intronic, intergenic, splicing, nonsynonymous, stopgain and frameshifts) based on RefSeq transcripts using Annovar31.
    RefSeq
    suggested: (RefSeq, RRID:SCR_003496)
    Additionally, Annovar was used to match general population frequencies from public databases (Exac, gnomAD, ESP6500, 1000g) and to prioritize rare, loss-of-function variants.
    Annovar
    suggested: (ANNOVAR, RRID:SCR_012821)
    Linear models adjusted for PC, age and sex were conducted in PLINK.
    PLINK
    suggested: (PLINK, RRID:SCR_001757)

    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
    NCT04326426Enrolling by invitationODYSSEY: A Study to Investigate the Efficacy of Tradipitant …

    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.

  3. Version published to 10.1101/2021.09.07.21263222 on medRxiv