Temporal associations of B and T cell immunity with robust vaccine responsiveness in a 16-week interval BNT162b2 regimen
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SciScore for 10.1101/2021.12.18.473317: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: EXPERIMENTAL MODEL AND SUBJECT DETAILS: Ethics Statement: All work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources CXCR3, CCR6, CXCR6 and CXCR5 antibodies were added in culture 15 min before stimulation. CXCR3suggested: NoneCCR6suggested: NoneCXCR6suggested: NoneCXCR5suggested: NoneExperimental Models: Cell Lines Sentences Resources Cell lines: 293T human embryonic kidney and HOS cells (obtained from … SciScore for 10.1101/2021.12.18.473317: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: EXPERIMENTAL MODEL AND SUBJECT DETAILS: Ethics Statement: All work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources CXCR3, CCR6, CXCR6 and CXCR5 antibodies were added in culture 15 min before stimulation. CXCR3suggested: NoneCCR6suggested: NoneCXCR6suggested: NoneCXCR5suggested: NoneExperimental Models: Cell Lines Sentences Resources Cell lines: 293T human embryonic kidney and HOS cells (obtained from ATCC) were maintained at 37°C under 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) (Wisent) containing 5% fetal bovine serum (FBS) (VWR) and 100 μg/mL of penicillin-streptomycin (Wisent). HOSsuggested: None293T-ACE2 cell line was previously reported (Prevost et al., 2020). 293T-ACE2suggested: NoneBriefly, 293T cells were transfected with the lentiviral vector pNL4.3 R-E-Luc plasmid (NIH AIDS Reagent Program) and a plasmid encoding for the full-length SARS-CoV-2 Spike D614G glycoprotein (Beaudoin-Bussieres et al., 2020; Prevost et al., 2020) at a ratio of 10:1. 293Tsuggested: NoneRecombinant DNA Sentences Resources Briefly, 293T cells were transfected with the lentiviral vector pNL4.3 R-E-Luc plasmid (NIH AIDS Reagent Program) and a plasmid encoding for the full-length SARS-CoV-2 Spike D614G glycoprotein (Beaudoin-Bussieres et al., 2020; Prevost et al., 2020) at a ratio of 10:1. pNL4.3suggested: NoneR-E-Lucsuggested: NoneSoftware and Algorithms Sentences Resources Stained PBMC samples were acquired on Symphony cytometer (BD Biosciences) and analyzed using FlowJo v10.8.0 software. FlowJosuggested: (FlowJo, RRID:SCR_008520)Statistics were analyzed using GraphPad Prism version 8.4.3 (GraphPad, San Diego, CA). GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Software scripts and visualization: Graphics and pie charts were generated using GraphPad PRISM version 8.4.1 and ggplot2 (v3.3.3) in R (v4.1.0). GraphPad PRISMsuggested: (GraphPad Prism, RRID:SCR_002798)ggplot2suggested: (ggplot2, RRID:SCR_014601)Heat maps were generated in R (v4.1.0) using the pheatmap package (v1.0.12). pheatmapsuggested: (pheatmap, RRID:SCR_016418)Uniform manifold approximation and projection (UMAP) was performed using package M3C (v1.14.0) on gated FCS files loaded through the flowCore package (v2.4.0). flowCoresuggested: (flowCore, RRID:SCR_002205)Scaling and logicle transformation of the flow cytometry data was applied using the FlowSOM (Quintelier et al., 2021) R package (v2.0.0). FlowSOMsuggested: (FlowSOM, RRID:SCR_016899)Clustering was achieved using Phenograph (v0.99.1) with the hyperparameter k (number of nearest-neighbors) set to 150). Phenographsuggested: (Phenograph, RRID:SCR_016919)Results from OddPub: Thank you for sharing your code.
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.
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