Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry

Article activity feed

1. 

   ScreenIT

   Jul 30, 2020

   SciScore for 10.1101/2020.07.29.227249: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Subsequently, the antibodies anti-ACE2 (1:100), S-RBD-His-tag (1:50), anti-LAMP1 (1:50) and anti-LC3b (1:50) were added and slides were incubated overnight at 4°C.	S-RBD-His-tag suggested: None anti-LAMP1 suggested: None anti-LC3b suggested: None
   Following blocking, membranes were incubated overnight at 4°C with the primary antibodies anti-ACE2 (1:1000), anti-LAMP1 (1:2000), anti-LC3b (1:1000) and anti-His-tag (1:1000).	anti-ACE2 suggested: None anti-His-tag suggested: (AnaSpec; EGT Group Cat# 29673-1000, RRID:AB_11232932)
   Experimental Models: Cell Lines
   Sentences	Resources
   immunofluorescence microscopy: For …

   SciScore for 10.1101/2020.07.29.227249: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Subsequently, the antibodies anti-ACE2 (1:100), S-RBD-His-tag (1:50), anti-LAMP1 (1:50) and anti-LC3b (1:50) were added and slides were incubated overnight at 4°C.	S-RBD-His-tag suggested: None anti-LAMP1 suggested: None anti-LC3b suggested: None
   Following blocking, membranes were incubated overnight at 4°C with the primary antibodies anti-ACE2 (1:1000), anti-LAMP1 (1:2000), anti-LC3b (1:1000) and anti-His-tag (1:1000).	anti-ACE2 suggested: None anti-His-tag suggested: (AnaSpec; EGT Group Cat# 29673-1000, RRID:AB_11232932)
   Experimental Models: Cell Lines
   Sentences	Resources
   immunofluorescence microscopy: For immunefluorescence, HUVEC cells were cultured into 8-well Lab-TekTM II Chamber Slides (NuncTM) and were then treated with either 17β-diol at 3nM or S-equol at 10nM.	HUVEC suggested: None
   Software and Algorithms
   Sentences	Resources
   Band intensity was quantified using ImageJ software.	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   Data were analyzed, and graphs were prepared with Prism 6.0 (GraphPad Software).	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   The OPLSAA based DoGlycans software was used for building all models35 (S-T1).	DoGlycans suggested: (doGlycans, RRID:SCR_015758)
   To address the structural interactions, we performed molecular dynamics simulations using GROMACS (v.2019.4)46 with the OPLS/AA force field parameters47.	GROMACS suggested: (GROMACS, RRID:SCR_014565)
   The PatchDock algorithm discard all unacceptable complex and results are assorted by geometry shape complementarity score.	PatchDock suggested: (PatchDock, RRID:SCR_017589)
   Molecular interactions were analyzed with LigPlot software58 and the pdb files required was constructed with fortran based own computer programs and the statistical data results.	LigPlot suggested: (LigPlot+, RRID:SCR_018249)

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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 pages 24, 32, 22 and 23. 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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   Read the original source
2. 

   ScreenIT

   Jul 30, 2020

   SciScore for 10.1101/2020.06.20.163097: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Myometrium tissue collection and preparation of the single-cell suspension: Normal myometrium was collected from the patients undergoing hysterectomy with informed consent. IRB: BIOS) program approved by the institutional review board, ethics approval, 17-22669.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   For the uterus dataset, we filtered out cells expressing more than 20% mitochondrial genes and used the standard Seurat pipeline to obtain the cell clusters.	Seurat suggested: (SEURAT, RRID:SCR_007322)

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   Results from OddPub: We did …

   SciScore for 10.1101/2020.06.20.163097: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Myometrium tissue collection and preparation of the single-cell suspension: Normal myometrium was collected from the patients undergoing hysterectomy with informed consent. IRB: BIOS) program approved by the institutional review board, ethics approval, 17-22669.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   For the uterus dataset, we filtered out cells expressing more than 20% mitochondrial genes and used the standard Seurat pipeline to obtain the cell clusters.	Seurat suggested: (SEURAT, RRID:SCR_007322)

   ---

   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: 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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2020.07.29.227249v1 on bioRxiv

   Jul 29, 2020