4 Matching Annotations
  1. Jul 2021
    1. Task related plugin for Obsidian.

      <small><cite class='h-cite via'> <span class='p-author h-card'>Eleanor Konik</span> in 2021-07-17: Obsidian Mobile, Community Events & Graph Tips (<time class='dt-published'>07/29/2021 11:06:38</time>)</cite></small>

  2. Feb 2021
    1. SciScore for 10.1101/2021.01.31.428824: (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

      <table><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Antibodies</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Four rounds of panning were used to isolate scFvs binding both MERS S2 and SARS-2 spike using the following solutions coated on high binding plates: 2 μg/ml anti-c-myc tag antibody (Invitrogen) to eliminate phage expressing no or truncated scFv (Round 1), 2 μg/ml MERS S2 (Round 2), 2 μg/ml SARS-2 spike (Round 3), and 0.4 μg/ml SARS-2 spike (Round 4).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-c-myc tag</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Duplicate serial dilutions of each full-length antibody were allowed to bind each coat, and the secondary antibody solution was a 1:1200 dilution of goat-anti-human IgG Fc-HRP (SouthernBiotech).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>IgG Fc-HRP ( SouthernBiotech) .</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Western blot of antibody binding to coronavirus spike proteins: Purified coronavirus spike proteins (SARS-2 HexaPro, SARS-2, MERS, and HKU1) were reduced and boiled, and 50 ng of each was subjected to SDS-PAGE and transfer to PVDF membranes in quadruplicate.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HKU1</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To determine the affinity of 3A3 Fab by BLI, anti-human IgG Fc sensors were coated with the anti-foldon antibody identified in this work (3E11) at 20nM in kinetic buffer.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>anti-human IgG</div><div>suggested: None</div></div><div style="margin-bottom:8px"><div>anti-foldon</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Cell Lines</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">MERS (18), HKU1 (18), and the SARS-2 variants HexaPro S2 (residues 697-1208 of the SARS-2 spike with an artificial signal peptide, proline substitutions at positions 817, 892, 899, 942, 986 and 987 and a C-terminal T4 fibritin domain, HRV3C cleavage site, 8xHisTag and TwinStrepTag), HexaPro RBD-locked-down (HexaPro with S383C-D985C substitutions), and aglycosylated HexaPro (HexaPro treated with Endo H overnight at 4 °C leaving only one N-acetylglucosamine attached to N-glycosylation site) as well as MERS S2-only (residues 763-1291 of MERS-2P with 8 additional stabilizing substitutions), MERS S2-apex-less (MERS S2-only construct with residues 811-824 replaced with GGSGGS and residues 1042-1073 replaced with a flexible linker) were expressed in Freestyle 293-F cells (ThermoFisher Scientific).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>293-F</div><div>suggested: RRID:CVCL_6642)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">On day 2 after transfection, HEK-293T-hACE2 cells (BEI, NR-52511), which stably expresses human ACE2, were stained with 1 μM CellTrace Far Red dye (Invitrogen, Ex/Em: 630/661 nm) in PBS for 20 minutes at room temperature, then quenched with DMEM with 10% heat-inactivated FBS for 5 minutes, and resuspended in fresh media.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK-293T-hACE2</div><div>suggested: None</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">expressing human ACE2 under an EF1a promoter was used to transduce HEK293T cells.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>HEK293T</div><div>suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Flow cytometry: On day 0, Expi-293 cells (ThermoFisher) were mock-transfected or transfected with pWT-SARS-2-spike (BEI NR-52514) or pD614G-SARS-2-spike (generated by site-directed mutagenesis).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>Expi-293</div><div>suggested: RRID:CVCL_D615)</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Experimental Models: Organisms/Strains</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Murine immunization: Three BALB/c mice were immunized subcutaneously with 5μg pre-fusion stabilized MERS S2 and 20 μg of ODN1826 + 100 μl of 2X Sigma Adjuvant System</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>BALB/c</div><div>suggested: None</div></div></td></tr><tr><th style="min-width:100px;text-align:center; padding-top:4px;" colspan="2">Software and Algorithms</th></tr><tr><td style="min-width:100px;text=align:center">Sentences</td><td style="min-width:100px;text-align:center">Resources</td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Images were collected with Zeiss LSM 710 confocal microscope (Carl Zeiss, Inc) and processed using ImageJ software (http://rsbweb.nih.gov/ij) (Fig. 2 and fig.</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>ImageJ</div><div>suggested: (ImageJ, RRID:SCR_003070)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The statistical significance of either HEK-ACE2 colocalization percentage or average cell size between different conditions was calculated with ANOVA using GraphPad Prism 7 (GraphPad Software).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>GraphPad Prism</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div><div style="margin-bottom:8px"><div>GraphPad</div><div>suggested: (GraphPad Prism, RRID:SCR_002798)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Spectra were manually assessed, and figures were prepared using HD-eXplosion (40) and PyMOL (41).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>PyMOL</div><div>suggested: (PyMOL, RRID:SCR_000305)</div></div></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Cells were washed again, then scanned for AF647 (640 nm excitation, 670/30 bandpass emission) fluorescence on a BD Fortessa flow cytometer and analyzed with FlowJo (Fig. 6B).</td><td style="min-width:100px;border-bottom:1px solid lightgray"><div style="margin-bottom:8px"><div>FlowJo</div><div>suggested: (FlowJo, RRID:SCR_008520)</div></div></td></tr></table>

      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:
      There are several limitations to this work as currently described. First, a structure showing the atomic details of 3A3 complexed with spike would provide additional insight into the mechanism of binding and neutralization. However, structures of antibodies bound to S2 are generally challenging to obtain with just one structure available of an antibody binding near the HR2 stem (28). It is possible that 3A3 binding distorts spike structure, disturbing otherwise ordered regions. Accordingly, additional efforts to better understanding the molecular underpinnings of 3A3/ spike interactions are underway. Second, while we have shown that 3A3 binds spike from all three highly pathogenic coronaviruses with similar affinities, we have only demonstrated its ability to neutralize SARS-2 spikes in vitro. Demonstration of broad neutralization in addition to broad recognition would increase the potential relevance of this epitope for future therapeutics. The 3A3 epitope is highly conserved, with pairwise comparisons showing between 56% and 100% identity to the SARS-2 epitope for MERS and SARS-1, respectively (fig. S14). Since 3A3 affinity for the least similar MERS spike is comparable to that for the SARS-2 spike and greater than for HKU1, it seems likely that binding and neutralization depend primarily on RBD position epitope accessibility. The most concerning emerging SARS-2 variants have one conservative substitution in this epitope in B.1.1.7, identified in the United Kingdom, and has...

      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 scite Reference Check: We found one citation with an erratum. We recommend checking the erratum to confirm that it does not impact the accuracy of your citation.

      <table style="border-collapse: collapse;"><tr><th style="min-width:95px; border: 1px solid lightgray; padding:2px">DOI</th><th style="min-width:95px; border: 1px solid lightgray; padding:2px">Status</th><th style="min-width:95px; border: 1px solid lightgray; padding:2px">Title</th></tr><tr><td style="min-width:95px; border: 1px solid lightgray; padding:2px">10.1371/journal.ppat.1000863</td><td style="min-width:95px; border: 1px solid lightgray; padding:2px">Has correction</td><td style="min-width:95px; border: 1px solid lightgray; padding:2px">In Vitro Reconstitution of SARS-Coronavirus mRNA Cap Methyla…</td></tr></table>
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  3. Jul 2019