21 Matching Annotations
  1. Dec 2022
    1. Please note, not all rigor criteria are appropriate for all manuscripts.

      Sciscore seems to have failed to be meaningful here

    2. ScreenIT Sep 27, 2021 SciScore for 10.1101/2021.09.22.461342: (What is this?)Please note, not all rigor criteria are appropriate for all manuscripts.

      Can we use any tools like this? E.g., Statcheck.io (for APA/Psych papers)

      somewhat important

    3. Is the study design appropriate and are the methods used valid? Yes

      as noted before, this yes/no tickboxing is generally not optimal for our case. These things are on a spectrum.

    4. Some details of the methods are lacking. For example, the MUpro provides two methods, it is necessary to specify which method was used in the analysis. The confidence score of each prediction should also be provided. Besides, some results from I-Mutant and MUpro were conflicting, the authors may want to discuss the discrepancy.

      again, the markdown numbering is failing here

    5. Discussion, revision and decision Discussion and Revision Author response We would like to thank the reviewers for their valuable comments. Below we provide pointwise response and the changes made in the revised manuscript. To Dr. Jyotsnamayee Sabat

      Nice, but

      1. I'd like to be able to see this full screen
      2. A heading/table of contents would be very helpful here

      fairly important

    6. PeerRef Dec 15, 2021 Discussion, revision and decision

      I would hope we could replace 'decision' with 'ratings and predictions' or something ... and make those ratings prominent


    7. Author response

      The 'order by recency' is good but sometimes limiting. I think readers would probably prefer to see the 'major comments and discussion' first, before the specific detailed small comments and clarification questions.


    8. Nov 26, 2021 Peer review report Reviewer: Hurng-Yi Wang Institution: Institute of Ecology and Evolutionary Biology, National Taiwan University email: hurngyi@gmail.com Section 1 – Serious concerns Do you have any serious concerns about the manuscript such as fraud, plagiarism, unethical or unsafe practices? No Have authors’ provided the necessary ethics approval (from authors’ institution or an ethics committee)? not applicable Section 2 – Language quality How would you rate the English language quality? Medium quality Section 3 – validity and reproducibility Does the work cite relevant and sufficient literature? No Is the study design appropriate and are the methods used valid? No Are the methods documented and analysis provided so that the study can be replicated? Yes Is the source data that underlies the result available so that the study can be … More Peer review report Reviewer: Hurng-Yi Wang Institution: Institute of Ecology and Evolutionary Biology, National Taiwan University email: hurngyi@gmail.com

      Nice. Is there a way we could put this at the top, or make a quick link to it?

      Ideally, this would have the ratings/rankings/predictions show up first on the page, as some sort of table (and also metadata if we dare to dream),


    9. Read the original source

      This is a bit misleading here. The 'original source' is basically the same stream of text

    10. I agree to change to Verified manuscript.

      what does this mean?

    11. and are shown below.

      these are not shown below. Are graphics possible here? Obviously a direct hyperlink to the revised section of the paper would be convenient here

    12. Pt-12:

      what do the prefixes like PT-12 mean here? I guess it's the reviewer number?

    13. The “Analysis of the Mutational Profile of Indian Isolates” should be moved to Materials and Methods.

      The markdown numbering failed here!

    14. Read the full article

      I clicked this link, and it is not coming up, or it's very slow

    15. Article activity feed Version 2 published on bioRxiv

      having trouble interpreting this. The linked version was published on Bioarxiv after the PeerRef? So which version was evaluated?

      OK, I guess the post-PeerRef version is published above ... so this is going from 'newest to oldest'. Maybe there's a way to make that clearer to someone visiting the page for the first time

    16. AgarwalNita Parekh

      why a 'full stop' (period) here after authors' names?

    17. Abstract

      abstract of which version?

    18. In this study we carried out the early distribution of clades and subclades state-wise based on shared mutations in Indian SARS-CoV-2 isolates collected (27 th Jan – 27 th May 2020). Phylogenetic analysis of these isolates indicates multiple independent sources of introduction of the virus in the country, while principal component analysis revealed some state-specific clusters. It is observed that clade 20A defining mutations C241T (ORF1ab: 5’ UTR), C3037T (ORF1ab: F924F), C14408T (ORF1ab: P4715L), and A23403G (S: D614G) are predominant in Indian isolates during this period. Higher number of coronavirus cases were observed in certain states, viz ., Delhi, Tamil Nadu, and Telangana. Genetic analysis of isolates from these states revealed a cluster with shared mutations, C6312A (ORF1ab: T2016K), C13730T (ORF1ab: A4489V), C23929T, and C28311T (N: P13L). Analysis of region-specific shared mutations carried out to understand the large number of deaths in Gujarat and Maharashtra identified shared mutations defining subclade, I/GJ-20A (C18877T, C22444T, G25563T (ORF3a: H57Q), C26735T, C28854T (N: S194L), C2836T) in Gujarat and two sets of co-occurring mutations C313T, C5700A (ORF1ab: A1812D) and A29827T, G29830T in Maharashtra. From the genetic analysis of mutation spectra of Indian isolates, the insights gained in its transmission, geographic distribution, containment, and impact are discussed.

      I really don't like this font, finding it very hard to read, but that's probably a taste thing. Still, I'd like if we could use a font that 'looks more like a journal'.

    19. Pt-13: I want to know how the representative sequences were selected for different states. Is it based on no. of sequences submitted or positivity rate of a particular region? All the Indian isolates available in GISAID for the period 27th Jan – 27th May 2020 were download and considered for analysis. NO state-wise selection was done.

      these authors seem to have use quotation the opposite way I would have done. I would have done

      reviewer's comment here

      My response here (unquoted)

    20. Demographic Analysis of Mutations in Indian SARS-CoV-2 Isolates

      Commenting on the format here

  2. Apr 2022
    1. The first intervention, surgical treatment, can’t even be seen on this scale, because it has such a small impact relative to other interventions. And the best strategy, educating high-risk groups, is estimated to be 1,400 times better than that. (It’s possible that these estimates might be inaccurate, or might not capture all of the relevant effects. But it seems likely that there are still big differences between interventions.)

      Some rigor might be hslpful here