874 Matching Annotations
  1. Jun 2022
    1. Our notes are things to use,not just things to collect.

      Many people take notes, they just don't know where they're taking them to. It's having a concrete use for them after you've written them down that makes all the difference. At this point, most would say that they do read back over them, but this generally creates a false sense of learning through familiarity. Better would be turning them into spaced repetition flashcards, or linking them to ideas and thoughts already in our field of knowledge to see if and where they fit into our worldview.

      link to - research on false feeling of knowledge by re-reading notes in Ahrens

    1. What's wrong with a simple, feel good movie?
    2. As has been mentioned this is a take on the Prince and the Pauper story that may not appeal to those who are into art films and like to sit around discussing and dissecting a film's philosophical nuances. If, on the other hand, you simply like a fun story, gorgeous sets, and yes, the occasional over-the-top scene, this can be a thoroughly enjoyable tale of a man who is willing to put the woman he loves ahead of himself.
  2. May 2022
    1. I suspect that rather than being totally dreary, this transcribing step can also be a creative step, and I will see patterns of thought, generate new ideas…

      On the value of revising and revisiting notes. Similar to Raymond Llull's combinatorial creativity, but in a different form which doesn't require memory the same way.

    1. Studying, done properly, is research,because it is about gaining insight that cannot be anticipated and willbe shared within the scientific community under public scrutiny.

    Tags

    Annotators

    1. or at least they pretend

      I don't think we're pretending. I know I'm not!

    2. Senior colleagues indicate that I should not have to balance out publishing in “traditional, peer-reviewed publications” as well as open, online spaces.

      Do your colleagues who read your work, annotate it, and comment on it not count as peer-review?

      Am I wasting my time by annotating all of this? :) (I don't think so...)

    1. He notes that authors of such projects should consider the return on investment. It take time to go through community feedback, so one needs to determine whether the pay off will be worthwhile. Nevertheless, if his next work is suitable for community review, he’d like to do it again.

      This is an apropos question. It is also somewhat contingent on what sort of platform the author "owns" to be able to do outreach and drive readers and participation.

    2. A short text "interview" with the authors of three works that posted versions of their books online for an open review via annotation.

      These could be added to the example and experience of Kathleen Fitzpatrick.

    1. I returned to another OER Learning Circle and wrote an ebook version of a Modern World History textbook. As I wrote this, I tested it out on my students. I taught them to use the annotation app, Hypothesis, and assigned them to highlight and comment on the chapters each week in preparation for class discussions. This had the dual benefits of engaging them with the content, and also indicating to me which parts of the text were working well and which needed improvement. Since I wasn't telling them what they had to highlight and respond to, I was able to see what elements caught students attention and interest. And possibly more important, I was able to "mind the gaps', and rework parts that were too confusing or too boring to get the attention I thought they deserved.

      This is an intriguing off-label use case for Hypothes.is which is within the realm of peer-review use cases.

      Dan is essentially using the idea of annotation as engagement within a textbook as a means of proactively improving it. He's mentioned it before in Hypothes.is Social (and Private) Annotation.

      Because one can actively see the gaps without readers necessarily being aware of their "review", this may be a far better method than asking for active reviews of materials.

      Reviewers are probably not as likely to actively mark sections they don't find engaging. Has anyone done research on this space for better improving texts? Certainly annotation provides a means for helping to do this.

    1. However, the degraded performance across all groups at 6 weeks suggests that continued engagement with memorised information is required for long-term retention of the information. Thus, students and instructors should exercise caution before employing any of the measured techniques in the hopes of obtaining a ‘silver bullet’ for quick acquisition and effortless recall of important data. Any system of memorization will likely require continued practice and revision in order to be effective.

      Abysmally sad that this is presented without the context of any of the work over the last century and a half of spaced repetition.

      I wonder that this point slipped past the reviewers and isn't at least discussed somewhat narratively here.

    1. Peer review report

      Reviewer: Ludo Waltman

      Institution: Leiden University

      email: waltmanlr@cwts.leidenuniv.nl

      ORCID: https://orcid.org/0000-0001-8249-1752

      I would like to note that I am an expert in the field of bibliometrics and that my review therefore focuses on the bibliometric aspects of this paper. I am not an expert on scoping reviews or on curcumin. I hope that other reviewers have expertise on these aspects of the paper.

      I am one of the developers of the VOSviewer software, which may perhaps be seen as a competing interest.


      General comments

      Please find below my detailed comments on the paper, including suggestions for improvements.

      “A study by Loannidis et al.”: ‘Loannidis’ should be ‘Ioannidis’.

      The author uses the Web of Science Core Collection. This database consists of a number of citation indexes (e.g., Science Citation Index, Social Sciences Citation Index, etc.). Depending on their subscription, different Web of Science users have access to different citation indexes. Please mention which citation indexes were used.

      The description of the search query in Section 2 is unclear, because the search query doesn’t seem to be restricted to COVID-19 research. The full search query should be reported in the main text of the paper (not only in Appendix 1).

      The VOSviewer visualizations presented in the paper are hard to read (especially Figures 1 and 2). The font size used in the visualizations needs to be increased. This can be done using the ‘Scale’ slider in VOSviewer. The author may also consider making interactive versions of the visualizations available online, so that readers can explore these visualizations in their web browser. A visualization can be made available online using the ‘Share’ button on the ‘File’ tab in VOSviewer.

      I found Section 3.2 to be quite confusing. This section is presented as a ‘bibliometric analysis of citations’. However, it is not clear to me whether Figures 1 and 2 show visualizations of citation networks or visualizations of co-authorship networks. Also, the results presented in Section 3.2 rely strongly on the total link strength attribute in VOSviewer. If the author wants to use this attribute, it needs to be explained to the reader how the total link strength is defined and how it can be interpreted. However, I think it is better not to use the total link strength. Presenting statistics based on publication and citation counts is more useful, since these statistics are easier to interpret.

      “Regarding keyword analysis, VOSviewer software features two options, one for keywords provided by the authors and the second for keywords provided by authors in addition to others extracted from title and abstract”: This is not correct. VOSviewer users need to choose between analyzing keywords (keywords provided by authors and/or keywords assigned algorithmically by Web of Science) and analyzing terms extracted from titles and/or abstracts. Combining these two analyses is not possible in VOSviewer. Also, while the author mentions a number of frequently occuring keywords, a visualization of the keyword co-occurrence network seems to be missing.

      To reduce the number of clusters in a VOSviewer visualization, the author increased the minimum cluster size. Instead of (or in addition to) increasing the minimum cluster size, my advice is to reduce the value of the resolution parameter. This can be done on the ‘Analysis’ tab in VOSviewer.

      The discussion section needs major improvements. This section provides a lot information that could better be presented in the introduction or methods sections.

      The conclusion section is very brief. The section needs to be extended and improved. The conclusion that the “VOSviewer software is very successful” doesn’t seem relevant, since the paper is not about evaluating the VOSviewer software.

      There is room for improving the writing style of the paper. In particular, my suggestion is to avoid the use of exclamation marks and the unnecessary use of capitals in the middle of a sentence (e.g., “found that Till 1 August 2021” should be “found that till 1 August 2021”). Also, there should be no colon at the end of a section heading.

      According to the data availability statement, “all data produced in the present study are available upon reasonable request to the authors”. Making data available upon request is poor practice. It is preferable to make data openly available in a data repository (e.g., Zenodo). However, the author should check whether data sharing is allowed in the case of Web of Science data. It probably violates the terms of use of Web of Science. If data sharing is not allowed, this needs to be reported in the data availability statement.

      According to the copyright statement, reuse is not allowed without permission. It is good practice to allow preprints to be reused provided that authors are properly acknowledged. I therefore recommend to attach a CC-BY license to the paper.


      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


      Language quality

      • How would you rate the English language quality? Low to medium quality, but I understand the content

      validity and reproducibility

      • Is the rationale for, and objectives of, the scoping review clearly stated? Yes

      • Are the methods documented and analysis provided so that replication can be conducted? No

      • Is the statistical analysis and its interpretation appropriate? Not applicable

      • Are quality of the figures and tables satisfactory? No

      • Are the conclusions adequately supported by the results presented in the review? Not applicable, since the conclusion section is extremely short

      • Are there any fundamental flaws or errors that make the scoping review invalid?

      Please see my comments above.


      Decision

      Requires revisions: The manuscript contains objective errors or fundamental flaws that must be addressed and/or major revisions are suggested.

    1. Peer review report

      Reviewer: Daniel Griffin, MD PhD, <br /> Institution: Columbia University ORCID: 0000-0001-5853-6906 email: danielgriffinmd@gmail.com, dgriffin@cumc.columbia.edu


      Please describe your research in a sentence or a few key words

      COIVD-19, general infectious disease, immunology, virology


      General comments

      The authors lay out a reasonable protocol for this type of investigation.


      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)? Yes

      Section 2 – Language quality

      • How would you rate the English language quality? High quality

      Section 3 – validity and reproducibility

      • Is the reasons for conducting the study and its objectives clearly explained? Yes

      • Is the study design appropriate? Yes

      • Are sufficient details provided so that the method can be replicated? Yes

      • Are datasets available so that others could use them? not applicable


      Section 4 – Suggestions

      • Based on your answers in section 3 how could the author improve the protocol? Fine as is.

      • Do you have any other feedback or comments for the Author?

      The authors lay out a reasonable protocol for this type of investigation that is based on a fairly standard approach with the standard GRADE grading.


      Section 5 – Decision

      Verified manuscript: The content is scientifically sound, only minor amendments (if any) are suggested.

  3. Apr 2022
    1. Peer review report

      Reviewer: Richard L. Guerrant Institution: University of Virginia email: guerrant@vrginia.edu


      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? Low to medium quality, but I understand the content

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? No — See comments
      • Are the methods documented and analysis provided so that the study can be replicated? No — See comments
      • Is the source data that underlies the result available so that the study can be replicated? not applicable
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? No — See comments
      • Are there any objective errors or fundamental flaws that make the research invalid? Yes, see comments below

      Section 4 – Suggestions

      • Based on your answers in section 3 how could the author improve the study?

      Major concerns include:

      1. Quantification of coliforms is key; if done as suggested by MPN method, actual projected counts should be put into a table and discussed by food type, pathogenic potential.

      2. Were any actual pathogens detected? (ex ETEC, EPEC, EAEC, EHEC); probes are not those typically used for that. Were any Shigella, Salmonella? Are other pathogens detected? If not, why not?

      3. Many statements are expressed as causal facts, but this is far from proven. Examples include ‘foodborne infections …have accelerated … resistance’ on page 1; ‘infections … are due to fast food ingredients;’ on page 2; these points require citation of documented data.

      4. At the bottom of page 2, the objective of ‘determining the origin’ is not addressed.

      5. Do you have any other feedback or comments for the Author? No

      Tighten statements, like the opening line of abstract to say more directly, ‘burden…compromises health.’


      Section 5 – Decision

      Requires revisions: The manuscript contains objective errors or fundamental flaws that must be addressed and/or major revisions are suggested.

    1. doi: https://doi.org/10.1038/d41586-021-02346-4

      https://www.nature.com/articles/d41586-021-02346-4

      Oddly this article doesn't cover academia.edu but includes ResearchGate which has a content-sharing partnership with the publisher SpringerNature.

      Matthews, D. (2021). Drowning in the literature? These smart software tools can help. Nature, 597(7874), 141–142. https://doi.org/10.1038/d41586-021-02346-4

    2. ResearchRabbit, which fully launched in August 2021, describes itself as “Spotify for papers”.

      Research Rabbit is a search engine for academic research that was launched in August of 2021 and bills itself as "Spotify for papers." It uses artificial intelligence to recommend related papers to researchers and updates those recommendations based on the contents of one's growing corpus of interest.

    3. Connected Papers uses the publicly available corpus compiled by Semantic Scholar — a tool set up in 2015 by the Allen Institute for Artificial Intelligence in Seattle, Washington — amounting to around 200 million articles, including preprints.

      Semantic Scholar is a digital tool created by the Allen Institute for Artificial Intelligence in Seattle, Washington in 2015. It's corpus is publicly available for search and is used by other tools including Connected Papers.

    4. Open Knowledge Maps, meanwhile, is built on top of the open-source Bielefeld Academic Search Engine, which boasts more than 270 million documents, including preprints, and is curated to remove spam.

      Open Knowledge Maps uses the open-source Bielefeld Academic Search Engine and in 2021 indicated that it covers 270 million documents including preprints. Open Knowledge Maps also curates its index to remove spam.


      How much spam is included in the journal article space? I've heard of incredibly low quality and poorly edited journals, so filtering those out may be fairly easy to do, but are there smaller levels of individual spam below that?

    5. Google Scholar does not disclose the size of its database, but it is widely acknowledged to be the biggest corpus in existence, with close to 400 million articles by one estimate (M. Gusenbauer Scientometrics 118, 177–214; 2019).

      Google Scholar was estimated to cover 400 million articles in 2019. It's acknowledged to be the largest research corpus, but the company doesn't publicly publish the size of its database.

    6. Besides published articles, Google Scholar might also pick up preprints as well as “low-quality theses and dissertations”, Tay says. Even so, “you get some gems you might not have seen”, he says. (Scopus, a competing literature database maintained by the Amsterdam-based publisher Elsevier, began incorporating preprints earlier this year, a spokesperson says. But it does not index theses and dissertations. “There will be titles that do not meet the Scopus standards but are covered by Google Scholar,” he says.)

      Scopus primarily covers regularly published journals with ISSN numbers and began including preprints in 2021, while Google Scholar has a broader net that also includes theses, dissertations, preprints, and books.

    7. Aaron Tay, a librarian at Singapore Management University who studies academic search tools, gets literature recommendations from both Twitter and Google Scholar, and finds that the latter often highlights the same articles as his human colleagues, albeit a few days later. Google Scholar “is almost always on target”, he says.

      Anecdotal evidence indicates that manual human curation as evinced by Twitter front runs Google Scholar by a few days.

    8. Another visual-mapping tool is Open Knowledge Maps, a service offered by a Vienna-based not-for-profit organization of the same name. It was founded in 2015 by Peter Kraker, a former scholarly-communication researcher at Graz University of Technology in Austria.

      https://openknowledgemaps.org/

      Open Knowledge maps is a visual literature search tool that is based on keywords rather than on a paper's title, author, or DOI. The service was founded in 2015 by Peter Kraker, a former scholarly communication researcher at Graz University of Technology.

    1. Peer review report

      Reviewer: Samuel Mayeden Institution: Ghana Health Service email: csmayeden@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)? Yes

      Section 2 – Language quality

      • How would you rate the English language quality? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? No

      Section 4 – Suggestions

      • Do you have any other feedback or comments for the Author?

      • Line 35, 36 and 37: Authors should be consistent in using odds ratios and/or p values to indicate associations.

      • Line 37 (Conclusion): Should align with objectives and results stated in abstract

      • 42: Keywords should emerge from the text of the abstract. Kindly review the keywords to align with the body of the abstract

      • Introduction: Has no concrete global, regional or local level statistics on the subject. It will be good to indicate some statistics of existing work to appropriately conceptualize your work.

      • The introduction is too long. It will be good to keep it within 2 pages

      • Line 73: It helps to move citation to the end of the sentence

      • Line 132: Indicate from which department(s) of the health facilities the participants were recruited

      • Methods: Needs lots of clarification. Authors have to indicate the process of sampling more clearly

      • What influenced the selection of the 32 facilities out of the 252

      • You indicated 15 clients from health centres and 22 clients from hospitals. Are these the authors’ assumptions? Was this calculated from the facility registers? If so what amount of data from which period was used to make the estimates

      • Line 154: Did each facility have a sampling frame? What was k?

      • Line 172: Which department were patient exiting from. Was it outpatients or laboratory only cases, or inpatients as well.

      • Line 174: Was scale adapted or developed by authors

      • Line 183-185: how many slides were reviewed. Why did you choose only malaria and TB.

      • Line 196: Is the score decided by researchers or it has been adopted or adapted

      • Line 205: Reference star grading system

      • Line 256: state p value as p<0.001


      Section 5 – Decision

      Verified manuscript: The content is scientifically sound, only minor amendments (if any) are suggested.

    1. Rating System: 0 = Painfully bad! Never worth watching. 1 = Bad. Only for the most dedicated fans. 2 = A mediocre episode, possibly worth skipping if new to Star Trek. 3 = Good! Generally enjoyable, worth watching if new to Star Trek. 4 = Great! An example of why we love Star Trek. 5 = One of the best. A classic.
    1. Peer review report

      Reviewer: Wei Zhang Institution: The First Affiliated Hospital of Hebei North University, Hebei Province, China. email: 15369318318@163.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)? *Yes

      Section 2 – Language quality

      • How would you rate the English language quality? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? not applicable
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? not applicable
      • Are there any objective errors or fundamental flaws that make the research invalid?

      Table 1 - The number of people in the gender section is wrong.


      Section 4 – Suggestions

      • Based on your answers in section 3 how could the author improve the study?

      (1)There is no "conclusion" in the abstract.

      (2)In order to make the study group comparable with the control group, should the patients in the control group be CSKP infected patients? Or the control group should at least be patients with bacterial infection.

      (3)The font in Table 2 is inconsistent with the original text.

      (4)The table format should be "three line table".

      (5)The number "0" can be added before some decimal points in Table 2.

      (6)The references are generally too old. It is suggested to increase the proportion of references published within 5 years.

      (7)It is suggested to write more specific experimental methods for amplifying KPC gene, such as primers, PCR reaction conditions and reaction system of KPC gene.

      (8)Have you done the drug sensitivity test of Klebsiella pneumoniae? If so, it is recommended to write the results in the article.


      Section 5 – Decision

      Verified with reservations: The content is scientifically sound but has shortcomings that could be improved by minor revisions.

    1. Peer review report

      Reviewer: Adam Marcus, co-founder Retraction Watch & Alison Abritis, PhD, researcher at Retraction Watch


      General comments

      Major Problems: I found serious deficits in both for this article, and thus I have serious concerns as to the usefulness of this article. Therefore, I have not proceeded in a line-by-line, as I consider the overall problems to be grave enough to require attention and revision before getting to lesser items of clarity.

      I would like to point out that the authors show a marvelous attention to their work, and they have much to contribute to the field of retraction studies, and I do honestly look forward to their future work. However, in order for the field to move ahead with accuracy and validity, we must no longer just rely on superficial number crunching, and must start including the complexities of publishing in our analyses, as difficult and labor-intensive as it might be.

      1) The authors stated that they used the search protocol (and therefore presumably the same dataset) as described in Toma & Padureanu, 2021, and do not indicate any process to compensate for its weaknesses. In the referenced study, the authors (same as for this article) utilized a PubMed search using only “Retracted Publication” in Publication Type. This search method is immediately insufficient, as some retracted articles are not bannered or indexed as retracted in PubMed. This issue is well-understood among scholars who search databases for retractions, and by now one would expect that these searches would strive to be more comprehensive.

      A better method, if one insists on restricting the search to PubMed, would have been to use Publication Type to search for “retracted publication,” and then to search for “retraction of publication,” and to compare the output to eliminate duplications. There are even more comprehensive ways to search PubMed, especially since some articles are retitled as “Withdrawn” – Elsevier, for example, uses the term instead of “Retracted” for papers removed within a year of their publication date – but do not come in searches for either publication type. Even better would have been to use databases with more comprehensive indexing of retractions.

      2) The authors are using the time from publication to retraction based on the notice dates and using them to indicate efficacy of oversight by publishers. However, this approach is seriously problematic. It takes no notice of when the publisher was first informed that the article was potentially compromised. Publishers who respond rapidly to information that affects years/decades old publications will inevitably show worse scores than those who are advised upon an article’s faults immediately upon its publication, but who drag their heels a few months in dealing with the problem.

      Second, there is little consistency in dealing with retractions between publishers, within the same publishers or even within the same journal. Under the same publisher, one journal editor may be highly responsive during their term, while the next editor may not be. Most problems with articles quite often are first addressed by contacting the authors and/or journal editors, and publishers – especially those with hundreds of journals – may not have any idea of the ensuing problem for weeks or months, if at all. Therefore, the larger publishers would be far more likely to show worse scores than publishers with few journals to manage oversight.

      Third, the dates on retraction notices are not always representative of when an article was watermarked or otherwise indicated as retracted. Elsevier journals often overwrite the html page of the original article with the retraction notice, leaving the original article’s date of publication alone. A separate retraction notice may not be published until days, weeks or even years after the article has been retracted. Springer and Sage have done this as well, as have other publishers – though not to the same extent (yet).

      Historically, The Journal of Biological Chemistry would publish a retraction notice and link it immediately to the original article, but a check of the article’s PDF would show it having been retracted days to weeks earlier. They have recently been acquired by Elsevier, so it is unknown how this trend will play out. And keep in mind, in some ways this is in itself not a bad thing – as it gives the user quicker notice that an article is unsuitable for citation, even while the notice itself is still undergoing revisions. It just makes tracking the time of publication to retraction especially difficult.

      3) As best as can be determined, the authors are taking the notices at face value, and that has been repeatedly shown to be flawed. Many notices are written as a cooperative effort between the authors and journal, regardless of who initiated the retraction and under the looming specter of potential litigation.

      Trying to establish who initiated a retraction process strictly by analyzing the notice language is destined to produce faulty conclusions. Looking just at PubPeer comments, questions about the data quality may be raised days/month/years before a retraction, with indications of having contacted the journal or publisher. And yet, an ensuing notice may be that the authors requested the retraction because of concerns about the data/image – where the backstory clearly shows that impetus for the retraction was prompted by a journal’s investigation of outside complaints. As an example, the recent glut of retractions of papers coming from paper mills often suggest the authors are requesting the retraction. This interpretation would be false, however, as those familiar with the backstory are aware that the driving force for many of these retractions were independent investigators contacting the journals/publishers for retraction of these manuscripts.

      Assigning the reason for retraction from only the text of the notice will absolutely skew results. As already stated, in many cases, journal editors and authors work together to produce the language. Thus, the notice may convey an innocuous but unquestionable cause (e.g., results not reproducible) because the fundamental reason (e.g., data/image was fabricated or falsified) is too difficult to prove to a reasonable degree. Even the use of the word “plagiarism” is triggering for authors’ reputations – and notices have been crafted to avoid any suggestion of such, with euphemisms that steer well clear of the “p” word. Furthermore, it has been well-documented that some retractions required by institutional findings of misconduct have used language in the notice indicating simple error or other innocuous reasons as the definitive cause.

      The authors also discuss changes in the quality of notices increasing or decreasing in publishers – but without knowing the backstory. Having more words in a notice or giving one or two specific causes cannot in itself be an indicator of the quality (i.e., accuracy) of said notice.

      4) The authors tend to infer that the lack of a retraction in a journal implies a degree of superiority over journals with retractions. Although they qualify it a bit ( “Are over 90% of journals without a retracted article perfect? It is a question that is quite difficult to answer at this time, but we believe that the opinion that, in reality, there are many more articles that should be retracted (Oransky et al. 2021) is justified and covered by the actual figures.”), the inference is naive. First, they have not looked at the number of corrections within these journals. Even ignoring that these corrections may be disproportionate within different journals and require responsive editorial staff, some journals have gone through what can only be called great contortions to issue corrections rather than retractions.

      Second, the lack of retractions in a journal speaks nothing to the quality of the articles therein. Predatory journals generally avoid issuing retractions, even when presented with outright proof of data fabrication or plagiarism. Meanwhile, high-quality journals are likely to have more, and possibly more astute, readers, who could be more adept at spotting errors that require retraction.

      Third, smaller publishers/journals may not have the fiscal resources to deal with the issues that come with a retraction. As an example, even though there was an institutional investigation finding data fabrication, at least one journal declined to issue a retraction for an article by Joachim Boldt (who has more than 160 retractions for misconduct) after his attorneys made threats of litigation.

      Simply put, the presence or lack of a retraction in a journal is no longer a reasonable speculation about the quality of the manuscripts or the efficiency of the editorial process.

      5) I am concerned that the authors appear to have made significant errors in their analysis of publishers. For example, they claim that neither PLOS nor Elsevier retracted papers in 2020 for problematic images. That assertion is demonstrably false.


      Decision

      Requires revisions: The manuscript contains objective errors or fundamental flaws that must be addressed and/or major revisions are suggested.

    1. Peer review report

      Reviewer: Yin Qianlan Institution: Navy Medical University email: yinqianlan@smmu.edu.cn


      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)? Yes

      Section 2 – Language quality

      • How would you rate the English language quality? High quality

      Section 3 – validity and reproducibility

      • Is the reasons for conducting the study and its objectives clearly explained? No

      • Is the study design appropriate? Yes

      • Are sufficient details provided so that the method can be replicated? Yes

      • Are datasets available so that others could use them? not applicable


      Section 4 – Suggestions

      • Based on your answers in section 3 how could the author improve the protocol?

      As an important part of a review is the declaration of the purpose, the introduction should be the core of the article. However, after reading the beginning of the paper, I could realize the seriousness of COVID-19, but I cannot see the key point of the research. There is a lot of data to emphasize the worse results, but I don’t know how this data contributed to the relationship between the major topic of Post-acute sequelae of COVID-19 and adverse psychiatric outcomes, for example, the introduction about the effect of therapies. Hence, more organized structure for the introduction of could be more concise and easier for readers.


      Section 5 – Decision

      Requires revisions: The manuscript contains objective errors or fundamental flaws that must be addressed and/or major revisions are suggested.

    1. Peer review report

      Reviewer: Argentina Felisbela Muianga,<br /> Institution: Instituto Nacional de Saúde-Maputo-Mozambique email: valiosa.muianga@gmail.com, Argentina.muianga@ins.gov.mz


      General comments

      The manuscript addresses a relevant subject that is still, in a way, little prioritized, therefore little developed and therefore raises the need for further in-depth studies to develop a good RDT that can detect infection in the most important phase of infection and ensure a better real-time response.


      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)? No, I did not see any approach on ethical aspects of the study. This should updated.

      Section 2 – Language quality

      • How would you rate the English language quality? High quality

      Section 3 – validity and reproducibility

      • Is the rationale for, and objectives of, the scoping review clearly stated? Yes

      • Are the methods documented and analysis provided so that replication can be conducted? Yes

      • Is the statistical analysis and its interpretation appropriate? Yes

      • Are quality of the figures and tables satisfactory? Yes

      • Are the conclusions adequately supported by the results presented in the review? Yes

      • Are there any fundamental flaws or errors that make the scoping review invalid? No


      Section 4 – Suggestions

      • Based on your answers in section 3 how could the author improve the study?

      I did not see information regarding to the type of sample used on the different platforms, since for the RDT the type of samples influences accessibility.

      How was the prototype evaluated, in terms of type of samples and environmental conditions?

      • Do you have any other feedback or comments for the Author?

      No


      Section 5 – Decision

      Verified manuscript: The content is scientifically sound, only minor amendments (if any) are suggested.

    2. Peer review report

      Reviewer: Sadia Ali Pereira,<br /> Institution: Instituto Nacional de Saúde, Mozambique email: Sadia.abdul.ali@gmail.com / sadia.pereira@ins.gov.mz


      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? High quality

      Section 3 – validity and reproducibility

      • Is the rationale for, and objectives of, the scoping review clearly stated? Yes

      • Are the methods documented and analysis provided so that replication can be conducted? No

      • Is the statistical analysis and its interpretation appropriate? Yes

      • Are quality of the figures and tables satisfactory? No

      It is difficult to read figure 4, on page 29 there is no legend of the figure, in figure 1 the pallet colours could have greater variation.

      • Are the conclusions adequately supported by the results presented in the review? No

      • Are there any fundamental flaws or errors that make the scoping review invalid? Not any major errors detected


      Section 4 – Suggestions

      • Based on your answers in section 3 how could the author improve the study?

      I would suggest improving the methodology and the criteria for articles selection/inclusion

      • Do you have any other feedback or comments for the Author?

      Will be helpful if the authors could better discussion the risk bias and applicability. Why select studies with patients with signs for CHIKV? What about asymptomatic? Not proper discussed the possibility of cross reactivity between other alphaviruses.


      Section 5 – Decision

      Verified with reservations: The content is scientifically sound but has shortcomings that could be improved by further studies and/or minor revisions.

  4. Mar 2022
    1. Peer review report

      Reviewer: Veena Nair Institution: UW Madison email: vnair@uwhealth.org


      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)? Yes

      Section 2 – Language quality

      • How would you rate the English language quality? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • Are the methods documented and analysis provided so that the study can be replicated?

      See comments below at the end of Section 3; some more methodological details could be provided.

      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? No

      In the demographics table, could you please add number of left versus right stroke patients, distribution of stroke location too. Thank you.

      In figure 1 I don’t see a L for left; perhaps missing in the pdf I have.

      • Are there any objective errors or fundamental flaws that make the research invalid? How could the author improve the study?

      It would be helpful to see the demographic characteristics of the normative database. Do the subjects in that database have a similar distribution of age and sex.

      Scanner variance is a known confound that studies must deal with; should we be concerned that the normative database was collected on a 7T whereas the current study’s data were all collected on a 3T? are there ways to do some kind of harmonization? Likewise, the multimodal Glasser atlas is based off of 21-35 old young healthy adults; but the variability in the current study population is large.

      In the Disconnectome map, what does each ‘map’ represent? Is it a structural connectivity map? What do the connections represent (fiber cross-sectional area, number of fibers etc.?). More details would be helpful.

      Based on Figure 4, prediction accuracy on the test set is low, at 22%; can this be improved by improvements in normalization? Perhaps by using a more age-appropriate template than the MNI152? [see for e.g., Mayo clinic template for older adults].


      Section 4 – Suggestions

      • Do you have any other feedback or comments for the Author?

      This is a very interesting study and the research question is an important one and very relevant to the field. Thank you.


      Section 5 – Decision

      Verified with reservations:The content is scientifically sound but has shortcomings that could be improved by further studies and/or minor revisions.

    1. Peer review report

      Reviewer: Dacre Knight, MD Institution: Mayo Clinic email: Knight.dacre@mayo.edu


      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? High quality

      Section 3 – validity and reproducibility

      • Is the reasons for conducting the study and its objectives clearly explained? Yes

      • Is the study design appropriate? Yes

      • Are sufficient details provided so that the method can be replicated? Yes

      • Are datasets available so that others could use them? not applicable


      Section 4 – Suggestions

      • Based on your answers in section 3 how could the author improve the protocol?

      There is a more specific definition of PASC that should be included (with reference). Need to list specific medical databases to search, not just “various”. PECO criteria needs to be listed, not only implied that it will be used.

      • Do you have any other suggestions, feedback, or comments for the Author?

      GRADE approach will be useful, as is mentioned along with narrative synthesis if needed. Strengths and limits seem accurate, good to list.


      Section 5 – Decision

      Verified with reservations: The content is scientifically sound but has shortcomings that could be improved by further studies and/or minor revisions.

    1. Peer review report

      Reviewer: Bertrand Fournier Institution: Potsdam University email: bfourni@gmail.com


      General comments

      This paper investigates context-dependencies in metacommunities using a modelling approach. The authors present a new metacommunity model (the Unified Metacommunity Model) that includes habitat heterogeneity, dispersal, specialization, and species interactions. The authors use this model to illustrate two forms of context-dependency: directional and reciprocal context-dependency. They present several simulations that illustrate these two aspects. The authors also discussed the implications of their results for future research in metacommunity dynamics. I overall enjoyed reading this manuscript which I consider as an interesting contribution to the field of metacommunity ecology. I think that it has a clear structure and is well-written. The data, illustrations, and tables are of good quality. The cited literature is appropriate. Overall, the work and methods meet the expected scientific standards, but several precisions are needed to allow the replication of the study. The model created in this study presents interesting adaptations of existing concepts and is one of the main strength of this study. Another strength of this work is that it investigates a known weakness of metacommunity ecology (context-dependency) and ecology in general and discuss potential ways to tackle this problem. Overall, I think that the paper is of direct interest to scientists working in the field of metacommunity ecology and can be interesting for a broader audience in various fields of ecology including community assembly, biodiversity, and metapopulation. I did not identify major flaws, but I have a few suggestion for minor improvements. I think that addressing these concerns can further improve this work. See my comments below for further details.


      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)? Yes


      Section 2 – Language quality

      • How would you rate the English language quality? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • Are the methods documented and analysis provided so that the study can be replicated? No
      • Is the source data that underlies the result available so that the study can be replicated? not applicable
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly. No

      Section 4 – Suggestions

      • Do you have any feedback or comments for the Author?

      Abstract:

      The use of abbreviation in the abstract is to me unnecessary and I encourage the authors to remove them (i.e. C-D). The mention of macro-variables got me confused. While it becomes clearer what those are later in the ms, I would suggest explicitly mentioning the four dimensions of the model (habitat heterogeneity, dispersal, specialization, and species interactions) in the abstract.

      Context-dependency in metacommunities:

      This section is nicely written. Please, consider providing a definition of directional and reciprocal context-dependency earlier in the text.

      Context-dependency in a model:

      This section clearly explains the functioning of the model and how it allows interactions among “macro-variables”. However, I would like to see more technical information because I don’t think that I would be able to replicate the same model with the information provided (either here or in the SupMat). I encourage the authors to add more detailed information about the functioning of the model (maybe as an additional document published at the same time as the models itself ...)

      Directional and reciprocal C-D:

      Nice section. I like the chosen examples for the two types of context-dependency.

      C-D in future metacommunity research:

      Also nicely written. Consider adding a few words about the implications of this work beyond the metacommunity framework.

      Fig. 3: Even with the explanation provided, I still struggle to understand the abbreviations (panels A-D).

      Fig. 4: Consider replacing the vector image by a raster image (png, jpeg...). While the quality is nice, it slows down the whole document.

      Fig. 4B: There is no legends for the R2 values (which values correspond to which line).


      Section 5 – Decision

      Verified with reservations: The content is scientifically sound, but has shortcomings that could be improved by further studies and/or minor revisions.

    1. Peer review report

      Reviewer: Cristian Malavert Institution: University of Buenos Aires, Argentina email: malavert@agro.uba.ar


      General comments

      Overall, the manuscript is very good. There are some things to improve and revise that will help to make the manuscript clearer.


      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? Low to medium quality, but I understand the content

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? No
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? No

      Section 4 – Suggestions

      - Based on your answers in section 3 how could the author improve the study?

      The authors could improve the work by redesigning the figures, many of the symbols are not understood. Organizing tables and explaining abbreviations only once, perhaps making a list of abbreviations used throughout the manuscript. Equations, many do not describe what the components correspond to, are not listed.

      Suggested edits and comments have been added to the manuscript. Comments taken from manuscript below:

      Materials and methods

      add location coordinates

      How many samples were used?

      Soil Physiochemical Parameter: can you explain briefly what the APHA method consists of?

      Experimental Procedures: How many replications were used??

      Root and Shoot growth: Where is the germination test?? what does the germination test consist of?

      Median germination time: Explain how T(50) is calculated?

      The GRI equation is not explained

      the SAG equation is not explained

      Please explain component of the equations: Corrected germination rate index, Timson’s Index, Modified Timson’s Index

      Figure 1: are they plants or seeds? also germination of which species?


      Section 5 – Decision

      Verified with reservations: The content is scientifically sound but has shortcomings that could be improved by further studies or minor revisions.

      The content has many errors, which I marked throughout the manuscript. Once these errors are corrected, the manuscript will look great

    2. Peer review report

      Reviewer: Dr.Debojyoti Moulick Institution: University of Kalyani


      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)? No, there is no Institutional affiliation, approval from ethical committee, and other disclosures (like details of chemicals) are missing.

      Section 2 – Language quality

      • How would you rate the English language quality? - low quality, the content is difficult to understand

      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? No
      • Is the source data that underlies the result available so that the study can be replicated? No
      • Is the statistical analysis and its interpretation appropriate? No, Statistical data should be incorporated, contrast and quality can be increased.
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? No. The research should consider recent literature in this area. The conclusion should contain the vision for the research with honest self-criticism.
      • Are there any objective errors or fundamental flaws that make the research invalid?

      The study does not satisfy ISTA rule. Methods should have references.

      https://www.seedtest.org/en/international-rules-for-seed-testing-_content---1--1083.html


      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      Introduction:

      “ Soil heavy metal concentrations may not however be totally due to industrial activities as some soils are originally ferruginous and therefore have increasingly high quantities of iron yet some others have increased levels of aluminium which predisposes such soils to more soil acidity (Ikhajiagbe,2016).”

      What about geogenic sources of Fe, Al? Please explain this.

      “Many studies have shown that application of growth regulators enhance plant growth and crop yield (Hernandel, 1997).”

      States many studies, yet there is only one reference which is a decade old. Please provide additional references.

      The introduction should describe the need for selecting Fe stress, role seed priming in synchronizing germination, stress tolerances. The section should also contain the level of Fe toxicity in “Local-Regional-Global” perspective.

      The aim of the study should be clearly presented.

      Materials and methods

      Please describe the selected variety

      “Sand and Iron (Fe) were determined…” The authors are required to disclose the comparison carried out among the obtained result (Fe content) and Fe content of SRMs/CRMs.

      Soil Priming Material

      Which is applicable, Soil or Seed priming?

      Why are only 3 doses selected?

      The number of treatment combinations should be included.

      Which seed priming method did the authors follow?

      Details of chemicals should be included.

      Which chlorophyll meter is used? please disclose with details.

      How many seedlings were considered for taking weight?

      Statistics are not adequate. Factors (GA, AA,IA and Fe stress) 4 factors and their respective interaction and individual effects can be understand if 2-WAY-ANOVA can be used.

      • Do you have any other feedback or comments for the Author?

      Title could be brief, short and attractive.

      Abstract: Punctuation should be improved.

      For Fe, the term ‘essential nutrient’ can be used rather than ‘micronutrient’ Keywords could be expanded


      Section 5 – Decision

      Requires revisions: The manuscript contains objective errors that must be addressed.

    1. Peer review report

      Reviewer: Wade H. Morris Institution: Georgia State University email: morriswh@gmail.com


      General comments

      The authors dove headfirst into Dalhousie’s archives, unpacking the subtle shifts in grading policy. Their work seems to be comparable to archaeologists, digging deep beneath mountains of primary sources to find nuggets of clues into Dalhousie’s grading evolution. I particularly liked when the authors were able to link these changes to student voices, as seen in moments when they referenced student publications.

      Ultimately, I kept coming back to one main comment that I wrote in the margins: “So what?” I would humbly suggest that the authors reflect on why this history matters to them. Granted, they do this in the conclusion, where they touch on Schneider & Hutt’s argument that grades evolved to increasingly be a form of external communication with audiences beyond school communities. Sure. But I want more. I wanted to see a new insight that this microhistory of Dalhousie significant to the history of Canada or the history of education more generally.

      If the authors are so inclined, there might be several approaches to transform this manuscript. I would suggest the following. First, instead of tracing the entire history of grading at the institution, choose one moment of change that you think is the most important. Perhaps in the 1920s and the lack of transparency in grading, or the post-war shift toward American grading. Second, show me – don’t tell me – what Dalhousie was like at this moment. Paint a picture of the institution with details about student demographics, curriculum, educational goals, the broader town, etc. Make the community come alive. Show me what makes Dalhousie unique from other institutions of higher ed. Once you establish that picture, perhaps you could link the change in grading practices to subtle changes at the university community, thereby establishing a before and after snapshot.

      This will require considerable amounts of work, and the skills of a historian. You will have to find primary and secondary sources that go far beyond what you’ve relied on thus far.

      In the end, I found myself wanting the authors to humanize this manuscript, meaning I wanted them to show me that changes in grading practices have tangible effects on real-life human beings. A humanization of their research would mean going narrower and deeper; or, in other words, eliminating much of what they have documented.

      However, if that is too tall of an order, I would ask that the authors clarify for themselves who this manuscript is for. Is this a chronicling of facts for an internal audience at Dalhousie’s faculty, alumni, and students? Fine. But my guess is that even members of the Dalhousie community want to read something relatable.


      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? There are a few nagging stylistic quirks. Most obvious to me, the authors switch into and out of present tense. Stick with past tense. Also, I would suggest that they remove the first person.

      Section 3 – validity and reproducibility

      • Does the manuscript contain any objective errors, fundamental flaws, or is key information missing?

      Not that I am aware.


      Section 4 – Decision

      Requires revisions: The manuscript contains objective errors or fundamental flaws that must be addressed and/or major revisions are suggested.

      I am suggesting revisions, although not because of objective errors. History is more of an art, in my opinion. With that in mind, I would suggest that the authors paint a more vivid picture (metaphorically) of Dalhousie, showing me how changes one moment of change in grading practices impacted the lives of human beings.

    1. En somme, les études sur la communication des élèves atteints d’autisme permettent de mettre en évidence l’importance d’un contexte riche en stimulations appropriées (sons et images), mais également une évidente « stabilité » de l’information à décoder, le suivi des émotions des personnages, le rôle de l’imitation dans les apprentissages. Ces résultats encouragent donc l’usage d’outils informatiques adéquats pour améliorer la communication sociale chez les enfants atteints d’autisme.

      L'association de deux sujets qui n'ont pas de corrélation vérifiéé, revient dans la conclusion en contradiction avec la conclusion de l'étude de Ramdoss, S et al.

    2. Nous allons montrer par une courte analyse de quelques études l’impact du travail éducatif informatisé dans l’apprentissage de la communication sociale chez des enfants atteints d’autisme.

      En contradiction avec l'hypothèse :

      Results suggest that CBI should not yet be considered a researched-based approach to teaching communication skills to individuals with ASD. However, CBI does seem a promising practice that warrants future research. Les résultats suggèrent que le CBI ne devrait pas encore être considéré comme un approche fondée sur la recherche pour enseigner les compétences en communication aux personnes ayant Troubles du Spectre Autistique. Cependant, le CBI semble être une pratique prometteuse qui justifie des recherches futures.

    1. Peer review report

      Reviewer: GE Rainger Institution: University of Birmingham, UK email: g.e.rainger@bham.ac.uk


      General comments

      The English is generally acceptable, but there are serious lapses of syntax throughout the manuscript that require revision.

      Some sections, e.g. the introduction revert to a bullet pointed format for conveying information from specific citations. If the authors choose to submit to a journal, this is not acceptable in many journal formats.

      Figures are not publication quality and do not conform to a standard format. They often show images of single cells or sections as evidence of complex biology which needs formalising into graphs which show outcomes of the analysis of multiple experiments.

      As far as I can see there is no statistical analysis of any of the data (at least as presented in the figures), it is unclear what statistical analysis has been conducted when the text states that significant effects have been observed.

      It is not clear how reproducible assays such as the in vitro EC injury model are and this sort of concern would need addressing.

      The discussion is unfocused. Having read the full manuscript I am not informed about what SAMD1 is, how it achieves extracellular distribution, how it functions in the localisation of LDL and formation of foam cells etc. There are many broad brush strokes here, but there is not enough mechanistic detail to provide convincing arguments for its functions as extrapolated by the authors.


      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)? No


      Requires revisions: No details of ethics and the manuscript contains objective errors that must be addressed

    2. Peer review report

      Reviewer: Yaw Asare Institution: ISD LMU email: yaw.asare@med.uni-muenchen.de


      General comments

      The current manuscript is very diffuse with many figures that should be merged to one main figure with a clear message. The reader is easily lost going through multiple figure panels conveying pieces of information. The manuscript will further benefit from reducing the length of the discussion.


      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? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? No

      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      The manuscript will further benefit from the following experiments:

      1) Assessing the effect of targeting SAMD1/LDL axis in neointima formation following arterial injury given the reduced LDL retention in injured carotids.

      2) Analyzing effects of PEG-fab inhibitors in early lesions induced by atherogenic diet.

      3) Describing the role of SAMD1 in VSMC foam cell formation.


      Section 5 – Decision

      Requires revisions: The manuscript contains objective errors that must be addressed

    1. We recently placed an order at the restaurant at 267 Northfield Rd, Bedford, Ohio, online through the store and the order was canceled, when we reached out to the store to see if there was a substitution problem or some other issue that could be resolved so that we could still get our food, the person (unknown) on the phone said that they asked the manager and that the manager said only "we're sorry there's nothing we can do". I asked to speak with them to get clarification and hopefully still go through with the order, and the employee I was talking to hung up the phone. Now, wanting to give them the benefit of the doubt, I attempted to redial 3 times which were not answered. the 4th went to a fax machine. I am not happy with this experience and I believe this information needed shared.

    1. Peer review report

      Reviewer: Barbara Ruaro Institution: University of Trieste email: barbara.ruaro@yahoo.it


      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)? Yes

      Section 2 – Language quality

      • How would you rate the English language quality?

      Low to medium quality, but I understand the content (e.g. Our study is the first clinical study in which Netrin-1 elevation was demonstrated in SSc patients. It is better “studied” than “demonstrated”


      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? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? No
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? No
      • Are there any objective errors or fundamental flaws that make the research invalid? No

      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      1) Abstract. Results There was no significant correlation between netrin-1 level, organ involvement in SSc, and MRS (p>0.05). Please clarify MRS acronym. Is it mRSS (modified Rodnan Skin Score)?

      2) Abstract. Conclusion: In this study, we found that there is a significant relationship between Netrin-1 levels and SSc disease. Our study is the first clinical study in which Netrin-1 elevation was demonstrated in SSc patients. Please in the last sentence use “elevation was shown”

      3) Systemic sclerosis (SSc), often called scleroderma, is an autoimmune, destructive systemic connective tissue disease characterized by organ fibrosis and vasculopathy. Pathophysiological mechanisms that may play a role in disease development include platelet activation, fibroblast proliferation, endothelial disruption, fetal microchimerism, and increased transforming growth factor-β. In addition, VEGF is an important signaling factor contributing to the pathogenesis of SSc, even in the earliest clinically detectable stages of the disease.[1] Please add some references.

      4) Introduction. In this study, we aimed to evaluate the levels of Netrin1 between SSc and healthy controls and to emphasize the role of the known effects of Netrin-1 in the pathophysiology of SSc, which increases VEGF and supports the fibrotic process. Please change “to evaluate the levels of Netrin1 between SSc and healthy controls” and write” to compare the levels of Netrin1 in SSc patients and healthy controls”

      5) Methods. Modified Rodnan scoring (MRS) was used for skin thickness scoring in SSc patients. For MRS, 17 body areas were evaluated and scored in the range of 0-51 points. Please use the acronym mRSS.

      6)Results. Please underline the statistical values to support the conclusions. 7) DISCUSSION SSc is a progressive disease that pathophysiologically starts with microvascular damage and then develops widespread fibrosis due to increased autoimmune response and inflammation.[18]. Please summarise and underlie here the most important data of the study.


      Section 5 – Decision

      Verified with reservations: The content is scientifically sound but has shortcomings that could be improved by further studies and/or minor revisions.

  5. Feb 2022
    1. Peer review report

      Reviewer: : Charlotte Martial Institution: University of Liège email: cmartial@uliege.be


      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)? Yes

      Section 2 – Language quality

      • How would you rate the English language quality? High quality (but English typos)

      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? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? No
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? No
      • Are there any objective errors or fundamental flaws that make the research invalid? No*

      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      I read with great interest this manuscript, studying a fascinating topic. Although this study is highly interesting and intriguing, I think that some major improvements could be made. Notably:

      The work does not cite relevant and sufficient literature. For instance, the authors do not cite a recent publication which aimed to induce OBE using hypnosis (Martial et al., Scientific Reports, 2019). Another example: The authors could have at least briefly discussed Parnia’s AWARE prospective study reporting OBE in NDE experiencers (Parnia et al., 2014). Besides, they sometimes cite some inappropriate references; I would like to invite the authors to cite rigorous and serious articles in the field. For example, they used Jourdan (2011) reference to draw a parallel with NDEs, however, Jourdan (2011) is not a reference article in the field…

      Importantly, it is worth mentioning that, so far, no rigorous empirical scientific study has shown evidence of veridical perceptions during OBE; according to me, it is not clear in the manuscript.

      Some limitations of the study are not mentioned in the discussion section.

      Some details of the study are missing. Notably, the description of the Table 6 is incomplete: what do the bold numbers mean? Another example: how did they recruit the participants –who are co-authors of the paper? Are they researchers?

      The conclusions they draw in the discussion are not based on the present findings; they extrapolate.

      • Do you have any other feedback or comments for the Author?

      page13: what do they mean by “general consensus”? This is not clear to me

      I would like to invite the authors to correct English typo and spelling errors (example: “We also thankS”)


      Section 5 – Decision

      Requires revisions: The manuscript contains objective errors that must be addressed

    2. Peer review report

      Reviewer: : Aminata Bicego Institution: University of Liège email: abicego@uliege.be


      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)? Yes

      Section 2 – Language quality

      • How would you rate the English language quality? - Low to medium quality, but I understand the content

      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? Yes
      • Are the methods documented and analysis provided so that the study can be replicated? no
      • Is the source data that underlies the result available so that the study can be replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? No*

      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      Abstract :

      L13 : what do the authors mean by “hypnotic induction”, is it hypnotic experience ? During a hypnosis session, the therapist starts by an induction and then makes some suggestions according to the goal that has been decided. It is not clear to what the “hypnosis induction” refers to.

      L16 : “under hypnosis” should be changed as it suggests that the individual who is in hypnosis is passive. I would suggest “in hypnosis”.

      Introduction:

      L 54-56 : there has been some recent literature on hypnosis and OBEs or NDEs. It would be interesting to add newer literature on that topic.

      L75 : if the study’s aim is to confirm Tressoldi and Del Prete (2007), then this study should be explicitly explained in detail. That way the reader understands better the present study.

      L76 : could the authors specify the suggestion used.

      L78 : the induction is not the only and principal part of the hypnotic sessions that impacts an individual perceptions but rather the suggestion that is used. This paragraph could be clearer in terms of methodology

      L79 to L95 : this should be in methods.

      Materials and Methods :

      L110 : can the authors define and detail “clinical level of medical or psychiatric disease”.

      L111 : took, should be written “take”. Throughout the manuscript there are language mistakes that have to be checked.

      L111 : can the authors be more specific on the “personal experience with hypnosis” ? What do you mean by experience ?

      Procedure :

      in general the procedure is not very clear. Some results appear in the section when they should be in the result section

      L125 : Can the authors explain why some participants had one or two sessions ?

      L127 : Can the supplementary Material be numbered.

      L129 to 132 : Have all participants been seen in real life? Were all of them called? If not, was it always the same people in person or on the phone? This part should be more specific.

      L130 : hypnotized should not be used. Same comment as comment L16.

      L140 : was the order of the picture position randomized ? If so it should be mentioned here.

      L164: Who did the authors know that the participants where in an OBE state ? What were the criteria ? Especially on the phone ?

      L174 : did the authors create the questions ? Do they come from a questionnaire ? This should be specified.

      L188 : this should be in results

      L191 : “... and give suggestion...” : It is confusing to use that word, comments, mught be more appropriate.

      L198: what are the eleven questions ?

      L208 : all the questionnaires used should also be described in material. The reader has no information on the minimal phenomenal selfhood, nor has he information about the “characteristics of spatial and temporal perception reported in NDEs”.

      L221 : how did the 3 decoys were selected ?

      L225 : I only see 2 authors, not three.

      L234 : a section with the statistical analyses should be written before the results.

      L241 : 52.4 % is not metionned in the table, this is confusing.

      L245 : this should be in the statistical analyses part, it is not a result per se.

      L260 : the table 3 should be more specific: define ES + formula, CI, BF, H1, H0. A table should be able to be read by itself.

      L277 : This part merits some clarifications : - Did the approval from the Ethical committee approved this part ? If so, did the participants signed an informed consent ? - What should they refer to when they answered the questions ? Did the ones that had an OBE had to refere to that episode ? And those who did not life an OBE ? What was the experience of reference ? - It there is no reference for the controls without an OBE expereince then is seems logical that they do not answer like the others.

      L304 : the % is not correct, is should be 46.6%

      L338 : With what material was the comparison made ? With the material from Jourdan (2011) or the participants that were contacted after the study ? This part should be clearer If the cmparison is made with Jourdan, then a table with the similaritie and differences could be added.

      L382 : “but his aim was not to confirm his knowledge, but to compare it with the participants’ experience” : this was not mentionned before. It is hard to understand as we have no information in the hypnostist knowledge or the comparison that is mentionned. Could the authors clarify ?

      L387 : Another limitation it the response expectancy during hypnosis. There is a large literature on the subject this should be discused in the limites. More so because all the subject had good knowledge about OBEs

      L412 : Is it acceptable to disclose the participants identity ?

      Page 5 : The authors mention in a foot note that some other informatio will be avaiable in a future publication but the publication has since been published. Furthermore, that publication is cited in the bibliography this is confusing.

      Table S1 : it is hard for the reader to understand to what the table refers to. GAPED has to be explained.


      Section 5 – Decision

      Verified with reservations: The content is scientifically sound, but has shortcomings that could be improved by further studies and/or minor revisions.

    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      IRB: This study was approved by the Institutional Review Board of the Emory University School of Medicine.

      Consent: IRB of Emory University School of Medicine gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

      Inclusion and Exclusion Criteria

      not detected.

      Attrition

      The first case was identified in September of 2006 , 13 cases were detected in 2007 , and 16 cases in 2008 across these two hospitals ( total of 30 with 120 matched controls) .

      Sex as a biological variable

      Mean Median 60 62 ( range from 27 to 90 ) Sex Female Male 25 ( 52 ) 23 ( 48 ) Site of isolation Urine

      Subject Demographics

      Age: not detected. Weight: not detected.

      Randomization

      Controls, patients without CRKP were randomly selected from a computerized list of inpatients who matched the case age (+/- 5 years), sex, and facility and whose admission date was within 48 hours of the date of the initial, positive culture.

      Blinding

      not detected.

      Power Analysis

      not detected.

      Replication

      not required.

      Data Information

      Availability: The comparison of clinical characteristics between cases and controls was made using Chi-Square (or It is made available under a CC-BY-NC-ND 4.0 International license .

      Identifiers: medRxiv preprint doi: https:// doi.org/10.1101/2022.02.08.22269570; this version posted February 9 , 2022 . https://doi.org/10.1101/2022.02.08.22269570

    1. Blog này được lập vào khoảng 2014. Tác giả tự giới thiệu sinh năm 1979, tức hồi anh ta 33 - 34 tuổi. Ở bài trước, được viết vào 1/2016, anh ta "tự ái" khi đọc bài ​Sự khốn cùng của “tư duy triệu phú” - Tuổi Trẻ Online bởi Đặng Hoàng Giang (1, 6, 2015). Ở vào thời điểm này (2021 - 2020), có lẽ anh đã "trưởng thành" hơn và suy nghĩ, nhận thức có hệ thống hơn. Như ở đây anh ta tìm hiểu về "kinh tế học" một cách nghiêm túc thay vì đọc mấy cuốn self-help vớ vẩn như trước đây?


      Ha,... ở tuổi 40 - 41, anh ấy thấy thấm thía hơn vai trò của sức khỏe, tập luyện thể dục thể thao đều đặn. Có lẽ anh ta bớt "ảo tưởng" và dần nhận ra điều gì là quan trọng hơn đối với cuộc sống của bản thân.

      Nhưng cái sơ đồ thì hết sức "buồn cười". Sức khỏe của bản thân sẽ đạt tới trạng thái tối ưu nhất trong một độ tuổi nhất định, có lẽ trong khoảng 15 - 25 tuổi. Sau tuổi đó dù có tập bao nhiêu đi chăng nữa, cũng không thể đạt được như vậy bởi thể chất được quy định bởi gen di truyền. Đó cũng là lý do tại sao, những vận động viên trong quá trình tập luyện, không may mắn bị chấn thương, họ buộc phải nghỉ 1 - 2 năm và sau đó không thể quay lại thi đấu được nữa. Một số người có thể trở thành huấn luyện viên, số khác thì chuyển nghề,... để hiểu có những thứ khi đã qua đi thì không thể lấy lại. (Ngoài thời gian thì còn là sức khỏe, trí tuệ, mối quan hệ,.... sau cùng mới là tiền bạc). Vì vậy nhận thức sớm, hiểu biết (sâu sắc) sớm là quan trọng để thay đổi sớm.

      Nhớ lại trong phần giới thiệu cuốn sách "Hiện tượng học về tinh thần" - Hegel, dịch giả Bùi Văn Nam Sơn chia sẻ:

      H. Schnädelbach kết luận quyển sách của mình về Hegel một cách mỉa mai: “Điều Hegel không nói ra [trong diễn văn ấy] là: khi trẻ thì ta còn nhiều mơ mộng, còn lớn rồi thì tỉnh mộng. Hệ thống của Hegel là một cơn mơ trí tuệ mà triết học phải biết thức tỉnh khi đã lớn khôn” (H. Schnädelbach: Hegel, 1999: 166).

      Một thông tin thêm là có những ngành học chuyên nghiên cứu về thể chất con người [[Tản mạn về Chuyện Đọc#^uga1qu]]

      Ở nước ngoài có một môn tên là động năng con người (human kinetic). Môn học ấy tập trung nghiên cứu về sự chuyển hoá của các dạng vật chất và năng lượng bên trong con người. Một người bạn của tôi nghiên cứu môn này với mục đích là để có được cơ thể khoẻ mạnh. Sau khi đọc hết một quyển sách, hắn tìm ra mấu chốt trọng tâm chỉ là ngủ sớm, dậy sớm, tập thể dục đều đặn, mỗi ngày uống một cốc nước cam. 99% lượng thông tin còn lại của quyển sách là nói về việc nếu bạn không làm như thế thì cơ thể sẽ thế nào.


      Ở bài Tốc độ của niềm tin P1 (Hệ thống niềm tin) | Chiến lược sống (8, 2020), anh ta trích dẫn cuốn sách "7 thói quen thành đạt" cùng với hình minh họa (figures), trích dẫn/highlights/ví dụ (do anh ta thêm vào), sơ đồ tư duy (mindmap) do anh ta tự vẽ. Thiếu sót đó là: nó không có trích dẫn tài liệu tham khảo. Và có lẽ do vốn tiếng anh hạn chế, nên anh ta không tìm hiểu và đào sâu hơn vào các tài liệu liên quan bằng tiếng anh (thứ sẽ không có nếu chỉ đọc bằng tiếng Việt), ví dụ bài phê bình cuốn sách "7 thói quen thành đạt" phía trên bằng tiếng anh (hoặc các ngôn ngữ khác)? Và phê bình cái sơ đồ quy luật (?!) "niềm tin" này mà anh ta sử dụng. Nó từ đâu? Có nghiên cứu (lý thuyết/thực nghiệm) củng cố nó?

      Anh ta (có lẽ?) không biết là mỗi chữ cái mà anh ta vẽ trên cái sơ đồ trên, tương đương với các lĩnh vực nghiên cứu liên quan với hàng trăm, ngàn, trăm ngàn bài nghiên cứu và các cuốn sách liên quan trong lĩnh vực học thuật. Và cái sơ đồ trên chỉ mang tính "quy giản" (reduction). Tin vào nó cũng tốt (với người không biết gì hay người muốn có một bức tranh tổng quát "nho nhỏ"). Chứ nó không có ý nghĩa về mặt kiến thức hay sự hiểu biết.


    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      IRB: The ethics committee approval of the research protocol was made by the Ankara City Hospital Consent: Informed consent was obtained from the patients to participate in the study.

      Inclusion and Exclusion Criteria

      not detected.

      Attrition

      Two publications are evaluating the association with Netrin-1 in bleomycin-induced lung fibrosis in mice and SSc lung cell culture in humans.

      Sex as a biological variable

      A total of 56 SSc patients (mean age: 48.08±13.59) consisting of 53 females and 3 males, who were followed up in the rheumatology department of Ankara city hospital, diagnosed according to the 2013 ACR (American College of Rheumatology)/EULAR (European League Against Rheumatism) SSc classification criteria were included in the study.

      Subject Demographics

      Age: For the control group, 58 healthy volunteers (mean age: 48.01±11.59 years) consisting of 54 females and 4 males were included in the study.

      Randomization

      not detected.

      Blinding

      not detected.

      Power Analysis

      not detected.

      Replication

      not required.

      Data Information

      Availability: It is made available under a CC-BY-NC-ND 4.0 International license .

      Identifiers: preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in medRxiv preprint doi: https:// doi.org/10.1101/2022.02.05.22270510; this version posted February 10, 2022. https://doi.org/10.1101/2022.02.05.22270510

    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      IRB: I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

      Field Sample Permit: The research has been conducted using the UK Biobank Resource and has been approved by the UK Biobank under Application no. 36226.

      Consent: I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

      Inclusion and Exclusion Criteria

      Similarly , individuals where a large proportion of SNPs could not be measured were excluded.

      Attrition

      not detected.

      Sex as a biological variable

      not detected.

      Subject Demographics

      Age: not detected.

      Weight: not detected.

      Randomization

      Mendelian randomization ( MR ) is a robust and accessible tool to examine the causal relationship between an exposure variable and an outcome from GWAS summary statistics. [ 19 ] We employed two-sample summary data Mendelian randomization to further validate causal effects of neutrophil cell count genes on the outcome of critical illness due to COVID-19

      Blinding

      not detected.

      Power Analysis

      not detected.

      Replication

      not required.

      Data Information

      Identifiers: medRxiv preprint doi: https:// doi.org/10.1101/2021.05.18.21256584; this version posted February 14 , 2022 . https://doi.org/10.1101/2021.05.18.21256584

      Identifiers: Manhattan plot of neutrophil cell count showing that we reproduce the reported CDK6 signal ( rs445 ) on chromosome 7 . rs445

    1. I would consider my Read Write Respond site as a ‘blog’, but agree with you that my Collect site is not really a blog. In some respects I would be happy enough to make it private is it is primarily my own secret garden with the gate left open. This is why I curate my monthly newsletter. It is a habit which I find forces me to look back through all the noise. I think this creates a clearer narrative to pick through than my multitude of links.

      Aaron Davis uses the review through his website's posts, bookmarks, etc. to create his newsletter as a means of reviewing what he's read and thought about.

    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      IRB: 234 Ethical clearance was obtained from the regional Ethical Review Board of Amhara

      Consent: The general aim and purpose of the study was described to each 239 eligible patient and all voluntary participants gave verbal informed consent prior to 240 enrolment.

      Inclusion and Exclusion Criteria

      Those 135 patients who were critically ill and unable to respond and those not voluntary to 136 participate were excluded.

      Attrition

      Those 135 patients who were critically ill and unable to respond and those not voluntary to 136 participate were excluded .

      Sex as a biological variable

      Sex Male Female Age group 18-24 25-44 ≥45

      Subject Demographics

      Age: 130 All adult patients ( aged ≥18 years ) who were using clinical laboratory services at 131 public health facilities of east Amhara , northeast Ethiopia were source population.

      Randomization

      132 Study population and eligibility criteria 133 Adult patients who received general laboratory services at the randomly selected 134 government health facilities during the study period were study population .

      Blinding

      not detected.

      Power Analysis

      not detected.

      Replication

      not required.

      Data Information

      Availability: It is made available under a CC-BY-NC-ND 4.0 International license .

      Identifiers: preprint doi: https:// doi.org/10.1101/2022.01.25.22269238; this version posted January 25 , 2022 . https://doi.org/10.1101/2022.01.25.22269238

    1. Peer review report

      Reviewer: Nidia Bañuelos Institution: University of Wisconsin-Madison email: nbanuelos@wisc.edu


      General comments

      Questions of how and why grading practices change over time, how students, faculty, and administrators respond to grades, and the external pressures on grading practices (e.g. war, graduate school requirements) are inherently interesting! The authors have clearly done a careful job of tracking these – often minute, and likely, difficult to follow – changes at Dalhousie University. The manuscript is well-written and relatively easy to follow.

      My biggest concern, reflected in the more detailed comments below, is that the authors could do a better job of explaining to the reader why these changes are interesting, important, and relevant to historians of higher education more broadly – even those who aren’t at Dalhousie. They do some of this at the very end of the paper and, indeed, this summing up of their findings and explanation of their relevance was my favorite part of the manuscript. I would suggest reorganizing the paper so that these bigger takeaways appear in the introduction and so that the reader is reminded of them at each major section break of the paper. For example, when the authors present a quote from a student who is concerned that grades have little to do with learning outcomes, they might remind us that one of their main arguments is that “decisions about university grading schemes had very little to do with actual pedagogy” (p. 15).

      As it is written, the manuscript sometimes reads like a list of facts about grading changes. But, I think a reframing that focuses on the general importance of these changes could make the entire piece more engaging. More on this below…


      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? High quality

      Section 3 – validity and reproducibility

      • Does the manuscript contain any objective errors, fundamental flaws, or is key information missing?

      While I don’t notice any “objective errors”, I do think the paper has a major flaw (i.e. little explanation of the broader significance of this case study) and could benefit from additional information about the institutional context, the archival material, and external influences on grading trends. (Please see below.)


      Section 4 – Suggestions

      • Based on your answer in section 3 how could the author improve the study?

      I. Most importantly, I would like to see an introduction that explains the authors’ general arguments about grading changes – including the trajectory of these changes at Dalhousie and why this arc contributes to our knowledge of the history of higher education more broadly. Then, the authors might continually remind us of the arc they present at the outset of their paper – especially when they are highlighting a piece of evidence that illustrates their central argument. To me, the quotes from students and faculty responding to grading changes are among the most interesting parts of the paper and placing these in additional context should make them shine even more brightly!

      II. I’d like to read a little more about Dalhousie itself – why it is either a remarkable or unremarkable place to study changes in grading policies. Is it representative of most Canadian universities and thus, a good example of how grading changes work in this national context? Is it unlike any other institution of higher education and thus, tells us something important about grades that we could not learn from other case studies? I don’t think this kind of description needs to be particularly long, but it should be a little more involved than the brief sentences the authors currently include (p.3, paragraph 1) and should explain the choice of this case.

      III. I’d also like to know more about the archival materials the authors used. The authors mention that they drew from “Senate minutes, university calendars, and student newspapers” (p. 3), but what kinds of conversations about grades did these materials include? At various points, the authors engage in “speculation” (e.g. p.4) about why a particular change occurred. This is just fine and, in fact, it’s good of the authors to remind us that they are not really sure why some of these shifts happened. But, they might go one step further and tell us why they have to speculate. Were explicit discussions of grading changes – including in inter- and intradepartmental letters and memo, reports, and other documents – not available in these archives? Why are these important discussions absent from the historical record?

      IV. At various points, the authors make references to the outside world – for example, WWII (p. 5), the Veteran’s Rehabilitation Act (pp. 6-7), and British versus American grading schemas (p. 6). But, these references are brief and seem almost off-handed. I know space is limited, but putting these grading changes in their broader context might help make the case for why this study is interesting and important. Are the changes in the 1940s, for example, related to the ascendance of one national graduate education model over another (e.g. American versus British)? Are there any data on how many Canadian undergraduates enrolled in British versus American graduate programs over time? If so, I would share any information you might have on these broader trends.

      Similarly, the authors make brief mention of the internal reaction to grade changes – quoting students or faculty minutes. But, it would be wonderful (space permitting) to have even more information the internal impact of these changes. Did they change faculty instructional practices? Did they seem to have any effect on students’ orientation to their learning? Did standardization reflect an increasing interdependence of departments, or did it contribute to their lessening autonomy? If the archival record doesn’t permit us to know these things, then this might be a limitation the authors note at the end of the manuscript. I noticed that the authors reference a secondary source on Dalhousie student experiences repeatedly (Waite, 1998). Even a little more from this text or another secondary source like it could help the reader better understand the impact of grade changes.

      • Do you have any other suggestions, feedback, or comments for the Author?

      This is a very nitpicky concern that doesn’t fit well elsewhere, so please take it with a grain of salt. I was surprised at the length of the reference list – it seemed quite short for a historical piece! I wonder, again, if more description of the archival material - including why you looked at these sources, in particular, and what was missing from the record – would help explain this and further convince the reader that you have all your bases covered.


      Section 5 – Decision

      Requires revisions: The manuscript contains objective errors or fundamental flaws that must be addressed and/or major revisions are suggested.

    1. Peer review report

      Reviewer: Champion Deivanayagam

      Institution: University of Alabama at Birmingham

      email: champy@uab.edu


      General comments

      Summary of the study: The authors begin the manuscript describing an effort to understand the various sizes of DMBT1 protein, namely variations in the copy numbers of SRCR repeats based on its DNA sequence variations among various groups. In this effort they have identified/chosen three major groups namely European (states in Figure 1of the manuscript they are European-Americans in Utah), African (Yoruba of Ibadan, Nigeria) and Asian (Chinese from Beijing). The observed high D value shown in Figure 1, they contend is the evidence for balancing selection (which this Reviewer has no expertise on). Based on this Tajima scores, they were able to identify two haplotypes, and this led to them arriving at SNP (rs11523871).

      Now comes the interesting part of parsing the copy number variations of DMBT1’s SRCR domains within these two haplotype clades, where they conclude that the SRCR copy numbers are population specific. Then looking at tissue specific expression of DMBT1, where they observe higher expression levels in some tissues such as lung, small intestine, colon, and minor salivary gland. More interestingly they observe that there exists no linear relationship that exists among the alleles and concluding that there is no plausible explanation for protein expression, but the selection locus rs11523861 somehow is related at balancing selection.

      In an attempt to determine the copy number variations, a small set of samples (8) were collected from saliva and analysed. In table 1 they summarize these findings, where they observe four different isoforms. They report that there is a strong linear relationship, but do not present a figure or other details, except statistical parameters to convince the reader. From here, they step into establishing alternative splicing as a possibility, where they use the H292 lung cell line model, and report in past tense that the H292 cell line was homozygous for the 11/10 SRCR domain repeats (Figure 4). While they could not conclude, it mentions that alternative splicing may play a minor role.

      Finally, this study attempts to use the results from the classic Stromberg lab study published in 2007, which enumerated various properties of Gp340, and classified them into 4 groups, and enumerated their affinities for various carbohydrates, Lewis antigens and compared the oral and lung Gp340. The authors here use western blots to determine if the short allele is different from the normal one. They use two knock-outs of surface components on S. mutans, SpaP and Cnm to show that the shorter alleles display no binding. In the same set of experiments, they also show that S. mutans adheres to mono and dimeric amylase.

      Finally, they conclude that some of the variations in adherence may be due to the carbohydrates present on the different DMBT1.


      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)? Yes

      Section 2 – Language quality

      • How would you rate the English language quality? Low to medium quality, but I understand the content

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes to a large extent
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? No
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly. Yes

      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      Additional experiments are needed to support the conclusions.

      Major Concerns:

      The research work presented here appears highly disjointed at times. While they begin this study to evaluate the need for copy numbers and how it could have been a part of selection process induced by a variety of factors, their analysis leads to Supplementary figure 1, where they identify two clades. From here they offer some evidence for the choice of rs11523861 to study the balancing selection. However, no concrete evidence is presented and/or discussed except peripherally. This Reviewer understands the effort, which is very interesting, however, without additional analysis the current form of results does not offer any new insights, and so the title is highly misleading.

      At this point, they move into CNV’s, whereby their own admission have used a very small sampling of 8 individuals and extrapolate their results to be conclusive. Further sampling and additional studies are necessary to complete this section.

      One solid set of results shown here are from the H292 lung cell line model, where they report different variations of the repeats. However, all analysis stops here, and conclusion is derived that alternative splicing is ruled out, but for a minimal role. Once again, the same pattern exists here to do an experiment, without further analysis and additional data, conclusions are drawn.

      Finally, from sequence analysis the authors step into protein-based assays to expose the role of S. mutans adherence on the presence and absence of its surface proteins SpaP and Cnm. Their conclusion that Cnm is the major adherent protein is also out of one single experiment. More importantly, their analysis of I-IV alleles (without explaining them), an extension of a previous well cited article, results in a conclusion that smaller allelles (???) do not adhere to saliva. In Table 1, the molecular weights of these isoforms are in alignment with the 14 SRCR domains, but for their carbohydrate decorations, with one exceptions of sample 6. Also, this Reviewer is not sure if this table corresponds to the 8 samples, they have used for CNV analysis and/or for the smaller/larger alleles they allude to in the western blot study.

      In summary this appears to be a manuscript that is not only disjointed, but also not detailed enough to warrant publication at this stage. If they could do additional analysis on each of the points raised, it would elevate the research and conclusions.

      Minor concerns: The manuscript is extremely poorly written and needs major revamping in order to produce a more concrete publication.

      Figure numbers and legends are often mixed up both in the text as well as in the legends. Figure 5 - Differential binding of S.mutans by DMBT1 isoforms in saliva: Overlay of individual saliva phenotypes with DMBT1 size isoforms I- IV with A) a biotinylated S. mutans SpaP A, Cnm strain and B) with DMBT1-specific antibodies. The positions of DMBT1, mono- and dimer amylase, and acidic PRP co-receptors are marked by arrows”. This bold line is not related to this figure but to the supplementary figure.

      There is no marker in these figure 5A so indicate the specific molecular weights. The isoform IV on the last lane seems to lightup with the lower MW DMBT1 (allele?). However, the conclusions presented show that lower isoforms do not bind well is contrary to the results presented here.

      Supplementary figure 2 should be in the main manuscript, even though this is not a new result, in combination with the other two, authors can summarize the results.

      Abbreviations should be in the expanded form the first time.

      Why do the authors use the SpaP A instead of SpaP?

      What do they mean by a biotinylated S. mutans SpaP A, Cnm strain?

      • Do you have any other feedback or comments for the Author?

      These copy numbers have always been fascinating not only on DMBT1 but on other proteins, yet to date we don’t have a handle on the type of selection. If these authors could provide additional analysis on why and how balance selection could have played a role it would be very important and could be extended to numerous other proteins.


      Section 5 – Decision

      Requires revisions

  6. Jan 2022
    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      Field Sample Permit: Our findings indicate a paucity of 217 research focusing on field trials and implementation studies related to CHIKV RDTs .

      IRB: I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

      Consent: I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

      Inclusion and Exclusion Criteria

      98 Articles were excluded if (i) the studies were reviews, case reports, or opinion articles; (ii) 99 the studies evaluated the performance of reverse transcription loop-mediated isothermal 100 amplification (RT-LAMP) assays; (iii) the studies were related to an outbreak investigation 101 without the evaluation of the accuracy of CHIKV RDTs; (iv) the studies used an inappropriate 102 study population (asymptomatic individuals); (v) the studies described inappropriate It is made available under a CC-BY-NC-ND 4.0 International license.

      Attrition

      Based on the tile and the abstract , 96 were excluded , with 89 full-text 158 articles retrieved and assessed for eligibility .

      Sex as a biological variable

      not detected.

      Subject Demographics

      Age: not detected. Weight: not detected.

      Randomization

      Similarly , there was a high risk of bias in 210 the patient selection domain because only three studies enrolled a consecutive or random 211 sample of eligible patients with suspicion of CHIKV infection to reduce the bias in the 212 diagnostic accuracy of the index test .

      Blinding

      not detected.

      Power Analysis

      not detected.

      Replication

      not required.

      Data Information

      Availability: The 90 Prisma-ScR checklist is available in the Supplementary material.

      Identifiers: medRxiv preprint doi: https:// doi.org/10.1101/2022.01.28.22270018; this version posted January 30 , 2022 . https://doi.org/10.1101/2022.01.28.22270018

    1. it is only in equity funds/hybrid aggressive funds that you can turn market volatility to your advantage, by investing on dips and lowering costs. In the absence of that volatility, you get no averaging benefit; in such funds, as long as your timeframe is right, it doesn’t matter whether you invest through SIP or lumpsum.

      SIP Averaging benefit in high volatility (aggressive hybrid funds)

      • ? role of correction
    1. Peer review report

      Reviewer: Jinbao Liao Institution: Jiangxi Normal University. email: jinbaoliao@163.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? Low to medium quality. I understand the content

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • 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? No
      • Is the source data that underlies the result available so that the study can be replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly. No

      Section 4 – Suggestions

      • Do you have any feedback or comments for the Author?

      Three basic models are used to study complex systems: dynamical system modelling, agent-based model, and complex networks. Dynamical system modelling uses top-down modelling ideas (modelling with macroscopic variables; based on mean-field ideas). The agent-based model uses bottom-up modelling ideas (modelling with micro variables; based on individual simulation ideas). Complex networks lie between dynamical system modelling and agent-based model (each individual interacts with each other, and the interactions are linked into edges to form a complex network). The paper 'Metacommunity research can benefit from including context-dependency' uses the agent-based model framework (NetLogo).

      The agent-based model framework in this paper incorporates four dimensions: inter-habitat differences (heterogeneity), dispersal (dispersal rate on the probability of colonizing rather than general mobility), specialization (breadth of species response to collection of diverse habitats), species Interactions (competition, predation, mutualism, parasitism et al. mutualism, parasitism et al.), and these dimensions have been more or less extensively studied in the dynamical system framework and the complex network framework. Therefore, the authors should discuss in detail how agent-based model framework has advantages over the most common frameworks currently used for ecosystem modelling (dynamical systems, complex networks).

      For example, for the dynamical system framework, recent studies suggest incorporating six modules (such as species interactions, dispersal, demography, evolution, environment and physiology) into the model to predict biodiversity (Norberg et al., 2012, Nature Climate Change; Urban et al., 2016, Science). For the complex network framework, early theoretical studies explored the effects of multiple relationship types or dispersal on complex networks (Holland & Hastings, 2008, Nature; Mougi & Kondoh, 2012, Science; Allesina & Tang, 2012, Nature).

      Moreover, the idea of agent-based model is derived from the theory of complex adaptive systems (e.g., Kondoh, 2003, Science), and the core idea of this framework is that adaptability creates complexity. Many studies have focused on the evolution of dispersal strategies within single species (Cote et al., 2017, Ecography), while theoretical studies on the evolution of dispersal in meta-communities remain rare. For the dispersal dimension (a key dimension of this paper), do authors consider the evolution of dispersal strategies.

      Finally, after reading this ms, it is really unclear what the model is and how to simulate the model. Maybe you should describe it in details following the ODD protocol for describing individual-based models (Grimm et al. 2006).


      Section 5 – Decision

      Requires revisions: The manuscript contains objective errors that must be addressed

    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      IRB: Institutional Review Board and all participants gave their signed informed consent.

      Consent: Institutional Review Board and all participants gave their signed informed consent.

      Inclusion and Exclusion Criteria

      83 years; 34 males; 57 righthanded , see Table 1 ) met the inclusion criteria: All patients were older than 18 years , presented with first-ever ischemic ( 83 % ) or haemorrhagic ( 17 % ) stroke and behavioural deficits as assessed by a neurological examination.

      Attrition

      Patients who had a history of neurological or psychiatric presentations ( e.g. transient ischemic attack) , multifocal or bilateral strokes , or had MRI contraindications ( e.g. claustrophobia , ferromagnetic objects ) were excluded from the analysis ( n = 131 patients , see the enrollment flowchart in the supplementary materials from Corbetta et al. 2015).

      Sex as a biological variable

      Handedness ( % right-handed ) 91.94 Sex ( % female ) 45.16 Abbreviations: SD = standard deviation It is made available under a CC-BY-NC 4.0 International license.

      Subject Demographics

      Age: 83 years; 34 males; 57 righthanded , see Table 1 ) met the inclusion criteria: All patients were older than 18 years , presented with first-ever ischemic ( 83 % ) or haemorrhagic ( 17 % ) stroke and behavioural deficits as assessed by a neurological examinatio .

      Randomization

      The task instructions require patients to place and remove the nine pegs one at a time and in random order as quickly as possible ( Mathiowetz et al. 1985; Oxford Grice et al. 2003).

      Blinding

      Two boardcertified neurologists ( Drs Corbetta and Carter ) reviewed all segmentations blinded to the individual behavioural data .

      Power Analysis

      We believe that adding other factors ( e.g. demographic , clinical , socioeconomic variables ) that likely interact with the recovery of patients can help us increase the model’s predictive power.

      Replication

      not required.

      Cell Line Authentication

      Authentication: However , most of the studies fall into one of the pitfalls that were described above ( i.e. overfitting , generalisability , and diaschisis ) as the models are not validated in an independent dataset.

      Code Information

      Identifiers: This procedure is available as supplementary code with the manuscript ( see https://github.com/lidulyan/Hierarchical-Linear- Regression-R- ).

      https://github.com/lidulyan/Hierarchical-Linear- Regression-R-

      Data Information

      Availability: Handedness ( % right-handed ) 91.94 Sex ( % female ) 45.16 Abbreviations: SD = standard deviation It is made available under a CC-BY-NC 4.0 International license .

      Identifiers: preprint doi: https:// doi.org/10.1101/2021.12.01.21267129; this version posted December 2 , 2021.

      https://doi.org/10.1101/2021.12.01.21267129

    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      Field Sample Permit: Collection of data for detecting cellular spatiotemporal condition supporting circularization For this purpose, online database and web server were used by taking specific queries like , RBP-types or lncRNAs to search out their special location inside cellular spaces

      Inclusion and Exclusion Criteria

      not required.

      Attrition

      not required.

      Sex as a biological variable

      not required.

      Subject Demographics

      Age: not required.

      Weight: not required.

      Randomization

      To reduce computational complexity in dealing with very large database where number of data is greater than 1000 , sample datasets were used through random selection of data from the original database .

      Blinding

      not detected.

      Power Analysis

      not detected.

      Replication

      not required.

      Data Information

      Identifiers: We analyzed the spread of this biomolecular entity outside and inside the sub- cellular space along with assimilating other reported pieces of information (e.g., about RBP molecules involved in circularization of such bioRxiv preprint doi: https:// doi.org/10.1101/2021.10.26.465935; this version posted October 26, 2021. https://doi.org/10.1101/2021.10.26.465935

    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      Field Sample Permit: Seeds of sorghum (Sorghum bicolor) were obtained from the seed collection unit of the Office of the Agricultural Development Programme, Benin City, Edo State, Nigeria. Ferruginous (or iron elevated) soil used in this present study was obtained from around the Life Sciences Faculty environment and pooled to obtain composite sample.

      Inclusion and Exclusion Criteria

      not required.

      Attrition

      not required.

      Sex as a biological variable

      not required.

      Subject Demographics

      Age: not required.

      Weight: not required.

      Randomization

      In order to confirm ferrugenicity, samples were collected from random areas and iron content was first confirmed in the area before more samples were collected and pooled.

      Blinding

      not detected.

      Power Analysis

      not detected.

      Replication

      The experiment was laid out incompletely randomized design in a factorial arrangement and replicated three times per treatment.

      Number: The experiment was laid out incompletely randomized design in a factorial arrangement and replicated three times per treatment .

      Data Information

      Availability: It is made available under aCC-BY 4.0 International license.

      Identifiers: preprint doi: https:// doi.org/10.1101/2021.11.22.469542; this version posted November 22 , 2021 .

      https://doi.org/10.1101/2021.11.22.469542

    1. Peer review report

      Reviewer: Dr. Pradeep G Kumar Institution: Rajiv Gandhi Centre for Biotechnology email: kumarp@rgcb.res.in


      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? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Not applicable
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? No

      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      • Do you have any other feedback or comments for the Author?

      Text requires improvement at some places (citing them is difficult as pages and lines are not numbered). Some examples are given below:

      .......was associated with molecular markers of the PGC...... (was associated with the expression of molecular???)

      Primordial germ cells (PGCs), the developmentally first founder cells of the germline, are induced from epiblast cells on around embryonic day (E)6.25 by external signals,

      Furthermore, it was shown for that male mouse ES cells cultured in serum that subjected to a chemical intervention, including a timed exposure to a combination of the a SIRT1 inhibitor Ex-527, the a DNA methyltransferase inhibitor RG-108 and the an electrophilic redox cycling compound tert-butylhydroquinone (tBHQ), was associated with induced the expression of molecular markers of the PGC


      Section 5 – Decision

      Verified manuscript

    2. Peer review report

      Reviewer: Takehiko Ogawa Institution: Yokohama City University email: ogawa@yokohama-cu.ac.jp


      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? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Almost Yes
      • Are the methods documented and analysis provided so that the study can be replicated? Almost Yes
      • Is the source data that underlies the result available so that the study can be replicated? I think, Yes
      • Is the statistical analysis and its interpretation appropriate? Not applicable
      • Is quality of the figures and tables satisfactory? Almost Yes
      • Are the conclusions adequately supported by the results? No
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly.

      I would like to request authors to test the validity of cells with spermatogonia-like morphology (CSM) as spermatogenic stem cells. For this, transplantation of CSM into the seminiferous tubules in the testis of recipient mice is necessary. This may be an additional work, but authenticity of CSM as SSCs cannot be claimed without such experiment. They may claim that in case of ES cells most experiments do not perform blastocyst injection experiment to confirm the pluripotency of ES cells. However, culture system for ES cells has a long history and was established as robust method to maintain their pluripotency. It is actually the 2iL system as shown in this study as well. In case of SSCs or GS cells, the culture system is still fragile in my understanding, compared to the 2iL. The spermatogenic ability that SSCs and GS cells have could be lost during the cultivation in many cases. In particular, chemical intervention shown in this study could disturb cell’s intrinsic system, which could make almost anything happen. The enhanced expression of Lhx1 also could be an aberrant result of such turmoil in the cells. I do not insist that is the case, but intentionally taking a position to be extremely skeptical to the results. In order to dispel such doubts, it is necessary to do the transplantation experiments and prove that the CSM maintained the spermatogenic ability as SSCs.


      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      Readers would wonder what the CSM is exactly. This naming means that CSM could be SSCs but possibly not, although they look like SSCs. It was honest naming but confusing in what the CSM really is. In order to start the experiment with CSM, authors should clear such ambiguous point. Thus, I recommend a transplantation experiment as stated above.

      • Do you have any other feedback or comments for the Author?

      In Page 6, it is described that medium change twice daily with a third of the volume at hour 8 and 16 was critical for the appearance of CSM. In case of the medium change with half of the volume every 12 hours, it was written that the CSM did not appeared at all. Authors argued that endogenously produced soluble factors might be the cause. I wonder what extent of difference could be there between the two method of culture medium change, regarding to the concentration of endogenously produced soluble factors. A simulation of the change in concentration of such hypothetical substances might help the speculation.


      Section 5 – Decision

      Requires revisions

    1. Peer review report

      Reviewer: Yuan Junpeng Institution: National Science Library, Chinese Academy of Sciences. email: yuanjp@mail.las.ac.cn


      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? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid?

      The research question of this article is not clear enough, and this paper is more like a report than a research paper. Since a lot of research about retraction haven been published, many characteristics of retraction have been analysed. There seem not enough new messages comes from this article.

      In addition, as ‘exploratory research’ defined by the title, the use of full data for analysis is more in line with the objectives of the title, instead of excluding other disciplines and restricting the analysis to human health. If the author’s goal is to analyse the characteristics of human health-related retractions, it is recommended to limit it in the title. The current topic is too general.


      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      It is recommended that the author properly point out what have and haven’t been done in this topic, and their specific contribution to the existing knowledge, so as to show the innovation of the research.

      It is recommended that the author clarify the research objectives and modify the title more in line with the content.

      • Do you have any other feedback or comments for the Author? No

      Section 5 – Decision

      Requires revisions

    1. 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? No
      • Are the conclusions adequately supported by the results? No
      • Are there any objective errors or fundamental flaws that make the research invalid?

      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      • Do you have any other feedback or comments for the Author?

      Agarwal and Parekh analyzed 685 SARS-CoV-2 isolates collected during 27th Jan - 27th May 2020 from India and described the distribution of virus strains and mutations across the country. While the information might be valuable to some local readers, the results are mainly descriptive and the data are a bit out of date. In addition, I have the following comments.

      1. 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.
      1. The “Analysis of the Mutational Profile of Indian Isolates” should be moved to Materials and Methods.
      1. The authors provided lengthy discussion about the effect of each mutation in some lineages, such as 20A and I/A3i. However, as these mutations are tightly linked, the effect of each individual mutation is difficult to access. It is possible that some of the mutations are just hitchhikers. They may want to address this alternative point.
      1. Several figures are confusing and lack detail. The diversity plots of Figure 3 and Figure 8 are hard to be precisely compared to the mutations that occurred among different plots. Phylogenetic trees, as well as their figure legends, are confusing, especially Figure 9 and Figure 10. For Figure 9, it is impossible to tell which mutation site had changed from C to T. For Figure 10, spots depicted in yellow are both position 29827 A>T and position 29830 G>T, green spot only notes as G, but A29827 is not mentioned in the figure. Furthermore, the mutation position of blue spot C cannot be found.
      1. Figure 9 and Figure 10 were not mentioned inside the text.
      1. The Top 10 mutations in PCA analysis are the mutations in 20A and I/A3i. It is reasonable to observed a clear association of the clusters with the clades. It is not clear, however, how these distribution correlate with lockdown, contact tracing and quarantine measures.

      Section 5 – Decision

      Requires revisions

    2. Peer review report

      Reviewer: Dr. Jyotsnamayee Sabat Institution: Regional VRDL, RMRC(ICMR). email: jyotsnasabat@yahoo.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? Good quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid?

      No such application was observed.


      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      They have analysed it in-depth and presented nicely.

      • Do you have any other feedback or comments for the Author?

      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.


      Section 5 – Decision

      Verified manuscript

    3. Peer review report

      Reviewer: Parvin Abraham Institution: MIMS Research Foundation, Calicut, Kerala, India. email: parvinabraham@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? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly. No

      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      The dataset is only from 27th Jan – 27th May 2020. Maybe they can include more Numbers.

      • Do you have any other feedback or comments for the Author? No

      Section 5 – Decision

      Verified manuscript

    1. Peer review report

      Reviewer: Dr. : Peter Dahlberg Institution: SLAC national laboratory email: pdahlb@slac.stanford.edu


      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? Low to medium quality. I have added several comments to section 4 as suggested edits.

      Section 3 – validity and reproducibility

      • Is the reason for developing a new method explained? Yes
      • Is the description of the method technically sound? Yes
      • Are sufficient details provided so that the method can be replicated? No
      • Is the source data that underlies the result available so that the study can be replicated? not applicable
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? No
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly. No

      Section 4 – Suggestions

      • In your opinion how could the author improve the method?

      The manuscript describes the progressive refinement method for sparse recovery. This approach uses minimal RAM while producing a finely discretized output for high density 3d fluorescence localizations. Furthermore, the approach does not require the PSF to be translationally independent. This is an assumption that is often made that simplifies the computation, but does not account for field dependent aberrations. There are several comments that I believe would improve what is overall strong manuscript. The most serious of which is addressed in 1a below.

      1. The two main claims of the manuscript are that the PRIS method requires less RAM than a brute force approach and that the algorithm functions for spatially varying PSFs. Neither of these claims are supported directly by the text or figures. a. Perhaps I missed it, but there were no field dependent aberrations in the simulations. If this is the case, how exactly has it been demonstrated that the approach works well for a spatially varying PSF? Because this is a central claim of the PRIS method, I think it is worth implementing. b. The authors describe a scenario of brute force solving of the inverse problem requiring 152.6 GB, while I have no doubt that the PRIS approach would require less RAM, the authors do not make it clear how much less. While I know that the reduction will depend on the exact implementation and the data at hand, a rough comparison of the RAM requirements would be helpful for the reader.

      2. Following algorithm 1, the authors introduce the “shrink” operator. A one line description would be helpful of what this operator does. As I understand it, it is a threshold of the output to keep the data output sparse.

      3. Following algorithm 1 and 2, the authors describe the use of “kicking.” They do a nice job of giving a brief description of what the “kicking” does (improve the convergence speed), but I am concerned because neither algorithm 1 or 2 shows kicking. The kicking is wrapped up in another conditional statement that is not shown in either algorithm. This is confusing for the reader. Perhaps a parenthetical should be added stating that the kicking is not shown in the algorithm.

      4. The code for the PRIS method should be made available publicly, both so the results can be replicated and also so that others can use the approach.

      • Do you have any other feedback or comments for the Author?

      Additionally, I have some minor text/figure edits

      1. In the title, the acronym PRIS is defined as “progressive refinement method on sparse recovery” however in the text it is “progressive refinement method for sparse recover” I think the wording in the text is correct.

      2. 5th paragraph of the introduction: “In principal” should be “In principle”

      3. Paragraph preceding section 3: “in case if a species” I think should read “in case a species”

      4. Throughout the figures, dark red, dark green, and dark blue are used over black and this is very difficult to see. For example, dashed red line in figure 2 on the right hand side, the cy5 and cy3 labels in figure 7, the dark blue box in figure 8.

      5. Throughout the figures there are also a lot of small symbols used. For example, Figure (a)-4 there are small (red?) marks on top of a red heat map. These are extremely difficult to see clearly.

      6. Figure 6c, it is very challenging to see differences in the distributions of points. I think this data would be better represented if additional histograms were shown.


      Section 5 – Decision

      Requires minor revisions

    2. Peer review report

      Reviewer: Dr. Christopher H. Bohrer Institution: NIH/NCI email: bohrerch@nih.gov


      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? High quality

      Section 3 – validity and reproducibility

      • Is the reason for developing a new method explained? Yes
      • Is the description of the method technically sound? Yes
      • Are sufficient details provided so that the method can be replicated? No
      • Is the source data that underlies the result available so that the study can be replicated? No
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? No
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly. No

      Section 4 – Suggestions

      • In your opinion how could the author improve the method?
      1. The approach is nice, but I really think they should highlight the advantage of their approach --- that is, perform a simulation with imperfect optics then apply the traditional methodologies as well as their own to show their superiority.

      2. The comparison to previous methodologies is nice, but the fact that they are different simulations with different parameters is a major problem --- for example, the photons used in their simulations are higher than used in the previous studies. Therefore, if they are going to compare, it should only be done if the methodologies were applied to the same data.

      3. A user guide with an example, walking through the specifics would aid this work greatly. For instance, it is unclear how one obtains the different matrices given their data --- though this is likely within the references. Additionally, if they want others to use the methodology, this is a must!

      4. Finally, though I don’t think they necessarily need to do this, but utilizing real experimental data to validate their approach would be nice. For instance, investigate the structure of the nuclear pore complex with the different methodologies --- a standard within the field.

      • Do you have any other feedback or comments for the Author? No

      Section 5 – Decision

      Requires revisions

    1. Peer review report

      Reviewer: Deyou Qiu Institution: Chinese Academy of Forestry. email: qiudy@caf.ac.cn


      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? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • 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 replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly. No

      Section 4 – Suggestions

      • In your opinion how could the author improve the study? No
      • Do you have any other feedback or comments for the Author?

      The resolution of Fig 3 is not good, could you pls improve it?


      Section 5 – Decision

      Requires revisions

    1. Peer review report

      Reviewer: Max Shokhirev Institution: Salk Institute for Biological Studies email: maxshok@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? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Some, but seems to be very limited in terms of biological literature.
      • Is the study design appropriate and are the methods used valid? Yes
      • Are the methods documented and analysis provided so that the study can be replicated? not applicable
      • Is the source data that underlies the result available so that the study can be replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? How could the author improve the study?

      The author has laid out a theoretical argument for senescence as a tradeoff between information capacity between epigenetic and non-epigenetic content.“A constraints-based theory of senescence: imbalance of epigenetic and non-epigenetic information in histone crosstalk.” This work is interesting, but is based on a superficial understanding of the biology underlying senescence/aging, makes several dangerous oversimplifications and assumptions, and does not provide any data or analysis to support the theory. I’ve laid out my comments for each section below:

      Sections 1.1-1.3

      The author only mentions the Hayflick limit as a biological reference for senescence. There is a very rich body of literature on senescence and aging that is completely overlooked here. The author should include additional references to reviews for senescence and aging to orient the reader to the complexity of these biological processes (e.g. PMC8658264, PMC7846274). Please clarify what you mean by senescence vs aging for both cells and individuals. Senescence is a natural biological process that cells/organisms use to turn off cell replication due to damage (e.g. telomere shortening, double-stranded breaks, etc.). Other cells can also facilitate this process through signaling (e.g. immune cells or contact inhibition). Aging is typically thought of as an organismal phenomenon, which is still poorly understood but is theorized to include tradeoffs (as you describe in section 1.2). It is also accepted that aging is cell, tissue, and organism specific. Since you talk about senescence and aging across both biological scales, it is important to define exactly what your theory pertains to.

      Section 1.4

      The author posits that senescence is an imbalance in information contents of histone post-translational modifications around transcription start sites. This is just one level of regulation, albeit an important one. The author seems to completely overlook many other types of regulation (e.g. microRNA, lincRNAs, metabolic/energetic constraints, non-proximal regulation at enhancers, higher ordered structure of the chromatin, post-translational regulation of proteins, and etc.). How can all of these other important levels of regulation fit into this theory? All have been implicated in senescence/aging in some form or another. The author further suggests that histone crosstalk information content can be decomposed into two unrelated components: epigenetic and non-epigenetic. The non-epigenetic component is described as “hologenic information content,” which stems from a previously published work by the author. Non-epigenetic is confusing in this context since really this is information content that stems from the synergies of individual cells to form a whole, e.g. the emergent information content that comes from many cells working together (or at least this is how I understand the underlying theory). This information content is important for the general maintenance and survival of the organism. The author should clarify this point further, since this seems to be one of the fundamental assertions being made in the paper. For example, bringing in the descriptions used in section 2, can further clarify these central points. In addition, the author states: “ Moreover, the sum decomposition in Eq. 1 implies that the growth in magnitude (bits) of the hologenic (i.e., non-epigenetic) component must be accompanied by a decrease in magnitude of the epigenetic component.” This is not necessarily true, since signaling is a separate biological process from the regulation of gene expression. In other words, both can increase or decrease simultaneously. For example, a healthy non-senescent immune cell can upregulate very specific transcriptional programs that lead to very complex signaling and extra-cellular interactions. You can argue that both represent an increase in information content for both the epigenetic and non-epigenetic “hologenic” components. In addition, as cells naturally senesce they are programmed to turn off cell-cycling while upregulating autophagy and repair processes. They may not upregulate extracellular signaling at this time, which would seem to contradict the author’s theory/statement. In this case, the simplification that all cells are the same is dangerous because it overlooks the tradeoff of information contents between cells. It also ignores important repair pathways (senescence being one of them), to deal with cells that have dysregulated their natural processes over time. It also overlooks the important action of immune cells that work to get rid of cancer and poorly-functioning cells. Also, it seems crosstalk, correlation, capacity, and content, are used interchangeably. Please clarify that these are all the same, or use one of these terms to avoid confusion.

      Section 1.5

      The author provides a general approach for measuring the log of the ratio of epigenetic and non-epigenetic capacities for a particular histone modification at three positions (i,j,k), and for some measured abundance of mRNA Y. Since we typically measure abundance of a particular modification genome-wide, and the mRNA level for tens of thousands of genes, how would a realistic equation look like (i.e. one that has 10k mRNA levels, and 10k histone positions)? In addition, the author does not explain how to combine correlations across multiple histone modifications. Please expand this section to make it relevant for real-world genome-wide measurements since this will be important for falsifying the theory. Since public datasets are available (e.g. the aging atlas https://doi.org/10.1093/nar/gkaa894), the author should show an example of how a dataset might be used to falsify or demonstrate the theory in more detail.

      Section 2.1

      The author uses correlation of the log ratio of the epigenetic and non-epigenetic content with age as a readout of “reassignment” of crosstalk/contents, arguing that for cancer cells this correlation should be essentially zero. This seems like an oversimplification of the “reassignment” process since senescence may occur in phases across the age of a cell/organism, and since there might be both increases and decreases in the log ratio of contents due to natural biological processes and variability. Would it not be better to measure the sum of changes in the log ratio or the difference between the log ratios at different ages?

      In addition, the biological age of a cell/tissue/organism can vary. For example, stem cells may have negligent aging, while other cells might age relatively quickly. Again, the author should clarify the context of age: are we measuring strictly chronological age correlation? Should we consider different correlations for each cell/tissue in the organism? What about tradeoffs in information content between cell types and tissues? In other words, it is unclear how the theory should be applied to biological systems.

      Section 2.2

      The author argues that senescence is an emergent property of the loss of information content for epigenetic histone crosstalk and an increase in information content of “hologenic” information content (e.g. cell signaling and anti-tumor signaling). I believe this premise does not stem from the reality of biological systems (see my comments for section 1.4). Also, this section seems to be contradicting the author’s conclusions and is very confusing. The author seems to argue that there is both more AND less constraint at the multi-cellular level (organismal)? Please clarify or remove this section.

      Section 2.3

      Senescence as transcriptional overregulation is vague. Here the author is arguing that as epigenetic constraint decreases, you have a decrease in precision (e.g. loss of regulation), but then you have a competing global or hologenic increase in constraints, which constrains the expression of genes for the overall benefit of the organism. A shift toward global constraint.

      Section 2.4

      This seems to be describing an illustrative real-world example? This section is incredibly specific and again only focuses on one possible mechanism and does not include any measured data or analysis. Please preface this section to explain that this is just one of many possible examples. Again, it will be good to provide other examples looking at other aspects of aging biology (not just histone modifications).

      Section 2.5-2.9,3

      This seems to be a general discussion. It would be easier to organize these sections into one discussion section for added clarity. Again, I would recommend not talking about sweeping statements like “Senesensce’s ultimate cause” and “Can senescence be stopped?” since this theory only addresses one small aspect of the biology underlying aging and senescence and does not address the heterogeneity of aging. These topics are controversial and should be addressed very carefully to avoid alienating the biological community.


      Section 4 – Decision

      Revisions required

    2. Peer review report

      Reviewer: Charles A. Schumpert Institution: University of South Carolina email: schumpca@email.sc.edu


      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? High quality

      Section 3 – validity and reproducibility

      • Does the work cite relevant and sufficient literature? Yes
      • Is the study design appropriate and are the methods used valid? Yes
      • Are the methods documented and analysis provided so that the study can be replicated? not applicable
      • Is the source data that underlies the result available so that the study can be replicated? Yes
      • Is the statistical analysis and its interpretation appropriate? Yes
      • Is quality of the figures and tables satisfactory? Yes
      • Are the conclusions adequately supported by the results? Yes
      • Are there any objective errors or fundamental flaws that make the research invalid? Please describe these thoroughly.

      Overall the manuscript is written brilliantly and provides excellent context to the audience about a complex theoretical biological concept. No flaws can be found, although one could argue against a few of the points in the assumptions used to construct the theory, there’s nothing illogical or irrational.


      Section 4 – Suggestions

      • In your opinion how could the author improve the study?

      The writing of the paper makes it easy to read, which can sometimes be a challenge with theoretical biology manuscripts. Potentially adding a bit more context on the various theories of aging may help demonstrate the marriage of the ideas into the theory he constructed.

      • Do you have any other feedback or comments for the Author? No

      Section 5 – Decision

      Verified manuscript

    1. SciScore rigor report

      Sciscore is an AI platform that assesses the rigor of the methods used in the manuscript. SciScore assists expert referees by finding and presenting information scattered throughout a manuscript in a simple format.


      Not required = Field is not applicable to this study

      Not detected = Field is applicable to this study, but not included.


      Ethics

      IRB: Samples and data collections were conducted according to the guidelines of the Declaration of Helsinki , and approved by the Ethics Committee Sciences et Santé Animale n°115 ( protocol code COVIFEL approved on 1 September 2020 , registered under SSA_2020_010 ) .

      Euthanasia Agents: Cells were then incubated for 72 h at 37 °C with 5 % of CO2 .

      Field Sample Permit: These experiments were approved by the Anses/ENVA/UPEC ethic committee and the French Ministry of Research ( Apafis n°24818-2020032710416319 ) .

      Consent: All sera from the first cohort , and whole blood samples from the second cohort , were obtained from the Toulouse hospital , where all patients give , by default , their consent for any biological material left over to be used for research purposes after all the clinical tests requested by doctors have been duly completed.

      Inclusion and Exclusion Criteria

      not detected.

      Attrition

      One additional conclusion that can be drawn from the comparison of the results of the RBD-ELISA with those of the Jurkat-S&R-flow test is that, whilst the two methods show similar sensitivities, the ELISA signals tend to saturate very rapidly, and are thus much less dynamic that those obtained by flow cytometry.

      Sex as a biological variable

      Of note, we did not notice an increased frequency of allo-reactivity in samples from women compared to men, which suggests that allo-reactivity after pregnancy is not a major cause in the origin of those allo-reactions.

      Subject Demographics

      Age: Experiments on virally-infected hamsters Eight week-old female Syrian golden hamsters ( Mesocricetus auratus , strain RjHan:AURA ) from Janviers’s breeding Center ( Le Genest , St Isle , France ) were housed in an animal-biosafety level 3 ( A-BSL3) , with ad libidum access to water and food.

      Randomization

      The results of the second cohort, which comprised a few Covid patients, but also a large proportion of blood samples randomly picked among those from patients hospitalized for conditions unrelated to Covid-19, yielded a much less clear picture than the first one.

      Blinding

      On the other hand, the situation was much less clear-cut for the cohort comprising blood samples picked more or less randomly and blindly among those available as left-overs from the hematology department and was, therefore, more akin to a ‘real’ population.

      Power Analysis

      not detected.

      Replication

      not required.

      Cell Line Authentication

      Contamination: The Jurkat-S and Jurkat-R cell lines were both checked for the absence of mycoplasma contamination using the HEK blue hTLR2 kit ( Invivogen , Toulouse , France ).

      Authentication: For the same reason , the blood samples for the experiment shown on Figure 3A were collected by one of the authors by simple finger-pricking.

  7. Dec 2021
    1. This book reminds me of me because I am funny. I like to joke around make funny faces and make people laugh. Yes I would recommend this book to reader’s ages 8-12 years old because it is hilarious and a good story. I think the drawings might interest the readers of this book.

      Recommendations

    2. My Favorite part is when teenagers are in a truck and there is a teenager in the back of the tuck who sprays something at Greg and Rowley and it was Halloween night and they said they was going to call the cop on them. I found Greg intersting because he was funny and he took things seriously. He says funny things and he is a nice kid and he knows what is right and what’s wrong. The illustrator used black and white drawings and stick men. I thought the illustrations were funny and some of them made me laugh.

      Evaluation + characters

    3. This book is about the first day Greg Heffley went to middle school. Greg thought he was sitting between two morons in the first day of middle school. It was Halloween night and Greg is dad favorite holiday is Halloween. Greg and Rowley were running away from a people with a chainsaw on Halloween night then Greg mom came and ask what is going on here.

      PLOT: Is this enough? Have you read it? Does it really capture the essence of the book?

    1. I would recommend this book. I think a good reader would like this book because they would understand it more. It would interest the reader. The plot is weird you never no what's going to happen next. The setting is in Camp Green Lake and the mountains. The author writes with simple words and it is easy to read.

      Recommendation

      What things DON'T belong in this paragraph?

    2. I really enjoyed reading this book because it was very interesting and it is a good book to read. My favorite part in the book is when they threw the shoes at Stanley because he fell funny. One of the characters reminded me of myself because I didn't know how to read like Zero, but now I do, and so does Zero because Stanley taught him. When I read this book I felt like I was there digging up holes and finding stuff underground.

      Evaluation + Characters

    3. This book is about a kid named Stanley Yalnats. One day he walked under the bridge and a kid had tossed some shoes off the bridge . They fell on Stanley and he fell when they fell on top of him. So about five minutes later the "'Police'" thought that he had stolen them, that's how he went to Camp Green Lake. When he went there he met a lot of people there. Their names were Zig-zag , Armpits , Zero , Twitch. They were good friends, but Zero didn't know how to read, so Caveman showed him. Stanley met them and they had to dig holes with his friends. About a year later Stanley left Camp Green Lake.

      Plot and characters. Is this first paragraph appealing? Does it capture the readers' attention? Why? Why not?

    1. I recommend this book because it has a positive story line. Lots of teenage girls would like this book because it is humorous but realistic. The plot would hold the interest of readers because it makes you laugh and think. I would also recommend this book to anyone who liked reading The Princess Diaries because it is by the same author.

      Recommendations

    2. I really enjoyed this book. It was very funny and genuine. Samantha was funny because of her attitude and her "protests" like wearing all black. This book was very well-written. It goes into great depth about how we look at things in life and has great characterization. Samantha changed and grew in the book. By the end, she looked at art and love very differently. I felt this book was easy to relate to because it isn't perfect like a Cinderella story. It describes how life really is and is a very positive story.

      Evaluation + Themes + Characters

    3. Samantha Madison is an outsider. She dresses all in black because she mourns the loss of the art supplies at her school. She is in love with her older sister's boyfriend and the enemy of Kris Parks (the most popular girl at school). After saving the president's life, Samantha's world turns upside down. She is now the most popular girl in the USA and appointed Teen Ambassador for the UN. And the president's son just might be in love with her. Samantha learns a lot about life, love and common sense - but does SHE love the president's son?

      PLOT: What details are included? What is left out? How does the reviewer avoid giving spoilers

    1. AIMOS. (2021, November 30). How can we connect #metascience to established #science fields? Find out at this afternoon’s session at #aimos2021 Remco Heesen @fallonmody Felipe Romeo will discuss. Come join us. #OpenScience #OpenData #reproducibility https://t.co/dEW2MkGNpx [Tweet]. @aimos_inc. https://twitter.com/aimos_inc/status/1465485732206850054

  8. Nov 2021
    1. I have no problem with publishers making a profit, or with peer reviewers doing their work for free. The problem I have is when there is such an enormous gap between those two positions.

      If publishers make billions in profit (and they do), while at the same time reviewers are doing a billion dollars worth of work for free, that seems like a broken system.

      I think there are parallels with how users contribute value to social media companies. In both cases, users/reviewers are getting some value in return, but most of the value that's captured goes to the publisher/tech company.

      I'd like to see a system where more of the value accrues to the reviewers. This could be in the form of direct payment, although this is probably less preferable because of the challenges of trying to convert the value of different kinds of peer review into a dollar amount.

      Another problem with simply paying reviewers is that it retains the status quo; we keep the same system with all of it's faults and redistribute profits. This is an OK option as it at least sees some of the value that normally accrues to publishers moving to reviewers.

      I also don’t believe that open access - in it’s current form - is a good option either. There are still enormous costs associated with publishing; the only difference is that those costs are now covered by institutions instead of the reader. The publisher still makes a heart-stopping profit.

      A more elegant solution, although more challenging, would be for academics to step away from publishers altogether and start their own journals, on their own terms.

    1. COVID-19 Living Evidence. (2021, November 12). As of 12.11.2021, we have indexed 257,633 publications: 18,674 pre-prints 238,959 peer-reviewed publications Pre-prints: BioRxiv, MedRxiv Peer-reviewed: PubMed, EMBASE, PsycINFO https://t.co/ytOhLG90Pi [Tweet]. @evidencelive. https://twitter.com/evidencelive/status/1459163720450519042