Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: UNDERSTANDING EXPERIMENTS AND RESEARCH PRACTICES FOR REPRODUCIBILITY: AN EXPLORATORY STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: - Clear and unambiguous, professional English used throughout.
    - Yes.
- Literature references, sufficient field background/context provided.
    - Yes, although I would have expected a comparison with related work.
- Professional article structure, figures, tables. Raw data shared.
    - All figures excluding Figure 9 have some minor issues, mostly resolution but sometimes a too small font.
    - I also find pie charts to sometimes not being able to represent percentages fairly, but that is mostly a personal preference.
- Self-contained with relevant results to hypotheses.
    - There are no hypotheses or research questions. See my comments.
Experimental design: - Original primary research within Aims and Scope of the journal.
    - Yes.
- Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
    - Missing. There are "investigated topics" in lines 45-49 but no RQs or hypotheses. I have several issues with this (see General comments).
- Rigorous investigation performed to a high technical & ethical standard.
    - There are no information on whether an IRB/ERB was present and, if positive, whether the study was evaluated in terms of ethics.
    - You declare to follow the national GDPR guidelines (DSGVO); however, one sentence worries me, and I hope that it is merely a language issue. Lines 169-171:
    - "Only those participants who read and agreed to the privacy policy were included in the final dataset."
    - As no question was mandatory, did you gather data in case participants did not consent to participate according to the privacy policy and discarded data afterwards? If positive, that is worrying.
    - Privacy policy is IMHO a weird term that is usually related to services. As researchers, we are also limited in which "policies" we want to set, for ethical reasons. I would still call this an informed consent.
- Methods described with sufficient detail & information to replicate.
    - Yes for the analysis method, although the paper misses details that are typical for survey research (response rate, number of excluded responses for each filtering criteria).
    - No for the survey construction (see General comments).
Validity of the findings: - Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
    - Yes.
- All underlying data have been provided; they are robust, statistically sound, & controlled.
    - The Jupyter notebook looks good to me.
- Conclusions are well stated, linked to original research question & limited to supporting results.
    - They are well stated, but the study overall is not properly framed. If the study is exploratory, it should be framed as such. If the study attempts to survey a population, as wording suggests, it has many unmentioned threats to validity (see General comments).
- Speculation is welcome, but should be identified as such.
    - Most the recommendations seem to come the authors personal beliefs and experiences; they do not seem to be constructed systematically.
Additional comments: The study reports on a questionnaire distributed to researchers  of various fields (n=101 complete responses) towards a better understanding of the reproducibility crisis, how to tackle the crisis, and how the FAIR principles are spread.
Overall, I appreciate the initiative and several of the questions asked in the questionnaire. The results are interesting, and I was surprised to see how (relatively!) widespread is the practice to repeat own experiments with respect to my field, where this is not the case.
The paper, however, lacks several details that, in my opinion, threaten how seriously we should consider the results, which are important but need to be contextualized. The most severe concern I have is that the study presents itself to describe a population (as in descriptive study, see, e.g., Pinsonneault, A., & Kraemer, K. (1993); or norm-seeking) if not even to explain phenomena (e.g., in line 124)). That is, the paper calls readers to evaluate the study in terms of reliability, validity and, in particular for validity, representativeness and external validity. These two are weak with 101 participants, gathered from a restrict pool, to represent at least 10 roles in at least 11 areas that range from biology to physics and computer science. While the sample is diverse, which would make an exploratory study interesting, the number of people for each possible settings make comparisons meaningless to generalize. How are the recommendation even applicable with such a sample that sparkled them?
My recommendation is to declare if this was an exploratory study, which might as well be given a lack of hypotheses and research questions, and to reframe the paper as such. Research questions can, of course, be part of an exploratory study, too, and I would recommend you to add them either in place of the investigated topics (45-49) or after them.
My second major concern lies in the questionnaire itself. The paper does not offer any explanation on how it was constructed. With all existing literature on survey construction, I was expecting some words on how the items were chosen, if any framework was followed, a conceptual model, prior literature; similarly for items: how the items are linked to research questions (or goals in your case) to represent what they are supposed to represent, how the scales were chosen to represent possible answers. Sometimes you use dichotomous/binary scales with a third "other" options, sometimes ordinal scales, sometimes what seem to be Likert scales. What drove the choice? Please inform us readers better in how we can trust the numbers that come out from your questionnaire, especially in what they are supposed to represent.
In line 146, you write that "A group of four researchers from Computer Science
146 and Biology first validated the survey before distributing it." I think you meant to write "piloted" instead of "validated" here, as validation would imply particular construction and statistical tests that would enhance the way we interpret the results.
I strongly suggest to rewrite lines 166-170 and to be careful in wording. For "ethics and consent", you are reporting that you are following privacy regulations (which is good, I commend you for this), but there is little else about ethics in here. Did you gather informed consent? Was there a need for an institutional review board to approve the study? Was there one at the institute (not having one would free you from seeking approval of one)? Please elaborate on ethics and consent. I interpret lines 169-170 to mean that data was gathered regardless of agreeing to the "privacy policy" or not, and was discarded in case no agreement was provided. I do not think that this is allowed under DSGVO/GDPR. Please specify.
I appreciate how you go into details in breaking down results, offering facets, going into details. When reading the dozens of percentages that you offer between line 191 and line 310, I was excited and surprised by several of them. I even annotated how interesting it would be to to group those in lines 238-244 by discipline. Then, I remembered about the sample, so how much sense did it make in the end to know, e.g., that "72% of PostDocs think that there is a reproducibility crisis", when this means that you found almost 13 (12.96) PostDocs who believe that there is a crisis?
The Discussion section lacks a comparison with related work. It seems that you spent a considerable time reviewing related work. Was there anything that is worth mentioning in the results you obtained? I would bet there is.
I am missing how the offered recommendations (362-486) were constructed, hopefully in a systematic way. The paper should explain the link between findings and recommendations. As written, they appear to be opinions, against which one can simply argue (e.g.: 429-434, VCS is not easy, especially Git, for those not in CS-related fields. Some people might need training to use VCS.).
Minor:
I commend you for clarifying on the differences between reproducibility and repeatability, so I recommend doing the same in the abstract to help readers to better understand your contents. People are still unclear on differences behind the meaning of these terms.
Consider adding "study" before "methods" in "and incomplete information in methods" (abstract)
Please clarify the term "metadata" in the abstract.
76-77, "We have proposed a definition of reproducibility and repeatability (Samuel, 2019) which is also inline with the definitions of NIST (Taylor and Kuyatt, 1994) and the Association for Computing Machinery (Result, 2017)." On the latter point, ACM itself recently agreed that its definitions for reproducibility and replicability were confusing (see version 1.1 from https://www.acm.org/publications/policies/artifact-review-and-badging-current). Please check that you are still aligned with ACM.
100-102, "However, a study on the reproducibility of Jupyter notebooks publicly available in Github indicates that [...] only 4.03% of them had the same results as the original run (Pimentel et al., 2019)." could you report (if any) why this happened? One would expect a Jupyter notebook to run the same everywhere.
461-464, the last sentence is confusing. A DOI helps to identify resources, not to preserve them. I know several people who believe that a DOI is a magic preservation mechanism, please help me to avoid this confusion further.

References
Pinsonneault, A., & Kraemer, K. (1993). Survey research methodology in management information systems: an assessment. Journal of management information systems, 10(2), 75-105.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: UNDERSTANDING EXPERIMENTS AND RESEARCH PRACTICES FOR REPRODUCIBILITY: AN EXPLORATORY STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: A few small issues here and there, please proofread the paper.

28 - things -> devices
45 - an exploratory study (Pinsonneault and Kraemer, 1993) -> as defined by Pinsonneault and Kraemer (1993)
48, 48, 265, 266, 270, and many other places -> consider putting al these links as footnotes or references. Also for 205-208
142 - once such tool -> one such tool
243 - build -> built
Table 1, Table 2 -> consider rounding percentages here as well

Disciplines are usually written lowercase (computer science, not Computer Science)
Experimental design: Thank you very much for specifying research questions. This and the conversion to exploratory study looks way better now, and reads more transparently.

I am not 100% convinced on the first part of RQ1. Given the large studies in Nature, would we really need it in a new exploratory study? As you require to answer positively to continue the survey, I propose "What leads to a reproducibility crisis in science?"
Validity of the findings: Conversion to exploratory study makes me see the report in a way better light.
Additional comments: Dear authors,

Thank you very much for following my recommendations. I am positively surprised by how much the manuscript has improved.

Apart from minor editing suggestions, I have nothing else to report.

Best regards


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: UNDERSTANDING EXPERIMENTS AND RESEARCH PRACTICES FOR REPRODUCIBILITY: AN EXPLORATORY STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript addresses an interesting and relevant topic in science. It is well written and a really nice review on what is being discussed an described with respect to reproducibility and related concepts.

While reading it, however, I had some issue with the term "crisis" that it is a bit hyperbolic. It is a term I expect in a brochure or manifest, not in a scientific paper. It is a strong word, which in the context of scientific paper requires much more substance than simple paraphrasing some citations that are included.  I have seen that previous reviewers made the same remark and with I can follow the arguments put forward in the rebuttal. However, given that the rebuttal is not part of the article and the strongness of the word "Crisis" remains, I would recommend that authors to elaborate a bit more on why it is a crisis and not just an area in dire need for improvement. If the authors decide to keep the term, I would suggest elaborating a bit more on why it is a crisis.
 Peng 2105 for example, argues nicely on the role of increased access to sensory data. Other citations - like this manuscript report on conducted survey's. With survey's the question remains, whether or not it is a real crisis and not a perceived crisis. e.g. as scientists do we need to change direction or better adapt to the inevitable growth and availability of technology to perform science. There are some citations (e.g. Atmanspacher and Maasen, 2016) that probably give substantial merit to using the term "crisis", however, those citations are paywalled and not part of my subscription plans and as a result, prevented me to access.

The question is whether the term "reproducibility crisis" is really needed. Without it, the paper has enough merit. It distracts from the main message. i.e. information technology brought an influx of new data and a massive scale, which needs new approaches to handle, process and disseminate. It reports back a survey on how scientists are affected with this increase of data and suggest countermeasures to improve capturing metadata to deals with this.
Experimental design: no comment
Validity of the findings: No comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSFECTION TYPES, METHODS AND STRATEGIES: A TECHNICAL REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript by Chong et al provides an overview of the transfection protocols used in modern laboratory practice. Transfection is a routine method utilised in a wide variety of cross-disciplinary studies, thus this topic is of broad interest and within the scope of the journal. Most of the literature available on this topic is focused on specific products or methods, while an unbiased summary of the field is needed. To my knowledge, such a summary has not been done recently, thus the review by Chong et al is relevant and up to date. The review cites recent publications representing a wide range of opinions in the field. The references are selected based on a stringent and unbiased criteria, the sources are adequately cited. The introduction clearly defines the purpose of the article and its target audience, the conclusions are logical. The review is definitely thorough and comprehensive, the wealth of information is carefully summarized, the text is overall logical and coherent, though some points might be improved. I would recommend this article for publication after a revision.

The following steps could be taken to strengthen the article:

Major English language revision. Grammar mistakes are frequent and the word choice is often imprecise, making the message hard to understand. Some examples include lines 47,60,79,88,325,587.

Paying attention to basic concepts and terminology. According to the introduction, the review is aimed at the wide variety of readers, including those new to the field of transfection. To fulfill this aim the review should accurately introduce the terminology and explain the underlying principles of the methods described before making any technical comparisons. Unfortunately, this is now missing. The article could be useful for the readers who already have some experience in the field, but is largely unsuitable for those unfamiliar with transfection principles.

The part “Common and special oligonucleotides (small ribonucleic acids, RNA)” is largely unclear. It would be useful to briefly introduce the readers to the structure of the small RNAs described (e.g. whether they are single-stranded or double stranded) and the molecular mechanisms of their activity in cells before making the comparison of their efficiency. “Common mimics/inhibitors” should be defined more clearly, possibly with some examples.

Minor remarks:

Figure 1 is not very informative and can be either omitted or expanded (e.g. some examples of each transfection type could be added);

The content of the tables sometimes duplicates the text in the main body of the article (e.g. Table 1 and line 194). Please, paraphrase;

In general, the tables are now very hard to read. Making the text in the tables more concise (e.g. by using bullet points instead of the plain text) would be much appreciated;

The descriptions of chemical structures (e.g. the part about LNAs, agomir/antagomir, etc.) are hard to understand and may require illustrations;
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSFECTION TYPES, METHODS AND STRATEGIES: A TECHNICAL REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	In the review by Zhong et al. the authors describe different transfection methods. The topic of the review is indeed of a great interest to scientific community as transfection is a widely used method with a variety of protocols and applications. This article indeed has the potential to be useful for a novice scientist who is starting to explore field of transfection. However, the organization of the entire manuscript can be improved as in the current state the review is a bit superficial and inaccurate. The main concern is that authors do not explain well the different processes and mechanisms that are foreseen in a technology of transfection. Transfection includes delivery, expression and possible integration, and these processes are not necessarily dependent on each other. The notion of integration is not explained well and sometimes is used inappropriately, e.g. in many cases authors refer to plasmid DNA transfection as a method for stable transfection with integration, which is not always the case.
2.	The English language needs proof-reading to ensure clear understanding of the review. Some examples where the language could be improved include lines 39, 52, 61, 70, 72, 79, 100, 112, 200, 275, 349, 371, 373, 455 – the current phrasing is incorrect or makes comprehension difficult. Here are some examples:
Line 52 integration in, not between
Line 100 Commonly used physical/mechanical transfection methods includes
3.	A brief introduction into the chapters of the review is missing. I would suggest to introduce to the readers that “first we are going to describe X, then Y followed by Z …”
Experimental design: 1.	Please describe in more details survey methodology. Were PRISMA guidelines followed? If so, please consider slightly modifying your Figure 2 intro classical PRISMA flow diagram (http://prisma-statement.org/PRISMAStatement/FlowDiagram), so your survey can be easily followed and repeated. Please indicate considered years of publications. What were the inclusion criteria that are briefly mentioned on line 79?
2.	Figure 1 is described by one phrase “transfection can stable or transient” and in this way is superfluous. Please consider either providing a more detailed classification to visualize “science of transfection” and to help understanding the field or removing the figure. Figure 3 can be improved to make it more informative. Methods can be sorted accordingly to their prevalence. For example, ballistic bombardment is probably not the first method to use among physical methods and it is not even mentioned in the text. Figure 4 can be structured better to make it easier to understand.
3.	Lines 46-54. This paragraph is a little bit confusing. Please either explain the notion of vehicle and vector before, or describe the difference between stable/transient transfection in terms of delivery in general with or without integration into the genome. I would also suggest providing examples when transient or stable transfection is applied, i.e. for what purposes.
-	Lines 46-48 In this phrasing the message is confusing. Does the “use of a vehicle or vector to carry the targeted nucleic acids into the nucleus” will result “in the stable integration of the foreign nucleic acids”? The delivery and integration are separate processes not necessarily dependent on each other. Please correct.
-	Lines 51-52 In this phrasing the message is incorrect. What do authors mean by “vehicle to transport the foreign nucleic acids”? How the nucleic acids are transported then? Liposomes, or calcium phosphate can also be named as delivery vehicles and as such does not assume stable transfection.
4.	Lines 132-141. The paragraph is again confusing. Do authors talk about viral or plasmid vectors, as they mentioned both and this results in misunderstanding. No attempt to structure the information is seen. Moreover, reading the text it seems that any DNA that gets into the nucleus is integrated (e.g. line 149) as the processes of delivery/expression/integration are not divided by authors. Plasmid vectors do not usually integrate into the host genome. Moreover, integration does not “mean” that vector has a specific promotor. Eukaryotic promotors ensure expression of transgene in host cell, independently of integration.  Finally, eukaryotic resistance gene and FP marker is not a common feature for all vectors. Please consider explaining in more details the structure and principles of viral and plasmid vectors, highlighting their main characteristics systematically, and explaining the processes of delivery, expression and possible integration separately.
5.	Lines 167-169. Small RNAs is a big group of different functional RNAs. Please detail about their nature, principles of work and what they are used for.
6.	Lines 211. Talking about combination of plasmid DNAs, authors do not mention the option of bicistronic vectors.
7.	Line 277. It is not clear what do authors meant by un-transfected control? A simple cell culture without any changes? How it would help assessing the transfection? Authors say that it gives information “whether the absence of transfection-related reagents or materials would exert any effects to the transfection outcomes”. How the absence of transfection itself and/or transfection reagent will have an effect on transfection outcome? Please reformulate.
8.	Lines 309-319 Fluoresce analysis of transfection efficiency is not limited to fluorescent dyes linked to DNA, the most common way to assess transfection + expression efficiency is the use of the plasmids that encode for FP.
Validity of the findings: 1.	The main focus of the review seems to be chemical methods of transfection, other topics related to transfection are much less explored. No protocols/principles of stable transfection were described in the review, which makes it less informative.  Authors only briefly mention “viral vectors” without discussing their use, comparing to other methods or highlighting the differences between different viral vectors. Why do authors decide to compare only chemical transfection in terms of efficiency for different cell lines? It would be very useful to discuss also the factors that affect the transfection efficiency of other transfection protocols.
Additional comments: Minor remarks:
Line 40 CRISPR is not the method itself, please correct.
Line 90 Viral transfection is not necessarily stable, e.g. adenoviruses. Please correct.
Line 105 Both necrotic and apoptotic death is possible after electrotransfection (PMID: 14646546).
Line 154 That is true only for DNA-based vectors with a potential to integrate.
Line 161 Again, not all DNA-based vectors are integrated into the genome.
Line 170 Mimic or antagonist of miRNA?
Lines 224-228 Is FRET-based measurement meant there by authors? Investigating PPI has many more approaches besides luciferase reporting system. I suggest either to make it more general, or to name at least some other approaches.
Line 248 Inhibitor or antagonist?
Line 260 plasmid-based transfection is not equal to stable transfection.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSFECTION TYPES, METHODS AND STRATEGIES: A TECHNICAL REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: Since the previous revision, the review by Chong at el has been significantly improved. The review is now easier to read, most of the previous remarks have been taken into account. Certain important clarifications have been added. Nevertheless, the article still has some space for improvement.

As a major remark, I would advise the authors to double-check all the essential terms used in the review and make sure all of them are clearly and unambiguously introduced and explained (especially before being referred to elsewhere in the text). For example, in lines 54-62 there is still a “mixture” of the terms “vector” and “delivery vehicle”, which can be highly confusing for the people new to the field.

The minor remarks include:

Lines 36: CRISPR- Cas9 technology is not classified as a transfection strategy.
Line 56: Grammatically Incorrect or incomplete sentence. Ranging from … (to?).
Lines 54-62: the terms “vector” and and “delivery vehicle”.
Line 102: retroviruses include lentiviruses, so “and” can not be used here.
Line 16: other drawbacks and difficulties of viral transfection could be added; the fact that not all viruses have integrases could also be mentioned.
Line 183: please, describe the viral-like vectors in more detail; the technology and its advantages are unclear now; in line 186 cell line examples could be added.
Line 203: a word missing.
Line 299: the gene for guigiing RNA is missing.
Lines 319-320: why in “particular cell types?” (Line 319);  Please, specify the cell type in the example which follows.
Line 463: Human primary stem cellS.
Line 511:  the cell lines should probably be called “immortalized”, not “secondary”.
Line 551: ...involving primary human myoblasts cells…, “cells” can be omitted.
Line 570: “Reduced or serum-free media are normally recommended…” What is meant by “reduced media” here? The paragraph elaborates only on the serum issue. Please, substitute for “serum-reduced” (if it is the case) or explain otherwise.
Line 590: complexes.
Line 655: correlated with.
Table 2: In the Electroporation column, Cell type should also be mentioned
Experimental design: Study design is adequate and raises no questions.
Validity of the findings: The goals set out in the introduction are close to be fully achieved.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSFECTION TYPES, METHODS AND STRATEGIES: A TECHNICAL REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: The review by Chong et al. has improved significantly from the previous version. The idea of the review is clear, the material is quite well organized and easy to read. Suffiecient background is provided. Probably, for a person unfamiliar with the field of transfection, this review will serve as a good help to dive into this topic. The Introduction adequately introduce the subject. The review will be ready for publication after some details have been corrected.
Minor corrections:
L. 13. I would use the term “deliver” instead of “insert”
L. 36-37. CRISPR is not a transfection strategy,
L. 54-62. Authors again do not explain the terms of “vector construct” and “transfection vehicle”. It seems that they confuse again the right terms. How DNA plasmid can be a vehicle itself? What if DNA plasmid is delivered via chemical vehicles? Please provide a clear explanation for the terms.
L. 59-62. The comparison makes no sense, one part is about promoter, another is about cellular entry. Viruses also facilitate the entrance into the cell, DNA plasmids within lipid complex can also have eukaryotic promotors.
L. 101-102. Lentivirus IS a retrovirus.
L. 109. Please, specify, which viruses carry an integrase.
P.1.1 Please, specify, what are the drawbacks of using viruses for stable transfection via genome integration. Talking about pros and cons of different commonly used viruses for transduction would be very helpful. Please mention the AAVs, one of the most common tools in gene therapy.
L. 126. Primary cells. If authors want to name difficult-to-transfect cell LINES that are easly electrotransfected, they can name B cell lines (PMID: 32999452).
L. 203. DNA integration into the genome.
L. 299. CRISPR/Cas9 and guide RNA genes.
L. 341. It seems that the described negative control is specific for small RNA transfection experiments, not for DNA plasmid transfection, for example. Please, specify or explain that as well as the notion of non-homology sequence.
L. 342. “interference to the host cells post-transfection” – please reformulate.
L. 357. Not all transfections are performed for the purpose of “post-transcriptional regulation”, please reformulate.
L. 379. in the case of fluorescence reporting gene (one of the most common case), flow cytometry quantifies cells that express a fluorescent gene, not “specially tagged cells”.
L.381-387. Apart immunoblotting, immunofluorescent staining is also commonly used to assess protein expression after transfection.
L. 461. Primary cells, not primary cell line.
L. 463-476. What about iPSCs transfection efficiencies?
L. 478, 481. Again, primary or stem cells.
L. 511, 525. I would suggest to avoid the term secondary and refer to them as “human cell lines”
Table 2. Electroporation: another influencing factor of electroporation condition is the number of pulses and cell type as well as for other transfection methods.
Fig. 2. MagneTofection; please, mention AAV.
Experimental design: The Survey Methodology is consistent with a comprehensive, unbiased coverage of the subject. The review is organized logically into coherent paragraphs/subsections.
Validity of the findings: The goals set out in the introduction are close to be fully achieved.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSFECTION TYPES, METHODS AND STRATEGIES: A TECHNICAL REVIEW
Review round: 3
Reviewer: 1

Output:
Basic reporting: The article has significantly improved after the second round of revision. All the reviewers' comments have been taken into account, the article is now much more accurate and new relevant information has been added, as well.
In the revised text, two very minor corrections should be made:
Line 185: Please, explain how the packaging capacity and viral tropism are related (if they are) or remove 'thus' (if they are not).
Lines 132 and 191 completely repeat each other. One should be removed.
Apart from these, the article is ready to be published in its current form and I believe that no further peer revision is required.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: TRANSFECTION TYPES, METHODS AND STRATEGIES: A TECHNICAL REVIEW
Review round: 3
Reviewer: 2

Output:
Basic reporting: The review is ready to be published, however, I would suggest authors to re-read carefully the manuscript as still some mistakes are remaining.

Line 135: the connection with previous sentence via “thus” is unclear; how packaging capacity and cell tropism are interconnected?
Lines 136-138: repetition, please delete.
Line 322: guide RNA is not equivalent to CRISPR, please correct.
Line 417: immunofluorescent staining does not require the specific antibodies to be fluorescently labelled, the use of secondary fluorescently labelled antibodies is possible – as secondary HRP-conjugated antibodies in immunoblotting. Please, correct.
Line 723: Please use “there is no single method” instead of “there is no a single method”
 Figure 2: magneTofection, not magnefofection, please correct.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE EXO70 GENE FAMILY IN GRAPE (VITIS VINIFERA L)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The abstract describes research context, briefly introduces the research method and states the research outcome and future expectation. In terms of the background context, it generally states the definition of EXO70 gene family, its function and the current inefficiency of knowledge on EXO70 gene family. After that, the abstract describes the process of the experiment and finally puts out the findings of the study comprehensively and coherently. In the final part, it provides us with the purpose and goal of this paper as well which makes sense to us what the authors are going to do.
    The introduction generally gives us a detailed description of EXO70 gene family including the definition, functions and its working essence by providing some examples, interpreting its discovery and development history, which I think makes us a relatively complete understanding and knowledge of EXO70 gene family
    This part first of all directly tells us two methods used to identify EXO70 genes and then a description of detailed procedures of how they carry out the experiment and do analysis. These processes are aligned in order of experimental logic and each analysis subsection is stated briefly and coherently. Analysis tools and techniques are also displayed in each analysis part so that we could get more idea of how they do it. Methods used are sound and data interpretation is up to the mark.
    The results part displays the outcome of the series of modelling analysis and test in the logic order in Methods part. The analysis results are put out by listing concrete data, including numeric data, statistical graphs and figures, in a specific and complete way to me.
    The discussion part discusses the findings discovered in the paper, including explaining how the findings come out and interpreting the results in more details, which gives us a supplementary understanding of the results obtained in the paper.
    Overall, the paper gives us a detailed understanding of the characteristics of EXO70 gene family by carrying out a series of experiment and statistical analysis in a logical order. Except for some minor errors, the paper is a complete, detailed one that interprets EXO70 gene family and leaves us open research areas to further explore the characteristics of EXO70 genes.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I have raised some related question which is mentioned in the detailed comments.
Point 1: Authors should carefully recheck the manuscript for the typos and scientific styles. For example, line-17 collinearity and selective pressure, codon bias, tissue expression and the like.
Point 2: The English was mostly understandable.
Point 3: Line 34-35, Please rephrase the sentence.
Line 35, When plants are under stresses, user stress??
Point 4: line 84, “and so on. And through”.?? rephrase
Point 5: In the material and method section, rephrase the heading 2.2
Point 6: line number 136, formatting error.
Point 7: In many paragraph repetitions of these words “In Addition, these results" etc.
Point 8: line 452-459, need to add more explanation with fold change.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE EXO70 GENE FAMILY IN GRAPE (VITIS VINIFERA L)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well written, although some typos and in few cases a clear form should be used, as mentioned in the comments.
The literature is enough rich
The article is well structurated
The article is an unique body and the studies conducted are coherently with the aims.
Experimental design: The experimental design, the methofs and the tools used are coherent
Validity of the findings: All data are strongly validated
Additional comments: Author you should consider that all the periods from line 195 to 207 are descriptions which deals with putative location of each gene; therefore, You must use a conditional form in the sentences in which you describe the results.
Line 198, delete the point from “…. abundant.in cytoplasm… “
Lines 199-201. Change the phrase from “VvEXO70-02, VvEXO70-03, VvEXO70-05, VvEXO70-07, VvEXO70-10 and VvEXO70-11 didn't exist in chloroplast but VvEXO70-08 was the highest abundant,” TO “VvEXO70-08 scored the highest probability to be present only in the chloroplast”
Line 201, delete the comma after the word abundant and insert the full stop.
Line 206, delete the full stop after the VvEXO70-05
Line 230 delete the word gene
Line 275 and 276, Authors use correct diction of  “the synonymous mutation frequency (dN) and the non-synonymous (dS)” therefore change as follow of  “the synonymous mutation frequency (ds) and the non-synonymous (dN)”. Correct in all other part of the text.
Line 276 mutation frequency (dS) and the ratio of dN/dS. The value of dN/dS plays an important role in gene
Caption of Figure 5. Correct this sentence in figure’s caption since it is not clear “Red indicates the lowest similarity, followed by orange, green and blue, indicating the decreasing similarity.” To avoid misunderstanding therefore change in “mutation, mainly including the synonymous mutation frequency (dS) and the non-synonymous (dN)”
Line 276 mutation frequency (dS) and the ratio of dN/dS. The value of dN/dS plays an important role in gene
Line 359 you should write in the extended form of the word Fig. 7: figure 7
Line 378: change from substances to proteins
Lines from 385 – 387: adjust better the phrase it is not clear!
Line 3091: what means etc. do you know publication related to other plant species or not?
Along the text after the first mention of Arabidopsis thaliana for the following time use A. thaliana in the italic form.
Caption of figure 7: Author you should insert the statistical analysis and indicate if the replication are generated from three biological replication or not.
Use italic form for all gene name
After the first mention of Arabidopsis thaliana all the time you mention this species you should use the contact form like A. thaliana, written in the italic form


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE EXO70 GENE FAMILY IN GRAPE (VITIS VINIFERA L)
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English language is clear enough but some sections of the article such as the discussion need to be improved.
Introduction and background showing perfectly the context of the study. The literature should be updated since most of them are before 2010, I think is also better to cite more the international published papers in this study.
The structure conforms the PeerJ standard.
Figures are relevant but the quality should be improved.
Experimental design: The research is so interesting and is within the scope of this journal.
Research is well defined and the methods is defined with suficient details.
Validity of the findings: The data provided are statistically sound and are robust. The discussion should be improved in the actual version is more reporting the results. Conclusions are well stated.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE EXO70 GENE FAMILY IN GRAPE (VITIS VINIFERA L)
Review round: 3
Reviewer: 1

Output:
Basic reporting: Now is ready for pubblication
Experimental design: it is ok
Validity of the findings: the area could be the plant molecular physiology
Additional comments: The manuscript was improved


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CHEMOSENSITIVITY AND ROLE OF SWIMMING LEGS OF MUD CRAB, SCYLLA PARAMAMOSAIN, IN FEEDING ACTIVITY AS DETERMINED BY ELECTROCARDIOGRAPHIC AND BEHAVIOURAL OBSERVATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is written in understandable English.

Sufficient back ground is provided.

Article structure and figures are fine.

Table 1 and 2 lack details, number of samples, mean of the value.

Average and standard error of pretest and test should be shown in the table or in a graph.

Behavioral result is qualitative but not quantitative. Number of trials and number of observations of behavior of interest should be provided.

I did not find raw data.

The manuscript is self-contained.
Experimental design: This is an original primary research within Aims and Scopes of PeerJ.

Main research question is simple, "Do dactyl of swimming leg have chemo sensory function in the green mud crab?" and well defined. Since the swimming leg is one of pleopods that had been reported as chemosensory organ and thus, the question is not so novel. However, testing swimming leg in this species is novel.

The experiments were performed rigorously and to a high technical standard. Ethical issue is fine.

Method description is fine.
Validity of the findings: Quantitative information of behavioral experiments (number of trial and observation and statistical test) are missing.

Main conclusion, "Dactyl of swimming leg has chemo sensory function in the green mud crab." is fine, however, the experiments in this research can not conclude that a part of bodies tested does not have mechano- or chemoreceptor. The part should be rewritten.
Additional comments: The manuscript entitled “Swimming legs are chemosensitive and involved in feeding in the mud crab Scylla paramamosain as　determined electrocardiography and behaviourally (#51510)” reports that the dactyls of the swimming legs of the mud crab have chemical sense. This finding is new and supported by the data presented. Electrocardiography is a reliable method when it shows positive response but we can not conclude that “the dactyls of swimming legs and the antennules are not mechanosensitive; the antennae are not chemosensitive based on the result. It is known that the antennule has mechanoreceptors in other decapods (ex. Kamio and Derby 2017). This is partially because electrocardiography is not direct measurement of chemosensory input in chemosensory neurons. It is a recording of changes in heart beat that is caused by input from the central nerve system that integrates multi-sensory inputs. Thus, negative data in electrocardiography does not mean that the crab is not sensing the stimuli. There might be sensory inputs that does not make changes in electrocardiograph. Overall, this manuscript has novel finding but need to correct overstatements. I recommend authors to rationalize the method, electrocardiography, explaining not only its strength but also its weakness. Behavioral result racks quantitative data. Please show data as table or graph. Please show number of crabs showed and did not show the response. I think this manuscript is publishable after revision.

Kamio, M. and C. D. Derby (2017). "Finding food: how marine invertebrates use chemical cues to track and select food." Natural Product Reports 34(5): 514-528.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CHEMOSENSITIVITY AND ROLE OF SWIMMING LEGS OF MUD CRAB, SCYLLA PARAMAMOSAIN, IN FEEDING ACTIVITY AS DETERMINED BY ELECTROCARDIOGRAPHIC AND BEHAVIOURAL OBSERVATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study characterises the sensory function of the appendages which is important and fundamental in understanding the feeding behaviour of mud crab. However, there is no clear problem or problem statement that emphasise on the needs or importance to perform this study, that is to determine the sensory function of appendages, hence making the study less interesting, and merely just characterising. It would be interesting to relate the problem of feeding of mud crab in nature or in aquaculture. For example slow eating behaviour of mud crab leads to nutrient leaching of feed that deteriorates water quality, hence reducing feed efficiency and increasing feed cost. By understanding the sensory function and feeding behaviour of mud crab in this study, feeds and feeding of mud crab can be optimized to cater its natural feeding physiology and behaviour. English is acceptable but there are some grammatical/typing errors that needs to be rechecked. Include more literature on the importance of the appendages and its sensitivity in feeding or daily activities. Also elaborate more on the fundamental concept of the methodology used especially on the electrocardiography and sensitivity so that readers have better understanding on the trend of the graph (electrocardiogram). The manuscript also lacks hypothesis in order to justify the results.
Experimental design: Experimental design should be explained in detail especially on the video recording of the feeding behaviour. What kind of feeding behaviour that was analysed? The chronology of procedure for stimulation of crab using touch and chemical is a little confusing. Was the cauterisation of antennules performed after touch stimuli and before chemical stimuli, OR even before the touch stimuli. Please be clear. Authors mentioned that all procedures were conducted according to the approved ethical standards, but was the cauterisation performed without any anaesthetic? Anatomy of mud crab showing the appendages will be helpful. At the current state of the manuscript, the only knowledge gap is that this study was conducted in some other crustacean species but has not been performed in S. paramamosain. As mentioned in the basic reporting, there is no clear problem or problem statement of the study, therefore the contribution towards filling the knowledge gap is not clear as well. In general, parameters studied in this work is insufficient as an original paper. Perhaps it is more suitable for short communication.
Validity of the findings: Authors claimed that the swimming legs were chemosensitive to sugarcane juice and salted fish, and the kicking motion was not triggered with a single touch stimuli. Just a thought, can it be that the single touch was just in a short moment (just a touch) and insufficient time to trigger a movement/reaction, while the sugarcane juice spreads throughout the water volume and stays for longer period of time, enough to trigger the chemoresceptor that is not from the swimming leg? Similar to the salted  fish flesh in regards to the chemosense, with the addition to being placed at the swimming leg long enough to trigger a reaction compared to the single touch stimuli, hence may be related to the flaw of experimental design? Possibly, an object without smell should be placed similarly as the salted fish flesh and clear water should be delivered at the appendages using a pipette such as for the sugarcane juice in order to omit the possibility of rheotaxis effect.  How confident are the authors to stand by the claims should be discussed in detail with supportive references since not much data were obtained from this study.
Additional comments: Most comment were covered by the 3 areas above.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CHEMOSENSITIVITY AND ROLE OF SWIMMING LEGS OF MUD CRAB, SCYLLA PARAMAMOSAIN, IN FEEDING ACTIVITY AS DETERMINED BY ELECTROCARDIOGRAPHIC AND BEHAVIOURAL OBSERVATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Description of results need to be modified.

(1) Result of behavioral experiment is only qualitative but not quantitative. Number of trials and number of occurrence of feeding behavior should be provided in the manuscript.

(2) Line 178 needs to be rewrite because T-test is not applicable on this data. This case compares 10 pre-test IBIs and a Test-beat (see table 1&2) from an animal. Thus, in table 1 and 2, * denotes that the Test-beat is out of 95% confidence interval calculated using 10 pre-test IBIs.
Experimental design: No comment
Validity of the findings: Description of results need to be modified.

(1) Result of behavioral experiment is only qualitative but not quantitative. Number of trials and number of occurrence of feeding behavior should be provided in the manuscript.

(2) Line 178 needs to be rewrite because T-test is not applicable on this data. This case compares 10 pre-test IBIs and a Test-beat (see table 1&2) from an animal. Thus, in table 1 and 2, * denotes that the Test-beat is out of 95% confidence interval calculated using 10 pre-test IBIs.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: CHEMOSENSITIVITY AND ROLE OF SWIMMING LEGS OF MUD CRAB, SCYLLA PARAMAMOSAIN, IN FEEDING ACTIVITY AS DETERMINED BY ELECTROCARDIOGRAPHIC AND BEHAVIOURAL OBSERVATIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors have made the necessary changes on the manuscript.
Experimental design: The experimental design was clearly explained and aligned with the objective of the study.
Validity of the findings: Findings are well discussed and concluded.
Additional comments: No comment.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: FIRST REMAINS OF THE ENORMOUS ALLIGATOROID DEINOSUCHUS FROM THE UPPER CRETACEOUS MENEFEE FORMATION, NEW MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: The geologic setting and fossil occurrence section requires a reorganization to better flow logically. The Systematic Paleontology section should not be split up. See specific comments on attached pdf.
Experimental design: The research question is not well defined or meaningful. A new specimen of Deinosuchus is identified without much discussion on its importance. The authors attempt to argue that this specimen is one of the oldest specimens in Laramidia, but do not comment on why this is important on the evolution of this taxon. See specific comments on attached pdf.
Validity of the findings: Conclusions are a bit confusing and not well supported by the data. The authors should expand their discussion to include  more robust comparisons to scutes to all species of Deinosuchus and to other closely related taxa. See specific comments on attached pdf.
Additional comments: See specific comments on attached pdf.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: FIRST REMAINS OF THE ENORMOUS ALLIGATOROID DEINOSUCHUS FROM THE UPPER CRETACEOUS MENEFEE FORMATION, NEW MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is fairly simple and straightforward: they report a new occurrence of a well-known organism represented by a few osteoderms, two vertebrae and a fragmentary tooth. The major new detail in the article is the claim that this is an older occurrence on the western side of the continent.  I have no disagreement with the technical details, except regarding some of the terminology for descriptions and age-ranges, detailed in the "validity" discussion below.
  The formatting, image quality, etc. seem fine. I would have preferred an additional image in Fig. 2 to show the thickness of the holotype osteoderm for comparison.
Experimental design: This is an observational report so "design" is not really relevant. It follows traditional formatting. The overall material is acceptable with a few minor issues below.
Validity of the findings: There is no doubt that the specimen reported are Deinosuchus osteoderms and vertebrae. However, I am not convinced they are very different from typical Deinosuchus riograndensis osteoderms (the vertebrae and tooth are nondescript). The authors here seem to imply they conform more closely with those of D. hatcheri based on "inflation." However that is not what I observe in their figure 1Cand 1F, and it is notable they do not figure a side view of the holotype D. hatcheri material to provide a comparison. I would like a bit more detailed measurement and imaging of this.
  Additionally, the age issue is interesting. Accepting their age for this occurrence at 79 Ma, that may indeed be old for the Laramida subcontinent, but it is 3 Ma younger than the oldest reported eastern occurrence. Three Ma is a significant difference which they gloss over by reporting their material as "roughly 80 million years (line 362)," and indicating age equivalence in their fig. 6.  I believe this is significant when we try to figure out the origins of Deinosuchus species: if they are all equally old occurrences it suggest a different pattern than if one population on the various sides of the seaway is older than the other. By selecting 79 Ma as the boundary of "older" and "middle" age populations, they may create a false impression of simultaneous appearances.  I would like it to be explicitly pointed out that this old Laramida occurrence is still notably younger than the oldest in Appalachia.
Additional comments: A few editing suggestions:

line 53 and elsewhere: there is no "middle Campanian" so I suggest "mid-Campanian" as the proper usage.
line 148 and elsewhere "in-situ" is thus.
line 171: the citations are in no order. Should be by date sequence.
line 189: cross-hatching misspelled
line 199: I'm not sure "inflated keel" is the correct term. Many 'derms lack keels at all, especially in the D. hatcheri type. Also, many osteoderms from Appalachia are quite thin (see Cossette and Brochu 2020, fig 26)
line 292: please note my comments about the age of this specimen. Note that 79 Ma does not "closely overlap" with the oldest Appalachian occurrence. This creates a false equivalency.
line 360: the term "associated skeleton" is a bit exaggerated for 6 'derms, 2 vertebrae and a fragment of tooth. This association is about 2% of the skeleton.
References: I notice there are no pages cited for Schwimmer (2002). it's 219 p.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: FIRST REMAINS OF THE ENORMOUS ALLIGATOROID DEINOSUCHUS FROM THE UPPER CRETACEOUS MENEFEE FORMATION, NEW MEXICO
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript was well-written and generally a good review for the limited scope of the paper. I see no issues with the structure of the manuscript or references included therein.  There are a few errors or stylistic points outlined below:

Line 20: add "partial" to “tooth".
Line 65: delete a ")".
Line 117: check style whether in situ should be italicized.
Line 122 (throughout) check spacing between measurements and units.
Line 201: "from one end of the centrum to the other” craniocaudal?
Experimental design: The experiment in this case is a comparison between scutes. Though I believe the authors have a strong argument for their identification, the comparisons are fairly short and qualitative. In fairness, this is not the author’s fault and directly related to the scrappy nature of the Deinosuchus fossil record. Also on line 215, the authors briefly introduce the tooth and mention that previous authors have used enamel thickness to identify species (though this criteria was recently rejected by Cossette and Brochu, 2020). The authors state “...an evaluation of enamel can be taken.”, but don’t provide measurements or comparisons on this matter.
Validity of the findings: I have no issues with the findings and conclusions. I believe the authors are cautious not to overinterpret their results.
Additional comments: Overall, it is a good manuscript that provides another data point for one of the most interesting Cretaceous species from North America.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ASSOCIATION BETWEEN BODY MASS INDEX AND BLOOD PRESSURE LEVELS ACROSS SOCIO-DEMOGRAPHIC GROUPS AND GEOGRAPHICAL SETTINGS: ANALYSIS OF POOLED DATA IN PERU
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study Association between body mass index and blood pressure levels across socio-demographic groups and geographical settings: analysis of pooled data in Peru seems interesting to me. The aim of this study is to assess the association between body mass index (BMI) and blood pressure levels, and how these associations vary between socioeconomic groups and geographical settings.
Experimental design: No comments
Validity of the findings: Mayor concern

It is not clear how the statistical models were constructed.

It would be important to know the models with their beta values and their statistical significance values.

In the supplementary document and specifically in model three, when the effect modification related with sex was evaluated, I wonder why the variable sex alone and its corresponding Beta value were not included as recommended. What statistical criteria were used to decide that there is an effect modification?

The authors did not mention why did not evaluate the presence of collinearity in the different models. Nor do authors mentioned anything in relation to the assumptions of the regression used.

I think that the section on limitations is needed, for example, would have been very enriching to include other types of variables such as dietary consumption, physical activity and some comorbidities as adjustment variables, since they are variables that are always measured almost as a rule in surveys.

Minor concern:
Check the numbers, since they do not match: Excluded 21,294, total evaluated, total analyzed 159,940

Regarding Tables 2 and 3, I suggest clarifying whether they are unadjusted estimates.

I think that in the discussion section it is necessary to include information on the possible mechanisms of how BMI causes the systolic and diastolic pressure levels to rise, supported in the literature.
Additional comments: The study Association between body mass index and blood pressure levels across socio-demographic groups and geographical settings: analysis of pooled data in Peru seems interesting to me. The aim of this study is to assess the association between body mass index (BMI) and blood pressure levels, and how these associations vary between socioeconomic groups and geographical settings.

Mayor concern

It is not clear how the statistical models were constructed.

It would be important to know the models with their beta values and their statistical significance values.

In the supplementary document and specifically in model three, when the effect modification related with sex was evaluated, I wonder why the variable sex alone and its corresponding Beta value were not included as recommended. What statistical criteria were used to decide that there is an effect modification?

The authors did not mention why did not evaluate the presence of collinearity in the different models. Nor do authors mentioned anything in relation to the assumptions of the regression used.

I think that the section on limitations is needed, for example, would have been very enriching to include other types of variables such as dietary consumption, physical activity and some comorbidities as adjustment variables, since they are variables that are always measured almost as a rule in surveys.

Minor concern:
Check the numbers, since they do not match: Excluded 21,294, total evaluated, total analyzed 159,940

Regarding Tables 2 and 3, I suggest clarifying whether they are unadjusted estimates.

I think that in the discussion section it is necessary to include information on the possible mechanisms of how BMI causes the systolic and diastolic pressure levels to rise, supported in the literature.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ASSOCIATION BETWEEN BODY MASS INDEX AND BLOOD PRESSURE LEVELS ACROSS SOCIO-DEMOGRAPHIC GROUPS AND GEOGRAPHICAL SETTINGS: ANALYSIS OF POOLED DATA IN PERU
Review round: 1
Reviewer: 2

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: The authors aimed to assess the association between body mass index and blood pressure levels across socio-demographic groups and geographical settings, by using data from different Peruvian Demographic Health Surveys. I would like to congratulate the authors for such an interesting topic and its novel approach. However, I believe that some aspects should be addressed in order to improve the final version.

Major comments:
1. I understand that the ENDES have different sampling frames for a group of years (eg. the sampling frame for 2018-2020 is different from other years). Polling data from years with different sampling frames could lead to incorrect estimates due to problems in weighting (at least this was considered on the first steps of the analysis. If so, please note the process for polling the data that you have performed)
2. How did you perform the t-test for svy? In addition, it is important to mention that the usual version of the Chi2 (pearson) is not adequate for svy analysis. The authors might have used the Rao-Scott chi-square test.

Minor comments:
Introduction
Lines 68-72: This sentence is too long. Please split it on -at least- two.

Methods:
Line 88: Please explain why you included adults aged 20 and over (and not 15 and over)
Lines 112-113: Please explain why you decided to categorize the education level in years instead of primary, secondary, university...


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ASSOCIATION BETWEEN BODY MASS INDEX AND BLOOD PRESSURE LEVELS ACROSS SOCIO-DEMOGRAPHIC GROUPS AND GEOGRAPHICAL SETTINGS: ANALYSIS OF POOLED DATA IN PERU
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments. My mayor concern were taken into account.
Experimental design: No comments
Validity of the findings: No comments
Additional comments: No comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: ASSOCIATION BETWEEN BODY MASS INDEX AND BLOOD PRESSURE LEVELS ACROSS SOCIO-DEMOGRAPHIC GROUPS AND GEOGRAPHICAL SETTINGS: ANALYSIS OF POOLED DATA IN PERU
Review round: 2
Reviewer: 2

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: The authors have responded to all comments and suggestions. I consider that the manuscript is now suitable for publication.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: WIDELY ASSUMED PHENOTYPIC ASSOCIATIONS IN CANNABIS SATIVA LACK A SHARED GENETIC BASIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment - nicely done - just have recommendations in next section for improving clarity
Experimental design: Recommend setting up the thesis of the paper more clearly. I see two main points: 1) Traits that are correlated may share common developmental pathways which would inhibit selecting for new combinations of traits. The authors investigated this by assessing the correlation in traits at early and later developmental time points and found that traits were not correlated, for the most part, and are likely inherited independently. The authors hit on this in several places, including the Conclusions section, but I would like to see the hypothesis clearly set up in the introduction.

2) Many commercially important traits in cannabis are expressed at maturity. If breeders could predict late stage expression via correlations with traits expressed earlier during development, selections could be made sooner and breeding cycles accelerated. The authors did the analysis to test this hypothesis (discussed on pg 13-14), but I would like to see the hypothesis set up in the introduction and then discuss whether the hypothesis is supported or rejected.  Similarly, the authors bring up the important point about identifying male and female plants - if early traits distinguished the sexes, males could be culled before contaminating field with pollen and reducing yield. Unfortunately, this doesn't appear to be the case, but their findings are valuable and bear reporting!

There is also the question of classification of plants. I don't see this as a major point of the paper since it has been covered extensively in other literature. However, it is relevant to introduce and re-emphasize that historical classifications and associated nomenclature are not supported by this investigation or other scientific work. Authors discuss findings related to this on p14 line 282-285, but need to give context as to why the findings are important.
Validity of the findings: p14, line 242-245 - seems like there are other explanations for lack of correlation between timepoints - were there differences in flower initiation time or maturation time? some plants "stretch" more than others - i.e., they grow more during the flowering stage than others - and there are also differences in apical dominance between varieties, which impacts the relationship between height and #nodes.
Additional comments: Minor edits

1. p6, line 47. need to add "possibly" or "may be" before "causally associated" since you aren't testing that specifically.
2. p6, line 62-63. wild populations that share ancestral traits would have a common ancestor and would not inherit independently.
3. p7, line 79-80. cite Laverty et al. and the BioRxiv papers that show the physical location of cannabinoid synthase genes
4. p8, line 98-100. cite Clarke and Merlin for the lineage definitions.
5. p13, line 217 add links
6. p20, line 371. THCA synthase may be a better competitor than CBDA synthase for the CBGA precursor, but THCAS could also be expressed at higher levels than CBDAS in these plants. Are there expression data that could help disambiguate?
7. p21, line 390. clarify what "this" is referring to in the introductory sentence
8. p21, replace "strain" with "variety" or "cultivar" as appropriate
9. p21, line 406-408. I agree that we need to do a better job of getting information out to the public and to make sure that we're doing all we can to make sure that research informs policy, medicine, etc.! Maybe break these two points into two sentences for clarity.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: WIDELY ASSUMED PHENOTYPIC ASSOCIATIONS IN CANNABIS SATIVA LACK A SHARED GENETIC BASIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written and describes all the methods clearly. The authors have looked extensively at the phenotypic and morphological changes in the inter-crossed lineages and performed correlation analysis.
Some concerns:

1) The authors need to change the title as they are not looking at any gene analysis of the species.
2) Grammatical errors in line 154 and line 368. Please check.
Experimental design: The experiments are well set up extensive endpoints have been measured.
It will be helpful if you can justify why you backcrossed male with female F1 offspring of the cross.
Validity of the findings: The authors have found some interesting results and point out a gap in the way cannabis nomenclature is adopted. The results can be further very useful in studies related to crossbreeding techniques in cannabis.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: WIDELY ASSUMED PHENOTYPIC ASSOCIATIONS IN CANNABIS SATIVA LACK A SHARED GENETIC BASIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Yes, meets the criterion.
Experimental design: Well designed research.
Validity of the findings: Data supported by valid evidence based research.
Additional comments: The manuscript entitled "Widely assumed phenotypic associations in Cannabis sativa---." is an important study conducted by the authors. The manuscript is well written, and research is well supported by data.
The manuscript can be accepted after minor revision.
Few typo errors need to be fixed.
Line 95 Give a period after the sentence 2012).
Line 218 R studio, give space
Line 468 D uppercase for difference
Line 500 G uppercase for geomorph


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PREVALENCE OF DEPRESSION AND ITS IMPACT ON QUALITY OF LIFE IN FRONTLINE OTORHINOLARYNGOLOGY NURSES DURING THE COVID-19 PANDEMIC IN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: This is an online survey, which aimed to examine the prevalence of depressive symptoms and its association with quality of life among frontline otorhinolaryngology (ENT) nurses in China during the COVID-19 pandemic. Though this is a well-organized manuscript, I have some comments for the authors for their consideration.
1. Authors mentioned that this is a national survey. However, subjects are from the online platform. How to define the “national survey” in this article?
2. Three additional questions were used, but not be validated. The Cronbach alpha value should be considered.
3. why do authors only use the first two items of WHOQOL- BREF? This is not a common way.
4. Authors mentioned that a total of 1,757 frontline ENT nurses participated in this study. However, I would like to know the response rate or completing rate. How many people refused to answer this survey? or How many questionnaires were eliminated due to the certain reasons, such as logistic errors, incomplete questionnaires?
5. Authors should describe the specific covariates. Please add them.
6. How do authors consider the collinearity? Such as a potential correlation between junior clinicians and working experience
7. Based on the criterion of P< 0.1, why not include the age (p=0.084) in the multiple logistic regression analysis.
8. Authors did not mention gender in this manuscript. I guess that all samples are female. But authors should describe this part.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PREVALENCE OF DEPRESSION AND ITS IMPACT ON QUALITY OF LIFE IN FRONTLINE OTORHINOLARYNGOLOGY NURSES DURING THE COVID-19 PANDEMIC IN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: The representativeness of the sample for otorhinolaryngology nurses during the COVID-19 pandemic in China is unclear, because there is no sampling frame. Selection bias exist.
Validity of the findings: no comment
Additional comments: This survey used snowball sampling and  WeChat-based Questionnaire Star program and investigated 1,757 frontline otorhinolaryngology nurses on depression symptoms and quality of life. Prevalence of depression symptoms in this population was estimated. However, I have several concerns as follows:
1. The representativeness of the sample for otorhinolaryngology nurses during the COVID-19 pandemic in China is unclear, because there is no sampling frame. How many provinces and hospitals involved? Selection bias exist.
2. Less information on quality control was provided. How did the investigators verify those who WeChat-based Questionnaire were otorhinolaryngology nurses? In adidition, because people with mental health problem tend to take part in this problem, is there any bias on this sample?
3.  The  online survey initiated by the Chinese Nursing Association Otolaryngology Branch between March 15 and March 20, in China. Actually from January, China has introduce a series of policies on the prevention and control of COVID-19 in each level of hospitals. Is there any evidence on the daily outpatient visit or the number of hospitalized patients in the hospitals and otolaryngology department? Because this may influence the clinical workload of the ENT units.
4. Besides primary and tertiary hospital settings, is there second-class hospitals included?
5. The authors used PHQ-9 to measure the severity of depression. The duration measured was within 2 weeks, which should be clarified.
6. The authors said "After controlling for covariates, nurses with depression were more likely to have overall lower QOL than those without". The covariates which controlled should be displayed. Besides, is this result showed in Table 1?
7. Table 2 showed the results of  multiple logistic regression analysis which examine the Independent correlates of depression. But I did not find the QOL in this model.
8. "All health professionals must have at least two weeks quarantine after they finished providing care to COVID-19 patients, which may put them in anxiety state and guilty feelings due to social stigma on their families." Is there any reference for this?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PREVALENCE OF DEPRESSION AND ITS IMPACT ON QUALITY OF LIFE IN FRONTLINE OTORHINOLARYNGOLOGY NURSES DURING THE COVID-19 PANDEMIC IN CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: none
Experimental design: none
Validity of the findings: none
Additional comments: none


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: PREVALENCE OF DEPRESSION AND ITS IMPACT ON QUALITY OF LIFE IN FRONTLINE OTORHINOLARYNGOLOGY NURSES DURING THE COVID-19 PANDEMIC IN CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thank the authors for considering my suggestions. I have several concerns before the publication:
1. The authors mentioned "the exclusion of participants with pre-existing mental health problems", how did they excluded participants with pre-existing mental health problems? On the contrary, I guess people with mental health problems were more likely to take part in this kind of survey, because they could be more concerned about their mental health.
2. The authors said "the data were collected online using smallball sampling with the Questionnaire Star program which has been widely used in many epidemiological studies. Therefore, certain variables, such as ... and participating hospitals, could not be recorded or calculated". Actually it is a limitation in the survey Questionnaire designing. They could have added items for information on participating hospitals and even the identity of participants.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EVALUATING ALTERNATIVE HYPOTHESES TO EXPLAIN THE DOWNWARD TREND IN THE INDICES OF THE COVID-19 PANDEMIC DEATH RATE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is, overall, well-written. However, the authors have assumed that the reader already has a relatively high background knowledge. It would be helpful if the introduction also explained some of the basics about recording of deaths from COVID-19 and the issues associated with this. In lines 36/37 it is stated that "an estimate of true death rate is rather difficult for several reasons." However, those reasons are not outlined (which they should be).

All terms should be defined, e.g. CFR, IFR, Rt.

The headings of the different hypotheses should be carried over to the results section as well. At the moment, the reader needs to refer back to earlier sections in order to remember which hypothesis is being discussed.
Experimental design: The experimental design is unusual in that a list of hypotheses is being tested using publicly-available information.

While the data sources have been identified in the main text, the actual original methodology is outlined in the supplementary files. I am unsure whether this is consistent with the style of the journal, but there at least needs to be some reference to the supplementary files.

It is unclear whether there was a systematic search for data, although the lack of a search strategy would indicate that this has not happened. This would be the expected standard to address the study questions. The authors need to clearly state why they haven't conducted a systematic review.
Validity of the findings: It is likely that the downward trend in COVID-19 death rate is multi-factorial, potentially contributed to by all the stated hypotheses. The authors state this and indicate the potential strength of support for each hypothesis. However, they also need to discuss the limitations of the study given the reliance on incomplete data. It would also be useful to discuss similar issues with previous newly-described infections.
Additional comments: The study question is important. This is a potentially useful paper in the context of the ongoing pandemic.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EVALUATING ALTERNATIVE HYPOTHESES TO EXPLAIN THE DOWNWARD TREND IN THE INDICES OF THE COVID-19 PANDEMIC DEATH RATE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an interesting paper, but it will take a lot of modification for this paper
Experimental design: This is an interesting paper, but it will take a lot of modification for this paper
Validity of the findings: This is an interesting paper, but it will take a lot of modification for this paper
Additional comments: This is an interesting paper, but it will take a lot of modification for this paper. The questions are attached in the pdf file


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: EVALUATING ALTERNATIVE HYPOTHESES TO EXPLAIN THE DOWNWARD TREND IN THE INDICES OF THE COVID-19 PANDEMIC DEATH RATE
Review round: 2
Reviewer: 1

Output:
Basic reporting: See general comments.
Experimental design: See general comments.
Validity of the findings: See general comments.
Additional comments: The article has presented clearly and in detail to the readers. My questions have been satisfactorily resolved, so I suggest accepting this version.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: AN INTEGRATED MODEL OF SEASONAL CHANGES IN STOCK COMPOSITION AND ABUNDANCE WITH AN APPLICATION TO CHINOOK SALMON
Review round: 1
Reviewer: 1

Output:
Basic reporting: Language is very clear and professional throughout. I have only very minor suggestions (though several), laid out below. The introduction and background are strong (again with some minor wording suggestions), the literature cited is appropriate, the structure is clear, and the figures are relevant and high quality. Raw data, along with code, are provided in a comprehensive GitHub repository, which is laudable.

Minor suggestions for text:

Line 37: May be appropriate to add a citation at end, or drop the language about "becom[ing] emblematic".

Line 49: As a practical matter, do ocean fisheries really operate "year-round" in these areas (winter fisheries are certainly rare coastwide, but perhaps less so in these areas)?

Line 50 and multiple times thereafter: I would suggest not using the term "mark" when referring to coded-wire tags (or to when later referring to fish being effectively marked by their genotypes), rather I would call both of these "tags". In the salmon management literature I am familiar with, "mark" seems generally reserved for externally visible, binary ways of distinguishing fish (e.g, adipose fin has either been clipped off or is present) and most commonly refers to the adipose fin clip, whereas a "tag" is often not externally visible and seemingly always encodes finer scale information (e.g. a CWT provides information on stock of origin, age, and often many other characteristics of the hatchery release group or wild fish tagging event it came from; even a FLOY tag conveys more than a simple binary 0/1 type of information) and most often refers to a CWT or to the genotype of a fish whose parents were also genotyped as part of a parentage based tagging program. In this context, the information provided by genotype in a GSI study seems much closer to a traditional "tag" than a traditional "mark". This would also be more consistent with how "mark" and "tag" are used on line 72, and when additional references are made later to mark-selective fisheries. However I realize things aren't always clear cut or terms used consistency, as highlighted by the fact pointed out on line 147 that the agency responsible for recovering coded-wire tags is called the Mark Recovery Program.

Line 62: replace "ress" with "in press" (or 2021 as appropriate)

Lines 72-73: While it is true that "mark-selective fisheries will result in differences in exploitation rates between marked indicator stocks and unmarked populations", the relevance here is not clear and I suggest dropping it (the part of this sentence about mass marking reducing the efficiency of CWT recovery is relevant and I suggest retaining that part). Although the authors do not directly suggest this, the complications posed by mark-selective fisheries are often a challenge to the CWT program that is brought up by advocates of replacing the CWT system with one based on genetics, implying that genetics can solve this particular problem. It is not obvious to me that genetics can do so -- the real problem is a lack of sampling of fish that are released rather than retained for potential sampling. In the absence of such sampling, a CWT-based approach may offer some advantages over a genetics-based approach when it comes to assessing mark-selective fisheries, since (despite problems in implementation) double-index tagging in combination with electronic tag detection may offer the best hopes for quantifying impacts of MSF, and it is not clear how electronic tag detection would work for genotypes. This is all quite aside from the main point of this paper, which is why I suggest simply dropping this clause.

Lines 75-76; Around here it is maybe worth more explicitly making the point (which is suggested earlier) that for "stocks" without tagging programs, GSI is the only way to get stock-specific information. On the other hand, is it worth discussing cases where genetic reporting groups may be more coarsely defined than some particular "stocks" of management interest (perhaps this is never an issue for the stocks of interest here, but is elsewhere in the range)?

Line 85: Though it's a bit hard to point to a direct line to a specific management action for either paper (or for Bellinger et al. 2015), Satterthwaite et al. 2014 (TAFS:143:117-133, http://dx.doi.org/10.1080/00028487.2013.837096) was probably more directly relevant to PFMC concerns and decision making than the cited 2015 paper.

Line 101: Are these tags "artificial" or just "physical" or "mechanical"?

Line 126: Presumably at least some (probably all to at least some extent) of these stocks are harvested in US fisheries as well as Canadian fisheries, even if you are not analyzing data from US fisheries?

Line 128: Can you provide a citation here that defines PFMAs?

Line 131-133: I'm not sure I understand what you are saying here. Area versus subarea has not been defined, I'm also not sure if PFMAs correspond to areas or subareas and whether catch regions are the same as areas, or an aggregation of areas. I'm assuming this is a case where managers place certain subareas in one larger area, when you think grouping them with a different area makes more geographic/ecological sense, but I'm not entirely clear on the wording and the hierarchy of scales.

Line 153: Was the contracted troller instructed to pursue their typical fishing strategy, and did they have incentives to maximize catch (e.g., pay per sample?). If fisheries in this area have minimum size limits or are mark-selective, was sampling done on all fish caught or only those which could have been retained in normal fishing?

Line 169: Are any guidelines provided on how to choose the one fish per day that is genetically sampled?

Line 175: Consider also denoting the "inside" regions on Figure 1.

Line 436: replace "ress" with "in press".

Figure S7: I would consider replacing "Composition" with "Proportion" on the y axis, since each panel only shows the proportions contributed by one stock rather than the total composition in an area (like Figure 3).

Figures in general: For figures with observational data plotted, consider whether approximate error bars could be added legibly (i.e. the error associated with individual observations, not just the model uncertainty ribbons).
Experimental design: This is original primary research with a well defined question, that addresses an identified knowledge gap (the distribution of many natural-origin Chinook stocks, and Chinook distributions at a finer patio-temporal scale than is usually studied. The work adheres to high technical and ethical standards.

The methods are generally described with sufficient detail and information to replicate, with the following exceptions:

Lines 203-207: Though the choices strike me as reasonable, can the authors say any more about how/why they chose these values of k?

In between lines 207 and 208 (not sure what happened to the line numbering here), more detail is needed on how the Dirichlet-multinomial allowed the model to "account for uncertainty in individual stock assignments" -- presumably it somehow made use of the posterior assignment probabilities coming out of cBAYES, but how? Especially since accounting for this uncertainty is highlighted in both the abstract (line 19) and introduction (line 116), it seems like more attention is warranted.

Somewhat similarly, the abstract (line 19) also highlights accounting for the uncertainty associated with annual variability in sampling effort, but this isn't really treated in much detail. Presumably, sampling effort relates to the total size of the n_j in equation 3a, and this leads to greater uncertainty when sampling is limited, but this isn't really made explicit. Also, it appears total catch C is assumed to be observed without error (equation 1a) but presumably there is some estimation involved in determining total catch for a sampling stratum, and the precision of this estimate probably also depends on sampling (though a different kind of sampling than the collection of tissues for genetic analysis). Finally, when calculating CPUE, uncertainty can be related to the total amount of effort, i.e. effort is itself a measure of how extensively the fishery has "sampled" the underlying abundance. A bit more clarity on which aspects of sampling effort were versus were not explicitly considered, and their consequences, might be informative.

Lines 211-212. I'm not entirely sure where the "very small values" were plugged in in place of zero "observations". It seems like the observations of zeros would be for certain n_j in equation 3a, in which case it seems like an integer value might be needed. Is it rather than some elements of theta (I wouldn't really call these observations) were fixed at 0.00001?
Validity of the findings: All data are provided, as is the code, which is laudable. The data are what they are, almost entirely collected from fishery-dependent surveys, thus there is no control (which isn't really meaningful for an observational study, but the reviewer guidelines ask about controls) and the statistical design makes good use of what is available. While the data are not the product of a designed experiment or even a sampling scheme optimized for the intended purpose,  this is pretty much state of the art as far as salmon ocean distribution data go, and comparable too many published studies.

Conclusions are well stated, linked to original research questions, and the difference between direct results and speculation are clear.

I did wonder a bit about the approach of starting from modeling total (relative) abundance by month/area along with stock proportions by month/area rather than modeling stock-specific abundance by area and then the resultant summed abundance and stock proportions. Mechanistically, total abundance must be driven by the sum of each stock's abundance. Assuming that stocks are similarly distributed across years, as stocks vary in their relative abundance, it seems that the spatial pattern in total abundance across space must also vary, which conflicts somewhat with assuming a constant smooth pattern across years. Perhaps the random effects (in CPUE and/or in the proportions) serve to sufficiently soak this up, and this assumption is needed for model tractability, but I'd like to see just a bit more discussion/justification of this approach. This may just be a point to address in the Discussion -- what are the advantages of trying to directly model area-specific abundance of individual stocks, and from that derive stock proportions versus modeling a typical distribution of total abundance over space and typical stock proportions in each area? Maybe referencing Figures S7 and S9-S11 and what they imply about how constant or variable stock composition tended to be across years in a particular month/area would shine light on how important this choice of approach might be?

Lines 429-440: This would requite speculating outside the realm of model outputs, but would including age as a covariate in these models change any of the interpretations here, and/or would the potential that distributions are age-specific affect how we interpret the patterns presented in this paper (and in fairness, many related papers), where all ages are combined? (I see age effects are brought up later, around line 475)

Circling back to lines 207-208, it is stated that a "benefit" of the approach is "account[ing] for uncertainty in individual stock assignments", so perhaps somewhere there should be a mention of how much uncertainty there actually was in stock assignments, and whether this has any meaningful impact on the results or how they should be interpreted.

Lines 488-490 seem like important points. That said, if there are stock-specific responses to environmental drivers, and stocks vary across years in their relative abundance, what does this mean for the advisability of modeling total abundance across space separately from stock proportions versus modeling stock-specific abundance across space and deriving stock proportions from that? I am not suggesting that the authors should be required to develop an alternate model from this starting point, simply suggesting some further discussion of the issue and the choices made.
Additional comments: An impressive amount of work, clearly communicated. My suggestions are mostly minor attempts to improve the clarity of presentation and to give a bit more discussion to the motivation for certain modeling choices.