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: A COMPARISON OF FOOD SOURCES OF NUDIBRANCH MOLLUSKS AT DIFFERENT DEPTHS OFF THE KURIL ISLANDS USING FATTY ACID TROPHIC MARKERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The work entitled “A comparison of food sources of nudibranch mollusks at different depths off the Kuril Islands using fatty acid trophic markers” by Anatolii Komisarenko and colleagues is written in a clear way with a suitable level of English (although I suggest some editing in the PDF file I am attaching with my comments) that confirms the relevance of using fatty acids as trophic markers to shed light over the feeding regimes of some deep-sea nudibranchs.
The manuscript is very well organised and easy to follow.
The introduction is concise, but it clearly prepares the reader for the content of the manuscript and provides a good level of background information about the topic, whose scientific content the author team is certainly familiar with (given their solid publication record on this topic).
The literature cited is adequate and up to date (both in the introduction and the discussion).
Figures are clear, but Figure 2 could benefit from being in colour to allow the reader to better discriminate the different species of nudibranchs in the scatter plot, as well as to identify the groups that were formed. If available, the authors could consider supplying colour pictures of the nudibranch species here addressed (everyone loves pictures of these wonderful marine invertebrates).
Table 1 can be improved by listing relevant ratios of some FA useful to discriminate species using FATM, as well as listing the sums of SFA, MUFA, PUFA and HUFA per species (and highlighting significant differences). In Table 1, significant differences should be signalled comparing all species vs. all species and not between shallow vs. deep sea species.
I could not access raw data, only an excel file with Supplementary Table 1 which are not raw data (I please ask the Editorial team to check if taw data is available).
Experimental design: The manuscript submitted is original, clearly within the scope of PeerJ and builds upon previous works of some of the co-authors that have a solid publication record on using FATM to shed light over the trophic regimes of nudibranchs. The manuscript has a well-defined research-question that contributes to advance the state of the art (and the authors clearly explain how they will do so).
While the research is sound, with high technical and ethical standard, there are some important details missing in the methods that require attention by the authors.
In the methods, the authors must detail what was the amount of sample injected for FA analysis? Was any internal standard used? Please clearly refer how fatty acids are expressed (I inferred these were relative abundances of the total pool of FA?) (please see the PDF file I am attaching with my comments).
The authors must explain how they could have performed a one-way ANOVA to compare the FA profile of different nudibranch species, when one of them (Aeolidia papillosa) has n=2? Please clarify this important issue. Performing a one-way PERMANOVA can be an option to compare the FA pool of each species as whole against each other to confirm or refute significant differences. However, n=2 for A. papillosa is a caveat for this and other statistical analysis… Please elaborate on this. Moreover, if raw data were % of FA was it not necessary to transform your data prior to analysis? Please confirm this, as well if the assumptions of ANOVA were always met so there was no need to perform non-parametric statistics (but first pay attention to the fact of n=2 for A. papillosa.
Validity of the findings: While the findings reported are certainly relevant, the authors must clarify the issues referred above concerning their statistical analysis. The authors may also consider suggesting the use of molecular barcodes of gut content of these nudibranchs in future studies to support their assumptions on the feeding regimes of these deep-sea species. The use of FATM provides indirect evidence (and the authors must be cautious when reporting their findings) of trophic interactions and may not be able to discriminate which prey is being ingested to genus or species level.
Additional comments: Given the issue I refer with your statistical analysis I consider that this study requires a major revision before being accepted for publication.
Please see the PDF file I am attaching with my 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: A COMPARISON OF FOOD SOURCES OF NUDIBRANCH MOLLUSKS AT DIFFERENT DEPTHS OFF THE KURIL ISLANDS USING FATTY ACID TROPHIC MARKERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a very interesting paper focused on the little-known topic dealing with the food preference of Nudibranchia. The trophism of five species is studied using the fatty acid trophic markers (FATM) that is poorly used in this group of mollusks. This is a still unexplored field and this work can be an excellent starting point. The English is good and the paper is well structured.

Anyway, I suggest to implement the data on the genera investigated and in general on the biological and ecological context dealing with the species investigated. In fact, I found that the technique used and the results obtained were well explained but the paper does not give the instrument to understand the biological question that is behind this paper. Why is it important to understand the trophism of these species, why and how it is useful the FATM to explore the ecology of these species. I found the paper difficult to follow. Increasing the references cited or reporting data on the state of the art on the knowledge on the diet of related species could be very useful to easily follow the paper and quickly understand the meaning of the study carried out. For example, as little is known to date about the diet of nudibranchs, I find it a bit superficial not to mention all the few works published to date, at least on the genera treated here. I suggested some of these papers directly on the attached pdf file.
Experimental design: It is not clearly reported in the text how many individuals were analyzed and the lack of any kind of pictures of the species investigated make this paper a bit abstract and too methodological. Furthermore, I think that these data should be included also because two of the five analyzed species are not identified at species level but reported as ‘sp.’.

Another point is about the comparison with different species from shallow water as A. papillosa and C. verrucosa. In fact, in the discussion section, you stated that: “Considering the close similarity between the FATM profiles of A. papillosa, C. verrucosa, and Dendronotus sp., we assume that the increased 22:5n-6 and C20 MUFAs levels in the deep-sea nudibranch Dendronotus sp. from the Sea of Okhotsk indicate its preying on sea anemones and/or anthoathecates hydroids, similarly to the shallow-water species, A. papillosa and C. verrucose.” This concept means that the FATM profiles are not so specific for the prey because the three species here discussed (Dendronotus sp., A. papillosa and C. verrucosa) are very distant in terms of evolution and diet and I would aspect to found differences in the FATM profiles. I think that this aspect should be better explained or clarified.
Validity of the findings: I really appreciated to read this paper that is focused on the important, and very hard to study, aspect of the trophism in nudibranchs. The fatty acid trophic markers (FATM) are a consolidated technique but still little used in this group of mollusks today and for this reason this paper is original and interesting. This work can be an excellent starting point to understand and fill the gap of knowledge on this unexplored field of study. Anyway, as I stated above, I think that the authors should make a little extra effort to better explain the biological question behind their work and allow the reader to understand the study done and its possible importance and applications.
Additional comments: Other minor comments are directly reported on 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: A COMPARISON OF FOOD SOURCES OF NUDIBRANCH MOLLUSKS AT DIFFERENT DEPTHS OFF THE KURIL ISLANDS USING FATTY ACID TROPHIC MARKERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have successfully addressed all issues raised on the first version of their study and significantly improved the overall quality of their work. Congratulations!
Experimental design: The number of specimens sampled is now clearly detailed, as well as the methods for FA analysis and statistical comparisons.
Validity of the findings: The findings reported are now much better framed and presented. The discussion of the manuscript is now clearer and easier to follow.
Additional comments: The Figures added to this revised version significantly improve the overall quality of the manuscript. Well done!
I recommend some minor corrections before acceptance of this manuscript (please see the PDF file I am attaching).


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: A COMPARISON OF FOOD SOURCES OF NUDIBRANCH MOLLUSKS AT DIFFERENT DEPTHS OFF THE KURIL ISLANDS USING FATTY ACID TROPHIC MARKERS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I thank the authors for the effort in reviewing the manuscript that now resulted to be really improved.
I like the manuscript as it is, and I do not have any other 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: GENOME-WIDE QTL MAPPING OF YIELD AND AGRONOMIC TRAITS IN TWO WIDELY ADAPTED WINTER WHEAT CULTIVARS FROM MULTIPLE MEGA-ENVIRONMENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The report is too long and hence difficult to grasp the main points. Please try to shorten the volume. In the result section for the MTAs, just focus on yield. And you may add those MTAS which are common with yield, days to heading, plant height and TKW. At the end of the day, we will not use any of the QTLs which are not linked to yield for practical breeding purposes.
2. Too many analysis and supplementary data have been presented. But in fact, the main Tables and graphs ( Tables S1, S2) and Figure S2 should be part of the main document.
3. A table showing the yield performance of the top 20 lines along with the parents across the 28 environments could be presented.
Experimental design: No comment
Validity of the findings: 1. too many analysis but lacks clear reporting. Some of the Tables and Figures should be part of the main document instead of Supplementary.
2. The conclusion part is weak. There are many reports that could lead to a clear recommendation along with the current result. Tell us specifically the MTAs which could be used in marker assisted breeding for yield under moisture stress.
Additional comments: Please try to shorten the volume. In the result section for the MTAs, just focus on yield. And you may add those MTAS which are common with yield, days to heading, plant height and TKW. At the end of the day, we will not use any of the QTLs which are not linked to yield for practical breeding purposes.
2. Too many analysis and supplementary data have been presented. But in fact, the main Tables and graphs ( Tables S1, S2) and Figure S2 should be part of the main document.
3. A table showing the yield performance of the top 20 lines along with the parents across the 28 environments could be presented.


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 QTL MAPPING OF YIELD AND AGRONOMIC TRAITS IN TWO WIDELY ADAPTED WINTER WHEAT CULTIVARS FROM MULTIPLE MEGA-ENVIRONMENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: This study by Dhakal et al. identified QTLs associated with yield, test weight, heading date and plant height across 28 diverse environments, followed by analyses of QTL pleiotropy and interactions of epistasis, epistasis-by-environment, and additive-by-environment. The field experiments were well designed and phenotypic data were collected and processed appropriately. The consistent QTLs detected in multiple environments would be useful for future cloning and breeding use. This paper was written in a straightforward way and well structured. Care must be taken to correct some minor language problems. In addition, I think that Tables S2 and S3 showed important information so may be included in the main text. Fig. S1c,d are not clear regarding the descriptive statistics.


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: THE REPORTING OF P VALUES, CONFIDENCE INTERVALS AND STATISTICAL SIGNIFICANCE IN PREVENTIVE VETERINARY MEDICINE (1997–2017)
Review round: 1
Reviewer: 1

Output:
Basic reporting: I thought the basic reporting was fine, though the review of previous work could have been more extensive. For example, the author said nothing about the banning of p-values in Basic and Applied Social Psychology in 2015.
Experimental design: I thought the sampling was fine, though limited. It isn’t clear to me why more journals were not sampled, which would have increased the generalizability of the findings. It also would have been nice to have had more explanation for the reasons that particular choices were made.
Validity of the findings: I thought there was a strangeness in the reporting of the findings. It is obvious that the authors do not favor p-values, and they are right in this. And I understand why the authors have some of their focus on using confidence intervals (CIs) as significance tests; they are right to be critical of this, and it matters, as I will explain in the general comments. But the authors fail to explain why their use of CIs is valid! I see this as a major failing, as I question that. What EXACTLY is the reader to conclude from a CI? Should the reader conclude that the population parameter of interest has a 95% chance of being within the CI? Of course not, that would be blatantly invalid. But if the reader is not to draw that invalid conclusion, then what, precisely, should the reader conclude? The point I am making is that the author’s use of CIs also is invalid. The authors should either (a) explain exactly how they are using CIs validly (which I don’t think they can do without watering down the gain to the point of triviality) or (b) dump the CIs. They could, for example, use the a priori procedure (by yours truly) to say how precise their data are.
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: THE REPORTING OF P VALUES, CONFIDENCE INTERVALS AND STATISTICAL SIGNIFICANCE IN PREVENTIVE VETERINARY MEDICINE (1997–2017)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is well-written, and relatively easy to read. The section with the results is a bit dense (quite a lot of numbers to process here), but I think the outcomes that are mentioned are relevant, so there's little that can be done. As is often the case, I found the figures easier to process than the written outcomes.

Although I'm generally quite positive about the paper, one of my main concerns deals with the amount of background information (see also general comments). Although I don't have to be convinced of the relevance of the research question, I think it might be good to add a bit more context to the reader who might be less familiar with issues surrounding inference. The issues are briefly mentioned, but personally I'd prefer a bit more context here: What is the problem with focussing on a binary outcome? For what problem would CIs be a solution? And, to be fair and balanced, are CIs without problems? Is there something wrong with p-values presented as inequalities? Long story short, I think it's important  to link the research questions to background information. Thus, the paper would not only present some outcomes about the (lack of) change in the reporting of inferential results, but at the same time make the reader familiar with some often debated issues in statistical literature.
Experimental design: I think the study is well-designed, so I have few comments about that. I was expecting an extensive analysis for the change of reporting practices over time, until I saw the Figures with the results, which immediately made clear that such an extensive analysis would be superfluous. Moreover, I appreciate the amount of detail of the Method, and the supplementary materials.
Validity of the findings: The results are interpreted quite carefully, and I've seen no clear cases of exaggeration or overgeneralization.
Additional comments: Review
First of all, I appreciate to have been given the opportunity to review this paper. In 2006, we’ve published a similar study on the use of p-values and CIs the psychology literature, and it is nice to see that such studies are also carried out in different fields. I also want to make clear that my expertise is in the use of statistical methods, but not in epidemiology or veterinary medicine, but for this paper that doesn’t matter too much, apart from some the fact that if I’d written this paper, I’ve leaned more on literature based on the reporting of inference in the social sciences.
I think this is quite a good paper, and I found it interesting to read. Actually, I have only one larger concern, and a few (very) minor issues. My main concern is that I think that more background information for this study would be helpful to understand why the study was conducted, and could be educational for the reader as well. To be clear, *I*  don’t have to be convinced of the importance of such a study, but I’m not sure whether a more substantively oriented person in this particular field is aware of all the discussions about how to report inferential results. Strengthening of the introduction could alleviate that issue. Of course, readers could read relevant and mentioned literature like Wasserstein and Lazar (2016) themselves, but I’d be in favour of giving a bit more context to the reader. Questions I’d like to have seen addressed are: What exactly is criticized about the reporting of inferential results? What’s wrong with p-values, or with a binary interpretation of them? Why are CIs seen as a useful alternative, and are they without criticism themselves?  [to be frank, I’ve been involved in some papers on the problems with the interpretation of CIs, so this remark may not be completely neutral. I do think though that we have to be careful in saying that the interpretation of p-values is often problematic (and it is!), and that therefore moving to CIs solves all problems] What’s wrong with interpretating a CI as if it were a significance test, given their technical relationship? Why would one not report a p-value as an inequality? What kind of a change over time could have been expected? Would one expect CIs for both common and not so common methods (and do they even exist for the latter)? All these issues come back to some extent in the results, but are not thoroughly discussed in the introduction. I think these could be better matched, with, as mentioned before, the additional benefit of making the paper more informative/educational. In case it wasn’t clear yet: By no means am I suggestion that the authors wouldn’t have good answers to these questions: I’m sure they have. I’d just like them to be more explicit about them. A related, but arguably less urgent point deals with the difference between NHST and significance testing (e.g., line 401). I’m pretty sure this will go over the heads of many readers, so I’d either leave this out, or explain the distinction a bit more.
Another, somewhat smaller issue, is that I think a rationale for focussing on p-values and CIs only is lacking. Although I can easily imagine a good justification (their frequency of use, or how often they are discussed in literature, for example), the paper just states that the focus will be on them. Why not include Bayesian statistics, for example? I’m not saying the authors should have done that, but I’d like to see a justification for their selection added,
I also have a few (very) minor issues:
94: While it may be postulated,  I think the comma is redundant, but then again, I’m no native speaker
394: p ≥.05 or p < 0.05. It’s not important at all, but I’d suggest to be consisted in whether or not a “0” proceeds a decimal number
Figure 1: I have no strong opinion about this, but I’m not sure whether this figure contains a lot of information. To me, it wasn’t hard to imagine how such a search process would look like, but maybe I’m biased because of my familiarity with such studies.
Figure 4: I think it would be helpful if a legend would be added to the figure. Of course, there were only three elements to remember, but generally I think it is easier to read a figure, rather than having to go to the text instead. Of course, this is also due to the incomprehensible habit of some publishers to present the text and the figures on separate pages: I would be so much easier if they would be presented in the same manner as they would in the eventual published paper.

To summarize, I think this is a decent paper, with the potential to be a good paper if the outcomes presented in the results section would have had a better link to issues discussed in the introduction.

I always sign my reviews.
Rink Hoekstra


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: THE REPORTING OF P VALUES, CONFIDENCE INTERVALS AND STATISTICAL SIGNIFICANCE IN PREVENTIVE VETERINARY MEDICINE (1997–2017)
Review round: 2
Reviewer: 1

Output:
Basic reporting: Fine
Experimental design: Fine
Validity of the findings: Fine
Additional comments: Well both myself and Rink Hoekstra commented on the confidence interval issue in the first round of reviews. I’m not really satisfied with the author’s response to our comments on that. However, I’d hate to see that disagreement scuttle the paper. Therefore, despite my lack of satisfaction on that issue, I’ll recommend publication. I hope that it influences the field away from p values.


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: THE REPORTING OF P VALUES, CONFIDENCE INTERVALS AND STATISTICAL SIGNIFICANCE IN PREVENTIVE VETERINARY MEDICINE (1997–2017)
Review round: 2
Reviewer: 2

Output:
Basic reporting: I have nothing to add to my previous remarks: this is all fine
Experimental design: Same here
Validity of the findings: Same here.
Additional comments: I appreciate the opportunity given to review this paper a second time. I think the authors did a good job in processing the comments by both myself and David Trafimow, and I think most issues have been dealt with properly.
I do want to note that the authors are clearly more optimistic about the usefulness of CIs than I am, which may come as now surprise given our papers on this issue. As Trafimow also pointed out, too often CIs are promoted as a valuable alternative for NHST, without explaining what one can validly conclude from a given CI. This is actually quite tricky, and makes, at least in my opinion, the use of CIs less attractive than many would think (and than I used to believe for quite a while as well). The answer given to Trafimow’s comment in the reply (point 3) is not completely convincing to me: “reasonably compatible” is not formally defined as far as I know, and I wouldn’t know how to use that, unless as an inverted test. Moreover, it suggest that values outside the interval are reasonably incompatible, which I’m not sure I agree with either, and it notably creates a dichotomy that CIs are often propagated to avoid.
But then again, I do agree that a relatively careful use of CIs is probably preferable over what we often see in substantive studies (as this study shows as well), so overall I think the added value of publishing this paper outweighs the fact that I do not fully agree with the authors’ assessment of CIs.
Best regards,
Rink Hoekstra


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: PROTEOMIC PROFILING OF THE ENDOGENOUS PEPTIDES OF MRSA AND MSSA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript utilizes LC-MS approach to profile endogenous peptides of MRSA and MSSA, aiming to provide a guidance for further mechanistic studies and treatments of S. aureus. They identified 292 MSSA-abundant endogenous peptides and 35 MRSA-abundant endogenous peptides with distinct potential characteristics. The manuscript is well organized and written. However, there are certain gaps and misleading parts in this manuscript, which need to be improved. The idea behind this manuscript is clear but still in early stages.

Concerns:
1. Introduction: this part is not well introduced, which couldn’t clearly express the purpose of this study. Why the authors preferred using peptidome approach, what’s the advantage of it. Are there published literatures talking about the importance of peptides in S. aureus, and their relationship with human diseases?
2. The resolution/quality of all the figures should be improved.
3. The authors should convert the supplementary files into more general formats, like excel.
Experimental design: Sample preparation:
1. the authors boiled the samples for 15 mins to eliminate proteolytic activity.  Will this step cause the denaturation of proteins or peptide or other artifacts?
2. Why not use any proteases inhibitors during sample processing?
3. The authors used a 30-kDa molecular weight cut-off filter to enrich the endogenous peptides, however, the supernatant may still contain other components, like protein, nucleic acid. Did the author carry out further steps to enrich the endogenous peptides before submitting to MS analysis? Why used a 30-kDa filter, which is much bigger than a typical peptide, there should be smaller cut-off filters.
Validity of the findings: Overall, this study presents descriptive data without any functional validation.
1. line 145, “A total of 1040 endogenous peptides from 282 proteins were identified”. I think the authors may mix the concepts between peptide and protein. When working with MS, usually the proteins will be digested into short peptides, and then matched back to identify the original protein. So here, the authors actually identified 282 proteins, not the real endogenous peptides. Even though the author could claim the peptides are generated by the 282 precursor proteins, how could the author make sure that all the peptides are naturally existing in S. aureus, not introduced by sample processing, like the procedure of boiling the sample for 15 mins. If so, the original purpose of this study should be questioned. Please explain it.
2. Also, in the abstract, the author mentioned they identified 1065 endogenous peptides, so what are the rest 25 peptides? (1065-1040=25).
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: PROTEOMIC PROFILING OF THE ENDOGENOUS PEPTIDES OF MRSA AND MSSA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well structured and written clearly with description of sufficient background.
Experimental design: Tu et al., compared endogenous peptidome profile of Methicillin-resistant S. aureus (MRSA) with the methicillin-susceptible S. aureus (MSSA) following appropriate experimental design including sample selection and experimental workflow as well as data analysis.
Validity of the findings: Tu et al., identified 1065 endogenous peptides from 282 proteins and further analyzed differentially expressed peptide features and precursor protein employing various bioinformatic tools.
The following minor comments may need to be addressed
1.	The MSSA has enriched motif but not for MRSA (Figure 3) which may be due to small number of identified peptides expressed in MRSA compared to MSSA. So, the authors may comment  the need for deeper peptide coverage.
2.	The authors may add more description in bioinformatics criteria including motif-x (line 203), normalization method or if any quantitative imputation is employed (Table S2).
3.	 The authors may provide the raw data and MaxQuant search result (txt folder) accessible for the community in addition to the identification result provided in supplementary table.
Additional comments: Overall, the study is well designed and written which may provide insight for further in-depth study of S. aureus peptidome and I recommend the manuscript 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: PROTEOMIC PROFILING OF THE ENDOGENOUS PEPTIDES OF MRSA AND MSSA
Review round: 1
Reviewer: 3

Output:
Basic reporting: There are some minor grammatical issues that needs to be rectified.

1) In the Abstract, line 26-27, Instead of writing "MSSA-abundant endogenous peptides have significantly enriched motif of VXXXK at the C-terminus", you can use "MSSA-abundant endogenous peptides have significantly enriched VXXXK motif at the C-terminus".

2) In the Introduction, line 34-35, Instead of writing "Gram-positive bacterium that is a common cause of human infections", you can use "Gram-positive bacterium that is a common cause of infections in humans"

3) Line 90, remove "the" from the sentence " the acetic acid was then to the lysate.

4) Line 159, remove "s" from lengths in the sentence "relatively short in lengths".

5) Throughout the manuscript, please use italics, whenever the name of the bacteria or the name of a gene is mentioned.

6) Space is missing at several places in the paragraphs when a reference has been inserted in brackets. For example: Line 47 "colonies(Akil and Muhlebach, 2018), Line 48 "thickened cell walls(Garcia et al., 2017) etc.
Experimental design: no comment
Validity of the findings: 1) In the Results section, Lines 166-167, simply because most of the analyzed peptides are acidic and have similar size, it cannot be generalized that they have similar properties. The sentence needs to be rephrased to make more sense.

2) In the Results section, Lines 223-224, "indicating that many precursor proteins were involved in ribosome or translational regulation". This sentence is not clear since ribosomes are the major components of translation. Does the authors mean "ribosome biogenesis ?". This is based on the fact that 13 peptides were found to be structural components of the ribosome.

3) In the Discussion, Lines 252-254, "MRSA-AEP may experience.........regulated by proteases". This statement is not clear and needs to be elaborated for a better understanding of the authors intensions.

4) In the Discussion, Lines 273-275, “In comparison with MRSA-AEP, MSSA-AEP has stronger ribosome related functions including promoting bacterial growth and resistance to antibiotics”. It is acceptable that MSSA-AEP has stronger ribosome related functions like promoting bacterial growth, but the authors does not show any evidence to state that it promotes resistance to antibiotics, though ribosome are targeted by a number of antibiotics.
Additional comments: Overall, the manuscript is well written and the role of endogenous peptides in the regulation of bacterial growth and immune responses were well explained. There are some minor issues in the results and discussion section that needs to be clarified in order to improve the quality of the manuscript. I recommend this article 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: PROTEOMIC PROFILING OF THE ENDOGENOUS PEPTIDES OF MRSA AND MSSA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors addressed my concerns.
I would suggest the authors change "1065 endogenous peptides" into "1040 endogenous peptides" in the abstract and introduction, which is more in line with the results.
Experimental design: The authors addressed my concerns.
Validity of the findings: The authors addressed my concerns.
Additional comments: The authors addressed my concerns.


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: TRANSLATION AND PSYCHOMETRIC VALIDATION OF THE PERSIAN VERSION OF THE QUESTIONNAIRE ON SMOKING URGES FOR ASSESSMENT OF CRAVING TO SMOKE AMONG UNIVERSITY STUDENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Literature Review can be improved.
Line 89-91: Author stated that QSU has been translated in different languages since this is a validation article why the validity (brief information) in different languages were not provided e.g., French (Dethier et al., 2014; Guillin et al., 2000), Spanish (Cepeda-Benito & Reig-Ferrer 2004), Portuguese (Araujo et al., 2007), Chinese (Yu et al., 2010), Italian (Teneggi et al., 2001), and German (Müller et al., 2001).

Line 93: Strengthen the rationale of this study is to encourage. i.e., line 93 Thus, suggesting the need for both suitable guidelines and also good screening for smoking cravings… smoking in Iran. This manuscript does not deal with guidelines but more towards validating QSU questionnaire. The word suitable guidelines should be omitted.

Line 106: “participation rate”, change to survey response rate.

Line 126: …urge, and .82 for expectancy .82- this is redundant

Line 125-126, 184: There is inconsistency throughout this manuscript in terms of numerical system (for example: either author use .71-US system or 0.71 alternative numerical system). Choose one system.
Experimental design: Line 156: Content Validity Index (Waltz & Bausell, 1981), can you include the proof of CVI information in your attachment?

RESULTS
-Add EFA results table especially factor loadings
-Add information of χ²/df in Table 1.
-Figure 1, Factor 1, and Factor 2 must be named.

Line 228-229 The factor loadings, standard errors, t-values, and p-values of the items are presented in Appendix. I could not find the information in Appendix

Reliability
Line 216-218, 223 Why are these words (RMSEA, CFI, TLI, SRMR) in italic?

Line 242: Why is … Cronbach’s alpha (Bonett & Wright, 2015) in italic?

Line 245-246 "For Factor 1 it was 0.94, for Factor 2 it was 0.97, and for the total construct Cronbach’s alpha was 0.95." I have some concerns as the reliability of Factor 2 is extremely high.
Please read Tavakol and Dennick (2011)
If alpha is too high it may suggest that some items are redundant as they are testing the same question but in a different guise. A maximum alpha value of 0.90 has been recommended (Streiner, 2003).
Validity of the findings: Impact and novelty are well-established but there are a few issues that need to be addressed.

DISCUSSION
Line 307-312-briefly discussed Factor 1 (5 items) and Factor 2 (7 items) but did not provide an explanation of the rationale as to why suddenly 1 item from Factor 1 loaded on Factor 2. An explanation or rationale is needed to justify this issue.

Line 322: Hu and Bentler (Hu & Bentler, 1999) changed to Hu and Bentler (1999).

Line 324: Kenny and McCoach (Kenny & McCoach, 2003) changed to Kenny and McCoach (2003)

Line 332: confirmatory factor analysis (eg., Brown, 2015), some researchers (e.g., Kline, 2015) Delete e.g.,

Line 361: might also need to use Beta (e.g., Revelle & Zinbarg, 2009) or Omega (e.g., Al Nima, 2020)… Delete e.g.,

Line 338-339: Worthington & Whittaker, 2006; Costello & Osborne, 2005; Henson & Roberts, 2006) changed to (Costello & Osborne, 2005; Henson & Roberts, 2006; Worthington & Whittaker, 2006).
Additional comments: Reference needs some attention. In-text citation needs attention.
Proofreading is stringly encourage.
There is major inconsistency throughout this manuscript in terms of the numerical system (for example: either use .71 (US system) or 0.71 alternative numerical system)


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: TRANSLATION AND PSYCHOMETRIC VALIDATION OF THE PERSIAN VERSION OF THE QUESTIONNAIRE ON SMOKING URGES FOR ASSESSMENT OF CRAVING TO SMOKE AMONG UNIVERSITY STUDENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Dear authors:
I have now reviewed your paper and recognize your manuscript addresses the interesting research question (psychometric validation). However, I can suggest several weaknesses in the manuscript.
* The quality of presentation.
* The presentation of manuscript contains unnecessary description and self-assertion (not supported by the current knowledge, not properly cited)
* Short paragraphs and lack of consistency between paragraph topics
Abstract
1.     Abstract is not balance.
2.     Abstract is not informative. For example, number of male and females, Cronbach coefficient, goodness of fit information can be added to abstract.

Introduction
3.     The first paragraph, Line 51, 52, the statements must be cited.  Also, when the authors talk about the Western and Eastern communities, such classifications must be relevant for study. However, we do not any specific design and outcomes related western or eastern. So, i suggest to delete some phrases.

4.     Authors must describe to justify the need for Persian version of measure. For example, if measures of the construct exist in the literature, explain the value added by your new scale. Revision requires theoretical understanding what is essential in the instrument for the targeted population. How might the new measure enhance the substantive knowledge base?

5.     In line 56, the authors must cited for both causes and associated, separately, or use one of the verbs.
6. The phrase of “in this context” is vague. Please, speak clearly. In which context?
Also, the measure, dimensions, and characteristics must be explained.

The final paragraph of introduction must be to aim and objectives.
Experimental design: Method
7. The sampling must be more explained.
8. The study period must be added
9. The authors must clearly stated inclusion and exclusion criteria.
10. Mean values must be stated with unit. Age mean values unit is age.

11.     Did you conduct a pilot or preliminary study before the main validation study to refer what is important a scale modification?
*     If your answer is positive, please describe how you conduct.

12.     Please describe more clearly about the statistical analysis. What is your criteria about the significant results? What is your plan to reach the aims?

13.    Your translation process did not meet standard guidelines. For example, Translation back-translation process, how did you conduct the translation back-translation process?
14.     Please, Report expectation related to the reliability of measures,
15. How you judged the normality?
16. As you aware, EFA and CFA methods do not suggested simultaneously. However, you did.

17.     Report the specific sampling strategy taken
18. Please report multicollinearity test
19. For all measure, report internal consistency, and higher scores demonstrations.
Validity of the findings: Results
20. Do not use of “We”. It is not good idea.

21.     Please use the APA or Journal Guideline in the report.

22.     Results of your study were not well-organized. I recommend

*     To concise the result, the correlation results can be illustrated in the table.
*     Describe your strategy and fit indices Criteria,
*    RMSEA must be accompanied by the 90% CI
*     In the results section, clearly state the results according to sequence in statistical analyses

23.     Report sufficient descriptive statistics—¬including means, standard deviations,
24.     SD has not unit (e.g., years). Please revise.
25.     Please provide more information about the internal consistency the overall measure, and its dimensions, separately. (Cr or omega)
26.     Please describe how you assessed discriminate validity.
27.     Test-Retest Reliability is important to present evidence for new scale.
28.     Was the sample size included in the analysis adequate? For continuous scores:
29.      Was an intraclass correlation coefficient (ICC) calculated?
30. Divergent validity, convergent validity, and AVE values must be generated. Currently, i cannot make a decision about the validity.
34.     Please, conduct a multicollinearity test.
35.     Please, address to categorical variable. (e.g., Gender, in sample). For example, is there statistically significance difference between male and females?
 37.     Add the new Persian version of the scale in appendix.
38. Report the concept(s) you are measuring. The exception to this rule is if you are specifically studying the properties of the scale in question rather than the concept(s) it measures.
39. Put a leading zero for indices that can take values greater than plus 1 or lower than minus 1 such as means, standard deviations, b, beta, and standard error. Do not put a leading zero for indices such as r, alpha, and p. However, journal rules may vary from this but they will then edit and change to their own liking.
40. Report two decimal places in general but three for p values and one for percentage values. At minimum, make sure to be consistent within different indices.
41. Please add the legend for figures.
Discussion
42.     Evaluate the strengths and limitations of the work.
43.     Conclusions are inadequately clear or sound or supported.

Reference
44.     Your references are included several Persian refs, that they cannot read by non-Persian speakers. Please, use the core references instead of those.
Additional comments: DEAR authors
i deeply suggest that you report the study based on STROBE checklist.
also; while your scale is related to health setting,we must be more sensitive about the validation.


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: TRANSLATION AND PSYCHOMETRIC VALIDATION OF THE PERSIAN VERSION OF THE QUESTIONNAIRE ON SMOKING URGES FOR ASSESSMENT OF CRAVING TO SMOKE AMONG UNIVERSITY STUDENTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The title seems incomplete without the target group and the aim to use the questionnaire. It is suggested to change the title into Translation and Validation of the Persian Version of the Questionnaire on Smoking Urges for Assessment of craving to smoke among university students.

The content of the abstract is inadequate to reflect the robustness of the method and synchronization of the findings. Do you do pre-testing analysis before proceed to confirmatory factor analysis? It is important steps in a translated version of the questionnaire, to ensure the content was well understood by the readers. You need to explain briefly the nature of the questionnaires that you had translated ie the number of items, the scoring or rating system applied, and how the confirmatory factor analysis was performed. Why do the respondents need to answer the Nicotine Dependency Syndrome Scale and the Self-Motivation for Smoke Cessation as well? Does it related to the topic of the study? Your statement in the result section needs to be briefed and consolidated. Your current findings are confusing.

The focus of the study was not well explained. Why the questionnaire is needed? Why can’t you use the available tool like Fagerstrom test and others that mentioned in the text? What is the strength of the chosen questionnaire as compared to others? What kind of theory supports your justification to use the questionnaire?
Experimental design: Study setting and participants: What is your study design? How did you determine the sample size for the study? How did you do the sampling method? We usually do not describe the findings in the method section. Thus, please delete the statement line 104 – 115. How long the data collection took place?

Validation measures: You need to explain in detail the translation and validation process which include 10 stages starting from preparation, forward translation, reconciliation, backward translation, backward translation review, harmonization, cognitive debriefing, review of cognitive debriefing result, and finalization, proof-read and finally preparing the final report. The information for NDSS and MSC might not be related to this study yet.

Data analysis: Did you check for multicollinearity between factors?

Any evidence of ethical clearance from the institution? Please provide the number of approval of ethical clearance.
Validity of the findings: The sociodemographic data is important, please include it in your result section (bring all the information from the method section). Please kindly explained the importance of Table 3. Why the plausible differences between individuals important in validation study?
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: TRANSLATION AND PSYCHOMETRIC VALIDATION OF THE PERSIAN VERSION OF THE QUESTIONNAIRE ON SMOKING URGES FOR ASSESSMENT OF CRAVING TO SMOKE AMONG UNIVERSITY STUDENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Dear authors
    I found the structure of the manuscript difficult the follow, somehow disorganized and scattered. Therefore, I suggest that the author(s) be very precise and simple on what they wanted to say/what they aimed. The basic structure of comparative research should be followed while providing the literature and purposes. The authors can apply the logical flow sample below to all manuscripts.

Also, statistical results such as fit indices in introduction section is bad idea.
Experimental design: Please, state the standard method that you utilized for transcultural process.
You must follow the standard method.
(SD years) is incorrect. SD has not unit.

Please, remove the second hand REFS. such as ghasemi...
please,cite tge primary Refs.
Validity of the findings: The method and result section need organization.
Additional comments: Discussion must be related to the results.
However, there are several results without discussed.
The limitation must be revised.


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: TRANSLATION AND PSYCHOMETRIC VALIDATION OF THE PERSIAN VERSION OF THE QUESTIONNAIRE ON SMOKING URGES FOR ASSESSMENT OF CRAVING TO SMOKE AMONG UNIVERSITY STUDENTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Clearer info described the workflow of taught and process. The literature references are provided adequately. Self-contained with relevant results to the hypothesis.
Experimental design: Methods described with sufficient detail and information to replicate.
Validity of the findings: All the underlying info has been provided. They are robust, statistically sound, and well presented.
Additional comments: In principle, I satisfy with all additional info and correction done. The info is clearer and had back up with the works of literature. I have no doubt to accept this piece of work for publication in this prestigious journal.


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: TRANSLATION AND PSYCHOMETRIC VALIDATION OF THE PERSIAN VERSION OF THE QUESTIONNAIRE ON SMOKING URGES FOR ASSESSMENT OF CRAVING TO SMOKE AMONG UNIVERSITY STUDENTS
Review round: 3
Reviewer: 1

Output:
Basic reporting: Line 117, add " there is" to no standard and validated ....
Line 128, change the word "received" to "provided". The participants received informed consent...
Line 138: a university student, and have started smoking regularly for at least one year. Please be more specific, the word “regularly” is quite vague a better description would be for example smoke daily or at least 1 pack of cigarettes a day would be more specific
Line 181-182: QSU 12-items Persian version was finalized after some minor revisions and corrections... so what are the revisions/correction give a few examples.
Line 251-251: The CFI value in the single-factor model was not good (.76), it was very good in the modified two-factor model (.97), and it was not acceptable in the original two-factor model (.86). These sentence could be rearranged in a better understandable manner.
For example, the CFI values for single-factor (.76), modified two-factor model (.97) and original two-factor model (.86) respectively. The general acceptable CFI value should be above .95 which is achieved by the modified two-factor model in our CFA analysis.

Figure 1, the legend is missing to explain what the numbers represent.

Line 273-274: The Cronbach’s alphas for Factor 1 (α = .94, mean scores = 5.55±.13) and Factor 2 (α = .97, mean score = 5.31±.48), and for the total construct (α = .95, mean scores = 5.41±.55)
Mean and SD are not needed here…

Line 292: Do you mean concurrent validity as opposed to convergent validity?
“are, the higher the nicotine dependency is. That is, indicating a fair convergent validity between…”

Line 388: negativly associate- missing an “e”
Line 404: Nevertheles,- missing an “e”
Line 447: Psyciatric- typo
Experimental design: No comment.
Validity of the findings: Conclusion are well stated but a few redundant words in line 566-567. Line 571-573. Kindly double check.

I would like to suggest another round of proof reading as there are grammatical and structural throughout this manuscript.
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: TRANSLATION AND PSYCHOMETRIC VALIDATION OF THE PERSIAN VERSION OF THE QUESTIONNAIRE ON SMOKING URGES FOR ASSESSMENT OF CRAVING TO SMOKE AMONG UNIVERSITY STUDENTS
Review round: 3
Reviewer: 2

Output:
Basic reporting: Currently, the manuscript has significantly promoted during review rounds.
Experimental design: I suggest the new title:
Psychometric Validation Currently, the manuscript has significantly promoted during review rounds
Validity of the findings: Currently, the manuscript has significantly promoted during review rounds
Additional comments: Currently, the manuscript has significantly promoted during review rounds


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: ESTABLISHMENT AND VALIDATION OF AN INDIVIDUALIZED MACROPHAGE-RELATED GENE SIGNATURE TO PREDICT OVERALL SURVIVAL IN PATIENTS WITH TRIPLE NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript needs heavy editing and improvement with respect to the use of professional English usage and sentence constructions. It made the flow of the paper very difficult to follow.
Even though the authors discussed TAMs in the introduction thoroughly, the authors in their introduction and discussion mentioned that they analyzed them based on "certain immune cells". Since this paper talks about TAMs in the introduction and does analysis based on macrophages it is very important to highlight what was the grouping criteria. Thus, it didn't make a strong rationale for their study.
Figures were not legible even at 200% zoom which makes it difficult to follow with the text.
Figure 3 needs to be completely changed as the labels do not match the text in the manuscript.
Experimental design: The authors did extensive analysis and validated their observations with multiple data sets and programs. This was one of the strongest points of this paper. I commend the detailed analysis and flow of the research rationale.
Methods are described in detail. Authors are suggested to add a Schematic of the Study Design and analysis used in the paper. It will be easier for readers to follow.
Validity of the findings: Personalized medicine is an upcoming field and providing immunotherapies to patients based on subclasses could be really helpful. The authors have done a good job in showing the novelty and robustness of their subclass analysis that could suggest which subclass of patients will fail for gemcitabine treatment and which subclass could benefit from Vinorelbine treatment.
The weakness of the paper is the disconnect between their discussion on TAMs whereas in the paper they described that they were distinguishing TNBC from the perspective of a "certain immune cell" without providing much context on what is this certain immune cell?
Additional comments: The authors provided a prognostic analysis on a TNBC patient's overall survival and resistance to gemcitabine with respect to immune cell infiltration. Such analysis is important as the tumor microenvironment has been shown to be involved in chemotherapy resistance.
All corrections that are required to be made in the paper could be found in the annotated 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: ESTABLISHMENT AND VALIDATION OF AN INDIVIDUALIZED MACROPHAGE-RELATED GENE SIGNATURE TO PREDICT OVERALL SURVIVAL IN PATIENTS WITH TRIPLE NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Comments to the authors:

Breast cancer is the most commonly occurring cancer in women and the second most common cancer overall. Therefore, studies that indicate new possible therapeutic targets or prognostic biomarker should be encouraged. In the present study, the authors use 6 kinds of immune cells composition analysis, WGCNA expression analysis, and other methods to screen out five macrophage-related hub genes that were associated with prognosis of triple negative breast cancer (TNBC). However, several points are to be considered.

Major comments

1-	Although the analysis of the blue module has pointed out the possible existence of other cell types in the tumor, the authors invest only in macrophages. At this point I have some questions:

a.	Why did the authors exclude the other cells from the analysis?

b.	Under these conditions, the enrichment analysis presented in Figure 1E shows biological processes associated with neutrophil function and other generic processes linked to immune response, but none directly associated with macrophage function. How do the authors explain this fact? Could other cells be involved?

c.	Did the authors perform analyzes in other molecular signature databases besides GO?

2.  The authors identify five hub genes (CD79A, CXCL13, IGLL5, LHFPL2 and PLEKHF1), which are referred to as macrophage-associated genes. However, it seems not to be very clear the association of these genes with macrophages. According to the Human Protein Atlas (https://www.proteinatlas.org) CD79A is expressed on B lymphocytes, LHFPL2 on dendritic cells and PLEKHF1 on T cells but not on macrophages. Thus, the authors should clarify what supports the statement that these genes are linked to macrophages and not to other cells.

3. Figure 3 is confused; the text order does not match the order of the panels. For example, figure 3D should be figure 3E and figure 3F should be figure 3H. Please check the entire figure 3.

4. Based on the GDSC database（https://www.cancerrxgene.org/) the authors evaluated the responses of two subgroups Cluster A and Cluster B that were previously clustered according to 5 hub gene to anticancer drugs. However, this tool has characterized 1000 human cancer cell lines and screened them with 100s of compounds. Considering that the focus of the study is on genes expressed by immune cells such as macrophages. How can drug testing in tumor cell lines be associated with the genes described in Cluster A and B of the present study? Furthermore, it would be interesting the authors to describe in more detail the methods of how they performed this analysis.

Minor comments

1.	Authors could indicate the meaning of acronyms in the abstract. For example, TNBC, BRCA and GDSC are without their description. Additionally, throughout the text this question is repeated. Please review the use of acronyms.

2.	Please increase the font size in the figures

3.	In figure 2D the authors could indicate the clusters as A and B.

4.	Authors could standardize the use of colors to indicate groups. For example, in Figure 2E cluster A is blue and cluster B yellow. Next in figure 2F cluster A is yellow and cluster B is blue. Standardization can help read the article.


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: ESTABLISHMENT AND VALIDATION OF AN INDIVIDUALIZED MACROPHAGE-RELATED GENE SIGNATURE TO PREDICT OVERALL SURVIVAL IN PATIENTS WITH TRIPLE NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article merits English revision. The authors must mention the limitations of solely using bioinformatics platforms. That information must the included in the discussion section. Regarding the structure of the figures, improving the resolution and quality of all figures is essential. Most of them is of low quality, which makes them unintelligible.
Experimental design: In the experimental design, please add a workflow to depict the study phases and number of samples used in each step.
Validity of the findings: The study provides a relevant research question. However, it is necessary to carry out an external validation of the findings to ensure a robust conclusion. We mean, the use of databases is associated with several limitations. Please, see the comments to the authors.
Additional comments: Su et al. evaluated an individualized gene signature related to macrophages to predict
overall survival in patients with triple negative breast cancer. The authors showed that they found five central prognostic genes associated with macrophages, and a prognostic model was constructed to predict the survival of patients with TNBC. However, the study lacks external validation to improve the study robustness to support the findings of the bioinformatics platforms. Some important points must be addressed to improve the quality of this study before the final recommendation as follows:

Comment:

•	Immune infiltration analysis and WGCNA screening of macrophage related genes in TNBC (line 209-210): The authors showed a gene signature in TNBC macrophage infiltrate. What is the immunological profile of this macrophage? M1 or M2? Based on that, an independent external validation of the signature is essential to support the conclusions.

•	The following confounding factors were not taken into account. Key points unadressed: 1) the duration of chemotherapy exposure and sample collection. 2) Type of chemotherapy regimen used. 3) Considering the chemotherapy is known to modulate the macrophage phenotype in tumor microenvironment, a group naive of treatment would be essential.


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: ESTABLISHMENT AND VALIDATION OF AN INDIVIDUALIZED MACROPHAGE-RELATED GENE SIGNATURE TO PREDICT OVERALL SURVIVAL IN PATIENTS WITH TRIPLE NEGATIVE BREAST CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have done a commendable job in increasing the quality of writing this paper. It was much easier to read and follow. Thank you for adding Fig 1 as it helps the reader to understand the paper.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Su P. et al did extensive analysis and validated their observations with multiple data sets and programs. This study is important in the field of developing personalized medicine against TNBC.

The authors have incorporated all the comments as suggested and it was a delight to read this modified version of the impactful study.


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: ESTABLISHMENT AND VALIDATION OF AN INDIVIDUALIZED MACROPHAGE-RELATED GENE SIGNATURE TO PREDICT OVERALL SURVIVAL IN PATIENTS WITH TRIPLE NEGATIVE BREAST CANCER
Review round: 2
Reviewer: 2

Output:
Basic reporting: none
Experimental design: none
Validity of the findings: none
Additional comments: Two major points remain unresolved:

1. It must be demonstrated that these 5 hub genes are expressed in macrophages. This can be done by rtPCR on differentiated M0, M1 or M2 macrophages, or use a public database with these cells, or use a single cell analysis of TAMs.

2. Drug testing is done on tumor cells, not macrophages. Are these genes also expressed in tumor cells? As a suggestion, this data could be removed from the article.


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: ESTABLISHMENT AND VALIDATION OF AN INDIVIDUALIZED MACROPHAGE-RELATED GENE SIGNATURE TO PREDICT OVERALL SURVIVAL IN PATIENTS WITH TRIPLE NEGATIVE BREAST CANCER
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The article can be accepted in its current form. However, as a suggestion I believe that use "hub genes associated with immune response" is more adequate.


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: SURVIVAL RATES OF ADULT AND JUVENILE GYRFALCONS IN ICELAND: ESTIMATES AND DRIVERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I have some general comments on suggestions for alternative wording in section 4, but otherwise the manuscript is clear and well written. Given that neither author is from an English speaking country, I commend you on your writing.

The references are appropriate given the subject matter and I noted no obvious omissions. Perhaps more detail could be provided about ringing procedures, or simply refer readers to another paper for more details.

I thought Table 1 could be moved to supplemental (most of the parameter estimates and credible intervals are already cited in the text), and that the regression coefficients for Model C could be better displayed as a violin plot. Regrettably, I don't code in STAN so I wasn't able to thoroughly review the materials in GitHUB, but I went to the website and examined all materials. Everything is well documented.

The results are clear, and except for a few issues noted in general comments, I think that the authors did an outstanding job.
Experimental design: Materials and Methods: From figure 2 it seems that the covariates were all standardized, but you should probably state that clearly in the Methods. And for the regression parameters in Table 1 to make sense, you will need to inform the reader of the means and SD’s for each variable (this could be provided as supplemental information).
Validity of the findings: Results: It seems odd in an elegant Bayesian analysis to dismiss something as potentially important (e.g. winter temperatures, winter precipitation) because the 95% CI barely touches, or doesn’t quite touch, 0 (Fisher would be smiling in his grave).

Table 1: What does a SE mean in a Bayesian context? The SD is equivalent to a SE based on maximum likelihood estimation; the SE is just confusing. For that matter, this is just a table of STAN output that isn’t that helpful. You already include many of the parameter estimates and credible intervals in the text. I recommend making violin or rainfall plots of the posteriors for B1, B2, and B3, which will confirm that all 3 effects are mostly positive, and if all 3 are standardized, then the ptarmigan effect isn’t that much more pronounced than the temperature or precipitation effects.

Discussion (line 136-137): “This average adult survival rate corresponds to a mean duration of the adult stage of 5.88 years, and thus an average lifespan given survival of 8 years.” First, which adult survival rate do you mean by “this” because earlier in the paragraph you cite 0.83 as your empirical estimate (0.830 for Model A, but 0.834 in Table 1 based on Model C), but you also cite 0.81 based on the meta analysis of Newton et al.
Using your Table 1 value of 0.834 and calculating mean future lifespan for a newly banded adult, I get 1/-ln(S2) = 5.51 years, not 5.88 (using 0.830 gives 5.37 years).
And using the formula: 1/-ln(S1) + S1/-ln(S2) + S1/ln(S1) gives 2.78 years predicted mean survival for a newly banded juvenile (formula from Seber 1973 cited in Anderson, 1975, Population Ecology of the Mallard V). Perhaps you used a different formula to calculate mean expected lifespan, but because you haven’t indicated how you did this calculation, it’s difficult to interpret if it is appropriate or not.

Discussion (lines 138-148): Here you discuss evidence for individual heterogeneity, but your survival model for adults did not include an effect of individual heterogeneity (although Kery & Schaub consider such models) and therefore there is no evidence of survival heterogeneity based on your analysis.

Discussion (lines 141-144): These are apparent survival probabilities only if dead recovery data are limited to the mark-recapture study area. If the data include dead recoveries from gyrfalcons that dispersed off the study area (or could have been recovered if they dispersed off the study area), then these are true survival probabilities. You mention recoveries of dead juveniles from off the study area, so it seems that these are true survival probabilities, and the Discussion should be modified appropriately (see also lines 162-164, 175-178).
Additional comments: Minor comments (recommended wording changes, other comments and suggestions):

Abstract (line 10): “especially for adults” or “especially of adults”

Abstract (line 12): use “encounters” instead of “recaptures” because dead recoveries are not really recaptures.

Abstract (line 14): Reword as “with weak positive effects of prey density (ptarmigan), winter temperatures, and winter precipitation on juvenile survival”

Introduction, paragraph 1: Here you point out that adult survival is expected to show less annual variation than juvenile survival, based on Pfister (1998), but you don’t fit models that estimate juvenile and adult annual survival as random effects, which would allow you to test this idea. It seems odd to include this in the Introduction, but then not follow up on it (I could see citing it in the Methods as justification for why you don’t bother considering temporal variation for adults, but here in the Intro it seems to set up a hypothesis that is never tested).

Intro (line 19): Reword to: “for building population projection models.”

Introduction (line 24): delete “territorial” because it isn’t necessary. Delete “both” because it is confusing (also in line 27).

Introduction (line 28): important for what? Consider adding “important for understanding annual population dynamics”.

Introduction (line 29-30): I would consider omitting “a large iconic bird of prey – the largest falcon –“ because it breaks the flow of the sentence.

Intro (line 32): add “to changing prey abundance” to the end of the sentence.

Fig 1: The scale on the right side is unnecessary and confusing.

Material and Methods (line 44-45): I recommend rewording this sentence as “We excluded data from 103 adult birds that were released into the wild after rehabilitation and 5 nestlings that were marked with improper sized rings.”

Results: consider referring to the survival estimates as probabilities rather than rates, since they are measured on the interval scale and not instantaneously.

Line 49: “…estimates of survival”

Line 96: delete “dynamics” and just say “reproductive densities”.

Line 98: change “is” to “are” to match the plural “conditions” earlier in the sentence.

Figure 2A y-axis legend should say “Predicted” rather than “Predator”; understanding the biological magnitude of this effect would be easier if you provided information to help interpret the X axis; e.g. “Standardized ptarmigan abundance of -1  and 2 were approximately #.#  and #.# individuals/km2, respectively.”

Discussion (line 183): replace “would likely enter predator demography through predator fecundity“ with “likely occur due to increased fecundity of gyrfalcons when ptarmigan are abundant.”


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: SURVIVAL RATES OF ADULT AND JUVENILE GYRFALCONS IN ICELAND: ESTIMATES AND DRIVERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1)	Line 42 reads “As can be seen in Fig. 1, most recaptures are dead recoveries”. However, I find it rather difficult to extract this information from the figure. Thus, could you please add numbers here for clarification?
2)	Although that might be my fault, I find Figure 1 rather difficult to interpret. On the y axis are plotted the years in which individuals have been observed (which usually was just one year), right? But what does the legend on the right mean? Could you please either revise the figure or add a sentence explaining it in more detail?
3)	In my opinion, the paragraph in lines 77-82 should rather be placed at/towards the end of the methods section as you otherwise jump between presenting the model and explaining how you fit it.
4)	Figure 2 (A): I suggest using the values from 0 to 1 as range of the y axis, or at least to ensure that the credibility intervals are fully displayed (which is not the case at the left boundary).
5)	Figure 2 (B): The figure should show the whole range of abundance values on the x axis.
6)	In my opinion, Table 1 could as well be placed in the Appendix. However, if you decide to keep it in the main text, it should display the same parameter estimates as the ones used for Figure 2 and presented in the text.
7)	I believe the effects of the weather covariates (model C) should also be visualized such that their relevance for survival can easily be grasped, although the figures might rather be added to the Appendix.
8)	Personally, I would find it quite helpful for the readers to include the transition matrix and the observation matrix in the main document as they nicely “summarize” the text and concentrate the parameters that are of interest. Why would you rather put them in the Appendix instead?
Experimental design: 1)	I am missing some sort of model comparison between model B and C (and possibly model A, although it is currently based on a somewhat larger data set, but could also be fitted on the smaller one). This would greatly help to assess the importance of the covariates for juvenile survival. Therefore, I suggest to perform some model selection first between the models A to C, and to then present the results of the chosen model (or at least either model B or C) in the main text. Currently, Figure 2A depends on different parameter estimates than those shown in Table 1, which can be rather confusing.
2)	ll. 40-41: Do I understand it correctly that data on 1816 individuals has been used for analysis, of which only 293 have been recaptured and all others have been observed once? Could you please clarify how often individuals have been resighted or recaptured alive, and how many have been recaptured dead? I believe additional descriptive statistics on the data are necessary here.
3)	In line 121 you present a different parameterization. The notation appears to be different to the one in line 91, why? And why has the covariate not been standardized in this model as well (cf. Figure A1 in SI)?
Validity of the findings: 1)	Regarding the effect of Ptarmigan abundance on the survival of juveniles (ll. 125-126): As the credible intervals are quite large, it is also possible that the abundance has no effect at all on survival. Therefore, I suggest formulating this result in a more cautious way (also in the abstract) and to point out the large uncertainty in the parameter estimate.
2)	In line 166, you call the effect of Ptarmigan abundance on survival “moderate”. I would disagree – if there is any effect at all, it is rather small. Could you hence please rephrase this sentence.
3)	The estimate of the probability of detection is very small (ll. 116-117). Is that realistic, i.e. are there similar results in other bird studies? How have the data been collected that the detection probability is so small, could you please elaborate on this?
4)	In lines 183-188 you discuss the results of weather effects on juvenile survival. However, as there are huge uncertainties in these effects, I rather believe that one cannot conclude anything from these results (at most some minor indication for a possible positive correlation). Therefore, I suggest rephrasing this paragraph. In addition, one could think of missing covariates or interaction terms that should be considered in the model, which otherwise might mask the true relationship between survival and weather.
Additional comments: Overall, I enjoyed reading the manuscript, which is well written and clear structured. Furthermore, the analysis is entirely reproducible as the data and code are available online.
However, I do have some concerns regarding the presentation of the findings which should be improved upon before acceptance. In particular, I believe that performing model comparison/selection would greatly improve the understanding of the variables’ relevance for juvenile survival, while the uncertainty in these parameter estimates should be stressed when presenting the results.


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: SURVIVAL RATES OF ADULT AND JUVENILE GYRFALCONS IN ICELAND: ESTIMATES AND DRIVERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The paper is very well written (I have only a few small suggestions for rewording in the Additional Comments section).
Experimental design: The analysis is appropriate, and the Bayes' factors added to the revision make it easier to interpret the covariate effects as being mostly uninformative. I also think that moving the transition and observation matrices from the supplemental materials to the methods makes the paper easier to understand.
Validity of the findings: The authors provide the first published estimates of survival for Icelandic gyrfalcons. Based on added interpretation provided in the revised Discussion, it seems likely that these estimates are very close to true survival (i.e., unlikely to be strongly impacted by emigration).
Additional comments: Thank you for the careful revision. I believe your paper has been improved through your efforts, and will make an important contribution to the literature about raptor population dynamics.

I have highlighted 3 sections of the revised text where the wording is a bit awkward, and one correction for a figure legend. I have provided suggested revisions, but the authors are also welcome to provide their own revisions. Suggestions are in the attached pdf document.


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: SURVIVAL RATES OF ADULT AND JUVENILE GYRFALCONS IN ICELAND: ESTIMATES AND DRIVERS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is well written and clearly structured. The authors adequately addressed my comments from the previous review and, in particular, modified some figures, moved some material to the Appendix and reinserted some information into the main text. Overall, the reporting is greatly improved and hence, I do not have any further suggestions or comments.
Experimental design: As suggested, the authors now systematically compare their models using Bayes factors. This allows for a more thorough assessment of the importance of the covariates for juvenile survival, increasing the quality of the paper. However, I do have one last question:
You write that for models B and C, you exclude 7 capture histories from the data, right? But do you fit model A (and S) on the full data set? Because this would mean that you compare a model fitted to the full data set (model A) to a model fitted to a reduced data set (model B). As far as I know, all models need to be fitted to the exact same data set for model comparison with the same number of observations. Is this the case in your analysis (or maybe I just missed something)?
Validity of the findings: The authors adequately addressed all my concerns from the previous review and stress the uncertainty within their modelling results. There is only one final point regarding possible weather effects on juvenile survival rates, which I think is important to discuss.
You now write that “We therefore disregard those weather effects on juvenile survival. This will undoubtedly simplify future models of gyrfalcon population dynamics.” While I agree that in your current analysis, no weather effects on survival can be detected, I would not dismiss possible weather effects from all future analyses. I was wondering if maybe there is a ‘better’ or more accurate way of including those weather variables in the model. For example, I was wondering if it might make a difference if instead of averaging those variables, you would sum the log-precipitation, or would define a variable counting the number of days on which the temperature is below/above a certain threshold. I do not expect you to rerun your analysis, but I believe that these different possibilities for the variables to enter the model (different transformations, interaction terms, etc.) should be noted and might be explored in future studies – at least if/as there are reasons to suspect that weather conditions influence survival.
Additional comments: I believe the manuscript has greatly improved. I only have two more comments, which I think should be addressed before a possible publication of the paper.


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: EFFECT OF MESOPOROUS BIOACTIVE GLASS ON ODONTOGENIC DIFFERENTIATION OF HUMAN DENTAL PULP STEM CELLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study investigated the effects of mesoporous bioactive glass (MBG) on odontogenic differentiation of human dental pulp stem cells. This work expands the applications of MBG to dental applications, and the results show the potential of MBG in dental pulp damage repair and regeneration. In my opinion, this paper could be accepted for publication in PeerJ after some issues are addressed. Here below are the specific comments:

Introduction

1. Line 49, the authors stated, “… the particles can be prepared into mesoporous materials with more uniform particle size, smaller pore size, and better dispersion by using sol-gel method combined with organic template technology.” Here the definition of MBG should be clarified. Actually, not all MBG have uniform particle size and better dispersion. Only these MBG produced under certain conditions have a uniform spherical shape and favorable dispersity (Ref. Porous bioactive glass micro- and nanospheres with controlled morphology: developments, properties and emerging biomedical applications, Mater. Horizons. 8 (2021) 300–335.). The authors should clarify this.
Experimental design: Methods

2. Section: 2.2 Physicochemical properties of MBG: The composition of 45S5 Bioglass and their particle size should be given. Also, why did the authors compare 45S5 Bioglass and MBG in terms of their pH and ion release behavior? The authors should clarify it.

3. Line 105 “The remaining solid bioglass powder was removed” here “bioglass” should be “MBG” if I understand correctly.

4. “MBG induced the formation of dental pulp dentine complex in rats”. I suggest that the authors could use a schematic to describe the process of in vivo study to help readers understand the procedure.
Validity of the findings: Results and discussion

5. Table 1, why the concentration of P decreased in MBG group compared to the control?

6. Line 241, “Traditional silicate glass has a complete network structure formed by -Si-O-Si- bridge oxygen bonds, which is relatively stable[13]. CTAB is introduced into the system to interrupt the covalent network structure, changing the -Si-O-Si- bridge oxygen bond into a non-bridging oxygen bond -Si-O-M+ (M+ is the modified cation), forming a partially open grid structure[14, 15].” Here the explanation was wrong. CTAB did not change the -Si-O-Si- bridge oxygen bond into a non-bridging oxygen bond -Si-O-M+ (M+ is the modified cation). The incorporated Ca changed it in your case.

7. Line 258, “ In this study, the effect of MBG on pH increase was significantly weaker than that of 45S5, suggesting that MBG has better biocompatibility with tissues and less influence on the growth of pulp cells in vivo.” It is not clear to me why the authors compared MBG with 45S5 Bioglass? Has 45S5 been used clinically? If in this case, I suggest that the authors should also compare MBG with 45S5 in cell and animal studies.
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: EFFECT OF MESOPOROUS BIOACTIVE GLASS ON ODONTOGENIC DIFFERENTIATION OF HUMAN DENTAL PULP STEM CELLS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this manuscript, the authors reported that MBG could induce the odontogenic differentiation of dental pulp cells and the formation of pulp dentin complex. This study provides a potential application of MBG that repairing and regenerating for dental tissue injurie. However, several points need to be clarified.
1.	The information of reagents, materials and instruments that mentioned in this manuscript should be supplied, such as manufacturer, code and country.
2.	The identification for hPDCs should be provide.
3.	Table 2, the mean and standard deviation of ion concentration of MBG extract  should be considered,
4.	The author mentioned that MBG has a large specific surface area, therefore the specific surface area and mesoporous size should be measured.
5.	The Figure 3 cannot support the author’s finding, like mineralized matrix with dentin tubule structure, and the residual MBG particles can’t be observed in the Figure 3. The author should provide more evidence to support the correctness of results.
Experimental design: no comment
Validity of the findings: no comment
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: EFFECT OF MESOPOROUS BIOACTIVE GLASS ON ODONTOGENIC DIFFERENTIATION OF HUMAN DENTAL PULP STEM CELLS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have well addressed my comments and questions. The paper can be accepted for publication.
Experimental design: The authors have well addressed my comments and questions. The paper can be accepted for publication.
Validity of the findings: The authors have well addressed my comments and questions. The paper can be accepted for publication.
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: EFFECT OF MESOPOROUS BIOACTIVE GLASS ON ODONTOGENIC DIFFERENTIATION OF HUMAN DENTAL PULP STEM CELLS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The revised manuscript has addressed most the comments and suggestions by the reviewers, thus, the reviewer recommends publication of current manuscript.
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: A DECREASE IN REPORTS ON ROAD-KILLED ANIMALS BASED ON CITIZEN SCIENCE DURING COVID-19 LOCKDOWN
Review round: 1
Reviewer: 1

Output:
Basic reporting: Language should be checked, particularly in some points that I highlight in specific comments, where the clarity should be enhanced.

Figure 1: In order to show the variation across years, I would plot average line + standard deviation bars, or authors can plot one black line for each year before 2020. This way it will be easier to detect differences in the number of reports between 2020 and previous years.

Figures 2 and 3: the font is really too small, it is impossible to read without zooming in. There is a typo in the bottom label “resondents” in both figures. Columns should be ordered less/same/more roadkills or more/same/less, to make it the understanding of the plots more intuitive.

What is the meaning of the last column of Table 1?
Experimental design: no comment
Validity of the findings: no comment
Additional comments: General comment:

The authors present an interesting work on the effect of lockdown on the number of reports of roadkilled animals. Generally, I think that the topic is interesting, however I have some concerns. My main concern is the language and the presentation of figures. Language should be checked, particularly in some points that I highlight in specific comments, where the clarity should be enhanced.

Figure 1: In order to show the variation across years, I would plot average line + standard deviation bars, or authors can plot one black line for each year before 2020. This way it will be easier to detect differences in the number of reports between 2020 and previous years.

Figures 2 and 3: the font is really too small, it is impossible to read without zooming in. There is a typo in the bottom label “resondents” in both figures. Columns should be ordered less/same/more roadkills or more/same/less, to make it the understanding of the plots more intuitive.

What is the meaning of the last column of Table 1?

My last concern is about discussion. It is a bit confusing, and I would rearrange it in order to avoid repetitions of result. The structure should reflect the main results: i) drop in roadkill reports ii) people moving less iii) people felt to report less roadkills even if their travelling did not change.

Specific comments:

Lines 50-52: The sentence is not clear, I would rephrase that. For instance, “roads” can’t “decrease in extent”: eventually the negative effect of roads can decrease. Additionally, the listed factors do not influence “behavior or habitats” but “activity and habitat suitability” might be preferable as terms. Rephrasing the sentence will help.

L52: Start the sentence with “Roads can have positive or negative influence on animals, depending on…”.

L66-67: Are all the project participant also writing this manuscript? Otherwise, the sentence should be rephrased because it seems that there are just two people in roadkill project (I see at least 4 on the website, so I suggest to rephrase the sentence to avoid misunderstandings).

L69: Rephrase this part of the sentence, it is not clear.

L 69: Sentence starting at the end of this line should start with “The project is its first stage, etc…”.

L79: change “amphibia” to “amphibians”

L79: “huntable” is not a good category. What is “huntable” in Austria may be not in other countries.

L81: “amphibians”

L81-83: I did not understand the sentence. There are many example of usefulness of citizen-science with many groups, not only amphibians. Additionally, why “citizens potentially also cover”? It seems that only the ones that report amphibians travel long distances, while it is not the case for the citizens reporting reptiles/mammals/etc… rephrase the sentence.

L 90-91: Merge the two sentences. In the second one the authors make an example with common toads even if second sentence is about non-amphibians.

L103-105: Too many “however”

L108: delete “your”

L122: “Mai”

L124-125: “You can find a translation of the survey in the appendix (Appendix 1).” -> “A translation of the survey is available in Appendix 1.”

L151-157: What is “F”? I see “Question 1, 1.1, etc” in appendix, no “F”.

L166: Since you shared the survey also with people not participating in the program, it is wrong to say that 77 is 43% of users (you may have also non-users as you state at line 138).

L170: “table” -> “Table” ?


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: A DECREASE IN REPORTS ON ROAD-KILLED ANIMALS BASED ON CITIZEN SCIENCE DURING COVID-19 LOCKDOWN
Review round: 1
Reviewer: 2

Output:
Basic reporting: Authors meet all basic reporting requirements of journal  - see general comments for author for full review.
Experimental design: Authors meet all experimental requirements of journal - see general comments for author for full review.
Validity of the findings: Authors meet all validity requirements of journal - see general comments for author for full review.
Additional comments: This study describes a decrease in reported roadkill observations in the Project Roadkill database during a COVID-19 lockdown in Austria and examines the underlying cause. The authors explore whether the decrease in reports was due to an actual decrease in roadkilled animals or due to fewer reports from volunteers in Project Roadkill. This is a novel and important study investigating the cause of a decrease of wildlife roadkill observations during COVID-19 lockdown. A few other papers have examined pre- and during-lockdown roadkill observations but have not explored the possibility that fewer roadkill reports were due to fewer volunteers collecting data. This is an interesting and novel topic and provides basic investigation on causes of fewer roadkill reports in Austria, however, the study could use deeper inspection on the following:

-	Though not the central question of the study, it would be interesting to see basic quantifications of changes between pre- and during lockdown observations by major taxon groups in Austria. These comparisons could reveal if there were differences in observations of different taxon groups in the two time periods. It could be especially interesting if there were differences in reported roadkill since authors found that many volunteers began walking/biking rather than driving.
-	Authors should  consider the more inclusive term “community scientist” or volunteer rather than “citizen scientist.” It has been widely accepted and used by many large voluntary science programs such as the U.S. Audubon: “As part of Audubon’s commitment to equity, diversity, and inclusion, we have transitioned from using the term “citizen science” to the more inclusive term “community science.” No matter where a volunteer was born, or how they came to the United States, we value their contribution to our science and conservation programs.” (https://debspark.audubon.org/news/why-were-changing-citizen-science-community-science#:~:text=As%20part%20of%20Audubon's%20commitment,to%20our%20science%20and%20conservation)
-	A more in-depth introduction to volunteer-based and opportunistic roadkill observation programs would be helpful so that those unfamiliar will have a better understanding of shortcomings and benefits – expand on lines 56-59 (e.g. Waetjen and Schilling 2017, Chyn et al. 2019, Pagany 2020, and many more). There are also a few other studies on the effect of COVID-19 lockdowns on roadkill numbers not described or cited (e.g. Shilling et al. 2021, Lopuki et al. 2021).
-	There is inconsistent usage of road-killed vs roadkilled. Both are valid but authors should choose one consistent spelling.
-	Awkward phrasing throughout (a few examples noted below in specific comments) and some sentences need restructuring – could use a revision focused on clarity and flow.
-	Figures 2-3: helpful visualizations, but since the frequency of daily routes is “reduced,” “no change,” “increased”, I think it would be more consistent (and smoother) if the number of reported roadkill is in a similar order of  “less roadkills,” “same,” then “more roadkills.”

Specific comments by line:

42: “life” vs “live”
60: “wildlife” (no cap)
66-67: Transition to last sentence is awkward and could be smoother.
68: Don’t need “as much as possible”
73: “In Project Roadkill?”
80: “suburban”
90-93: Restructure sentences for clarity. Grammar is a little unclear.
94-98: Restructure for clarity – run on sentence.
107-109: Verbose/wordy – revise for clarity.
110: Delete “a”
124: “May”
166: Cite ‘gmodels’ developers
202: “Chi-square”
215: “We got a similar picture when we asked for” – a bit colloquial. Revise with more technical language.
234: “fewer” vs “less”
300: “roadkills”