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: DEVELOPMENT AND VALIDATION OF A NOVEL RISK SCORE TO PREDICT 5-YEAR MORTALITY IN PATIENTS WITH ACUTE MYOCARDIAL INFARCTION IN CHINA: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.The details of missing value for each variables should be complemented in a separate table.
2.The polishing of the language and presentation of the manuscript is necessary.
Experimental design: 1.The author needs to explain whether the sample size is sufficient and how to calculate the sample size.
2.Whether the enrolled patients included both type 1 and type 2 AMI. In view of the significant differences in the pathogenesis between the two types, it may not be appropriate to use a universal model.
3. In the final model, it may not be appropriate to directly include the continuous variable, but the continuous variable can be transformed into the classification variable into the final model. eg, if the glucose was included in the model as a continuous variable, whether it meant that the higher glucose was, the higher the mortality rate was, and the lowerthe glucose was, the lower the mortality was. It is obviously unreasonable.
Validity of the findings: CAMI score was designed to predict the prognosis of Chinese patients with AMI as stated by the author in the Discussion part. The comparison of prediction performance between C2ABS2-GLPK and CAMI scores need to be conducted, if possible.
Additional comments: The present study aimed to construct a prediction nomogram to predict the 5-year all-cause mortality of AMI. The subjects were hospitalized between January 2013 and December 2017, and the follow-up was completed in December 2019, which meant we didn't know exactly if the most of subjects hospitalized after 2015 died five years later. The follow-up can be continued in the future.


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: DEVELOPMENT AND VALIDATION OF A NOVEL RISK SCORE TO PREDICT 5-YEAR MORTALITY IN PATIENTS WITH ACUTE MYOCARDIAL INFARCTION IN CHINA: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well constructed and the study flowchart is nice and clear, however English writing can be improved.
There are A LOT of figures and tables and I'm not sure all are needed or provide interpretable information. Please review what you would like to include and their relevance to the findings in the manuscript.

The risk score is reported as a continuous number going up into the hundreds, yet in Figure 4 it is also referred to as a % predicted risk. How was an absolute risk obtained from a Cox model that provides relative risks?
Also, the three final risk bands that are produced include a huge range of risk in the intermediate risk group (4.3-26.5% 5-year risk of death). Please comment on how useful the risk bands are likely to be in clinical practice.

Calibration is assessed, which is good. Please show calibration plots in terms of cumulative probability, not survival. With the current calibration plots, the groups are all squashed into the low risk/high survival end of the scale, and we miss seeing just how accurate risk is predicted in the relevant risk range. Also, the production of calibration plots mean the risk has been converted to absolute risk, so how come the score is reported in the unhelpful scale that goes up into the hundreds?
Calibration is quantified with the calibration slope and intercept, and thank you for including the intercept. It is often overlooked but is vital to show the accuracy of the risk estimates.  Here, intercepts were typically far from 0, with values of 0.2-0.4, showing likely overestimation of risk, yet it is not mentioned in the interpretation of the results. Please include.

Why are both the c-statistic and the AUROC calculated? And reported interchangeably?

Hazard ratios don't need to be reported to 3 decimal places (see Table 2). Given the small cohort and low number of events, I suggest 1dp would be appropriate.
Experimental design: Patients were excluded from the study cohort if their length of stay was <1 day.  The number excluded on this basis were low but please clarify how many of these were due to the patient dying?

The risk score aims to predict risk of death over 5 years. How many people had the opportunity for 5 years of follow-up?

One of the rationales for developing this score is that a score is needed to predict death during the in-patient stay as well as in the longer period.  Yet it is only ever tested in the medium to longer term. I couldn't see where it's performance was assessed for in-hospital or convalescent phase post-MI.  Please clarify exactly when the score is intended to be used and the results of the assessment that support such use.

A variable in the final model was "PCI (immediate or delayed)". How delayed?  This would also impact on when the score can be used. (as it can't be applied if it needs information about something that happens in the future).
Validity of the findings: The study followed the TRIPOD guidance for reporting of prognostic models, which is great to see. Derivation and validation cohorts were clearly defined and used from the outset, and sensitivity analyses were clearly reported.  It was also good that the authors compared the new score to a selection of existing scores for this patient group. The new score derived from the type of cohort used to test it in will always have an advantage over completely independent scores but there was still a point to be made over the better discrimination of the new score over GRACE, at least.

Importantly, the limitations of the study are well described.

There was a lot of variable selection which I'd question is statistically appropriate. However, the goal of a prognostic model is to predict risk, as opposed to the etiological or statistical importance of individual predictors, so an allowance for that can be made. And in terms of performance, the ability of the new score to discriminate, or rank, risk seems well supported.  Calibration, or accuracy, of risk appears ok but we can't really assess it given the format of the calibration plots and information that is currently provided.
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: PECAN AGROFORESTRY SYSTEMS IMPROVE SOIL QUALITY BY STIMULATING ENZYME ACTIVITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript named “Pecan Agroforestry Systems Improve the Soil Quality by Stimulating the Enzyme Activity” was interesting to readers. In this manuscript, the English language is clear and relatively professional, but it still needs to be improved to ensure that an international audience can clearly understand your text. More importantly, there are some Chinese expressions in your manuscript. Some examples where the language could be improved include lines 51, 92-92, 218-219, 231-232 and so on. The current phrasing makes comprehension difficult. I suggest you have a colleague who is proficient in English and familiar with the subject matter review your manuscript, or contact a professional editing service.
    Intro & background shows in context. Literature is relevant but the formation in text and part of references is relatively poor. For examples in line 53, 55, 66, 116 and so on. I suggest you should check the literatures in text and part of references carefully to promise the formation is correct and consistent.
    The structure of manuscript conforms to Peerj standards. Figures are relevant and well labelled and described but not high quality because of poor definition. I suggest you can import figures as the .tif or .png.
   Raw data supplied is complete.
Experimental design: This manuscript is within the scope of Peerj. Research questions were well defined, relevant and meaningful. It is stated how the research fills an identified knowledge gap. Rigorous investigation performed to a high technical & ethical standard. Methods described information to replicate but with insufficient detail in dealing samples and determination methods. The process of the field sampling and sample handling in lab were described not clear. In addition, the determination of soil enzyme activity is not detailed enough. Finally, there are no references about determination method of each index. I suggest you should add relevant literatures.
Validity of the findings: The findings in this manuscript was meaningful and instructive to some extent. All underlying data have been provided; they are robust, statistically sound. Conclusions are well stated, linked to original research question & limited to supporting results.
Additional comments: Abstract:
1. In background, I suggest you should rewrite because the current background and purpose are not related to research content. More importantly, “the formation of a mechanism that drives the organic combination of multi-industries” was not studied in manuscript, so I suggest you delete this sentence.
2. In results, there are some uncommon abbreviations which was not spelled out at first use, such as kinds of soil enzymes. Finally, the last sentence is suggested to be deleted because it has a poor correlation with previous contents and it do not belong to your results just literature review for other references.
Introduction:
1.Line 50: I suggest you should add some new and relevant references to ensure domestic and foreign research progress to be shown adequately.
2.Line 51:Repalce the ”maintenance” to “increase”.
3.Line53: Revise “to improve” to “to be improved”. The formation of “Q. S. Li et al., 2018” is wrong, please correct it. So was the Line 55, 66,116, 239.
4.Line63: There was no reference named “Chen et al., 2017”, please delete it or replace it.
Materials & Methods:
1.Line92-93: There are some grammatical mistakes. Foe example, there are some simple sentences without coordinating conjunctions. Please revise them.
2.Line103:In text, the “0~20cm” and “0-20cm” appear many times, but their formation do not keep consistent. Please revise them.
3.Line 110:The “water content (MC)” may is the “water content (WC)”. Please revise it.
4.Line133:the software that is used to the PCA analysis needs to be noted.
Results:
1.Line153:Please correct “the same layers” to “same layer”.
2.Line158: ”(p<0.05)” is “(p<0.05)”. In the following manuscript, there are many mistakes, such as “(p<0.05)” or “(P<0.05)”. Please revise them to “(p<0.05)”.
3.Line164: Please replace “Correlation study” to “Correlations”.
4.Line181:Please revise “between the PPS, PPL, and CK agroforestry systems” to “among PPS, PPL, CK”.
5.Line187: I suggest you can combine this paragraph and paragraph in line164.
Discussion:
1.Line218: Please revise the “Ca and Mg content” to “contents of Ca and Mg”.
2.Line231:Delete “furthermore” and revise the “and played” to “which plays”.
3.Line233:Please revise the “agroforestry cultivation of” to “with the cultivation of”.
Conclusions:
1.Line263: Please replace the “impacts on” to “changes of”.


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: PECAN AGROFORESTRY SYSTEMS IMPROVE SOIL QUALITY BY STIMULATING ENZYME ACTIVITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper presents an interesting topic of the impact of pecan agroforestry systems on the soil quality by stimulating enzyme activity, which could help gain insights into optimized land utilization and the promotion of stand growth. The soil physical and chemical indicators of different treatments were measured, the correlations were analyzed between soil physicochemical properties and soil enzymes, the author must dig deeper into the innovation points and draw conclusions from their data. Another obvious problem with this paper is the lack of logic, many paragraphs are confusing and beyond comprehension.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Abstract：
Line 27-30，The abbreviation are unnecessary.
Line 32, 35 & 36, Please define “C”, “N”, “P”, “TP”, “TN”, “AK”, “TC”, “S-UE”, “S-AKP”, and “S-NAG” when they are first used. Please check such errors throughout the manuscript.
Line 32-36, Please reorganize your main conclusions to make them not so confused.
Line 39, “root interactions and the microbial compositions”. The conclusions are overstated.  I suggest that you improve the description to provide more significance of your study.

Introduction：
Line 50. Delete “-”
Line 53, 55, 61 & 66, In-text citations should be corrected to consistent format according to the author guidelines. Please check such errors throughout the manuscript.
Line 61-62. An explanation of why the soil quality improved through soil enzymes should be provided.
Line 44-84 There is too much unnecessary information, while some important terms and information are left unexplained. Consider merging some paragraphs to make the introduction more focused

Materials & Methods
Line 103. Please leave a blank space between numbers and units.
Line 124. Please introduce the determination method of soil enzyme activity, not just the name of the company.
Line 127-133. Please pay attention to the paragraph format and carefully modify it according to the author guidelines.
Line 110. MC is the abbreviation of water content? Please provide abbreviate form in common use.

Results

Line 142 & Line 146. “(P < 0.05)”, Pay attention to the use of space symbols.
Line 157 Delete “from”.
Line 180-193. The authors should clearly present the results of statistical analyses, main effects and comparison between different treatments should also be reported clearly.

Discussion
Line 201 More discussion and interpretation on the soil quality affected by agroforestry system should be provided in comparison with the other agricultural soils.

References
Line 280. The references in this study should be updated according to checking the recent published literature.
Line 346 & 402. Before submitting a manuscript, be sure that the list of references is properly prepared and formatted.

Figures and Tables
1. The statistical analysis of Figure 3 was plainly unreasonable. Soil enzymes were measured at a depth of 0-20 cm, not include 20-40 and 40-60 cm.
2. Please add the title of X axis in the Figure 1, 2 & 3.
3. All the tables should be revised for the inconsistent format
4. Table 1, 2 & 3 are not necessary since the information is presented in Figure 1, 2 & 3.

Language
It is noted that your manuscript needs careful editing by someone with expertise in technical English editing paying particular attention to English grammar, spelling, and sentence structure so that the goals and results of the study are clear to the reader.


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: PECAN AGROFORESTRY SYSTEMS IMPROVE SOIL QUALITY BY STIMULATING ENZYME ACTIVITY
Review round: 1
Reviewer: 3

Output:
Basic reporting: Background, abstract and introduction part of the manuscript is well written as per the requirement of the topic.
Manuscript is structured as per the journal standards. Whereas, the main headings and the references given in running text of manuscript needs to follow journal pattern.
Avoid repetition of the text given in line number 75-80 (Introduction), which is related to the methodology, so it should be place under Materials & Methods heading.
Figures and tables have relevance to the research and are in required quality.
However, there have some sort of scope to improvement in language as comments give in sticky notes on the manuscript (pdf file). Minor corrections also have to incorporate in the manuscript as per comments given on pdf file of manuscript.
I thanks for the providing raw data, all figures and tables in separate files.
Experimental design: Original research is in the scope of the journal.
The topic of the research has scope in widely adoption of the agroforestry systems for conservation of natural resources especially soil quality and health.
Manuscript hypothesis were well designed by the authors and discussed well.
S sampling method: why this method is used for the study. Needs to give reference of that method.
Soil preparation method for analysing physico-chemical and enzyme activity needs to check and confirm it. (Soil samples were dried for determination of physicochemical properties and kept in refrigerator at 4° C for determining enzyme activities)
Methods used for the determination of soil physicochemical properties and enzyme activities as given with sufficient reference information.
Analysis of the data is done by using standard statistical tools.
Validity of the findings: The research includes very interesting idea and it has wide scope in further research such as belowground interactions between tree-crop components of the agroforestry systems.
The literature provided in the manuscript is sufficient and backing the current research.
The research is replicated well for minimizing the errors in outcomes of the study.
The data given in manuscript is sufficient, analysed by statistical tools as per requirements and nicely illustrated in the manuscript.
In 20-40 and 40-60 cm soil depth: When BD has positive correlation with Ca and Mg, then how MC is positively correlated with Ca and Mg? (Line 172-1174)
Use correct short forms of the different agroforestry systems given in manuscript. (Line 139)
Additional comments: Overall, the manuscript is well written and has wide scope as per journals requirement. It has further scope in advance research in belowground tree – crop interactions.
Manuscript has some major mistakes need to check and correct them for improving standard of the paper and journal.
Authors need to follow journal pattern in case of manuscript headings and reference style.
Manuscript needs revision as per comments given on 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: PECAN AGROFORESTRY SYSTEMS IMPROVE SOIL QUALITY BY STIMULATING ENZYME ACTIVITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript named “Pecan Agroforestry Systems Improve the Soil Quality by Stimulating the Enzyme Activity” has been resubmitted for publication in Peerj. This manuscript has really improved after revision. And authors replied to reviewers and included into the text most of these comments. However not all of them were considered in the manuscript.
Experimental design: After revision, research questions were better defined and relevant. Methods described information to replicate with more details in dealing samples and determination methods. The process of the field sampling and sample handling in lab were described more clearly. In addition, the determination of soil enzyme activity is detailed enough. Finally, there are some relevant references about determination method for each index. Overall, authors did a good work during the process of revision.
Validity of the findings: The findings in this manuscript was meaningful and instructive to some extent. All underlying data have been provided; they are robust, statistically sound. Conclusions are well stated, linked to original research question & limited to supporting results.
Additional comments: Abstract:
No comments.
Introduction:
1.Line 59: Please revised the “pecanS” to “pecans”.
Materials & Methods:
1.Line85: Delete the “,” in phase of “115 °36' E,”.
2.Line85: Please explain the meaning of “experences”. Maybe there is some spelling mistake for this word. Please amend it.
Results:
1. Line148: Please revised “(p<0.05)” to “(p<0.05)”. Statistical probability is p (small + italic). In the following manuscript, there are many mistakes, such as “(p<0.05)”. Please revise them to “(p<0.05, small + italic)”. Last time, the formation of “p” changed, after this comment was copied to system. So the italic “p” was not obvious.
2.Line185: Please replace “Correlation study” to “Correlations”.
3.Line 202-203: Please revised “TC and TN, Ca and Mg contents” and “the Ca and Mg contents” to “contents of TC and TN, Ca and Mg” and “contents of Ca and Mg”. Because “TC and TN, Ca and Mg contents” and “the Ca and Mg contents” are the translations according to Chinese. So was the “The AK, TN, and TC contents” in Line 283-284. Please correct it.
Discussion:
1. Line 252: Please add the “.” behind “the soil (Rudolph et al,. 2013)”.
2. Line 283: Delete the “,” behind the “TN”.
Conclusions:
No comments.


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

Input:
Title: PECAN AGROFORESTRY SYSTEMS IMPROVE SOIL QUALITY BY STIMULATING ENZYME ACTIVITY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript named “Pecan Agroforestry Systems Improve the Soil Quality by Stimulating the Enzyme Activity” presents an interesting topic and have a good writing. In the present status of the manuscript, I suggest a minor revision should be made before the publication in PeerJ.
Experimental design: The revised manuscript is within Aims and Scope of the journal. Research questions were well defined, relevant and meaningful. It is stated how the research fills an identified knowledge gap. Rigorous investigation performed to a high technical & ethical standard. In addition, I suggest you should add references or websites of meteorological data sources.
Validity of the findings: The findings in this manuscript was meaningful and instructive to some extent. All underlying data have been provided; they are robust, statistically sound. Conclusions are well stated, linked to original research question & limited to supporting results.
Additional comments: Introduction：
Line 58-69. The font size of this paragraph should be consistent.

Materials & Methods
Line 86-88. Add references or websites of meteorological data sources.

Results
Line 146. Delete “the”.
Line 185-186. Please simplify the headline.

Conclusions
Line 294-296. This section mainly introduces the important progress and significance of the research, please modify the unnecessary description.


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: RNA SEQUENCING-BASED EXPLORATION OF THE EFFECTS OF BLUE LASER IRRADIATION ON MRNAS INVOLVED IN FUNCTIONAL METABOLITES OF D. OFFICINALES
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. In line 102, the format for units need to be written correctly, such as
“ 1 g L−1 ” “ 6 g L−1 ” need to be revised as “ 1 g·L−1 ” “6 g·L−1” et al.
2. In line 132, “P value” needs to be revised as “P-value”, and in the whole manuscript, please unified the writing, modify “qPCR” as “qRT-PCR”.
3. Table 1 has no lncRNA result in the table and the whole manuscript also has no lncRNA analysis, please explain it or delete it.
4. A uniform format is needed for the “References” part.
5. The legend in Figures 3A-3C was not complete, please explain clearly.
Experimental design: 1. Why the author selected the tissue culture seedlings of D. officinale in the incubator for 60 days to sequencing and assay the different functional metabolites.
Validity of the findings: 1. In the results, actually, in line 180 “differentially expressed genes” need to be as “differentially expressed mRNA”. And we suggested that this paragraph could merge with line 236. For another, we want to know why to choose the top 10 up- and down-regulated DEG mRNAs analysis under different light treatments. Why didn’t choose specific expression genes to analyze under the blue laser?
2. In line 446, How to establish a blue laser signal network, the discussion part needs to be explained clearly.
Additional comments: 1. In line 310, what's the criterion of the 9 groups mRNAs to further verify by qRT-PCR should be mentioned.
2. In the discussion, in line 325, the conclusion is not correct: “D. officinale responds to blue lasers through cutin, suberine, and wax biosynthesis ”, from the manuscript have no direct evidence to prove that, this is a hypothesis, and probably exist, please consider.


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: RNA SEQUENCING-BASED EXPLORATION OF THE EFFECTS OF BLUE LASER IRRADIATION ON MRNAS INVOLVED IN FUNCTIONAL METABOLITES OF D. OFFICINALES
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear and unambiguous
Experimental design: Research question well defined, relevant & meaningful
Validity of the findings: Impact and novelty not assessed.
Additional comments: 1.In line 17, when the abbreviated noun “ LB-B, LB-W and W-B” first appears, please mark the full name.
2.In line 157, Please explain the use of the ACTN gene as the reference gene for qRT-PCR.
3.In line 169, “the number of red leaves under the blue laser treatment was greater than that under the blue and white light”, there was a statistical analysis? Please write out the statistics on the number of plants.
4.The focus of the research is not prominent and too protracted, so it is suggested that integrate the expression of differential genes and secondary metabolite contents into one graph for comparative analysis, so that the results will be more intuitive, clear and easy to understand for other readers.


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: RNA SEQUENCING-BASED EXPLORATION OF THE EFFECTS OF BLUE LASER IRRADIATION ON MRNAS INVOLVED IN FUNCTIONAL METABOLITES OF D. OFFICINALES
Review round: 1
Reviewer: 3

Output:
Basic reporting: This article presents the D. officinale growth under blue laser, blue and white light. According to the results from RNA-seq, Physiological and biochemical experiment, the author find that blue laser is more efficient in production of metabolites in D. officinale. This research is interesting, however, the paper is poorly written, I suggest the author should make major revision to meet the magazine requirement.
Experimental design: It is well designed
Validity of the findings: The finding is interesting.
Additional comments: 1.The introduction is too long, too many information about laser light, I suggest to add some information on light effect on plant growth and metabolites production.
2.Why did the author focus on blue light, how about other light quality including red, green and yellow light on the growth of D. officinale. The paper discuss red light on anthocyanin biosythesis.
3.The author should do correlation between RNA-Seq data and qRT-PCR.
4.The phenotype of D. officinale under difffferent light treatments showed the leave color after blue laser light treatment is much deeper, which may revealed that the anthocyanin is much higher in this treatment. I suggest to assay the anthocyanin content in different treatment.
5.In the discussion part, I suggest the author should put the light effect on plant forward, then discuss on RNA-Seq, and functional metabolic material.
6.The author discuss a lot on ROS and enzymatic and nonenzymatic antioxidant systems including GSH, so I prefer to see those data in the manuscript.
7.I suggest the author should disuss more deeply which combined the RNA-Seq data and the the physiological and biochemical result more closely. Such as POD content and its relationship with the POD biosynthesis genes.
8.The reference of 336-339 is missing or wrong cited, it make me confused.
9.The color of different treatment should be consistent, the white treatment is in green color in the figure 5, but in white light in figure 6.
10.Table 1:have you done IncRNA experiement?
11.Table S2: which does the FR1, FR4 mean?
12.Table S4: is the FPKM vale or log2fold change value?


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: RNA SEQUENCING-BASED EXPLORATION OF THE EFFECTS OF BLUE LASER IRRADIATION ON MRNAS INVOLVED IN FUNCTIONAL METABOLITES OF D. OFFICINALES
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
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: RNA SEQUENCING-BASED EXPLORATION OF THE EFFECTS OF BLUE LASER IRRADIATION ON MRNAS INVOLVED IN FUNCTIONAL METABOLITES OF D. OFFICINALES
Review round: 2
Reviewer: 2

Output:
Basic reporting: Professional article structure, figures, tables
Experimental design: Methods described with sufficient detail & information to replicate
Validity of the findings: Conclusions are well stated
Additional comments: No additional comments


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

Input:
Title: HUMAN-WILDLIFE CONFLICTS WITH CROCODILIANS, CETACEANS AND OTTERS IN THE TROPICS AND SUBTROPICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English language used is clear and unambiguous.

Authors have included conflicts regarding only mammals and reptiles. Other classes have not been included. Birds, most importantly cormorants and pelicans, are often involved in conflicts. Other than this, Field context and references have been sufficiently described.

The structure of the article is very good. Raw data have been shared.

The manuscript reports results related to the study's aims.
Experimental design: The manuscript's subjects falls well within the aims and scope of the journal.

The research question is rather simple, however, authors failed to adequately explain what they mean by "freshwater piscivores". They claimed that  they reviewed and study the conflict between stakeholders and freshwater piscivores. And they proceed by including mammal and reptile species. Classes such as the birds have not been included, although bird species such as cormorants and pelican are important fish predators in freshwater ecosystems. Authors need to clarify in the Introduction (and then throughout the manuscript) what they mean by the term "freshwater piscivores". Lines 42, 43, 47, 49, 64, 67 need to be revised. They should also convincingly report why they did not include birds or piscivores from other vertebrate classes.

In lines 79-80 of Materials & Methods they reported that they searched the literature by including species name. This approach did not allow for discovering all piscivores. I would suggest to perform a more general search before narrowing down at the species level.

Other than the above, research is rigorous and methods of analysis well described and replicable.
Validity of the findings: All findings, according to the study aims and as describes in Materials & Methods, have been provided, analysed and presented in a robust and sound manner.

Discussion and Conclusions support the results.
Additional comments: Lines 31 and 222: When someone see an article about piscivores, they do not expect to read about their effect on livestock. Please explain, in the Introduction and Discussion, which species predate on livestock and to what extend.

Line 108: Give the survey instrument in a supplementary file.

Lines 135-138: Give references for all stated software.

Line 158: Differences are significant, but towards which direction? Did the severity of conflict increase with threatened status or vice versa? This could have important conservation implications and should also be highlighted in the Discussion. Authors refer to this only on the Conclusions (lines 334-336), without giving any further information or explanations.


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: HUMAN-WILDLIFE CONFLICTS WITH CROCODILIANS, CETACEANS AND OTTERS IN THE TROPICS AND SUBTROPICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Dear editor, dear authors,

many thanks for giving me the opportunity to review the manuscript entitled "Human-wildlife conflicts with freshwater piscivores". Resolving human-piscivore conflict is certainly a relevant topic. The manuscript is overal well written and uses professional English. Minor inaccuracies, missing words etc. are marked in the attached PDF document. The second research question, which deals with the severity of conflict and IUCN red list status, requires more context. The literature references section should be checked for uniformity in line with the PeerJ requirements. The article structure, figures, tables etc. is professional. The authors focus on negative implications for human when dealing with the topic "human-wildlife conflict", but could do a better job in describing associated (negative) implications for the relevant wildlife species. The authors could do a better job in connecting their case study from the Amazon to their worldwide review on human piscivor conflict. Please find specific comments in the attached PDF document.
Experimental design: The research question number 2 would require some more context in the introduction. Otherwise it remains difficult to comprehend why this analysis was conducted. The authors could give some more context why the various statistical analyses are conducted in the section "data analysis", l. 125 ff.
Validity of the findings: The underlying data have been provided. The benefit to literature is stated. Underlying data have been provided and seem to be sound.
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: SEASONAL VARIATIONS AND CO-OCCURRENCE NETWORKS OF BACTERIAL COMMUNITIES IN THE WATER AND SEDIMENT OF ARTIFICIAL HABITAT IN LAOSHAN BAY, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article in general is understandable but some changes need to be done for a better understanding.

The article is very well supported with references. However, the way in which some of these references are cited needs to be checked, and some references are missing.
In particular, in the discussion section I recommend the authors to try to use better the references in the context of their study. In some cases, they just mention the results of previous studies. I encourage them to try to link all this information.

In general, the structure of the article follows the standards of the Journal and the study sequences have been deposited in NCBI for public accessibility.
The results presented are mostly supported by figures or tables, with some exception. New figures need to be performed to support some results mentioned in the manuscript, while some others should be re-done and displayed in a clearer way.
Experimental design: The authors take the most of the sequencing technologies to bring a step forward the study on artificial reefs from a microbiological perspective.

In principle, the experiment is well designed, but more explanation on the co-occurrence networks analyses and clarifications are needed. For example in the study design, the number of samples, replicates, and samples used in networks analyes need to be cleared in the manuscript. Moreover, I recommend the authors to explain the theresholds used to define dominant bacteria, and the reasons why they decided to based their research only on this fraction of the bacterial community.
Validity of the findings: The analyses are appropriate for this research. However, some missing information is needed and the interpretation and discussion of these results is confusing. Moreover this issue extends also to the conclusion, which in principle is well stated and connected to the original question of the research, but it is based on these confusing results,thus losing its validity.
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: SEASONAL VARIATIONS AND CO-OCCURRENCE NETWORKS OF BACTERIAL COMMUNITIES IN THE WATER AND SEDIMENT OF ARTIFICIAL HABITAT IN LAOSHAN BAY, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Even though I’m not English native speaker, I think that the MS is clear on the use of English.
In the abstract section the most relevant data found should be showed. Bacterial communities must be displayed among sampling sites (habitats) to understand possible differences.
Introduction and background sections are well presented to show their finding within the proposed study field, with adequate and relevant literature.
Materials and methods showed clear definition of sampling site, design structure and data analysis. Some clarifications are needed, which are detailed in the correspond section of this review.
In results, relevant data are showed. However, does not follow a clear pattern from previous section. Some adjustments may be necessary to provide a better progress of results from applied methodologies.
Regarding to conclusions, authors should stress out the importance of dominant bacterial communities, specially associated with their ecological role in both water and sediment samples.
Figures and tables have well definition and are relevant for the aim of this MS. Its necessary include some elements in legends.
Support data were revised and easily find out.
In general, the MS provide valuable information, with plausible relationship among habitats for bacterial communities and environmental factors. Especially for the last ones, which it is hard to find out.
Experimental design: This section was well performed, just need some clarifications to be completely understanding.
Validity of the findings: All findings are relevant, especially because contemplate interesting variables such as environmental factors, examination of bacterial communities from microbiological data for different habitats.
Conclusions should be better oriented to understand why some bacterial communities are present in evaluated areas. Probably a good explanation of their ecological role could express better their findings.
Additional comments: General comment of the MS
This MS provide valuable information, with plausible relationship among habitats for bacterial communities and environmental factors. Especially for the last ones, which it is hard to find out.
All editorial criteria were revised.
The current MS should be improved upon before acceptance. Some comments and suggestions are below detailed.

Abstract
In this section more robust data are need, please show valuable data that you have reach to give robustness to this section. Also, bacterial communities must be displayed among sampling sites (habitats) to understand possible differences.

Introduction
This section is well presented, with adequate literature.
Specific point:
Line 51 (Sun et al., 2017), please check publication year. Its does not match with reference (2019)

Material and methods
Here its possible to find a clear definition of sampling site, design structure and data analysis.
However, some clarifications are need.
Specific points
Lines 104-106. First, within samples for water and sediment among season are 24, according to description provided. Then, the number of 32 samples are not clear from where it comes.
Line 111. May its necessary to include 1L instead of other part.
Line 113. Is necessary to describe why a grab sediment sampler was used. This tool is commonly used but generates some resuspension of sediment particles, that might could affected bacterial taxa identification in sediment samples.
Line 125. Check publication year of (State Bureau of Quality and Technical Supervision of China, 2007), its does not match with reference (2001).

Results
This section showed relevant data. However, does not follow a clear pattern from previous section. Some adjustments may be necessary to provide a better progress of results from applied methodologies.
Specific points
Line 190. Table 1 is mentioned, but from this table its not possible determine differences among habitats.
Line 193. May the word “much” should be removed
Line 194. Its possible to stress that a seasonal pattern could be observed.
Line 197-198. Seasonal variations of phylum are not clear as described (“evident”) in these lines, especially for those collected from sediment samples. Also, areas are used as check point. I think that are you talking about seasons?
Line 203-207. The fact that 4 phylum on water samples counts for over 70% of total abundance should be incorporated. The same facts should be stressed for sediment samples. Then this could be a first approach to diversity among sites
Line 206. Given percentages are associated to total abundance?
Line 207. Why Cloroflexi is particularly mentioned?
Line 210. Table 2 does not show mentioned facts.
Line 214. Include bacterial within “ten classes”.
Line 215-217. An explanation of how or why described differences of bacterial communities among areas were found.
Line 227-228. More than OTUs explanations, classes must be stressed out. May be is better to explain that 3 mentioned OTUs belongs to a clade in sediment, for example.
Line 237-240. Described OTUs abundance among seasons and networks are not easy to understand because there is no data available to figure out.

Discussion
In this section a good discussion could be find out. However, I think that bacterial communities and their interaction with habitats must be highly described, to understand why some communities are present or not in evaluated areas.
Specific points
Line 270. “Highly of endemism” should be well described.
Line 276. What “inconformity” means?
Line 276-278. Firmicutes abundance is well described among areas, but its ecological role does not, then just a simple result is showed instead of a discussion (in concordance with the general comments of this section).
Line 287-289. Re-write this paragraph, because it’s difficult to understand why 5 phyla in water had high abundance compared with phyla from sediment samples. I can´t see the relation with 16 shared Phylum. Then, why the abundance of Proteobacteria is described as a main factor to explain the above-mentioned facts. Again, the ecological role of this phylum should provide a better idea about it.
Line 292. “Some assumptions were reasonable”. I don’t understand this sentence.
(Ye et al., 2007), publication year must be verified from reference, does not match.
Line 304. (Margesin et al., 2009) is not in reference. (Margesin, 2009)?
Line 336. What do you want to say with “sufficient nutrition”?
Line 338-339. (Brandt et al., 2016) is not in reference. (Brandt and House, 2016)?
Line 371. What do you want to say with “mature”? could you explain this term. Do you want to say something like stable?
Line 376. (Faust and Raes et al., 2012), delete “et al.”
Line 386. (Caron et al., 2009) is not in reference. (Caron and Countway, 2009)?

Conclusions
Here authors should stress out the importance of dominant bacterial communities, regarding to it ecological role in both water and sediment samples.
Line 403. “mature” term must be clarified.

Reference
Some ones must be revised
Lines: 443, 448, 469, 471, 530, 603, 606.

Figures
Fig 1. To provide a better comparison point, Shannon index values from sediment should be located over the ones from water. Also values and bars (mean and SD?) should be explained in the legend of this figure.
Fig 3. Principal coordinates analysis (PCoA) plots of bacterial communities in the (a) water and (b) sediment of artificial reefs. Why fig 3a has water and sediment samples?
Fig 6. In the legend, “Positive and negative lines are represented by the gray solid lines and black dotted lines.”. Respectively?, should be included after “dotted lines, ”

Tables
Some extra information should be included in legends, same as in supplementary figures and tables.

Table 1.  P values, what it means?. It corresponds to differences among seasons for each index.
Table 2. Describe what is F, R and P values.
Table 3. Describe what is r and P values.

Fig S1. Describe what are CR, RR, TA and AA


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: SEASONAL VARIATIONS AND CO-OCCURRENCE NETWORKS OF BACTERIAL COMMUNITIES IN THE WATER AND SEDIMENT OF ARTIFICIAL HABITAT IN LAOSHAN BAY, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have incorporated many changes making the manuscript more understandable. However, there are still a few details they should pay attention on.
For example, they still use the term "interaction" in the abstract and the Keywords sections, and I would recommend the authors to change it by correlation or at least specify that they mean potential interactions.
Experimental design: I appreciate the authors did clarify many things they were asked to.
Nevertheless, there is some inconsistencies related to the networks analyses. First of all (lines 238 and next), they said that the networks were built in Cytoscape, but they don't mention the tool in Cytoscape for doing so. Maybe they want to say that they used Cytoscape to visualize the networks.
Next, they explain clearly how they calculate the Spearman correlation and how they selected the significant correlations, and they cited a paper by Cheung et al. (2018). However, in this paper, Cheung et al. calculated the networks using the SparCC R package. Either way, calculating "manually" the correlation networks or by using the SparCC R package is correct. But I recommend the authors to be clear in this part, and whatever the way they calculate the networks was they have to explain it and cite it properly.

Moreover, in the Results, in line 337 the authors introduced the concept of "the most abundant OTUs in the network". It is not clear what do they mean with this. Each of the OTUs usually appear once in the ecological networks representing one single node. I believe that the authors mean the OTUs in the networks that presented the highest abundance. In any case, they should either rephrase or explain how they defined the most abundant OTUs in the network.

Finally, in line 357 they wrote "the capital keystone". I recommend the authors to define what is it the capital keystone.
Validity of the findings: no comment
Additional comments: In line 61 replace "which" by "being"
Sentence in lines 77-78 is not clear
Line 185 change "was" by "were"
Line 160 Spearman with capital S
Line 354 replace "of more" by "higher"
Line 358 remove "which"
Line 412: what do they mean by "five-sixteenths phyla"?
Line 415: replace "which" by "might"
Line 535: I think the authors mean "needed" instead of "suggested"
Line 546: change "varied" by "variation in"
Line 551: the authors said "influencing microorganisms". I recommend they specify if they influenced microorganisms from sediments or from seawater.
Line 586: Indicate the lowest taxonomical rank the OTU17592 belongs to, as done for the others.
Line 619: at the end of the sentence that stated that "rare microbiomes might act to stabilize the community", please indicate the reference.
Line 658: ARs "are" an important artificial habitats in marine "fisheries"
Moreover, the reference they include to cite Cytoscape is not correct, and they should include the one provided by https://cytoscape.org/


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: SEASONAL VARIATIONS AND CO-OCCURRENCE NETWORKS OF BACTERIAL COMMUNITIES IN THE WATER AND SEDIMENT OF ARTIFICIAL HABITAT IN LAOSHAN BAY, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Suggestions were carefully considered, especially in abstract, results and conclusions.
Also, modifications of figures and tables has been considered, complemented with some new or modified figures, that reach better understanding of this MS.
In general, the MS provide relevant information within ARs habitats for bacterial communities and environmental factors.
Experimental design: This section was well performed since first draft, with clear and accurate clarifications of referee's observations
Validity of the findings: Results are relevant, especially because contemplate interesting variables such as environmental factors, examination of bacterial communities from microbiological data for different habitats among ARs.
Adjustments on results and discussion sections has been highly improved
Additional comments: The current MS version correctly reach some previous observations and provide to readers a better description of interesting 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: DEVELOPMENTAL EXPOSURE TO THE DE-71 MIXTURE OF POLYBROMINATED DIPHENYL ETHER (PBDE) FLAME RETARDANTS INDUCE A COMPLEX PATTERN OF ENDOCRINE DISRUPTING EFFECTS IN RATS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper reports interesting findings on the effects on reproductive development by the PBDE mixture DE-71, an important global pollutants.
While the results are clearly reported and thoroughly discussed, there are number of problems with study design and interpretation that the Authors need to clarify before recommending the paper for publication.
In its present form, the study can be considered as a pilot trial, prompting toward further investigation.
Experimental design: The sudy design is straightforward, but there are some questions.
- How the dose levels were selected? The lowest dose level (20 mg/kg bw) seems pretty high in comparison with both expected PBDE exposure and nOAEL/LOAEL in previous experimental studies. For instance, EFSA (already in 2011) concluded that the highest exposure to individual major PBDE congeners never exceeded 0.02 mg/kg bw, 3 orders of magnitude lower that 20 mg/kg) and BMDL10 ranging from 0.012 to 1.7 mg/kg bw (3 to 1 order of magnitude lower than 20 mg/kg bw).
RTHe Authors are therefore invited to carefully justify the relevance of the dose range selected
- The choice of endpoints is sound but limited. I understand that the Authors wanted to assess effects on reproductive development, excluding the thyroid and the liver that are well-recognized PBDE targets. I concur with  the Authors that more information is needed on PBDE ffects on reproductive development.
Nevertheless is somehow surprising that no investigation was carried on well-known targets of endocrine disruption, siuch as uterus and testis;, no attempts to perform simple quantitative histology were done with prostate and ovary and no hormone measurements were performed.
Overall the many animals (9-12 per litter as I understand from Table 1) seem to have been underxploited.
The Authors shoulsd explain why few (albeit relevant) endpoints were selected
- Finally, data listed in Table 1 look strange: the average perinatal mortality ranges 20-30% in the Control, 420 and 60 mg/kg bw groups, while the postnatal mortality ranges 15-23% in the same groups. These figures seem very high and in the meanwhile have high SD. Can the Authors explain?
Validity of the findings: The findings obtained in the given experimental conditions are valid, properly  analysed and reported.
Nevertheless, the Authors need adress questions on the relevance of findings derivingfrom problems in the study design, in particular
- relevance of selected dose levels
- restricted range of findings.
Additional issues
- Actually, 20 mg/kg bw is the NOAEL of this study (no attempt to derive a BMD). This is pretty high, as PBDE may affect, thyroid (and other tissues, such as liver and thymus, see e,g.  DOI: 10.1016/j.fct.2013.02.056) at definitely lower levels. Moreover, most effects are observed at 60 mg/kg bw, i.e., with a concurrent general toxicity (although I agree with the Authors that reproductive effects may not be due to general toxicity).
The conclusion seems that reproductive development is not a sensitive target for PBDE. What's the Authors opinion?
- Figure 4: where are the data for the lowest dose level (the most interesting one)? There seems to be a trend toward reduced mammary parameters in females , albeit not significant. Is it the case to attempt a BMD estinate (with values from the 20 mg/kg group, of course)?
What is the rationale to combine gfemales and males as their endocrine regulation is different.
- The two most sensitive endpoints (detected also at the intermediate dose level) are reduced AGD in both sexes and reduced mammary growth parameters (only a trend but in both sexs). These effects fit in a overall picture of general "hormone-inhibiting"effect on both sexes.
In the discussion the Authors do not mention the interactions of PBDE with PXR and CoAR; could these explain the observed effects?
Also thyroid has a modulating effect on reproductive development at early life stages (see e.g., DOI: 10.3389/fendo.2021.736505. Overall, the Authors are invited to discuss the overall picture of effects observed in light of mechanisms other than estrogenicity/androgenicity.
Additional comments: In its present form, the study can be considered as a pilot trial, prompting toward further investigation, pending the replies to the doubts raised above.


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

Input:
Title: DEVELOPMENTAL EXPOSURE TO THE DE-71 MIXTURE OF POLYBROMINATED DIPHENYL ETHER (PBDE) FLAME RETARDANTS INDUCE A COMPLEX PATTERN OF ENDOCRINE DISRUPTING EFFECTS IN RATS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Generally speaking, this manuscript is clearly written in professional English and of good format.
Experimental design: PBDEs are widely used flame retardants in daily life and industry and have been demonstrated to harm human and animals' health. Though using PBDEs have been restricted since 2019, humans are still facing exposures to PBDEs in the environment, both indoor and outdoor. This study uses DE71, a mixture of PBDEs, to investigate endocrine disruption effects of developmental exposure to PBDEs in rats. After determining doses of DE71 used in the experiments, anogenital distance, nipple retention, relative prostate weight, mammary gland development were measured in the offspring after perinatal exposure to DE-71, of differential treatment period, respectively.
Validity of the findings: This study has demonstrated that developmental exposure to DE-71causes endocrine disruptive effects in both male and female rats of complex mechanisms to be unveiled. In general, their experimental results support the findings.
Additional comments: There are minor points I’d like to mention. 1) In Line 306, the sentence "..., so too have several compounds with known estrogenic potentials, ..." is confusing, please double check. 2) In Line 318, "mechanismor" should be "mechanism or" with a space in between.


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: DEVELOPMENTAL EXPOSURE TO THE DE-71 MIXTURE OF POLYBROMINATED DIPHENYL ETHER (PBDE) FLAME RETARDANTS INDUCE A COMPLEX PATTERN OF ENDOCRINE DISRUPTING EFFECTS IN RATS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Data from 20 mg/kg dose group is missing.
Experimental design: Authors must be more detailed/specific about what new information was provided in their work.
Validity of the findings: Data in one table does not show asterisks that are indicated in the caption.
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: DEVELOPMENTAL EXPOSURE TO THE DE-71 MIXTURE OF POLYBROMINATED DIPHENYL ETHER (PBDE) FLAME RETARDANTS INDUCE A COMPLEX PATTERN OF ENDOCRINE DISRUPTING EFFECTS IN RATS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The Authors replied to comments in an adequate way. The revised paper can be accepted for publication
Experimental design: he Authors replied to comments in an adequate way. The revised paper can be accepted for publication
Validity of the findings: he Authors replied to comments in an adequate way. The revised 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: PREDICTING CONTINUOUS GROUND REACTION FORCES FROM ACCELEROMETERS DURING UPHILL AND DOWNHILL RUNNING: A RECURRENT NEURAL NETWORK SOLUTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: No Comment
Experimental design: No Comment
Validity of the findings: This study uses LSTM neural networks to predict GRF characteristics from sacral IMUs and temporal gait characteristics from shoe IMUs.  This work is novel and the question is highly relevant for bringing gait analysis out of the lab. The study should be published with minor revisions.

Justification for application to track and trail running is limited not everyone is interested in trail running, however, there is certainly good application for clinical, rehab and geriatric applications.  These could be identified to augment the justification

One methodological question.  Is it necessary to align IMU and treadmill frames of reference?  The neural network can likely learn the patterns regardless of this alignment, but would prediction be better if this step was performed.  Certainly in non-lab situations this alignment will not be possible since one does not know substrate orientation.  Please discuss this point in the MS.

The authors discuss the methods poor ability to detect the presence of an impact peak?  Were results better for heel strike runners vs. midfoot (who normally have much lower impact peaks)?  Did filtering at 30Hz or 20Hz remove impact peaks?  Please discuss the effects of filtering on this pattern in the paragraph (lines 316-330)

Error metrics (Table 3) show good predictability for most of the metrics with the exception of loading rate.  This will be strongly influenced by filtering of impact peaks.  Please address this.

To what extent are results influenced by duration of the trials?  I would expect that trail running on varied terrain will result in substantially altered GRF for subsequent footfalls.  Could you address how this results might differ with more variable input data?

The authors are correct to discuss the effect of attachment methods for the IMUs.  In addition there is likely variation in skin movement at different body sites (and among subjects) depending on the quantity and properties of subcutaneous fascia. Some of this can addressed by comparing the vibrational frequencies of the IMUs.  See Smeathers JE, (1989). Proceedings of the Institute of Mechanical Engineers, 203: 181-186. Also see Smith http://hdl.handle.net/2436/623290.  Please address this variable in the discussion.
Additional comments: Minor point:

Insert 2 commas in the sentence lines 272-5 “..network, given ….sacral acceleration, can predict”


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: PREDICTING CONTINUOUS GROUND REACTION FORCES FROM ACCELEROMETERS DURING UPHILL AND DOWNHILL RUNNING: A RECURRENT NEURAL NETWORK SOLUTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: -The document is well-written and easy to follow.
-Figures are well-designed and add to the strength of the manuscript.
-Sample data is not misleading.
-Models and raw data are freely available online via the provided GitHub link, as well as thorough documentation.
-Manuscript is appropriately self-contained. Extensions from original hypothesis (i.e. exploring accuracy of individual models, excluding foot strike info) are very appropriate.
Experimental design: -Manuscript fits within the aims and scope of the journal.
-Research question is well defined, relevant, and meaningful.
-Approach is technically sound and ethical – recommendations for utilizing machine learning for studies of human biomechanics have been followed.
-Methods are described in sufficient detail to replicate.
Validity of the findings: -Manuscript is valuable, as the data are readily available, methodology is clear, and documentation of approach is abundant.
-Data are provided via GitHub link.
-Conclusions are well stated, linked to original research question, and are limited to the supporting results.
Additional comments: While I am not an expert in machine learning approaches, I was able to understand the methods used by this research team and the findings/limitations. Below are a few comments/suggestions/questions that I hope the authors can use to improve the manuscript.

Line 64: The argument is made in the manuscript that other approaches require normalizing waveforms to the duration of the step prevent the calculation of temporal biomechanical variables. However, if the duration is known (and used to perform the normalization), can’t temporal variables be calculated?

Line 89: If GRF is calculated ‘only’ during the stance phase, isn’t that as good as calculating for the entire cycle since GRF = 0 during the flight phase? Not sure I’m missing something here…

Line 121: I was surprised that only bi-axial accelerometers were used – would the authors expect results to change if 3 axes of data were available?

Lines 129-134: Is there any other motivation to filtering cut-off values other than improving the prediction accuracy? Why not the same cut-off for both systems?

Data Processing: Was any attempt made to ensure the accelerometers were mounted the same on everyone (i.e. same sensor to segment alignment)? Was there a chance that sensors were placed slightly out of alignment (if assuming a physical alignment with body structures)? If so, how would that affect the results here?

Data Processing: Overall, there seems to be many choices made in order to get the best results possible (cut-off values, window size, making negative accelerations = 0). Is this common? Is there a systematic way to make these choices?

Discussion: As a reader, I am left wondering what features were most valuable for accurately predicting the nGRF. I would imagine that a simple model with participant mass, height (leg length), running speed, stride frequency, and slope would do pretty well in predicting the nGRF waveform – how much value do the accelerometer features add?

Line 356: The citation of Vitali et al. 2019 is incorrect for the sentence – Vitali and colleagues did not use GPS and tested more than 3 subjects.

Thank you for providing all the data, code, and tutorial – this manuscript motivated me to download and try out Python for the first time.


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: CHARACTERISTICS OF CENTRAL AMERICAN BROCKET DEER RESTING SITES IN A TROPICAL MOUNTAIN CLOUD FOREST IN EASTERN MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Ref: Manuscript # 61216-v0

In this manuscript Vazquez et al. evaluate the attributes at the landscape and microhabitat levels that drive the selection of resting sites by Mazama temama. This work is based on commendable sampling and analytical efforts and provides important information on a barely studied species.

Having said that, I think this manuscript needs to be improved before publication. My main concerns relate to the way the hypothesis has been laid out and even most importantly the context within which the data is discussed. Finally, I, of course, understand the challenges of writing in a second language, but the manuscript would benefit from a thorough review of the writing (some comments and suggestions about this issue in the attached pdf).

Main comments

Introduction

Lines 60-61 I suggest improving the hypothesis. I think that it could be something like “we hypothesized that the distribution and structure of resting sites would be driven by variables related to access to food, water and protection from predators” From here authors could derived specific predictions about the variables affecting the distribution and structure of resting sites (e.g., distance to the water in resting sites would be shorter than for random sites). I encourage the authors to polish their working hypothesis and present predictions; by doing this they would certainly improve the quality of the manuscript. Moreover, such improvement will help them to structure the manuscript in clearer and more concise way.

In lines 149-150 authors state that they used several variables to describe thermal cover; the problem here is that in the introduction authors only mention food, water, and protection from predators; so, thermal cover must be included in the intro.

Methods

There is a missing piece in the methods. Basically, there is no mention to how authors designed the transect survey. Starting points and direction were randomly selected? Please include this information.

Methods to evaluate microhabitat need to be better organized. Begin by clarifying which variables were used to describe water, food, and protection. For instance, “we evaluated access to the water by measuring the following variables…”, and so on for each resource. Also, I could not find any variable linked to food; please explain why + variables related to food are missing.
Authors state that they calculated the understory density, coverage, height, and species richness; and that these variables were then used to describe thermal cover. How is species richness related to thermal cover? Also, there is no mention to thermal cover in the introduction.

I think authors might want to explain in a more friendly way what was specifically tested with their methods; in some cases, this is done nicely, but in other cases I found statements like “we calculated the homogeneous K and L…” difficult to understand because I do not how they contribute to the story.

Finally, it is not clear why you looked at scraps, branches removed, compacted litter, and preference for bedding below a tree and/or tree fern species. How does this part of your analysis fit the introduction?

Results

Just difficult to follow and could be more informative. As a reader what I would like to see in the results are effect sizes and odds. For instance, cover was XX times higher in resting sites compared to random sites. Or the odds of finding a resting site increased by XX with every meter closest to a water source. Those are, I think, the kind of data that highlight the importance of your work. In fact, that sort of data are the ones that could have an impact on conservation and management actions.

Discussion
In the discussion, please delete the first paragraph (lines 202-208). There is no need to spend a whole paragraph trying to defend your sample size.

Authors mention core areas several times; but core areas need to be defined in some way. What represents a core area for your species, and why?

Authors refer to a shift (line 220), but they are referring to what it seems some level of habitat selection (“Despite the availability of different vegetation types, a relatively high percentage of resting sites were found in Mexican beech forest habitats”).
Is this the shift that authors mention? If so, that´s not a shift.

On the other hand, if deer shifted habitat use (¿?), then, they are not habitat specialists as you claim. Again, in lines 228-240, authors state that evergreen forest was avoided but because of human activity and the fact that such habitat has been heavily impacted. So, deer is not selecting against evergreen forest because some intrinsic variable; it is avoiding it because it is dangerous. Or even worst, you did not detect resting sites there because animals are just being poached. So, it seems that the context does not support your claim about habitat specialization of this deer. All this confusion must be clarified before publication because is a clear weakness in the interpretation of the results.

Lines 225-227 how is that the use of ravines reflect antipredator behavior?

Paragraph beginning in Line 257 mentions the importance of thermal and concealment cover, but only discusses concealment and ends mentioning that “As a forest specialist, it is not surprising that this species prefers forest habitat to rest” So, how is this final statement related to thermal and concealment cover?

Lines 265-270 introduce something defined as “general habitat” Not sure why this is important. I suggest authors delete this paragraph. Similarly, lines 271-275 mention some behavioral attributes of the species that make deer difficult to observe and highlight the importance of tracks to detect resting sites and how thorough the survey was. How is this related to your discussion of the results?

Minor comments

Line 27-28 Habitat features might define resting sites, but they are not resting sites. Please rephrase this sentence.
Line 32 “Resting sites were aggregated at distances below one km.” Unclear, please rephrase.
Lines 32-33 “Vegetation type and elevation affected resting site distribution at a landscape scale”. Authors need to state how these variables affected the distribution of resting sites.
Line 33 “all resting sites displayed similar values” What are the values?
Lines 38-40 “preserving Mexican beech forest and oak forest and protecting deer from poaching in core resting site areas are particularly crucial” Why? Can you link resting sites to some key demographic parameter?

In general, the abstract needs to be more informative.

Lines 54-55 delete the sentence “Several authors have described the characteristics of resting sites for many species, but this does not include Central American brocket deer” Start the paragraph with the second sentence but remove “this species” and include Central America brocket deer instead.

Line 79 what is the difference between bedding and resting sites? If none, then use only one term. If there is a difference, then define each type of site.

Lines 111-112 How is that roads and villages are classified as types of vegetation? I suggest changing the name of the variable from Vegetation type to something else.

Lines 114-116 Authors converted a continue quantitative variable into a categorical one; by doing so, they lose a lot of information. Please support your decision.

Lines 127 and 129 Please explain what the role of cartesian coordinates is in these 2 models.

Line 139 please explain how deer footpaths and slope are connected to water, food, or protection requirements.

Lines 287-288 “...alleviate potential human-wildlife conflicts” This manuscript is not about human-wildlife conflict. Please delete.

Legends for all tables and figures need to be more self-explanatory. Moreover, several components of the tables are difficult to interpret. For instance, Table 1 what are Pars and M3value?; Table T2, need to define what each C is, and also define the interaction term.
Figure 6, axes labels are illegible; in some figures I cannot figure it out what the grey shaded areas are; in general, what are you showing with those figures? Explain in the legends.

Figure 3, I am not sure why it is important; I would suggest deleting it. Green scale almost impossible to see. Also, it seems that you are using different font sizes or styles here (e.g., vegetation vs hillside and elevation). Is elevation in meters (see the color key)?


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: CHARACTERISTICS OF CENTRAL AMERICAN BROCKET DEER RESTING SITES IN A TROPICAL MOUNTAIN CLOUD FOREST IN EASTERN MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English is generally good but could be improved with revision by a native speaker.
Some references appear to be incomplete; they may be doctoral theses, but it is not clear from the information provided. The reference Aranda(2012) (line 84) is missing from the bibliography.
The article structure, figures and tables correspond to the way an article should be written. Raw data is supplied.
It is self-contained wih relevant results to hypotheses.
Experimental design: It is original research within the Aims and Scope of the journal. This manuscript deals with a study of resting places in the Central American brocket deer (Mazama temama) in Mexico. Given our lack of knowledge of the biology of all species of brocket deer, it is a welcome addition to our understanding of the species.
Methods: Resting sites: more detail should be provided about the methodology used in the field. The authors state that they sampled along 32 transects of 500 m each over a period of almost 1 ½ years. They do not say how the transects were laid out, what separation was between them, whether each transect was sampled once or more often, how often observations were made or in what seasons. They do not indicate the seasonality of the study area, whether it has a wet and dry season or relatively warmer and cooler seasons.

Resting site distribution: the authors state that they compared the number of pixels in each class of vegetation with the number of pixels containing resting sites. Could they clarify the size of pixels they are talking about so that we can understand the scale of the habitat that they are comparing?
Model fitting and diagnostics: the authors state that they used Poisson models to explain the distribution. Are they talking about Poisson regressions for GLMs? This is not clear, and as these are very complicated statistics for the general reader, they should clarify exactly what type of model they are using. The description of the difference among the four models themselves is clear. However, Lurking variables and second order K functions are not familiar concepts and a little explanation would be in order.
Microhabitat: The descriptions and variables measured are well done, but more descriptive detail would be very helpful. In line 151 they say they looked at “scraps”; I assume they mean scrapes. What kind of scrapes are these? Are they marks on trees, described in gray and red brockets, where the deer scrape the bark with their incisors and then rub their foreheads or are they scrapes on the ground as made by pawing the ground? They mentioned the presence of fecal pellets as part of the identification of bedding sites (lines 79-80), but they do not mention the presence of latrines near the bedding sites. The use of latrines, probably for scent-marking has been described in red and gray brocket deer (M. americana and M. gouazoubira) (Black-Decima & Santana, 2011 (Acta Theriol (2011) 56:179–187 DOI 10.1007/s13364-010-0017-6); Rivero et et al 2004, 2005 (Eur J Wildl Res (2004) 50: 161–167
DOI 10.1007/s10344-004-0064-x; Mammalia 69 (2) : 169-183 ). This information would be helpful for a general understanding of the biology of brocket deer.
Validity of the findings: Results: Resting site distribution and Landscape variables. The distribution of resting sites is very interesting (Fig,2A). However, one immediately wants to see a map of the study area and compare it with this distribution. It takes awhile to realize that these maps seem to be in Fig. 3, as the coordinates coincide. This information should be in the figure legend for Fig. 3 and should be referenced in the text near the description of the resting sites. The legend in Fig. 3A could be improved as the lines and colors are very close together and hard to distinguish. A map of the study area with the resting sides superimposed would be helpful.
Model fitting and diagnostics: The model fitting seems to be fine, especially if there is a sentence about Lurking variables in the methods section or here.
Microhabitat: The analysis is good. Again, it would be very interesting to know whether latrines or marked trees were found near the resting sites. The statistics also corroborate their findings. Again, inhomogenous second order K functions are not common knowledge and a little explanation is in order.
The statistical comparion is clear, and Fig.6 is potentially clear and valuable. However, the quality of the figure is poor; it is too small, it is impossible to read and it is too low resolution.
The conclusions are valid and well linked to the original question.
Discussion and possible speculation:
With respect to th discussion, the points raised are clear and valuable. However, it would be interesting to know if the authors observed any instances of scent-marking of trees and latrines to add to the general biology. It would also be interesting to know if they made any estimates of the number of deer that used these resting sites, considering previous abundance measurements and considering the solitary nature of these deer. Reyna-Hurtado & Sanchez-Pinzon (2019) consider the density of M. temama in the Chakamul region of Mexio to be 0.9-1.5 deer/km2. This would correspond to around 1 individual in the smaller region of Fig. 2A and 3-4 in the larger region. These may represent the home ranges of very few individuals. Further studies using camara traps might yield valuable information about this little-known species.
Additional comments: I am happy to see field work on brocket deer and I hope the author continues her work in more detail.


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: CHARACTERISTICS OF CENTRAL AMERICAN BROCKET DEER RESTING SITES IN A TROPICAL MOUNTAIN CLOUD FOREST IN EASTERN MEXICO
Review round: 1
Reviewer: 3

Output:
Basic reporting: Introduction
There is way too little information in the introduction section.  The authors need to establish why this study is important and how it has ecological implications for this species.  A much more thorough review of the literatures is necessary for publication.  There should be at least 4 paragraphs detailing the importance of this topic based on extensive literature review.  Paragraphs need to be a minimum of 3 sentences.
Methods
The study area description is also severely lacking.  The writing is poorly structured and the information about the area is at a bare minimum.  What about predator presence?  This paper is about resting sites, which are important for survival, yet there is nothing about the potential predators in the area.  I recommend including more information about the area regarding seasonality, precipitation, temperatures, topography, population characteristics, predator presence, etc.  In its current form, I know very little information about the area.
The writing needs major work and is not suitable for publication, throughout the manuscript.  See manuscripts in this journal and others for examples.
The results need to be much more detailed and really describe all the major findings of each analysis.
The authors state that the sites were located in a year but say otherwise in the methods section.
The discussion is much more thorough than any other portion of the paper.  However, the authors need to tie everything together at the end better.  Describe why this is pertinent information for the management of the species.
Tables need to be reformatted so everything is very clear.  Also, where are the headings for tables?
The figures need to be redone so that each axis is clear and wording is not clumped along axes.  Figure 2 needs a scale.  Where are the headings/descriptions?
Experimental design: The limited information regarding the collection of data seems appropriate, although more information is needed to truly assess this.  How were the transects distributed?  Were they covering an equal representation of habitat types available in the study area?  What time of year were they conducted?
Why did you use a point pattern analysis?  This needs to be justified.  Many would just use logistic regression frameworks to compare the used vs random locations of resting sites.  See Smith et al. 2015 in The Journal of Wildlife Management for an example of more common analyses used for this type of work.  The descriptions of the analysis are bare minimum and don’t really allow the reader to understand exactly what you are doing.  The authors need to be very thorough with describing the analysis and the math behind it.
What is the purpose of using NDVI?  If this is a forested area, NDVI is just going to show the values from the forest and not the understory.  This is why it is important to thoroughly describe your study area.  NDVI in treed areas is not useful for studying ungulates unless the trees are a primary source of vegetation.  If they are not, then NDVI values need to be regressed against a tree cover layer so that they are adjusted.  However, in dense canopy forests, this is still not going to give an accurate representation of vegetation quality in the area.  Given the low number of sites, vegetation sampling at each site would have been much more valuable.  As it stands, NDVI appears basically useless for this analysis.
There are way too many vegetation types for the amount of sites you have.  When dealing with small sample sizes, categorical variables severely limit what you can accomplish.  Also, roads and disturbances should be treated as distance to variables.  Similarly, treat aspect as a continuous variable.  Turn aspect into cosine and sine of aspect variables using the raster calculator.  You can also turn aspect into a single, continuous variable.  Elevation should not be set as a categorical variable.  Make it continuous.  Keep in mind this is will help strengthen your models.
How large are pixel sizes for each of your layers and how large are your resting and random sites?
How were your microhabitat variables used to describe thermal cover?
What does “looked at scraps, branches removed, etc” mean in regards to this analysis?
How are you analyzing the vegetation portion of the analysis?
Were variables tested for correlation?  It’s also not appropriate to just test for all variables in a single model.  The authors need to test many different combinations because variables will interact differently with each other and could lead to skewed results.
Validity of the findings: The results are poorly stated and are hurt in part by the lack of explanations within the methods sections.
The discussion does a good job of relating the results to literature and the ecology of the species, but it is difficult to determine the validity of these findings when the methods are so poorly constructed.
Additional comments: Overall, I think there is some interesting and worthwhile data present in this study, however, in its current format it is not publishable.  Significant adjustments need to be done to the manuscript’s writing style and much more clarity needs to be provided throughout.  I thought the discussion was the most structured and well written portion of the paper, while the introduction was severely lacking background information.  The methods are very difficult to process in their current forms.  It is not clear at all what you are trying to accomplish and there are many flaws in the habitat analyses.  The analyses as stated do not seem appropriate for this work and need to be revised and at a minimum made clearer.  With the right analyses, this data is certainly publishable.  Consider using logistic regression analyses for the habitat portions.


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: CHARACTERISTICS OF CENTRAL AMERICAN BROCKET DEER RESTING SITES IN A TROPICAL MOUNTAIN CLOUD FOREST IN EASTERN MEXICO
Review round: 2
Reviewer: 1

Output:
Basic reporting: Ref: Manuscript # 61216-v0-Rev

I appreciate the efforts made by the authors to improve the quality of the ms following my advice and the advice provided by other reviewers.

Some comments about the reviewed version,

Lines 42-43. What is the evidence that shows that current conservation problems result in part from consumption during the Pleistocene? If there is no evidence, please remove this statement.

Line 48 – “Resting sites have important effects on survival and fitness; they provide adults” provide references that support this statement.

Lines 59-60 delete the word “apex”; just say that domestic dogs also kill deer.

Line 66 – Why resting sites must offer food?

Lines 126-132 So, you surveyed a total of 32 transects over 8 field seasons. Basically 4 transects per field season. Is this correct? If yes, write it in the ms, if not also explain (maybe you could state on average 4 transects per field season or numbers of transects surveyed ranged between X and X per field season)

Line 202-203 You repeat 3 times (results, discussion line 222, and conclusion) that you found for the very first time a latrine for the species. This is completely anecdotical and unimportant. I suggest you mention this finding one time maybe in the results, and that should do it.

Line 209-211 you state that the “probability to find a resting site was (…) negatively associated with pine forest, houses and roads and grazing” So a pixel occupied by a house showed a low probability to present a resting site. But pixels were 30 m2; so 6x5 m basically the size of a very small house. I am sure you were not expecting to find a resting site in a house. Why are houses part of the analyses? The same for roads. Also, you need to define “grazing”. Did you mean grazing areas?

Line 222-226 Please delete; your work is not about latrines and their function.

Line 236 delete “apex”. In fact, if pumas inhabit the area, dogs are not the apex predators.

Line 238-242 delete, your work is not about diet.

Lines 243-250 How do you interpret this result?

Line 272 – dogs were introduced previously; delete scientific name.

Line 283 – Unclear. Please cite work where managers use “habitat limitations” to protect populations.

Lines 294-295 – Authors conclude “Therefore, we suggest preserving the existing forests, with a special interest in Mexican beech forest and oak forest to improve the
species conservation status.” How is that preserving what it exists will improve the conservation status of the deer? Please explain.

Please check the English; it has been improved, but there sentences with verbs in past and present tense, repeated words within clauses, and sentences that are too long and should be broken into 2 or 3 sentences.
Experimental design: see 1
Validity of the findings: see 1
Additional comments: NA


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: CHARACTERISTICS OF CENTRAL AMERICAN BROCKET DEER RESTING SITES IN A TROPICAL MOUNTAIN CLOUD FOREST IN EASTERN MEXICO
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been greatly improved from the original version presented. However, the English is still a problem. Throughout the manuscript there are many grammatical errors such as lack of correspondence of verb forms with subjects and sentences that are so long as to be difficult to understand. The manuscript needs to be corrected by a native English speaker. The literature has been well covered, the background and structure are fine. The analysis has been greatly improved as well as the figures. One small correction: on line 112 the authors refer to jaguarundi (Herpailurus yagouaroundi). The scientific name has been changed to Puma yagouaroundi. The other problem I have is with Figure 5. The legend states that it shows the L function of the distribution of resting sites; however, the title of the graph is Fecal pellet groups (L function). Are they talking about resting sites or fecal pellet groups?
Experimental design: The experimental design is clearer now than in the first version. The description of the methods is greatly improved.
Validity of the findings: This section is fine.
Additional comments: I hope the authors will continue their investigations of brocket deer, as so much is still unknown abouth them.


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: COMPARATIVE GENOMICS OF THE BLACK ROT PATHOGEN XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AND NON-PATHOGENIC CO-INHABITANT XANTHOMONAS MELONIS FROM TRINIDAD REVEAL UNIQUE PATHOGENICITY DETERMINANTS AND SECRETION SYSTEM PROFILES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written.  In fact, the introduction which focuses on the virulence and pathogenicity of members of the genus Xanthomonas is one of the most comprehensive I have ever read.  It is succinct and well-formulated.  The manuscript has a professional structure containing both tables and figures.  The raw data are provided.  Again the hypotheses are clearly presented.
Experimental design: The methodology described in this manuscript is based on bioinformatics, i.e. the authors use a number of computer programmes to analyse sequence data.  This is a standard approach in this type of research and are described in sufficient detail to be repeated.  The research question is well defined and relevant.

I have one question regarding Xmel.  Very little information is provided on this species (in the introduction and discussion sections).  The authors isolated it together with Xcc - is the association between Xmel and Xcc common, i.e. has it been reported elsewhere? The authors assume Xmel is non-pathogenic (and based on their results it lacks a number of key pathogenicity traits) but can one be sure without preforming inoculations?  What would have been really interesting is to co-inoculate the species and determine if the severity is increased.  This has been shown with other pathogens notably Ps. savastanoi pv. savastanoi.
Validity of the findings: The results are novel - the authors add to genome sequence information on additional strains of Xcc and of Xmel.  The analyses of pathogenicity and virulence factors are comprehensive and provide novel results.  The conclusions are well stated.
Additional comments: Line 108 - sentence is incomplete
Lines 477 and 716 - the word "species" is redundant - arboricola is the species
In the phylogenetic tree (Fig. 1) please indicate the type strains with the subscript T
Table 3 is confusing.  Add the word "strains" in the first line, i.e. Xcc strains;  Xmel strains
In Fig. 5A and 6A - what do the different colours mean?
Underneath Fig 6B indicate which strains are Xcc and Xmel
In Fig 8 what is A and B?
Again in Fig 9 indicate which strains are Xcc and which are Xmel


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: COMPARATIVE GENOMICS OF THE BLACK ROT PATHOGEN XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AND NON-PATHOGENIC CO-INHABITANT XANTHOMONAS MELONIS FROM TRINIDAD REVEAL UNIQUE PATHOGENICITY DETERMINANTS AND SECRETION SYSTEM PROFILES
Review round: 1
Reviewer: 2

Output:
Basic reporting: There is a scope and need to make the abstract and whole manuscript clearer and concise.

The title is also lengthier. There is also need a proper introduction to non-pathogenic Xanthomonas (NPX) in the introduction.

How authors are differentiating pesticides and fungicides? I can understand...copper, fungicide, bactericide...but what is the connection with fungicide...

In several instances, can finding results being repeated in discussion...

231 line...lastn?

Line 579 mentioning that native hrp ...were longer than references...is not clear...

The manuscript is written very roughly with lots of grammatical mistakes and incomplete sentences and typing errors (LN: 231, 430). Species name must be italic (LN: 57). Abbreviations are not introduced properly (LN: 67, 91-93).
Experimental design: 1.	How authors used bioanalyzer for quality check of genomic DNA...it is not clear...
2.	Absence of a phylogenetic tree based on core-genome and authors have just relied on MLST data set.
3.	Phylogenetic analyses (Figure 1) have missed many of the representative species of Xanthomonas genus. It needs to be revised according to the latest taxonomic classification of genus Xanthomonas.
4.	LN: 223-224, Mention Blast coverage and percentage identity cut-off values used for the presence/absence of secretion system genes. Also, mention which type of Blast was used.
5.	How meaningful is the findings related to genome dynamics (structure, IS elements, and plasmids) just based on draft genome sequences?
Validity of the findings: 1	The authors have mentioned that the three X. melonis isolates to be non-pathogenic only based on the absence of T3SS but as the strains were isolated from infected plants there is a lack of pathogenicity studies and also HR response in the context of T3SS
2	The plasmid prediction profile done by the authors is very vague and does not add any relevance to the study. In some cases, (CaNP1C) coverage is very low. They might refer to more reliable plasmid prediction tools.
3	Data represented in Table 1 and LN: 278-279 should be verified.
4	LN: 170-171, which one of the sequenced strains was taken from the previous study? Mention in the manuscript.
5	LN: 183, what do mean by QC>30? Write clearly.
6	Revise Figure 5 and 6 legends to mention what the color codes represent.
7	Figure 11 – why the contig containing metB is missing in Xcc (B)? Is contig altogether missing?
Additional comments: None


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

Input:
Title: COMPARATIVE GENOMICS OF THE BLACK ROT PATHOGEN XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AND NON-PATHOGENIC CO-INHABITANT XANTHOMONAS MELONIS FROM TRINIDAD REVEAL UNIQUE PATHOGENICITY DETERMINANTS AND SECRETION SYSTEM PROFILES
Review round: 2
Reviewer: 1

Output:
Basic reporting: As this is a revision of a previous version, I reviewed the paper  and then read the authors response to the reviewers comments.  The only question I still have is that in the abstract the authors make the following statement:  "Xmel strains were confirmed to be non-pathogenic by pathogenicity assays." - yet they do not include these trials in the materials and methods section.  Unless this was done previously.
Experimental design: The experimental design answers the research questions posed and where necessary the information requested by the reviewers has been addressed.
Validity of the findings: The results are novel and supported by the data generated in their study.
Additional comments: In my opinion, the manuscript has addressed the concerned raised by previous reviewers and should now be accepted for publication.

regards
Teresa