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

Input:
Title: A NEW NEMATODE SPECIES, CHROMADORINA TANGAROA SP. NOV. (CHROMADORIDA: CHROMADORIDAE) FROM THE HULL OF A RESEARCH VESSEL, NEW ZEALAND
Review round: 1
Reviewer: 3

Output:
Basic reporting: The description of a new nematode species is basically well done following nematological requriements; the distributional information is of general interest.

The manuscript widely meets all the parts relevant for the basic recording though I have some remarks see below. The manuscript is concisely written for most parts, the literature used is of relevance and mostly properly cited (some references used in the text are missing in the reference list - please check lines 44, 76, 117 and 175); the figures and data given are appropriate.

Adressing the evaluation of the self-containment with relevant results to hypotheses -  due to the bipartite character of the paper and basically, with the new description of a species -  not a point that can and must be adressed in the manuscript, to my opinion.
Experimental design: Experimental design
Since this is a new description of a species – there is no direct research question, no research gaps other than that this species is new and thus has to be described to fill a so far unknown knowledge gap.
As already mentioned, the data are sufficient for the species new description and follow common standards of nematode species description.
Methods – sorting, slide preparation and measurements (inclusively magnification) could be given in more detail to my opinion. How have nematodes been separated from the macrophytes – sieving, centrifugation, have samples been stained, etc?
The biogeography part lacks investigation – as already mentioned, this is one difficult to handle point of the manuscript – since the discussion is about the dispersal and distribution, but the species dispersal is nothing which has been investigated in the study.
Validity of the findings: The new species descriptions based on morphological data alone seems to be justified with regard to the differentiation of four other species with similar male supplements.
As also mentioned, conclusion is difficult to handle since there is no original research question other than the species description – deals with the biogeography part of the paper.
And this final comment address once again my major point of concern – the bipartite paper – mixing a species new description with some biogeographical aspects. Maybe choice of another section heading (biogeography aspects) could circumvent this issue if this finds editor’s (journal) approval?
Additional comments: Some more basic remarks on the manuscript - Difficulties arose for me as a reviewer confronted with the two differnt contents of the manuscript - the species description and the (potential) dispersal, where yet the latter has not actually been investigated. To my opinion, in order to combine these two different contents in one manuscript, an approach might help to overcome this issue, namely, slightly deviating naming of sections – e.g. instead of results, which are generally lacking in this paper, taxonomy or species description as one section title, and instead of discussion – ecology or biogeography – but only if this would meet editor’s or journal’s agreement.

This “two parted content” causes my only one major concern for accepting publication after minor revision; since the distribution has actually not been investigated and is more a side effect discussion of the taxa adressed within the species description. Nevertheless, both parts are of relevance and informative for nematode taxonomy and biogeography.

Additional remarks:

Please correct:
author of order - line 99,
subfamily name - line 101,
a instead of A for Cobb’s measures line 79.

Suggestions for the introduction: I would recommend to distinguish between biofilm and biofouling – what are the differences? Are biofilms or macroalgae “aufwuchs” automatically biofouling substrates? One to two sentences on this topic would be helpful to my opinion – e.g. “Introduction” starts with 32 with biofouling though “this biofouling communities” are not well introduced and explained; biofouling to my understanding is something which degrades “technical materials” – is this given for the macrophytes and their inhabitants with regard to ship vessels? Please clarify this passage on the biofouling” vs. biofilm or macrophyte dwellers.

I would also suggest to position “Etymology” –  before “type locality” at the beginning of the species description (e.g. line 122).

Wording: though it is commonly used I would recommend to clarify what a homogenous cuticle is in the context of the Chromadorida taxa – namely a homogenous punctuation or homogenously punctated cuticle (line 104, line 135). Please avoid homogenous cuticle.

Discussion:
e.g. omit 218-225 somehow redundant - see  introduction; not essential information to my opinion

Rearrangement of paragraph from 239 consecutive to line 217 – might fit better considering readability.

One question came to my mind when reading the manuscript – what do we know of other marine Chromadorina species recorded from New Zealand, are the common, widely distributed, restricted to some specific areas, can their distribution give indication / speculation of narrow ranges etc.
It would be of interest to have some additional information on this, if available, somewhere within the ecological part.


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

Input:
Title: TRANSCULTURAL ADAPTATION AND VALIDATION OF THE QUESTIONNAIRE “URGENCY, WEAK STREAM, INCOMPLETE EMPTYING AND NOCTURIA (UWIN)” FOR THE BRAZILIAN PORTUGUESE
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The English language should be improved. Prosfessional English translator should be consulted.
2.Reference is ok.
3.Figures or tables are good.
Experimental design: 1. Research object and question is clear.
2. Ethic issue is ok.
3. The numbers of sample size should be calculated.
Validity of the findings: 1. The conclusion is clear.
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: TRANSCULTURAL ADAPTATION AND VALIDATION OF THE QUESTIONNAIRE “URGENCY, WEAK STREAM, INCOMPLETE EMPTYING AND NOCTURIA (UWIN)” FOR THE BRAZILIAN PORTUGUESE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have justified in detail the need to carry out the work of transcultural adaptation of the UWIN instrument, and it has relevant practical and socio-sanitary implications.
It is a well-written English manuscript with an adequate structure. Bibliographic references used to justify this research are relevant and updated. These are correctly written following the formal recommendations of the journal.
Experimental design: The research question is relevant and well defined.
The article has a rigorous methodology in relation to the translation and validation process. It has been carried out following the COSMIN indications, which ensures alignment with the basic principles of validation studies.
The use of external and objective information such as the urinary flow study constitutes a strong point of this work not previously carried out to assess the criterion-validity and the diagnostic value of the instrument.
Validity of the findings: From my point of view, the results of this research have practical relevance for severe cases of LUTS screening, and as described in the manuscript it can serve as a first-level tool in populations/communities with few resources in Brazil.
Absolutely in accordance with its use as an easy and simple screening tool, prior to other more complex and expensive clinical tests.
The conclusions are clear and respond to the objectives set.
Additional comments: First of all, I would like to congratulate the author on the work. It has a practical application and relevance. The text is clearly written, and it is well understood, despite the specific terminology of the valuation studies.
I would like to make some suggestions that could help the potential reader improve their understanding of the text:
- First, I consider necessary a more detailed description of the instrument and its interpretation as well as the metric properties of other validated versions. For example, it appears in step 2 of the methodology that a score above 8 in UWIN-Br is considered "serious." I believe that I should explain it previously in the introduction when describing the instrument.
- It would be interesting to show the descriptive data of the sample, such as educational level, as you indicate in the discussion that it can be a relevant reason for the work. There are no data on body composition, comorbidities, etc. that are interesting to characterize the sample. I CANNOT find it in table 1 as you indicate. Please, revise.
- Could you report the possible ceiling or floor effects on the different items of the instrument? I have not found any information about it in the manuscript
- You should report the values of the Measurement Error (SEM; MDC…) to know the thresholds of the error and its potential influence on the interpretation of the scores. This is relevant information for readers.
- Line 257. Put reference 18 in hyper index format.
- It would also be interesting to offer the results of a Bland-Altman graph of the UWIN instrument test-retest, in order to know the temporal stability of the scores.


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: TRANSCULTURAL ADAPTATION AND VALIDATION OF THE QUESTIONNAIRE “URGENCY, WEAK STREAM, INCOMPLETE EMPTYING AND NOCTURIA (UWIN)” FOR THE BRAZILIAN PORTUGUESE
Review round: 1
Reviewer: 3

Output:
Basic reporting: I commend the authors for their extensive data set and analysis.  In addition, the manuscript is clearly written in professional, unambiguous language.
Experimental design: The study did achieve its stated aims and objectives
Validity of the findings: The study is well designed
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: TRANSCULTURAL ADAPTATION AND VALIDATION OF THE QUESTIONNAIRE “URGENCY, WEAK STREAM, INCOMPLETE EMPTYING AND NOCTURIA (UWIN)” FOR THE BRAZILIAN PORTUGUESE
Review round: 1
Reviewer: 4

Output:
Basic reporting: This is adequate
Experimental design: These are adequate
Validity of the findings: This is adequate
Additional comments: The papers is well written and well presented. The message is not new and has been published before. The validation of the UWIN -br questionnaire is well described. It maybe useful for the author to say something about the validation of the IPSS-br which is used in the study. It is noteable that while the Spearmans correlation of 0.804 is given , the next most commonly used measure the sensitivity and specifity of UWIN-br score against IPSS is not given.This would enhence the results. The ROC of  89% has no corresponding results table.The data on the uroflometry appears to have been underutilised in this study and could strengthen further evidence of the accuracy of the UWIN-br. The duration of the IPSS in contrast to the UWIN-br should have  p value computed, as well as patient acceptability for both IPSS and the UWIN -br is not given.The study focuses on quantitative data mainly, and says little on the qualitative data which is key in these types of studies.Overall this is a well written paper, with  good scientific rigor. these addition would serve to improve it further


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: TRANSCULTURAL ADAPTATION AND VALIDATION OF THE QUESTIONNAIRE “URGENCY, WEAK STREAM, INCOMPLETE EMPTYING AND NOCTURIA (UWIN)” FOR THE BRAZILIAN PORTUGUESE
Review round: 2
Reviewer: 1

Output:
Basic reporting: 1. Please consider to change the term ' International Prostatism Symptom Score' in Line 22 to 'International Prostate Symptom Score'
2. Please check the sentence after the full stop in Line 88.[2000). followed the recommended steps..........']. Is it a sentence? if yes, the first letter after full stop should be a block letter.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: TRANSCULTURAL ADAPTATION AND VALIDATION OF THE QUESTIONNAIRE “URGENCY, WEAK STREAM, INCOMPLETE EMPTYING AND NOCTURIA (UWIN)” FOR THE BRAZILIAN PORTUGUESE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The English writting has been reviewed satisfactorily. References are adequate and have been added some relevant news.
Experimental design: Author should describe the method to justify the study sample size.
Validity of the findings: The use of this questionnaire is relevant in the clinical practica in Brazil.
It could be interesting to include a user's guide for this new version, in order to improve its applicability.
Additional comments: I congratulate the authors for their review. They have attended the comments made by this reviewer, and hace included new information that provides relevant data for the research.
However, calculating the sample size and not having data on temporal stability can reduce the power of the study.


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

Input:
Title: TRANSCULTURAL ADAPTATION AND VALIDATION OF THE QUESTIONNAIRE “URGENCY, WEAK STREAM, INCOMPLETE EMPTYING AND NOCTURIA (UWIN)” FOR THE BRAZILIAN PORTUGUESE
Review round: 3
Reviewer: 1

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK
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: REVEALING THE SELECTIVE MECHANISMS OF INHIBITORS TO PARP-1 AND PARP-2 VIA MULTIPLE COMPUTATIONAL METHODS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In the manuscript titled “Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods”. The authors performed a series of molecular modeling techniques to reveal the selective mechanisms. The article deals with a very interesting topic with quite understandable and comprehensively explained.
Experimental design: The computational methods of docking, classical MD simulations, aMD simulations follow well-established protocols, and are appropriate for explore the selective mechanisms of inhibitors to PARP-1 and PARP-2.Some minor revisions are still requested before it can be published.

1.	The format of △EvdW, △Eelec in table 1 is inconsistent with in notes, please change the capital English letters to italic.
2.	The number of equations in line 210-217 is not correct. As an example, the equation in line 210 should be “(7)”.
Validity of the findings: The raw data were provided and the results were reliable.
Additional comments: Overall this paper meets the criteria for publication with minor revisions.


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: REVEALING THE SELECTIVE MECHANISMS OF INHIBITORS TO PARP-1 AND PARP-2 VIA MULTIPLE COMPUTATIONAL METHODS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Pass: the manuscript is generally well-written, and the data presented in a clear and readily-understood fashion by experts in the field.
Experimental design: Pass: The research question (explaining the molecular-level mechanism of selective inhibition) is well defined and meaningful. The methods employed are well-established and appears rigorously applied.
Validity of the findings: Pass: The conclusions reached are consistent with the results obtained from simulations, and are valid insofar as the basic assumptions underlying the simulation methodology itself (such as forcefield employed, timescale sampled) are valid.
Additional comments: This manuscript details a set of computational approaches employed to explore the selective
inhibition mechanisms of the ligand NMS-P118, and attempts to provide molecular-level explanations for its selective inhibition of PARP-1 over PARP-2. Classical equilibrium MD simulations suggest that preferential NMS-P118 binding to PARP-1 over PARP-2 was controlled by the conformational changes of helix alpha-F. Accelerated MD simulations, supplemented by free energy calculations of the conformations of the proteins expressed in principal component space (PC1 vs PC2), provide further details of the conformational changes induced by binding of PARP-1 and PARP-2 to the ligands NMS-P118 and Niraparib.

The methodology adopted is well-established and appears rigorous, with sufficient simulation trajectory lengths employed. The manuscript is generally well-written and the data presented clearly. I recommend publication in its present form. There is a  minor error: the x-axis of Figure 10A should read "PC1".


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: REVEALING THE SELECTIVE MECHANISMS OF INHIBITORS TO PARP-1 AND PARP-2 VIA MULTIPLE COMPUTATIONAL METHODS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The work is presented well
Experimental design: The manuscript presents a comprehensive computational studies of the complexes formed by PARP-1 (an important drug target) and PARP-2 with selective and nonelective inhibitors. The work is relevant and rigorous.
Validity of the findings: no comment
Additional comments: In this manuscript Hu et al. present a comprehensive computational study on the mechanisms underlaying selective inhibition of PARP-1 over PARP-2 from the small-molecule inhibitor NMS-P118. I think the overall study is well performed and deserves to be published in PeerJ after the following minor issues are considered:

1)	The authors should discuss better their findings in the context of the inhibitory mechanisms. What is the inhibitory mechanism? Competitive? Non-competitive? Other? How does the higher PARP-2 flexibility induced by NMS-P118 affect inhibition?
2)	Figure 1A should contain a close up view of the active site with displayed residues that are important for catalysis
3)	The authors mentioned the existence of a few non-specific (Niraparib, Talazoparib and rucaparib) and specific (WD2000-012547, BYK204165 and NMS-P118) PARP-1 inhibitors? Why they only focused on Niraparib and NMS-P118?


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: REVEALING THE SELECTIVE MECHANISMS OF INHIBITORS TO PARP-1 AND PARP-2 VIA MULTIPLE COMPUTATIONAL METHODS
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: REVEALING THE SELECTIVE MECHANISMS OF INHIBITORS TO PARP-1 AND PARP-2 VIA MULTIPLE COMPUTATIONAL METHODS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed my concerns
Experimental design: The authors have addressed my concerns
Validity of the findings: The authors have addressed my concerns
Additional comments: The authors have addressed my concerns


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

Input:
Title: PLANT-DERIVED ANGIOGENIN FUSION PROTEIN’S CYTOPROTECTIVE EFFECT ON TRABECULAR MESHWORK DAMAGE INDUCED BY BENZALKONIUM CHLORIDE IN MICE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Poor English was used.
Experimental design: Authors need to plan some more experiments (mentioned in comments to the author) to full fill their statements
Validity of the findings: The authors over-interpreted their results
Additional comments: Abstract: Background: Adding one sentence about “ANG cytoprotective activity” which is previously published would connect in a better way.

Authors need to check the sentences carefully for ex. “The cytoprotective effect of ANG on TM resulted from a reduction in ultrastructural changes and retained outflow function” . The authors have written the paper with poor English. Need to improve.

Authors did not mention the purpose of ANG fusion protein (ANG-FcK) over the Rh-ANG.

Insert scale in the images

Fig.3A&B: It seems ANG or ANG-FcK did not show any prominent anti-fibrotic effects. Any prominent reduction in Col-I staining is observed up on ANG/ANG-FcK treatment in BAK treated TM tissues. Authors encouraged to examine more ECM markers in these tissues like fibronectin, Col-IV, laminin, elastin etc which help to give a broad statement like anti-fibrotic effect. Even alpha-SMA staining not convincing to the authors statement.

Fig.3C: The low number of green florescent beads were observed in the BAK treated group compared to the control group. This method (outflow) little bit subjective as there are low and high flow regions in 360-degree circumference of the TM. It might possible that the low number of beads in BAK treated group might be due to the plane of the TM section the authors observed. Did authors observe the bead distribution in continuous parallel sections? If so giving the cumulative bead distribution data, more appropriate in this case or observing the distribution of the beads in TM flat whole mounts will give a better idea.


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: PLANT-DERIVED ANGIOGENIN FUSION PROTEIN’S CYTOPROTECTIVE EFFECT ON TRABECULAR MESHWORK DAMAGE INDUCED BY BENZALKONIUM CHLORIDE IN MICE
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	The supplemental figure did not download properly or it was formatted wrong because it appeared dark and greyed and was difficult to read.
2.	Figure 1B, label the treatment and stain in the figure.
3.	Figure 2B, each graph should be a separate B, C, D and referenced so in the text of the Results section for clarity.
4.	Figure 3, label which antibody was used for each panel in the figure.
5.	Starting at line 263, it would be helpful to introduce the experiment of why beads are being injected into the eye first. So, I would suggest switching the sentence starting at Line 265 with the sentence starting at line 263.
Experimental design: How were the statistics done for the IOP data? Was an ANOVA calculated at each timepoint?
Validity of the findings: Conclusions are well stated.
Additional comments: Jeong et al evaluated the cytoprotective effect of ANG on TM damage induced by BAK. Overall the manuscript was well written, and experiments performed appropriately.


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: PLANT-DERIVED ANGIOGENIN FUSION PROTEIN’S CYTOPROTECTIVE EFFECT ON TRABECULAR MESHWORK DAMAGE INDUCED BY BENZALKONIUM CHLORIDE IN MICE
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: no comment
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: PLANT-DERIVED ANGIOGENIN FUSION PROTEIN’S CYTOPROTECTIVE EFFECT ON TRABECULAR MESHWORK DAMAGE INDUCED BY BENZALKONIUM CHLORIDE IN MICE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Pass
Experimental design: Pass
Validity of the findings: Pass
Additional comments: The authors have addressed all of my concerns.


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

Input:
Title: COMPARATIVE ANALYSIS OF FOUR ZANTEDESCHIA CHLOROPLAST GENOMES: EXPANSION AND CONTRACTION OF THE IR REGION, PHYLOGENETIC ANALYSES AND SSR GENETIC DIVERSITY ASSESSMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: yes
Experimental design: yes
Validity of the findings: yes
Additional comments: These cp  genomes were well assembled (de novo) and the variations were also fully examined, so I support publication of this study.


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

Input:
Title: COMPARATIVE ANALYSIS OF FOUR ZANTEDESCHIA CHLOROPLAST GENOMES: EXPANSION AND CONTRACTION OF THE IR REGION, PHYLOGENETIC ANALYSES AND SSR GENETIC DIVERSITY ASSESSMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: The whole English expression is fair, some places need to improve. Please do more polishings work on this.

the background about the mechanism and meaning of SSRs is not enough in the introduction parts.

The figures of four cp genome are high repeated. And they will not supply more useful information for the readers.
Experimental design: The whole design is good, And the extra SSR markers are used to re-test the meaning of them are nice for readers.
Validity of the findings: Sequencing the complete cp genomes have become more and more easy and popular in land plants. However, the whole analysis is still focusing on data reporting. Except the SSRs part, all other findings are repeated from previous reports or the same as them. There are no exciting findings from the cp genome work.
Additional comments: Dear authors,

The manuscript from He et al. as "Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment". In this paper, the authors finished four full cp genome in Zantedeschia genus by using the NGS method and did comparisons analysis across many different species. It is always good to get the genome data from different plant groups. That will supply more genomic information for many different researchers. But the whole analysis from this ms is not exciting because all parts are following the same styles from many other plant cp genome paper as data reporting.  The whole MS is data descriptions and comparisons. And the only good point is deep into the SSR analysis with more populations data. In all, it is will be nice as the data reporting paper, not as the research paper.

Major parts:
Introduction:
As many papers reported, the cp genomes have been published from thousands of plant. The whole research style is almost the same as each other.  From the introduction, methods, results and discussion, all parts are following the same pattern. We can not get any valuable scientific view after the reading. If the whole design is as data reporting, it should be fine.
The authors used the SSR in their title, then the SSR should be the valuable point to deep into. The introduction part should extend this part to interest the readers.
It is also nice to extend the point about using the cp genome as a marker to explore the phylogeny and barcoding of this confused groups for hybridization and all kinds of breeding.
Discussion:
IR dynamic variation is really nice to discuss, but in this ms, the authors just put the number here. we did not see any mechanism about it.
The mechanism of SSR and utility of them should be discussed.

Minor point
1. please make it uniform for using the "cp" and "chloroplast"

2. please add the source of those plants. where and how you get them? how to plant them in the lab?

3. the CTAB method is used to extract the total DNA. it is confused to say "Total genomic DNA 49 was isolated from fresh leaves of these seedlings, using a modified cetyltrimethyl ammonium 50 bromide (CTAB) method (Doyle 1987) to construct chloroplast DNA libraries." It seems as cp DNA libraries.

4 "Insertion/deletion polymorphisms (indels) were identified using DnaSP", how did you do the alignment at here?

5. the sampling analysis of SSR should be in the method part, you put them as in the results part.

6. line 147 to 152: the divergent was relatively large? it should be compared with some markers. what kinds of data do you use to cmpare?

7. the SSR from mononucleotide repeats is also more like as the error from DNA replication. this may be not good to use as markers.

8. English writing in someplace should be improved.


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

Input:
Title: COMPARATIVE ANALYSIS OF FOUR ZANTEDESCHIA CHLOROPLAST GENOMES: EXPANSION AND CONTRACTION OF THE IR REGION, PHYLOGENETIC ANALYSES AND SSR GENETIC DIVERSITY ASSESSMENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: There is no problem with the structure, figures, tables and reference citations of this article. I could only suggest that the authors may probably like to improve some of their English statements of the 'Introduction' part.
Experimental design: The experiments and analysis are very standard.
Validity of the findings: All findings and conclusions are precise and well supported by the corresponding data in the paper.
Additional comments: Interesting little article, congratulations!


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 ANALYSIS OF FOUR ZANTEDESCHIA CHLOROPLAST GENOMES: EXPANSION AND CONTRACTION OF THE IR REGION, PHYLOGENETIC ANALYSES AND SSR GENETIC DIVERSITY ASSESSMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: good
Experimental design: finished
Validity of the findings: good
Additional comments: no


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 ANALYSIS OF FOUR ZANTEDESCHIA CHLOROPLAST GENOMES: EXPANSION AND CONTRACTION OF THE IR REGION, PHYLOGENETIC ANALYSES AND SSR GENETIC DIVERSITY ASSESSMENT
Review round: 2
Reviewer: 2

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: CREATININE IS A BIOCHEMICAL MARKER FOR ASSESSING HOW UNTRAINED PEOPLE ADAPT TO FITNESS TRAINING LOADS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Whereas the text is generally well written, there are some grammar mistakes throughout the manuscript which should be corrected Some examples are in L113, L128-129, L116-117, L150-151, L216, L240 and L284.

Abstract:
L41: What does the term ‘PM’ mean?

Your introduction is logical and well structured although it needs more detail. Specifically, a brief description of the sport/activity used to implement the exercise in the participants is needed. Why power fitness was selected as the specific tool to develop this study? Stating that it is mainly anaerobic is important but providing more details is needed.
By the way, the term ‘power fitness’ is used to mention a specific sport/physical activity but it is not. At least it is not known as it has been named in the current manuscript in the international research community. May the authors change this term to ‘resistance training’ throughout the text?
L75: I think that authors refer to ‘high-intensity’ sports rather than ‘high-speed’ sports.
L83-86: If there are results they should be indicated although they would be scarce.
Experimental design: The methods are not sufficiently described.
L 107: What does the term ‘PM’ mean?
L108: The method of ‘control testing’ is just explained through a reference (Shaner et al., 2014) which is not even in the references section. An explanation of this method is needed.
L112: an explanation of the method used is needed.
L113-115: it is not clear which method of anthropometry measurement was used. It should be specified and explained.
L116: the kinetic method mentioned should be explained and referenced.
L121: A reference is needed here.
L124: Why ‘Ra=0.72’ and ‘Ra=0.53? These terms should be explained. How this coefficient is assessed?
L127: ‘reducing almost twice’? I think that this expression is not correct.
L124: What is the evidence for the use of this strategy of training load combination? Can this be based on the findings of a previous study?
L124: If in this paragraph, authors are referring to a modification of the training regime with respect to the control group, it should be clarified.
Considering that main group participants used a different
L150: I’m not sure whether the training characteristics of the main group reflects a higher intensity and a lower volume than the training characteristics of the control group. In this sense, reducing the length of the rest periods implies a decrease of intensity and not the opposite. Training intensity is also related to the movement velocity and in this case this velocity is lower in the main group. Therefore, I think that authors may need to value whether it may need to be necessary to change this expression (‘high volume-low intensity vs low volume-high intensity’).
L151: I don’t understand the reference to ‘conventional indicator of power fitness’, specially when referring to a comparison of different types of training load combinations. May the author clarify this aspect?
Which exercises were used? May the authors indicate a description of the exercises used? How many sets per session did each group conduct?
L151-155: This paragraph somehow repeats what was stated in a previous paragraph (L124-129). They may be rephrased.
L160: I think that the term ‘using well-known methods’ may need to be removed.
L164-165: I think that this sentence should be removed because it repeats part of the previous text.
Validity of the findings: Results.

L189: a mention to the table where this explanation can be checked might be worth.
L191: I don’t understand the expression ‘the number of which depend on the…’. Please, clarify.
L190-194: This paragraph is difficult to understand. May the authors clarify it?
L205-211: This paragraph pertains rather to the discussion section.
L219-228: This paragraph pertains rather to the discussion section.

Discussion and conclusion.

The discussion is well structured and explained although I miss some references related to the resistance training methods which induces muscle hypertrophy and the relationships with the methods used in the current study. More specifically, I am concerned with the relationship of training intensity and volume made by authors and their findings. In this sense, a comparison with existing studies may be worth.

I think that some of the conclusions are not summarizing the main findings of this study and they are relying on other aspects which does not really reflect what has been found in the current study.
L309-312: This sentence is not clear. Please rephrase.
Additional comments: The present study deals with a very important topic regarding creatinine related adaptations to different types of training load combinations in non-trained population. Its findings are interesting and it is generally well written although it contains some issues that should be addressed.
1.	The most important issue is the lack of description of some methods of analysis (i.e., the method used to assess the strength capability).
2.	The next important issue is the lack of a wider description of the training methods used in order to understand better what participants did. Furthermore, the concept of low training volume-high intensity vs high volume-low intensity is not clear with respect to the training characteristics described and they need to be clarified.
3.	The next important issue is that the term used by authors (‘power fitness’) to define the type of physical activity practised by participants is not common in the international research community and it may involve misunderstanding among readers of this manuscript.
4.	The last but not less important issue is that I miss some references in the discussion related to the resistance training methods which induces muscle hypertrophy and the relationships with the methods used in the current study.


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

Input:
Title: CREATININE IS A BIOCHEMICAL MARKER FOR ASSESSING HOW UNTRAINED PEOPLE ADAPT TO FITNESS TRAINING LOADS
Review round: 1
Reviewer: 2

Output:
Basic reporting: this manuscript requires basic science reporting.

1. It's very hard to follow the manuscript. each sentence is too long and sometimes the whole paragraph ends with a single sentence. I would suggest the authors write the manuscript simple basic scientific language so that everyone in the scientific community understands.
Experimental design: I think original primary research is very interesting and comes under the aims and scope of the journal.

The research question which is addressed in this manuscript is very interesting and useful information for the assessment of adaptive body changes during power fitness training.

The experimental design was good and authors have followed all the ethics while performing the experiments.
Validity of the findings: The original findings in the manuscript are novel and will have an impact on the scientific community and society.

Along with the creatine levels, authors also have measured the adaptive body changes maximal muscle strength growth and circumference body size to correlate their results.
Additional comments: The manuscript titles as "Creatinine is one of the biochemical markers for assessing the processes of untrained people adaptation to power fitness training loads" focused on the to study the changes in creatinine concentration in blood serum as a marker for the assessment of adaptive body changes during power fitness training. The authors have nicely planned and executed the experiments. I have a few concerns regarding some of the points made in the manuscript. In my opinion, the manuscript looks better if the authors address the following issue I have.

1. t's very hard to follow the manuscript. Each sentence is too long and sometimes the whole paragraph ends with a single sentence. I would suggest the authors write the manuscript simple basic scientific language so that everyone in the scientific community understands.

2. There is no figure legends for Figure 1 and 2. Also no legends for Tables 1,2. it's hard to follow them without the legends.

3. some of the numbers in table 2 are very hard to follow because in the manuscript text authors have discussed these numbers as percentage increment for every parameter but in the table, they reported as numbers. I would suggest include these numbers in the text as well in brackets or include percentage increment numbers in table 2.

4. Authors haven't mentioned anywhere what is Ra, how they calculate to be 0.72 or 0.53?

5. The authors should include the significance of the work in the Abstract conclusion and also at the end of the discussion.

I think after careful consideration and going through the manuscript, the manuscript is ready to accept in this journal only after fixing errors.


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: CREATININE IS A BIOCHEMICAL MARKER FOR ASSESSING HOW UNTRAINED PEOPLE ADAPT TO FITNESS TRAINING LOADS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: Some references which were not written by English were hard to check experimental methods for reviewers or readers.
Validity of the findings: The results including tables and figures were limited to supporting the conclusion.
Additional comments: In the current manuscript, objective data and strong evidence in tables and figures were inadequate to support the conclusion. I suggest that authors should provide significant results and appropriate statistical analysis to confirm that the blood creatinine raising was accompanied by muscle mass increasing or training load etc.


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: CREATININE IS A BIOCHEMICAL MARKER FOR ASSESSING HOW UNTRAINED PEOPLE ADAPT TO FITNESS TRAINING LOADS
Review round: 2
Reviewer: 1

Output:
Basic reporting: After asking authors to include an explanation regarding the concept of 'power fitness', authors refused to provide it arguing that in Ukraine it is well known and failing to realize that the current journal has an international audience.
Experimental design: No comment
Validity of the findings: No comment.
Additional comments: Whereas authors have corrected some of the issues reported previously, they refused to provide an explanation regarding the concept of 'power fitness' arguing that in Ukraine it is well known and failing to realize that the current journal has an international audience.

Minor comments:
L88-91: Again, if there are few results they should be indicated. If there are not any studies related, it should be indicated rather than ‘few’.


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: CREATININE IS A BIOCHEMICAL MARKER FOR ASSESSING HOW UNTRAINED PEOPLE ADAPT TO FITNESS TRAINING LOADS
Review round: 2
Reviewer: 2

Output:
Basic reporting: the new manuscript much better in terms of the language and references and structure of the manuscript.
Experimental design: Methods and results are well described.
Validity of the findings: The original findings in the manuscript are novel and will have an impact on the scientific community and society.

Along with the creatine levels, authors also have measured the adaptive body changes maximal muscle strength growth and circumference body size to correlate their results.
Additional comments: The manuscript titles as "Creatinine is one of the biochemical markers for assessing the processes of untrained people adaptation to power fitness training loads" focused on the to study the changes in creatinine concentration in blood serum as a marker for the assessment of adaptive body changes during power fitness training. After careful consideration of the author's response to reviewers' comments, now the manuscript looks much better in terms of the data representation and conclusion. I would recommend accepting the manuscript with the current state. I don't have any comments now.


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: CREATININE IS A BIOCHEMICAL MARKER FOR ASSESSING HOW UNTRAINED PEOPLE ADAPT TO FITNESS TRAINING LOADS
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I think that the current study has substantially improved its quality during the review process and it is interesting for both practitioners and research community.


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: IN SILICO ANALYSIS ON THE FUNCTIONAL AND STRUCTURAL IMPACT OF RAD50 MUTATIONS INVOLVED IN DNA STRAND BREAK REPAIR
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper the authors collected known mutations for the Rad50 gene from either literature or a SNP database and annotated them using bioinformatics tools and databases, gathering information on how likely they are to be pathogenic, on the potential mechanism(s) of pathogenicity and on predicted changes in stability. They also investigated the structure by generating a partial model of the structure of Rad50 and annotated different predicted structural domains.

The paper is mostly clearly written, however the language and flow could be improved in some areas, especially regarding the Methods which are a bit short. Lines 223-234 are not detailed enough, (for instance 226-227 - what does consolidating similar mutations mean?). I especially find it difficult to understand how these mutations from different organisms are put together to gain a more general understanding (see below).

The authors generate a structural model of part of the Rad50 protein, however they don’t really use it to discuss the results and so it’s left hanging. I’d recommend integrating it better in the discussion.

The results section is short and mostly a summary of Table 2, but I feel their work could be better contextualised (see below).

Regarding table 2, the authors lists a number of functional sites possibly affected by the mutations ("Affected functional sites"), however it's not clear to me where this information comes from.

No raw data are provided in machine-readable format, even though most data (maybe except the full MSA) are present in form of word documents.
Experimental design: The aim of the study is to “identify the functional and structural effects of amino acid mutations in Rad50 gathered from exhaustive literature review and SNP database search”. While the matter is clear, it feels more like a review article than an original research article; the authors gather known SNPs/mutations for Rad50 and annotate them using some bioinformatics tool. While there is some content in their work, it feels like the research question is only superficially explored as no other validation of their findings is performed.

The researchers collect mutations of Rad50 in human and ortholog proteins, put them all together in the same pool and carry on with their analysis. I feel like a strong assumption is being made here: all mutations are taken together, without considering that they actually do come from different organisms and they are then discussed as a bulk, as if they were from a single organism or of exactly the same protein. This makes discussing the “structural and functional effects of aminoacid mutations” challenging, since it ignores the fact that a mutation might behave differently in different organisms because the protein and the more overall cellular and physiological environment are different and this should be taken into account. For instance, a mutation that is damaging in yeast Rad50 could be compensated by another substitution in human. The authors should state more clearly if they are considering a reference organism and contextualise their findings in this direction, or can make a better point of the fact that the mutations are affecting all the proteins in the family in the same way.

The authors discuss only 43 of the identified mutations since are those that have been seen to have a more important effect in the phenotype. However - again, the question remains if they are damaging in the phenotypes of all the organisms they have considered or only one/some, and/or if some of the other discarded mutations could actually be pathogenic in other organisms.
Validity of the findings: The researchers use a consensus prediction tool to assess pathogenicity. From reading the paper, I’m not sure whether their prediction are performed applying non-human mutations to the human sequence (the legend of table 2 is not very clear on this matter) or if the original organism’s wild-type protein sequence was used as a reference. If so, it should be noted that many of the tools were explicitly trained and validated on data from humans and are designed to work on human proteins, therefore it raises the question of how transferable they are to sequences from other species. This should be discussed in the paper if necessary.

The authors express some considerations on the performance of the in-silico analyses respect to the experimental findings. Even ignoring the transferability issues I’ve raised above, it’s not surprising the methods aren’t completely accurate - but it should be noted that data from a single protein aren't enough to make general claims.
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: IN SILICO ANALYSIS ON THE FUNCTIONAL AND STRUCTURAL IMPACT OF RAD50 MUTATIONS INVOLVED IN DNA STRAND BREAK REPAIR
Review round: 1
Reviewer: 2

Output:
Basic reporting: The work presented here is based on a classic approach, but  the authors did a remarkable job. One of the difficulties of in silico approaches is to see the limitations of approaches and analyses. Here, there are no such problems. The whole process is well brought into context.
Experimental design: The design is rigorous and well balanced.
Validity of the findings: The design is simple and clear, so the results are of similar quality. The conclusions are well stated.
Additional comments: A  pleasant article to read. Well detailed and rigorous.


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: IN SILICO ANALYSIS ON THE FUNCTIONAL AND STRUCTURAL IMPACT OF RAD50 MUTATIONS INVOLVED IN DNA STRAND BREAK REPAIR
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thanks to the authors for revising the paper and making an effort towards addressing my comments. Despite the paper has improved in different aspects, some critical key points still remain.

In terms of basic reporting, I feel the form of the article has improved – the methods section is now more clear and allowed me to understand much more of the experimental design. This withstanding there still are some mistakes in the article text that the authors should address through another round proofreading or by asking a native speaker to proofread it. The way the results and discussion are written is a bit misleading – sometimes it’s difficult to understand when the authors refer to their predictions and when they refer to experimental evidence.

The authors have added the raw data they got from their analyses – it’s in a machine-readable format even though not the easiest one (i.e. CSV or at least Excel files would be preferable) but it’s there.
Experimental design: I feel like the methods are much better described now

The authors use evidence from other organisms, even evolutionary distant from human,  to validate the findings of their in silico approach in human. The effect of a mutation can’t be transferred that easily from organism to organism, for instance because of i) compensatory effects due to other changes in the sequence ii) compensatory effects in other proteins (for instance in surfaces that mediates binding) iii) the fact that related proteins don’t have necessarily perfectly superimposable function iv) the fact that there might be other compensatory mechanisms that mask effects of a loss-of-function mutation differently in different organisms. The opposite is also true - mutations that aren’t deleterious in other organisms might be deleterious in human.

The authors here i) derive a collection of mutations from different organisms, focusing on the most damaging mutations, ii) use bioinformatics predictors to assess the impact of these mutations in humans, iii) use evidence mostly from other organisms to validate their finding. The other studies that are linked by the authors follow a different approach: they derive potentially interesting SNPs from different sources, use bioinformatics predictors to understand which one could be the most damaging, collect evidence that such mutations can be deleterious in human. In the present work the approach is the opposite: predictions are used to validate findings from literature rather than the opposite.
Validity of the findings: Until the authors can’t clearly demonstrate this step, i.e. validate that the mutations they find are damaging in human or at least very sound reasons for which these mutations can be transferred, I feel like the research question remains too superficially explored.
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: IN SILICO ANALYSIS ON THE FUNCTIONAL AND STRUCTURAL IMPACT OF RAD50 MUTATIONS INVOLVED IN DNA STRAND BREAK REPAIR
Review round: 2
Reviewer: 2

Output:
Basic reporting: There is an absence of literature references in the Results section.
There are numerous grammatical errors that need to be addressed.
Experimental design: This seems ok.
Validity of the findings: I am not sure of the validity of the findings or maybe that the validity of the findings are not currently stated. Whereas the prediction software does a good job of identifying mutations to conserved motifs within the Rad50 ABC ATPase and their effects on the core ATP binding and hydrolysis activity, other alterations of function are also noted which have not been described in the literature. To the best of my knowledge Rad50 is not a substrate for PKA or casein kinase II and it is not myristolylated. These predicted effects are probably false positives from the prediction and are being presented as valid results. Thus, the results and discussion need to be reworked to more clearly reflect what are validated and unvalidated findings from the prediction.
Additional comments: If I am understanding the “Analyses of Rad50 mutation deleterious effects” subsection of the Results, bioinformatics predicts that mutations in human Rad50 can have certain effects. For example, mutations in the Walker A affect catalytic and allosteric site, which has been shown. Do the authors next suggest that mutations in this region  affect N-myristolylation, casein kinase II  and protein kinase A phosphorylation of Rad50? Is Rad50 the substrate for these enzymes? Are this predictions biologically relevant? Similar statements are made about the coiled-coil domain and signature motif. It seems that some of the predictions are valid and others are not based on what is known about Rad50 structure/function.

The “Limitations of in silico predictions” subsection of the Discussion section needs to be greatly expanded to include more possible problems with the Results (see above). Again, I am not aware of any literature data that states that Rad50 is a substrate for PKA, casein kinase II, N-myrstolylation, etc. Too much weight is given to what is probably false positives from the prediction software.

In the Results section, the “Analysis of protein domains” subsection needs references. There are numerous crystal structures of Rad50 from archaea, bacteria, and a thermophilic eukarya. These features were also previously identified >19 years ago, and their role in Rad50 function is the subject of many of the mutations used in this study.
Generally, the Results section needs referencing.

The sentence on lines 412 and 413 is incorrect. The globular ABC ATPase head domain is formed by the N- and C-terminus. The Zn-hook is in the middle of the primary structure.

The Walker B mutation E1232Q (T. maritima E798Q) is ATPase dead. The analysis of this mutation in the Discussion (line 452-457) is incorrect. In general, more care has to be taken in describing the underlying effect of the mutations.

The sentence starting “Our analysis using PredictSNP have identified three mutations” on line 457 is confusing and maybe a bit misleading. CFTR is a member of the ABC ATPase superfamily like Rad50. Mutations in CFTR that result in some cases of CF have been made in Rad50 and analyzed as the references imply.

D1238N is a known mutation in Rad50 that has been observed in breast cancer. It effect has nothing to do with FHA binding. Studies by the Nelson lab utilizing T4 Rad50 have shown that it has problems with ATP hydrolysis.

On line 79, Carney at al reference is not formatted properly.
Line 96 should read “one of the most common types of genetic”.
Line 105 should read “the accelerating number of known SNPs have made it”.
Line 171, I am not sure what is meant by “mutations have been proceeded with pairwise alignment”.
Line 174 should read “mutations in human were manually refined,”.
Line 292 should read “literature pertaining to the topic was exhaustively”.
Line 322 should read “The regions with no 3D structure”.
Line 323 should read “which were mainly predicted to”.
Line 410 should read “Rad50 is a member of the”.
References in the Discussion are not consistently formatted.


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: IN SILICO ANALYSIS ON THE FUNCTIONAL AND STRUCTURAL IMPACT OF RAD50 MUTATIONS INVOLVED IN DNA STRAND BREAK REPAIR
Review round: 3
Reviewer: 1

Output:
Basic reporting: Thanks to the authors for their resubmission.

Writing quality has improved from the last revision, even though the text isn't always easy to follow and contains mistakes. For instance (but not limited to) these sentences require attention:

171-172 "From this
172 analysis, we identified equivalent site of mutation in human. "
204 Prediction of deleterious effects of the identified Rad50 mutations were carried out
225 This is achieved by providing a general pathogenicity prediction
251 & Casadio, 2005) using default setting
Sequence homology search of the human Rad50 protein was performed against
267 NCBI nonredundant protein databases (equal and lesser 1E-05) (what's equal or lesser?)
342 All of these 42 mutations (based on human equivalent mutations) (these are human mutations derived from non-human ones)
Experimental design: I feel the authors haven't completely addressed the transferability issue and how it affects the choice of mutations and the interpretation of results - see below
Validity of the findings: The way in which the results are exposed is clearer but still a bit misleading, in that they are written in a way that suggests me that these are confirmed consolidated results while they are actually predictions. This is for instance the case in:

"mutations located at Walker A (Figure 2a) affect catalytic and allosteric site, loss or
gain of methylation, alteration of DNA binding, metal binding, ordered interface and the loss of relative solvent accessibility"
"These mutations were found to affect ATP binding site motif, N-myristolylation, casein kinase II (CK2), protein kinase A (PKA) phosphorylation site and Forkhead-associated (FHA) functional sites"
"These mutations were found to affect ATP binding site motif, N-myristolylation, casein kinase II (CK2), protein kinase A (PKA) phosphorylation site and Forkhead-associated (FHA) functional sites"
"We have also identified K6E, K132E and K105E mutations occurred at the coil-coiled domain or ATPase domain to be deleterious"
The authors should better cross-reference these findings with what is known in the literature (for instance they should at least provide evidence that binding/PTM sites they have predicted to be damaged by the mutations exist and are important)

The authors haven't really addressed my point on the transferability of the mutations they find and how this affects the selection of the mutations to be studied. This effect is also not considered in the interpretation of the results. This is especially evident for instance in the "Limitations of in silico prediction" section. While I agree that bioinformatics predictors aren't perfect, comparing prediction in human with experimental results in other organisms isn't really fair because of transferability issues (see my last revision). I don't think it's surprising that the predictors predict more damaging mutations in conserved sites, since they are typically important for function/structure and so mutations in them are more likely to be damaging. For less conserved regions, the effect in vivo is also likely to be more context-dependent (hence the transferability issue becomes even more important).
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: IN SILICO ANALYSIS ON THE FUNCTIONAL AND STRUCTURAL IMPACT OF RAD50 MUTATIONS INVOLVED IN DNA STRAND BREAK REPAIR
Review round: 4
Reviewer: 1

Output:
Basic reporting: I feel the reporting has improved to a point that is acceptable for publication
Experimental design: the reporting is clear enough that now predictions and experimental data are clearly distinguishable
Validity of the findings: The author have briefly acknowledged the issues on transferability, even though they are not well-integrated with the rest of the discussion. It's enough for a pass, even though I'd advise them to integrate them better in the discussion. I don't think this would be worth of another round of revisions.
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 MILK MICROBIOTA ASSOCIATED WITH EARLY COLONIZATION OF THE NEONATAL GUT IN MEXICAN NEWBORNS
Review round: 1
Reviewer: 1

Output:
Basic reporting: a.	There are several instances as described below in the Genereal comments in which the sentence structure is awkward or needs to be edited to be easily read.
b.	Intro and background provide sufficient context.
Experimental design: a.	There are just a few questions in regards to the methods but with some revision, there is sufficient detail and information.
Validity of the findings: a.	The authors have provided a report on a study that examines the milk microbiota and infant fecal microbiota in a self-reported healthy Mexican cohort of mother/infant dyads during the first 6 days postpartum/infant life.
b.	The authors provide speculation about the roles milk bacteria play in the early colonization of the infant’s gastrointestinal microbiome.
c.	Caution, however, needs to be heeded in not using words that reflect causality and instead describe results as associations/correlations.
d.	In the conclusion, I think it would be better to say that they have provided evidence rather than “confirmed” that milk is the main source of bacteria that colonize the infant’s GI tract.
Additional comments: Abstract

Ln 20: Would recommend changing the word “gut” to “gastrointestinal tract” throughout the manuscript.

Line 20-22: Sentence reads awkwardly. Maybe change “Even though” to “However”?

Ln 25: In abstract, don’t need the use of “The” in the “The human milk…”. Actually, this is common throughout manuscript and there are several instances where this needs to be edited.

Line 27: “dominated the human milk bacterial community.” Did these bacteria actually “dominate” the community or were they more “prevalent”? or both?

Ln 29: Would recommend changing the word “breast” in “breast milk…” to “human” throughout manuscript.

Ln 29: How was neonatal gut microbiota associated with delivery mode? With microbial diversity?

Ln 44: please check to see whether ‘in utero’ should be italicized.

Ln 52-58. This is a very long sentence. To help with the readability of this sentence, please consider creating two sentences, perhaps by separating in line 53.

Line 63: change “to” to “with”

Line 72: “microbiota” is a noun; perhaps better to use “microbial”

Line 77-80: There have also been studies in the USA by this group (Hunt et al. 2011, Williams et al. 2017 and 2019, Lackey et al. 2019)

Methods

Line 109: How long after the infant was fed? Immediately following?
Line 112: How were feces sampled? Using a sterile scoop, spatula, or swab of some sort? How soon after infant defecated were samples collected?
Line 118 and 120: What temperature was milk centrifuged at?
Line 124: “QIAmp” should be “QIAamp”.

Line 126: Negative controls were used during the DNA extraction but were they also sequenced?

Line 136-138: Should be two sentences or separated by semicolon before “nuclease free sterile water was used.”

Line 140: How were PCR amplicons quantitated? Or were equal volumes pooled?

Line 165: Might be better to describe Chao 1 as a richness estimator

Results

Line 220: For neonate description, would be helpful to separate out female and male by delivery mode.

Line 228-230: When I look at Figure S1, I see a continued upward trend as the read depth goes out to 20,000 reads. Perhaps I am misinterpreting what the authors are meaning when they say 96.7% of total samples did not show new Observed_otus?

Figure 1:
-	“Human” and “Neonatal” should start with lowercase letters

Line 234: “being this the only phylum with statistically significant difference” seems awkward in the sentence.

Figure 3:
-	Next to last sentence, “H” needs to be capitalized in “human”, plus missing a space to separate sentences.

Line 275: “Only the Shannon and Simpson indexes showed higher…” This is confusing since the sentence before says that richness was higher in the milk microbial community. But then the next sentence says with BH correction, there were no significant differences.

Table S5: Something doesn’t seem right in this table. Both observed and Chao 1 richness estimators are around 60-75 but in looking at the rarefaction curves in Figure S1, the average seems like it would be greater than that. Also, in looking at 3A, the median or mean line is much higher.
Additionally, I would also like to see the SD or SEM for the values in Table S5.
There is also something odd about the high values for Shannon and Simpson. They do not match the boxplots in 3A as well.
I am guessing that the alpha diversity indices were calculated at the otu level, but even as such there is discrepancy between Figure 3A and the table.

Additionally, were the sample read counts rarefied or normalized somehow prior to calculation of alpha diversity? Read depth seemed to be quite varied across samples and read depth can have a significant impact of diversity indices.
If read counts were not rarefied, did the authors check to see if read depth contributed to the overall community structure and result in biases in diversity analysis? Were there differences in read count by sample type or delivery mode?

Line 279: There does appear to be grouping but there is not a “clear separation. It would also be helpful to the reader if the colors were consistent between Fig3A and 3B for human milk and stool groups.

Figure 3B – Is this a different ordination plot than Figure S2? The PC axes have different percentages. And if different, what is Figure S2 displaying? How does this provide “more precise information”?

Line 280: Isn’t Adonis a PERMANOVA? Did the authors mean anosim instead of Adonis test for similarity?

Line 286: Delivery mode is associated with bacterial richness and diversity. The word “influenced” suggests causality and thus, should not be used.

Line 288: Once again, there appears to something off about the values in Table S6. Why are these alpha diversity values so different from Table S5 which is also different from Figure 3A? They also seem quite different from Figure 4.

What is the difference between S3A and S3B? I did not find the legend for the Supplemental figures.

Line 300-302: Although evaluating relationships with maternal age is interesting, what about time postpartum? Human milk composition undergoes a lot of compositional change over the first week of lactation. This would be of great interest to evaluate as well.

In addition to maternal age, what about testing for relationships with parity? And this information, i.e. description of parity for the population, should also be included in Table 1.

Line 315: Table S7, it might just be alterations in the table due to a different computer, but the columns should be widened so the text in a word doesn’t wrap to the next line.
Also, the row of Bacteroidetes has an extra column between “Genus/species” and “Human milk”

I also don’t understand what the OTUs count represents in Table S7. Are these the number of reads attributed to each genus or species? Is it the total read count across all samples?
What are these numbers?

Line 316: I think this sentence is missing a “that” or “which” before the “originated from the human milk”.

Line 318 (Figure S6): I wonder what associations are present between mode of delivery and amount of contribution from milk microbiota. And is the day postpartum associated with increasing or decreasing contributions of milk bacteria to the infant microbial community? Did the authors examine these factors for association with amount of milk bacteria that contributes to infant fecal microbial community?

Line 319: “came from other unknown source no characterized in this work” does not make sense the way it is worded; needs to be edited.

Line 320-323: Not clear what this sentence means. Is it saying that the bacteria in the fecal samples that were identified as coming from an unknown source and not human milk were mainly taxonomically identified as being from the Clostridiales order? Maybe what is missing is “The taxonomic analysis of the bacteria in the fecal samples…”

Figure 6B: Bar label needs to be corrected to “Unknown Source Group” by adding an ‘n’ at end of “Unknow”.

Line 325: “Predicted” should not be capitalized.

Table S8: Should the differences between means in the table correspond to the right side of Figure 7? The values don’t seem to match up. In addition, Table S8 discusses q-values but there is not a column for the q-value.
Under ‘Corrected p-value’ column the “-3” is superscripted on all except one value. Please make consistent.
Spacing in “Antigen processing and presentation” is different in this cell as compared to others.

Discussion

Line 343 (Table 2): Under the ‘Method’ column, to be consistent, shouldn’t the Asnicar reference be “Illumina/Metagenome”

Line 347: It is unclear in Hunt et al. 2011 which, if any, milk samples were collected during the first 30 days postpartum. According to Williams et al. J Human Lact 2017, which utilized the same milk samples, the average time postpartum was around 5 mo.

Line 359: “Chan el al., 2016” needs to be edited to be ‘Chan et al., 2016’

Line 368-371: This sentence doesn’t quite read correctly, i.e. the section on “core microbiota” added of a pan-microbiota”

Line 389: Although the references appear to be in chronological order, it might be more helpful to the reader to have the references in the order of the populations or conversely, put the populations in order of the references.

Line 406: Which bacteria are being referred to by “its” in “its ability to use” HMO? I don’t think the bacteria mentioned above utilize HMO. I think the Hunt et al. 2012 article describes Staphylococcus increasing in concentration but not actually utilizing the HMO. The Yu paper describes Bifidobacteria utilizing HMO. I also don’t know that the Rocha Martin manuscript provides evidence of use of fatty acids as energy sources. I didn’t do a thorough read but at first glance this reference doesn’t seem to describe this.

Line 414-417: What about the possibility that these bacteria are in other parts of the GI tract?

Line 419-420: “We try” seems awkward; maybe “We wanted to replicate” would read better?
This whole sentence needs to be reworded as the sentence construction is awkward.

Line 425-429: In this study, both bacteria from skin and bacteria from within the mammary gland would be present in the milk sample. Thus, bacteria in skin would be included in the milk microbiota observed in source tracker.

Line 448-450: This sentence reads awkwardly.

Line 460: “et la.” should be “et al.”

Line 464: Did all of the vaginal births occur at home? If not and some of the vaginal births occurred in the hospital as well, delivery mode and site of birth are potentially two different factors.

Line 471: maybe change “being the peroxisomes…” to “with the peroxisomes being one of the main …”

Line 473: change “mother” to “mother’s”

Line 482: significantly increased from what? Or compared to what? Milk bacterial communities?

Line 499, 524: Once again, would caution against using the word “influence(s)” and instead use words that reflect that these are associations and/or correlations.

References

There are several citations in which the journal titles need to be italicized. Additionally, the sentence case format is not consistent across references. And there are some references that have capitalization of some words in the middle of the sentences.
Here are just a few examples:
Line 798: odd capitalization of “Are” in the middle of the title.
Line 848: “Normal Pregnancy”

Line 805, 892, 924: need line space between references.


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 MILK MICROBIOTA ASSOCIATED WITH EARLY COLONIZATION OF THE NEONATAL GUT IN MEXICAN NEWBORNS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript submitted by Corona-Cervantes et al. describes the structure and, to a limited extent, predicted genetic capacity of bacterial communities detected in maternal milk samples and infant faecal samples from a Mexican cohort.
The language used is of a good standard and is clear and unambiguous. I would guess that English is not the main authors first language and there are minor points throughout the manuscript that might have been worded slightly differently by a native English speaker, but these differences do not impact on the legibility of the manuscript (for example, lines 97/98: 'Apgar score greater than 7 at minute 5 after born.' could be worded as '...at 5 minutes after birth.' Also line 462: 'markedly modules' could be 'markedly modulates'.)
The structure of the manuscript is good. Figures and tables are appropriate and well presented (having said that, Tables 2 and 3 feel like they belong in a review rather than a research paper, but they do work well in this study). The study includes appropriate literature and background/context. The results and hypothesis align and raw data is appropriately archived (and available).

Note: Fig 3 legend. Penultimate sentence. Insert a space after the full stop and add a capital h for ‘Human…’

Line 408: There appears to be a 'stray' reference [48].

Line 460: Dominguez-Bello et al (not et la).
Experimental design: The research question is defined and given the possibility of different microbial communities within different ethnic/cultural groups (with unique dietary and behavioural traits) it is relevant to carry out studies that focus on previously under or not-reported cohorts.
The methods used are appropriate for the study and appear to be technically well done. Method details are suitable.

Further comments below:

The materials/methods noted that Blank extraction controls were carried out - were they negative? If not, how was environmental contamination controlled for?

It appears that two DNA extraction methods were utilised for milk and faecal samples. Neither appear to include physical disruption (some kind of physical disruption is often recommended, particularly for bacteria such as bifidobacteria. For example see: Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ, Scott KP. Microbiome. 2015 Jun 22;3:26. doi: 10.1186/s40168-015-0087-4. eCollection 2015.
16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

Could any of the differences, particularly diversity, between the milk and faecal microbiomes be due to the different methods used to extract genomic DNA?

Was there a rationale behind the use of qiime v1.9 rather than the updated qiime2? The updated package includes sequence error correction algorithms (such as dada2, which incorporates a ‘pyro’ option for analysing PGM data). Error correction can reduce the 'tail' of 'rare species' and thus have an impact on diversity measurements. However, as long as  all samples are analysed using the same methods comparisons should still be valid (as is the case for this study).

Fig 3: Does significance in the two alpha diversity metrics that include components of richness and evenness suggest that much of the difference in diversity between the milk and faecal samples is due to higher evenness in the milk samples? This could be tested by running Pielou’s evenness test in qiime.

Is there a rationale behind the use of different ‘types’ of figure when describing alpha diversity between milk/faeces groups and vaginal/c-section groups? Also, why include Simpson and Shannon indices only for the milk/faeces comparison?

Fig 5. What does the tree/cladogram next to the heat map represent? Is the clustering based on average relative abundance?

Obviously it is extremely difficult to design and carry out microbiota-based experiments with high power to detect differences between groups (given inter-individual variation). But, were any power calculations carried out prior to commencing the study?

Why use syber green mixes for amplification prior to sequence library preparation? Might it have been better to use a high fidelity taq?

I was not aware that FastQC could be used to trim reads to a set length (I've always used this program to carry out quality control analyses). The Babraham Institute (who created FastQC) also supply 'Trim Galore' for sequence trimming.
Validity of the findings: The discussion notes low relative abundance of Bifidobacteria and Lactobacillus in comparison with other studies. Could this be an impact of the DNA extraction methods chosen for the current study? Indeed a lack of standardised methods makes comparisons between studies quite difficult at the best of times.

The study conclusions are appropriate and well supported. There is some speculation, and this is identified.

Overall the study adds to the knowledge of milk and infant faecal microbiota composition (particularly for a previously unreported study group) and provides valuable information relating to the colonisation of the human gut.
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 MILK MICROBIOTA ASSOCIATED WITH EARLY COLONIZATION OF THE NEONATAL GUT IN MEXICAN NEWBORNS
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1)	In general, the first half of the paper does not focus on the main Aim (sharing of milk/gut taxa). I recommend focusing on your main Aim and most novel findings, rather than descriptive results and associations that are already well known and not your main purpose.

2)	Introduction: This was hard to follow at times. The first paragraph does not effectively present the current theories for the origins of milk bacteria. While the main theories are both mentioned (entero-mammary pathway and exogeneous origins) they are presented separately in a way that makes the paragraph contradict itself. Also, the ‘prebiotic’ function of milk (via oligosaccharides) is not mentioned. Midway through the second paragraph, the origins of milk bacteria are discussed again – this was already discussed in the previous paragraph and should be moved or omitted. In the final paragraph, the statement of the study Aim does not mention sharing of milk/gut bacteria. Isn’t this the primary Aim?

3)	In general, the discussion is quite long and could be condensed substantially. Also, please revise the opening paragraph of the discussion to clearly state your main findings.
Experimental design: 4)	Authors do not address the well-known contamination problem associated with low biomass samples. They mention that negative controls have been added during sequencing, however there is no mention on whether any kit contaminants were identified in the negative controls. The authors should reanalyse their data and discard any OTUs identified in the negative control and in the samples or use a different accepted method for decontamination using their negative controls, such as the use of the decontam package in R.

5)	Other methodological issues:

a)	Line99 Do mothers delivering by c-section receive antibiotics in Mexico? (Antibiotic use is mentioned as an exclusion criterion – please clarify.)
b)	Line115 Were samples really processed for DNA extraction within 24 hours of collection? Normally samples are processed in batches (or ideally, all at once) to reduce variability. Please clarify and explain.
c)	The authors have shown a detailed description of laboratory methods, however an explanation of what “equal amounts” of each barcoded amplicon means [in Ln 120] is needed. Ideally, this should be an equal mass rather than volume of each sample/amplicon to avoid biases in sequencing (Particularly since stool and milk usually have very different DNA concentrations).
d)	Authors have used an older version of QIIME that has been depreciated as of January 1, 2018. I would recommend reanalysing with the most recent version of QIIME2.
e)	Normalization methods are not described. The sequences generated belong to different sample types with very different microbial biomass. This needs to be taken into account when pre-processing the sequences, calculating relative abundances and correlation analyses.
f)	Authors mentioned FastQC was used to trim the sequences of low quality. As far as I am aware, fastQC is a QC tool that just estimates the quality of sequences and does not have any trimming parameters. Could the authors please confirm what tool was used for trimming of the sequences?
g)	Ln 230: It is unclear from the authors description whether rarefaction was performed (and to what depth) or if sequencing depth was accounted for using a different method. Accounting for this is particularly important with variable sequencing depths, and the rarefaction curves in Fig S1 indicate to me that samples were variable in sequencing depth. Also, for a number of samples, the rarefaction curves do not reach a plateau which does not support the authors’ statement that “The rarefaction curves indicate that depth of sequencing coverage was acceptable” (Line228)
h)	Ln 199: The authors mention both the use of PERMANOVA and Adonis, but both are the same statistical analysis (permutational multivariate ANOVA). Either PERMANOVA was performed using the Adonis function in R or using some other program. Since they are the same analysis, ideally only one should be reported. [Adonis is the name of the function for this analysis used in the vegan package in R, while PERMANOVA is the general acronym for the analysis (Anderson, M.J., Wiley StatsRef: Statistics Reference Online, 2014, pp. 1-15)]
i)	Ln 168: Euclidean distance is separate from UniFrac distance (you cannot do a UniFrac analysis with Euclidean distance) – Recommend clarifying which was used for beta-diversity.
Validity of the findings: 6)	The conclusion is too strong. This study is inferring the source of bacteria bioinformatically using 16S (not strain-level) data, without analysing any additional/alternative sources. It is important to acknowledge that this study cannot prove or quantify the ‘vertical transfer’ of bacteria from breast milk to the infant gut, and that the co-occurrence of similar bacteria could also simply reflect colonization of mother and infant by the same bacteria from their shared environment.

7)	Using the same method (SourceTracker), Pannaraj et al. estimated that 28% of infant gut bacteria originated from breast milk. The current study estimates 68%. This is a very large difference. Please discuss.

8)	It is very well known that method of delivery influences the infant gut microbiome. One of the strongest and most consistently identified differences is the depletion of Bacteroides taxa in CS-born infants. It is strange that this was not found in the current study. Please confirm and comment on this.

9)	Figure 3b consists of 3 PCoA plots, where the authors explain a clear difference in the 2nd plot of 3b. Do the other 2 PCoA plots explain any other variance between the samples? the authors do not explain the other PCoA plots.

10)	The results paragraph starting at L269 and related TableS5: only p-values are reported; this is not very meaningful. Please report effect sizes and include (especially in the table!) a measure of variation.
Additional comments: Corona-Cervantes and colleagues used 16S rRNA sequencing of the V3 region to profile the microbiota of human milk and neonatal stool from 67 Mexican mother-infant dyads. Similar larger studies have been performed, albeit in different settings. The authors claim that their results indicate 68% of bacterial taxa from the infant gut originate from breast milk and interpret this as evidence of vertical transfer, stating that their study “confirms that breast milk is the main source of bacteria that colonize the neonatal gastrointestinal tract from the first days of life.” I think this statement is probably too strong. Overall, the manuscript needs editing for language and flow as it is overly long, and hard to follow in places. I have quite a few questions and concerns about the methodology and presentation of results.

MAJOR concerns are listed in the sections above. Other MINOR concerns are:

11)	The term “increase” is misused multiple times when comparing milk to gut data. “Increase” implies a change over time. You are comparing different sample types, so should refer to “higher” or “lower” levels.

12)	Line252 I don’t understand this statement; please explain.

13)	Line266 You mention “three-fold” but earlier mention that a LDA threshold of 3.5 was used. Please clarify.

14)	Fig S2 – please add effect sizes and p-values on the figure.

15)	FigS5 – bar graph is not an effective visualization of this data.

16)	Fig S6 – large number of pie graphs is not an effective visualization of this data.

17)	Do you think that primer differences (you analysed V3, several of the cited studies used V4) might contribute to the different composition you observed?

18)	Line389 – please carefully check the cited references here. At least one does not include breast milk analysis.

19)	Line 473: do the authors believe that bacteria are metabolically active in the milk (which is continuously produced and ejected frequently), to the extent of influencing short chain fatty acid content?


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 MILK MICROBIOTA ASSOCIATED WITH EARLY COLONIZATION OF THE NEONATAL GUT IN MEXICAN NEWBORNS
Review round: 2
Reviewer: 1

Output:
Basic reporting: There are still several sentences that would be helpful to restructure or reword for ease of reading.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I thank the authors for revising the manuscript and providing thorough responses to my questions.

I just have a few additional comments.

Line 126: I thank the authors for providing information to me about the negatives. I think other readers will want to know this information too. Please add in the methods or in the results that since DNA was neither detected by 260 nm absorbance nor a 281 amplicon observed, the negatives were not sequenced.

Line 168: Were samples that had less than 10,000 sequences removed?

Line 320: Not sure having the absolute counts in Table S7 is very helpful; couldn’t these numbers be biased due to high variation in read counts per sample?

Line 414: I do not think the Hunt paper describes Staphylococcus “using” HMO; only that growth increased in the presence of HMO.

There are several instances that the grammar and sentence structure is awkward. I have included a few examples.
Line 354: seems to be missing a few words, e.g. “postpartum in a Canadian population… postpartum in an Irish population”

Line 428-431: This sentence is really long and doesn’t read quite right. Perhaps it would help to split it into two sentences, e.g. “In Mexico, mothers habitually do not thoroughly cleanse their breasts before breastfeeding. For this reason and because we wanted to know the bacterial composition transferred from mother to neonate during the process of breastfeeding, in our study the mothers did not clean their breast prior to sample collection.”

Line 454: “in a report made in Canadian women…” Awkward sentence structure, as the report was not made in Canadian women. “Conversely, in a report by Urbaniak and coworkers (2016), no differences were identified in a Canadian population.”

Line 459: Maybe reword or remove comma to read “The same group also reported…”

Line 461: Start a new sentence at “They suggest that physiological …”

Line 580: extra “B” in title.


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 MILK MICROBIOTA ASSOCIATED WITH EARLY COLONIZATION OF THE NEONATAL GUT IN MEXICAN NEWBORNS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors can be applauded for answering all the questions of the reviewers and making the necessary changes
Experimental design: The authors have clarified many aspects of the experimental design.
Validity of the findings: The authors have answers all the questions from the reviewers and clarified the findings with more analyses.
Additional comments: no comments


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

Input:
Title: A WITHIN-SUBJECT COMPARISON OF DIFFERENT RELAXATION THERAPIES IN ELICITING PHYSIOLOGICAL AND PSYCHOLOGICAL CHANGES IN YOUNG WOMEN
Review round: 1
Reviewer: 1

Output:
Basic reporting: I think this is a very interesting study, given the elegance of its design. It can be useful for clinical practice, both with healthy and ill populations.

However, I think the paper needs editing to be more understandable. Sentences should be shorter and more direct. Too many sentences with “and.” Results should be discussed more clearly.

Not trying to be flip, but I would just like to see tighter editing. In the Discussion section, too much is made of a Chinese study. I would rather see more discussion of the relationship (or lack thereof) of perceived relaxation and physiological measures.
Experimental design: Not sure how “Stairway to Heaven” (Led Zeppelin) can be characterized as “oriental” or meet the physiological criteria you state. However, it is a wonderful song.
Validity of the findings: Again, I think you Results & Discussion section need more editing. More direct discussion of each finding, eg, perceived relaxation and physio measures.
Additional comments: I really like your study in conceptualization, design and implementation. I feel it has implications for clinical practice, especially for high risk pregnancies. Would just like to see tighter writing with more concise organization.


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

Input:
Title: A WITHIN-SUBJECT COMPARISON OF DIFFERENT RELAXATION THERAPIES IN ELICITING PHYSIOLOGICAL AND PSYCHOLOGICAL CHANGES IN YOUNG WOMEN
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: General comments
This manuscript aims at comparing the effects of five relaxation interventions on physiological markers and perception of stress in women of reproductive age. Authors manage to fulfill sufficiently their aim.

Minor comments
(lines 96÷98) Please, provide supporting reference;
(l446÷448) add reference details;
(l160) … Sheri Menelli in 2004. Provide a regular reference;
(l177) In a study in Singapore… Provide supporting reference;
(l180) … Philips Hue system. Add instrument’s details;
(Relaxation Lighting) Did Relaxation Lighting last 7’, as well?
(l414) add reference details.