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

Input:
Title: THE ASSOCIATION OF EGF RS2237051 VARIANT, SERUM EGF LEVELS AND GENERALIZED AGGRESSIVE PERIODONTITIS: A PRELIMINARY STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Authors used 216 patients with GAgP and 138 healthy controls to investigate the association of the EGF rs2237051 variants, serum EGF levels, and Chinese patients with GAgP. Authors concluded that there is a significant association between the genotypes of EGF rs2237051 and GAgP risks as well as serum EGF levels, and showed that the level of serum EGF was increased in patients with GAgP patients. However, authors couldn’t provide the paragraph of conclusion or describe the conclusion in the final sentence of abstract.

In the conclusion paragraph of main text, authors made a statement that Chinese patients presenting with the variants of EGF rs2237051 are associated with increased risk for GAgP due to increased levels of serum EGF. However, I didn’t agree this statement. The relationship between EGF rs2237051 polymorphisms and serum level of EGF was only found in GAgP group but not in the control group. There were no significant effect of interaction between rs2237051 polymorphisms and serum level of EGF on the development of GAgP by the results of univariate and multivariate logistic regression analysis. I mean that an increase of serum EGF level could be an independent risk factor for the development of GAgP Especially, no evidence was reported that polymorphisms in EGF rs2237051 gene was the only one mechanism causing the elevation of serum EGF level. I thought that this statement was overestimated the relationship between EGF rs2237051 variants, EGF serum level, and GAgP risks.

The goodness-of-fit test for testing the Hardy-Weinberg equilibrium was very important in the analysis of genetic susceptibility. Please provide it. If the results could not fit the Hardy-Weinberg equilibrium, please discuss their effects on the study findings.

The description in some sentences of results were not confirmed by the data in tables. Please see the following:
Line 144: Individuals with a BMI≥18.5 and <24.9 kg/m2 did not present with GAgP, whereas those with a BMI<18.5 kg/m2 (P=0.9964) did. However, participants with BMI<18.5 kg/m2 could be defined as a reference group. Therefore, the content in this sentence was not confirmed by the table 2.
Line 165: The serum EGF concentration in total subjects with the AA genotype of EGF rs2237051 was 2.86 pg/ml higher than that in the subjects with AG and GG genotypes (adjusted β=2.86; 95% 167 CI: 0.88, 4.84).   Line 168: The serum EGF concentration in patients with GAgP with the AA genotype was 4.70 pg/ml higher than that in patients with the AG and GG genotypes after adjustment of age, gender and BMI (adjusted β=4.70; 95% CI: 2.09, 7.31).      I thought that authors might misunderstand the meanings of beta value in the regression equation. Please ask an expert of statistics for help to revise the description.

I suggested that authors can discuss the differences between salivary EGF, gingival EGF, and serum EGF in the roles of GAgP development.

Line 228: Please change the term of “Reference” as “References”.

Line 268: I suggested that “: official journal of the American Association of Oral and Maxillofacial Surgeons” can be deleted.

Line 288: It was needed to add a space between “Communicatoins” and “317:887-892.”.

The data presentation of statistics on table 2 were not a typical style. Please ask an expert of statistics for help to revise them.

On table 1, the mean value of attachment loss in control group was 0.00. In my knowledge, it was little impossible that the general control group could get the data like this. Please verify this data. If it was true, the control group had a very good oral health and some bias could be happened. It might need another control group recruited from the general population to validate the findings in this study.

On the notes of table 3 and 4, I suggested that “Adjust I model adjust for:” and “Adjust II model adjust for: can be revised as “Model I was adjusted for“ and “Model II was adjusted for”, respectively.
Experimental design: Authors reported that periodontal parameters (plaque index, PD, AL, BI) were clinically evaluated by two skilled examiners. However, no evaluated results in the consistence between these two examiners were reported in this study. In addition, I suggested that authors can determine the association between EGF rs2237051 variants and periodontal parameters and the correlation between serum EGF levels and periodontal parameters. The distributions of different allele frequencies and the results of genetic recessive model should be added in table 1.

Authors reported that the controls were volunteers from the staff and student population of the hospital. It was not clear what knid of plans did authors make for the invitation of volunteers. It was possible that an information bias could be caused by the hospital staff and students which were attracted by a free oral health examination. In the section of discussion, authors also gave a statement that selection bias could be identified in this study. According to the study design of epidemiology, information bias and selection bias could not be adjusted by the statistical analysis and after the participants’ recruitment into this study. I strongly suggested that authors shall discuss the effects of these two types of bias on the findings of the present study.

In multivariate regression analysis, an increase in serum EGF levels by one and five units should be recognized as the same variable using the different expression pattern. Therefore, it was not suitable that these two data were included in the same statistical analysis.

Please give an explanation why authors would like to use model I and model II in the statistical analysis of table 3 and 4. No special discussion for the roles of BMI in the development of GAgP was found in this study.
Validity of the findings: Some statistical analysis were not completed in the present study. I suggested that the results and conclusion shall be revised according to the updated statistical analysis and discussion.
Additional comments: The sample size is not so big. Some statistical analysis were not completed in the present study. The information bias and selection bias could be possible identified from the present study. The mean age of healthy controls was less than 36 years in the present study. These participants might potentially have been subjects with periodontitis but have not manifested signs and symptoms yet. I suggested that authors can modify the title according to the final data analysis and add a description of “a preliminary study” before the end of 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: THE ASSOCIATION OF EGF RS2237051 VARIANT, SERUM EGF LEVELS AND GENERALIZED AGGRESSIVE PERIODONTITIS: A PRELIMINARY STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors addressed the comments raised by editing the manuscript accordingly.
More details have been provided concerning:
- the rationale to study EGF serum levels,
- the correlation of their findings with what is already known concerning EGF/FGF polymorphisms and the phenotypes reported in this study
The abstract has been improved
Experimental design: Comments have been addressed.
Validity of the findings: The authors addressed the issues raised.
Additional comments: The manuscript was significantly 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: THE ASSOCIATION OF EGF RS2237051 VARIANT, SERUM EGF LEVELS AND GENERALIZED AGGRESSIVE PERIODONTITIS: A PRELIMINARY STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors already revised this manuscript according to my comments. Authors also replied my questions point-by-point. I am satisfied with the revision. However, there is a very minor question for this manuscript.

Line 203: I suggest that authors shall indicate the exact variant (allele G or A) of carriers of EGF rs2237051............
Experimental design: No more question.
Validity of the findings: No more question.
Additional comments: No more question.


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

Input:
Title: THE CASE FOR EXTENDED LIFESPAN IN COOPERATIVELY BREEDING MAMMALS: A RE-APPRAISAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is well written and unambiguous, revealing that the author does not agree with previously published findings and that this paper, serves as a commentary on earlier published work.
Experimental design: This paper focuses upon an interesting idea raised by Austad, Healy and others that social /herd living animals have enhanced longevity relative to more solitary species.  The author specifically focuses on those species that show cooperative breeding and uses as a data source the information accrued by de Magalhaes on the AnAge website.  I have one major concern that I am sure the author can easily address, assuming he has not yet already done this. That is has he undertaken the appropriate power analyses to evaluate if he would be able to pick up a statistically significant difference between cooperative breeders and non-cooperative breeders if there indeed was one?  With such limited data sets and relatively unreliable maximum lifespan estimates for some of the species (small sample sizes, not kept long enough in captivity to get an accurate estimate of max. lifespan) does he truly have enough power to categorically state there is no small, significant biologically meaningful difference between these two modes of behavior.
The authors also do not distinguish between eusocial and cooperative breeding.
Validity of the findings: If Dr Thorley has done the power analyses and determined the power needed to yield a significant change and met those criteria, I would be in strong support of publication. Without this analyses it is impossible to gauge the scientific merits of these findings.
Additional comments: Minor comments:-
The author cites Dammann's critique of the Ruby et al., paper without also citing the response to that commentary that refutes their claims by using additional analyses, creating a subjective bias in favor of the conclusions of this paper.
Data from solitary species, especially fossorial or strictly subterranean rodents in Walker's book and on the AnAge website differ greatly, reflecting the anecdotal nature of maximum lifespans with few substantiated records of truly maximum lifespan.  No mention is made how these widely different data sets for often the same species are reconciled.


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

Input:
Title: THE CASE FOR EXTENDED LIFESPAN IN COOPERATIVELY BREEDING MAMMALS: A RE-APPRAISAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: All good here
Experimental design: Conceptual issues aside (see general comments), here are some technical suggestions:
-	Habitat categories are somewhat confounded with fossoriality. Arboreal or semi-arboreal species cannot be fossorial. Have you checked the VIFs for these models?
-	You provide subsequent tests separating by family. What about providing an additional test where you only test this idea among terrestrial species and group them by fossorial or not? This seems like a better dataset for this question given the indication that fossoriality is an issue.
-	MCMCglmm uses a Bayesian framework so it seems weird to refer to the p-values it provides in the same way you refer to those provided by the other (frequentist) methods. At the very least, it would be important to remind the readers in the manuscript what the p-value means in the MCMCglmm context. I would even suggest that model selection in that case would be better done using BIC or log-likelihood.
-	On that regard… the stats you report in Table 1 suggest that you ran a fully parameterized model and simply reported its findings without attempts to reduce the models by removing non-significant terms – or using BIC-based model selection (please excuse me if I am missing something). If that is the case, then this could be problematic for your particular claim of a null result. For example, in the caper findings we see a marginal p-value for cooperative breeding (0.09) that could potentially cross the 0.05 threshold if non-informative parameters were to be removed from the model. Did you try that? The same could be said for the credible interval of coop bdg in the MCMCglmm output. It seems important to check that things don’t change after applying proper model selection algorithms
-	It would also be nice to incorporate phylogenetic uncertainty into your analyses.
Validity of the findings: See general comments
Additional comments: In “Do cooperatively… live longer” the author critically re-evaluates the link between sociality and lifespan. There are several things to like about this paper, including the author’s care to redefine fossoriality as applicable only to species that spend significant amounts of time foraging underground (a more conservative definition than previous studies), the confirmation of findings with multiple statistical methods and the explicit correction for sample size in the estimate of lifespan. Other than a few minor technical comments provided below, I find the statistical approach sound. I am also quite aware that in this particular case, a null result is important and should be published. Having said that, there is one critical aspect of this study (and its predecessors) that casts a significant shadow on this entire discussion: estimating lifespan from data points collected in captivity simply does not seem to capture what the underlying hypothesis is all about. Conditions in captivity are incredibly different than in the wild: researchers are explicitly making active efforts to keep captive individuals alive, well-nourished and free from disease. At best, captive measures could be seen as a metric of lifespan potential, which is what the author has done, and differences between species could be interpreted as differences in how long a life cycle could be. In my opinion, though, the problem here is that the hypothesis being tested is likely to relate not to ultimate potential but to expressed one. As the title says, the idea being tested is not about how different species can live under idealized conditions but rather about whether social species actually do live longer in the wild. Sociality is thought to buffer the very things that captive conditions eliminate (disease, predation, food stress) so it is not very convincing to say that you don’t see any differences between social and non-social species when you take all of those issues away. This, to me, seems like a critical flaw even if, as the author explicitly mentions in the conclusion, you are only trying to point out that you think there is no evidence for a positive effect of cooperative breeding on lifespan in mammals.


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

Input:
Title: THE CASE FOR EXTENDED LIFESPAN IN COOPERATIVELY BREEDING MAMMALS: A RE-APPRAISAL
Review round: 1
Reviewer: 3

Output:
Basic reporting: This paper is a re-appraisal of a previous analysis Healy 2015. However while this analysis does indeed reanalyse the question referred to in that analysis I believe it misrepresents both Williams and Shattuck’s and my comments and the appropriate context needs to be given here. See "General comments for the author" for more information.
Experimental design: See "General comments for the author" for other comments relating to category definitions.

Line 122-125: While I understand the retention of a the Cape mole-rat is due to the lack of information regarding African mole-rats, to show that the inclusion of this species does not affect the results a sensitivity analysis should be run with this species removed.

Line 135-137: How exactly was Subterranean defined. For example, is it defined differently to that stated in Healy et al 2014. Given that these definitions are the main difference to the previous analysis they need to be clear.

Lines 147: Was lifespan z-transformed, if not why not?

Line 158-162: Give how many chains were run and how convergence between chains was tested.

Lines 164-173: Why was the residual and t-test approach used instead of adding an additional cooperative breeding term in the general model. Also why was phylogeny not corrected, particular as the PLMM models show high phylogenetic signals.
Validity of the findings: All data have been provided, apart from some issue I have mentioned (convergence testing, number of chains, use of t-test) in Experimental design, the general analysis are statistically sound. See below regarding to how the conclusions are stated and linked to the litrature.
Additional comments: When I was asked to review this paper I was very happy to see that someone had reanalysed a comparative analysis that formed part of a comment and response to an article I published on maximum lifespan in 2014. In particular, the comment (Williams and Shattuck 2015) and response (Healy 2015) were both relatively limited analysis that mainly served to raise the issue that sociality may be a confounding factor for increased lifespan in fossorial mammals. While this analysis does indeed reanalyse the question using a different categorisation of sociality, something I greatly welcome, unfortunately I believe it misrepresents both Williams and Shattuck’s and my comments and I this needs to be put into its proper context and given a tone that appropriately reflects this context.

To give the full context the analysis this paper sets out to conduct a re-appraisal of is my 2015 analysis (Eusociality but not fossoriality drives longevity in small mammals). My 2015 analysis was published as a reply to Williams and Shattuck’s comment and analysis (Ecology, longevity and naked mole-rats: confounding effects of sociality?) which in turn was a comment in relation to the original manuscript Healy et al. 2014 (Ecology and mode-of-life explain lifespan variation in birds and mammals). In this string of analysis Williams and Shattuck highlighted the potentially confounding effect of sociality and showed it had a positive effect on lifespan using a new dataset derived from, but with several important changes, the original dataset in Healy et al. 2014. These changes consisted of using different categorisations for fossoriality and only focused on small mammals (< 60kg) with the potential for fossoriality. My 2015 analysis simply reanalysed the data using a MCMCglmm approach which also incorporated error associated with phylogenetic relationships. My analysis found that fossoriality no longer had a significant effect on lifespan while sociality did.

This manuscript here needs to clearly highlight this context in several ways. For example, while the origin of this analysis stems from Williams and Shattuck 2015, this work is only mentioned in passing in the last paragraph of the discussion (the reference is also missing from the reference list). This paper needs to refer to Williams and Shattuck 2015 throughout and be clear with regards to that being the initial and main analysis with regards to the Healy et al 2014 string of analysis associated with sociality. I think it would also greatly benefit this manuscript to focus on how the analysis here builds on, but differs, from their analysis, and to a lesser degree to Healy 2015 (which only differed to Williams and Shattuck 2015 by using a MCMCglmm approach). Furthermore, the tone of this manuscript should more clearly recognise that these comments were never intended as a final say or anything more than the start of a conversation regarding the role of sociality in comparative analysis of lifespan. In fact, the final paragraph of Healy 2015 highlights this “Williams and Shattuck’s work helpfully extends our analysis to include eusociality; however, the lack of correlation between fossoriality and longevity in this dataset requires further attention given the predicted reduction of extrinsic mortality associated with burrowing. Analysis of fossorial species in other groups such as reptiles, along with the inclusion of more detailed life-history data, may yield more insights into the role of fossoriality in life-history evolution.”

Overall, I think the tone of this manuscript of setting Healy 2015 up as a stand alone analysis to be taken apart misses on the opportunity to build a more constructive paper highlighting the clear gaps in both those previous analysis and to point a more constructive way forward for the field. In particular, I think this paper would be greatly improved if it focused on a message such as “Here we use a more stringent definition of sociality along with a definition of fossoriality more closely related to the original fossoriality in Healy et al 2014 to test the role of cooperative breeding and fossoriality in driving longevity. We also extend the analysis to mammalian groups with no fossorial species to test whether cooperative breeding is associated with increased lifespan across mammals.” By framing it this way the focus would be squarely on the work presented here and not on the limitations of previous short comments and replies.

I give more detailed comments below.

Lines 86-91: mention the more relaxed definition of fossorial used in the 2015 analysis. I refer the author to Williams and Shattuck 2015 who combined the original fossorial and semi-fossorial categories from the Healy et al 2014 into one category. I agree that this is too relaxed a definition and a more restricted term, as used here, is more appropriate for the question. However, Williams and Shattuck 2015 need to be cited here, and the fact that a fossorial category, similar to the one used here, was initially used in the 2014 manuscript.

Lines 95-100: It should be mentioned that, while sample size was not included as a factor, it was considered in the methods of Williams and Shattuck 2015 and Healy et al 2014, with Healy 2015 using the data from Williams and Shattuck 2015. As it stands it reads as if no consideration was made for sample size or data quality in previous analysis.

Lines 100-103: Again out of context this line misses the reasoning from Williams and Shattuck 2015 for not including Callitrichid primates. I refer the author to thier paper which mentions “Since fossorial and eusocial-like species are restricted to smaller body sizes, we do not include mammals larger than 60 kg, a boundary that is approached by the largest semi-fossorial and eusocial-like mammals, aardvarks and humans, respectively.”

Line 195-198: Healy (2015), following from the data from Williams and Shattuck 2015, does not incorporate foraging mode directly as the analysis was conducted on a sub group effectively excluding arboreal species. Hence, to suggest that these analysis failed to control for variation in foraging mode is misleading. I also don’t understand the comment regarding the failing to consider the leveraging effect of exceptionally long lived specie, such as the naked mole rat, given these species were central to the discussion and analysis of Healy et al 2014, Williams and Shattuck 2015 and Healy 2015. Furthermore, my 2015 paper specifically tests the effects of incorporating uncertainty from phylogenetic relationships, to help account for such “outlier groups”. Also it is not clear how this outlier leverage effect was controlled for in a way that was not controlled for previously. I would suggest removing this line.

Line 211-219: It should be mentioned that the definition of cooperative breeding here may be more relaxed than Williams and Shattuck 2015. It would be useful to compare the species defined as eusocial in Williams and Shattuck 2015 to the species defined as cooperative breeding here to see if there is a difference as this might also explain the different results.

Line 221-232: The author suggests here that the previous analysis were in affect pre-mature. This again ignores the context of both comments and also the fact that both papers highlight that more work needs to be done, again referring to my 20015 comment I end on the note “Analysis of fossorial species in other groups such as reptiles, along with the inclusion of more detailed life-history data, may yield more insights into the role of fossoriality in life-history evolution “. I suggest a more constructive tone should be used in this paragraph pointing towards how the field may advance. For example, it could refer to recent relationship found between fossoriality and life span in reptiles (Stark et al 2018). Unnecessary tone of what the author determines as useful or not useful are not helpful here in my opinion. For example, the comments “This being the case, it not it is not particularly useful, for example, to claim that placental moles are on average characteristically short-lived in the context of all mammals (as per Williams & Shattuck 2015). For one, moles are rarely studied, and a cursory glance at another ageing database (Jones et al. 2009) indicates that one of the few well-studied species, the European mole Talpa europaea (not present in this study), can live for seven years, a relatively long time for an 80g insectivore.”. For one, placental moles are indeed on average characteristically short-lived in the context of all mammals. Using your example an 80g mammal living for 7 years would still have a negative residual based on the Healy et al 2014 analysis. Hence, while 7 years might be relatively long for an 80g insectivore it is not long in the context of all mammals. This statement doesn’t so much bother me in its inaccuracies but more so in its tone and quite frankly aggressive tone to another author when it is in no way merited. I think it would be far more helpful to make the useful and important point regarding the difficulties and pitfalls of using maximum lifespan measured for species that have not received much research attention.

Lines 235-236: The author suggest there is little evidence that cooperatively breeding mammals live longer despite the fact that their own models found a significant (and may still be so in the Bayesian model if the chains never converged), albeit small, effect for this. This is clear cheering picking of the results, especially given the context of results in other papers. It would be more consistent to say that the effects of cooperative breeding on longevity are inconsistent across models here and in all cases there is only small effect sizes related to them.

Lines 237-239: “Future studies assessing the role of sociality or mode of life on lifespan variation should consider the availability and quality of data before conducting large-scale comparative analyses.” While this is true, and normally I would not think anything about this statement, given the tone of this manuscript this reads as if previous studies have ignored this. Given the wealth of comparative analysis which strongly point the dangers and pitfalls of using maximum longevity, such as from Anage itself, I think a rephrasing this to “Echoing previous studies (de Magalhães et al 2007), future studies assessing the role ….”

Kevin Healy


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

Input:
Title: THE CASE FOR EXTENDED LIFESPAN IN COOPERATIVELY BREEDING MAMMALS: A RE-APPRAISAL
Review round: 2
Reviewer: 1

Output:
Basic reporting: For the most part OK, a few typos/grammatical errors that should be picked up in final revision
Experimental design: All good
Validity of the findings: With caveats that the maximum lifespan data set may not be as accurate given that these are captive records and AnAge has not necessarily updated as things have changed.  It is a vast improvement on Walker's
Additional comments: The authors have addressed some of my comments or at least provided a convincing rebuttal.

The track changes version is not identical to the PDF!  For example line 55 includes the Damman and Ruby response citations, while in the track changes version it does not and is far less confusing to read.  It seems very strange to have a set of references cited for a finding, in this case mortality rate followed by a “but see”.  If you want to make a comment about these data write a sentence to state your position, as it stands this is most confusing to the reader.

There are also several grammatical errors or typos. For example Line 157 “In general information The only exception to this data restriction”; eLine 210. .. “had a positive effect on maximum lifespan that was positive”.. the sentence should end at maximum lifespan.

It is my understanding that Damman et al has shown that cooperative breeder Fukomys anselli live 20 years as do the solitary spalax, so in many cases of the small subterranean cohort, lifespans are likely to be underestimates.  This should be strongly emphasized but does not detract from the analyses undertaken using the not so up to date AnAge data set.


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

Input:
Title: THE CASE FOR EXTENDED LIFESPAN IN COOPERATIVELY BREEDING MAMMALS: A RE-APPRAISAL
Review round: 2
Reviewer: 2

Output:
Basic reporting: Overall the author has toned down the article and placed the previous analysis into a better context, however there are still a few issues with regards to this that I highlight below. The focus on using just MCMCglmm does simplify the analysis and makes the results more easily interpretable.

I outline my comments in more detail below.
Experimental design: Overall, I think that these analysis are generally sound. However I do think given the context of this paper that the issue of captivity as highlighted by another review should be handled better. I would also like to point out the power analysis suggested is possible (a power analysis is simply simulation of how many more such species would need to exist and does not require more species to actually exist). However I do agree it is not a trivial problem to fix for phylogenetic comparative model (although still possible).
Validity of the findings: As the main goal of this paper is to re-analysis previous questions and updating their shortcomings regarding data quality and the definition of terms, I think it is important to address the comments of reviewer two explicitly in the analysis. The comment outlines that comparing cooperative breeders and non-cooperative breeders from captivity data may have an addition problem due to the usual effects of using captivity data for maximum longevity. In effect, we expect that cooperative breeders would not greatly increase maximum longevity in captivity when compared to non-cooperative breeders. If this was the case and the majority of the data was from captive sources any increase in maximum lifespan associated with cooperative breeders could easily be masked in the analysis. I suggest including captive versus non-captive as an additional explanatory factor in the analysis with an interaction term with cooperative breeding. If this really is an issue you would expect a negative interaction associated with non-captive measures of longevity for non-cooperative breeders.
Additional comments: In Figure 1 there are OLS lines fitted for each order, yet the analysis is a MCMCglmm. I imagine this is a hangover from the previous iteration of the paper were OLS models were used. I would recommend removing these fitted OLS lines and only used estimated from the main MCMCglmm model. It would also be far more informative for the reader if both cooperative and fossorial species were marked out in the graph and the overall mass longevity line fits for both cooperative breeding and fossoriality were included.

With regards to the response from the author“In my opinion not enough was done to control for sample size, as I try to make clear in the introduction (line 137).” in relation to my comment that sample size was considered in the previous papers. I would like to point out that in Healy et al 2014 two analysis were run; one using max longevity for species with only 10 records (small) and a second analysis that only included species with 100 records (large). This effectively boils down to include an explanatory factor of sample size with two levels (even if they are not explicitly included in the model we effectively manually partitioning variance in the data). In this analysis, while an explanatory variable for sample size is included, it only has three levels, so to suggest, as the author does, that this analysis has fixed the problem of sample size in a way that others have not is over egging the contribution in my opinion. It would be comparable to someone re-running the authors analysis with sample size included as a continuous variable and suggesting that “although previous studies tried to overcome possible issues of sample size” “not enough was done to control for sample size”. I would suggest to tone down the line 214-224 to something along the lines of “included sample size in their analysis, using sensitivity analysis relating to sample size, here we explicitly include sample size in each model.”

Minor comments.
Line 247: remove “In general information”
Line 380 “Healey” should read as “Healy”
Line 381-382: I assume there is a mistake in the numbers for the chains as 105000 iterations with a burnin of 5000 and thining of 100 would only generate 1000 posterior samples for each parameter and not 200000
Line 383: Gelman-Rubin statistic needs citation.
Line 552: For clarity include “compared to non-cooperative breeders” in the line “The only family where cooperatively breeding species appear to live longer is in the bathyergid mole-rats.”


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: PLASMA ANTIOXIDANTS AND OXIDATIVE STRESS STATUS IN OBESE WOMEN: CORRELATION WITH CARDIOPULMONARY RESPONSE
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	Some language issues should be corrected, for example:
•	Introduction, Line 2: “dynamics factors that have” should read “dynamic factors have”
•	Introduction, Line 50 can be rephrased to clarify to “When energy intake is high and energy expenditure is low….1”
•	Introduction, Line 53: “that presence” can be changed to read: “the occurrence of chronic inflammation present in adipose….”
•	Introduction, Line 60-61 should be changed to: “Eventually, the elevated levels of ROS in a biological system could lead to an oxidative state.”
•	Methods, Line 184: “as unit per milliliter” should be “units”
•	Methods, Line 198: “Ramp protocol…” should be “The Ramp protocol”
•	Methods, Line 203: “of antioxidant and oxidative stress status with CPET” should change to “of antioxidant and oxidative stress and CPET”
•	Results, Line 228, 230, 233, 235, 245 the use of the words “decrease”, “change”, “increase” is not appropriate as it reflects a time component. It should rather be replaced with “lower”, “difference”, “higher” etc. Also check Discussion, Line 287, 296
•	Discussion, Line 276-277: “Subsequently, lead to the elevated level of reactive oxygen species in the biological system result in oxidative stress state.” This sentence can be rephrased as follows: “These complications may include the elevation of reactive oxygen species and ultimately result in an oxidative stress state.”
•	Some abbreviations were not explained upon first use, e.g. IL-6, TNF-α in the introduction and ABTS and FRAP in the abstract.

2.	The introduction/background is sufficient to supply context, but some clarification is needed as indicated below. The references used are appropriate but some statements were not referenced and the reference style used in the reference list is not consistent.
•	Sometimes the one idea does not flow to the next. Remember that each paragraph should be a unity describing an idea. For example in paragraph 2 the theme is mostly on inflammation, but at the end of that paragraph oxidative stress comes into play, while the whole third paragraph focus on oxidative stress. Also keep in mind that inflammation is not central to this article since it was not measured.
•	In the introduction, the oxidative stress markers measured in the study was not introduced. When referring to previous studies in which these markers were measured, gives credence to your work.
•	Sometimes it works better if the motivation moves on to the aim and not the other way around as it is currently stated in the last paragraph of the Introduction.
•	In paragraph 2, Line 55 the following was stated: “An imbalance between pro-inflammatory and anti-inflammatory cytokines, in favour of the former, is thought to be the cause for the development of metabolic and cardiovascular disorders including atherogenesis.” Just keep in mind that multiple factors contribute the development of CVDs. Yes inflammation is a contributing factor, but not the only factor.
•	The following statements needs references:
o	Line 38: “Obesity is considered as a 21st-century epidemic worldwide.
o	Line 44-46: “ …in which low physical activity coupled with high consumption of energy-dense food over the needs of an individual would cause excess adipose tissue deposition in the body.”
o	Line 54-55: “…in which the enlarge adipocytes release pro-inflammatory cytokines such as IL-6 and TNF-α.”
o	Line 60-61: “Eventually, the elevated levels of ROS in the biological system could lead to oxidative stress state.”
o	Also check statements in Line 63-63, line 64-65, Line 70-71.
•	In the reference list the following references lack page numbers or DOI numbers: Awad, Bunsawat, Cepeda-Lopez, Chan, Cole, Csige, Gustafson, Kawasaki, Kowalska, Limberaki, Lubkowska, Pizzino, Steinberg, Van Gaal

3.	As indicated above, sometimes the one idea does not flow to the next. Please refer to examples given below:
•	The first few lines (Line 268-279) of the discussion if mainly repetitive of the introduction. Also when the authors get to what they found some aspects of the results section is repeated, without immediately telling the reader why their findings is important.
•	It may also help to structure the paragraphs similarly. Start off with what you found. How does it compare to known literature. If it is contradictory – why? What possible mechanisms may be at play?
4.	The resolution of the figure were not good and the text is quite small.
5.	The raw data was supplied
Experimental design: 1.	This article is original primary research and within the scope of the journal.
2.	The research question was well defined, it is relevant and meaningful and it was stated how the research fills a gap in knowledge.
3.	The investigation method complies to ethical standards but needs some clarification:
•	The sample size was rather small, did you have enough power to address your hypothesis?
•	Which guidelines were used for BMI classifications?
•	It would have been interesting to see if the oxidative stress and antioxidant markers change after CPET
•	For anthropometry, which guidelines and instruments were used?
•	 In the statistical analyses section it was stated that “All analyses were performed in triplicate” Does that refer to the biochemical analysis or the statistical analysis?
•	Which of the variables did not display a normal distribution? It is not clear when Pearson vs Spearman correlations were used?
Validity of the findings: 1.	Limited information is available on the link between oxidative stress and cardiopulmonary fitness and body composition, especially in females and therefore this study is beneficial to fill this gap.
2.	All underlying data have been provided but I do have some concerns:
•	The difference in age of the groups, may be an bigger issue than indicated in the strengths and limitations of the study. Age, especially in women aged 19-55 may be a huge confounder when considering different hormonal levels in women in this age range. Do you have data on estradiol available? Or if the data of the main findings are normally distrusted, I would suggest adjusting for age in partial correlations (you may even consider data transformation).
•	It is stated in the discussion in line 304 that CAT is more stable than SOD and GPx, please clarify?
•	If a finding is not statistically significant, it should not be used to make an argument, please refer to lines 311 – 313 and line 372.
•	The conclusion is a bit bold, and should be rephrased and toned down. This was cross-sectional work on a very small sample and does not show any predictive value.
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: PLASMA ANTIOXIDANTS AND OXIDATIVE STRESS STATUS IN OBESE WOMEN: CORRELATION WITH CARDIOPULMONARY RESPONSE
Review round: 1
Reviewer: 2

Output:
Basic reporting: English.  The article needs editing. I include some suggestions (but not exhaustive editing) in comments to the authors.

References.  Nothing to add

Structure and organization of the article. It  has an acceptable format and the figures and tables re relevant.

Hypothesis. The article contains a hypothesis and results relevant to it.

Discussion. The results need to be better discussed and some paragraphs reorganized. At points the information given in the discussion is not directly related to their results.
Experimental design: Aims of the journal .The manuscript conforms to the aims and scope of the journal.

Scientific question. It is clearly indicated: it aims to fill the gap in knowledge on the relationship between oxidative status and cardiopulmonary fitness in relation to obesity.

Ethical and technical standards.  The work conforms to the ethical standards and it has been conducted rigorously. I miss data on the diet and the level of physical fitness of the studied population and the fact that they have age differences. I appreciate that these aspects have been discussed as a limitation by the authors. I suggest that they can statistically re-analyze some of their results taking into account age and may be menopause (suggestions included in comments to the authors).

Methods. The methods have been described rigorously. I make some suggestions to the authors to include some details regarding th formula of the parameters used in the CPFT, which I think could improve the manuscript.
Validity of the findings: The manuscript adds the novelty to assess the possible relationship between oxidative status and cardiopulmonary function in obese women. Although the results do not allow for a global conclusion, since they did not assess the previous level of fitness (which may have an impact on the antioxidant status of the women), the data presented are relevant of interest to researchers in the field and provide ground for further studies.

Robustness of the data. The data are statistically sound. I think there are relevant data what can be easily included: I suggest to add the Skeletal Muscle Mass/body weight, Fat mass/body weight.

Conclusions. I think the authors have to be more cautious about the conclusions. The data indicate that in relation to obesity there is decrease in some antioxidants and an increase in catalase activity, likely due to a compensatory response. However, the assumption that catalase can predict metabolic disorders and complications, I think it is not supported by the data provided. There are many questions remaining (different ages of the population, level of fitness), which may have influenced. I think they should restrict to their original question and discuss what aspects remain in speculative field.
Additional comments: English. Editing by a native English speaker would improve the clarity of the manuscript and help the readier. Below I suggest a few modifications.
Line 25. Plasma samples were “separated”. I suggest to change to: were “obtained by centrifugation”
Line 39. Sociocultural dynamics factors that have been associated with….  I suggest to change to:  “Sociocultural factors have been associated with…. “
Line 42:” lead to”.  I suggest to change to: “contribute to”
Line 46: “What is more”. I suggest to delete this. This applies to similar sentences (i.e. in the abstract, in lines 70 and 346).
Line 67. The uncontrolled increase of oxidative “stress”. I think it is more correct to talk about increase in oxidative “damage”, since oxidative stress is just the disbalance between ROS production and elimination leading to damage to macromolecules.
Line 92. “Staffs” has to be changed to “Staff” (it is singular)
Line 111. Plasma layers were separated. I think you can delete “layers”
Line 187. “The exercise physiologist conducted CPET at the”.  I suggest to change to: “CPET was conducted at the”
Line 325. “Ill interactions”. May be you can change to “abnormal interactions”.
Line 354. “lower in female youth”. I suggest to change to: “lower in young OB females”
Abbreviations. Some  have to be included before in the text, such as NW, OB, OW, CPET

Abstract . It can be improved. I suggest to expand it  with additional information on methods (i.e. what oxidative balance and cardiopulmonary  parameters were assessed)

Methods. I suggest to include in methods if you asked about menopause, I also propose to include the formula of some of the parameters measured in the exercise testing, (i.e. the oxygen pulse; metabolic equivalents, peak oxygen consumption). I think this would help the reader.

Results. I think there are relevant data what can be easily included: I suggest to add the Skeletal Muscle Mass/body weight, Fat mass/body weight; You indicate that a drawback of the study is the fact that you found significant differences in age between the 3 groups.  I suggest to re-analyze  statistically the results taking into account age: 1) the relationship between age and the plasma parameters and 2) relationship between age and some of the cardiopulmonary parameters measured in CPET
Did you ask about menopause? If you can add some information it would improve the manuscript (either in the discussion if you did not ask about this, or if you know you can check if it influenced the results).

Discussion. I suggest to include the following aspects. !) to discuss on the type of antioxidants which are evaluated by FRAP and ABTS (low molecular weight antioxidants? Vitamins? ). This can be informative; 2) the possibility that you did not find differences in oxidative damage or ROS due to methodology (may be the method is not accurate enough to detect small differences, taking into account that ROS are highly unstable?
Lines 273-277. “Expansion of adipose tissues may activate inflammatory cascades that lead to secretion of adipocytokines, and together with changes in lipid and glucose metabolisms (Gustafon, 2010) may give rise to other complications when responses are uncontrolled. Subsequently, lead to the elevated level of reactive oxygen species in the biological system result in oxidative stress state”. I think this sentences need to be rephrased and organized  according to the sequence of events: adipose tissue expansion, increase of pro-inflammatory adipokines, macrophage infiltration, ROS increase and tissue damage (also induced by alterations in lipid and glucose metabolism).


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: PLASMA ANTIOXIDANTS AND OXIDATIVE STRESS STATUS IN OBESE WOMEN: CORRELATION WITH CARDIOPULMONARY RESPONSE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thank you for your efforts in fixing the language errors. I did notice some minor issues that still needs ratification:
•	Line 236: “The mean BMI for the study was” should be changed to “The mean BMI for the study population was”
•	Line 302: “Yet, majority” should be changed to “Yet, the majority”
•	Line 427: “OB individual” should be “OB individuals”
Experimental design: Thank you for your efforts in clarifying the mentioned issues on your experimental design. There are still some issues that I would like to bring to your attention:
•	Please add the power calculation to manuscript.
•	You indicated that you added a footnote to show the normal distribution when spearman vs Pearson correlations were used, but it was in fact not added.
•	Line 37 and Line 288: You refer to Pearsons’ partial correlations. It should only be Partial correlations.”
•	Line 278-279: It was stated: “Data from the antioxidant activities and oxidative stress parameters together with the CPET parameters were compared to determine the relationship between the various parameters.”  This is not stated correctly. You did not compare these variables, but investigated associations/relationships/correlations between CPET parameters and markers of antioxidant activities and oxidative stress.
Validity of the findings: Thank you for your efforts in correcting the issues raised. Regarding the conclusion, you summarized the correlations found in the study, but you did not indicate what this mean? You should also conclude on that.
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: PLASMA ANTIOXIDANTS AND OXIDATIVE STRESS STATUS IN OBESE WOMEN: CORRELATION WITH CARDIOPULMONARY RESPONSE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Adequate
Experimental design: Adequate
Validity of the findings: Adequate
Additional comments: The manuscript has been markedly improved and I think it deserves publication. I only suggest changing the conclusions, which I think are still a bit confusing. I suggest the modification of the following sentences:

Abstract: Lines 40-41. “Results from this study indicate potential correlation between redox status and cardiopulmonary response.  However, validation of this cross-sectional data in a larger sample size and population would shed more light on the observed results”. I suggest to change to : “Our results indicate a lower cardiovascular fitness and antioxidant capacity in obese women; the higher catalase may be a compensatory mechanism. The correlations between antioxidants and cardiopulmonary responses deserve further analysis in a larger population”.

Conclusion. Lies 433-437. “In conclusion, female subjects who are obese showed higher CAT activity than normal weight subjects, despite the reduced non-enzymatic antioxidants activities and their metabolic responses were low, reflected by the levels of peak oxygen consumption and metabolic equivalents.  The ABTS, CAT and SOD correlated negatively with oxygen pulse and cardiac output, peak oxygen consumption and respiratory frequency, respectively. Future studies should take…”.     I suggest changing to:   “Obese women exhibited reduced cardiopulmonary fitness and antioxidant capacity, while catalase was increased, possibly as compensatory mechanism. The negative relationship between some antioxidants and cardio-pulmonary responses to exercise, deserve further investigation, taking  …

Minor comments:
Abstract line 44. I suggest deleting the word “parameters”
Line 317. The sentence   “that even with excessive dietary consumption of antioxidants-rich food”. I suggest changing to:    “that even with high dietary consumption of antioxidant-rich foods”.


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

Input:
Title: THE INFLUENCE OF SURROUNDING LAND COVER ON WETLAND HABITAT CONDITIONS: A CASE STUDY OF INLAND WETLANDS IN SOUTH KOREA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study evaluated the current status and factors which influenced for these status of wetlands in whole of South Korea using national inventory. Wetland is one of the most threatened ecosystem worldwide so conservation strategy is strongly needed. Nation-scale assessment like this study is the important first step so I could find the significance of this study. The manuscript is satisfied basic criteria of PeerJ, English, construction of Introduction with literatures are clear. All figures and Tables are significant for this study. Data sets were basically opened in local languages from Open Data Potal in South Korea so readers could access that.
Experimental design: The aim of study and approach are significant, analytical approach is basically acceptable. However, there are several problems especially on data management.

First, authors used rank of wetland condition using scoring system by governmental criterions (L131-). This system itself is good to evaluate the condition of wetland quickly, but not suite for additional statistical analysis I think. For example, authors used wetland size as explanatory variable in the catchment and that strongly influence for the wetland rank (Table 3). However, that is already included the wetland ranking definition (L135). That is problem because in theory same value was used both explanatory variable and objective variable. Even authors integrated these wetlands within the catchment, I think that essential problem could not clear.

Second, relate to the first problem, authors used wetland size within the catchment as explanatory variable. However, this values include several types of wetland which have different origins i.e. riparian, lakes etc.. Each type could have different effects for the condition of target wetland I think. Authors should divide that variables at least natural and human-made.

Third is on spatial analysis. Authors treated all wetland as independence one. In other words, authors did not consider the spatial autocorrelation of distribution of wetland. Unfortunately authors did not show the distribution pattern of each origin type of wetland, I imagine same origin type could located closely. Authors should clear that problem.

Forth is the lack of explain of used data set. I surmise authors selected used explanatory variables based on VIF for statistical analysis (L185) but there are no specific mention of results of VIF analysis. In the result section authors showed the map which showed relationship between wetland and land cover (Figure 1) but no mention which types were removed in statistical analysis. Authors should explain what variables are correlated with removed variables such as cropland cover, forest, population.

Almost of all problems were caused by statistical analysis for wetland ranking. In my opinion, that part is not important for this study. Summarize and overview of wetland inventory itself has significance for the aim of this study namely. For this aim, descriptive statistics, i.e. without complex analysis is adequate.
Validity of the findings: There are some problems on statistical analysis so I could not evaluate the findings from these. I could evaluate the results of overview of wetland condition with nation wide. Summarize and overview of inventory itself is significant as nation wide assessment of wetland.
Additional comments: In this section I would like to take specific comments.

L60,
What are assessment tools? Please explain with come example.

L87-88,
Please explain why authors focused the importance of these points from several un-evaluated contents on wetlands.
There are many types of “spatial pattern”. For example, density, location information with majority land use are all spatial pattern. Please explain more details.

L111-,
Why authors used the category IV? Please explain more details.

L114-
Is there any references on that survey methods?

L135-,
How to select these 8 categories? Please explain more details.
Among these category, academic or educational values are difficult to evaluate. How to evaluate that?

L150-, Table 2,
How to decide these criterions to define rank A-D?

L185- Please show here which variables were removed.


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

Input:
Title: THE INFLUENCE OF SURROUNDING LAND COVER ON WETLAND HABITAT CONDITIONS: A CASE STUDY OF INLAND WETLANDS IN SOUTH KOREA
Review round: 1
Reviewer: 2

Output:
Basic reporting: I have not properly corrected the English writing since it is not my native language, but I think an English editing effort is needed.

Line 96. Please, add your hypotheses at the end of the Introduction section.
Experimental design: The M&M section should be improved: Lines 135-146. Justify and explain why you choose each wetland characteristic and how they were recorded.
Validity of the findings: To improve the Discussion:

Line 331. I think it would be worthy to comment of the effects of soil erosion from agricultural bare soils and its effects on wetlands.

Line 358. Please, offer here the most important wetland restoration and preservation measures to carry out in view of your results.
Additional comments: Title: The influence of size and surrounding land cover on wetland habitat conditions: a case study of inland wetlands in South Korea

The subject of this manuscript falls within the general scope of PeerJ. The manuscript is an original contribution to the preservation status of inland wetlands and environmental factor influencing on it. I recommend the publication of this manuscript in PeerJ after mayor revisions.

Abstract

Please, clarify in the Abstract that we are analyzing only inland wetlands and no coastal intertidal wetlands.

Lines 35-36. Rewrite and clarify this sentence: ‘We also found that the presence of protected areas is affected positively´

Lines 39-40. Keywords should be in alphabetical order. Please, avoid words already included in the title.

Introduction

Line 54. ‘National wetland inventory is’ should change to ‘National wetland inventories are’.

Lines 65-66. ‘(62%). While in Asia’ should change to ‘(62%), while in Asia’.

Line 88. Please, include a paragraph about the effects of surrounding lands on wetland preservation.

Line 96. Please, add your hypotheses at the end of the Introduction section.

Materials and Methods

Line 106. Delete ‘the’ before ‘wetland’.

Line 121-122. ‘Smaller wetlands or ponds (< 400 m2) were not included in the following delineation process’. Explain why, please.

Line 129. Please, add the author name for the first time you cite every species. Ex. ‘Moliniopsis japonica’.

Lines 135-146. Justify and explain why you choose each wetland characteristic and how they were recorded.

Results

Line 197. ‘Korean peninsula’ should change to ‘Korean Peninsula’.

Line 205. Were these ‘brackish’ wetland intertidal salt marshes? Were you including coastal wetlands in your study? Please, clarify. You are talking about ‘estuaries’ in Line 265…

Lines 240-260. Please add the ‘n’ date to the results of correlation analyses.

Discussion

Lines 288-290.’ Rice paddies were included in the category of wetland types; however, only part of the rice paddies and abandoned fields were included in the current wetland inventory’. Please, explain why.

Line 331. I think it would be worthy to comment of the effects of soil erosion from agricultural bare soils and its effects on wetlands.

Line 358. Please, offer here the most important wetland restoration and preservation measures to carry out in view of your results.

Tables

Table 3. Indicate what ‘β’ is.

Figures

Figure

I have not properly corrected the English writing since it is not my native language, but I think an English editing effort is needed.


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

Input:
Title: THE INFLUENCE OF SURROUNDING LAND COVER ON WETLAND HABITAT CONDITIONS: A CASE STUDY OF INLAND WETLANDS IN SOUTH KOREA
Review round: 2
Reviewer: 1

Output:
Basic reporting: In the first round I could not find any severe problem on the criteria of basic repotting. However in that round I found one dead link on the website (http://map.ngii.go.kr). Please check and show the final date of access. Authors should revise that to keep data accessibility.
Experimental design: The problems on analytical design which I indicated previous round were basically revised. On the VIF, I would like to recommend author to show there are no removed variables in the text, or show the table which snow the VIF values as supplemental material.
Validity of the findings: Discussion section and recommendation are basically adequate. However, I would like to request author more deep discussion in some points.

L329-332, Same as the bareland which showed latter, please discuss about the mechanism why natural vegetation could positively influence for the wetland condition. Currently authors showed the just result only.

L355-356, Please explain what is a gap more specific. This point is important to enhance the inventory work I think.
Additional comments: No additional comments


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

Input:
Title: THE INFLUENCE OF SURROUNDING LAND COVER ON WETLAND HABITAT CONDITIONS: A CASE STUDY OF INLAND WETLANDS IN SOUTH KOREA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have already answered correctly to my previous comments.
Experimental design: The authors have already answered correctly to my previous comments.
Validity of the findings: The authors have already answered correctly to my previous comments.
Additional comments: The authors have already answered correctly to my previous 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 NEW GENUS OF SINOGALEASPIDS (GALEASPIDA, STEM-GNATHOSTOMATA) FROM THE SILURIAN PERIOD IN JIANGXI, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: see general author notes
Experimental design: see general author notes
Validity of the findings: see general author notes
Additional comments: Shan et al describe some new sinogaleaspid fossil material identifying new taxa. These taxa are placed in taxonomic framework, subjected to a phylogenetic analysis, and discussed in the context of galeaspid evolution. I am happy to recommend publication of this manuscript in PeerJ following some minor revisions (listed below).
1. If Shuyuidae is a new family, it will also need a taxonomic diagnosis.
2. Some aspects of the taxonomy would benefit from highlighting the key synapomorphies that distinguish taxa. For example, what are the unambiguous synapomorphies of the revised Sinogaleaspididae? Can the authors confirm that developed median dorsal canals and more than 2 pairs of median transverse canals are not observed in any other galeaspids? A remarks section for Rumporostralis would help to highlight the unambiguous and unique syanpomorphy defining the genus.
3. The final discussion and conclusions section makes some interpretations beyond the available data. Given the phylogenetic analysis and its taxonomic scope, it is possible to infer or describe the evolution of sensory line patterns WITHIN galeaspids, but it is certainly not possible to identify or infer ancestral conditions for vertebrates without a much bigger analysis including a broader range of clades. I suggest removing this final observation - the manuscript happily stands alone with out it.
4. I don't quite understand the choice of the phylogenetic matrix. The authors use Gai and Zhu 2005, but why not use Zhu and Gai 2006? The later has a broader range of genera included and a more exhaustive character list.

More minor points:
L36 accumulative is not the correct word
L32 are not is
L44 delete the
L64 excursions is not the right word
L140 acanthous might not the best word choice here
L206 "as for the type species" but this IS the type species. Did you mean to refer to a previous diagnosis?
L256 The extension of the anterior end of the median dorsal opening terminal on the head shield- this character needs consideration from a taxonomic perspective. Could it be an artifact of preservation? Some of your specimens show incompleteness in this region
L307 be careful of the word 'cracked'. This implies some sort of destructive force, when I think the intention is to describe the position of the median opening as reaching the anterior margin of the headshield
L353-L359 This is a fascinating subject, but needs more thorough data and consideration before definitive conclusions are drawn
L406 have not has
L476. Abbreviations
Figure 7. This is a beautiful figure. Given the discussion of sensory line patterns, it might make sense to include that information in this phylogeny some how.


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 GENUS OF SINOGALEASPIDS (GALEASPIDA, STEM-GNATHOSTOMATA) FROM THE SILURIAN PERIOD IN JIANGXI, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall the study is well described and executed. However, the text would benefit from the use of clearer English throughout, perhaps a re-edit and read through, this would clarify some meanings and descriptions and enhance the flow of the text in places.
Experimental design: The study aims to describe two new galeaspid species and place them within the phylogenetic context of the Eugaleaspidiformes. I believe the text could put more emphasis on our previous gaps in knowledge and how their contribution alleviates this. All other methods are well descried, with a clear systematic palaeontology section.
Validity of the findings: no comment
Additional comments: Overview
The paper introduces and describes two new species of galeaspids from the Lower Silurian of Jiangxi, China. The two new taxon are notable as their median dorsal openings are positioned at the very anterior end of the head shield, creating a break in the rostral end of the shield. The presence of  3-8 pairs of transverse commissures in the new taxon supports the presence of these in sinogaleaspids, which is not seen in other galeaspids taxa. The authors then incorporate the new taxa into a phylogeny of Eugaleaspidiformes erecting 5 new characters and determine the monophyly of the Sinigaleaspidae (to the exclusion of Shuyu zhejiangensis and Meishanaspis lehmani).
Overall the study is well described and executed. However, the text would benefit from the use of clearer English throughout, perhaps a re-edit and read through, this would clarify some meanings and descriptions and enhance the flow of the text in places.
The study aims to describe two new galeaspid species and place them within the phylogenetic context of the Eugaleaspidiformes. I believe the text could put more emphasis on our previous gaps in knowledge and how their contribution alleviates this. All other methods are well descried, with a clear systematic palaeontology section.
Below are general comments on sections, or specific lines
Abstract: The abstract could be improved by a clearer introduction to the animals being studied and place the new galeaspids taxa into their wider context.
Introduction: More of a general introduction would help non-specialists. Perhaps a phylogeny of early vertebrates with an introduction into their anatomy (especially galeaspids anatomy) would make your paper more accessible to non-specialists. I think the text would also benefit from an introduction to galeaspids phylogenetics, what has been done in the past? Where are the Eugaleaspidiformes placed within the Galeaspida?  What are the previous contradictions in their phylogenetic relationships that your study may alleviate?
L43: “we use the synchrotron X-ray tomographic microscopy (SRXTM) to characterize the cranial
anatomy of Shuyu zhejiangensis and provide the crucial fossil evidence for the
 culmination of stepwise anatomical changes towards crown gnathostomes “ This sentence is slightly misleading, as it reads as if you are doing this in this paper and you do not state that Shuyu is within the Sinogaleaspididae and thus the Eugaleaspidiformes. I would suggest stating that SRXTM has been used to reveal the cranial anatomy of Shuyu, a Sinogaleaspididae, which in turn has provided valuable characters and anatomy within the galeaspids and for comparison with other early vertebrate groups ( Gai et al… etc ) – thus highlighting the groups importance.
L46: perhaps detail the characters that demonstrate the step-by-step transition from jawless to jawed vertebrates – this would emphasize why this group is important.
L49-63:  this section is bit dense with lots of taxonomic names – would a diagram help with demonstrating what the taxa look like or the conflicting phylogenetic position of taxa in past studies? See Sansom (2009), Randle & Sansom (2017), Glinskiy (2019) – they provide conflicting previous topologies – this helps to show where the controversy is and thus increases the importance of your study.
L54-55: is this paraphylic grouping based upon phylogeny or taxonomy?
L74-75: “The new
materials of sinogaleaspids were collected”, try “The new sinogaleaspid material was collected”
L101: material not materials
L119: you say all characters are unordered but in SI character list it says character 4 is ordered?
L119: please don’t use the term “basal” not useful when talking about taxa phylogenetically, perhaps use “deepest branching” or “considered sister taxon to….”, or “plesiomorphic”
L121: why are these galeaspids selected as outgroup taxa? I think an explanation/justification here would be good. Is it based on previous interpretations of anatomy, previous phylogenetic studies, stratigraphy?
L139: “Small to medium-sized galeaspids
” –this isn’t that informative when you have given no introduction to what the size range is for galeaspids – perhaps put a measurement or size range for the headshields, or state the size.
L142: “orbital opening a little big, round” – this doesn’t make sense
L160: “basal” – try “Shuyuidae are positioned as the sister to all other Eugaleaspididiformes, and lack the typical eugaleaspid-type sensory canal pattern”
Line 165: sp. Lartin - latin
L174: try “its posterior margin ends before the level of the orbital opening anterior margin”
L175: “orbital opening fair big, round, dorsal positioned” – doesn’t really make sense
L177: “sensory system developed” – developed compared to what?
L181: sp “chamber” – “chambers”
L246 & 248 sp. in the holotype
L252: with the long axis
L253: axis of the median dorsal opening

L307: is cracked the correct work here? Cracked would suggest it is broken and not an anatomical feature.
L313: are not is
L328: in the following aspects:
L329: more slender not “much slenderer”
L338: exists
L338-343: what are these similarities differences
L350: “the relative size of the head-shield seems to be a reliable
species diagnostic in osteostracans and galeaspids” – should size be used as a diagnostic feature…. Have you compared the relative proportions of some of the features? If is scales completely and has no anatomical distinguishing features should it be considered a different species?
L358: remove “of”
L367: “diversified” - diverse
L399: why was the monophyly questioned? Many of the galeaspids papers referenced are in chinese so it may be a good idea to explain why this was questioned? Was it taxonomically, phylogenetically? Why?
L401-403: “In our cladogram, the monophly of the Sinogaleaspidae is robustly supported, if we remove Shuyu zhejiangensis and Meishanaspis lehmani from this group (Fig. 7)” what support measures are there to support this, I think it would add support to this statement if you include branch support statistics?
L458: “Within galeaspids, the number, placement and branching pattern of the sensory canals vary significantly in different groups, even if the species are closely related” – interesting point, which is true in other ostracoderm clades i.e. heterostracans. I wonder then how phylogenetically informative sensory canal pattern characters are?

L508: “but is very common in heterostracans” – heterostracans commonly have 3-4 median transverse commissures. Why do you think the sinogaleaspids have up to 8?
L505 & L530: on line 505 you mention 3-8 pairs median transverse commissures and on L530 you state its 6-8 pairs -  this needs clarifying
Phylogenetic characters
Characters: Overall the character list could do with explanations of the character codings – if you have used other studies characters and character codings you need to reference these with the original character numbers, This makes it clearer and more reproducible. If you’ve made any changes again state what these are and why (see below for further comments).
Figures
Fig 1: Colour combination – red and brown aren’t the best especially for colour blind peeps, also a fair bit of white space – could you remove the bounding box around China and squash it up a bit better. Key could be clearer – it’s hard to see what things are, distinguish from the different rock types.
Fig. 7. Usually the tree length and number of most parsimonious trees the strict consensus is constructed from is reported in the figure legend. It would also be good to see the branch support statistics on the tree (such as bremer decay and bootstrap values)
Comments on Character List
Appendix I
Characters used for the phylogentic analysis of the Eugaleaspiforms by Gai et al.(2005)
  All characters except Character 4 are unordered – why is 4 ordered and all others not?
1. Shape of median dorsal opening: (0) round; (1) transverse oval (width>lengh); (2) longitudinal oval (length>width).
2. Longitudinal oval dorsal opening: (0) not slit-like (length/width<5); (1) slit-like (length/width>5) – why have you used this – why 5?
3. Anterior end of median dorsal opening: (0) subterminal; (1) terminal; (2) far from rostral margin of shield.
4. Posterior end of median dorsal opening: (0) in front of or level with anterior margin of orbital opening; (1) between the centre and anterior margin of orbital opening; (2) between the centre and posterior margin of orbital opening. (ordered)
5. First median transverse canals (mtc1): (0) present; (1) absent. Doesn’t change the meaning of the character but conventionally (0) is absent and (1) present
6. Third median transverse canals (mtc3): (0) present; (1) absent.
7. Posterior supraorbital canals (soc2): (0) present; (1) absent.
8. Ltca: (0) present; (1) absent.
9. Ltcb: (0) present; (1) absent.
10. Ltcc: (0) present; (1) absent.
11. Ltc4: (0) present; (1) absent.
12. Median dorsal canals: (0) not developed; (1) developed. What does developed and not developed mean?
13. Corner: (0) present; (1) absent. Corner of what?
14. Extending direction of corner: (0) projeccting laterally; (1) projecting backward.
15. Inner corner: (0) present; (1) absent.
16. Shape of inner corner: (0) broad leaf-shaped; (1) spine-shaped.
17. Ratio between preorbital length and post-orbital length in mid-line larger than 0.9: (0) no; (1) yes. Again why 0.9 –what’s the significance of 0.9?
18. Ratio between preorbital length and post-orbital length in mid-line larger than 1.1: (0) no; (1) yes. Same as previous comment
19. Pineal organ: (0) on front of or level with posterior margin of orbital opening; (1) behind posterior margin of orbital opening.
20. Ratio between pre-pineal length and post-pineal length in mid-line of cephalic shield larger than 1.0: (0) no; (1) yes.
21. Rostral process: (0) absent; (1) present. You have switched the codings around here
22. Shape of cephalic shield: (0) nearly triangular; (1) nearly semicircular; (2) nearly oval; (3) nearly trapezoid.
23. Edge of cephalic shield: (0) serrated; (1) smooth.
24. Anterior supraorbital canals: (0) exitence; (1) absence. Should this be present/ absent?
25. V-shaped  Posterior supraorbital canals: (0) yes; (1) no.
26. The rostral margin is splitted by the median dorsal opening: (0) yes; (1) no. Sp. split
27. The ornamentation of the head-shield: (0) star-shaped tubercles; (1) tiny granular tubercles （2）coarse granular tubercles
28. the number of mtc: (0)one (1) two; (2) more than two; Again why just more than two – would be good with character explanations!


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

Input:
Title: A NEW GENUS OF SINOGALEASPIDS (GALEASPIDA, STEM-GNATHOSTOMATA) FROM THE SILURIAN PERIOD IN JIANGXI, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: I carefully read “A new genus of sinogaleaspids (Galeaspida, stem-Gnathostomata) from the Silurian of Jiangxi, China”.  In this manuscript, Gai and colleagues describe new galeaspid materials from the Lower Silurian Xikeng Formation in Jiangxi Province, China.  On the basis of these materials, Gai and colleagues: a) assign the form previously known as Sinogaleaspis xikengensis to a new genus Rumporostralis; b) name an additional species of Rumporostralis, R. shipanensis; c) provide general discussion of the lateral line morphology and small size variations in galeaspids; and d) present a new phylogenetic analysis of eugaleaspidiforms.

I find the components a–c sound and well reasoned. In particular, the sensory canals in galeaspids are among the topics ripe for comparison and discussion in a widely accessible international journal. Although comparison is rather superficial, and although this comparison should be enhanced with citations to new papers and the broader literature on the topic (such as King et al. Palaeontology 61, 325–358, and general discussion of dermal plate homology in stem gnathostomes), I welcome this contribution.

I recommend the authors consider some presentation problems identified in text and figures, and address some issues with the phylogenetic analysis. The manuscript is written with some clarity overall, but suffers here and there for the lack of better terminologies to describe morphology or the refusal to use simpler, clearer language.  Diagnosis needs to be differential against coeval galeaspids and closely related, con-familial taxa, and should indicate which, if any, is an autapomorphy.  Figure 1 has many problems.  I suggest the authors use clearer legends for the stratigraphic column, and remove international borders in dispute, which have no relevance whatsoever to the content of the paper. For particular comments, please refer to the following sections and the file attached with my suggestions.
Experimental design: The analytical design has some flaws that need to be addressed.
1)	I understand that there is little to do about the high taxon:character ratio in galeaspids, but some characters are clearly duplicates and others are non-independent of each other.
2)	Appendix says character 4 is ordered, but the main text states all characters were treated unordered.
3)	Characters 17 and 18 give weight to the taxa with ratio lower than 0.9 (scoring “0” for both characters, even though character 18 is dependent on 17).
4)	Character 26 overlaps with character 3.
5)	Character 28 repeats characters 5 and 6.

The text argues that it “robustly support” monophyly of sinogaleaspidiids. Any measure for this? Decay index or bootstrap?
Validity of the findings: It is difficult to assess taxonomic validity without differential diagnosis. Again, diagnosis needs to be differential against coeval galeaspids and closely related, con-familial taxa, and should indicate which, if any, is an autapomorphy.  If difficult to do this in text, consider presenting a table comparing these forms.
Additional comments: Gai and colleagues use “basal” a lot as descriptive term. This is not recommended. Shuyuiids are equally "basal" as non-shuyuiid eugaleaspidiforms because one can simply rotate the tree at the node.  Perhaps the authors mean that shuyuiids are nested outside all other eugaleaspidiforms?

Similarly, Taxa do NOT form a clade BY a synapomorphy.  Taxa DO form a clade WITH a synapomorphy.

Figure 1: Different rock types cannot be distinguished because patterns are minute and all similar from fine sandstone to quartz sandstone.  Please amend and differentiate better.
What are the differences between the sold and broken horizontal lines? Unconformity?
What are the vertical lines?  Gaps?
What do the colors represent?
Fish legend on the stratigraphic column seems to be aligned with a green layer.
Academic journals are not suitable in showing international boundaries that are in disputes (inset having a large blank showing the southern islands and Taiwan, with a line drawn around them, which are not necessary to the context of the paper).  PeerJ should not and cannot endorse any stance on international politics by publishing such map.  Show the entire region in the map, or only show the mainland China.


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 GENUS OF SINOGALEASPIDS (GALEASPIDA, STEM-GNATHOSTOMATA) FROM THE SILURIAN PERIOD IN JIANGXI, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is much improved - regarding grammar and language

The amended figures are a lot clearer and add value to the manuscript
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have taken the majority of the reviewers suggestions on board. I have 2 minor notes to make about the figures:

Figure 2 - Silurian not Siluric in stratigraphic column

Figure 7 - Perhaps state that the bremer values are above branches, whereas bootstrap values are below?


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 GENUS OF SINOGALEASPIDS (GALEASPIDA, STEM-GNATHOSTOMATA) FROM THE SILURIAN PERIOD IN JIANGXI, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I read the revised version of the manuscript "A new genus of sinogaleaspids (Galeaspida, stem-Gnathostomata) from the Silurian of Jiangxi, China" and reviewed the responses submitted by the authors.  I note that the authors put some efforts into incorporating our suggestions.  However, I found some of these modifications introduced new sources of confusion, and in the end, problems have multiplied.

Major concerns include:

The most serious error is in "differential diagnoses."  The authors did not understand the difference between synapomorphy and autapomorphy, and include in diagnosis traits like "synapomorphy with other eugaleaspiforms" or "plesiomorphy".  Symplesiomorphic character can be used in differential diagnosis, but it makes no sense to include "plesiomorphy" without specifying what this plesiomorphic trait excludes.  In any case, differential diagnosis must state which trait excludes what taxa.  Some of these confusions may be clarified if the authors list (in addition to or parallel with diagnosis) parsimoniously constrained syn-/autapomorphies.

Description is repetitive and redundant, because the authors repeat the same information for two species of Rumporostralis.  I have difficult time figuring out what is shared and what is not between the species.  This part of the paper is still quite confusing, but needs not be.  Please set the text in comparative framework, and do not just list morphological traits as they come to you.  You said something once, why say it again?

In Description, the authors provide maximum and minimum values of measurements.  This may be precise but not accurate: the authors describe the known range of size as a systematic trait, but this is just a sample from a much larger population.  Also, in this format, I have no idea if these measurements kept in proportions or not.  Why not present ratio values?  Do they vary linearly?

Rostral margin "split" or "pierced" by the medial dorsal opening.  These words are as poor choices as "cracked."  The opening reaches the rostral margin.  The margin is disrupted, or it remains unclosed.

Shuyuids as the "deepest" branching galeaspids -- this is still misleading.  Non-shuyuid eugaleaspiforms comprise a clade equally deep as shuyuids.  They are nested outside (or form a sister group to) all other eugaleaspiforms.  They form one of the earliest diverging, and deepest branching eugaleaspiform clades, but they are not "the" deepest branching or earliest diverging.

Figure 1 is still difficult to decode, even with the legend.  The lithographic symbols are too small to see, and the patterns blend in when multiple layers are stacked together.  Please use more intuitive design.

Figure 3D, 4A, B -- "Neural canal" is supposedly preserved in these specimens, but the canal (nc.p) is unclear in pictures and I am not sure if this is simply an embayment of the posterior margin of the headshield.
Experimental design: No comment.
Validity of the findings: I think the authors have made improvement on the phylogenetic analysis, and the current version is sufficient.
Additional comments: Description is poorly executed here and there.  Many grammatical comments were made on the pdf file, so please refer to those.  Some major comments include:

Description
Redundant and repetitive.  Re-organize information content for conciseness.

Throughout: "Oralopharyngeal"
Why not "oropharyngeal"?

Throughout: "naturally" "natural"
I have no idea what this means.

L 269 "...rapidly tapered off..."
Poor word choice.  Rapidly means time.  In this case, some alternatives should be considered, such as "acutely."

L308: "...pass through..."
Poor word choice.

L461: "...to cover a larger morphospace..."
This is not about morphospace occupation, and it is not ecomorphological context.  A certain cladistically defined lineage is found to embrace greater morphological variations than previously anticipated.  So morphospace itself is not expanded; rather, its systematic compositions were modified.

For more specific comments, see the pdf attached.


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 GENUS OF SINOGALEASPIDS (GALEASPIDA, STEM-GNATHOSTOMATA) FROM THE SILURIAN PERIOD IN JIANGXI, CHINA
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors carefully considered all the comments and questions raised, and addressed them adequately in the manuscript.  The text could benefit further from editor's help for a clearer language, but the paper already reads much better than the initial submitted version.  I have no further request.


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: PERSONALIZED ANALYSIS OF BREAST CANCER USING SAMPLE-SPECIFIC NETWORKS
Review round: 1
Reviewer: 1

Output:
Basic reporting: -	The authors build individual-level gene expression networks in order to find breast cancer-specific interactions and pathways related to tumor staging and subtypes. The manuscript addresses a relevant topic to the scientific community and the study is scientifically sound, but some improvements and clarifications need to be performed to the presentation of the study. In particular, the authors perform a standard bioinformatics analysis, where the novelty is not properly highlighted. I think that it would be very interesting to conduct a network analysis to find communities in the PPI network and investigate the behavior of modules/genes that are co-expressed, co-localized in the PPI network and that could share functionality, specifically related also to the topic under study, that is breast cancer and its heterogeneity. Indeed, there is a new and cutting-edge field of medical research, called network medicine, whose basic idea is that human diseases are rarely caused by single molecular determinant, but more likely influenced by a network of interacting molecular determinants with the propensity to cluster together in the human interactome.
-	The authors addressed a relevant and interesting topic that fits well a new and cutting-edge field of network medicine (see for example reference [1-3]). This aspect should be discussed and highlighted in the Introduction or in the Discussion (example at line 292).

References
1.	Albert-László Barabási et al. “Network medicine: a network-based approach to human disease” Nature Reviews Genetics volume 12, pages 56–68 (2011) https://doi.org/10.1038/nrg2918
2.	Conte et al. (2019) “A paradigm shift in medicine: a comprehensive review of network-based approaches”.  Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms. Article num: 194416 https://doi.org/10.1016/j.bbagrm.2019.194416
3.	Fiscon et al. (2018). “Network-based approaches to explore complex biological systems towards network medicine”. MDPI Genes, 9(9), 437.https://doi.org/10.3390/genes9090437
Experimental design: - In the framework of network medicine, many network-based methods have been developed to aid in understanding molecular-level underpinnings complex human diseases. In particular, for what concerns the building and analysis of gene co-expression networks (see reference [3]), the two widespread algorithms are SWIM (see reference [4]) and WGCNA (see reference [5]). SWIM is a software able to extract from complex correlation networks the so-called “switch genes” that could be associated to the transition from physiological to a pathological condition. Among its several applications, SWIM was applied to study a large panel of gene expression data of tumors from TCGA, including breast cancer. WGCNA is a software exploited for describing the correlation patterns among genes and that can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Both algorithms (see references [4-5]) I think should be mentioned in the Discussion, for example at line 311-312 when the authors claim: “Many studies have shown that network-based methods are more robust and effective than single-gene-based methods”
- From all the considerations explained above, I think that could be very interesting and thus strongly recommend for the authors to apply WGCNA software to study and deeply analyze their correlation networks. By using WGCNA the author will be able to find network modules and also identify which are those modules that are more correlated (and thus strongly associated) for example with the tumor staging, or also to other clinical traits of interest.
- For what concerns pathway the pathway enrichment analysis, did the authors make use of some tool/R package as enrichR? If yes, it should be specified.

References
4.	Paci, P. et al. (2017) "SWIM: a computational tool to unveiling crucial nodes in complex biological networks." Scientific reports 7: 44797. https://www.nature.com/articles/srep44797
5.	Langfelder, P., Horvath, S. (2008) WGCNA: an R package for weighted correlation network analysis.BMC Bioinformatics 9, 559. https://doi.org/10.1186/1471-2105-9-559
Validity of the findings: As mentioned in the “experimental design” section, the obtained results and their interpretation could be extended by exploiting the WGCNA analysis. For example, it could be also really interesting to check if the key genes identified by the authors for breast stages and for subtypes form unique modules in the human interactome.
Additional comments: -	Figures quality is too low and should be improved, in particular:
o	Figure 1: panel A bottom: “significanc” should be “significance; panel B bottom: plot of survival analysis is not visible.
o	Figure 2: network edges could be colored by p-value.
o	Figure S1: networks are barely readable, it is not informative in this form.
-	In general, the authors should check the English language and the form of the entire paper avoiding careless errors, missing commas, and confusing sentences that should be reworded in order to make them clearer. In the following, I have just reported some examples.
-	Check all the commas. Add a comma before “and” whenever more than two elements have been listed (E.g. line 51, line 250, etc…)
-	Line 34: missing space between 24% and among
-	Line 42, 83: missing references
-	Line 314-315: please reformulate the sentence, it is not clear and appears a truncated phrase.


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: PERSONALIZED ANALYSIS OF BREAST CANCER USING SAMPLE-SPECIFIC NETWORKS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Adopting a sample-specific networks, the authors further investigated the breast cancer specific networks in various aspects including cancer stage, subtype, pathway and survival. In general, the study was designed reasonable and the findings were valuable to the research field.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Here are still some spaces for improving the article:
1.	The text was not clear enough,
a.	First of all, the term individual-level network was not quite meaningful without clear explanation in this manuscript. The reference [7] was the paper brings up the network method. The title was “Personalized characterization of diseases using sample-specific networks” which is different from the citated reference. Please double check.
b.	Are the 186 KEGG pathways involved in this paper breast cancer related? It should be described clearly. Line 96.
c.	The description of the network construction was not clear. For example: “significant perturbations of co-expression”, line 110. What are the n reference samples? Are they the normal samples? Line 113.
d.	I suggest putting more details into section “Identification of stage/subtype-related gene-gene interaction networks”. The authors mentioned some important genes were selected and used for the analysis. However, the details for identifying stage/subtype-related specific networks are needed.
e.	Similarly, I suggest adding some more details in “Survival analysis by the Cox regression model” section. How the individual-level networks used for this analysis.
2.	The validation,
GSE3494 was mentioned to be used as validation data set. From line 171 to line 173, only one sentence here describing the validation process.
The question is, did you apply the Cox model or the network method on this data set, which means did you fit a specific Cox model over the GSE3494 data or used the Cox model based on 1093 samples.
From the text I assume you fitted a new model. In this case, I think this data set is not used for validation. It is just a second data set for the survival analysis because there is no comparison can be taken between them.
3.	The other parts of the manuscript should be revised correspondingly.


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: PERSONALIZED ANALYSIS OF BREAST CANCER USING SAMPLE-SPECIFIC NETWORKS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author carefully   addressed all my comments, thus I suggest to accept the manuscript
Experimental design: The author carefully   addressed all my comments, thus I suggest to accept the manuscript
Validity of the findings: The author carefully   addressed all my comments, thus I suggest to accept the manuscript
Additional comments: The author carefully   addressed all my comments, thus I suggest to accept the manuscript