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: GROWTH RATE AND LOCOMOTOR PERFORMANCE TRADEOFF IS NOT UNIVERSAL IN BIRDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is an interesting study. I have only some few minor comments. I have also provided some minor corrections on the ms itself.
I have provided an alternative title.

Intra and interspecific results are mixed sometimes without clearly differentiating between the two (e.g. L 69-71).
L90: In L78 it was flight muscle mass, not ratio. Please clarify which was the variable tested.
L97: Body mass seems to be taken from different sources. Please clarify (I suppose it is because it is for different sets of species).
L136-144: I have not found information on the amount of variance explained by the models. P-values are not enough.


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: GROWTH RATE AND LOCOMOTOR PERFORMANCE TRADEOFF IS NOT UNIVERSAL IN BIRDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have provided an updated manuscript, and I am pleased with the changes that have been made. The inclusion of effect sizes, p-values, and model summaries in the main body of the text has greatly improved readability and the ease of interpretation of the models. Furthermore, the use of more mass-independent metrics of wing morphology and muscle size have improved the statistics. Overall, I am pleased with the changes that the authors have provided.


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: PERMUTATION-BASED METHODS FOR MEDIATION ANALYSIS IN STUDIES WITH SMALL SAMPLE SIZES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: Some clarifications should be given why correlations of .15 and .60 were used instead of .10 and .50, which would be in line with Cohen's cutoffs for small and large effects.

Some more details should be provided about the permuation used in the current manuscript.
Validity of the findings: No comment.
Additional comments: For small sample sizes, Bayesian Analysis may be a better altertnative than bootstrapping. This could be mentioned in the discussion.

Table 2 and 3 lack the information given in the first row of table 1.

The mansucript could beneifit from a an illustrative example.

It was not clear to me what is meant by a_1 = a and gamma_3 = b and a_1 = b and gamma_3 = a in line 219 and 220.

Thank you for the opportunity to review this mansucript.


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: PERMUTATION-BASED METHODS FOR MEDIATION ANALYSIS IN STUDIES WITH SMALL SAMPLE SIZES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is clearly written and uses common terminology in the field of mediation analysis. The manuscript consults relevant literature for the research question. The structure of the paper is clear, and the paper is self-contained.
I have a few suggestions for improvement:

- MacKinnon & Taylor (2012) make a distinction between approximate and exact permutation tests. Given the sample sizes in the current manuscript, I assume the permutation tests are approximate, but it would be nice to mention if this is the case explicitly. Furthermore, Line 282 incorrectly states that Taylor and MacKinnon (2012) did not report Type I error rates.

-It is unclear why the PSRM uses absolute values for Step 7 instead of raw values. Can the authors explain this choice?
Experimental design: The research question is defined clearly, and there is no doubt that this paper fills a gap in the literature. The choice of the set of models and conditions to examine in the simulation study is appropriate. Parameter combinations are described in sufficient detail for other researchers to replicate the simulation study, however, it would be nice to include code for executing the analyses using each method tested in the simulation study.
Validity of the findings: The conclusions are well stated, linked to original research question and limited to supporting results.
The findings in Lines 291-293 confirm findings from previous literature about the bias-corrected bootstrap having excessive Type I error rates (MacKinnon, Lockwood, & Williams, 2004; Fritz, Taylor, & MacKinnon, 2012), and the citations of papers that found the same should be included.

Recommended reference to add:

Fritz, M. S., Taylor, A. B., & MacKinnon, D. P. (2012). Explanation of two anomalous results in statistical mediation analysis. Multivariate behavioral research, 47(1), 61-87.
Additional comments: More details about how to interpret Figure 4 (e.g., picking one bubble and describing what it’s size and location mean) would be helpful .


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: PERMUTATION-BASED METHODS FOR MEDIATION ANALYSIS IN STUDIES WITH SMALL SAMPLE SIZES
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is all fine.
Experimental design: I wonder what the usefulness of presenting the IERM is (See general comments).
Validity of the findings: Please supply computer code used to verify validity and reproducibility.
Additional comments: General Points

1.	What’s the difference between IERM and PSRM other than the additional tests on alpha and gamma at the end in step 7? If that’s the only difference then
a.	just say so and omit the re-explanation of the steps.
b.	If the additional tests for alpha and gamma are needed to guarantee the mediation effect is zero, as stated in line 140, then is IERM even useful? Why would you ever use this test?

2.	Lines 327-334: If you knew that IERM was unsuitable a priori then why propose it as a method in the first place? Your arguments in this paragraph seem be sufficient to rule it out as a useful tool for the purposes of testing your target hypothesis so why bother with the permutation tests? Why not just give readers the logical explanation and done?

3.	Line 272: With power so low, are these tests any use at all?! Would you recommend the, as useful in practice?

4.	Is 100 a “small” sample size in psychology experiments? What is a typical sample size in the kinds of studies this work is aimed at?

5.	Why does the bootstrap lead to biased results? What is it about the permutation tests that makes them free from this particular shortcoming?

6.	Could you supply computer code for your simulations? Given that the results are specific to the inputs it would be useful if readers wish to apply your tests to their own studies with different characteristics.

Specific Points

7.	Line 100 (or vicinity): State the hypotheses explicitly , I.e., H0 = … and H1 = … . This will make it obvious what you mean by ‘null’ and ‘full’ model.
8.	Add C to Fig 1.
9.	Vanderweele and Vansteelandt, 2009 not in references.
10.	Line 124: Yhat and Mhat are from the full or reduced model?
11.	Line 129: What is gamma3 orig? This symbol was not introduced.
12.	Line 202: “significant” should be “significance”.


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: PERMUTATION-BASED METHODS FOR MEDIATION ANALYSIS IN STUDIES WITH SMALL SAMPLE SIZES
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I was a reviewer of a previous version of the manuscript and found the authors were responsive in addressing the concerns raised in the previous round by the editor and the reviewers. The current version is an improvement over the previous one. This work will make an important contribution to the literature on mediation analysis. Thus, I strongly suggest to accept this manuscript for publication in its current form.


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

Input:
Title: PERMUTATION-BASED METHODS FOR MEDIATION ANALYSIS IN STUDIES WITH SMALL SAMPLE SIZES
Review round: 2
Reviewer: 2

Output:
Basic reporting: - Please reference the github repository with your code in the manuscript so future readers have access.
Experimental design: Fine
Validity of the findings: Fine
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: SOCIAL RANK OVERRIDES ENVIRONMENTAL AND COMMUNITY FLUCTUATIONS IN DETERMINING MEAT ACCESS BY FEMALE CHIMPANZEES IN THE TAÏ NATIONAL PARK, CÔTE D’IVOIRE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall: strong. I have made some suggestions for providing a more detailed context for the study by referencing some key papers on the topic (see General comments).

Re the raw data: It might help to provide a ‘legend’ for all the variables within each file (or as a separate text document to accompany all files), briefly explaining what they are and how they were coded.
Experimental design: Rigorous and appropriate. Very interesting study! (see some specific comments further below)
Validity of the findings: Given the large dataset originating from two separate chimpanzee communities, this is a robust analysis which has important implications for our understanding of female chimpanzee feeding ecology and how that interacts with social dynamics in the context of meat sharing. The discussion is clear and avoids the pitfall of over-speculation very well.
Additional comments: General comments

Line-by-line:
L32/3: check for sentence structure/grammar and paraphrase for clarity (‘the effect on meat access found different results’).

L47: ‘chimpanzee understanding’ is a bit ambiguous; the understanding of chimpanzee behavioural ecology (or whatever) would be clearer. Having said that as a final sentence of an abstract this is not very informative; may be instead of saying ‘we discuss findings and offer implications’ you could just state what is the main implication you have identified.

L63-65: When giving average amount consumed per year might be helpful to specify these data come specifically from Tai in the text. Otherwise it sounds like this applies to chimpanzees everywhere. It would also be good to acknowledge there is considerable variation in frequency of hunting and amount of meat intake across study sites.

L70. Please replace ‘gender’ with ‘sex’ (here and throughout the MS). With animals we cannot easily discern their gender, we can only observe their biological sex. This is an important distinction.

L79, 88 etc.: Here and throughout the MS and in the list of references please correct ‘Thompson’ to ‘Emery Thompson’ (no hyphen) for the last name of the relevant author.

L69-72: Here or elsewhere in the MS where relevant (perhaps in the Discussion) it would be useful to provide a more detailed review and comparison with data on sex differences in hunting/consumption to encompass observations from other study sites. E.g., new data on higher than usual hunting by females are available for Fongoli: Pruetz et al. 2015 Roy Soc Open Science.

L99: I find the use of the term ‘cheating’ potentially misleading and unnecessarily ambiguous (and also perhaps inaccurately anthropomorphic). I see no need to define individuals getting access to meat that they did not participate in capturing as ‘cheating’. The use of this word can be read as implying that they somehow ‘trick’ others. That’s hardly the case. This is very much a stylistic preference/issue but I do think the text will be clearer and more precise without this ‘term’.

L106-109: This statement, while technically correct for the case of Tai chimpanzees, skirts around the larger issue of the assumptions and validity of the ‘meat-for-sex’ hypothesis. It should be made more explicitly clear that this only applies to long-term patterns observed at Tai (as opposed to direct short-term tests of this hypothesis at Tai or all the tests at other study sites that have failed to support the hypothesis: Gombe & Kanyawara). Along these lines, the absence of a reference to the paper, which examines this idea at great detail, is puzzling: I think you need to address this gap here or in the Discussion by directly contrasting your findings to those from Gombe & Kanyawara (Gilby et al. 2010 J Hum Evol).

L126: The hypothesis that higher-ranking females are more likely to be present during a meat eating event (H1) is interesting but I think needs a stronger/clearer rationale. What is the mechanism you envisage here? Given the fission-fusion system of chimpanzees, the implication of your hypothesis is that simply higher-ranking females are more gregarious than low-ranking females, is it not? I think this is worth elaborating on so that the context of this hypothesis is clearer to readers. Are there comparable evidence to review from other study sites to suggest rank-differences in gregariousness/space use that you can use to frame this H1 in context? You discuss gregariousness in the Discussion but I think it would be useful to introduce the concept of fission-fusion and sex differences in gregariousness in the introduction when formulating your H1 (you don’t mention the ‘fission-fusion’ social system of chimpanzees at all in your entire paper – I think this is relevant background information).

L182: ‘We constructed two models’ is sufficient (no need for ‘and analysed’).

L192: Clarify what you mean when you say the hierarchies ‘reached significance’ (i.e. they were significantly linear?).

L214: ‘on the day’ (not ‘at the day’)

L276: Why could the rank effects differ between North and South – provide a rationale for including this interaction term, please.

L280: A more appropriate test for this would be to examine the variance inflation factors for the model (VIF). Which you have done later in the text (L324-232) – so why mention Pearson here?

L328/9: Could you clarify how you checked that specifically (e.g., which package/function?).

L375: Principal, not ‘principle’.


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: SOCIAL RANK OVERRIDES ENVIRONMENTAL AND COMMUNITY FLUCTUATIONS IN DETERMINING MEAT ACCESS BY FEMALE CHIMPANZEES IN THE TAÏ NATIONAL PARK, CÔTE D’IVOIRE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper tests the hypothesis that dominance rank in female chimpanzees increases their access to meat, which is interesting because male chimpanzees primarily hunt and possess meat, so females would have to get meat through sharing and/or tolerated theft. The authors find support that high-ranking females are more likely to be present when meat-eating occurs and are more likely to obtain a share.
This is an interesting article but has two major issues that should be addressed. First, while these analyses include lots of control variables, they are not carefully thought out with respect to their ability to test the hypotheses. The authors find that dominance rank influences female presence at meat-eating events, but they do not test whether high-ranking females are also simply more likely to be observed (e.g., if they are more gregarious) even when meat eating is not occurring. It was also not clearly stated specifically why they were testing this hypothesis. With respect to meat access, they authors find that dominance rank influences getting meat. This is certainly interesting, but the authors fail to provide any context for why this occurs. This should start with a clearer definition of what the outcome variable actually is because it is variably described as “got meat or not”, “did or did not receive meat”, “eating [or accessing] meat”. Did this refer simply to eating meat at all (i.e., could be by the female’s own capture) or does it mean receiving it from someone else? Prior studies of meat sharing in chimpanzees suggest that begging intensity is an important determinant of who gets meat. Since the authors collected data on begging, they should determine whether the rank effect could be driven by begging. Similarly, if sharing was the main thing that was accounting for female meat-eating, then it would be useful to determine whether kinship could explain some of this (i.e., high ranking females receiving meat from their sons). Throughout the discussion, the authors never do discuss explanations for HOW high-ranking females get more meat. There is a brief reference to contest competition, but is there evidence that these females are getting their meat by taking it from other females?
The second issue is that while the authors do cite studies of other chimpanzee populations for general things, they pointedly ignored highly-relevant literature on hunting and meat-sharing from other sites. In particular, the extensive work by Ian Gilby has not been cited at all, and there is only one passing reference to the work by Mitani & Watts. These scholars have made some important critiques and have made different conclusions, so ignoring their work yields a highly biased review.
Experimental design: see above
Validity of the findings: see above
Additional comments: Lines 61-65: I don’t immediately have access to the textbook cited here, but these numbers seem very high. “Up to 9% of their activity budget” is vague – does this refer to hunting? Or meat eating? Over what time frame? Surely they are not eating meat for >1 hr per day. This is probably meant to say that in some months, the chimpanzees spend up to 9% of their feeding time feeding on meat. The statement about caloric amounts also doesn’t make sense as written, so it must be per episode and/or perhaps across all individuals of each sex. By the data reported here, there are about 20 meat-eating episodes per year, so to get to 186g/day, males would have to eat 3.4 kg per episode!
Line 65-68. Grammatically incorrect. Please revise.
Line 70. Please use sex and not gender. Gender refers specifically to identity.
Lines 103-105. As written, this sentence contradicts itself with respect to whether females or males receive more
Lines 113-115. This sentence appears out of place as written
Lines 191-192. Please clarify which measure did not reach significance (e.g., I assume you mean linearity).
It seems ok to address the uncertainty of dominance ranks by assigning categorical ranks. However, the method for assigning high/middle/low is vague, and if the data were not sufficient to assign a linear hierarchy, it is not clear how well these will represent the data. Given the assumption that ranks are stable from year to year, I recommend to combine 2-3 years in order to generate more reliability in assessments. In the present method, it is unclear how many females fell into each category and if this varied a lot from year to year.
Line 218: This sentence appears to give a prediction rather than a declarative statement so should be reworded to make this clear.
Line 235: did this include pregnant females with swellings?
Line 250: in the interests of avoiding an overparameterized model, I suggest deleting the community size variable. The rationale given in the first sentence is really only about how many individuals can participate in hunting, thus the number of males present should already take care of this. With that variable and community ID, it is not clear what the significance of community size would be. [I see now that this was excluded from the first model…I suggest simply eliminating it entirely]
Line 264: clarify “accessibility”, as this sentence appears to contradict another sentence in this paragraph: do they hunt more with lower or higher FAI?
Line 271: correct “colleges” to “colleagues”.
Line 351: shouldn’t this be number of males present (not in the community)?
Lines 409-412: but there is no evidence that these females receive meat because of contest competition is there?
Lines 426-428: this sentence needs more explanation
Lines 426-430: but you’ve shown in this paper that the hierarchy is often not linear.


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: SOCIAL RANK OVERRIDES ENVIRONMENTAL AND COMMUNITY FLUCTUATIONS IN DETERMINING MEAT ACCESS BY FEMALE CHIMPANZEES IN THE TAÏ NATIONAL PARK, CÔTE D’IVOIRE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Both the introduction and the discussion have been revised to provide detailed context and interpretation. A very strong revision!
Experimental design: Good as before!
Validity of the findings: Yes. As before - this is a strong study and an important contribution.
Additional comments: Thank you for this thorough revision. I think you've addressed all the comments well and the paper is now a much more comprehensive piece of writing, making the most of this amazing dataset.


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: HIGH VARIABILITY WITHIN PET FOODS PREVENTS THE IDENTIFICATION OF NATIVE SPECIES IN PET CATS’ DIETS USING ISOTOPIC EVALUATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is well written and has appropriate contextualization either for the scientific inquiries as for the methods. However there are some corrections to be made.

The delta (δ) symbol should be italicized throughout. See Bond and Hobson (2012) for guidance on recommended isotope ratio terminology.
* Bond AL, Hobson KA (2012). Reporting stable-isotope ratios in ecology: Recommended terminology, guidelines and best practices. Waterbirds 35:324–331. doi: 10.1675/063.035.0213

Pay attention to superscripts and subscripts.

Improve plots, they are not publishable. Letters and symbols could be larger; use black for letters and lines to make it clearer; correct delta symbols and put mass numbers in superscript; and so on.

Line 145: “0.1‰ δ13C and 0.2‰ δ15N” should be “0.1‰ for δ13C and 0.2‰ for δ15N”, with delta symbols in italic and the mass numbers in superscript.

Line 153: “+1.9‰ δ15N and +2.6‰ δ13C” should be “+1.9‰ for δ15N and +2.6‰ for δ13C”, with delta symbols in italic and the mass numbers in superscript.

Line 154: “δ15N” should be with delta symbols in italic and the mass numbers in superscript.

Line 155: “+3.2‰ δ15N and +2.6‰ δ13C” should be “+3.2‰ for δ15N and +2.6‰ for δ13C”, should be with delta symbols in italic and the mass numbers in superscript.

Lines 166 – 168: Revise the subscripts of C3 and C4, and the superscript and italics of δ13C, throughout the text.

Lines 197 - 198: I think the δ13C and δ15N results would be better presented as follows:
Instead of “Values for all potential 198 native prey from the southeastern US ranged from -17.7‰ to -25.3‰ δ13C and 2.0‰ to 9.5‰ δ15N”
I suggest “Values of δ13C and δ15N for all potential 198 native prey from the southeastern US ranged from -17.7‰ to -25.3‰ and 2.0‰ to 9.5‰, respectively.”
This can be done for all δ13C and δ15N results throughout the text.

Line 198: Add standard deviation in the native prey isotopic values averages.

Line 208: “carbon” should be in lowercase.

Lines 295 - 298: It is unclear what you meant here, maybe you could re-write it.

Lines 318 – 319: Unclear.
Experimental design: I have a few questions regarding the MixSIAR model.

Have you considered using the median proportion values from the MixSIAR output for the cats classification and evaluation of their diets, instead of the posterior density plots? (see Galera et al. 2019). Maybe the posterior density plots could be included in the supplemental material to make more room for the isospace plots and MixSIAR output values. Normally the posterior density plots are used as a visual diagnostic of the model, but not the main result of it.

What were the Geweke and Gelman-Rubin diagnostic tests results? (see Galera et al. 2019).

How did you set the Markov Chain Monte Carlo (MCMC) in your models?

Have you classified cats prior to the MixSIAR modelling and then prepared four sets of sources, mixtures and discrimination sheets to run? If yes, what criteria did you use? Or you ran all the data at once and then proceeded with the classification. Explain it better please.

You could add a third tracer to your model, like C:N ratio, to allow a better distinction between cat food and native prey.

Lines 149 – 152: About the discrimination factor, have you considered using an average of all Pet Food cats? Another option would be using a discrimination factor from native felids from the literature.

Lines 247 – 249: The native prey data varied the same as the cat food. More tracers (like C:N ratio) and larger MCMC might be considered to improve the MixSIAR model in this case.
Validity of the findings: The scientific question and the methods chosen are very pertinent. The authors present robust data, but skipped information regarding the handling of it. There are missing important information about the MixSIAR model that would elucidate some of the limitations faced in the analysis.
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: HIGH VARIABILITY WITHIN PET FOODS PREVENTS THE IDENTIFICATION OF NATIVE SPECIES IN PET CATS’ DIETS USING ISOTOPIC EVALUATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript discussed an important topic, the diet content of domestic animals, and should be of interest to readers of the journal as to society in general. Strengths for the study are the knowledge gap identified by the fact that the isotopic composition of cat hairs was not enough to determine the cat diet.
Concerns are that the results related to the research question (the ecological impact of domestic cats preying on wildlife) were not well discussed. And as the authors state, it is already know that it is very difficult to access the wild prey consumption by cats (line 360; 364-366).

The second part of the Title gives a big attention on the fact that the pet foods are sold as a different product of what they are in truth. However, this aspect of result and the consequences of that to cat health was not discussed throughout the text. I suggest including this aspect on the text or changing the title.

In general, the Introduction is appropriately referenced. The structure of the article is conformed to the acceptable format of the Journal.

The axes of the template of Figure 3 (A1, B1, C1, D1) has not a good resolution on page 42.

In some parts of text the English was not clear. I suggest an English revision. I have made a number of suggestions bellow where improvements could be made.
Overall suggestions:
Line 68 – change impact “from” to impact “of”
Line 71 – insert “that” after suggest
Line 93 – change “studying” to “study”
Line 98 – change “out of” to “the”
Line 135 – change “allowing” to “dry”, and remove “to dry”
Line 140/141 – insert a space after the numbers
Line 145, 153, 154 (and elsewhere) – Subscribe the numbers “13” of δ13C and “15” of δ15N
Line 166, 167 – change “C3” to “C3”and “C4” to “C4”
Line 179 – delete “of the area”
Line 296 – change “potentially” to “potential”
Line 326: delete “an”
Experimental design: The statistical analysis on Materials and Methods section are poorly described. There is not sufficient detail about the determination of isotopic composition. The authors should include the equation used to calculate the isotopic ratios of the cat hairs as the cat food.
The author should use a reference to support the statement of lines 93-95. The paper of Ehleringer et al., 2015, for example, talks about how the use of stable isotope technique can identify differences between source and product. (Ehleringer JR, Chesson LA, Valenzuela LO, Tipple BJ, Martinelli LA. 2015. Stable isotopes trace the truth: from adulterated foods to crime scenes. Elements 11(4):259–264).

The study mentioned that the samples were send to different research centers (Center for Stable Isotope Biogeochemistry and Elemtex Stable Isotope Analysis). The analysis performed in each center used the same process to determine the isotopic composition? That information should be mentioned on the text.

The authors have conducted the research with ethical standards in the field.
Validity of the findings: The conclusions were appropriately stated, however, it was poorly linked to the original research question. It should explore the ecological aspects of those results since the author’s main concern regarding cat diets are the impact on wildlife.
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: HIGH VARIABILITY WITHIN PET FOODS PREVENTS THE IDENTIFICATION OF NATIVE SPECIES IN PET CATS’ DIETS USING ISOTOPIC EVALUATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The paper is well reported and the figures have been improved. I still have a few comments that can be found in the reviewing PDF.
Experimental design: Material and methods have been improved and made clearer.
Validity of the findings: The idea of the paper is very interesting. Results are compelling and may serve as basis for further studies on the impacts of pet cats on wildlife.
Additional comments: I think the manuscript is almost ready to be published. Take into consideration the comments I've made in the reviewing PDF.


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

Input:
Title: HIGH VARIABILITY WITHIN PET FOODS PREVENTS THE IDENTIFICATION OF NATIVE SPECIES IN PET CATS’ DIETS USING ISOTOPIC EVALUATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: The first sentence of the Introduction section should be appropriately referenced. For example, by the work of Medina (2011) used bellow.
You have made a better connection of the results with the research question, however I suggest that you improve the evidence of domestic cats affecting wildlife at lines 61-69 to provide more justification for your study. For example, what are the consequences of native species extirpation and threaten?

English written:
Lines 64-66: Note that the word “severe” is used three times in a row.
Synonyms for this word could be “alarming”, “critical”, “strong”, “intense”.
The use of the word “island” on lines 66 and 67 seams to be redundant.
Experimental design: Line 216: Please, specify the 112 food samples from UK. Are them dry cat food or wet cat food?
Validity of the findings: Lines 288-290: I suggest reformulating the sentence since the difficulty to determine the impact of domestic cat over native species is not just consequence of the isotope analysis it can be also related to the behavior of the domestic cats that in some cases do not ingest the species they might be hunting - and not eating.

Lines 291-292: Explore the fact that the access to the pet food labels would help to understand the high variability of isotopic carbon composition between different cat foods and the results interpretation, however there is a lack of information about the main sources of protein, carbohydrates, and others on pet food labels (Aro Galera, 2019). Besides the information of ingredients listed on labels can be incomplete.

The information stated on lines 324-326 can be controversial. The main object of your study is the diet of domestic cats and not the influence of human foods on wild animals.
Although in your study you found that the isotopic technic was not enough to answer the main work question (discern the proportion of pet food and native prey source), the composition of carbon isotopes to provide information about the base of a food webs in diets of many animals can be appropriate for others situations (Post, 2002. Ecology v 83, Issue 3 - https://doi.org/10.1890/0012-9658(2002)083[0703:USITET]2.0.CO;2
). Please make that clear in your text.
Additional comments: You have changed the original Tittle but I would suggest a shorter tittle. The words “cat” and “diet” are repeated twice each. You could remove the first line “Isotopic evaluation of cat diet” and leave just “High variability within pet foods prevents the identification of native species in pet cats’ diets using isotopic evaluations”

Note that one of the basic conditions of using stable isotopes on diet studies is that the possible source of food to the animal in study have different isotope value, so that you have a clear answer for the research. Remember to make that clear to the readers.


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

Input:
Title: PREDICTING HEDGEHOG MORTALITY RISKS ON BRITISH ROADS USING HABITAT SUITABILITY MODELLING
Review round: 1
Reviewer: 1

Output:
Basic reporting: -	The language is clear, professional and easy to understand.
-	The authors give a very good introduction to road ecology and describe the problems associated with roadkills in a very succinct way. However, I would recommend that citizen science be described either in the introduction or later in the material and methods section. The advantages and disadvantages of this method and its influence on the data. Additionally, literature references are okay in general, although more sources on citizen science and how it is used to study roadkills could be added.
-	The article is structured as usual. However, I noticed that the authors don't mention all supplementary materials in the text. Thus, references to Supplementary 3, 4, 6 and 7 are missing in the text. Please add this accordingly or reduce the Supplementary materials. Besides, Supplementary 7 is missing completely.
-	Figure 1: For me personally this graphic is too overloaded. The variables could be removed and placed in a separate table. Additionally, I would describe the properties of the variables in such a table, because they are missing in the text. For example, I am not familiar with the difference between improved and rough grassland or the characteristics of a "B road". I would like to ask you to add this as it will make the results of the study easier to understand. Especially as a person outside the UK, the road classes are not self-explanatory.
-	Figure 2: From my point of view, a classic bar chart would be more appropriate here. For example, average number of hedgehogs per month. But this is optional and probably a subjective assessment.
-	The study seems to be self-contained.
Experimental design: -	The research presented is within the scope and aims of PeerJ.
-	From my point of view, the scientific question is very well chosen and can be answered with the methods presented. The research gap has also been highlighted very well in the introduction.
-	In principle, the methods are described appropriately and at a high technical level. Nevertheless, I miss some important details to make the study reproducible.
o	The data were collected in various citizen science projects. Please describe briefly what the data collection looks like in the individual projects and how they may differ from each other. If the data collection differs, how were these differences addressed in the analysis?
o	How many years of data collection were done, you mention from 2000 onward? Again, this probably differs from project to project, please describe this in the text.
o	How do the different projects geographically cover the nation? Are there strong differences? If so, does this have a strong influence on the data?
o	In general, the sources of the data should be described in detail. For example, where does the data for variables such as landcover, street properties, etc. come from?
o	Line 91: Just a little note, what is NBN gateway?
Validity of the findings: -	Raw data: Only the x- and y-coordinates can be found in the Excel table. In order to be able to understand the study, many things would have to be added here. For example, I lack the number of individuals per point, the source of the point, since data from several projects with different survey methods have been used. In addition, please add the data on the variables used, such as the landcover.
-	Since your study is based on citizen science data, please elaborate also on the citizens behavior and how this could have influenced your results. You start to address this issue in line 257 and 321, but I would suggest to elaborate on that. For example, it could be that it is easier for citizens to find road-killed hedgehogs in suburban areas than on highways and that’s why there is at the end a high probability of road-killed hedgehogs in suburban areas in your results and not because many hedgehogs were killed in this area.
Additional comments: o	I do not understand the sentence in line 248-250. Could you please rephrase the sentence?
o	Line 294: There is a typo in “measured”.
o	Line 335: I think here is a word missing


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

Input:
Title: PREDICTING HEDGEHOG MORTALITY RISKS ON BRITISH ROADS USING HABITAT SUITABILITY MODELLING
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript entitled “Predicting hedgehog mortality risks on British roads using habitat suitability modeling” provided a good overview about the factors related to hedgehog road mortality in Britain and showed some recent approach with habitat suitability models. The importance of this study is that it used a species as a model that suffers a population decline. And, it used a citizen science database, that provided a large amount of information and sometimes is neglected.
Experimental design: One important issue is that authors need to standardize the concepts: road collision, roadkills, road casualties. It is better to use the same concept for the same meaning.
I commented below point-to-point. However, there are some general issues. The introduction is well written and pointed out the main information. The authors just need to improve the goals in the last paragraph and to clarify the main hypotheses (for example, I understand that road types represent different traffic volumes, but it is not clear in the manuscript. In some places, minor roads can have more traffic than major ones. It is important to clarify why you are using this road type classification instead of traffic volume, for example).
Methods need some improvement related especially to the description of the database and clarify the way to calculate some metrics (I mentioned below one by one).
Validity of the findings: The findings are very relevant to the understanding of the relationship between roads and hedgehogs.  The conclusions are well stated.
Additional comments: 2.    Between lines 39 and 48, some references can be replaced by some more current ones. Authors can cite some chapters from the Handbook of Road Ecology (van der ree et al. 2015) instead of van der Ree et al. 2011, for example.
3.    Lines 45- 49: The sentence is related to the impact of wildlife-vehicle collisions. Then it is important to clarify mitigation measures for what! I recommend including mitigation measures ”for reducing animal-vehicle collisions”...
4.    Line 53: Replace “gloal” by global
5.    Lines 54-56: I agree that, in general, researchers and stakeholders are more worried about mitigating large mammal collisions, but authors should make a review about small mammals researches and rewrite the beginning of the sentence. Some studies can be cited here about a formal investigation related to small animals. One example is a book of Roads and Ecological Infrastructure: Concepts and Applications for Small Animals (by Kimberly M. Andrews, Priya Nanjappa, and Seth P. D. Riley. 2015). Furthermore, I made a quick search on google scholar and there are a lot of studies considering roads and small mammals.

6.    Lines 66-68: There is a lack of reference in this sentence. I suggest to include some example of the use of these models for the general use (first sentence) and the roadkill prediction (last sentence). Some examples for the roadkill context are: Fabrizio et al. 2018 (https://doi.org/10.1007/s10344-018-1241-7) and Santos et al. 2013 (https://doi.org/10.1371/journal.pone.0079967)

7.    Lines 84-86: The last paragraph of the introduction could be used to introduce the reader for what the authors did. The goals must be clear and I suggest to improve the paragraph, including some extra information about the study.

8.    Line 88: Hedgehog roadkill data: improving the data description. How many records were considered? When were the records collected (which years, for example)? There is “from 2000 onwards”, however, this is not good to understand the duration of data collection.

9.    Line 88: Is there any possibility of double counting in the dataset as data came from different projects?

10.    Line 95: It is important to understand the question at comment 8 to understand the temporal analysis. Please, clarify this section.

11.    Line 121: Sorry, but I do not understand what “B roads” are.

12.    Line 130: As the reference is In Review, it is important to explain a little bit more about the method or change the sequence of sentences. Suggestion: firstly, explain how the model works and secondly explain that the approach is developed by Bellamy (In Review).

13.    Line 152: How were “collision risk ratio” calculated? Clarify the way that you calculated it and why you did that. Firstly, I understood that it was calculated for all roads, but in the results, it is not clear because different types of roads have different collision risk ratio.

14.    Line 168: Please, clarify how this “inter-annual persistence of roadkill” was calculated. Is it just the record presence?

15.    Line 181: In Figure 2: Is the y-axis the number of road casualties recorded? Clarify it in the figure.

16.    Lines 182-183: What does explain this result: The national, minor roads and all roads models performed well with AUC scores higher than 0.70, while the major roads and B road models performed less well (AUC ≤ 0.6)? It is nothing about what differ these roads.

17.    Figure 3 is not cited anywhere, except Figure 3C. If the other parts are not cited, I presume that there are not important for the results. In this figure, there is another question:

First: graphs (Figure3C and Figure3D) do not have a good resolution. Improve them if you will maintain them.
Second: authors are assessing Habitat suitability indices. Then, why are they calling the probability of occurrence in Figure 3 graphs? They did not model occurrence probability and they did not mention it anytime in the manuscript.

18.    Lines 213 and 215: It is a correlation level: why did authors indicate R2?
19.    Lines 236-238: Authors could include in this part that this information is also important to plan temporal mitigation measures since this animal has a very defined risk season.
20.    Line 292: authors can mention that there are studies that tested the effectiveness of mitigation and there are some successful examples.
21.    Line 294: Replace “meansured” by measured
22.    Line 295: Authors are writing that their models did not correctly predict hedgehog collision risk, as they wrote: “if the model has correctly predicted areas of hedgehog roadkill”. However, they showed the AUC values and the models were good predictors. I suggest rewriting this sentence.
23.    Line 307: It depends on the kind of speed data. Some references show speed limit is not a good predictor for road collisions because it does not express the real speed.
24.    Line 340: Greater monitoring of road casualties does not mean that mitigation measures will be effective. I recommend rewrite the last sentence.
25.    Resolution of figure 5 is not good.
Supplementary information
26.    As I pointed out at the beginning of the comments, the information on supplementary 3 is what I would like to read on the Hedgehog roadkill data section.
27.    Supplementary 5 has the same problem of “probability of occurrence” concept mentioned in comment 17.
28.    Supplementary 20: include the scale.


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

Input:
Title: PREDICTING HEDGEHOG MORTALITY RISKS ON BRITISH ROADS USING HABITAT SUITABILITY MODELLING
Review round: 2
Reviewer: 1

Output:
Basic reporting: First of all, I would like to thank the authors very much for responding to all the comments and for writing a very detailed reply letter. In my view, only two of my previous stated comments were not addressed in the revision:

o The data were collected in various citizen science projects. Please describe briefly what the data collection looks like in the individual projects and how they may differ from each other. If the data collection differs, how were these differences addressed in the analysis?

o How do the different projects geographically cover the nation? Are there strong differences? If so, does this have a strong influence on the data?
Experimental design: no comment
Validity of the findings: no comment
Additional comments: -	Line 82-85: Please rephrase the sentence. In the current structure, the listing is difficult to understand.
-	Line 90: Please change “Heigle” to “Heigl” in both references.
-	Line 99: In my view, “ecological resource” is not the appropriate term. I suggest to use “data resource”.
-	Line 125: Cannot find the mentioned information about the data sources used in the supplementary. Please add the information as mentioned in the rebuttal letter.
-	Line 336-338: How is this information linked to roadkilled hedgehogs?
-	Line 351: Please change “supplementary 19” to “supplementary 18”.


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: CLINICAL CHARACTERISTICS AND PROGNOSTIC VALUE OF MEX3A MRNA IN LIVER CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript needs significant improvement on the language throughout.
Experimental design: Methods are not sufficiently described, for instance do not refer the normal samples that are used (number, etc).
RFS cannot be performed for stage IV patients, so these cases must be excluded from this analysis.
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: CLINICAL CHARACTERISTICS AND PROGNOSTIC VALUE OF MEX3A MRNA IN LIVER CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: Yang et al. analyzed the RNA expression of MEX3A in TCGA data base and conclude that MEX3A expression is correlated to the disease development of live cancer and could be used as a prognosis markers. This is an interesting study and could be further improved.

1, The English need to be further edited by native speaker. For example, line 64, “The low overall 1-year survival for liver cancer confuse us all the time.” Line 83, “it’s an essential future challenge that is evaluating its potential as a biomarker for progression or prognosis of the disease and exploring its contribution to  carcinogenics”
Experimental design: 3, Different statistics methods are mixed in Figure 1. Why and how are they selected?
Validity of the findings: 4, Fig.1, all fonts are too small. Please also clearly labelled all the single panels using A, B, C,… and provide clear description of each small panels in the figure legends.  For comparison between multiple groups, it’s important to clearly label which two groups are compared.

5, Fig. 2, 3 and 4,  please clearly labelled all the single panels using A, B, C,… and Figure legends as requested as above.
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: CLINICAL CHARACTERISTICS AND PROGNOSTIC VALUE OF MEX3A MRNA IN LIVER CANCER
Review round: 1
Reviewer: 3

Output:
Basic reporting: See the general comments
Experimental design: See the general comments
Validity of the findings: See the general comments
Additional comments: In this manuscript, Yang and co-workers reported the relationship between MEX3A mRNA expression level and clinical characteristics in liver cancer patients. The statistical results indicate that the MEX2A expression level can be used as an independent factor to predict the prognosis of liver cancer. This manuscript is somehow poorly written. There are numerous grammatical and stylistic errors as well. Some of the language mistakes cause the interpretation of experimental results confusing and ambiguous. I strongly recommend the authors to fix the errors and carefully proof-read before its resubmission to the journal. Overall, this is an important study and the findings are interesting. However, the lack of details of data collection and the ambiguous interpretations of the statistical results make it less convincible. Besides the language, the questions/suggestions for this research are listed below.

1.	The definition of MEX3A expression level is not clear. The authors mentioned that the MEX3A RNA-Seq expression data were obtained from the TCGA without any further description that how the expression level was measured. For example, the y-axes of boxplots in Figure1 are labeled as mRNA expression of MEX3A, but the values are meaningless without explanation. Please specify what method was used to measure the MEX3A expression level and describe the expression level data in the method section with more details.

2.	The MEX3A expression level is classified into two groups as high and low. The authors claimed that "measurement of reasonable median value that served as a cutoff to divide the samples into high and low MEX3A expression groups". However, the cutoff point (median value) is not reported in the manuscript.

3.	The experimental method section is too brief, especially for the data collection part. More details are required to make the results solid. For example, based on the plots in the manuscript, it looks like the MEX3A mRNA expression level was measured in both normal tissue and tumor and statistically compared. However, no information is mentioned in the method section.

4.	The interpretation of the statistical results is ambiguous and confusing. For example, "The MEX3A mRNA expression level was significant(ly) upregulated in liver cancer". Does it mean that the MEX3A expression level in the tumors is higher than the normal tissues, or the MEX3A expression level in patients with liver cancer is higher than the normal people? "The results of ROC curve reveal that MEX3A mRNA had moderate diagnostic ability in patients with live cancer". However, the ROC curve only indicates that the tissue with high MEX3A expression is more likely to be a tumor. So I don't see the potential of MEX3A as a biomarker to diagnose the liver cancer.

5.	The percentage data reported in table 2 are confusing without description. Please explain in the table caption.


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: CLINICAL CHARACTERISTICS AND PROGNOSTIC VALUE OF MEX3A MRNA IN LIVER CANCER
Review round: 1
Reviewer: 4

Output:
Basic reporting: This manuscript focusses on role of RNA binding protein on cancer, specifically on liver cancer. Authors have chosen. The is manuscript was well written with professional language. However, the authors can improve sentence formation. Authors. Literature work is thorough with up to date references. Introduction part was very well written with background information of cancer and RNA binding proteins. Tables and figures are represented well with clear legends, marking, and labels. Authors have shown that the expression of MEX3A mRNA can be used as a prognostic molecule for liver cancer.
Experimental design: Manuscript meets the aims and scope of the journal and experimental designs are well presented. Authors have used adequate methodology to verify the differences in the expression of MEX3A in patients with multiple differences not only in age but also in cancer stage, gender, Overall survival etc. Authors have used a large data sets for their analysis. Authors are encouraged to use other profiling techniques such as Immunohistochemistry and metabolite profiling to identify potential targets for cancer studies.
Validity of the findings: Results part was written well and study shows original results from designed experiments. Some of the discussion part can be easily kept into introduction. Authors attempt to do comparative study with other similar work was appreciable but the discussion can be shortened and focus more on their findings. When discussing some of the results, authors should cite particular figure or table in the discussion. It will be interesting to learn about what is the mechanism of MEX3A and also studies based on knockouts of MEX3 family proteins. The OS and RFS results are encouraging showing the significance of MEX3A mRNA expression in relation to survival in liver cancer patients.
Additional comments: This manuscript was focused on investigating the role of MEX3A mRNA in liver cancer and how the expression variation can be used for prognosis. Introduction part was very well writtern. Experimental procedures and results section were written well. However, Care needs to be taken in terms of sentence formation and grammar. Some areas of the discussion part should be placed into introduction.  Overall the manuscript was well written with minor revisions required. Please see comments from the attachment.  Authors should also provide some future work on how they will use this molecule to future studies on liver cancer.


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: CLINICAL CHARACTERISTICS AND PROGNOSTIC VALUE OF MEX3A MRNA IN LIVER CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The clarity of the manuscript improved significantly with revision. The message is novel and relevant. The study is well performed with a relevant number of samples.


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: CLINICAL CHARACTERISTICS AND PROGNOSTIC VALUE OF MEX3A MRNA IN LIVER CANCER
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript clearly reported the potential of MEX3A in liver cancer diagnosis.
Experimental design: The work is well designed.
Validity of the findings: Data is prepared is a standard way.
Additional comments: The authors well addressed my concerns.


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

Input:
Title: CLINICAL CHARACTERISTICS AND PROGNOSTIC VALUE OF MEX3A MRNA IN LIVER CANCER
Review round: 2
Reviewer: 3

Output:
Basic reporting: See the general comments
Experimental design: See the general comments
Validity of the findings: See the general comments
Additional comments: In this resubmission, the authors added more details in the method section. The detailed description of data collection and statistical methods make the results much clearer. The statistical results clearly indicate that MEX3A mRNA expression associated with the survival rate of liver cancer patients and it could be used as an independent predictor of liver cancer prognosis. The conclusion is more convincing than the original version. Overall, the authors addressed the questions from reviewers properly, and the resubmission is well written. I recommend that the paper should be accepted for publication in its present form.


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

Input:
Title: VARIABILITY OF SOIL CARBON AND NITROGEN STOCKS AFTER CONVERSION OF NATURAL FOREST TO PLANTATIONS IN EASTERN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors addressed an interesting topic that soil carbon and nitrogen stock responded to forest conversion in different altitudes. Generally, this is a traditional issue how plantations change soil carbon and nutrient pool. They found natural forests have a better capacity to accumulate soil carbon and nitrogen. Although this conclusion is not quit novelty, the paper provided rich data in understanding the relationships between afforestation or reforestation and soil carbon pool dynamics.
Experimental design: The description of methods is extremely poor. Line 99-100, the authors declared “six depth layers 0–10, 10–20, 20–40, 40–60, 60–80 and 80–100 cm along soil profiles”, but I can only see the results from two layers. Moreover, no detail information was given in lab-determining elements and other parameters. No sample site descriptions and any other detail information to tell reader about reasonable or statistical sampling. I can not judge the scientific property of sampling.
Validity of the findings: The results did not follow the methods. The interesting results is carbon stoke distribution along soil profile, especially the deep soil. However, I can only see the top soil. Line 140 “Plantation age and elevation were positively correlated with….”, if this is the case, how many plantations with different age or different elevations in a sample region? I don’t think “land use change” is a good phrase to express forest conversion.
Additional comments: Many abbreviations have no primary words, which limited the readable of whole paper. Scientific hypothesis should be listed in the section of Introduction. Most part of the paper paid more attention to carbon, less attention to nitrogen. Line 91-93, the three questions are too normal. Every papers about this direction can give these questions. Some deep objectives should be listed.
I think if the authors can add the detail information about materials and methods, and carbon and nitrogen stock along whole soil profile 0-100. If do so, the paper could be acceptable.


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: VARIABILITY OF SOIL CARBON AND NITROGEN STOCKS AFTER CONVERSION OF NATURAL FOREST TO PLANTATIONS IN EASTERN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper investigated differences between the natural forests and plantation forests at four sites and tried to explore the factor affecting these differences. The experimental design and field measurements seem no problem. But I have some concerns with the current version of the manuscript. Particularly, the discussion section requires a thorough revision. Some conclusions and explanations are also very far-fetched. The authors should revise it and make it much clearer.
Experimental design: L27 five sites, L97 six forest sites. So how many forest sites did you have?
L97: you only use the 0-10 cm and 10-20 cm soil data in this paper. So even though you collected six layers soil samples, I think these could not be included in the total samples 252.
Does all of the samples is taken at the same time?
You should point out the layers of topsoil and subsoil.
L106-107: it’s better to use the formula editor to generate it.
Table 2: As far as my knowledge goes, the age of Dinghushan plantation forest is at least 60 years, you should check it again.
Validity of the findings: It seems no problems.
Additional comments: L30: which one was decreased?
L36-39: This sentence is too long.
L39: Please add the abbreviation of MAT and MAP.
L40: the first letter of the word should use upper case or lower case consistently.
L44: should be nitrogen
L46-48: I think you should state the reason why the soil N accessibility is limited. The logic is not right.
L69-71: Land use change, reforestation, afforestation, land conversation and forest management, they are different concept. You should make sure which kind of it in your paper and don’t mix it up.
L51-52, L63-67, L84-86: These sentences represent the similar meaning. Please revised it carefully.
L88: it should be “it’s”. it should be “plantation forests”.
L93: replace by How
L97: Although we know the meaning of PF. You should explain the abbreviation because it is the first appear.
L115: check citation for SPSS version 20.0. Systat Statistical Software Package for Windows?
L124: Remove “interestingly”
L121-124: which figure or table showed this result?
L129-130: this sentence belongs to the next section.
L135: I think you can separate this section into two parts or you can put the results of changes in affecting factor into the l section, this may be better. This results portion is some kind of simple.
L136: This result “Soil C and N stock varied significantly (P<0.05, for all) with site” belongs to the last section.
L156-162, L167-169: these sentences are a little repetitive.
L170: change the word of “prediction”
L180: It should be “Wang”
L170-172: the ages of this plantation forests are different, so it meaningful to compare these together?
I recommend to use the annual accumulate rate if you want to compare different species function.
L184-186: what does these percentage mean?
L188-189: the hypothesis should be proposed in the introduction section.
L193-195: This explanation is very far-fetched.
L218-219: How can you get this conclusion?
L246: this data (189 m) is not matched with the Table 2 (275 m).
L359-360: “forests have below-ground C and N processes which promote better accumulation in the soil”. How about the plantation forests?
The discussion part should also be revised with more explicit explanations of your findings.


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: VARIABILITY OF SOIL CARBON AND NITROGEN STOCKS AFTER CONVERSION OF NATURAL FOREST TO PLANTATIONS IN EASTERN CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The language needs to be improved. Generally speaking, academic papers use the present or past tense.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Line 96: The authors collect a total of 252 samples from NF and PF stand of each site in August 2017. Six forest sites were selected as experimental plots including Jianfengling (JF), Dinghushan (DH), Huitong (HT), and Qingyuan (QY), across eastern China forest (Fig. 1, Table1).
(1) Please give more details about collection area.
(2) How many samples chose from each forest site, and give the approximate location?
(3) 252 samples are sufficient for this article to get the conclusions. Please explain their rationality.

Line 145 In the discussion, the authors investigate the effects of different factors on soil C, N stock, respectively. The study provides an overview of the current spatial distribution and soil stocks of C and N, as well as the eﬀects of environmental factors on soil C and N stocks and indicated that although MAT and MAP are the most important factors aﬀecting the variations in soil C and N, their vertical and horizontal distribution diﬀered in various aspects.
(1) However, in the natural environment, the soil C, N stock is affected by the multi-factors. If possible, the authors can discuss more factors.
(2) “ MAT and MAP are the most important factors aﬀecting the variations in soil C and N”
How do they affect the soil C, N stock? Please try to explore the mechanism of synergism.


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: SOIL TEMPERATURES AND ACTIVE CARBON COMPONENTS AS KEY DRIVERS OF C STOCK DYNAMICS BETWEEN TWO DIFFERENT STAND AGES OF LARIX PRINCIPIS-RUPPRECHTII PLANTATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors examine the impacts of stand age on soil carbon in a Larch forest. The authors seek to assess differences in C stocks in stands with trees that are 40- and 24-year-old. They also examine variability in soil and microclimate conditions and potential explanations for differences between stands. The description and presentation of the results should be more specific to address all four study objectives outlined by the authors. Further work is necessary to ensure that conclusions are direct and clear.

General comments:
1. There are some areas where some clarification is needed to better convey scientific terminology throughout all sections. For example, in lines 69-70 “environmental variables C pool is affected by the dynamic of actively C components”, it is unclear what the components is being referred to and how they are varying temporally. There are several other areas that use similarly vague terminology. I’ve included some other lines in the specific comments.
2. While the authors set out with 4 study objectives, the importance of these objectives and the background can be hampered by too superficial of sentence phrasing. Throughout the introduction, there are often sentences that often indicate the importance of a process without providing context. For example, line 45 indicates “Many forests, especially plantation forests, are managed for particular age structures.” This does not help me understand whether I should expect the younger or older stand in the study to reflect management practices. It is hard for the reader to gather the importance of the study. Other examples include lines 45-47, 59-60, 67-68, 77-78.
3. The discussion would benefit from a clearer interpretation of the results that relates back to the big picture and original objectives. More citations would be useful. For example, lines 270-282 have a series of competing explanations for the impacts of soil and microclimatic conditions of soil carbon. It can be a little confusing for remembering the differences between the stands and the main take away.
4. The study would benefit from clear, direct conclusions (lines 333-44). The conclusions section largely repeats results and provides open ended, vague explanations for carbon dynamics in the two stands. It is difficult to keep track of what the “difference in crown cover” or “difference in litter input” is for the two stands (lines 343-344). Furthermore, objective 4 (evaluate strategies for storing C in managed forests) is not discussed entirely and there are no conclusions about strategies. This objective seems particularly useful for providing more context for the study.

Specific comments: Please clarify phrasing with more detail and clear definition.
Line 57: “combination of factors”. What factors?
Line 59: “interactions between human activities and environmental factors and their effects on forest function and dynamics” What interactions and effects?
Line 292: “different seasons” What seasons?
Line 335: clearly state how and what environmental factors, active C pools impacted carbon
Experimental design: Overall the experimental methods and objectives are sound. The authors’ data and analysis would be useful for understanding the carbon balance in managed forest plantations. However, some issues with basic reporting hamper the reporting of the research and its relevance.
Validity of the findings: The results and conclusions could be clarified and more specific. The data provided is well organized, but needs a little more clarification in the metadata.

General comments
1. The full statistical test should be reported not just the p value. For example, it would be good to see the test statistic (ex, t-statistic with degrees of freedom) in addition to the p value for open and thorough reporting of statistical analysis. It would also be good to use a consistent number of significant digits. In some areas, p values are reported as <0.01 and others p=0.009. It would also be helpful include the mean in some comparisons rather than percent differences (for example lines 192-200, line 212).

2. The provided data has a column that identifies each sample does not have any explanation for each identifier. It appears there is an indication of stand age, stand replicate, and sample replicate. However, it is not possible to confirm this and stand/age replicates may be confounded depending on user interpretation. I recommend breaking identifiers up into separate columns and having a brief explanation for what each identifier represents.

3.There is also no PLFA mass data included.

Specific comments:
Table 1: error in numbers. Trees are listed as >2000 meters in height.
Line 270-2782: Need to expand on reasoning behind the crown and branch height influences on soil temperature. There are also many explanations for the differences in soil temperature. While the temperature is significantly different, there is little functional difference in the difference between the mean soil temperature (0.4 C), less than half of the typical diurnal range in temperature for in both stands. The difference appears to be driven by the spring, but the seasonality and implications for soil carbon are not discussed. The higher soil moisture discussed in the 278-282 would increase thermal conductivity, but lower thermal conductivity as a result of litter is a line of reasoning for the higher soil temperature.
In figure 8: correlations are shown in cases where high correlation is expected. For example, DOC is used directly in the calculation of ratio of DOC/DON and thus there is a high correlation. Other significant correlations often have a huge variability and vary non-linearly. Units would also be helpful.
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: SOIL TEMPERATURES AND ACTIVE CARBON COMPONENTS AS KEY DRIVERS OF C STOCK DYNAMICS BETWEEN TWO DIFFERENT STAND AGES OF LARIX PRINCIPIS-RUPPRECHTII PLANTATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: Ma, and colleagues investigate changes in several soil properties including soil organic carbon in forest ecosystem across two different stand ages. In particular, the study compared 40-year old growth forest against 24-year-old  plantation of Larix species in North China to show that old growth forest tend to store more carbon, which is likely associated with low microbial activities in old growth forests. In addition, the study found that soil temperature and soil moisture content were higher in old growth forests. While quantifying the carbon content of soil across different forest age is an important topic for understanding ecosystem health and climate change mitigation, there are several study limitation that need to be addressed prior to publication. In addition, the English language need to be thoroughly revised since I found several typos and grammatical errors.

Major comments:
1.	While the study report differences in several soil attributes (organic carbon, pH, soil temperature, microbes etc) between two forest types with the findings that old growth forest are more resilient and store more carbon compared to planted forests, the mechanisms driving these changes are not well justified and explained. It seems abit counterintuitive to think that soil moisture, soil temperature and soil nitrogen would increase in old growth forest but still be able to hold for carbon in soils. One of the argument as suggested by the authors was that more C were accumulated in recalcitrant pools which are less vulnerable to microbial activity. While I agree with the authors justification, it is unclear how they determine the amount of C stored in recalcitrant pool. Since old growth forest have high litter input compared to planted forests, which could lead to more organic matter retention in labile pools leading to higher rate of decomposition.
2.	It is unclear why there would be such a huge difference in the pH of the soil between the old growth and planted forest (see figure 2b), particularly in the month of June. Since both soil contain same species and given that the environmental conditions are quite similar, there is no justification of these difference. It is also unclear how the increase/decrease in pH would play an important role in ecosystem management (i.e. through increase or decrease in microbial activity).
3.	The authors also simply report findings from their experimental studies and never try to put the outcomes of the study in the larger context. I think the authors should flesh out how/whether retaining the old growth forests is better for climate change mitigation compared to regrowing forests. For example, there are several studies that suggest that after an initial release of carbon following forest harvest, forest ecosystems are able to retain or even gain more carbon in plant and soil following plantation (see Dangal et al. 2014). However, the authors fail to include the legacy effects of forest harvest and regrowth on net carbon sequestration in soils.
4.	The results of this study show that both temperature and soil moisture increase in old growth forests. However, the authors fail to clearly provide a justification of why both temperature and soil moisture increase. I believe that if there is an increase in temperature, there should be less soil moisture as an increase in temperature increase the vapor pressure deficit increasing the atmospheric demand of water vapor.
5.	The writing need to be thoroughly revised. There are several grammatical errors that can be improved by contacting a native speaker to comment/revise the manuscript. Also, I found that there are Chinese language inserted in figure captions (please see figure 2).

Other comments
Ln 27: Is it a good idea to report temperature increase in percent? It is really surprising to me that a 2.9% increase in temperature was significant?
Ln 35: 3300 Pg C is not an accurate number. There is actually a large uncertainty in the total carbon stored in soil that could range from 411-2111 PgC (see Tian et al. 2015).
Ln 41: I disagree if forest soil store the largest amount of carbon. How about wetlands or even grasslands?. It is really important to know if you are talking about per unit area storage or total storage.
Ln 49-52: I do not think this study is focused on understanding the effects of different management in forest carbon. Is this paragraph even important?
Ln 69. Please revise this sentence. For example: “Forest C pools can also be affected by the dynamics of active C components”.
Ln 69: revise actively to active.
 Ln 212-214: There is only a result of soil pH changes but no mention of soil moisture changes.
Ln 334: correct “retults” to “results”

Dangal et al. (2014) Effects of agriculture and timber harvest on carbon sequestration in the eastern US Forest. JGR-Biogeosciences
Tian et al. (2015) Global patterns and controls of soil organic carbon dynamics as simulated by multiple terrestrial biosphere models: Current status and future directions
Experimental design: Since the authors are comparing planted vs old growth forest, the experimental design does not apply
Validity of the findings: This is a reporting paper with a strong measurement data. So, the findings are valid but the authors need to put those findings in the larger context by comparing with similar results from other studies
Additional comments: see basic reporting


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: DIFFERENTIALLY EXPRESSED GENES AND KEY MOLECULES OF BRCA1/2-MUTANT BREAST CANCER: EVIDENCE FROM BIOINFORMATICS ANALYSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is clear and most of the time direct to the point. The authors used professional, clear and unambiguous, English language. However, occasionally there were some redundant words as indicated in the general comments. Most of the references were relevant to the topic except in few occasions. The authors used a good article structure which includes the relevant figures and tables. But some of the figures were not in a high resolution. In addition, the legend for figure 5 has insufficient description. The results were relevant to the original hypothesis nevertheless; the hypothesis is not very clear in the introduction. Background in the abstract needs more details as well as the introduction needs more details.  I suggest adding descriptions in line 21-22 in the abstract and in the line 68-73 in the introduction. Also it is better to write more about the justification for the study and demonstrate adequate relevant literature.
Experimental design: The Peer Journal’s aim and scope is publishing articles in the Biological Sciences, Environmental Sciences, Medical Sciences, and Health Sciences. The current manuscript is a part of the Medical Sciences, and Health Sciences. Therefore, the research is within the aim and scope of the peer journal. The research is defined and meaningful, as well as it is relevant and adding to the scientific knowledge. However, I think the data analysis needs more elaboration. The research is bioinformatics based analysis and most of the used software are well defined. There were no human materials used in this study. So the study in line with the ethical standard. The methods were not described in details and it needs more elaboration and description. The over all data have some degree of novelty.
Validity of the findings: Most of the underlying data were robust and controlled. But most of the figures are not in a very high resolution form. I suggest using a higher resolution form or improving the resolution, especially for the Kaplan-Meier figures. There is no clear conclusion at the end of the article which can summarize the findings.
Additional comments: Abstract:
Line 21. The background in the abstract is insufficient. I suggest to add one or two sentences to reflect on the subject.

Line 37, remove the words “For example”.
Introduction
•	Line 64, remove the word mainly.
•	Line 66, the sentence “In fact, this limits the opportunity of prevention for BRCA1/2-mutant breast cancer and other tumors such as breast cancer”, it is better to add other tumors.
•	Line 70. the sentence “treatment of breast cancer, especially for some hereditary breast cancer and sporadic breast cancer…) is repetitive with redundant words. It is better to change as “treatment of BC, especially for some hereditary and sporadic BC….)
•	Line 73, it is better to add a reference.

Methods
•	Line 89. No mention for the source of other groups (WT& Control).
•	Line 123, the sentence “specializes survival analysis” needs to be cleared. specializes for survival analysis

Results
•	Line 128 there is no need to repeat the abbreviation “breast cancer (BC)”
•	Line 131, be consistent in writing the BRCA1/2 “BRCA1&BRCA2 mutations”
•	Line 162, use the Italian uppercase letter for the BRCA1/2-

Discussion
•	Line 212, the sentence “TNBC accounts for about 70% and 20% of BRCA1 and BRCA2 mutation carriers” is in accurate so please review this statement
•	Line 255, Italian CCNE1
•	Line 273 the sentence “has attracted a lot of research enthusiasm. reported that TTK could regulate the growth” doesn’t make sense.


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: DIFFERENTIALLY EXPRESSED GENES AND KEY MOLECULES OF BRCA1/2-MUTANT BREAST CANCER: EVIDENCE FROM BIOINFORMATICS ANALYSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comments
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Major Comments:
1) In the methodology section, can the authors elaborate on the ethnic sub-division of the control, Wt and Mutant breast cancer RNA-Seq data? The distinction is important to understand because as authors already mentioned that there is "paucity in data pertaining to ethnical risks with BRCA1/2". Further it is important to observe if the ethnic classification lowers the "N" in differential analysis following inclusion and exclusion criteria. It is also important to know if the authors have performed the PPI integration of differentially expressed genes within the ethnical groups of control vs Wt vs MUT, if it was not done can authors justify the exclusion, especially when it is known to have BRCA1/2 has ethnic risk factors associated with it

2)Could authors provide more detailed description of the RNA-seq data they have obtained from cbiportal? Was it single cell RNA-seq data?How many reads were done on the cells? what was the quality of the data? what kind of algorithm was used for the comparative transcriptome analysis? Was the data obtained from several different research labs? what were the statistical common factors amongst the digital gene expression of the RNA-seq data? what was the method of collection and what measures were undertaken to prevent batch effects and the normalization procedures for the data obtained from different sources?

3)By authors confession in discussion section "lack of adequate BRCA1/2 mutant cases for accurate survival" it is important to further know the statistical confidence level of the predictive model that authors have laid in the manuscript. Can authors comment on the what percentage of confidence do they exude in utilizing the CCNE1, NPBWR1 and TTK genes in prognosis and diagnosis of breast cancer and if that confidence level is enough for a clinical prediction?

4)The genes such as TTK and GRP7 that authors claim to serve as diagnostic markers for BRCA1 breast cancer have previously been studied in the incidence of breast cancer as clinical targets, considering what is already known about these genes/protein products in breast cancer can author comment/defend the merit and novelty of the current study? and how does the study differ from the plethora of literature already available?

Minor comments:
1) Authors please check for some grammatical errors


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

Input:
Title: DIFFERENTIALLY EXPRESSED GENES AND KEY MOLECULES OF BRCA1/2-MUTANT BREAST CANCER: EVIDENCE FROM BIOINFORMATICS ANALYSES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I re-reviewed the article. It has been improved and the English language also has been improved greatly. Most of the highlighted comments have been addressed. The article now is ready to be published.
Experimental design: The methods and experiments section  have been improved. Most of the highlighted comments have been addressed. The article now is ready to be published.
Validity of the findings: The article has been improved and the English language also has been improved greatly. Most of the highlighted comments have been addressed. The article now is ready to be published.
Additional comments: The methods and experiments section  have been improved. Most of the highlighted comments have been addressed. The article now is ready to be published.