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

Input:
Title: DEVELOPMENT OF A PREOPERATIVE INDEX-BASED NOMOGRAM FOR THE PREDICTION OF HYPOKALEMIA IN PATIENTS WITH PITUITARY ADENOMA: A RETROSPECTIVE COHORT STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: Detailed comments as below.
Experimental design: Detailed comments as below.
Validity of the findings: Detailed comments as below.
Additional comments: 1. Line 62-63, it is inappropriate to describe both ROC and AUC are used to assess the performance, because AUC is an indicator and ROC is a method which can generate AUC.

2. Given the small sample size of validation set and the lack of external validation set, the conclusion should be made with caution. It is overstated to say “can facilitate the prediction of hypokalemia”.

3. Please follow the TRIPOD statement to write this paper. For this revision, please attach the corresponding TRIPOD list.

4. Introduction. It remains unclear why hypokalemia is a concern of postoperative patients with pituitary adenoma, and a further question is why preoperative could be used to predict postoperative hypokalemia. These are important for this research topic. The authors should also briefly review risk factors and reasons for postoperative hypokalemia in patients with pituitary adenoma.

5. Line 130, please specify the design of this study.

6. Line 130-141, please provide detailed inclusion and exclusion criteria.

7. A fatal methodological limitation is the small sample sizes, limiting the generalizability of the predictive model developed. Please also provide the 95%CI of AUC, due to this reason, I speculate the lower limit of AUC is lower than recommended.

8. For addressing missing values, please provide rationales for the use of multivariate normal imputation method. It seems no supporting evidence for random missing. The authors may consider to repeat the analysis with the complete dataset to do a sensitivity analysis.


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

Input:
Title: DEVELOPMENT OF A PREOPERATIVE INDEX-BASED NOMOGRAM FOR THE PREDICTION OF HYPOKALEMIA IN PATIENTS WITH PITUITARY ADENOMA: A RETROSPECTIVE COHORT STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English were used throughout in this manuscript. Literature references, sufficient field background/context provided.
Experimental design: Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, & controlled.
Additional comments: This study aimed to develop and validate a preoperative indices-based nomogram for the prediction of postoperative hypokalemia in patients with pituitary adenoma (PA). 205 patients were retrospectively collected in this study, and a nomogram prediction model was trained and validated. The AUCs of the nomogram model for predicting postoperative hypokalemia were 0.871 and 0.753 in the training and validation sets, respectively. This suggests that the authors have built a relatively good prediction model.
Overall, the study was well designed and the usage of statistical analysis was comprehensive. But there are small problems:
1) Variables that are not statistically significant in Table 2, such as serum potassium and CK, are not recommended to be included in Nomogram.
2) It is recommended that the report of the manuscript refer to TRIPOD "Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD): the TRIPOD statement". And the PROBAST (prediction model risk of bias assessment tool) was recommended to evaluate the risk of bias for this manuscript.


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

Input:
Title: DEVELOPMENT OF A PREOPERATIVE INDEX-BASED NOMOGRAM FOR THE PREDICTION OF HYPOKALEMIA IN PATIENTS WITH PITUITARY ADENOMA: A RETROSPECTIVE COHORT STUDY
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors have addressed my concerns. I have no fruther comments.
Experimental design: The authors have addressed my concerns. I have no fruther comments.
Validity of the findings: The authors have addressed my concerns. I have no fruther comments.
Additional comments: The authors have addressed my concerns. I have no fruther 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: MALDI-TOF MS AS A METHOD FOR RAPID IDENTIFICATION OF PHYTOPHTHORA DE BARY, 1876
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study by Bozik and colleagues shed light into the application of routine MALDI-TOF mass spectrometry for the rapid identification of Phytophthora species.

The manuscript is clear, straightforward and the data support the primary hypothesis.
Experimental design: The experiments have been conducted diligently with appropriate statistical analyses.
Validity of the findings: The data support the research hypothesis.
Additional comments: It would be of importance to include a flow diagram displaying the route for identification from isolation from plants into MALDI analyses.


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: MALDI-TOF MS AS A METHOD FOR RAPID IDENTIFICATION OF PHYTOPHTHORA DE BARY, 1876
Review round: 1
Reviewer: 2

Output:
Basic reporting: Title
1.MALDI-TOF MS as a method for rapid identification of
Phytophthora species
ex. Please  inform  author and year. ex.  Phytophora  Bary, 1986

2. Correct throughout the text (M / Z), correct is italic.
Experimental design: MALDI-TOF MS as a method for rapid identification of Phytophthora species.

It is a tool that is evolving mainly in the microbiological part, fungi and Bacteria. The article is to be congratulated both on the materials and methods. They used a (Byotiper) database to compare with spectra, which is essential for verification.

MALDI TOF tool has an advantage over molecular biology, as it is very fast and efficient, that's why I find the article very innovative and attractive.

Material and method well based, correctly describing the steps of the protocol process.
Validity of the findings: The conclusions are well formulated, linked to the original research question and limited to supporting results.
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: FROM DATA COMPILATION TO MODEL VALIDATION: COMPARING THREE ECOSYSTEM MODELS OF THE TASMAN AND GOLDEN BAYS, NEW ZEALAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: Page 18 lbe 418 missed links/reference to Table twice.

AM is largely a predatory/prey fisheries model. The limitations in terms of the role that the AM model is to play in ecosystem based management is not clearly defined, although it is presented in the context of broader EBM.

Many useful experiments have been run and results are reported. However, the discussion of what this means is weak.

Conclusion missing.
Experimental design: There is circular thinking in the experimental design. While the three models are independent in principle, parameters from AM were used to populate EWE and SS.

If three models are compared, it would be good to include a table that compares the models, beyond the strengths/weaknesses on particular items.

If this is the best contemporary 'what-if' model then more attention could be given to the actual dynamic structures that are at work. It remais a black box expert model with regard to its dyamic capacity.

Calibration and testing of extremes are described in a useful manner.

Connectivity and Influence (6.3) p22 reports findings but there is no conclusion from this paragraphs either. What do the authors learn from this?

Ecosystem based management (EBM) in the introduction includes multiple activties, but the model is fisheries oriented. Seagrass and algae are narrowly included. Considerable assumptions and adjustments had to be made to prevent crashing the model. These considerations should be clearly listed in Discussion and thereafter the Conclusions.
Validity of the findings: The link between the findings and the discussion is not strong.

The conclusion is missing altogether.

The recommendation in the abstract doesn't clearly line up with discussion, given that conclusion is missing. 'We recommend that scenarios relating to ecosystem dynamics of the TBGB ecosystem incorporate initialisation uncertainty, oceanographic uncertainty, and compare responses across all three models where it is possible to do so."
Additional comments: The process of testing the Atlantis model for this bay is very useful. The comparison with the other models is less evident.  When would the authors recommend use the AM model and when does it come with caution?

A summary table of comparision between the models might help.

A conclusion is essential.

Mentioning of the national science challenge Sustainable Seas in the abstract doesn't seem relevant. Perhaps move this to the introduction. While acknowledged that the research is incremental, it seems important to position the contribution and the limitation of this model to tie the introduction and the Discussion (Conclusion?) together.


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: FROM DATA COMPILATION TO MODEL VALIDATION: COMPARING THREE ECOSYSTEM MODELS OF THE TASMAN AND GOLDEN BAYS, NEW ZEALAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: -	Figure 3 can be moved to the Appendix (if it is not of course providing any critical information for the model excluding assumptions/inputs).
-	I am not sure how to interpret Figure 4 without looking at the text. Would be nice to provide some complementary explanation in the Figure caption.
-	Page 18 has multiple formatting issues. Page 32 has several English issue.
Experimental design: -	The abstract is not self-descriptive. What is the aims of this research and what is its contribution and industrial application?
-	Page 4, it is important to add some information about the methods used for developing the Atlantis model and if it is too difficult to fit the observation, then how we can rely on the results of scenario?
Validity of the findings: -	The goodness of calibration has not been reported. By looking at the literature and the values of model outputs in Figure 5, the error looks quite big. Therefore, without providing this type of statics it is hard to say how good the model is calibrated.
-	Page 20, 21, was the sensitivity test global or local? What method has been used in what range?
-	The managerial implications of this study should be well-explained according to aforementioned results. What advantage industry and practitioners can gain from the findings of your study? What are the specific action plans based on the research findings? These should be addressed.
-	The limitations need to be highlighted. Furthermore, the suggestions for future studies could be carefully expanded.
Additional comments: This study aims to Compare three ecosystem models of the Tasman and Golden Bays. The authors have explained the standard tests of models and compared the results of certain scenarios across three. The results are interesting and can contribute to the literature of ecological modeling. Please see few suggestions and 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: FROM DATA COMPILATION TO MODEL VALIDATION: COMPARING THREE ECOSYSTEM MODELS OF THE TASMAN AND GOLDEN BAYS, NEW ZEALAND
Review round: 2
Reviewer: 1

Output:
Basic reporting: This article meets all the requested standards.
Experimental design: The authors have addressed all these points in the revised manuscript.
Validity of the findings: To the best of my knowledge the method and results are valid.
Additional comments: Thanks for your responses and clarifications. The text reads very well after the revision.


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: ASSESSMENT OF AGRO-MORPHOLOGICAL, PHYSIOLOGICAL AND YIELD TRAITS DIVERSITY AMONG TROPICAL RICE
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The information in the manuscript is really helpful for future rice breeders to plan shorter duration high yielding variety development.


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: ASSESSMENT OF AGRO-MORPHOLOGICAL, PHYSIOLOGICAL AND YIELD TRAITS DIVERSITY AMONG TROPICAL RICE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The two references, Foley et al. (2011) and Lesk et al. (2016), are rather old to support the authors' claim that the current level of rice productivity is not enough. Consider adding a more recent reference if available. Similarly, Ray et al., (2012) is almost a ten years old reference. Is the current situation for rice yield stagnation the same as in 2012? Consider updating the reference, if possible. I highly encourage you to cite more up-to-date references when referring to agricultural statistics or the current state of farming.

In the Results section, do not repeat the numbers reported in the Tables in the text. This will hinder readability.

Figure 2: The correlation values are too small and not visible at all.

Figure 3: Define what A to H are referring to.

Figure 4: Define what A to D are referring to. Same for Figure 5.

Figure 6: Clarify what each rectangle, triangle, and circle is referring to.
Experimental design: Explain how the 74 genotypes were chosen. Were they chosen randomly or based on some criterion? This was not clear to me.

Many indices appeared in the manuscript. I did not understand the difference between additive response indices, vigor response indices, total response indices, and cumulative response indices. Or are they the same index?

I did not understand what does it mean by values > (population mean + SD), ≤ (population mean + SD) and values ≥ (population mean - SD) and < (population means - SD) in L207. I suggest rephrasing this part or provide a cartoon that explains this cutoff criterion visually.
Validity of the findings: No comment.
Additional comments: The authors evaluated 74 indica rice genotypes for morphological, physiological, and yield related phenotypes. Overall, the manuscript is well written and structured. Below are my additional comments.

L93: This sentence is a bit confusing. Did the author mean that, contrary to the rice producers in the USA, Asian rice producers do not prefer short-duration rice genotypes? If so, add a term Asia, outside of the US, or something similar.

L133: Did you mean relative humidity?

L182: RStudio is an integrated development environment for R. So you have to provide the R version the authors used for the analysis rather than the RStudio version.

L185: Panicle length was significant for the year x cultivars interaction rather than year itself. According to Table 1, the year effect is significant for spikelet fertility too.

L189: The term tolerance seems not adequate here.

L400: Remove "(".


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: ASSESSMENT OF AGRO-MORPHOLOGICAL, PHYSIOLOGICAL AND YIELD TRAITS DIVERSITY AMONG TROPICAL RICE
Review round: 1
Reviewer: 3

Output:
Basic reporting: Manuscript (MS) entitled «Assessment of agro-morphological, physiological and yield traits diversity among tropical rice» aimed to evaluate the variation of some traits related to yield in a wide range of tropical rice genotypes in order to identify the best individuals usable in a breeding program. It is well documented that rice is almost the main food wolrdwide but its production does not meet the demand of the growing population. Therefore, deciphering the genetic potential hidden in the germplasm is relevant for identifying elite accessions which can be used to implement a breeding program. From this point of view, the approach described in this well written MS is scientifically sound, the methodology is appropriate and significant results were recorded. Despite these significant acheivements, the paper needs slight modifications before it can be considered for publication in «Peer J».
Specific comments
Please see the attached word document of the MS.
Experimental design: The experimental was well conducted and appropriate.
Validity of the findings: The findings are relevant for the scientific community, the curator and the breeders as well.
Additional comments: Please see the attached documents.


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: PEPPER ROOT ROT RESISTANCE AND PEPPER YIELD ARE ENHANCED THROUGH BIOLOGICAL AGENT G15 SOIL AMELIORATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article was written in clear, unambiguous, technically correct English and conforms to professional standards of courtesy and expression. Neverthelee I suggest some small improvements, which are listed in the attached file, in order to improve grammar and some scientific expressions. For example, throughout the paper the Authors use the phrase sp for species. I think it would be more correct to add a point after sp (writing sp.) because it is an abbreviation.
Some of the paragraph titles could be improved as listed in the attached file. For example, for Line 169 I would suggest: the title of the paragraph could be improved writing as follows: Impacts of G15-treatment on pepper root rot, biological characteristics, and yield.
Furthermore, only for the sake of clarity,  I suggest not to point out at the control as a "control treatment", but as a condition, because control is more a condition than a treatment. (Please, see the attached file)
Literature references are well structured and up-to-date, although I suggest for lines 259-265 to add any reference about the relation between ammonia N decreasing and root rot prevention, which seems to be a key role of G15 to prevent root rot? (Please, see the attached file)
Experimental design: As I listed in the attached file, I only suggest to spend a few words about your G15 fertilizers in Mat&Met too? You told about it in the Introduction, but I think a few words in the first paragraph of the Mat and Met section would fit.
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: PEPPER ROOT ROT RESISTANCE AND PEPPER YIELD ARE ENHANCED THROUGH BIOLOGICAL AGENT G15 SOIL AMELIORATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper describes the effect of a biological fertilizer on pepper growth and the impact on microbial community and soil composition. In general it is consize, well written, and clearly structured. The introduction contains information of papers in Chines, which are hard to consult by non-Chinese people. More information regarding Bjerkandera would have been useful. The figures are of low quality. In contrast to what the paper describes, there is no comprehensive analysis of root rot resistance, only circumstantial data of the relative abundance of Fusarium (not absolute numbers), and an unclear way of disease monitoring. I added details in the end.
Experimental design: The topic of the paper is relevant because Biological control of plant disease is becoming more and more important. However, I have some concerns regarding the experimental set-up:
- Only 1 (pooled) soil sample per plot was analyzed for microbial community composition?
- The microbial community composition should have been analyzed before inoculation as well to be absolutely sure that changes in microbial community are due to inoculum
- Only 1 plant per plot was measured (see also remark below)? This is very strange. Was it a healthy or diseased plant? Considering the biological variation In plant growth, the number of plants analyzed is too limited
- The authors indicate that the control field was plowed and treated in the same way, but without adding the inoculum. However, the inoculum doesn’t only contain G15, but also  contains pig manure, straw, urea,…
- Microbial community is examined at 1 time point only. At least the situation before inoculation should be included to see what the dynamics are due to the inoculum. In addition, how can we be sure that the starting situation of C and G are exactly the same?
Validity of the findings: The relevance of their findings could be discussed more clearly in the discussion. Furthermore, a lot of the differences on soil content (and hence microbial community) is probably due to organic compounds that are added to the microbial inoculum, rather than the microbial strain itself. This is not discussed at all.
Some unexpected results (low alpha diversity, low number of genera,…) are not mentioned in discussion. The discussion contains statements that are not backed up by data, e.g. L222 (number of pathogenic bacteria is not analyzed), L236 (disease resistance mechanism cannot be explored with microbial community analysis), biological agent G15 refers to the microorganisms, but this is applied together with organic compounds (manure,….) and therefore not possible to point to the microorganism as the major driver of these differences.
Additional comments: Other general and minor remarks
General remarks:
-	Yield increases but also looked at damage? Maybe more PGP effect?
-	A lot of references to papers (and patent? Hard to look up the content of this patent) in Chinese: not the best suited because a large part of the scientific community cannot consult these papers. In most cases these references can be changed by alternatives or excluded. It also seems that there are a lot of self-citation
-	Check spelling and correct use of all family, genus, and species names, also in reference list
-	Check citations and references. For instance, Fravel et al. 2005 is not in reference list
-	Materials and methods could use more specific information for some crucial aspects (e.g. how many plants per plot, determination of disease index,…)
-	Table legends should contain all information to interpret data, not a summary or conclusion of data

Abstract:
-	Increased richness of beneficial bacteria is mentioned twice (L22, 27): combine

Introduction:
-	Confusing start: Hymeophora subfamily? F. verticilliodes=F.moniliforme?;
-	L37: “The pathogen invades”: specify “these fungal pathogens…”
-	L47: not all of these references seem to be crucial, please avoid papers in Chinese for reason mentioned above
-	L47: Ikeda 2010
-	L53. Amyloliquefaciens; also in corresponding reference
-	L55: revise
-	L56: all references needed? Here I would expect a good review pointing to mode of action of BCOs

Materials and methods
-	L85: how was the chemical composition assessed?
-	L98: how many plants per plot of 300 m2? In table 1, it seems to be only 1 plant? Otherwise it would have been mentioned that the data in Table1 represents the averaged of X plants, and also a std dev would have been expected
-	L102-103: “after selecting three batches”?? not clear
-	How is plant height and root length measured? Authors provide data that are accurate to 0.01 cm?? I’m not sure if this is feasible.
-	It is nor indicated how disease is monitored
-	L112: stored
-	L114: why sieving before DNA extraction? Could this create a bias? Why DNA extraction of entire soil sample?
-	L131: specify length of DNA fragments extracted from gel
-	It would have been better to do the Illumina analysis in duplicate (two technical repeats for each DNA sample)

Results:
-	First title is not appropriate: the impact of root rot is not analyzed in detail.
-	Table 1 could also include averages and stddevs of the 3 analyses per treatment; similar remarks for Tabe2
-	L173-174: not clear how disease index or control effect is determined.
-	L180: not described how interaction was assessed
-	Table 3: 4 digits after comma? Sometimes 2 or 0 digits after comma? This should be cleaned up
-	Quality of figures could be improved regarding resolution as well as font size/readability (in particular for fig 2 and 4)
-	Unexpected that only 1 bacterial phylum was found?


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: PEPPER ROOT ROT RESISTANCE AND PEPPER YIELD ARE ENHANCED THROUGH BIOLOGICAL AGENT G15 SOIL AMELIORATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The article was written in clear, unambiguous, technically correct English and conforms to professional standards of courtesy and expression.
The Authors agreed with all of my suggestions and changed the paper accordingly. Probably just for material mistakes, a few of my previous suggestions were not fulfilled. That is the list:

Introduction
line 41. and chlamydospores to the (please, remove “the” as I suggested in my previous review, because to overwinter is a verb) overwinter in the….
Line 85. the grown plants, (please, add a comma before thus, not after it, as I suggested) thus maintaining

Mat & Met
Line 104 …… pig manure, straw,. (would you like to specify instead of using etc.?),
Line 104. ……….. , which (please, add “which” preceded by a comma) are necessary ……...
Line 107.  ….. remove one of the “to”
Line 145.        ……..water and fertilizer,  (would you please, avoid etc. and specify thoroughly),

Results
Line 238.      bacteria had an (please, remove n) richness of more….

Discussions.
Line 272, 275, 276. ……. the G15-treatment (I would leave G15 treated here, because “G treated” works as an adjective) plants
Line 285.  ….. of the G15-treatment (I would leave G15 treated here because it works as an adjective) soils were ….
Experimental design: No comment.
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: ASSOCIATION BETWEEN DIETARY INFLAMMATORY INDEX AND TYPE 2 DIABETES MELLITUS IN XINJIANG UYGHUR AUTONOMOUS REGION, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: In relation to methods:
I suggest the authors include in the section: Dietary Assessment (line 67) references of the validated FFQ and about Physical Activity (line 121).
Validity of the findings: The authors applied appropriate statistical test.
The data are robust and the conclusion support the originate question investigated.
The limitations of the study were clearly pointed out in the text.
 But in the section Conclusion: line 242 the authors described “...that a diet with a high pro-potential is associated with an increased risk of T2DM.” I suggest include the word inflammatory:
I would recommend something like:  “a diet with a pro-inflammatory potential is associated with an increased risk of T2DM...”.
Additional comments: I think this manuscript has interesting 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: ASSOCIATION BETWEEN DIETARY INFLAMMATORY INDEX AND TYPE 2 DIABETES MELLITUS IN XINJIANG UYGHUR AUTONOMOUS REGION, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1)	Table1: Firstly, rounding digits should be consistent, for example, most of the numbers are rounded to one digit, but for Kazak T2DM group, the percentage is 9.55. Secondly, in the footnote, it is unclear how the continuous variables were compared. For footnote A, if the authors added the comparison method to the Method Section, it’ll be unnesscrary to include this footnote. Footnote B should be removed and just add it right behind the variable name, just like the other variables.
2)	Table2: Firstly, the title should be revised to ‘baseline characteristics of study population by Dietary Inflammatory Index(DII) categorization’, Secondly, it should be quintiles instead of quartiles. Thirdly, the cutoff of categories should be listed as ‘<-5.33’,’-5.33— 1.34’,’1.35-1.31’ etc., but not the exact number alone. Fourthly, for glucose, are these mean and standard error?
3)	Figure1: Title should be revised, also there is no need to list the categories of each covariate. In addition, the exact numbers of odds ratio and its 95% CI isn’t listed throughout the paper.
4)	Figure2: Instead of having a plot and a table pasted together, this figure can be revised as a forest plot: showing the odds ratio of the outcome with T2DM vs no T2DM for patients in vs. out of the respective subgroups. (e.g. show the variables and categories in the left column, and then another column to show the number of OR(95% CI), the last column would be the plot. Again no need to list the categories of each covariate.
5)	Figure 3: Can be listed as a supplemental figure, but not a main figure.
Experimental design: 1)	In the statistical method section, please specify which comparisons tests were used in table1. In addition, the authors performed parametric tests for the comparisons, but it is unclear if the normality assumption was checked for the continuous variables.
2)	In the statistical method section, how did the authors decide which variables to include in the multivariable model? Moreover, the authors should list the multivariable adjustments used.
3)	The authors should be cautious about stating something is significant. I suggest that authors to revise the statement as p<0.05 was considered to be ‘significantly’ significant’ in line 132. This language should be revised throughout the paper.
4)	In the sensitivity analysis part, the authors used two different ways, using imputation and E-values, however, it is unclear how the imputations were performed, and if there are missing values in the raw data, the missing percentage of each variables should be reported.
Validity of the findings: 1)	In the results section, the authors summarized some findings from table1 and table2. For example, in line 146, the authors stated that ‘subjects with Hui or Uyghur ethnicity had higher prevalence of T2DM’. However, this is not safe to draw this conclusion. Firstly, the authors should add the reference group; Secondly, in comparisons consisting of two or more categorical independent variables, such as age group, BMI, ethnicity, education level, etc., a one-way ANOVA would not be suitable to draw this conclusion, post hoc multiple comparison tests should be performed to acquire correct p-values.
2)	In line 144, the authors mentioned the age of the participants ranged from 45-60 years old, however in Table1, it did show the study has included patients <45 years old. This should be revised to be consistent.
3)	When stating the findings is statistically significant or evident, if the tests were performed, the corresponding p-values should be included.
4)	In Line 155, the authors reported the odds ratios for all of the groups, but only included the 95% CI for the 5th quintile. It is unclear if the other odds ratios are statistically significant; and in line 157, the authors only reported the odds ratio for the 5th quintile. It would be better if the authors could show these as a table or figure, instead of listing it in the text.
5)	In line 156, ‘co-variables’ should be revised to ‘covariates’. In line 157, ‘over 50% greater odds of having’ is not accurate.
6)	It is not clear how the stratified analysis was done.
7)	The interpretation about E-values is not clear enough.
Additional comments: This study discussed the association between pro-inflammatory diet and having T2DM in Xinjiang district of China, which provide valuable information for further studies. However, it still requires revisions.


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

Input:
Title: ASSOCIATION BETWEEN DIETARY INFLAMMATORY INDEX AND TYPE 2 DIABETES MELLITUS IN XINJIANG UYGHUR AUTONOMOUS REGION, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: 1. In table1, 'referent' should be revised as 'reference'.
2. In table2, the statistics should be specified for glucose, eg., 'glucose(mmol/L), mean(SD)'.
3. In statistical analysis section, line 139, 'Values  were determined using a student’s t-test for continuous variables and Chi-square test for categorical variables', where 'values' should be revised as 'P-values'. In addition, the authors should also add a sentence stating the normality was checked using xxx test.
4. It was not clear how the stratified analyses were performed, was the comparison being made between model with/without interaction terms?
5. In the sensitivity analysis section, the authors stated that multiple imputation was performed, however, the authors failed to stating the results for the model after imputation. Were there any differences between the models before and after imputation?
Validity of the findings: no comment
Additional comments: Thank you for addressing my questions.


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: STABLE ISOTOPE ANALYSES IDENTIFY TROPHIC NICHE PARTITIONING BETWEEN SYMPATRIC TERRESTRIAL VERTEBRATES IN COASTAL SALTMARSHES WITH DIFFERING OILING HISTORIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The writing is clear with only a few minor grammatical mistakes. The literature is cited appropriately to provide supporting information or support inferences. Results are self-contained and relevant to hypotheses, but I suggest a reworking of hypotheses or objectives which will affect the organization of subsequent sections (see general comments to authors). Figures and tables are appropriate and professionally made. However, I suggest moving Fig S1 to the main body of the paper following the map figure, thus making it Fig 2 and shifting the remaining figures one spot. In that figure, the primary producer or consumer data should either be overlain on the bird or rat panels (preferred) or come as panel a. If included as a separate panel, the y-axis scale should be the same as the other other two taxon-specific panels.
Experimental design: This research is original and within the aims and scope of the journal. The research questions are well defined, although I think the order and focus should be shifted (see general comments to author). Stable isotope and statistical methods are described in sufficient detail.Appropriate inferences are drawn from the data, but I feel the authors have been a little too conservative in discussing their findings.
Validity of the findings: All data are presented in either raw or summarized forms. The design is robust and appropriate controls exists within the authors' field experiment. Conclusions are mostly well-stated, but data need to be interpreted more completely in the Discussion. The authors tend to restate hypotheses and results in the Discussion and only draw limited and conservative inferences from their work.
Additional comments: The Moyo et al. study is well-designed with a sound approach. It fits well within the scope of PeerJ and is likely to be well-cited once published. The paper is generally well-written, with only a few minor grammatical or punctuation errors, and the authors do not attempt to draw inferences beyond their data. I do think some restructuring of the manuscript prior to publication will improve its readability and make it more impactful. Part of that involves the tail end of the introduction and the remaining reorganization suggestions are for the discussion. I detail these more substantive suggested changes below, followed by a list of more minor suggested edits.

The introduction focuses on the usage of indicator species to examine anthropogenic stressors and then moves into the specific utilization of seaside sparrows and rice rats as indicator species of Deepwater Horizon Oil Spill (DWH) impacts on Louisiana (LA) marsh food webs. However, the authors actually do not explicitly state that is how they are employing their two study species; they leave out a much needed statement about food webs. I feel they should also state that in the case of many anthropogenic stressors researchers often focus on direct acute affects versus more indirect chronic effects. Their study is an excellent example of the latter. If they stated that more explicitly I think it would allow them to more easily draw inference from their data in the discussion.

Another area of the introduction that I feel needs some attention is the statement of hypotheses. As written, they are a mix of null hypotheses and predictions. To avoid that confusion, why not just state the objectives of the study? Toward that end, I would start with the first objective being to estimate d13C and d15N for basal endmembers and primary consumers. The second objective would be to estimate species-specific trophic position and isotopic niche width for seaside sparrows and rice rats from unoiled (control) sites. The final objective would be to test for differences in basal endmembers as well as between seaside sparrows and rice rats, between control and oiled sites. I would focus less on the idea that these two species likely interact trophically, but instead focus on their roles as common, generalist mesopredators in the LA marsh ecosystem which makes them ideal model species to examine indirect chronic effects of the DWH on LA marsh food webs. And by stating the approach via objectives, it removes the need or tendency to repeat the hypotheses in the discussion, or list them parenthetically in the results.

One reason to suggest the first objective was to examine differences in basal endmembers and primary consumers between terrestrial and aquatic habitats, as well as between control and oiled sites (which are the preferred terms versus oiled and unoiled), is because those data are what the entire study hinges upon. The authors should be commended for conducting that sampling as too often authors attempt to borrow literature values instead of conducting contemporary sampling. It is actually unclear whether basal endmembers and primary consumers were sampled at each site. If both were sampled as suspected, then and the data for controlled and oiled sites are combined in the biplot in Fig S1C. I suggest this figure be moved to the main body of the manuscript and appear as Fig 2, just after the map figure. If they exist, the data for control versus oiled sites should be displayed separately, either as Panel A of that figure or overlain on the sparrow or rat panels. One reason to display control and oiled sites separately is that if petrocarbon from DWH was assimilated into the marsh food web at oiled sites, then the d13C signature should be depleted. Regardless, differences in d13C and d15N should be tested with ANOVA between control and oiled sites to determine whether significant differences existed in basal endmembers or primary consumers.

Different terminology is utilized throughout the intro, methods, and discussion to refer to trophic niche or isotopic niche. Mostly, the term “foraging niche” is utilized, but this is a misnomer. Elsewhere, “trophic niche” or “foraging trophic niche” are utilized, but the preferred term is “trophic niche.” When the SEA or isotope data are being utilized to draw inference about the trophic niches of the two model species, then “isotopic niche” should be utilized, which should be stated is a proxy for trophic niche based on d13C and d15N data.

One bit of information that is not included in the results is the size range of sparrows and rats. Did the authors test for effects of animal size on d13C or d15N values? Ontogenetic shifts in diet often can add a source of error that should be accounted for. This can be accomplished by detrending the data or adding animal size as a covariate in statistical analyses.

In the discussion, there is too much restatement of hypotheses from the intro and too much restatement of results. Instead, the authors should focus on the inferences from the significant findings of their study. They demonstrated significant differences in trophic position, isotopic niche breath, and even trophic overlap between species between control and oiled sites. Instead of focusing on the caveats associated with those findings, I would focus on the remarkability of persistent food web effects despite the time since the spill, weathering of oil, and other factors that add considerable process error to the system. Furthermore, there are interesting patterns in there data that suggest shifts to more generalism even 5-7 years after the DWH in their study species. While there is touched upon in the discussion, very little ecological theory is discussed as to why this may be an important indication of food web effects. The authors state that their sparrows and rats are being utilized as indicator species, but they do not do much in the form of stating what they are actually indicating.

Other authors have reported persistent food web effects of the DWH in different habitats or systems than the marsh, but the Moyo et al. do not cite or discuss that literature, which hurts the discussion. Lastly, I would return to the theme of acute direct versus chronic indirect of the spill. Their study nicely demonstrates the potential for the latter in the LA marsh food web, but they fail to mention or discuss that.

Minor comments:
line 32: “species-specific” is redundant with niche

lines 35-38: This is written as if it was the main objective of the study, but the paper does not support that as written.

line 43: “though” should be replaced with “although” throughout.

line 54: Should be Deepwater Horizon Oil Spill (DWH) here, then DWH thereafter, with Deepwater Horizon italicized.

lines 55-56: “which lasted for several months” appears twice

line 61: What is meant by “penetrated deep into the marsh?” What dimension is being referred to here and what is meant by deep?

lines 62-65: Subordinate clause (about oiling) does not match the main clause here (about general contaminant effects).

line 68: Are these animals truly ubiquitous, or just common in these habitats?

line 69: For example indicates this refers to the previous statement, but here that is not true.

line 80: I am not sure what a life history ecology is. Do you mean feeding ecology and life history?

line 81: This is the first time you have used trophic versus foraging niches. Trophic is more accurate and should be utilized throughout.

line 83: What about morphology and physiology? There are intrinsic factors that are overlooked here.

line 115: See comment about line 83 text. Here other factors are mentioned.

line 118: Should be hypothesized, past tense, but I think it would be better to phrase these as study objectives instead of hypotheses.

line 137: (Cooney et al. 2015)

line 142-143: …were sampled on private or public land…

line 152: …2015, 2016, and 2017…

line 152: The saltmarsh in this area is either dominated by smooth cordgrass, Spartina alterniflora, or co-dominated by smooth cordgrass and black needlerush, Juncus roemerianus.

line 162: Sites not Site

line 167: Need to indicate mean (+/- dispersion measure) here for PAH values.

line 233: represented BY the…

line 233: encompassing approximately 40%...

line 251: Need to present basal endmember and primary consumer data first.

line 252: Trophic position not positions

line 269: Why add the word “previously” here?

line 269: It is unclear what tables S1-S3 are actually showing because they lack captions.

line 275: isotopic niche instead of isotopic foraging niche

lines 276-280: Strike second and fourth sentences of this paragraph.

line 291: No overlap measure provided in the table for this first set of CIs.

lines 296-297: … the feeding ecology of terrestrial omnivores IS often flexible and dependent…

line 312: Not consistent; half a trophic position lower. Why? Were the same tissues analyzed in both studies? Where same TDFs used in both studies? Did basal endmember values differ?

lines 318-320: Run-on sentence

line 334: glean food?

lines 340-341: This suggests trophic niches are not fully segregated between these species despite observed differences in trophic position and resource use (alpha).

lines 342 and 343: marsh not march

line 365-366. Post-spill declines in the abundance of terrestrial invertebrates, such as insects and spiders, also were reported for Louisiana marshes after DWH.

lines 383-385: See comment above for lines 340-341.


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: STABLE ISOTOPE ANALYSES IDENTIFY TROPHIC NICHE PARTITIONING BETWEEN SYMPATRIC TERRESTRIAL VERTEBRATES IN COASTAL SALTMARSHES WITH DIFFERING OILING HISTORIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The writing in this paper meets these criteria.   I noted only a couple of little problems, below.  Literature is cited correctly and the paper directly addresses specific hypotheses.
Experimental design: Research is well designed and appropriately sampled.  Statistical tests are appropriate.
Validity of the findings: Experimental data are well analyzed and significance of the results is well tested, documented and explained.
Additional comments: Clear hypotheses are articulated and I like the way the results and discussions sections are organized to address each one.

Lines 296-297--  In coastal marsh ecosystems, the feeding ecology of terrestrial omnivores are often flexible and are dependent on environmental conditions (Ruiter, Wolters & Moore, 2005).   Relative to what other environments?

Discusion line 354-357.  Interesting that the consumption of terrestrial resouces in oils sites was due to less abuncance of aqutic prey items even 5 years after the oil spill.  Is this in the abstract?   Seem important.

Repeated phrase lines 54-57.   Specifically, the Deepwater Horizon disaster, which lasted for several months, was the largest (> 700 000 m3 of crude oil) marine oil
 spill in the history of the United States of America, which lasted for several months (Crone &
57 Tolstoy, 2010).


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: STABLE ISOTOPE ANALYSES IDENTIFY TROPHIC NICHE PARTITIONING BETWEEN SYMPATRIC TERRESTRIAL VERTEBRATES IN COASTAL SALTMARSHES WITH DIFFERING OILING HISTORIES
Review round: 1
Reviewer: 3

Output:
Basic reporting: I found parts of the manusript confusingly worded and at times had a hard time sorting out the authors’ intention.  I also think that the manuscript would be greatly improved by adding some basic background on the sites and the two species targeted.
Experimental design: The authors provided insufficient detail on the study sites and how similar or different the individual sites were, both within and between years.  A critical step was to combine all of the oiled and all of the unoiled sites, but no justification was provided other than the need to increase sample size.  At the least, some assessment of differences among sites should be provided.
Validity of the findings: I had a hard time seeing some of the patterns described.  That’s not to say that the findings are incorrect, but at the least the figures and text need to be reworked to provide a clear and consistent scientific message.
Additional comments: This is an interesting set of isotopic measurements intended to help shed light on the impact of oil deposition on marsh foodwebs.  Unfortunately, I found many parts of the manuscript and its figures difficult to follow and was frustrated by having to parse the text and figures carefully to try to figure out the authors’ message.  This manuscript does have promise, but I recommend a thorough revision of the text and figures, and addition of some critical contextual information on the populations and communities studied.

A number of more specific comments and suggestions follow.

Abstract, lines 42-43:  This sentence is an example of the sort of imprecision I struggled with.  Should this sentence be read to mean that sparrows from unoiled sites had wider niches than rats collected from unoiled sites (ignoring the animals from oiled sites) or that sparrows from all sites had wider niches than rats from the unoiled sites.  As written, the sentence can be read either way, leaving the reader to puzzle out the meaning.  The next sentence does imply that the first reading is the correct one, but many readers will come to that only after spending time and energy trying to sort out the meaning of the earlier sentence.

Lines 67-69:  A few words about the life history of the sparrows and rats would help.  Do they have similar life spans?  Do they mature at similar rates?

Lines 75-76:  Did oiling alter sparrow and rat abundance along with the abundances of their potential prey?  If so, how do you distinguish between impacts of intra- and inter-specific competition?

Line 80:  Indeed!  A bit more background on the life histories of the two species would be very helpful here.

Lines 124-125:  I found this sentence very confusing!  The absolute overlap of species A’s niche with that of species B has to be equivalent to the overlap of species B’s niche with that of species A.  What actually matters, and what the authors are after here, is the degree of niche overlap relative to a species’ overall niche.  That is, it’s the relative, not absolute overlap that matters, but that subtlety is missing here.

Lines 130-140:  A couple of sentences on the life histories and populations of the two species would be helpful here.  What is their typical life span?  Were the animals sampled in 2017 descendants of the ones sampled in 2015, or part of the same cohort?  All of these details are important context for discussing the trophic ecology of these animals.

Lines 164-165:  I can’t sort out the dimensions of the plot given this description. The bit in parentheses is particularly cryptic.

Lines 169-171:  What about the animals?  Are they long-lived enough that the animals sampled for this study may have also been present in 2010?

Lines 173-174:  Many more details are needed here.  For example, were collections carried out at the same time of year in all years?  Were the animals collected all of similar size?  Were the size/mass of the animals measured?  Were the animals sacrificed after sampling or released?

Line 198:  The equation is missing a factor of 1000

Lines 210-213:  Did you first test for differences among sites?  I realize that sample numbers may have been low in some cases, but this should be done before lumping data in this way.

Lines 244-247:  This definition makes sense and should have been presented earlier to avoid the confusion I noted above (lines 124-125).

Line 262:  I don’t see this at all.  If anything, 2015 looks like the outlier, with what look like appreeciably higher alpha values than in 2016 and 2017.  In any case, it’s hard to make this comparison visually given the layout and the visual confusion created by the asterisks, which have nothing to do with this comparison.  See below for other comments on Figure 2.

Lines 285-287:  This should be evident in Fig 3, but only 2015 shows the asymmetric overlap described in the text.  In fact, there’s minimal if any overlap between the species’ isotopically defined niches in 2016 and 2017.  This deserves a bit more description and explanation.

Lines 287-293:  It’s interesting that there appears to be no niche overlap at all in 2016;  this seems interesting and relevant and should be noted.

Lines 309-310:  This statement is a bit misleading since the two spp. differed significantly between oiled sites in 2015.  In other words, only one of the six comparisons (2015, unoiled sites) showed no significant difference in trophic position.

Line 320:  Fig. 2, not Fig. 3 is the relevant one here.

Lines 338-340:  As noted above, this isn’t evident in Fig. 3, where two of the three years show minimal if any niche overlap (2016 and 2017) at unoiled sites.

Lines 342-346:  What about the role or intraspecific competition in this system?  Did the population density of either species vary between years?   For that matter, did food abundance vary between years?

Lines 377-380:  These are factors that really should have been addressed earlier!  I was curious about differences among sites when I saw that they had been grouped simply by oiling history (see above re: lines 210-213), and I’m now left to wonder how similar the different sites actually were.  At the least, some assessment of the community, and the population densities of the two target species and their likely food sources would be helpful.

Figure 2:  Why the modal value?  There may well be a good reason for this, but wouldn’t it make more sense to show the mean or median value?  I’m also puzzled by the choice of modal value for a continuous variable;  were the data binned in some way?

Figure 2:  The asterisks mark cases where the two species differ significantly within a habitat, but the figure is also used to discuss differences between years within a habitat (e.g., Line 262).  This makes for a confusing figure that forces the reader to parse the data for him/herself.  I strongly recommend exploring clearer ways to present the data graphically.

Figure 2:  The sparrow and rat symbols should be offset (jiggled) slightly so that the error bars can be clearly distinguished.  As presented, it’s hard to tell which bars go with which symbols.

Figure 3:  The numeric labels are far too small for legibility, and the d13C label on the horizontal axis really should be closer to the horizontal axis of panel C.

============End of Review====================


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: STABLE ISOTOPE ANALYSES IDENTIFY TROPHIC NICHE PARTITIONING BETWEEN SYMPATRIC TERRESTRIAL VERTEBRATES IN COASTAL SALTMARSHES WITH DIFFERING OILING HISTORIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have revised the paper following reviewer guidance and in my opinion the paper is acceptable for publication.
Experimental design: The authors have revised the paper following reviewer guidance and in my opinion the paper is acceptable for publication.
Validity of the findings: The authors have revised the paper following reviewer guidance and in my opinion the paper is acceptable for publication.
Additional comments: The authors have revised the paper following reviewer guidance and in my opinion the paper is acceptable for publication.


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

Input:
Title: STABLE ISOTOPE ANALYSES IDENTIFY TROPHIC NICHE PARTITIONING BETWEEN SYMPATRIC TERRESTRIAL VERTEBRATES IN COASTAL SALTMARSHES WITH DIFFERING OILING HISTORIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: This revised version is well written and much clearer than the original submission.
Experimental design: The authors have added detail on the study sites and have successfully reworked the text for clarity.
Validity of the findings: The revised figures and manuscript organization address my earlier concerns with the original submission.
Additional comments: This is an interesting set of isotopic measurements intended to help shed light on the impact of oil deposition on marsh foodwebs.  This revision addresses the concerns I had with the original submission.  I have only minor comments and suggestions for the authors:

Lines 225-227:  how was the POM removed from the filters?  Since particles are trapped in the filter matrix as well as on the filter surface, it’s common to simply combust the filter rather than trying to remove material from it.

Lines 372-381:  Did the absolute isotope values differ between studies, or was this contrast arise strictly in the calculation of TP?

Figure 2:  It would be easier to compare between oiled and unoiled sites visually if unfilled versions the same symbols (square, circle, triangle) were used (colored blue, of course).

============End of Review====================


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: DAIRY MANAGEMENT PRACTICES ASSOCIATED WITH MULTI-DRUG RESISTANT FECAL COMMENSALS AND SALMONELLA IN CULL COWS: A MACHINE LEARNING APPROACH
Review round: 1
Reviewer: 1

Output:
Basic reporting: Thank you for the opportunity to read this paper. I found it interesting, well written and relevant. The background content, references and cited literature appear to be sufficient. I have a number of comments / suggestions regarding the presentation of the data and reporting of data which i address in the general comments. The results presented are relevant to the proposed hypotheses in the paper.

There is a problem in the reporting of data and significant digits, how the graphs are presented, and such throughout the paper. These are discussed later below. I encourage the authors to be mindful of every number typed/presented in the paper and their associated error reported to ensure their reporting is consistent not only from a ‘significant figures’ perspective, but meaningful. It does not, for example make sense to report tens of cows to 4 significant figures.

I also have some challenges with some of the figures presented in this submission. While I appreciate the importance of the decision tree figure(s) in the submission, much of the presentation should be compressed and more easy to read. As is, it is very difficult to absorb and will likely detract some readers, which would be unfortunate since it is very rich in data and valuable. Details are provided further below.
Experimental design: The paper straddles both data science techniques and practical questions related to dairy sciences. It does, however, raise the challenge in the extent of expertise needed to understand the submission if readers are unfamiliar with either dairy sciences or machine learning. I commend the authors attempts in trying to bridge this gap.

The research conducted on exploring the need to understand the relationships between herd metrics and bacteria is important and this research meets an unmet need in further uncovering the relationships between culled cattle and these 3 important strains. The methods in the paper were sufficiently described such that the result could be replicated, however, the authors have not made their code available for testing / review on public platforms (eg., GitHub). While it is understandable that the data itself may not be sharable, the primary codes/routines could be easily shared and I would encourage the authors to do so.
Validity of the findings: The findings in the paper appear to make sense and the discussion/conclusions drawn from them are largely reasonable. There are a few exceptions to this noted below.
Additional comments: General Comments to Author

I provide a line-by-line assessment of this paper.

Title: consider a colon instead of a comma before ‘machine learning’.

Abstract:
L54: “In contrast, …” this sentence could be written more clearly. Also, the phrase “may reflect economic decisions…” needs to be used carefully. We do not know what motivates farmers to cull. This reason (economic) may be just one of several.

Introduction:
L66: “… a serious threat…” authors should consider adding what that threat actually is for readers unfamiliar with this problem/challenge.
L75: .. 31.X% should be used if using a CI of 26.0-35.0 (specify the value X).

Materials & Methods
L161: I don’t believe MIC was defined yet.
L190-193: It is not clear to me that there are two classifications defined here, which makes the “Fifth” classification defined in the following sentence unclear. It would be helpful to write out the 2 specific classifications.
L216: it would be helpful to know the grid search algorithm used here. It *could* be confused with a manual grid search.
L228: Consider the precise use of ‘Gini Impurity’ to completely avoid possible confusion for readers unfamiliar with this metric.

Results
L239: Here is an example of inconsistent sig figs. (24% +/- 2.81, should be 24.X % +/- 2.8). I encourage the authors to be mindful of significant figures and their reporting throughout the entire text. For example, L 242 reports 31.09% +/- 3.00 but I highly doubt one can be accurate to within 3 sig figs in the error here. Same challenges in L265 onwards.

L296: It would be helpful fo the reader to know if values of 0.47 to 0.74 (and their precision) are acceptable or unacceptable ranges of sensitivity in this (diary science) context. In some medical fields 0.7 would be considered ‘poor’ whereas in other areas they might be considered ‘fair’.

L304: insert “Gini”
L308: It may be helpful to have defined entropy score previously in the methods section along with the Gini impurity.

L393: Sentence requires “The” (or something else before “Algorithms”)
L412: This sentence could be controversial and it may be wise to state that culling due to economic factors is perhaps but one of multiple reasons for culling.

Conclusions: no comments

References: appear to be in order

Figures
Figure1: Caption and Figure – no comments
Figure 2: This figure is important and it would be in the authors best interest to make this as easy as possible to digest. Some suggestions include color coding instead of text to define class, use heat-map instead of reporting actual Gini, replace ‘No resistance’ with “NR”, use ‘n’ instead of ‘samples’, and use the same size box if possible. Also, there are some issues with sig.figs (eg., why is Gini 0.64 in one box and 0.798 in another?).

Figure3: again, sig figs for values should be consistent.

Figure 4: no comments.

Figure 5: I am not sure it is necessarily to provide 10 plots here, and I think it may be more instructive to see these sensitivities in relations to other features. It should be possible to, for example, provide multiple plots on a single axes since values/ranges in y are comparable for many investigated.

Figure 6 and 7: no comments

Tables:
Table 1: no comments, nice work!
Remaining tables – no. comments


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

Input:
Title: DAIRY MANAGEMENT PRACTICES ASSOCIATED WITH MULTI-DRUG RESISTANT FECAL COMMENSALS AND SALMONELLA IN CULL COWS: A MACHINE LEARNING APPROACH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript was wrote with an acceptable english. The literature references and the introduction is clear to understand the manuscript. The figure  and table was sufficient to understand the result in the manuscript.
Experimental design: I consider that method used was sufficient to complete aims of the manuscript.
Validity of the findings: no comment
Additional comments: The manuscript describe the association of herd management practices and antimicrobial resistance phenotype of Salmonella, E. coli and Enterococcus isolates from cows (fecal samples). The results and the methods used in the paper are clear. I consider that the paper is very interesting.


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: DAIRY MANAGEMENT PRACTICES ASSOCIATED WITH MULTI-DRUG RESISTANT FECAL COMMENSALS AND SALMONELLA IN CULL COWS: A MACHINE LEARNING APPROACH
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1)The greatest strength of this article is the clear description of the 3 decision tree algorithms, and its application in classifying/ranking the herd and individual cow features to explain the shedding of multi/antimicrobial drug resistance organisms from cull cows, a potential transmission risk to humans.
2)The language used is crisp and clear to me. Various methodologies - the data collection using surveys – fecal sample collection - antimicrobial resistance profiling - machine learning techniques used, are explained appropriately. Readers in our field should be able to grasp the key findings from the neatly organized figures and tables, provided they grasp the tree classification methodologies used. Introduction, background, and references used are appropriate.
Experimental design: 1)Sub-sections a) farm surveys and sampling, bacteriological culture, and antimicrobial susceptibility testing are described with appropriate details, to ensure the repeatability of the experiments.
2)Having 5 different classifications for drug resistance is appropriate to discern both herd and individual cow level features contributing to MDR/AMR/No resistance.
3)Hyper-tuning (grid-search) ensuring the selection of appropriate criteria. Influential metrics like gini, SHAP are discussed in sufficient detail and can be easily perceived by the reader.
4)All the relevant features pertaining to decision tree, random forest and gradient boosting have been harnessed meticulously, in describing the plausible herd management and individual cow factors affecting MDR organism’s shedding.
Validity of the findings: 1)I think the authors should discuss the reasons (even though it is conjecture) why high rolling herd average milk production is the number one feature explaining MDR, when decision tree is used. I would think that higher rolling herd averages are associated with larger herd sizes, which indeed provide an opportunity for resistant bacteria to spread profusely. Do you agree, else provide a reason for this.
2)Similarly higher culling %, culling frequency will naturally group those herds as high risk herds for MDR bacterial shedding. Higher the culling %  higher the probability to find MDR. Discuss how this will be helpful in formulating policies for the data-informed risk assessment tool you talk about in conclusion.
3)It is counter-intuitive to me, when you say that number culled per day is negatively associated with MDR shedding, while culled % is positively associated. Isn’t number culled per day used to calculate culling % on a farm. Help me out here. So what is your suggestion to farms with regards to culling policy and MDR risk profiling? Cull lesser % of herd?
Additional comments: 1)Consider shortening the title of the manuscript. Do you need to mention the fecal samples were collected from cull dairy cows?
2)Lines 72 to 75. What is a probable explanation for the 10 fold increase in Salmonella shedding prevalence between Abu Aboud et al. 2016 (3.42%) & Pereira et al. 2019 (31%)?
3)Introduction is concise and to the point. Good job.
4)Line 126. Introduce your abbreviation for extra-label drug use (ELDU), here.
5)Line 208-210. So models RF and GB prevented overfitting (limitation of DTC), isn’t it?
6)Line 307. Which tables represent the trees generated by all the 5 models?
7)Line 321. Did you mean collectively instead of separately? Figure 3 description from “.. cal” is missing.
8)Line 328-330 – Chalk method seems to be relevant feature in Salmonella too?
9)Legends for figures 5 and 7 should be larger
10)What is the standard error for the partial dependence features shown in figures 5 and 7? Will it be affected by the number of herds (6) included in your study?


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

Input:
Title: DAIRY MANAGEMENT PRACTICES ASSOCIATED WITH MULTI-DRUG RESISTANT FECAL COMMENSALS AND SALMONELLA IN CULL COWS: A MACHINE LEARNING APPROACH
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thank you for the opportunity to read this resubmitted paper.

- The resubmission reads well, literature cited appears up to date, the structure of the paper is appropriate.
- I commend the authors for publishing their scripts for other investigators to explore, validate and test
- I commend the authors for addressing challenges with the figures. Figure 2 is much improved, but also contains a lot of ‘dead space’ between figures and the font is very small and difficult to read. I would strongly recommend the authors obtain professional support for this figure
- There remains still some challenges with presenting numerical values, such as in line 270 onwards. Can the authors confidently state errors can be reported to within 4 significant figures, eg. 50.00% ±11.18 ? Most likely errors are no more precise than 2 sig. figs. L281 reports 42.3%±9.68 which is simply wrong. I strongly recommend the authors refer to guidelines such as the ISO GUM, AIP data representation standards for reporting numerical results, or another reference and very carefully review every number presented in their findings.
Experimental design: - There are no concerns on the experimental design. Nice work!
Validity of the findings: - There are no concerns on the validity and impact of these findings. It is a nice paper and will have value in the community.
Additional comments: I provide a line-by-line response
L35: consider using a dash (-) or bracket to separate ‘machine learning algoriths’ from the 3 types you investigate
L91: Random Forest is capitalized here and not elsewhere. Would be good to be consistent.
L392: consider replacing ‘if’ with ‘whether’ and pluralizing ‘reveal’
L394: sentence is awkward with comma after Athough. Consider re-writing.
L399: Consider replacing “Machine learning algorithms” with ‘The three machine learning algorithms tested in this study”
L410: “milk”? production?
L414: An increased percent cull and rate would reflect…?
L416: Consider inserting “total” number culled.
L419: needs a period to close sentence.
L423: Please rewrite/edit the sentence more clearly.
L430: Please rewrite/edit this sentence more clearly.


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: DAIRY MANAGEMENT PRACTICES ASSOCIATED WITH MULTI-DRUG RESISTANT FECAL COMMENSALS AND SALMONELLA IN CULL COWS: A MACHINE LEARNING APPROACH
Review round: 2
Reviewer: 2

Output:
Basic reporting: Not Applicable
Experimental design: Not Applicable
Validity of the findings: Not Applicable
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: VERTICAL ESCAPE TACTICS AND MOVEMENT POTENTIAL OF ORTHOCONIC CEPHALOPODS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is part of a series of groundbreaking papers recently published by the first author and cooperators about mode of life and the functionality of the shell architecture of ectocochleate cephalopods. The research question, followed in the manuscript, is what, if at all, is the adaptive value of the orthocone cephalopod shell. Repeated, independent re-evolution of this shell form suggests an adaptive value. The method, how this hypothesis is answered combines traditional ideas, namely the reconstruction of a physical shell model, with up-to date computational methods and statistical tests. In combination these methods give surprising results and new insights.
The original idea of an advantage of orthoconic cephalopods by rapid vertical escape from pelagic predators, which in contrast often have a mode of life optimized for rapid horizontal hunting is compelling and the authors support their hypothesis with a robust set of data. Also, the results clearly support the hypothesis that orthococonic shells give an advantage for low-cost vertical movement.
All underlying data supporting their hypothesis and have been provided in detail (including raw data) by and statistical error margins are well documented.
The conclusions are well stated and the manuscript, generally is written in a clear language without redundancy and unnecessary detail. The figures are clear, relevant and of high quality. The figure captures are easily readable.
I have only one very minor suggestion:
Baird et al (1989) described syn-vivo epizoans on Palaeozoic orthocones. The growth directions of the bryozoans, described therein could be used to support the arguments of the authors (Baird, G. C., Brett, C. E., & Frey, R. C. (1989). Hitchhiking epizoans on orthoconic cephalopods: preliminary review of the evidence and its implications. Senckenbergiana lethaea, 69(5-6), 439-465.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: At line 324 "However, this is .." it is not clear what the "this" refers to.


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: VERTICAL ESCAPE TACTICS AND MOVEMENT POTENTIAL OF ORTHOCONIC CEPHALOPODS
Review round: 1
Reviewer: 2

Output:
Basic reporting: First, I want to congratulate the authors for this very interesting article. The manuscript is well written and presents an innovative approach. I am looking forward to it being published. During the revision, I came across some issues which need to be addressed.

Some of the references could be expanded. In particular, some additional references for nautiloid cephalopods should be cited apart from the Treatise and Kröger, Servais & Zhang 2009. In addition, some important literature on hydrostatics and locomotion of orthoconic cephalopods is missing and should at least be cited somewhere or discussed. Some suggestions:

Schmidt 1930, Über die Bewegungsweise der Schalencephalopoden. Paläontologische Zeitschrift 12, 194–208 [in German].
Teichert 1933, Der Bau der actinoceroiden Cephalopoden. Palaeontographica, Abt. A 78, 111–230 [in German].
Flower 1955, Cameral deposits in orthoconic nautiloids. Geological Magazine 92, 89–103.
Crick 1988, Buoyancy regulation and macroevolution in nautiloid cephalopods. Senckenbergiana lethaea 69, 13–42.
Chamberlain 1993, Locomotion in ancient seas: constraint and opportunity in cephalopod adaptive design. Geobios 15, 49–61.

Further literature suggestions in the relevant comments below.
Experimental design: The manuscript presents an innovative approach for testing hypotheses on the mode of life of orthoconic cephalopods. Orthocones are highly abundant in some localities during the Palaeozoic and the same morphotype reappeared during the Mesozoic in heteromorph ammonites. Thus, identifying the locomotory constraints of orthocones is important for our understanding of these past ecosystems. However, this is complicated by a lack of modern analogues, and hence, their swimming capabilities and ecological roles are poorly understood. This manuscript therefore offers a refreshing new perspective on this topic, including new tools to test hypotheses.

I have nothing to add to the experiments themselves, except that you may need to explain better the rationale behind testing a sinking model, since this would not be relevant for the vertical escape hypothesis. I understand why you did it, but I still cannot quite see the connection of this part of the results to the conclusions. What alternative results could have been expected other than slowly accelerating sinking in a stable position? Would have different results changed your conclusions in any way? If not, why do it in the first place?

Perhaps it would be great to upload part of the video footage somewhere and link it in the article?

I also want to add some thoughts, which you may incorporate into the manuscript, use them as inspiration for future studies, or simply discard them. I am not sure if further experiments are feasible, they may be out of scope for the current study. Right now, you tested three models with considerable positive buoyancy and one model with only very slight negative buoyancy. From these experiments, I find it difficult to interpret whether orthocones were better adapted to upwards or downwards movement. If vertical escape tactics were one of the primary drivers for orthoconic conch shapes, then I would expect the shell to be optimized for rapid upward movement. However, if downward movement is more stable, then I would expect that escape tactics are only a secondary advantage. You mention that downward movement would be difficult because of the position of the hyponome. However, you already suggested active buoyancy regulation in ammonites (Peterman et al. 2021), and it has also been proposed in various nautiloid groups with orthoconic conchs and very large siphuncles (e.g., actinocerids and endocerids, see Kröger 2003, The size of the siphuncle in cephalopod evolution, Senckenbergiana lethaea 83, 39–52). Thus, they were maybe able to achieve higher degrees of negative buoyancy and consequently, higher accelerations in downward direction? Obviously, this depends on the rates of chamber filling, which is another issue. One could test whether orthocones are better adapted to downward or upward movement, perhaps at different speeds. Intuitively, I would say downward is more optimal, though it may depend on the shape of the soft body and would thus be difficult to test. What is also not tested (for obvious reasons I suppose) is sinking or rising at slow but constant speed, as the animals may have used small bursts of the hyponome as a brake in either direction. This may be out of scope for the current article, but perhaps provides some ideas for future studies!
Validity of the findings: I am not sure if vertical escape movements were the main drivers for the evolution of orthoconic conch shapes, though you make a compelling case that this was at least possible. It appears to me that vertical escape movements would only work in a completely straight conch, but how would evolution go from a tightly coiled to a straight conch then? Either there would be a direct “switch” between coiled and orthoconic (which seems unlikely to me), or successive evolutionary stages of uncoiling, but those cyrtoconic intermediate stages probably could not employ vertical escape tactics, so there must be another evolutionary advantage. In addition, many orthocones are not completely straight, but at least slightly curved, though often this is only visible in very long fragments. Would these curved conchs not impede vertical escape tactics? Perhaps feeding strategies were more important, e.g., filter feeders moving up and down or pouncing on benthic prey as you mention already. In any case, orthocones show such a diversity in external and internal structures during the Palaeozoic, that they must have played different ecological roles (also indicated by their facies distributions). Thus, my recommendation is that you discuss in more detail other advantages of an energy efficient vertical movement capability in orthocones. Perhaps make it clear that vertical escape tactics were likely not the only evolutionary reason for orthoconic conchs, but you show that despite the seemingly clumsy and awkward vertical orientation (this seems to be one of the main reasons why older publications categorically excluded this possibility!), they were not as slow or unmaneuverable as one would think. Furthermore, I recommend that you point out more clearly at the beginning that you are only testing a very specific conch shape, namely a slender smooth orthocone with a compressed cross section and without counterweight. Especially the part with the compressed cross section should be mentioned somewhere, as at least to me – being relatively unfamiliar with Baculites – it was not clear at the beginning and I had to look it up. There are so many other shell characteristics that may have an influence, such as cross section shape, expansion rate, annulations, ribs, longitudinal ornament, apertural modifications, conch curvature, mass distribution (i.e., deposits), etc. Perhaps you could try to assess the potential impact of these characters on your conclusions, thus allowing for a more differentiated picture, which of your findings can likely be generalized for most orthocones and which cannot. Obviously, testing all this with additional experiments would be out of scope of your study. Nevertheless, this is a great first step, opening up new opportunities to identify the influence of these traits on hydrodynamics of orthocones and our understanding of the palaeoecological role of this morphotype!
Additional comments: Multiple times throughout the manuscript, you state that the orientation of orthocones was vertical or near vertical, citing Peterman et al. (2019). While I liked the latter article a lot, I do not think that it can be concluded from this alone that all orthocones had vertical orientations. For example, you assume a very long body chamber of at least 33% in your other paper, but from my experience, many (at least Palaeozoic) orthocones have shorter body chambers (e.g., the endocerid Anthoceras vaginatum has an estimated body chamber length between 16% to 20% of the total conch length, see Kröger 2012, The “Vaginaten”: the dominant cephalopods of the Baltoscandian Mid Ordovician endocerid limestone, GFF 134, 115–132). Shorter body chambers would allow more apical chambers to be filled with cameral or endosiphuncular deposits, potentially adding enough ballast for a horizontal orientation. A hypothetical vertical orientation would also make it impossible for endocerids to empty their chambers, because they have extremely long septal necks (thus, they could not accumulate enough gas in the phragmocone to become buoyant, unless they had a different mode of chamber formation than Nautilus). In most endocerid species, the siphuncle touches the ventral shell wall, and thus, a horizontal orientation would conveniently allow for complete chamber emptying. Anyway, I just wanted to highlight that we cannot rule out horizontal modes of life for at least some orthocones. You mention already colour markings and cameral/endosiphuncular deposits, but you need to be careful that you do not contradict yourselves: Sometimes you mention possible horizontal alternative orientations, but on other occasions you appear to suggest that significant deviations from a vertical position were not possible at all. Therefore, I propose that you try to be more consistent on this issue. For example, you could mention potential horizontal orientations already in the introduction when talking about orientation first. Then, you could make it clear that you refer to vertical (unballasted?) orthocones during the remainder of the text.

Further minor comments:

Title and elsewhere: The term “orthocone” is a noun, while “orthoconic” is the corresponding adjective (see Flower 1964 or Treatise). Hence, I suggest using either “orthoconic cephalopods” or “orthocones”, depending on context. For the title, the former would be appropriate. Please check throughout the manuscript.

Line 50: To a reader unfamiliar with cephalopods, it may appear as if a tightly coiled conch evolved only during the Devonian – however, this happened multiple times as well: Tarphycerida in the Early Ordovician (e.g., Teichert et al. 1964), independently the Uranoceratidae in the late Ordovician (Kröger 2013: The cephalopods of the Boda Limestone, Late Ordovician, of Dalarna, Sweden, European Journal of Taxonomy 41, 1–110), the Lituitida in the Middle Ordovician (particularly Cyclolituites, Sweet 1958, The Middle Ordovician of the Oslo region, Norway, Norsk Geologisk Tidsskrift 38, 1–178; note that the group is now thought to be derived from the Orthocerida rather than the Tarphycerida), Hercoceratidae in the Early Devonian (Turek 2007, Systematic position and variability of the Devonian nautiloids Hercoceras and Ptenoceras from the Prague Basin (Czech Republic), Bulletin of Geosciences 82, 1–10) and of course the Nautilida in the Devonian (or Silurian?), which may originated from one of the above groups or independently from somewhere within the Orthocerida (Kröger, Vinther & Fuchs 2011). Thus, orthoconic and coiled forms coexisted essentially continuously starting from the Early Ordovician, but probably occupied different habitats and ecological roles.

Line 97: This is not so clear - earlier publications have also seen them as bottom dwellers (e.g., Teichert 1967, Major features of cephalopod evolution. University of Kansas Department of Geology, Special Publication 2, 162–210) or active swimmers (e.g., Holland 1987, The nautiloid cephalopods: a strange success, Journal of the Geological Society, London 144, 1–15). One recent publication interpreted endocerids as pelagic suspension feeders (Mironenko 2020, Endocerids: suspension feeding nautiloids?, Historical Biology 32, 281–289), although the latter results are somewhat speculative. In general, the mode of life of orthoconic cephalopods is poorly understood and palaeobiological studies are lacking. It seems likely that different lifestyles existed - this is also indicated by the diverse siphuncular structures found in Palaeozoic orthocones.

Line 246: I suggest you use meters instead of foot to describe the depth of the pool.

Line 376: Conch curvature could also be added to this list, for very slightly cyrtoconic forms.

Line 429: Just a thought: wouldn’t the airfoil-like cross section help the animal to move in horizontal (i.e. forward/dorsal) direction?

Line 460: There are also well documented cases of sublethal injuries in Palaeozoic endocerids (Kröger 2011, Size matters – Analysis of shell repair scars in endocerid cephalopods, Fossil Record 14, 109–118) and orthocerids (Kröger 2004, Large shell injuries in Middle Ordovician Orthocerida (Nautiloidea, Cephalopoda), GFF 126, 311–316), as well as Devonian orthocerids, bactritids and ammonoids (Klug 2007, Sublethal injuries in Early Devonian cephalopod shells from Morocco, Acta Palaeontologica Polonica 52, 749–759). Note that in the latter study, there was no difference found between the frequencies of injuries in straight and coiled conchs.

Line 471: Why would the predator not just turn around to follow the orthocone? At some point, it will hit the surface without further room to escape. Perhaps these evasion tactics were more useful against benthic or demersal predators?

Line 505: You may also cite Klug et al. (2021, Failed prey or peculiar necrolysis? Isolated ammonite soft body from the Late Jurassic of Eichstätt (Germany) with complete digestive tract and male reproductive organs, Swiss Journal of Palaeontology 140, 3).

Line 506: See Doguzhaeva & Mapes (2015, The Body Chamber Length Variations and Muscle and Mantle Attachments in Ammonoids, in: Klug et al. (eds.), Ammonoid Paleobiology: From Anatomy to Ecology, Topics in Geobiology 43, 545–584) for details on ammonoid muscle attachments.

Line 509: Just as a clarification, there are also orthocones within other nautiloid groups, e.g., Ellesmerocerida (even in the Cambrian, such as Ectenolites), Cyrtocerinida (e.g., Bathmoceras), Oncocerida (Jovellaniidae) and Bisonocerida (e.g., Allotrioceras). The Riocerida and Dissidocerida are also predominantly orthoconic. Thus, there is a variety of with diverse siphuncular morphologies (though you are correct that where known, orthocones seem to have relatively small retractor muscles, see also King & Evans 2019, High-level classification of the nautiloid cephalopods: a proposal
for the revision of the Treatise Part K, Swiss Journal of Palaeontology, 138, 65–85).

Fig. 4-5: Please adjust the position of the subfigure labels (A-D) to be consistent across figures. Additionally, please use a sans-serif font in the axis labels of Fig. 5. Lastly, to avoid confusion, it may be a good idea to place the legend in Fig. 5C at the bottom end of the figures, since it applies to all subfigures (even if two colors only appear in 5C).


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: VERTICAL ESCAPE TACTICS AND MOVEMENT POTENTIAL OF ORTHOCONIC CEPHALOPODS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well written and structured. The figures are high-quality and easy to read.
Experimental design: The design of the experiments seems well suited to addressing the major goal of establishing limitations on the vertical movement of orthoconic shells.
Validity of the findings: The conclusions regarding vertical acceleration and passive downward movement relative to the potential ecology seem justified although the conclusions about the ability to dodge predators seems highly speculative.
Additional comments: The authors have conducted an interesting study into the hydrodynamics of accelerating orthocones. By utilizing a clever system of weights and cavities within a 3D print of a Baculites, they were able to compare vertical movement speed between several different acceleration types. The MS is well written with well-made figures and is easy to understand. My major criticism of this MS is that all of this good work is seemingly done in service of a story that his heavy on speculation and not very convincing. This focus on predation and the evolution of orthocones as a function of vertical escape is never really explained. Overall, I would suggest minor revisions since the science presented here seems sound but the discussion is a bit weak.

In the discussion, the authors mention past research that relates the evolution of increased coiling in early ammonoids to the evolution of quick, nektonic predators. But the authors suggest that the opposite trend, from spiral to straight shells is also, to some degree, a function of nektonic predators. Maybe this innate high stability of these forms permitting a low-energy lifestyle is the driving force here and perhaps the lack of maneuverability seen in orthocones relative to spiral shells is an indication that predation wasn’t a significant evolutionary pressure? In this case the speed in upward movement is just due to the conical shape that is not necessarily an adaptation to movement as it is a necessary consequence of the accretionary growth of the animal.

All of this speculation about dodging predators seems to assume that a predator could not reorient itself in the water and simply chase the orthocone whose only escape vector is up, which would bring it closer to the surface-water interface where it would likely be fairly easy prey. Then factoring into this, the fact that the actual distance traveled from the beginning of acceleration in real life would not be constant, as in the model since the buoyant force is constant, but would “pulsed” due to the jet. How far could it travel on a single pulse? Is it possible to very roughly estimate this?

A few other minor things:
Is there a kind of missed opportunity here in not simulating the downward movement of the animal as you did the upward movement? Of course this would have been an overestimate of downward movement since hooking the hyponome around the aperture would displace the thrust vector from the center of rotation but even as a “best-case” scenario it might have been interesting in constraining possible speeds.

I believe the stability index you use (Eq. 3) is the one Okamoto suggested in his chapter: Theoretical modeling of ammonoid morphology in Ammonoid Paleobiology. Maybe cite this.

On line 229 you mention the 3D prints have watertight voids. Are these not printed with a support material? If so how did you remove it?

You mention that only a relatively small amount of mass, ~0.26% of the organisms mass (does this just mean soft-body mass?) is required for a negatively buoyant condition. Do you know how large the crop of Baculites was? If it was filled do you think it would have been enough mass to cause the animal to sink?

Line 429, you say that Baculites is similar in shape to an airfoil. I don’t really follow what you mean here. Are you talking about the dorsal/ventral wall thickness?

Line 487, you say the animal would have to rotate it’s head 90 degrees but since they are in water couldn’t it also just rotate it’s entire body 90 degrees and attack with that orientation?

Lines 530-540 A couple of times in the MS you mention ecological saturation. I think this needs to be explained a bit more. Planktonic and demersal habitats are fairly commonly suggested for planispiral forms as well. What exactly is the niche the orthocones are filling that other forms could not?

Line 533 What is the vertical motility of planispiral ammonoids? You didn’t test this and I don’t see a real comparison from the literature. Is there another paper you’re referring to here?