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: EARLY MIOCENE REMAINS OF MELISSIODON FROM MOKRÁ-QUARRY (MORAVIA, CZECH REPUBLIC) SHED LIGHT ON THE EVOLUTIONARY HISTORY OF THE RARE CRICETID GENUS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors present a precise work and describe in detail an important fossil collection attributed to the rodent Melissiodon (Lower Miocene, Czech Republic).

Their work is divided into 5 parts:

1 The introduction briefly introduces the genus, but expands on the history of the supra-generic affiliation of Melissiodon. A second chapter, entitled "the genus Melissiodon", takes up the genus again, commenting on its geographical and stratigraphic distribution.
(see § GENERAL COMMENTS)

2 a short § Material & Methods. The information necessary for a good understanding of the article is included, but it needs implementations (see § GENERAL COMMENTS)

3 A systematic section with very detailed descriptions.

4 The Discussion includes in a first part a comparison of the morphometric characteristics of the populations assigned to Melissiodon in Europe. On the basis of these results a sub-section proposes different hypotheses concerning the evolution of the genus in the Miocene (see § GENERAL COMMENTS). They end with paleoecological notes.

5-The conclusion summarises the main results and opens the way for further research

I'm not in a good position to comment on the quality of the English, but I think some smoothing is necessary.

Similarly, minor errors appear throughout the text (spaces, Melissiodon not in italics), but these are easy to detect after re-reading.

The list of references needs to be checked (e.g. De bruijn et al. 2013 is missing).

The figures are of good quality (see § GENERAL COMMENTS).
Experimental design: The authors use a standard but very detailed method of morphometric comparison. The arguments of the authors are then, from a taxonomic point of view, well argued.

The authors refer to five references to support their chrono- and biostratigraphic work. I think that a more precise discussion on the age of important localities is necessary, especially when the work proposes to follow the evolution of the genus during the lower Miocene (see § GENERAL COMMENTS)
Validity of the findings: The strongness of the article is the detailed description of the fossils, which allows us to demonstrate a great  (taxonomic?) variability within the European populations at the end of the Miocene. The data necessary for a good understanding of the article have been provided.

I do have one major criticism. This concerns the correlations of the localities located in the text and presented in figure 5. I have detailed in the § GENERAL COMMENTS
Additional comments: This genus Melissiodon disappears at the end of the Lower Miocene, although it survived the cricetid vacuum. The locality in the Czech Republic studied is of this age. From a paleogeographical point of view the locality is also important. In my opinion, it is very interesting to work on this genus, whose species M. dominans probably does not correspond to a biological reality, as the authors state. This work is therefore also important for the understanding of faunal exchanges in Europe.

In the following I provide some comments

FIGURES

I think the article would benefit from a supplementary table where the morphometric characteristics of the important populations are summarised. This would help the reader to better follow the taxonomic discussion.

INTRODUCTION

The introduction and the part "the genus Melissiodon" seem to me too long. It would be possible to include the long part corresponding to the family attributions in a remark of the systematic §. Melissiodon is referred by De Bruijn et al. 2013 to Kargi 2 (not 1)

MATERIAL & METHODS

In my opinion, these biochronological proposals should be reworked as a matter of priority. This is important because it is the basis of the discussion. I am not going to discuss everything here but, for example, it seems to me wrong to put Glovelier on the same level as Forsthart. I refer the authors to Kälin & Kempf (2009). A useful figure can also be found in Prieto et al (2018: fig. 9). It also seems unwise to limit oneself to placing Vieux-Collonges in MN 5 without further discussion. I refer the authors to Prieto et al. (2022) and the references therein. What is the argument for placing Béon 2 younger than the Central European sites? I'll leave it at that, but I advise a much more rigorous argumentation.

DISCUSSION

In the course of the discussion, there are numerous references to fossils whose study would shed light on the evolution of the genus (e.g. pp. 509-511). First of all, it is obvious that new data shed more light on the problem. Above all it gives the reader a taste of incompleteness. I would save this for the conclusion in fact. This is found in the § paleoecology.

The authors situate Melissiodon de Kargi at the beginning, but do not return to it. Why not?

Kälin, D. and Kempf, O. 2009. High-resolution stratigraphy from the continental record of the Middle Miocene northern Alpine Foreland Basin of Switzerland. Neues Jahrbuch für Geologie und Paläontologie, Abhandlungen 254 (1/2): 177-235.
Prieto, J., Lu, X.-Y., Maridet, O., Becker, D., Pirkenseer, C., Rauber, G., and Peláez-Campomanes, P. 2018. New data on the Miocene dormouse Simplomys García-Paredes, 2009 from the peri-alpine basins of Switzerland and Germany: palaeodiversity of a rare genus in Central Europe. Palaeobiodiversity and Palaeoenvironments 99 (3): 527-543.
Prieto, J., Rummel, M., Scholz, H., and Mein, P. 2022. A new middle Miocene lineage based on taxonomic revision of the large and rare cricetid-rodent genus Lartetomys. Palaeobiodiversity and Palaeoenvironments 102 (1): 223-236.


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 COVID-19 RISK ASSESSMENT MODEL FOR PARTICIPANTS AT OUTDOOR MUSIC FESTIVALS: EVALUATION OF THE VALIDITY AND CONTROL MEASURE EFFECTIVENESS BASED ON TWO ACTUAL EVENTS IN JAPAN AND SPAIN
Review round: 1
Reviewer: 1

Output:
Basic reporting: This work pertains to a small-scale covid risk assessment study of a group of people. Overall the work is clear and unambiguous. A group of people has been for COVID infection when without precautionary measures. The outbreak has been modeled cluster outbreak model. The study claims to have achieved a 94% reduction in the cases if proper measures are put into place.
1. The introduction is weak.
2. How, this study can be helpful to other areas with similar settings is also not properly mentioned.
3. This is one such study, how it can be globally applied has not been discussed in detail.
4. Modeling approach is not clear. The methodology behind it is not clear.
5. This work is just reporting its results. The discussion needs to be discussed in reference to relevant published work. It must not only stick its results to delta strain. What about other strains, e.g., omicron
6. As a global pandemic, the results of this study must be applicable to the majority of regions where COVID is prevalent.
7. Uncertianities of this work, should be placed as a separate section.
Experimental design: The experimental design is very restricted. It is still not clear how a separate secluded event can be used for the global management of this pandemic. Either, the authors need to substantiate their claims, or there must be others ways to validate this work.
Some more Statistical techniques need to be used. Why this model has been used may kindly be discussed.
In the model development section, a reader is confused, about what actually has been used from the statistical techniques. It is requested to simplify this section.
Overall methods sections needs to be elaborated.
Validity of the findings: The results need to be validated with some separate random events. It is very important. It is requested to keep a global perspective into consideration. Studies from Asia, South Asia, and the Asia Pacific as well as from Europe and the Americas can be used to discuss. As said, methods sections need to be elaborately discussed.
Further, the discussion section has to include global studies and the results must be validated/ discussed with those.
Additional comments: Overall, the work requires substantial restructuring and additions, to stand as a global level COVID management model 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: DEVELOPMENT OF A COVID-19 RISK ASSESSMENT MODEL FOR PARTICIPANTS AT OUTDOOR MUSIC FESTIVALS: EVALUATION OF THE VALIDITY AND CONTROL MEASURE EFFECTIVENESS BASED ON TWO ACTUAL EVENTS IN JAPAN AND SPAIN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The reporting of the study is good. Overall the work is a case study, wherein participants have been in a festival and with and without measures, their vulnerability to covid infection has been determined. The conduct of the study of the fine. However, I have reservations about the novelty of the work.
Experimental design: The design of the study has some issues. Can a single event consisting of over 7000 people be used to prepare a risk model for a pandemic such as COVID needs to be substantiated with similar works from other parts of the world. As a single event the design of the experiment is clear and understandable.
Validity of the findings: Again, as far as the single event findings are concerned can be used to model the COVID-19 pandemic is questionable. COVID -19 depends has been observed to depend on various parameters about what has been used to evaluate the risk in this study. Therefore the veracity of the usefulness of this study needs to be substantiated by other global studies similarly carried out in other parts of the World. The discussion needs to be very strong substantiated by the facts and figures from other published work.
Additional comments: The title is very simple, "Development of a COVID-19 risk-assessment model for participants at an outdoor music festival: Evaluation of the validity and control measure effectiveness".

You need to revise it so that it reflects that this is a study that has global implications. Overall huge emphasis needs to be drawn on the usefulness of this study for other regions of the world, taking into consideration all the factors that govern the risk of a population to covid-19


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 COVID-19 RISK ASSESSMENT MODEL FOR PARTICIPANTS AT OUTDOOR MUSIC FESTIVALS: EVALUATION OF THE VALIDITY AND CONTROL MEASURE EFFECTIVENESS BASED ON TWO ACTUAL EVENTS IN JAPAN AND SPAIN
Review round: 3
Reviewer: 1

Output:
Basic reporting: The manuscript has been improved a lot. The analysis of two case studies, Japan and Spain has added huge value to its content
Experimental design: The design of the experiment is acceptable
Validity of the findings: The results are well validated.
Additional comments: I recommend its acceptance in current form


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

Input:
Title: DEVELOPMENT OF A COVID-19 RISK ASSESSMENT MODEL FOR PARTICIPANTS AT OUTDOOR MUSIC FESTIVALS: EVALUATION OF THE VALIDITY AND CONTROL MEASURE EFFECTIVENESS BASED ON TWO ACTUAL EVENTS IN JAPAN AND SPAIN
Review round: 3
Reviewer: 2

Output:
Basic reporting: The authors have considered all the comments, I had previously asked them to incorporate.
Experimental design: Using two case studies, the manuscript has significantly improved in experimental design
Validity of the findings: The results can be now applied to other areas of the Globe for pandemic/ epidemic control measure.
Additional comments: I thank and congratulate the authors for working out on their manuscript and submitting the revised version.


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: ONE STEP FURTHER IN BIOMECHANICAL MODELS IN PALAEONTOLOGY: A NONLINEAR FINITE ELEMENT ANALYSIS REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: The basic reporting is mostly strong, however, there are quite a few grammatical problems that do need to be addressed to make the article clearer. I recommend that the article is proof-read before publication.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Summary:
This paper presents a review of ways in which non-linear approaches can (and arguably should) be incorporated into zoological, and by extension paleontological, FEA. I think that such a review is timely and will be very useful to other workers. Non-linear FEA is hardly ever used in zoo/paleo modelling, and while it is often unnecessary, sometimes its inclusion will be essential. This review provides an overview of these situations.

While I like this work and think that it could be an important reference for many people, at the moment, I think it is something of a missed opportunity. This is because I disagree that the main reason that biologists don’t use non-linear FEA is because of the computational cost, although this can certainly be a factor. Instead, I think the main reason is a widespread ignorance about how FE problems are set up and solved, and that people are generally unaware that they could or should be using non-linear methods. Therefore, I think that this review could do more to educate readers on these fundamentals. If this was added, I believe that the value of the paper would increase substantially.

More detailed comments:
I find that the paper is well-written overall, however, there are quite a lot of small grammatical mistakes (too many for me to list here) that can obscure your meaning. It’s mostly things like missing articles, subject/verb disagreements, or synonyms with subtly different meanings to the one that is intended; they’re small things, but given that this is quite a technical topic where logic is paramount, they should be fixed. Therefore, I suggest that the manuscript would benefit from further proof-reading, either by a professional or a colleague with a pedantic love of grammar.

A few times: The word ‘stablish’ appears, and it is unclear whether this is supposed to say ‘establish’ (verb: to set up), or ‘stable-ish’ (not a real word, but would be commonly understood to mean a configuration of bodies that is somewhat stable, but wobbly). I expect it’s the former, because on line 241 you say “to stablish”, but until then I’d assumed it was the latter. Given that this word appears in the context of setting up contact problems it needs to be clarified, as either interpretation could work.

Introduction, first paragraph: While I don’t find that there’s anything particularly wrong with what is written here, I think you need to expand your text by stepping back even further and explaining more plainly how FE models are constructed, and where the linear/non-linear equations are brought into this process. As it stands, you seem to be assuming quite a lot of prior knowledge of FEA, and that biologists will have an intuitive grasp of linear vs. non-linear problems: in my experience this is not often true. My overwhelming suspicion is that most paleo FE users make linear models not because they are trying to keep the model simple, as you suppose, but rather, they are genuinely unaware of the differences between linear and non-linear FEA and why one might be more appropriate than the other for their analysis. It just so happens to be the case that most problems that have been looked at by paleontologists to date CAN be treated as static, linear problems, so few have had any reason to explore the methods further. You can therefore use this paper as an opportunity to send out a warning as well as highlighting the wider range of questions that can be asked with FEA.

You have a good explanation of what a linear model is on line 190, so perhaps you could move this forward to your introduction? Defining both linear and non-linear models in plain language right at the start would be helpful for your readers. You could perhaps also include some brief examples (without leaning heavily on physics or engineering terminology) of what a non-linear model for zoo/paleo FEA might look like, and explain how the key variable that’s different between linear/non-linear models is how certain aspects of the input/output change with time. I know that you address this in detail later, but I think you’re more likely to retain readers if they can instantly see how this issue is applicable to their studies.

L70: I’ve never thought of Anderson and Westneat’s (2007) model as a finite element model of trusses! I suppose it is the equivalent of that, in that there are four trusses joined at nodes, but the authors never called their model FEA, and the purpose of this model (per my reading) is to understand the rotational motion of those bars based on rigid body displacement. Given that the nodal displacements in this model are large, and that large displacement problems are a specific candidate for using non-linear models, I wonder if citing this paper as an example of 1D FEA isn’t going to get too confusing for people? Because it isn’t something that people are going to envision as FEA, even though technically it is a model made from four 1D elements connected by nodes. That said, I don’t have a better suggestion; I’m not aware of other models that have used trusses in biomechanical analyses.

L88-90: “These kinds of elements … cannot be called as 2D elements because they use the equations of plane elasticity”. This needs further expansion for it to make sense; if these elements are not 3D and not 2D, then what are they? It follows that they are not 3D if they are defined and solving only in the x-y plane, but as this is written it doesn’t explain why one can’t call plane elements 2D elements. Do you mean that they are not 2D in the sense that they are defined with a (small) third dimension thickness? Don’t most commercial solvers still list these under 2D elements?

Fig 2: You need to use the caption to define and explain the letters and colors in this figure. If force is F and displacement is u, then I’m assuming K is some sort of stiffness modulus? I’m also assuming that the orange line is an approximation of the response, the true version of which is the black line (and therefore i represents the iterative steps needed to converge on it?). Without defining all of these parts, the figure is more confusing than it is helpful. (The same comment applies to figure three, but with more letters to define. While many people are likely to be familiar with an elastic-plastic stress/strain curve from high school, the hyperelastic one will be less familiar and needs the terms defining – is W the strain energy function?)

L123: If this review is pitched at biologists, you might have to help them through concepts like Hooke’s Law, which they might be unfamiliar with, or have not encountered for a long time. Here, instead of “The relationship between stress and strain is not following the linear Hooke’s law”, you could say “When a material is non-linear, the strain it experiences is not proportional to the stress applied”. You could follow this with an “i.e. the material does not conform to Hooke’s Law” if you wanted to. I think the point I’m trying to make is that it’ll be easier for non-physicists/engineers if you lead with a simple explanation.

L127: Similarly, you should probably also explain what the small strain theory is. If people are unaware of this assumption, they’re going to be unaware that they’re violating it in certain models, and I think this is behind a lot of the inappropriate use of linear models in bio FEA.
L165: Can you give a more straightforward description of hyperelasticity first, before defining it precisely? For example, something like “A hyperelastic material is one that shows extreme elastic behaviour, in that it is able to return to its original shape even after experiencing very high strains of up to X%”

L166: Can you explain what a strain energy function is? My understanding is that it refers to the elastic potential energy built up in the structure, but beyond that I’ll admit not really knowing how it works.

L167: “…it uses the large deformation theory described above”. Except you didn’t really describe the large deformation theory, beyond “the deformed and undeformed configurations of the body under analysis are notably different”. This doesn’t really explain what the theory is, and all that was done in the section above (L125-131) was state that it should be used when the assumptions of the small strain theory are violated, which as per my last comment, also was not described.

L199: I find that many non-engineers are unfamiliar with the concept of buckling, and struggle to understand it until they’re given an example that they will have encountered in day-to-day life (at which point they recognise it instantly). I don’t think that figure 4 really helps to elucidate things either, because if people don’t appreciate the difference between bending and buckling (and most biologists won’t), then Fig. 4b will just look like bending. I know that your point with the figure is to illustrate the differences between the linear and non-linear solution rather than how buckling is different to bending, but I fear that this could get lost if people are confused about what they’re looking at. Could you show a photograph of a buckled structure in Fig. 4, alongside a common example in the text? My go-to for a buckling column is how a drinking straw or soda can will suddenly fold if you compress it lengthways. Is there an everyday example that you could give for a sheet?

L235-241: This is a very long sentence that doesn’t resolve. Please revise.

L267: “…which can be an appropriate simplification if this is validated experimentally.” I think this is an important observation, and I am pleased that you have made it. I wonder if it’s worth pointing out that none of the validation studies that came out in the period where they were popular (c. 2005-15) considered whether non-linear models were more accurate than linear ones (at least, not to my knowledge). Of course, many of these models were deemed to be ‘good enough’ and wouldn’t be candidates for non-linear properties anyway, which is the point that you’re making here; however, would a call for some more experimental testing of non-linear models in non-medical, biological FEA be prudent? I feel like you’re getting at this in your closing sentence (L280-282), but you don’t quite say it. Indeed, is it sensible for paleontologists to use the methods you describe before any non-linear validation studies have been performed?

L285: “fossildiagenesi” Should be diagenesis?

L303: Another obvious one that springs to mind is the wing bones of pterosaurs; although their mass is likely to be lower than the other examples that you have given, the bone walls are substantially thinner, and their high aspect ratio makes buckling a real concern. Colin Palmer has done some work on this that you could look up, although I can’t recall the exact references right now (and I don’t remember FEA being used).


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: ONE STEP FURTHER IN BIOMECHANICAL MODELS IN PALAEONTOLOGY: A NONLINEAR FINITE ELEMENT ANALYSIS REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: The review considers the use of non-linear approaches in finite element modelling, with the aim of introducing the potential of these approaches to a palaeontological audience. This is clear in the introduction, as is the motivation of the study. Later, the 'palaeontological audience' is more broadly interpreted as palaeo, archaeology, and zoology, which is, in reality, the audience the review is aimed at.
There is scope for a review of this nature. As the author points out, most studies and most previous reviews have focused on linear static methods in the bio- and historical sciences. Yet in medical sciences, non-linear approaches are more commonplace. The review will be of interest to the field.
For the most part a description of the mathematical and computatinal underpinnings are matched to the relevant biological structure or approach (although see below where these links could be stronger or clearer).
Experimental design: In a short review such as this it's impossible to capture the breadth of the field. However the examples chosen do span taxonomic groups and different approaches. I don't have any concerns about this. The references seem adequately cited. Organisation seems logical.
Validity of the findings: So this is where I have the majority of comments. My overwhelming feeling when finishing reading the manuscript was, we can do all of this, but *should* we do all of this, and do we *need* to do all of this? This is because one thing that's missing from the whole review is a discussion of validation. The non-linear approaches are introduced, there’s a discussion of which materials, tissues or structures and loading scenarios might lend themselves to a non-linear approach – I have no qualms about this. But, do we need to introduce this level of complexity to get the results we need? There are some mentions of this in the text, but the danger is that a reader may interpret this paper to think that one must apply these approaches to get a more accurate and realistic result. But is this really the case? In most instances we don’t know. Take the PDL as an example. We could define the PDL as a contact surface, but do we need to define this as a contact surface to get the most accurate results? Do we need to actually introduce such complexity into our models? Likewise, we could introduce muscles as non-linear features, but actually some elastic linear studies have got really quite good results using subject specific models, detailed material properties and applying muscle forces directly to the model. Take Panagiotopoulou et al. 2017 (https://www.sciencedirect.com/science/article/pii/S0944200616301805) as a good example of a linear elastic model where computational strain values that match those measured in vivo with a high degree of accuracy. Explores the role of the PDL again using a linear elastic noncontact approach (Panagiotopoulou et al. 2019) https://www.frontiersin.org/articles/10.3389/fbioe.2019.00269/full
This review needs to acknowledge the lack of understanding of how much introducing non-linear methods improves accuracy or predictability of models.

Sections on plastic deformation (line 151 onwards) and buckling (line 189 onwards). These sections need to acknowledge that plastic behaviours in materials such as dentine or enamel represent the extremes of the loading environment rather than everyday behaviour. Likewise simulations of buckling in structures such as limb bones would also represent extreme loading conditions at the point of critical failure. Neither would be useful simulations to understand everyday loading behaviours. Further on the point of buckling, I'm not convinced that a rigid upright column is the appropriate model to represent a multi-jointed musculoskeletal system such as the limb. Why for example might it be useful to test if the bones of dinosaurs or mastodons are affected by buckling? Surely this would tell us the maximum loads that could be experienced but equally this could be achieved simply by running simulations of individual limb bones and seeing which one reaches critical failure first? In both this context of plastic deformation and buckling the review needs to be careful not to mislead the reader that such non-linear simulations would represent everyday behavioural functions.

More specific comments:
Line 19  - assuming linear elasticity in bone is not a simplification for most loading scenarios (avoiding large loads).
Lines 23-25 – also we use linear models because we understand the properties of these materials better than those with non-linear properties? And, we’ve performed validation studies in some models that show that the results are appropriate for the question of interest.
Lines 76 to 104. There’s some repetition in these three paragraphs (see comments on my PDF).
Lines 279 to 282. Picking up on the question of muscles again, if it's not clear how soft tissues can accurately be predicted in fossils, then surely we should be avoiding modelling these soft tissues using non-linear material properties because this has the potential to introduce more error to our models?
Line 330 – section 5.4. I think the section on using contacts could be more nuanced. For example, I think it's a good idea to include contact surfaces when modelling multi bone structures with joints and range of motion, such as the carpal bones of the wrist or the bones of the foot (as examples presented here). However, going back to my original point about the PDL, do we need to model adjacent materials that lack articulations as contact surfaces? Studies that have tried to model sutures in different ways for example using contact surfaces or springs, have shown variable results. It goes back to the point about whether introducing more complexity is really worth the extra time and effort and computational power and if this is going to produce a more accurate result, and indeed whether a more accurate result is actually warranted by the question at hand. A good example of this is modelling fossils, where we do not know material property values or the true extent of soft tissues and therefore muscle input forces with a high degree of accuracy. Is it therefore necessary to introduce other complex features when we know our results will not represent the absolute stresses and strains student structure in life?
I have a few different comments on the figures. I’ve added these to pdf.
Additional comments: N/A


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: ONE STEP FURTHER IN BIOMECHANICAL MODELS IN PALAEONTOLOGY: A NONLINEAR FINITE ELEMENT ANALYSIS REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is a useful review and one that I would like to see published. Following the first review, my main concern was that the author make it clear that they are showcasing the overlooked potential and importance of non-linear FE models rather than appearing to advocate without bias for their use. In this revised version, I am happy to see that the author has modified the text to make the review closer to the former rather than the latter. This is particularly clear in the Abstract and at the end of the Introduction.

As it stands, I am content that this revised manuscript serves the purpose of outlining the usefulness of non-linear models. There are still a few queries and adjustments I would like the author to make before publication - outlined below.
Experimental design: No comment.
Validity of the findings: Line 32 - when you say "mathematical nonlinearities are natural in physical models and the assumption of nonlinearilty...[etc]" by 'physical models', do you mean organisms and biological systems? When I see the word 'models' I think of mathematical/computational constructs, but I think you mean something different here?

Line 38 onwwards - if palaeontologists are unaware of non-linear models, then they cannot ignore something they are not aware of. I suggest instead of ignore, phrase this as something like: "...most palaeontologists do not have a deep understanding of how FEA problems are defined and solved, and many are not aware of the potential of non-linear modelling."

Line 41 onwards: "Including non-linearities in palaeoanthropological models can improve the results obtained in skulls when modelling skulls by considering sutures, thus making the behaviour of the model closer to reality." If you want to convince palaeo/anthro people to use non-linear models, you need to add a reference to show how this is indeed the case (maybe from the human/medical literature?).

Line 103 onwards: "In most of the biological models modelling bone structures, shells have been the prefered option." Preferred on what basis? Accurate geometry or performance? I can see how this will work for a thin later of cortex and underlying cancellous bone, but surely shells are not preferred when dealing with thick cortical bone for example? This sentence needs clarifying why shells are preferred and whether this is the case for all bony structures.

4.2	Non-linearities in Geometry: Buckling - this section should refer to Figure 4 I presume (not figure 3).

4.3	Non-linearities in contacts - likewise in this section should refer to Figure 5.

5.1	Non-linear soft tissues - it would be great at the end of this section to include some references of biomedical models that have succesfully included non-linear materials - to guide the reader to further recommended reading.

Regarding buckling - the modified figure is helpful. And I understand how buckling may be important for the slender long bones of some birds and pterosaurs. Arthropod cuticle could be another good model strucutre. However I'm still not convinced that buckling is an important selective criterion for the thick long bones of high body mass dinosaurs and proboscideans. Are buckling injuries recorded in the human and veterinary literature? I need some more evidence before dinosaurs and mammals are used as exemplars.
Additional comments: Line 80: kind should be kinds

Finally -  the review ends abruptly. It would benefit from a short conclusion paragraph. I suggest the author add this to summarise their ideas and suggestions. (I should have suggested this in the first review - it was an oversight on my part).


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

Input:
Title: INDIVIDUAL-LEVEL SPECIALISATION AND INTERSPECIFIC RESOURCE PARTITIONING IN BEES REVEALED BY POLLEN DNA METABARCODING
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study uses state-of-the-art data and methods to further our understanding of how foraging preferences vary within and between closely related bee species. I found this manuscript well written and appropriately structured, besides it follows logically from prior knowledge. In general, the citation of previous work is satisfactory, however, I notice relevant papers regarding the use of DNA metabarcoding to answer similar questions are missing in the list, such as Pornon et al., 2016, 2017 and 2019; and Lucas et al., 2018. The deposited data is accessible, and the figures and tables supporting the findings are clear and readable.

I only have a few concerns regarding some aspects of the abstract and the general background:

L. 20, 31: Please mention what “temporal scales” means here. After reading the entire manuscript, I suggest avoiding this term in the abstract as it can lead to confusion. Please specify in the abstract what you refer to with the temporal scale clearly.
L. 82-84: It is not clear the difference between these two statements; do you mean a change in the diet width vs. a displacement of the diet in the niche axis?
L. 92-93: Please provide a reference for this statement. The two studies cited do not address the effects of between-individual variation on the structure of plant-pollinator networks.
L. 97: Before reading the methods, it is not well understood what “mostly solitary” here means, please reword it.
Experimental design: The research questions are clearly identified and timely; and the motivation for the work is adequately explained. In some cases, more information and details are necessary to improve understanding of the methodology section and for the study to be replicated. My most important concern is related to the insufficient sample size to characterize intraspecific variation in plant resource use and to infer patterns of interspecific resource partitioning. Authors should identify the potential limitations within this research design, which may influence the main outcomes of the study. I believe this study has the potential to advance the field provided these methodological issues can be addressed somehow. More details about this major issue and other minor comments and suggestions:

L. 114: Please provide more phenological characteristics of the three Ceratina species: approximate start and end dates of their activity season, how different are their phenologies?
L. 25-26: Replace “comprises of” with “comprises”.
L. 130: The exact number of sheaves used and the spatial scale (i.e., the size of the study area) should be stated. Also, more details about how these sheaves were spatially distributed (i.e., distance apart) are needed. Could different nesting cavities be used by the same female? How could authors identify whether different nests were constructed by the same or different females?
L. 134: How much time did the sheaves spend in the field? I other words, how much time did the bees have to occupy the artificial nests?
L. 136-137: Only those occupied artificial nest with a female inside were collected? Did you use the artificial nests that were occupied but no female was found inside?
L. 142: How was the relative brood cell age estimated? What relative measure did you use?
L. 144: Replace “has” with “had”.
L. 147-149: I am not sure if this sample size for each bee species is enough to characterize intraspecific variation reliably (only 17, 36 and 13 nests in the case of the first phase of the study; and 17, 23 and 6 females in the second phase). The authors should account for the limitations regarding this small sample size when discussing their results and drawing general conclusions about patterns of intra- and inter-specific variation in resource use.
L. 152: Here the spatial scale is provided, please provide this kind of information also for the first phase of the study.
L. 161-162: I have the same concern regarding the sample size (L. 147-149). Besides, some additional information is needed. How many times was each bee captured during the four days? Please provide a mean value to give an idea of how strong your data on repeated measures of pollen composition from the same female are. It seems that only a few females from each species were recaptured and for most of them you only have one measure.
L. 245-246: Why did you use Pianka’s overlap index? Please provide a justification for using this specific index.
L. 256: How was the average age of the brood cells specified? Which measure did you use?
L. 258: Remove “used”.
L. 259-260: Here and before, it should be clearer what are you testing with each analysis and specifically, which are the response and explanatory variables. In its current form, it makes model construction difficult to understand. For instance, does "to analyse these data at the level of individual brood cells" means "to analyze whether pollen composition differ among brood cells within each nest"?
L. 268-270: What are the predictor variables here?
Validity of the findings: The results are clearly presented, although the clarity of the writing about statistical procedures leading to these results should be improved as stated before. In general, the discussion is well-structured and sound. However, the limitations regarding the insufficient sample size should be stressed out and considered when formulating the conclusions. Based on the results obtained with this sample size, the discussion and main conclusions in their current form may be overreached.

Below I list specific comments and suggestions:

L. 312-313: Maybe this result is due to a low availability of plant resources at that moment?
L. 322-323: How are these results affected by the fact that for most females you collected pollen only once or twice (i.e., you do not have a high number of repeated measures) to evaluate intra-individual differences?
L. 353: I don’t think this study address specifically how resource use varies “through an individual’s lifetime”. Please remove this or focus only on what it is assessed, that is the variation within and between individuals from the same species, and between different species.
L. 362-363: This statement is maybe too speculative and general at this point of the discussion; I suggest removing it and focusing on the main findings here. Nonetheless, I think it is an interesting point to develop later in the discussion.
L. 379-380: To what extent can these differences between the three Ceratina species be attributed to different sample sizes among these species? Besides, more details about the spatial scale of sampling (see comment on L. 130) for the three species are necessary to interpret these results. How were the nests and the individual bees from the different species spatially distributed? Did they show a similar spatial distribution? How could this affect to the intraspecific differences in plant resource use? I mean, I would expect individuals from the same bee species which were flying in distant places to differ more in their resource use than individuals from the same bee species flying in nearby places, just because a matter of local resource availability.
L. 388: Was it tested in this study or only based on previous work?
L. 393-394: I don't think these findings are comparable considering the huge differences in biological characteristics of the two genera, Ceratina and Apis. Please consider removing this example or rewording it to make clear how they are related.
L. 409-412: Could this preference for Echium vulgare be related to a higher relative abundance in the study site?
L. 423: Replace “it’s” with “its”.
L. 423-424: I think it should be indicated here that a high level of specialization in the pollinator assemblage would be also negative from the plant’s perspective, as plant species can be more vulnerable to fluctuations in their pollinator species’ abundance.
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: INDIVIDUAL-LEVEL SPECIALISATION AND INTERSPECIFIC RESOURCE PARTITIONING IN BEES REVEALED BY POLLEN DNA METABARCODING
Review round: 1
Reviewer: 2

Output:
Basic reporting: I reviewed the manuscript entitled “Individual-level specialization and interspecific resource partitioning in bees revealed by pollen DNA metabarcoding”. In this manuscript the authors deepen into the field of inter and intra-specific variability in the dietary specialization of three bee species of the genus Ceratina.
This is a high-quality research, well-performed and interesting. The overall quality of the writing is very good. My major comment is that in the text sometimes is not clear that the focus is on inter and intra-specific differences, and too much weight is given to the intra-specific level. Is true that this is the main novelty of the article, but more cohesiveness has to be given throughout the text.
I propose a reformulation of the introduction. To put what is now the fourth paragraph as the second, as it is still general. And to give a line to the text that is less focused on the intra-specific differences, to lead the reader to expect that you deal with both, intra- and inter-specific differences in your study. Moreover, the results section is very complex and there are certain results that appear in the discussion and I do not have the impression of having read them in results section, such as the comparison between pollen from bee bodies, cells within nests and nests. May be a table or a figure summarizing all the comparisons you did would help the reader, just conceptual.
The first part of the discussion could be more clear. It is reporting the results and putting them together, but it’s difficult to understand.
Experimental design: Methods in general are very well explained and explained in a high detail, which is great. Still, some points need clarification. The mantel tests need to be better explained. As they are right now is not clear what are the introduced data, and so what is the information extracted from them. And a big part of the article relies on this results.
Validity of the findings: The results of this study are highly relevant, and are supported by the data.
Additional comments: Minor comments:
Please check the format of the references throughout the text (parentheses).
Line 43: “disconnect” -> “disconnection”
Line 46: this line is confusing. The previous sentence is about specialization as a concept, and this is about generalist individuals, but is introduced too roughly.
Line 52: “a large amount of evidence”. Then you should give more references.
Line 66-70. The line about plant fitness is cutting the text. It should me moved elsewhere.
Line 73: remove “on the other hand”.
Line 118: remove “whose relative age is easy to determine, the”. Is redundant with the information given before.
Line 130: “several hundred sheaves’. Could you be more specific?
Line 133. A subset of the occupied nests. Could you be more specific? Just to have an idea.
Lines 213-244. Generate a new subsection in methods called data processing, or data cleaning?
Lines 305-308. Non-significant p-values should be regarded as “no evidence”, not as “little evidence” or “effect to a limited degree”. In the second part of the methods is well-done, no significant results = no effect.
Figure 3. I recommend to modify the legend as to move the legend of the lower row of graphs. I printed the manuscript in black and white and it was challenging to understand the figure from the legend. If the information of the variable employed in each graphs is situated next to them, there will be no confusion.
Lines 357-358. This is very important and is not given sufficient weight in the redaction of the discussion.
Lines 33-385. Please clarify, the sentence is not clear.
Line 423. It’s -> its
Line 470. Number of avenues


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: INDIVIDUAL-LEVEL SPECIALISATION AND INTERSPECIFIC RESOURCE PARTITIONING IN BEES REVEALED BY POLLEN DNA METABARCODING
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors addressed properly all the comments raised in the first round of revision.
The article is coherent, well explained and well performed troughout. It is a pleasure to read and very interesting. Congratulations for all this great work!

One spelling mistake in line 453: "Alium" should be "Allium".
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No comment


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

Input:
Title: SKIMMING FOR BARCODES: RAPID PRODUCTION OF MITOCHONDRIAL GENOME AND NUCLEAR RIBOSOMAL REPEAT REFERENCE MARKERS THROUGH SHALLOW SHOTGUN SEQUENCING
Review round: 1
Reviewer: 1

Output:
Basic reporting: I believe that the indtroduction will benefit if the authors gave it a little more structure. Maybe in a time line sense i.e. , first mention traditional barcoding COI and Sanger sequencing ( third praragraph in the manuscript), then the importance of  barcode and metadata, followed by other types of barcoding like eDNA, then the disadvantages and finishing with the aim of this study.
Experimental design: no comment
Validity of the findings: I was looking for a phylogentic tree, but there is none, I think it is important to add a phylogenetic tree with other previously sequenced sister species to furhter validate the authors findings. Please also provide the alingement used for the tree inference
Additional comments: The article provides a novel and cheaper methodology to optimeze the power of sequencing and use it to contribute to the biological databases and collections. It will improve with just a small extra analysis that will not consume a lot of exta time and resources.


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: SKIMMING FOR BARCODES: RAPID PRODUCTION OF MITOCHONDRIAL GENOME AND NUCLEAR RIBOSOMAL REPEAT REFERENCE MARKERS THROUGH SHALLOW SHOTGUN SEQUENCING
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is written in clear English and is technically correct. Appropriate literature is cited. The figures and tables are well constructed, high quality, and provide relevant information. The results follow stated objectives and the overall hypothesis that genome skimming could be utilized to obtain full mitochondrial genomes and ribosomal RNA genes simultaneously.
Experimental design: The authors have described the knowledge gap they are targeting with their research well. High technical standards were followed in both lab methods as well as bioinformatics, and all are described in sufficient detail.
Validity of the findings: A difference in procedures followed between mechanical and enzymatic shearing makes the direct comparison of these methods obscure. The authors point out this potential problem, but this comparison is weakened.
Additional comments: This is a clearly and concisely written paper that explores several variables that contribute to successful genome skimming to obtain barcode markers across museum vouchered fish taxa. The results suggest that the methods work under varying (and realistic) DNA concentrations, extraction and shearing methods.

In the abstract, it may be more logical to discuss the aspects being tested in the order in which they occur in the process (DNA extraction, DNA input concentration, then shearing), as was done in the Introduction.


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: SKIMMING FOR BARCODES: RAPID PRODUCTION OF MITOCHONDRIAL GENOME AND NUCLEAR RIBOSOMAL REPEAT REFERENCE MARKERS THROUGH SHALLOW SHOTGUN SEQUENCING
Review round: 1
Reviewer: 3

Output:
Basic reporting: Well-written in clear, unambiguous English. Introduction and background information are relevant and well-presented, making a strong case for the method presented. The manuscript structure conforms with PeerJ and general scientific publication standards. The two figures are well-done and relevant to illustrate taxonomic diversity and mt-genome annotation. Raw data, annotated assemblies and specimen metadata are all clearly linked to and accessible. Supplementary Tables S3 and S4 could do with a bit more context / explanation of what they present. If I understood S3 correctly, I'm not sure that all numbers in there are correct (no cost difference between enzymatic and Covaris shearing).
Experimental design: Original research that is well within scope of the journal. Research questions (e.g., “Can we generate multi-gene markers from collection specimens with genome skimming?”, “Is there a difference in DNA shearing method applied?”) are well defined and relevant, advancing our understanding of how to generate reference sequences for, e.g., eDNA studies. The investigation is sufficiently rigorous, with the main caveat being that multiple variables (DNA extraction method, DNA concentrations, DNA fragmentation method) were changed at the same time, which makes it impossible to correlate a particular change with the result (e.g., read coverage or recovery of the mt-genome). However, no significant differences in results were detected in any case – “it always worked, no matter what”. The methods are described in sufficient detail (additional info on flow cell type and read de-duplication would be helpful).
Validity of the findings: All underlying data have been detailed and are accessible, even at the review stage. The data are robust and sound. Replication of the genome skimming approach is explicitly justified by extending it to include ribosomal data. The conclusions are clear, supported by the data and answering the original research questions. The study provides an outlook on scaling up the approach, pointing to data for 384 samples not presented in this manuscript. However, this is not a major point of this manuscript and acceptable (the provided bioproject seems to include not only the data presented in this study, but also these additional unpublished data).
Additional comments: This manuscript makes a very compelling case for generating DNA reference sequences for molecular species identifications that are backed by verifiable voucher specimens, have all relevant specimen data included and are not limited to one particular molecular marker. These are exactly the drawbacks of existing “reference” sequences, and reading the abstract I thought “Yes, finally a paper that is to the point!”. Well done!
In terms of experimental design, I wish the study would have had more samples and only changed one variable (parameter) at a time to enable correlations between the variable and the outcome. This would be relevant when looking at performance and optimisation of workflows in more detail (which isn’t the topic of this manuscript, it aims at demonstrating the principle). As this study seems to have used only high-quality DNA extracts (from presumably frozen tissue samples), the outcome has always been successful and there is no apparent need for or difference between different approaches. When working with more degraded DNA (older specimens; formalin-fixed; stored at room temperature) and scaling up, this will be come more relevant – maybe the topic of a future paper.
I’ve placed various comments directly in the PDF file for consideration or information, but none of them should preclude this manuscript from getting published. It’s a good paper, and I’m looking forward to being able to cite it.


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: SKIMMING FOR BARCODES: RAPID PRODUCTION OF MITOCHONDRIAL GENOME AND NUCLEAR RIBOSOMAL REPEAT REFERENCE MARKERS THROUGH SHALLOW SHOTGUN SEQUENCING
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed all the introduction comets
Experimental design: Have no comments
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: EPIGENETIC MODIFICATION MECHANISM OF HISTONE DEMETHYLASE KDM1A IN REGULATING CARDIOMYOCYTE APOPTOSIS AFTER MYOCARDIAL ISCHEMIA-REPERFUSION INJURY
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this work, they revealed the mechanism by which KDM1A inhibits SOX9 transcription by reducing H3K4me3 in the SOX9 promoter region and thus promotes cardiomyocyte apoptosis after MIRI. By and large, the language of the manuscript is of good quality and the pictures are well laid out.
Experimental design: 1.In the abstract, “HE-1 cells” or “HL-1 cells”?
2.In cell transfection, they didn’t indicate the time of cell transfection. How long were the cells transfected before CIP-455 was used and how long was the CIP-455 treatment? What’s the rationale for using CIP-455 to treat cells?
3.In ELISA assay, they should describe how the cell supernatant was obtained.
4.In ine 128, they should detail the relationship between the time of transfection and the time of model processing.
5.What treatments were the cells subjected to before experiments such as ELISA were performed? The relevant information is severely lacking in the manuscript.
6.In line 215, after the transfection of pcDNA3.1-KDM1A, the protein expression of KDM1A needs to be detected.
7.More details about Blank are needed. And what is “CPI”?
8.In line 241, changes of SOX9 should be detected after CPI-455 treatment.
9.Since the relationship between KDM1A and SOX9 has been reported (line 321), I wonder what is the innovative point of this study then?
10.They performed their experiments in cell models, however, they didn’t design relevant animal experiments to verify their results.
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: EPIGENETIC MODIFICATION MECHANISM OF HISTONE DEMETHYLASE KDM1A IN REGULATING CARDIOMYOCYTE APOPTOSIS AFTER MYOCARDIAL ISCHEMIA-REPERFUSION INJURY
Review round: 1
Reviewer: 2

Output:
Basic reporting: In general, the overall quality of the manuscript is impressive and the study content meets the requirements of Peer J. The introduction and background sections provide the necessary information and the picture quality is up to standard. Besides, description of the method and the results in the manuscript is clearly presented and shows enough details for other researchers to refer. However, there are some details that need to be revised.
Experimental design: 1.Line 44. What is “HE-1 cells”? The cells included in this study may be HL-1 cells, I guess.
2.Line 45. Please give the full name of “SOX9”.
3.Line 128. What is “pcDNA3.1-NC”?
4.Line 135. The number of cells used in ELISA assay should be given.
Validity of the findings: 5.line 335-342. The authors should further discuss the limitations of the study in the conclusion part; after all, this study is based on cell experiments and the authors didn’t validate this mechanism in any animal or clinical experiment.
6.Fig 1-5. Please give the full name of abbreviations in graphs in the figure notes (such as LDH, AST, etc.). And, since the specific p-value is shown in Figs, "* p < 0.05" should be deleted from the figure notes.
7.Fig.2. After overexpressing KDM1A, Western blotting for detecting its protein expression is needed.
8.Fig.5. The P-value in 5F is displayed incorrectly, and the strikethrough is misused as an underscore.
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: EPIGENETIC MODIFICATION MECHANISM OF HISTONE DEMETHYLASE KDM1A IN REGULATING CARDIOMYOCYTE APOPTOSIS AFTER MYOCARDIAL ISCHEMIA-REPERFUSION INJURY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors wrote a short yet complete manuscript. While this is overall comprehensible in all its parts, I must recommend English language editing to improve the clarify of certain sections, particularly the abstract, introduction, and conclusions, which can be hard to parse. There are also several typos (i.e.  Line 91: two extra characters at the start; Line 99: missing space after H3K4). Of note, I encourage the authors to be more specific when describing earlier findings (i.e. Lines 94 and 96: clarify what "implicate" and "is necessary' mean in this context by indicating the specific findings of the references cited therein; Line 110: what does "regulate" mean here? Promote/inhibit?)

The literature cited is sufficient yet I notice a bias towards very recent reports. I recommend that more attention is based to the seminal findings in the field: for instance, I/R injury was first described in the 80's (PMID: 3769170).

The figures are well structured, but the authors should modify all bar graphs to show overlayed individual data points as per the policy of PeerJ. I also could not find the raw data for Figures 4 and 5 in the same way done for Figs. 1-3; please amend to allow their examination. Furthermore, WB raw data are provided only for the representative WB experiment; please supply the images also for the other replicates used for quantifications.
Experimental design: The question being studied is clearly stated and of interest, though the ambition of the study is very limited in looking at the regulation of a specific gene rather than the global changes that are induced following KDM5A down regulation in H/R. The authors do admit this in the conclusions, though.

From an experimental perspective my main concern is that atrial-like HL-1 cells are not a great model for H/R: not only they are hardly comparable to normal cardiomyocytes, but they are less sensitive to H/R than other more physiologically-relevant cardiac cell lines such as ventricular-like H9C2, see for reference PMID: 25450968. Authors are encouraged to validate key findings in this second cell line or, even better, in iPSC-derived cardiomyocytes and/or primary cardiomyocytes

Other important remarks:

H3K4me3 levels by WB should be presented alongside total H3, which is a better loading control than GAPDH. Indeed, consistent extraction of histones is challenging using conventional buffers such as RIPA that have physiologic pH: acid extraction is the preferred method for accurate histone WB, see PMIDs: 17545981 and this protocol from Abcam, the supplier the authors use for their histone antibodies: https://www.abcam.com/protocols/histone-extraction-protocol-for-western-blot

I am confused as to why in Fig 2E the gating thresholds for the oe-KDM1A condition are very different from the control and NC conditions: were these experiments run on separate days? If not what else explains the overall increased Annexin V and PI signals in the KDM1A conditions? A similar inconsistency is noted in Fig 4E.

I noticed Figs 1 and 2 use the vewry same raw data for the Blank and H/R conditions: were the experiments run at the same time?

The raw data for what the authors define as biological replicates are exceedingly close to one another, much more than it can be possible in my experience. This is particularly true for RT-qPCR Ct values, which are all within 0,5-1 of one another for both the housekeeping and genes of interest. Perhaps the authors consider biological replicates as multiple wells from the same culture? If so I recommend that key experiments are repeated at least twice in separate cultures (i.e. different passages of HL1 cells), so as to account for inter-experimental variability rather than intra-experimental one, which is much less meaningful.

In Fig. 3B findings would be strengthened by also reporting results for an unrelated genomic region (i.e. a non H3K4me3-marked domain on or around SOX9).

Finally, I have several requests for clarifications regarding the methods:
- Line 128: please provide the RefSeq ID for the specific cDNAs (and if possible deposit the plasmids to Addgene as per PeerJ policies).
-  Line 128: I assume that pcDNA3.1-NC is for negative control - was this an empty plasmid? If so using an unrelated protein would have been preferable as control and could be added for at least key experiments
- Line 163: please provide further details about the cytometer used, for instance the lasers and optical filter configurations
- Line 182: for the loading control did the author strip and reprobe the same membrane used the protein of interest? Or were membranes cut in pieces based on the anticipated MW?
- Line 187: clarify sonicator model and conditions used
- Table 1: the size of some RT-qPCR amplicons seems way too big (i.e. 2.6 kb for KDM1A). Please check the sequences or clarify
Validity of the findings: As mentioned above I could not examine the raw data for Figs 4-5 as well as raw data for all WB. I also await for clarification on experimental and analytical designs that are key to make a complete assessment of the robustness of the study.

From the figures presented the main conclusion of the study appears to be generally supported, and there is no ove-rinterpetation of the data.
Additional comments: NA


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

Input:
Title: EPIGENETIC MODIFICATION MECHANISM OF HISTONE DEMETHYLASE KDM1A IN REGULATING CARDIOMYOCYTE APOPTOSIS AFTER MYOCARDIAL ISCHEMIA-REPERFUSION INJURY
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
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: EPIGENETIC MODIFICATION MECHANISM OF HISTONE DEMETHYLASE KDM1A IN REGULATING CARDIOMYOCYTE APOPTOSIS AFTER MYOCARDIAL ISCHEMIA-REPERFUSION INJURY
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: No comment.


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

Input:
Title: IN SILICO TESTING OF FLAVONOIDS AS POTENTIAL INHIBITORS OF PROTEASE AND HELICASE DOMAINS OF DENGUE AND ZIKA VIRUSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This well written manuscript describes the in silico based discovery of some compunds with activity against the dengue and zika viruses proteins.

While the computational data certainly looks promising, the authors did not demonstrate biological efficacy of any of the discovered molecules.

To be considered for publication, I recommend that the authors demonstrate antiviral efficacy of at least one of the identified compounds in a cell based system. Dengue and Zika have several excellent model systems which can be handled at BSL-2 and could be used for this.

I cannot recommend this manuscript for publication without at least the proof of concept that the computational approach was able to identify a compound with antiviral activity in a biological system.


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

Input:
Title: IN SILICO TESTING OF FLAVONOIDS AS POTENTIAL INHIBITORS OF PROTEASE AND HELICASE DOMAINS OF DENGUE AND ZIKA VIRUSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: minor mistakes

1.  line 30: like in the background, please change this statement as some antivirals exist and developed this year. " have been approved"
2. line 35 molecular dynamic simulations
3. line 29: why only microcephaly as there are many public health issues with Zika and Dengue.
Experimental design: the experimental design looks fine.,
Validity of the findings: results look expected
there should be validation of the models like positive and negative control.
Additional comments: No additional comments


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

Input:
Title: IN SILICO TESTING OF FLAVONOIDS AS POTENTIAL INHIBITORS OF PROTEASE AND HELICASE DOMAINS OF DENGUE AND ZIKA VIRUSES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The research topic is timely. The results are exposed, and the discussion is written clearly. The literature references are appropriate and correct. However, the quality of the manuscript, including writing quality, figure captions, and table captions, needs to be significantly improved.

Some of the writing issues:
Abstract:
1.	Methods. Methods (written twice)
2.	Discussion: The analyzes on MOD10? (correct it)

Lines:
36: Methods. Methods (written twice)
144-146: (Structure the sentence correctly)
165-166: populated ligand pose from ADFR was selected as then (the ?) initial conformation.
384: useful to test, a evaluate new. (correct it)

Tables:

In supplemental tables S3 and S4, what are these numbers (percentages?) Write that in the figure caption.

In table S7, figure caption (3rd line):  fo domain III  (of ?)

Figures:

No figure captions for the supplemental figures. Isn't it very confusing without the figure captions?

Figure S4: What are red and black trajectories in the RMSD vs time graphs? (DENV3 or 4?)
Experimental design: In this study, the authors explored the binding mechanism of various compounds as potential inhibitors of protease and helicase domains of dengue and Zika viruses via molecular docking and MD simulations. Here, the authors used the flavonoids previously shown to inhibit the dengue virus serotype 2 replication in vitro to identify the specific target domains in DENV and ZIKV. Here, the authors chose to explore the NS3-pro and NS3-hel regions for the binding activity of flavonoids. What is the rationale for using the biggest binding sites for helicases? There is no necessary reason for doing this because binding sites of this size are not usually actual binding sites for small molecules.

In the abstract, the author mentioned that molecular dynamics analysis was carried out using UCSF DOCK. Later in the main text, they said that they also used the AMBER20 suite for MD simulations. Can you explain more clearly which one of these you used? If you are used both, why? AMBER20 suite itself is good enough for end-to-end MD simulations.
Validity of the findings: Molecular docking and MD simulations identified that quercetin derivatives could inhibit the DENV infections via interaction with NS3-pro in DENV3 and DENV4 serotypes. These findings were clearly stated, and the discussion was written clearly and concisely. The conclusions are sound.
However, in addition to the MMGBSA calculations, hydrogen bond analysis is recommended for the protein-ligand complex. It would give a better idea of the strength of hydrogen bond interaction.
Additional comments: I support its publication in PeerJ after

1.	significantly improving the writing quality, figure, and table captions.
2.	hydrogen bond analysis for the protein-ligand complex.


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: RANDOMIZED FEASIBILITY TRIAL OF THE SCLERODERMA PATIENT-CENTERED INTERVENTION NETWORK HAND EXERCISE PROGRAM (SPIN-HAND)
Review round: 1
Reviewer: 1

Output:
Basic reporting: meet the standard. good English.
Experimental design: 1. please stated the drop-out criteria for the subjects. clearly define the research question, relevant and meaningful.
2. please explain: how do the authors make sure the correct exercise has been done by participants?
Validity of the findings: 1. the data about disease characteristics: almost all standard deviation (SD) is more than half of the mean. Could you please clarify why this happens?
2. the author did not give the post-exercise data of EQ-5D
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: RANDOMIZED FEASIBILITY TRIAL OF THE SCLERODERMA PATIENT-CENTERED INTERVENTION NETWORK HAND EXERCISE PROGRAM (SPIN-HAND)
Review round: 1
Reviewer: 2

Output:
Basic reporting: This feasibility trial attempts to analyze the characteristic of the scleroderma patient-centered intervention network hand exercise program on its usability.
The article seems to be almost easily readable, even though in some parts appears hard to follow the description of the SPIN Cohort and SPIN-HAND Feasibility Trial Participants. The references appear almost all up to date.
Experimental design: About the Keywords, it is preferable to choose between MeSH terms.

Introduction:
- line 186 "Previously, three RCTs...". In the text, there is a description of only two RCTs. But the two articles cited appears as a couple of article on this theme and also not the most recent. Which is the third? Also, more recent examples in the literature should be considered.
- line 200 "... to care as usual...". Is not described what the Authors identify as usual because in most of the cases the rehabilitation management of the hand is absent.

Intervention: the description of the 4 modules should include also the timing that the patient spend on each of them. There is a minimum time?
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: RANDOMIZED FEASIBILITY TRIAL OF THE SCLERODERMA PATIENT-CENTERED INTERVENTION NETWORK HAND EXERCISE PROGRAM (SPIN-HAND)
Review round: 1
Reviewer: 3

Output:
Basic reporting: A loss of 20% or greater to follow-up should be a concern of possibility of bias (Schulz & Grimes, 2002). While Table 1 provided useful information on all participants and confirms the success of the randomization process, the substantial proportion of loss to follow-up means that information presented in Table 1 does not adequately describe the analytic sample nor reflect the comparability of the trial groups. The descriptive statistics of analyzed sample and those who are lost to follow-up should be presented separately.

More details are needed about the SPIN’s hand exercise program in the introduction section, such as how SPIN-HAND program components compared with other existing interventions and routine care, online program versus facility or home-based delivery. Some of the information from ‘background and rationale’ section from the research protocol could be incorporated into the introduction.

Lines 186-189, please be more specific about the methodological shortcomings.

It would be helpful to present, briefly, the characteristics of the 6 patients who participated in the feasibility interview in the results section.
Experimental design: The manuscript reported a pilot study, assessing the feasibility for conducting a full-scale randomized controlled trial of an online intervention of SPIN-HAND Program to improve physical function and HRQoL among systemic sclerosis patients. The authors reported a relatively high overall satisfaction and good technical feasibility among patients who completed post-intervention interview. However, these results must be interpreted in light of low consent rate (60%) among those who randomized to intervention, high attrition (7 out of 15 consented patients did not complete 3-month follow-up assessment), and low utilization rates among consented patients (only 5 logged in more than twice). Although the authors acknowledged these limitations, and proposed ways to improve uptake and utilization in the future study, these numbers appeared to indicate a rather unfavorable perspective for a larger RCT. If patients will have to be willing to try the program to be eligible (lines 489-492), the proportion of the 1800 patients who could meet the eligibility criteria may be much lower than 35% as indicated by the authors. This could be further complicated by the potential high lost to follow-up and low adherence to intervention, problems not uncommon in internet-based interventional studies.
Validity of the findings: Table 3 showed that the mean CHFS score at month 3 for intervention patients was higher than control, and the mean CHFS score increased over the study period. A quick look at the raw data, among the 8 patients who completed 3-month follow-up assessment, only 2 had improved/maintained the same level physical function in the hands over baseline (as assessed by the CHFS), while 6 out 12 in the routine care group maintained or had improved physical function. In another words, the patients in the intervention armed were more likely to experience deteriorated hand function after intervention! These numbers showed no sign of the efficacy of the intervention. According to the effect size and standard deviation from Rannou et al study, the sample size of the present study was clearly insufficient to detect the difference in hand function and other functional health outcomes. The author may want to acknowledge the limitations, remove non-feasibility related outcomes from the manuscript, and focus on feasibility measures.
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: RANDOMIZED FEASIBILITY TRIAL OF THE SCLERODERMA PATIENT-CENTERED INTERVENTION NETWORK HAND EXERCISE PROGRAM (SPIN-HAND)
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: revision already made and it can full-fills the requirements


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: RANDOMIZED FEASIBILITY TRIAL OF THE SCLERODERMA PATIENT-CENTERED INTERVENTION NETWORK HAND EXERCISE PROGRAM (SPIN-HAND)
Review round: 2
Reviewer: 2

Output:
Basic reporting: Thanks to the Authors for this improved version of the Paper previously submitted to the Journal.
Based on the answers to the reviewers, I shall raise some hints and questions to the Authors as follow reported.
Experimental design: Clarifications on answers to the Editor comments:
1) "I am a bit confused as to the division of the participants. For the 9 participants who were randomized to the intervention, but did not consent to the intervention, how did they log in and access the materials for the intervention without consenting?", if I correctly understood, this could raise possible ethical problems. We can't conceal the information about the treatment on the basis that the patients don't fall into the treatment group. The patients must have full information about the design of the study in order to express valid informed consent. Please describe better on it.

2) About this point “Characteristics of participants assigned to the intervention and control groups were generally similar with exception of the Modified Rodnan Skin Score, which was substantially higher in the control group.” I think is better to specify it on the limits section of the study.

Clarifications on answers to the first Reviewer:
1) The drop-out criteria appear not yet well clarified.

Clarifications on answers to the second Reviewer:
1) Keywords are useful for the indexing of the article. So, terms not included in the MeSH term list are possible but is necessary that terms should have a probability to come in the mind of the possible readers to write it in the search string.

2) Filippetti M. et al in 2020 published an RCT on the effect of a tailored home-based exercise program in patients with systemic sclerosis (DOI: 10.1111/sms.1370). That study included aerobic, resistance training, and hand exercise. I think that also this study could be included as a rational basis to justify the improvement of knowledge on self-administered treatment protocols on these patients.

Clarifications on answers to the third Reviewer:
None.
Validity of the findings: No comment o it.
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: RANDOMIZED FEASIBILITY TRIAL OF THE SCLERODERMA PATIENT-CENTERED INTERVENTION NETWORK HAND EXERCISE PROGRAM (SPIN-HAND)
Review round: 2
Reviewer: 3

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
Additional comments: The authors have addressed my questions sufficiently, I have no further 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: FACTORS LIMITING REPRODUCTIVE SUCCESS IN URBAN GREYLAG GEESE (ANSER ANSER)
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: Line 104: about the hypotheses, this section of the manuscript should be deeply rethink/reshaped. The referred hypotheses should be better stated as questions/tasks or points guiding the manuscript methodological design.

(1) In the newly colonized area, an increasing population size of Greylag Geese leads to an increase in the number of breeding pairs as more offspring can be recruited into the breeding population.

There are two main factor influencing population growth (total number, be aware of the effective population size that is what actually represents the reproductive potential of the demo):
 i) Natural increment of the population by the increment of the number pairs
 ii) inmigration
If the population is growing but not the number of breeding pairs then the increase in the population is due to inmigration, birds than for some reasons do not breed, is it not happening? How an increment in the population size cannot lead to the increment of the breeding pairs and the total population size? The relationship cause-consequence here is not clear and it should be clarified.

(2) Fledging success of individual goose pairs decreases due to density dependence.
Since you are not measuring any other ecological parameter than number of birds you can find a correlation between fledging success and density but you cannot discard other factors acting against individual goose pairs fledging success.
How does this hypothesis relate/contradict with point (1)?

(3) Pairs that emigrate with young goslings to a new brood rearing areas will have a lower fledging success because they are more likely to lose young during the journey.

This can be tested as a hypothesis. Nevertheless, these movements are happening in about 4 Km from the breeding site an in the text it is referred as an emigration. I think the concepts of local displacements/emigration etc should be reviewed carefully and use the appropriate one. Since the movements of some pairs to other near areas seems not to be dangerous, then is there an alternative route to get to the new location?

(4) There is an optimal brood size which yields the highest fledging success.
This statement is tautologic, since there is always an "optimal" brood size (or range) which lead to the highest fledging success.

(5) On an individual level, the probability of a hatchling to fledge decreases with the following variables or a combination thereof:
a) an increasing local population size;
b) the number of breeding pairs in a population

(is it independent from a?)

c) emigration (see hypothesis 3)

Is not redundant to question 3?

d) a higher number of hatchlings
e) the increasing number of Egyptian Geese due to competition or agonistic behaviour. Regarding individual pairs, fledging success

These points are an extension of the question No 2.

(6) will increase with breeding experience and

This statement is tautologic, do not reproductive success always correlate with parents experience?

(7) will be overall higher for pairs which bred more often
This is related to point 6.
Validity of the findings: Figure 3 b,d and e are not convincing, even though the adjusted line shows a tendency the conclusions should be taken carefully since the visual inspection of the graph show a cloud-like dispersion of the observations. It would benefit if the dots are presented in a darker colour along with the corresponding regression coefficients.
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: FACTORS LIMITING REPRODUCTIVE SUCCESS IN URBAN GREYLAG GEESE (ANSER ANSER)
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is a paper describing reproductive success in a population of urban greylag geese in the city of Stuttgart, where individuals have been monitored since the establishment. This long-term dataset (17 years) provides a good opportunity to understand processes in an increasing goose population and the related reproductive success of individuals and possible impacting factors.

Some general comments:

o	I’m not familiar with the format of this journal, but it looks a bit strange with figure legend in-between the written text. Fine if this is the standard.

o	The Introduction will be improved from some re-structuring.  E.g., a detailed description of barnacle geese is given, but the full story is not completed but continues with information from the snow goose. I suggest that the authors more specifically list the various possible factors affecting reproductive success (RS) in more general terms regarding birds, and then provides some examples where geese are the main examples.

o	I think the Discussion is too long, with too many references to other bird species than geese. I acknowledge the authors overview in the field, but some of it appears not directly relevant. However, I leave for the Editor to judge the length of the Discussion in light of the journal style. If it is OK, then fine with me!

Specific comment referring to lines in the document:

Lines 28-29: Add that also the adult survival is high?

Line 35: “regulation” instead of “management” ?

Lines 36-38: write more precisely that the shift to agriculture is a reason for population increase (shift the order of the statements)

Lines 46-47: Describe briefly the mechanisms for density dependence in this case

Lines 47-49: How? (effect on RS)

Line 54: add “..of the annual cycle and locations as well”.

Lines 58-60: There is nothing about hunting in the Owen & Black paper on barnacle geese? I think the Danish group lead by Jesper Madsen may have some better and alternative references on pink-footed geese.

Line 63: use “estimated” or “counted” for the 300 individuals in Caerlaverock, as the 2nd WW apparently also had an effect on where the geese stayed during these years.

Line 64: slower rate; what are the numbers?

Lines 84-85: present what the arguments for the optimal clutch size are

Line 101: …fledged in the same area, adding…

Lines 105-107: other way around? More recruited leads to population increase.

Line 107: …individual goose pairs decrease over time due to…

Line 110: (4) explain what the logic is behind this

Line 112: …thereof due to density dependence mechanisms…

Lines 114-116: use the same format at in (1)-(5)

Line 121: do the urban parks also include ponds and open water?

Line 124: last sentence, it is obvious, delete?

Line 130: 300 pairs, from how many individual originally? What is known?

Line 131: how large proportion?

Line 137: the predators – both raptors and terrestrial?

Line 139: ….leading to higher nest densities.

Line 140: when disperse – winter/summer?

Line 144: use “introduced” instead of “occurred”?

Line 147: add average clutch sizes

Line 149:…breeding advantage due to diverse nesting site preferences.

Line 152: use “as a consequence of” instead of “during”

Line 162: …highest estimate based on goose counts during a given year….

Line 164: …Directive and also used by…

Line 168: How long is the narrow time period?

Line 177: Somewhat unclear what the local population is – define…. What if some geese were breeding elsewhere not detected in the study? Maybe add some distance information to clarify and define what the local population size is?

Line 183: adjust the text as the real number of eggs hatched was not possible to count as there were no entrance on the breeding island.

Line 185: define period for survival to fledging

Lines 201-207: the abbreviation of concepts, understand the need to shorten for the tables etc. (model presentations), but one word would be much better – e.g. HA= hatchlings, etc. They can still be defined in the text, but this will be easier for the general reader to follow and understand which  variables are included in the different models.

Line 222: How many geese were observed in 1988?

Lines 230-231: …three years from 2016 to 2019 their numbers doubled….

Line 232: delete “a high of”…

Lines 269-273: say something about the large brood sizes with hatchlings that are well above the normal clutch size.

Lines 277-283: some of this is already said above, delete and add “strong” etc. in the results described above instead, for a more streamlined text.

Lines 313-314: describe the mechanisms behind this statement

Line 317: see also some of the work from the Dutch team on Svalbard (1998, Nor. Polar Skrifter), may be information also referred to at this point.

Lines 317-319: add a question mark or re-write

Lines 331-333: see also the Black paper from 1998 about the colonization process on Svalbard for barnacle geese.

Line 359: but what is the detectability for families dispersing?

Line 367: add why so large broods

Lines 371-372: but geese also use body reserves for egg-development, reserves that may be gained elsewhere. Explain.

Lines 392-393: delete the parenthesis defining the M1 model, or say with words

Lines 405-410: but what about the dilution effect for the broods when more goose families are present, could that have an effect?

Line 412: use “larger” instead of “more”

Line 415: …indicus have been shown to be influenced by the ages…

Conclusion: most of this is more like a summary rather than a conclusion. The authors should have another look at this section.

Line 450. Use “suggesting” instead of “hinting towards”?

Line 452: Difficult to predict generally for all colonies – this is one case only. What about the exponential increase of barnacle geese in e.g. Malmö? No need to describe that example, but be more careful to suggest generality based on one case only.


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: FACTORS LIMITING REPRODUCTIVE SUCCESS IN URBAN GREYLAG GEESE (ANSER ANSER)
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have considered the main points raised in the first round of review. Nevertheless, in my opinion, some important aspects still need consideration before recommending the manuscript for publication.
The manuscript would benefit of a couple of sentences clearly explaining the benefit of using fledging success and hatchling survival, the different information they provide separately and the things the readers need to be aware at the time to interpret the results. As I understand it, the complexity of the models (number of variables) behind the estimation of these indexes make the difference, right?
I have to stress the point of referring to the movements 4 km away from the Max-Eyth Lake emigration and not dispersion. Since birds return to their original breeding place the movement is not an emigration, "Across all years, a total of 13 different breeding pairs emigrated, some of which emigrated repeatedly in several years. From 2016 onwards, fewer geese emigrated, ranging between one and three pairs each year." I think the authors need to go over the concepts and refer to what they are describing in the manuscript correctly.
Regarding the Figure 3 (panels b and d) I would still suggest to use different colours for a range of number of hatchlings, using shading intensity is misleading and create a bias in the data interpretation; this information should be clearly stated in the figure caption.
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: 'no comment'


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

Input:
Title: HMGB1-ACTIVATIED NLRP3 INFLAMMASOME INDUCES THROMBOCYTOPENIA IN HEATSTROKE RAT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The abstract is poorly written in places - especially the methods - should replace "reflected" with a more appropriate term such as measured, analysed.

The introduction provides a good analysis of the background but doesn't really explain why it is important.  The aims and hypothesis need to be more explicitly stated
Experimental design: The experiments are appropriate to address the research question and well designed and performed to a high technical ad ethical standard.

Some clarification is required regarding the specificity of the reagents used - e.g. are the neutralising/blocking antibodies specific for rats.
Validity of the findings: The data is clearly presented and described

Experiments were only conducted once but appear to be robust

The authors must justify the statistical analysis used.  Can they confirm if analysis of the normality of the data performed.  Given that small group sizes (n=6) were used it would be more appropriate to use non- parametric tests such as Mann Whitney and Kruskall- Wallis.

The majority of the discussion and conclusions are clear and well stated.  However some paragraphs need some attention (starting line 346 and 354) as it is not clear what point is being made.
Additional comments: A well executed study with interesting results however it could explain what the implications of the work is and how it could be used to develop therapies.

The English requires some attention in the Abstract, Introduction and Discussion - it would improve the clarity of manuscript.  Some odd phrases e.g. line 296.

Could include some comment of the limitations of the study