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: LEARNING TO PERFORM ROLE-FILLER BINDING WITH SCHEMATIC KNOWLEDGE
Review round: 2
Reviewer: 2

Output:
Basic reporting: This paper reports artificial neural network simulation results exploring various network architectures in search of one that can learn to process encoded “word” sequences in such a way so as to allow the network to correctly identify the word that fills a particular event schema role that is queried after sequence presentation. Importantly, a network is sought which can learn this task (1) without roles being explicitly labeled in the word sequence and (2) in a way that generalizes to arbitrary role-filler combinations (i.e., exhibits combinatoric generalization).

This revision is substantially improved in comparison to the previous manuscript. Additional technical details, needed for both understanding and replication, have been provided. The authors are more explicit about what is meant by “role-filler binding”, which is critical given the existence of multiple perspectives on this notion. The revision does a better job of situating the reported work in relation to previously published results. There appears to be a greater appreciation for the importance of the statistical structure of training patterns in networks of this kind, as well as the ways in which such structure can thwart combinatoric generalization, but the document still lacks a clear discussion of how the reported results could be largely explained by the differences in sensitivity to statistical structure across the network architectures. Indeed, the addition of a simulation experiment intended to show some retention of the statistical structure of training patterns, while welcome, seems to miss the fundamental contention between sensitivity to statistical regularities and the target goal of perfectly general role-filler binding. This last issue is discussed, below.
Experimental design: As previously mentioned, important details concerning the discussed simulations, which were elided in the previous draft, have been included in this revision.

Some of these details reveal potential imbalances across compared training regimens. For example, the variation in filler vocabulary sizes could influence the reported results, even beyond chance performance rates, given that word outputs were determined by a “code book” look-up over vocabulary items. Still, it is unlikely that any effects arising from these imbalances fully explain the important reported differences in performance.

The added analysis, intended to demonstrate sensitivity to the statistical structure of training patterns even in the network architectures that exhibited the strongest combinatoric generalization, is problematic. While the analysis is appropriate for showing that some sensitivity to the training distribution was acquired, the learned statistical structure is trivial, and focusing on such trivial learning suggests a lack of understanding of why an analysis of this kind is important. The focal conceptual issue, here, is discussed below.
Validity of the findings: As in the previous draft, the reported findings are certainly valuable, but the paper is still somewhat unclear about why the architectures that performed particularly well did so. The reader is told that these results indicate that an “external memory” is important for generalization, but the reader is not led to understand what distinguishes an “external memory” from other network structures. It is quite likely that the benefit of an “external memory” arises from its insensitivity to the statistical structure of training patterns. As suggested in a previous review:

“From this perspective, the network architectures that succeed, in this paper, are those that contain a mechanism to retain filler vectors, as they were presented to the network, without distorting them based on the learned expected distribution of such vectors. Fast weights change in essentially the same way in response to a given input vector regardless of the past distribution of such input vectors. The reduced NTM contains explicit registers for maintaining arbitrary vectors. From this perspective, the inclusion of mechanisms that are insensitive to spurious correlations — they do not learn statistical regularities that are present in the training examples — are important for role-filler binding that generalizes in a combinatoric way.”

The added experiment intended to show that some statistical structure was learned only demonstrates that the most obvious properties of training patterns (the mean values of the output elements) are retained. This distracts the reader from the fundamental opposition between statistical learning and truly general role-filler binding (particularly with novel filler vectors). A network that learns from training patterns that Anna is always the emcee will exhibit that knowledge in its performance, and it will, thus, have a more difficult time when presented with inputs that indicate that Belle is the emcee. If a network shows no difference in performance across fillers, even when training data reflects biases for certain roles to take on certain fillers, then the network is not exhibiting sensitivity to the correlations inherent in the network’s experiences. There appears to be an essential trade-off, here.

This is one reason why having an explicit criterion for the presence of role-filler binding capability is important. There is a “competence” view (embraced in this manuscript) that suggests that role-filler binding only exists when all fillers are managed equally well (e.g., perfectly). But this approach to role-filler binding runs counter to observed human behavior. People will have more difficulty remembering, and respond slower, to a stimulus like “the criminal arrested the officer” than to a stimulus like “the officer arrested the criminal”. Now, people can parse and understand the first of these two sentences, demonstrating some capability to overcome the statistical regularities of past experiences, but they do not perform equally well regardless of the nature of the fillers. This leads to a “performance” view of role-filler binding, which allows for sensitivity to statistical structure by slightly degrading combinatoric generalization.

The newly added experiment uses “ambiguous” inputs for an important reason. If the identity of the poet is not mentioned in the input, but Carter was almost always the poet during training, then presenting a query about the identity of the poet should show a bias toward a Carter response, if the “performance” perspective is taken. As presented in this draft, using “ambiguous” inputs seems superfluous, as all that is being demonstrated is the learning of the mean output values during training — not any correlations between roles and fillers. (The Sentence Gestalt network demonstrated this kind of statistical learning.) Thus, it seems as if the design of this added experiment is based on some misunderstanding of the importance of the trade-off between sensitivity to training distributions and clean combinatoric generalization. A better demonstration would be to bias the training data (e.g., the poet is usually Carter) and compare the cosine distance to the nearest vocabulary item when tested on an input indicating that Belle was the poet versus Carter. If the network correctly identifies Belle as the poet when she is, but the output vector is farther from the Belle vector in comparison to the Carter case, then the network is demonstrating combinatoric generalization while exhibiting some sensitivity to the training distribution.

I suspect that a reasonable balance in this trade-off can be more easily had in networks that have some part that is insensitive to training statistics (i.e., the “external memory”) and some part of the network that learns training correlations (e.g., other weights).
Additional comments: In summary, this is work that is generally worthy of publication, though a better experimental design to show sensitivity to training distributions would be welcome. The paper could also be further strengthened by discussing the trade-off between learning correlations and avoiding the trap of “spurious correlations” that hinder robust combinatoric generalization.


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: LEARNING TO PERFORM ROLE-FILLER BINDING WITH SCHEMATIC KNOWLEDGE
Review round: 2
Reviewer: 3

Output:
Basic reporting: See below.
Experimental design: See below.
Validity of the findings: See below.
Additional comments: Review of “Learning to perform role-binding…” for PeerJ

I reviewed a previous version of this paper. After reading this version many of my previous concerns still stand.

One problem with the paper is that while the ms. starts by describing dynamic role-filler binding, it then presents a definition of role-binding that is definitely not dynamic. It’s fine to define role-filler binding in a new way, but it should be clearly contrasted with the way it is conventionally defined. Especially, when initial text refers to conventional discussion.

On p. 2 the reference to the definition of role-filler binding by Holyoak and Hummel is incomplete. Hummel and Holyoak also argued that role-filler binding must be dynamic. It is misleading to give the current definition of role-biding following a discussion of Holyoak and Hummel, when half of Holyoak and Hummel’s definition is left out. The current definition is an odd one to have been motivated to by Holyoak and Hummel.

The discussion of prior would once again benefit from more careful reading of the cited work. First off, I don’t think anyone has claimed (and certainly not the papers cited in the first paragraph of the Related work section) that: “Connectionist models were traditionally thought to be unable to represent these symbolic relations, because of an ability to independently represent roles and  fillers”. I think “inability” is intended rather than “ability”, but either way the papers don’t argue that traditional connectionist models can’t independently represent roles and fillers (that’s easy, just have one node for the role and one for the filler). What they argue is that traditional connectionist networks can’t bind independent representations of roles to fillers dynamically. That’s a major point in this area.

Second, the discussion of Doumas et al. (2008) is again wrong. First, the sequence of comparisons are not hand-crafted (except in the first sim, then second sim shows they don’t have to be), and the comparison is only important for learning the relations in the first place, not for binding. Second, the binding signal emerges as a function of the architecture (layers of laterally inhibititive units and separate banks). If the architeture means hand-crafted, then your model is hand-crafted too (see organisation, learning rules, etc.).

Finally, I think my original points about the limitations of the current simulations still stand. I wrote:
“Third, the result in the paper seems very likely the result of the model learning to ignore certain bits of information when asking certain questions, rather than literal role-binding. This result was also reported in the cited Puebla et al. paper. In that paper, the finding was that when all fillers appeared in all roles with roughly similar frequency—as actually occurs in the current model as the small distributed encoding space of possible fillers (50 nodes) and large numbers of generated fillers almost assures all of the 50 nodes appeared in each role (though not in all possible combinations); this process is called spanning the input space and the practice as it relates to role-filler binding is covered in the previous literature suggested by the previous reviewer (Doumas & Hummel, 2012)—the model effectively learned to ignore context when answering specific questions. For example, if trained that a set of 4 people go to four coffee shops and order 4 different things and all combinations are roughly equally present in training, the model learns to return a copy of the y item in the sentence “x ordered y” in response to the question, “what was ordered?”. The problem is that then the model loses the capacity to learn any systematic context effects. If the model is then trained that John always orders cake when he goes to the coffee shop (“John went to the coffee shop” “John ordered cake”), the model is no more likely to return cake as, say, carrots when given the sentence “John went to the coffee shop” and asked “what did John order”. In other words, training as the done in the current paper, makes the model insensitive to context, while training with specific systematic statistical regularities (as in the other Puebla et al. sims) makes the model fail at returning the correct items when the statistically regular role-bindings are violated.”

I think that the correlation violation results are interesting. There are clear differences between the correlation violation used in Puebla et al. and in the current paper, however. More importantly, it’s not clear why the particular test of the network’s ability to retain statistical information was used rather than a simpler one. Based on the Puebla et al. tests, the test that should be run is as follows: the model is trained on a bunch of inputs where John orders cake (and only cake) at the coffee shop, and other people order other stuff. The network is trained to a point where when told John orders pie at the coffee shop and it returns pie to the question what did John order. Then the network is told John was at the coffee shop and asked what John ordered. Does it then return cake, or has this information been lost. Whey wasn’t this simple simulation used rather than the present one?

Second, the model succeeds in binding “novel” roles to fillers only in the unlimited training, when there are no systematic fillers used. That seems to suggest that the generalisation occurs when the model learns to ignore the filler information. I am skeptical that the unlimited training model could perform as it did if there were systematic statistical properties of the fillers of specific roles.

Also, I think it’s rather misleading to claim that the model is using unseen fillers when it used a pool of input that were clearly spanned (using only 50 inputs to code the fillers means likely each unit was the answer to each question at least once during training; again, see the spanning the input space point I made in my previous review). In the context of the literature on role-filler binding, unseen inputs mean units not used during training, not unseen combinations of units. The claim about novel fillers should be amended to something like “novel combinations of previously trained units”.


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: LEARNING TO PERFORM ROLE-FILLER BINDING WITH SCHEMATIC KNOWLEDGE
Review round: 3
Reviewer: 1

Output:
Basic reporting: This is the second submitted revision of a paper that reports artificial neural network simulation results which explore various network architectures in search of one that can learn to process encoded “word” sequences in such a way so as to allow the network to correctly identify the word that fills a particular event schema role that is queried after sequence presentation. Importantly, a network is sought which can learn this task (1) without roles being explicitly labeled in the word sequence and (2) in a way that generalizes to arbitrary role-filler combinations (i.e., exhibits combinatoric generalization).

As described below, this draft is greatly improved in comparison to the previous revision. In the judgement of this reviewer, this manuscript is worthy of publication, with any remaining contentious issues addressed through conversations between scholars in the literature.
Experimental design: The reported simulation experiments are well described. Previously elided details are now present. Concerns over imbalances in training set sizes have been explicitly discussed, adequately addressing worries about confounds.

Most importantly, the provided analyses that are intended to demonstrate sensitivity to the statistical structure of sets of training patterns, even in some of the network architectures that exhibited the strongest combinatoric generalization, are substantially improved. While some might argue for more concise methods to demonstrate sensitivity to “spurious correlations”, the logic behind the experimental designs used in this revision is certainly sound, and the results are compelling. Furthermore, the justifications for the designs reflect a deeper understanding of the theoretical issues being confronted through the provided analyses.
Validity of the findings: In a review of a previous draft of this manuscript, it was noted that the article’s discussion of the key differences between architectures likely responsible for differences in behavior failed to succinctly reflect important general insights into the causes of the reported results. That review suggested:

“From this perspective, the network architectures that succeed, in this paper, are those that contain a mechanism to retain filler vectors, as they were presented to the network, without distorting them based on the learned expected distribution of such vectors. Fast weights change in essentially the same way in response to a given input vector regardless of the past distribution of such input vectors. The reduced NTM contains explicit registers for maintaining arbitrary vectors. From this perspective, the inclusion of mechanisms that are insensitive to spurious correlations — they do not learn statistical regularities that are present in the training examples — are important for role-filler binding that generalizes in a combinatoric way.”

This critique has been fully addressed in the current revision. The issues are clearly discussed, and they are further explored in the context of the new simulations focusing on the learning of statistical relationships.

In the judgment of this reviewer, the phenomena of interest have been adequately demonstrated and discussed. While the terms used to describe these phenomena are appropriately defined and associated with their use in the literature, it is possible that other readers will still take issue with the reported findings due only to differences in preferred meanings of terms. The existence of conflicting viewpoints in the literature likely makes this problem impossible to avoid. In this reviewer’s opinion, the current revision is sufficiently clear with regard to the project’s goals and the validity of the associated findings in the context of those goals.
Additional comments: In summary, this is work that is worthy of publication. Previously raised concerns have been addressed in this revision, and no new problems are seen to have been introduced.


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: POST-EMERGENCE SEEDLING DAMAGE DUE TO VERTEBRATE PESTS AND ITS IMPACT ON SOYBEAN ESTABLISHMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is generally well-written, and the introduction clearly shows the context for the paper and shows the need for this research.  However, in some places editing for correct English language would be helpful. There are several minor misspellings (e.g. “sobean” on line 38, “majour” on line 49, “assesed” on line 170, “thier” on line 282, etc). There are also some cases of awkward wording (e.g. line 105, “was occurred” on line 171, etc).

Tables and Figures:
Table 1: It is unclear in the table (and also from the methods section) what exactly the F and p values refer to. Does this p value indicate a significant difference in emergence by year as indicated on line 124, or does it have to do with a difference by distance to the canal/residential areas?

Figures 3, 4, and 5 are very useful in visualizing the damage described in the paper.
Experimental design: The author clearly defined their research question, and I am convinced that this research is important and will be useful to inform future studies. I was unclear, however, about some aspects of the study design. In some cases, this may just require further explanation in the methods section.
1.	Lines 94-97 describe damage characteristic to hares and pigeons. Do you have a citation to support this, or did you do direct observations of vertebrates damaging plants? If so, this should be described in the methods. How can you rule out damage by other types of vertebrates (such as Corvidae mentioned on lines 226-232)?
2.	More description of the study site is needed. I cannot determine what type of habitat immediately surrounds each of the study plots. Figure 1 makes it seem that each plot is embedded within a larger agricultural field. Was the entire area planted in soybeans, or just the small plots? In addition, the size of experimental plots (line 78) seems quite small. Is this typical of the area? The size of the plot determines the amount of edge habitat, and edge effects may influence the amount and type of damage you see per plot.
3.	The terminology used in line 84 is misleading as this seems to be a purely observational study. Perhaps the authors mean “study design” or something similar instead of “experimental device?”
4.	Lines 117-119 need further clarification. Do you mean that you transformed the data in order to fit a normal distribution? What exactly did you test with the ANOVA? Just differences in damage between years?
5.	Lines 138-140 describe the effect of distance to residential area on damage, but the data are not shown. Table 1 further lists the distances to residential areas and canal for each plot. It is unclear why the data referred to in lines 138-140 are not shown when they seem to be relevant to the study. If the authors do not wish to discuss this part of the study, I suggest they remove mention of the distance effect from both the results and discussion.
Validity of the findings: Assuming the authors can justify their characterization of damage due to hares and pigeons, I found the conclusions to be well supported and explained. The authors are clear about the relatively limited scale of this study and the need for future research, but their findings represent a useful contribution to the field of study.
Additional comments: I enjoyed reading this manuscript, and found it to be fairly clear and concise. My main concerns, as stated above, are related to the justification and description of the study design. In particular, I believe the author should spend much more time explaining how certain types of damage were linked to pigeons vs hares, as this is the main premise of the study.


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

Input:
Title: POST-EMERGENCE SEEDLING DAMAGE DUE TO VERTEBRATE PESTS AND ITS IMPACT ON SOYBEAN ESTABLISHMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comments, see general comments
Experimental design: no comment
Validity of the findings: The observations are limited to one site and two years only and no particularly significant outputs or crop practices which may reduce vertebrate pest damage are supplied.
Additional comments: The manuscript supplies new information about soybean damage by two major Vertebrate Pests: the common wood pigeon (Columba palumbus) and the European hare (Lepus europaeus). The observations are limited to one site and two years only and no particularly significant outputs or crop practices which may reduce vertebrate pest damage are supplied. The reader cannot understand if the reported significant damage rates resulted in any impact on final crop stand and on yield, in terms of quantity and quality.
Material and Methods and other sections need improvements. Nevertheless information supplied represents a contribution to vertebrate pest risk assessment in soybean; at least if data will be analyzed alongside many more future data.
Therefore manuscript publication is encouraged
M&M
A complete description of material and methods should be given. Any method you use in a scientific research has to be objective, effective and replicable by anyone; therefore, all the details needed to evaluate and replicate the experiment have to be given.
All the agronomic characteristics should be given:
-	Soybean variety
-	Sowing date
-	Seed density
-	Soil texture of sampling site – variety, ...)
-	…….....

At least a short description of plants in the woody strip (bushes, trees, hedgerow nearby Midi canal) should be given (e,g. main plant species, were they high?,...)

A specific table completely separated by results should be prepared.

Current Table 1 is mixing M&M information with results and this should be avoided.

In order to improve this, I would suggest to have a Table 1 associated to M&M, with coordinates of sampling sites and the main agronomic characteristics; a second Table will give the results.

Another important factor to be considered is the presence of alternative food sources for wild fauna; other soybean fields.

L 117-118 If data didn’t meet the Normality assumption a non-parametric approach should be applied

RESULTS

L 122: The author reports information related to M&M (Cv ES Pallador); please move this information to M&M as above suggested;
L 139-140 This was the most interesting factor to show (compared to year not so interesting), why didn't the author provide at least a graph with distance from naturalistic or residential areas plotted to damage?

Discussion

L 168 – 164: it is truethat  little is known on the impact of birds and wild animals on the very early stage of field  crops but a little bit more than reported is known in Europe ; long term studies on maize damage at early stages have shown that bird/wild animal damage was low; therefore some references about maize should be added;
L 198-200 unjustified statement; please add data demonstrating the statement; there are few significant outputs of this work: why did not you present data to justify this factor effect? The reader cannot actually understand; please add relevant analyzes;
L 221-222 unjustified statement; please add reference
L 231 Negligible not negligeble
L 261 . 262: unjustified statement; please supply data demonstrating this
In  order to exploit experimental results it would be useful  to demonstrate:
-	the effect of plant damage reported in Table 1 on plant mortality and final plant density (crop stand);
-	the effect of vertebrate pest damage at early stages on yield.

Conclusion

The word IPM has never been used in the text!!  The author should add something about implications of the study results for IPM implementation (solution to contrast vertebrate pest damages in soybean)

L 268 which is the insight for future research? No spatial factor demonstrated or different effect on crop yield depending on damaged crop stage.

L273-274: Why didn't the author give an example of the output of the model using  the data base of the present work?

References
Some references does not allow to find the cited publication (e.g. Wise, K., 2018. Open Field Study with “Avipel Shield” Seed Treatment on Field Corn to Deter Birds from Feeding on Corn Seed and Corn Seedlings

Table 1: Damage by wood pigeon and hare should be identified in the columns.


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: POST-EMERGENCE SEEDLING DAMAGE DUE TO VERTEBRATE PESTS AND ITS IMPACT ON SOYBEAN ESTABLISHMENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript entitled “Post-emergence seedling damage due to vertebrate pests and its impact on soybean establishment” is well written with clear and professional English. Introduction and background of the study are adequately provided in the manuscript and relevant prior literature are appropriately referenced
Experimental design: Methods are described with sufficient information to be reproducible by another investigator. However, certain parts need to be explained in detail (See comments).
Validity of the findings: Results and conclusions are well stated and sufficiently discussed. The manuscript can be accepted after minor revision
Additional comments: Line 17: Mention the name of the authority after each scientific names at lease first time in abstract and on main text (Also add the same in Line 126)
“The common wood Pigeon (Columba palumbus…………) and the European hare (Lepus europaeus…………..)”

Line 49: change ‘majour’ to word ‘major’
Line 62 add space between ‘and2020’
Line 185-186: the sentence need to be modified as “the spotted dove, Spilopelia chinensis (Scopoli) and feral pigeon, Columba livia Gmelin……”

Line 187: Delete the sentence “and with late sowing dates”. It seems meaningless here.

Line 193: Mention the Scientific name of “European hares”.
Methodology of damage assessment in case of European hares is not clear. How the damage was assessed? How many times in a day? How did author know that the damage was due to European hares?

Line 200: (data not shown): Without data, how can author make such sentences?


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: POST-EMERGENCE SEEDLING DAMAGE DUE TO VERTEBRATE PESTS AND ITS IMPACT ON SOYBEAN ESTABLISHMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: I Think this is an overall improved manuscript, and the author made the suggested changes well. There are still a few (mainly small) issues to be addressed, as listed below.

•	Line 28, Add the word “for” after “compensate”
•	Line 33, make “crop” plural
•	Line 35, make “purpose” plural

•	In the new manuscript, the author clarifies on lines 103-105 that they used preliminary observations to identify types of damage by pigeons vs hares. However, they deleted the description of the types of damage typically caused by each, which should still be included in this paper. I see these descriptions are now in the results section. Since these are being reported as results, it seems like the authors should provide more information in the methods about their preliminary observations (e.g. how long did they watch for, did they ever see other wildlife in the field that didn’t damage the crops, etc). Alternatively, the authors could move the descriptions of types of damage to the methods section only, and then explain that they used their knowledge of the type of damage caused by pigeons vs. hares to categorize the damage data they collected and reported in this experiment.

•	On line 133 and elsewhere, the author refers to damage due to birds. Earlier you claim that all damage was specifically due to the Common wood pigeon, so please be more specific here and replace “birds” with pigeon or Common wood pigeon. Otherwise it seems that this could be caused by other bird species, which would be an important distinction.

•	The figure captions are cut off in my version of the PDF so I cannot read them to tell if they have been changed.

•	I understand the author’s reluctance to address the effect of the distance to residential area on damage due to the small sample size, and I commend them for including these data in the supplementary table. However, the reader needs to understand this limitation as well, especially since the author has still included a statement on lines 141-145 about their findings about the distance effect. I think the author needs to explain to readers that these are just observed patterns from the data, but that the sample size is too small to conduct a robust statistical test. This could potentially even go in the methods section under the statistical analysis subheading, so it is presented early on and the author is explicit about it. Alternatively, the author could opt to remove these findings from both the results and discussion section.
Experimental design: see above
Validity of the findings: see above
Additional comments: see above


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: POST-EMERGENCE SEEDLING DAMAGE DUE TO VERTEBRATE PESTS AND ITS IMPACT ON SOYBEAN ESTABLISHMENT
Review round: 2
Reviewer: 2

Output:
Basic reporting: manuscript OK
Experimental design: manuscript OK
Validity of the findings: OK
Additional comments: The author properly addressed the comments. The manuscript can be accepted after a further minir revision:

Please replace

Dimitri, G., Yuri, V., Albores-Barajas, N., Emilio, B., Lorenzo, V., Cecilia, S., 2012. Feral Pigeons: Problems, Dynamics and Control Methods, Integrated PestManagement and Pest Control Current and Future Tactics Dr. Sonia Soloneski(Ed.), ISBN: 978-953-51-0050-8, InTech,.

with

Giunchi, D., Albores-Barajas Y.V, Baldaccini N.E., Vanni, L., Soldatini, C., S., 2012. Feral Pigeons: Problems, Dynamics and Control Methods, Integrated PestManagement and Pest Control Current and Future Tactics Dr. Sonia Soloneski(Ed.), ISBN: 978-953-51-301 0050-8, InTech


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: LIGNINOLYTIC ACTIVITY OF THE PENICILLIUM CHRYSOGENUM AND PLEUROTUS OSTREATUS FUNGI INVOLVED IN THE BIOTRANSFORMATION OF SYNTHETIC MULTI-WALLED CARBON NANOTUBES MODIFY ITS TOXICITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The topic of biotransformaton of MWCN by fungi is very crucial for the environmental helath. This study
investigated the ability of fungi to MWCNTs biotransformation by peroxidases induction and
evaluation in vivo of its toxicity using Caenorhabditis elegans as a model. The manuscript was overall well organized and easy to follow. Some comments listed below may be helpful to improve the manuscript.
1.	Fig. 1 cannot clearly show the growth trend. It is recommended to set a breakpoint on the ordinate.
2.	Fig. 2A and Fig. 2B are almost identical, please ensure the raw data.
3.	There are many kinds of fungi, why choose Pleurotus ostreatus and Penicillum chrysogenum as the research objects.
4.	L109 Need to supplement the culture deposit number of GenBank.
5.	L136 The ɛ of laccase is wrong. Please re-calculate laccase activity.
6.	Please elaborate the significance of the research in the nature environment in "Results and Discussion".
7.     I suggest anthors to improve the sharpness of Figure. 3.


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: LIGNINOLYTIC ACTIVITY OF THE PENICILLIUM CHRYSOGENUM AND PLEUROTUS OSTREATUS FUNGI INVOLVED IN THE BIOTRANSFORMATION OF SYNTHETIC MULTI-WALLED CARBON NANOTUBES MODIFY ITS TOXICITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is written in clear, professional English.
The text of the article is supported by a sufficient number of references to modern scientific publications.
The structure of the article meets the existing requirements, the figures are relevant, of sufficient resolution.
In order for the results to confirm the hypotheses put forward by the authors, additional controls are required. Questions on setting controls have been added to the "Validity of the Findings" section.
Experimental design: The article corresponds to the Biological Sciences.
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
The technical level of experimental work is sufficient to achieve these goals.
It is necessary to describe more clearly the methods for separating MWCNTs from the cells of fungal cultures; it is not clear what was analyzed - pure MWCNTs without organic matter or MWCNTs with cells. How did you get rid of organic matter?
Validity of the findings: 1.Fig. 1. The dry weight is given in grams, for what volume? It is better to give the biomass concentration in g / l.
2. Fig. 2. Ligninolytic activities on P. chrysogenum and P. ostreatus cultures grown in presence of MWCNTs: The black line on the graph corresponds to the MWCNTs. In this case, what was the carbon source for the fungi, was it a yeast extract? When glucose and lignin were added, was it yeast extract + glucose, etc.?
3. Fig. 3. Raman spectra of P. ostreatus and P. chrysogenum cultures grown with MWCNT supplementation: The figure shows the Raman spectrum of MWCNTs modified under the influence of fungal cultures? In this case, adjustments should be made to the caption to the figure; from the caption, one might think that this is a spectrum of fungal cells. I believe that control of MWCNT should be presented in these media, but without fungal cultures, 0 and 28 days.
4. Fig. 4. How was MWCNT separated from lignin? Precisely the spectra of MWCNTs are presented, without lignin impurity? Where is the spectrum of pure MWCNTs without lignin?
5. Fig. 5. What is shown in the figure K-M and H-O - these are nanotubes? It should be pointed out, it is not clear from the figure. The figure caption indicates that these are images of fungal cultures. In the rest of the drawings, is it the backing grid or cells? It should be pointed out. The images must be signed, at first glance they are incomprehensible, only nanotube aggregates are clearly identified.
6. Fig. 6. Data missing: 0 day for cultures + MWCNT + glucose, cultures + MWCNT + glucose + lignin. Or it is incomprehensibly described in the figure captions. How was point 0 taken - is it a culture medium containing nutrients (yeast extract?) and an inoculum, or pure MWCNT + lignin?
7. Fig. 9. There is no data on how the culture medium of pure fungal cultures affects the worms (without the addition of MWCNT).
8. Fig. 10. It should be clearer to decipher a, b, c, d in the figure (or more clearly describe the statistical analysis in the Materials and Methods). How were the units of fluorescence correlated with the number of living worms? Was the increase in fluorescence due to more live worms, or due to oxidative stress?
9. How to explain that MWCNT + glucose gives an increased fluorescence of recombinant worms (Fig. 10), while glucose in the fungal cultivation medium suppresses the activity of the studied enzymes (Fig. 2)? According to the authors, these enzymes modifying MWCNTs and increasing their toxicity (line 380-383) which leads to oxidative stress and increased fluorescence of the worms. It is worth discussing these results in more detail.
Additional comments: I believe that the article should clearly indicate whether the modification of MWCNTs was studied without admixture of cells and organic matter, in this case, describe in Materials and methods how the MWCNTs were separated from cells that could partially be in the culture medium, forming aggregates with MWCNTs. Then it is necessary to correct the captions to the figures, to avoid phrases like "Raman spectra of P. ostreatus and P. chrysogenum cultures ..."


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: LIGNINOLYTIC ACTIVITY OF THE PENICILLIUM CHRYSOGENUM AND PLEUROTUS OSTREATUS FUNGI INVOLVED IN THE BIOTRANSFORMATION OF SYNTHETIC MULTI-WALLED CARBON NANOTUBES MODIFY ITS TOXICITY
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overall, the English language is OK.
The introduction must contain the remarks of "mycoremediation."  Mushroom is used for the one of the main strain for that.
Experimental design: The manuscript meets the aims and scope of the journal.
Some data for the conclusion are missing; mass balance for the degradation (GC data needed).
It is unclear why the growth curves are the same between glucose and lignin as well as other experimental sets (Fig. 1).
For TGA analyses, the physical mix of mycelium and MWCNT must be included in the experimental sets for comparing to 28 day data.
Fig. 7 is too complicated; it should be rearranged for clear results.
Validity of the findings: The data for fungal growth and enzyme production are ambiguous. The authors should explain how the three ligninolytic enzymes attack the lignin and CNT based on the enzyme production.
In Fig. 2, A and B are the same. The growth patterns are the same btw the two strains, but the enzyme production patterns are rather different. This phenomena should be comprehensively discussed with appropriate references.
The mass balance are missing and the metabolite data should be included for the conclusion.
Additional comments: The topic is interesting and suitable for the journal. However, it cannot be published unless some data and comprehensive discussion are to be supported.


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: LIGNINOLYTIC ACTIVITY OF THE PENICILLIUM CHRYSOGENUM AND PLEUROTUS OSTREATUS FUNGI INVOLVED IN THE BIOTRANSFORMATION OF SYNTHETIC MULTI-WALLED CARBON NANOTUBES MODIFY ITS TOXICITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The necessary explanations and corrections were made in the text of the manuscript.
Validity of the findings: There are no comments on the revised manuscript.
Additional comments: I thank the authors for the attentive attitude to comments and questions. All necessary changes have been made to the manuscript. I believe that the revised manuscript can be accepted for publication.


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

Input:
Title: LIGNINOLYTIC ACTIVITY OF THE PENICILLIUM CHRYSOGENUM AND PLEUROTUS OSTREATUS FUNGI INVOLVED IN THE BIOTRANSFORMATION OF SYNTHETIC MULTI-WALLED CARBON NANOTUBES MODIFY ITS TOXICITY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Overall, all the comments were clearly answered.
Experimental design: Some comments are well answered and others revised with detailed info.
Validity of the findings: Results and discussion were cleared revised.
Additional comments: The revised manuscript was overall well organized and easy to read. It can be published as it is.


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: NUTRITIONAL CONTENT OF TOTOABA MACDONALDI (GILBERT, 1890), ANTIOXIDANTS AND LIPID PEROXIDATION IN MUSCLE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Basic reporting is at the high level in the manuscript. Paper is well structured and quite well written, though some broken sentences do occur, and paper requires extensive proof reading for the minor typos and minor lexical improvement ( I marked some of the issues in the pdf attached).
I think that introduction should be restructured, to show the importance of studying oxidative stress and antioxidants, especially in application to totoaba. Now the introduction is quite disconnected from the research hypothesis. Also, since we are talking about totoaba here, I think it is important to mention connections between the totoaba fishing an expiration of the vaquita. Also please note that some references consistently failed to render properly (see annotated pdf).
Experimental design: I think design and statistical analysis are sound enough, but I would like to have more explanations regarding two following points:
1) why authors limited amount of the GLM's analysed is only 5 per enzyme? why not to run more models say with bootstrapping and then select the best ones based on AIC?
2) Please explain better how have you address unequal amount of the specimens in the different samples (i.e. from different ontogenetic stages or habitats. Also please check if all the raw data is attached.
Validity of the findings: I think findings of the paper are well supported by the analysis. I am especially excited about ecological and ecotoxicological implications of the paper, regarding the totoaba's oxidative stress reaction to the extraneous factors.
Additional comments: I would like to congratulate authors on a brilliant paper, dealing with such valuable and vulnerable species of the aquaculturaly important species. I think you done a great job showing ecotoxicological and environmental drivers behind the levels of the oxidative stress in totoaba. Please make larger emphasis on this part of your findings in the text (see pdf attached for the 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: NUTRITIONAL CONTENT OF TOTOABA MACDONALDI (GILBERT, 1890), ANTIOXIDANTS AND LIPID PEROXIDATION IN MUSCLE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic reporting: The report was fairly written with good English not confusing to the reader. Introduction and background of the study were averagely well written and referenced to explain why and purpose of the research. Standard laboratory analytical methods were applied  under materials and methods. Figures and Tables were fairly clearly displayed and presented, respectively. Raw data were also supplied.
Experimental design: Experimental design: The primary research was original and within the scope of the Journal. The major weakness of the study is experimental design. Further studies should be done with an acceptable design to discuss results better. This is also to assist in the repeatability of the research.
Validity of the findings: Validity of findings: Findings of the research were  fairly valid based on the statistical analyses employed after data collection.
Conclusions require slight modifications depending on specific objectives of the study.
Additional comments: General comments: The authors analyzed and compared the antoxidant enzyme activities and lipid peroxidation levels in the muscle of totoaba, endemic species of fish found in Gulf California. Samples of the fish were collected from different locations and seasons along the route which the fish migrate to assess potential variation in nutritional content based on when or where the fish was caught. The paper is publishable but some issues as follows have to be addressed:
1.	Title: Authors have to explain why title has reference and the way it was framed; why not as an instance: Effect of different locations and seasons on antioxidant enzyme activities and lipid peroxidation levels in the muscle of Totoaba Macdonaldi from Gulf California? Or Nutritional content of Totoaba Macdonaldi 2: Antioxidants and Lipid Peroxidation in the Muscle

2.	Introduction: Objectives/aims written at the end of introduction requires modification. They could be listed as specific objectives (lines 76 to 79).

3.	Materials and methods: Line 84: The statement with exclamation ‘Error-reference not found’ should be deleted or else authors would want readers to suggest references for them.

ii. What method of sampling was employed? Line 93-94 showed that gill net was used. Source of the net should be mentioned for the purpose of repeatability. Line 96-liquid nitrogen from where? Line 125: cited reference is better written once than repetition e.g. Perky et al. (Perky et al., 2000), Reference inside bracket should be enough
iii. Authors should explain why the study has no identifiable experimental design. The statistical analysis was quite complex!

4.	Results and discussion: Authors tried to present and discussed the results and the findings fairly well. However, it would have been better with experimental design.

5.	Conclusions: There should be slight modifications in the conclusion bearing in mind that conclusions from research studies are made considering the specific objectives and the various findings as discussed under results and discussion. Statement of lines 335-337 is a strong point under the conclusion.

6.	References: Authors tried in the listing of the references for the report. However, three references were discovered not listed but cited inside text: Mala et al., 1997-line 42; Konietzko and Schwertz, 2016- line 50; Mexico’s….2001-line 46


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: NUTRITIONAL CONTENT OF TOTOABA MACDONALDI (GILBERT, 1890), ANTIOXIDANTS AND LIPID PEROXIDATION IN MUSCLE
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: General comments:
The results obtained are good and useful information and it is appropriate for publication.

Introduction: it is mentioned that there is a different paper regarding the nutritional aspect. So, i think this paper can be independent without reference to another unpublished paper. It is ok to state that there will be another paper regarding the nutrition value, but no refer to them since it's not published yet.
- line 51-52 “...however, information...is scarce” this sentence is not needed in this part, because the main study is in stress oxidative and enzymatic antioxidants.
- Line 56-57: “...thus, the aim of this study...of totoaba.” also the same. The aim of the study is to study the stress oxidative and antioxidants and it is already well mentioned in line 76.
- Line 58: content of trace element (accompanying paper). I think its not appropriate to cite unpublished paper, I suggest only focus on antioxidants and lipid peroxidation.

Materials and Methods:
- Sampling (line 82): change to “sample collection and preparation”
- Sample preparation: Join the sampling section. Is there any reference for this technique to prepare the muscle sample?
- Part of sampling explanation in statistical analysis (line 173-179) should be moved as first part of “sample collection and preparation”
- What about the replication of the analysis? Its not mentioned in  the manuscript
- Wavelength of spectro. I think it would be better if the word “wavelength” is mentioned everytime the wavelength number is mentioned.  For example: line 133 “... at 530 nm wavelength”.
- The 3 seasons sampling. It is mentioned that in summer, fish go deeper (line 68-69). Is this the main reason no sample was done in summer? If yes, I think it should be stated clearly in the sample collection section.
- Line 176: “Figure 1 accompanying paper” is not necessarily needed.

Results:
- Line 201, why aren't all genders found in all seasons? Are there any specific reasons?
- it is confusing and difficult to understand as a reader because they are mixed. it would be better  if the results are separated and compared for each habitat in separate sections or subheadings:
Estuaries
Rocky area
Continental area
- line 222 and 226, k=9, if I understand it well, table 3 shows the k should be 10. please check and confirm

Discussion: well described

Conclusion: the conclusion is not in a good order. Conclusion should be made based on the results obtained.
- The first sentence can be a suggestion after conclusion is stated.
- Omega-6 HUFAs were not studied in this study, so its not necessary to refer this in conclusion
- Line 335 should be mentioned firstly.

Figure and table
- Table 2: It will be easier to read if the data is shown in mean with standard deviation. why the data are not shown in mean with the standard deviation? Is there any specific reason?
- Table 3: line 1 (Table 3) the tile should be "Table 3. Statistics of ..."


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: NUTRITIONAL CONTENT OF TOTOABA MACDONALDI (GILBERT, 1890), ANTIOXIDANTS AND LIPID PEROXIDATION IN MUSCLE
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: The aspect of experimental design has been addressed.
Validity of the findings: The findings are valid.
Additional comments: No comments.


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

Input:
Title: NUTRITIONAL CONTENT OF TOTOABA MACDONALDI (GILBERT, 1890), ANTIOXIDANTS AND LIPID PEROXIDATION IN MUSCLE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Clear and well-described
Experimental design: has been improved
Validity of the findings: well described
Additional comments: Thank you for the revision. Please find some minor comments. I hope it can improve the manuscript for better understanding for the reader.

Introduction:
Line 81: please add “which affect the quality of their muscle”  AFTER  “...biological factors throughout its lifespan.”
Line 85: “when and where” change to “season and location”

Materials and Methods:
Line 97: “Filed”, change to “field”
Line 132-190: please include the repetition in the analysis of parameters conducted, is it 2 replication or three replication.

Results, discussion and conclusion: well-described.


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: TRANSCRIPTOME ANALYSIS REVEALED GENE REGULATORY NETWORK INVOLVED IN PEG-INDUCED DROUGHT STRESS IN TARTARY BUCKWHEAT (FAGOPYRUM TARARICUM)
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this manuscript, authors presented some work regarding Transcriptome analysis revealed gene regulatory network involved in PEG-induced drought stress in tartary buckwheat (Fagopyrum Tararicum Gaerth). There are the following important issues in the manuscript.
1. Abstract
The abstract must be self-contained and concisely describe the reason for the work, methodology, results, and conclusions.
2. Introduction:
Lines 46-50: You should provide the literature you cite.
Lines 57-61: Do you want to express some drought induced genes in Tartary buckwheat have been identified. You should provide the literature you cite.
Your introduction needs more detail. I suggest that you improve the whole description to provide more justiﬁcation for your study (Have the physiological and transcriptional changes of Tartary Buckwheat under drought stress been explored (Lines 55-57)? Whether the transcriptome analysis of Tartary Buckwheat under drought stress has been reported? Is there any difference between this study and the previous report? Why should the author do this research again?).
In addition, the author did not elaborate the present research progress of Tartary buckwheat clearly. Many important transcription factor families that regulate growth and development and resist environmental stress have been identified in Tartary buckwheat, including AP2/ERF, BHLH, NAC, ARF, et al. Meanwhile, transcriptome analysis related to Tartary buckwheat development have also been reported (Liu et al. Insights into the correlation between Physiological changes in and seed development of tartary buckwheat (Fagopyrum tataricum Gaertn.). BMC Genomics (2018) 19: 648). The public information would be helpful identifying important candidate genes.
The author does not clarify the scientific problems of this study in the introduction. The introduction part is not well written and needs to be rearranged.
Lines 20, 38, 40, and many more, including lines 174, 185 and so on. Instead of »tartary buckwheat« correct to »Tartary buckwheat«, where applicable. In difference to »common buckwheat« (with lower-case first letter), »Tartary buckwheat« should be in English always written by upper-case first letter; this way of writing was internationally accepted, among others in the discussion on International Buckwheat Research Association (IBRA) Assembly in 2013, as word »Tartary« comes from the name of the Tartar people.
3. Methods:
Line 94: Why choose these four time points (0 h, 1 h, 3 h, and 6 h)?
Whether the author uploaded the raw data?
4. Results:
Lines 185-195: The descriptive results of physiological indexes after drought stress were provided. What readers want to know is how to explain the fluctuation of these physiological indexes and whether there is a reasonable explanation. Is there any change in the phenotype of Tartary buckwheat after drought treatment for different time?
Lines 213-215 and so on: Spaces are required between numbers and units.
Line 307: Should it be NECD or NCED?
5. Figures:
In Figure 2 and figure 3, there should be a space between the number and the unit in the abscissa
Figures 1, 2, 8, and 9 have multiple parts. Each figure with multiple parts should have alphabetical (e.g. A, B, C) labels on each part and all parts of each single figure should be submitted together in one file. In this case:
The 5 parts of Figure 1 should be labeled A-E.
The 5 parts of Figure 2 should be labeled A-E.
The 18 parts of Figure 8 should be labeled A-R.
The 7 parts of Figure 9 should be labeled A-G.
Please provide replacement figures measuring minimum 900 pixels and maximum 3000 pixels on all sides, saved as PNG, EPS, or PDF (vector images only) file format without excess white space around the images.
Text and figures legends should also be adjusted appropriately
6. References:
Please check the style of references. There are many references with incomplete formatting and missing page numbers, for example, “Abdel-Ghany SE, Ullah F, Ben-Hur A, and Reddy ASN. 2020. Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress. Int J Mol Sci 21. 10.3390/ijms21030772”.
7. Language
The English language should be improved to ensure that an international audience can clearly understand your text. Some examples where the language could be improved include lines 199, 174-176, 177– the current phrasing makes comprehension diﬃcult.


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: TRANSCRIPTOME ANALYSIS REVEALED GENE REGULATORY NETWORK INVOLVED IN PEG-INDUCED DROUGHT STRESS IN TARTARY BUCKWHEAT (FAGOPYRUM TARARICUM)
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1.English language and style. Moderate English changes required .
2.Introduction part must be significantly improved, some background of candidate genes should be added, for example: what is the candidate genes and why it needs to identify etc.
3.Are the methods adequately described?
4.Is the research design appropriate?
5.Why choose Jinqiaomai2 as the material?
6.The discussion part must be improved. In this study, the relationship between physiological changes and transcriptome data, and changes in gene expression under drought stress?
7.Supplement LEA protein expression experiment.
8. Authors must be highlighted the significant results found in this study as a conclusion.


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: TRANSCRIPTOME ANALYSIS REVEALED GENE REGULATORY NETWORK INVOLVED IN PEG-INDUCED DROUGHT STRESS IN TARTARY BUCKWHEAT (FAGOPYRUM TARARICUM)
Review round: 1
Reviewer: 3

Output:
Basic reporting: Drought is a major environmental factor can influence yield and quality of crop. The work used the transcriptome to analyze the effects of drought on gene expression in Tartary buckwheat. The overall design and experiment of this paper are relatively complete. But there are some small questions that need to be answered.
Experimental design: This study design is accord with the standard experimental design of transcriptom.
Validity of the findings: 1.	Line 251, sight maybe wrong, should be slight.
2.	Finally, the transcription factors selected by you may be involved in Tartary buckwheat drought stress. You should verify the expression of these transcription factors again by qRT-PCR.
3.	In the third paragraph of the results you don't seem to have written about gene expression, so the subtitle might leave out the “global analysis of gene expression”.
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: TRANSCRIPTOME ANALYSIS REVEALED GENE REGULATORY NETWORK INVOLVED IN PEG-INDUCED DROUGHT STRESS IN TARTARY BUCKWHEAT (FAGOPYRUM TARARICUM)
Review round: 2
Reviewer: 1

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


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

Input:
Title: TRANSCRIPTOME ANALYSIS REVEALED GENE REGULATORY NETWORK INVOLVED IN PEG-INDUCED DROUGHT STRESS IN TARTARY BUCKWHEAT (FAGOPYRUM TARARICUM)
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have adequately addressed all of my comments and suggestions.


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: TRANSCRIPTOME ANALYSIS REVEALED GENE REGULATORY NETWORK INVOLVED IN PEG-INDUCED DROUGHT STRESS IN TARTARY BUCKWHEAT (FAGOPYRUM TARARICUM)
Review round: 2
Reviewer: 3

Output:
Basic reporting: The revised manuscript satisfied with my suggestion and reach the requirement of acceptance.
Experimental design: The revised manuscript satisfied with my suggestion and reach the requirement of acceptance.
Validity of the findings: The revised manuscript satisfied with my suggestion and reach the requirement of acceptance.
Additional comments: The revised manuscript satisfied with my suggestion and reach the requirement of acceptance.


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: SYSTEMATIC ANALYSIS OF JMJC GENE FAMILY AND STRESS-RESPONSE EXPRESSION OF KDM5 SUBFAMILY GENES IN BRASSICA NAPUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript studied Jumonji C (JmjC) proteins in plant development and stress response
through the removal of lysine methylation from histones. Real-time quantitative polymerase chain reaction (RT-qPCR) and some bioinformatic prediction tools were used to support the functional Group-KDM5 genes responded to in various stress responses.
The manuscript provided basic provide a basis for future functional characterization of the Jumonji C (JmjC) proteins in stress response.

The introduction does well organize paragraphs in order to emphasize the necessity of this study. Literature is well referenced and relevant on studied topic. Discussion part repeated some data mentioned in result part. Shorten discussion part is recommended.
Experimental design: Methods was described with sufficient detail and experimental/bioinformatics tools used in this research was well defined, relevant and meaningful.
Validity of the findings: The impact and novelty of this manuscript are assessed. Overall, this manuscript was qualified for publication with minor revision.
Minor comments:
 Figure 8: the graphs are too small to read out.  I recommend that the data can be illustrated as different figures for drought, high temperature and NaCl stress. Adding axis title
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: SYSTEMATIC ANALYSIS OF JMJC GENE FAMILY AND STRESS-RESPONSE EXPRESSION OF KDM5 SUBFAMILY GENES IN BRASSICA NAPUS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors present a systematic analysis in Brassica napus of the JmjC gene family and an analysis of the KDM5 subfamily gene responses to stress. They made a comparative analysis of the genes members conservation based on phylogeny and protein structure/motif comparison and using the parental genome relatives. Although the bootstrap values were sometime weak, the topology found was coherent with previous work or confirmed by analyses focused on each clade. Therefore, the presented data is sound as an analysis of the redundancy and expansion of the JmJC gene family in the alloaphiployd B. napus and not for an evolutionary work as is stated in some sentences. Such study provides a frame to analyse the functional conservation of a group of paralogs as provided by the authors, by studying the response of the KDM5 members to stress.
Experimental design: The experiments was well conducted
Validity of the findings: The data are sound and well support the manuscript. However, they do not support any analysis of family evolution and should remain as a comparative analysis of the JmJC in Brassica napus. As stated before, the bootstrap values are low and only the large clade and few subclades are support. So all statement about family evolution should be remove from the text, especially when the authors do not discuss the low value of some branches. In addition, a paragraph of the discussion is redundant and should be remove for a clear reading of the manuscript.
Additional comments: The presented data is sound as an analysis of the redundancy and expansion of the JmJC gene family in the alloaphiployd B. napus and not for an evolutionary work as is stated in some sentences. Such study provides a frame to analyse the functional conservation of a group of paralogs as provided by studying the response of the KDM5 members to stress.

Major comments
Figure 8 is of bad quality and could not be read and checked
Rewrite the end of the background in the abstract, please. The sentence starting line 80 is better appropriate “The protein organization and function of JmjC domain in Brassica species and its relative relationship with model plant Arabidopsis….”
Line 185, please rewrite the last sentence of the paragraph
Line 366 please add “might indicate” instead of indicate
It is not clear to me what is discuss in beginning of the paragraph “Conservation and Function of JmjC Proteins of B. napus” starting line 381. The information is repetitive with the above introduction and results. I suggest the author to remove this part until line 421
Instead, the author could discuss about the reduction/expansion of some clade depending of the function of their known paralogues in Arabidopis or Rice development or about similar observation found for the mads-box family by Wu et al (even if their title is not right).
Line 425 should be rewritten and the evolution idea removed
Minor comments
Line 127, add the substrates used
Please indicate the title of the C column in supplementary data1
Sup figure have poor bootstrap value and cannot be used to draw any conclusion
Line 475 replace evolutional by divergent


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: SYSTEMATIC ANALYSIS OF JMJC GENE FAMILY AND STRESS-RESPONSE EXPRESSION OF KDM5 SUBFAMILY GENES IN BRASSICA NAPUS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: JmjC homologous proteins play critical roles in plant development and stress response. The manuscript by He et al. reports a genome-wide survey and analyses of this gene family in Brassica napus genome. Firstly, the work performed a genome-wide identification of the JmjC homologous genes in B. napus genome, and then performed the phylogenetic and genomic analysis (chromosomal distribution, gene and protein structure analysis) of the candidates, followed by the expression profile analysis of the KDM5 subfamily under drought, high temperature, and NaCl stresses by qRT-PCR. The methods in this study are relevant and are well applied for most of the study. This type of study falls within the scope of PeerJ. The major results of this study are based on Bioinformatics analysis, which is an important fundament for further functional researches of the candidate BnJmjCs in the future. However, the manuscript is mainly descriptive, and is not well organized with many grammatical in the whole text. Some major points listed below should be corrected before it could be accepted for publication in this journal.

Major comments:
1.	Line 1, the title of this ms needs to be correct, as its meaning is obscure.
2.	Line 25, “JmjC domain” should be “JmjC proteins”?
3.	Line 26, “Arabidopsis” should be in italic. And this problem should be amended in the whole text.
4.	Line 28-30, the current content in this part did not describe the main ideas and methods applied in this study well. Thus, it should be re-wrote.
5.	“Results” part in “Abstract”, the main results of this study are not summarized well and are not highlighted enough.
6.	Line 32, the statement of “These genes were grouped into seven clades base on the analyzation for JmjC sequences” is unconvincing, as mentioned in the main text, the classification of this gene family was based on the phylogenetic analysis?
7.	Line 36-37, the statement of “Furthermore, BrKDM5 genes were examined under stress conditions due to their crucial functions in H3K4 demethylation” is meaningless. The authors should focus on the result of this analyses here, and should illustrate the detail stress treatments as well.
8.	Overall, the contents in “INTRODUCTION” section is not well organized, especially these in line 59-85. Moreover, the contents in this section is too long, it is better to compress it. The authors should focus on the theme of this study, and highlight the KDMs instead of the other histone modification events.
9.	Line 130-133, the description about the identification of candidate JmjC protein sequences is not clear. Moreover, “O. sativa” in line 133 should be in full name instead of abbreviation for the first time in the ms.
10.	Line 160, “3 days” should be “at 3 days”?
11.	Line 161, “in 40 °C” should be “at 40 °C”?
12.	Line 168-169, it is better to use at least two reference genes in the qRT-PCR analysis.
13.	Line 177, “C-genomics” and “A-genomics” should be “C subgenome” and “A subgenome” or “Cn subgenome” and “An subgenome”.
14.	In the section of “Chromosome Maps of JmjC Genes in Brassica”, it’s better to describe the nomenclature method of the candidates and supplied a table to show the major features of the candidates.
15.	Line 196-197, why the proteins should be renamed in this part?
16.	Line 197, “hasthe” should be “has the”. Moreover, why the NJ tree is better than the ML tree? What is the reason? In general, it is more credible if the results got from different methods were the same or very similar. Furthermore, in line 139-145, “Analysis of JmjC sequences” in the method section, the authors just described the method used for constructing the NJ tree. The method of constructing ML phylogenetic tree was not supplied.
17.	The authors stated in line 101-103 that the Arabidopsis JmjC proteins were divided into five subfamilies. However, in line 199-200, this gene family was divided into seven subfamilies. Why the KDM5 and Jmic domain-only subfamilies were classified into two subfamilies respectively? As shown in Figure 2, the bootstrap value of KDM5A clade is very low, so, what is your criterion to divide the KDM5 subfamily into KDM5A and B subfamilies?
18.	Line 244-248, the authors should focus on their own results in the “Result” section. In general, it is not allowed to cite the results from any reference in this part. If there is any extensional meaning about your result, it is better to discuss it in the “Discussion” section.
19.	Line 354, the title of “KDM5 Expression in Abiotic Stress” is very strange. What’s your mean? Moreover, there are many grammar mistakes in the contents of this section.
20.	Line 355, “KDM5 genes” should be “KDM5 homologous genes”. Accordingly, the authors should uniform the name about this issue in the whole text.
21.	Line 364, the meaning of “Under drought 5 or/and 10 day” and “drought 15” are confusing.
22.	Line 379, “an subgenome” should be “An subgenome”? And the naming style of the two subgenomes of B. napus should be uniformed in the whole text.
23.	Line 380, the authors should describe the method to calculate the “retention rates” in “Method”.
24.	Line 396-397, what’s your mean about “Gene duplication events were confirmed by Yang et al. (Yang et al., 2008) and Sun et al. (Sun et al., 2015)”?
25.	Line 422, “base on” should be “based on”?
26.	Figure 5 is too large. And the authors should indicate the meanings of the labels and/or marks in the figures, such as the triangle in Figure 5H, etc.
27.	The letters of A-T are not necessary in Figure 8-10. And the words of “Drought stress”, “High temperature stress” and “ NaCl stress” should be removed from these figures respectively.
28.	There are many grammatical mistakes in this paper. I recommend language editing for this paper.


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: SYSTEMATIC ANALYSIS OF JMJC GENE FAMILY AND STRESS-RESPONSE EXPRESSION OF KDM5 SUBFAMILY GENES IN BRASSICA NAPUS
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Comments to the Author (s):

Many of my comments have been addressed. The quality of this manuscript had been greatly improved this time. I think that this new revision can be accepted for publication now. However, there still are some problems which should be addressed before it can be published.

Major comments:
1. As I have stated in the first round, there are many mistakes in English style and grammar that can be found throughout the manuscript. For example, line 30, “synonymous” should be “Synonymous”; line 32, “the expression level” should be “the expression levels”, line 40 “treatment” should be “treatments”; line 345, “day” should be “days”; line 348, “BnJMJ16;a, BnJMJ17a/b and BnJMJ18;a expression was induced” should be “ the expressions of BnJMJ16;a, BnJMJ17a/b and BnJMJ18;a expression were induced…”, etc. Therefore, I suggested the writing needs to be thoroughly checked and substantially improved by an English language editing company, again.

2. line 37, the statement of “exceeded whole genome level” is obscure. It is better to state or define it more clearly to avoid confuse.

3. Line 39-40, the sentence of “Furthermore, BrKDM5 subfamily genes were examined under stress conditions” should be deleted from this section.

4. Line 44, “expression profiles indicated that” could be “expression profiles of many …”

5. Last time, I have suggested that “Overall, the contents in INTRODUCTION section is not well organized. Moreover, the contents in this section is too long, it is better to compress it. The authors should focus on the theme of this study, and highlight the KDMs instead of the other histone modification events.” Although the authors have did some amends in this part, the problems that I mentioned last time are still existed here. The length is too long, such as the second paragraph has up to 48 lines. The contents in this part should focus on “JmjC proteins” or “KDM proteins”. In addition, as we know, the last paragraph in “INTRODUCTION” section is generally about the aim and main researches in the ms. However, these contents were missed in this ms.

6. Line 114, “Oryza sativa sequences” should be “The JmjC protein sequences in Oryza sativa…”.

7. Line 126, “The resulting files” should be “The multiple sequence alignment result…”. Moreover, in general, the bootstrap test in ML analyses is 100 replicates. Are you sure you used “1000 replicates”?

8. Line 128, please check whether you used the CDS sequences of the candidates to create the logo maps? It should be proteins sequences in Figure 3 to 7?

9. Line 161-162, the statement of “and 8 genes were still on scaffolds, in which 5 were from Cn subgenome and 2 from An subgenome” is right? 5+2=7?

10. Line 167-168, “Four tandem JmjC genes pairs located on chromosomes A03, A09, and C03 in B. rapa (Fig. 1).” should be “Four tandem JmjC genes pairs located on chromosomes A03, A09, and C03 in B. napus”?

11. There are still many mistakes in the section of “Stress-response expression of KDM5 subfamily genes”, such as line 324, “under salt, drought and high temperature” should be “under salt, drought and high temperature treatments”; line 345, the meaning of “drought 15” is confusing, etc.

12. The A-D parts in Figure 1 should be presented in four parts instead of A/B and C/D (two parts).


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

Input:
Title: THE CLASSIFICATION OF EEG-BASED WINKING SIGNALS: A TRANSFER LEARNING AND RANDOM FOREST PIPELINE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is largely unambiguous and with sufficient background. The hypothesis and results are convincing to a large extent. Nevertheless, the author  might consider reviewing the following.

Consider changing the sentence in lines 68-70 to "Particularly, a successful BCI primarily has two main requirements including a set of suitable electroencephalogram (EEG) features and an efficient machine-learning algorithm to classify the extracted features."

Also note that Transfer Learning does not apply only to CNN models or computer vision as implied in lines 76 and 164. It can be applied to other deep learning architectures.

Change "myriad" in line 111 to "several" or "a number of".

Please modify the statement, "It is worth noting that such a pipeline has yet been investigated with regards to wink-based EEG signals" in lines 114-115 to something like this: "It is worth noting that this is the first study to investigate such a machine learning pipeline with regards to wink-based EEG signals".

Change "till" in line 131 to "and".

Please delete "to transpire" in line 184.

Correct the spelling for "Inception" spelled as "Ineption" in Figure 5.
Experimental design: The technical and ethical standard of the work is acceptable. However, the methods need to clarified.

i) For instance, the method of transfer learning used was not fully described.
Were the retained pretrained layers' weights frozen or not during training of the classifiers? What is the justification for the approach adopted? E.g., performance reasons?

Further, there other clarifications that need to be provided to facilitate replication of results.

ii) What is the justification for the addition of RF classifier in the classification pipeline?
Was the performance of the TL models investigated in exclusion of the RF classifier?
What is the performance of the different TL models in that scenario?

iii) More so, you might want to check the performance of the RF classifier alone (i.e., in exclusion of TL).

The performance values realized from (ii) and (iii) could serve as a reference to demonstrate the benefit of the methods (combining TL and RF) applied in this study.

iv) Please include specificity and ROC AUC metrics to the performance evaluation metrics.  In particular, It would be nice to consider specificity alongside the sensitivity values except the classes are balanced in the datasets.
Validity of the findings: The conclusion is in line with the aim of the study. However, clarification of the issues raised in the experimental design can improve the significance of findings.
Additional comments: No additional comments


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

Input:
Title: THE CLASSIFICATION OF EEG-BASED WINKING SIGNALS: A TRANSFER LEARNING AND RANDOM FOREST PIPELINE
Review round: 1
Reviewer: 2

Output:
Basic reporting: A critical concern in this manuscript is that the authors used a very poor English to present. There are a lot of grammatical errors and typos. It is hard to follow and capture the ideas with poor English. Therefore, the authors should have an extensive revision on the English. It is important if it can be checked by a native speaker or English editing service.
Literature review are weak. The authors should show more latest works on the different feature extraction and classification techniques for EEG signals system.
Quality of figures should be improved. Now resolution is low.
Experimental design: The authors should release source codes for replicate the results.
How many experts were used for labeling? How to decide the experts?
Random algorithm has been used in previous works for classification of EEG. Thus the authors should refer more works to attract broader readership.
Validity of the findings: The authors have not compared their performance results with the previous works on the same problem. Therefore, it is not enough to convince the impact of the study.
The authors should have some independent tests on the model.
More discussions need to be added.
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: THE CLASSIFICATION OF EEG-BASED WINKING SIGNALS: A TRANSFER LEARNING AND RANDOM FOREST PIPELINE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thanks to the author.
The concerns raised in my previous review have been largely attended to.
Experimental design: No additional comments.
Validity of the findings: No additional comments.
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: AGGRESSIVENESS-RELATED BEHAVIOURAL TYPES IN THE PEARLY RAZORFISH
Review round: 1
Reviewer: 1

Output:
Basic reporting: - Basic reporting is generaly fine.

- Some article should be added. In particular articles realted to ecological aspects of aggresiveness in similar marine species and studies that criticize the mirror test.

- Hypotheses should be better contextualized
Experimental design: - Research within the scope of journal

- Some work to be done on contextualizing research hypotheses

- Information is sufficient to replicate the study
Validity of the findings: - The finding are valid and correctly exposed to the reader.

- A specific paragraph should be added to address limitations and possible biases of sampling methods.
Additional comments: I read with great interest the paper entitled “Aggressiveness-related behavioural types in the pearly razorfish”. I think it is an interesting study that deals with individual personality of a very interesting model system. I think the model system presented in this paper and the methodological approach is a very promising research tool and I hope my comments will help the authors to improve the quality of the manuscript.

The topic in interesting and timely, however I have several major concerns that are listed below together with some minor comments.

1) I think the title needs some rethinking. The paper investigates the behavior of fish in front of a mirror and the results do not demonstrate that this is “aggressiveness-related”. It is an open discussion in the literature. The authors reported some papers about it (e.g., Balzarini et al. 2014), but I think they cannot demonstrate if the behaviours presented here are aggressiveness-related or not. This aspect should be made clear.

2) I would avoid terms such as “for the first time” or “novel”. I think it is not necessary.

3) The introduction ends with the statement of the working hypotheses. However, I think a that the introduction needs more work to better prepare the reader for the working hypotheses. The great part of the information is already in the introduction, but needs a better logical structure. I tried to make some suggestion in the following points.

4) The first paragraph of the introduction introduces the topic of personality trait, but I think that “Behavioural types and syndromes are widespread across taxa (Réale et al., 2007), although its causes and consequences in marine fish species have scarcely poorly considered (Hutchings, Bishop McGregor-Shaw, 1999; de Jong et al., 2009; Millot et al., 2014)” is not a good justification for the study. What I mean is that the first paragraph of the introduction should end with the overall importance of the study, but I think the fact that something is scarcely considered in marine fishes is (by itself) not a major justification to investigate it. I think this paragraph should be refocused by removing all technical information related to “R”, which suits more in the methods.

5) Conrad et al 2011 is used as main reference for personality traits, however I think Réale et al 2010 should also considered here. Moreover, several sentences need a proper reference such as lines 62-63. Please check the rest of the manuscript for similar situations.

6) There is an open discussion in the literature regarding the mirror test. I think the author did a good but not complete job in addressing it. Please check this paper:
Li, C.-Y., C. Curtis, and R. L. Earley. 2018. Nonreversing mirrors elicit
behaviour that more accurately predicts performance against live
opponents. Animal Behaviour 137:95–105.
Did you use a normal or non-reversing mirror in your experiments?

7) Regarding working hypothesis (ii) I think this is something well established, but still worth testing. However, the authors should do a better job in introducing previous studies and also the concept of resource holding potential, which is totally missing in the paper.

8) Regarding working hypothesis (iii) I think also in this case a better introduction into the logic of the hypothesis is needed earlier in the text.

9) I have an overall major concern about the sampling method. Did you think about a possible sampling bias associated to the fishing technique? This aspect should be addressed in the paper. You explicitly say that fishing selects specific behaviours at the end of the discussion. What is the impact on such bias on your interpretations?

10) The PCA approach is interesting, but why did you decide to do that? I think it would be more interesting to run one model for each behavior and discuss the results independently. This could be more important at the moment to discuss possible problems related to the mirror test.

11) You have working es so I would not suggest to write the second paragraph on the discussion on a methodological aspect (lines 367-382).

12) I think a “limitations” paragraph is needed in the discussion

13) I would suggest the following references:

- https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12176
Instead of Arlinghaus et al. 2016

- https://afspubs.onlinelibrary.wiley.com/doi/abs/10.1002/tafs.10160
I think this study regarding a lack of repeatability for the mirror test in zebrafish is worth to be cited. Moreover, some aspect of the selection could be related to the concepts in Arlinghaus et al. 2017.

- https://www.sciencedirect.com/science/article/abs/pii/S0003347217300817
Sociability in your mirror test could be considered or at least mentioned

- https://jeb.biologists.org/content/220/24/4624.short
I think an interesting topic related to the razorfish could be related to the effects of aggressiveness and daily activity rhythms (I have seen you already publish a paper about daily activity rhythms in razorfish). I think this paper could be interesting (despite it deals with lobsters) because it is about a burrowing species such as the razorfish, which forms dominance hierarchy with the same ecological functions as in razorfish. Maybe is worth to be mentioned in the discussion instead of the paragraph related to genetic mechanisms, which comes out of the blue.

MINOR COMMENTS
- I think you could define if and what kind of swimming you recorded in from of the mirror (e.g., parallel swimming”). This aspect is tackled in one of the paper you cited (Balzarini et al. 2014) and I think could be interesting to better support whether the mirror test you used here.
- What does (4-6) represents in line 119?
- What does 1080p/30 in line 225 mean?
- I think it could be worthy to present supplementary videos regarding the behaviours characterized in the mirror test.
- Lines 311-312 (is that useful?). I would rather present range of values.
- Lines 384-385. This is not true. You did not validate the results
- Lines 402. Also isolation in an aquarium increase stress and anxiety in fish.
- Lines 499-508. It seems to come out of the blue


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: AGGRESSIVENESS-RELATED BEHAVIOURAL TYPES IN THE PEARLY RAZORFISH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language needs some improvement – there are a few typos but also some grammatical errors. I provide some specific examples in detail below.
Figures 4c and 5c are missing the Y-axis label.
The Discussion section could be better structured and more focused on the original research questions.
Experimental design: There are well defined and relevant research questions and the experimental design is adequate to answer them. The methodology, including data analysis is well described.
Validity of the findings: Results are statistically sound, and their interpretation is meaningful. Some directions for future studies are provided and discussed.

Line 20 – consider replacing “in” before pearly razorfish with “of”
Keywords – consider replacing keywords already present in the title
Line 53 – Please rephrase
Line 97 – replace “big” with “larger”
Line 98 – replace “small” with “smaller”
Line 103 – Delete “the leave”
Line 185 – 187 – Rephrase
Line 191 – Replace “trails” with “trials”
Line 191 – How can you say that it was the optimal arena? How did you measure their performance? This 120L arena was at most the best of the tested arenas but this does not necessarily mean it is the optimal. More information on this could be added in the supplements
Line 197-198 – “…pearly razorfish habitat and to allowing the fish to use the sand as refuge.” suggest changing to “…pearly razorfish habitat, allowing the fish to use the sand as refuge.”

Line 202 – “…water of the aquariums was changed…”

Line 212 – “…with an average total length (TL) of 15.2 ± 2.4 cm and…”

Line 215 – Please present the results for the statistical tests

Line 238 – How was the time of the test defined? Was it random? Did each fish had the test at the same time every day?

Line 263 – Why not consider time of day as well? (See previous comment)

Line 296 – Replace “dan” with “than”

Line 390 – Consider replacing “since” with “given that”

Line 394/396 – Not very clear, please rephrase

Line 491/492 – “For example…” – IMO this sentence could be removed since it does not add much relevant information to what is stated before.

Line 515 – Please provide references
Additional comments: Besides the general comments on Basic Reporting, Experimental design and Validity of Findings I have some specific comments that I would like the authors to address


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: AGGRESSIVENESS-RELATED BEHAVIOURAL TYPES IN THE PEARLY RAZORFISH
Review round: 2
Reviewer: 1

Output:
Basic reporting: Basic reporting is fine and readability is good.
Experimental design: Well explained and with all the major elements to replicate it.
Validity of the findings: Finding are robust, but sometimes overstated.
Additional comments: I think the quality and clarity of the paper strongly increased. However, I still have some concern regarding the way in which the mirror test is presented and discussed.

I am not sure that you can claim that what you measure is aggressive-related. The only way would be to see if exist a correlation between the mirror test and the rank in dyadic encounters or in a dominance hierarchy. I think it is still a valid and appropriate test to assess repeatability of behavior, but I think “aggressive-related” is not the best way to refer to it in the title. Maybe you can simply refer to the mirror test. I am not questioning your results, but I am simply not convinced that the scientific discussion on the validity of this test is over. Therefore, the title of the paper is referring to something that you are not demonstrating with your results. I would strongly suggest to change the title to something like: “The mirror test suggests the existence of aggressiveness-related behavioural types in the pearly razorfish”. In this way you still have “aggression” in the title, but you clearly say how you measured it.

I think you cannot say what you say in lines 625-629. You did not measure stress and you did not validate the mirror test with other approaches to be sure that you are measuring aggressiveness (the same for the rest of the paper). I think more caution is needed in the way in which the results are discussed. They are valid results and they open a variety of opportunity for future studies, but I think some sentences as the once highlighted above are overstated.

Regarding the use of the PCA I suggest to refer to this recent guide where there is a specific section on the use of PCA in statistical analysis related to animal personality (https://onlinelibrary.wiley.com/doi/full/10.1111/eth.13082).

Some minor comments:
- In lines 252 I suppose you are referring only to fish. There is a lot of literature about lobsters that you are not citing. So, I would specify you are only referring to fish.

- RHP stays for Resource Holding Potential and not for resource retention power.

- Line 753: hierarchy is not a property of a population

- Line 891-893: Yes, it is a promising avenue of research, but I think you need to say why and maybe provide a reference?