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: PERIPHERAL-PHYSIOLOGICAL AND NEURAL CORRELATES OF THE FLOW EXPERIENCE WHILE PLAYING VIDEO GAMES: A COMPREHENSIVE REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: First, I would like to thanks the authors for extensively revising their manuscript according to both reviewers’ recommendations. I believe that the manuscript greatly improved as it now shows a clearer structure, a more in-depth discussion of both theoretical assumptions and observed findings, and a more comprehensive review of the literature. Therefore, I would only like to make some minor final remarks and recommendations before the manuscript can be published:
1.	I noticed some grammatical errors and spelling mistakes throughout the manuscript, which is why I would recommend to have a native speaker proof-read its final version before publication. Examples: leave out ‘either’ (line 100); repeat ‘on’ after ‘as well as’ (line 162); use ‘for the creation of a flow state’ or ‘for creating a flow state’ (line 163); spell U-shaped either consistently with an uppercase or lowercase U (e.g., lines 207 & 211); ‘A significant effect was neither found for…, nor for…’ (lines 224-226); ‘noted’ instead of ‘considered’ (line 256); ‘associated with’ (line 321); ‘capacity’ (line 340) does not seem to be the right word (do you mean the skill to correctly judge the appropriate difficulty level for oneself or the opportunity to pick a difficulty level oneself?); plural ‘flow scores… were’ (lines 413-414); ‘flow as measured by…’ (line 430); ‘a mental arithmetic task’ since the task has not been described beforehand (line 464);  ‘higher left temporal cortex alpha activity, which reflects decreased cortical activity in this region, is associated with improved performance, as it represents reduced internal verbalization and increased visual-spatial processing in the right hemisphere’ (lines 531-534); ‘a 7-second video clip’ ‘table tennis’ (line 549); ‘was to be expected in the more difficult condition’ (lines 574-575); ‘which increase with increasing difficulty’ (line 576); ‘the flow and anxiety condition’ (line 579); ‘as compared to’ rather than ‘than’ (line 580); leave out ‘alone’ or replace with ‘on its own accord’ (line 620); ‘playing in 2D’ (line 666); ‘The observed co-activation… aligns’ (line 756-757); ‘flow was found to be associated with’ (line 759); ‘a purely effortful mental experience’ (line 766); ‘practice’ instead of ‘exercise’ (line 789); ‘mind-wandering’ (line 801); ‘body- and self-awareness (line 807); ‘role’ (line 163 and 819); ‘some studies…, other studies…’ (lines 832-833); ‘in which’ instead of ‘where’ (line 833); leave out ‘of’ (line 840); ‘neural activity’ (line 849); ‘…, given the different physiological and cognitive demands of the flow-inducing activity, …’ (lines 850- 851). Moreover, ‘e.g.’ is normally followed by a comma and the gerund is preceded by one (e.g., lines 885-886 ‘…, reporting medium levels of performance’), and an enumeration of three or more things requires a comma before the ‘and’ (e.g., line 122); please make sure to put these commas throughout the manuscript. Also, check the blanks between words as you tend to sometimes either put too many (e.g., lines 236, 267, 486, 498, 513, 649, 660, 742, 841, 886, 892) or none (e.g., lines 44, 469, 470, 486). There are also some stylistic mistakes: In line 355, there is a semicolon that does not seem to make sense; FKS in line 91 is underlined for some reason; the dash once comes with blanks and sometimes without. I do not claim to have found everything, so I strongly recommend the authors to also proof-read their manuscript in terms of formal and stylistic requirements once more.
2.	I have some remaining issues with the introduction: ‘Why do we seek activities that make us happy?’ does not inspire interest in the reader as the answer is in the question; I would suggest to just leave it out (line 37-38).
Further, I believe there is still a misconception about processing fluency as well as about antecedents, components, and consequences of flow reflected in the text. Processing fluency is a dimension of flow, just like absorption and enjoyment (i.e., broader than the nine components), and is directly reflected in some of the flow components such as sense of clear goals and immediate feedback. Thus, there is no ‘state termed processing fluency’ (line 40-41), but processing fluency is part of the definition of the flow state and should appear together with enjoyment and absorption in lines 38-39. ‘Stemming from intrinsic motivation’, however, in my opinion does not necessarily belong in the definition itself, as intrinsic motivation is an antecedent (and maybe also a consequence) of flow – therefore it should be mentioned later on together with the first three key components (not dimensions!) as potential antecedents in lines 54-55. Importantly, each antecedent of flow (e.g., clear goals when starting the flow activity) at the same time serves as an experiential component (e.g., the perception of clear goals during flow in this activity). To make this clearer, I would reword lines 54-56 as ‘Whereas all nine key components reflect the subjective experience during flow, the first three (balance between skills and challenges, clear goals, and immediate feedback) can in a more objective sense also be understood as activity-related preconditions for flow. Moreover, in relation to the person, intrinsic motivation for the activity can facilitate a flow experience (Csikszentmihalyi, 1975). Optimal skill-challenge balance, though, is considered to be the main antecedent for entering a flow state…’.
3.	I would also suggest to re-structure the introduction to make it easier to follow for the reader: After you introduce the flow channel model and potential modulators of the relationship it predicts between flow and skill-challenge balance (lines 59-75), explain how this theoretical framework can be relatively easily implemented in the context of computer gaming (‘…could facilitate the propensity to experience flow. – new paragraph – Despite such potential modulators, the relationship between skill-challenge balance and flow postulated in the flow channel model affords an approach for experimentally manipulating flow by presenting different challenge levels. Even though inducing flow under controlled laboratory conditions has been considered difficult (reference please!), game-based paradigms are especially promising as a) the difficulty level of a game can relatively easily be manipulated to achieve skill-challenge balance, and b) gaming can be considered a typical flow-inducing activity’; then go on with the reasons why video gaming is a great flow activity from lines 104-112 and 132-133, and follow up with the manipulation approaches from lines 113-118). Please make sure to include all three approaches, namely also the medium challenge level-approach (Rheinberg and Vollmeyer, 2003), in lines 113-117 – and then move lines 124-126 up as an example (‘For instance, Rheinberg and Vollmeyer…’). In the next paragraph, you can then give three interesting areas of application for experimental flow research with computer games: a) understanding peak performances, b) potential use of flow in therapeutic settings, and c) maximization of game enjoyment. Thus, put lines 75-84, lines 131-148 and lines 149-153 next, respectively (with appropriate connecting passages of course). Then, you can come to the methodological challenge this research faces and its potential solution in the form of psychophysiological or neural indicators for flow, pointing out why the reader should be interested in what is about to follow in your literature review (e.g., ‘In order to successfully study research questions related to flow and performance, therapeutic use, or gamer experience, the experimental paradigm must be accompanied by a valid measurement of the flow state.’; move lines 85-103 here – how flow used to be measured with self-reports, how this is problematic and warrants additional psychophysiological and neural measures; now also briefly mention the dual-task approach from line 156-158 and in doing so, please spell out ‘dual-task approach’). And then you can end with lines 158-171.
4.	There are some minor unclarities left in the introduction: ‘Autotelic experience’ (line 52) – this term needs to either be explained (Greek: ‘auto’=self, ‘telos’=goal) or reworded as ‘intrinsic enjoyment, which is more self-explanatory. In lines 67-68, it is ‘activities that were subjectively evaluated as important to succeed in’ ¬– this way, the obtained result (low demands/flow) becomes more understandable. The FSS (lines 90-91) was developed in the context of sport, but can be and is often applied to other flow activities, just like the FKS. The FKS is called Flow Sort Scale in English and should therefore also be abbreviated to FSS and not FKS. The FQ (lines 668-669) is missing in this section and should be introduced with the ESM as it was originally developed for ESM studies (lines 85-88). Effectance motivation might as well be explained using the term ‘feeling of control’ instead of ‘empowerment’, pointing out the link to this flow component. The TOJ (lines 143-148) needs a bit more explanation, since the loss of a sense of time during flow would suggest that a flow experience actually diminishes the performance in a temporal judgement test. Similarly, the reasoning why autonomy is suggested as an important determinant of flow needs to be briefly given (lines 119-120, lines 340-341). And I am painfully aware of the difficulties to distinguish flow and immersion in video gaming, but since the term immersion is later brought up, there needs to be one or two comprehensive sentences about this (‘Some studies (ref.) implemented an additional immersion condition, which was aimed at transporting the player’s mind into the virtual world by manipulating factors like graphics, sound, and gameplay (ref.). Immersion is an important concept in VR and computer gaming research and seems closely connected to flow in these activity contexts, as both pertain to a pleasant, absorbed mental state common in gamers. However, flow and immersion can be distinguished due to subtle structural differences (for further information on this, please see Michailidis, Balaguer-Ballester, & He, 2018).’.
Experimental design: I am very happy to see that the authors put in the additional effort to extend their literature research to other databases and to revise the presentation of their inclusion criteria. The methodology is now much clearer and more convincing. I also find the new structure of the presentation of the findings much easier to follow for the reader. Again, I would like to commend the authors for the successful revision, and only have minor remarks to add:
1.	I believe some section need a bit more clarification: In line 182, the term ‘exergames’ may need a short explanation and the confounding factors could be accompanied by examples (e.g., movement effects, processing of social interaction, …), in order to explain to the reader why the 35 papers were excluded, to be as transparent and detailed as possible with the exclusion criteria; in lines 204-205, I would write ‘that the experience of challenge during flow induces a certain amount of stress’ (lines 204-205) since ‘stress’ and ‘challenge’ cannot be used interchangeably in some theories; in line 206 and 207, I find ‘fast/slow response system’ to be better terms, respectively; in line 228 and 556, please leave out ‘emotional’ as flow is not an emotional state; in line 236, you state that flow was assessed in the study and later go on to say that flow was actually not assessed with a questionnaire (line 239); you may want to say that there was a flow, immersion, and boredom condition, but no measurement of self-reported flow?; in line 445, please write ‘a first person shooter (FPS) game’; lines 447-449 could use an example to clarify what is meant by ‘game events that contribute to factors  described by Csikszentmihalyi’; in line 433 the name of the FPS game, in line 419 the name of the videogame, and in line 656 the name of the flow scale is missing.
2.	I find it a bit adverse to first give interpretation of the HRV indices and later on discuss those interpretations. I would be upfront with the controversial aspects here: ‘To investigate the relationship between flow and ANS activation, cardiovascular measures are oftentimes assessed, given that heart rate variability, which pertains to fluctuations in the time intervals of adjacent heartbeats, is traditionally seen as an indicator to dismantle PSNS and SNS activation. Thus, high-frequency HRV can be considered a direct measure of parasympathetic activation, whereas low frequency HRV has long been interpreted as reflecting sympathetic influences, rendering the HF/LF ratio an indicator for autonomic balance between SNS and PSNS. However, it is important to note that this interpretation of LF-HRV and LF/HF ratio is controversial…’ and follow it up with the information from lines 293-301. After this clarification, you can go on to report De Manzano et al. (2010) and later Chanel et al. (2011).
3.	Sometimes it is unclear how certain constructs related to flow were measured, given that they could be measured both with self-reports and physiological indicators. For instance, in line 277 do you mean self-reported positive affect and effortless attention? Same for line 321: How was the decrease in mental effort assessed? In line 416 you mean the last 30 seconds of the flow condition, and in line 478, you mean the flow score? Similarly, in line 500, do you mean in the flow condition, and in line 501, correlations between the flow score and DMN activity? What is the attention score referred to in line 595? In line 868, I assume you mean ‘…does not guarantee that a person will enter a flow state in the flow condition.’. In line 489, you mean a flow score – or is the flow index something else? And in line 615, what do you mean by ‘moments of flow’ since as of now flow cannot be captured with high temporal accuracy?
4.	I would re-structure and re-word certain lines to clarify their meaning: In lines 200-201, I would suggest. ‘In contrast to the notion that the attentional focus during flow is essentially effortless, Keller and colleagues (2011) argued that flow involves considerable mental effort due to the high degree of involvement along with the challenging nature of the task.’; in line 234, ‘EDA measures increased with the game’s difficulty level, indicating heightening arousal’; in lines 323-329, ‘The different findings show that during… participants may not perceive as much stress…. It should also be noted, that Keller’s study involved a relatively small number of participants and operationalized flow through the flow condition, without actually measuring self-reported flow experiences, which might affect the validity of their findings.’ (On a side-note, if this operationalization is used, the analyses is most likely not correlational.); in line 401, ‘the activity of the DMN is thought to decrease’ since you are still stating assumptions and not findings at this point; in line 459-461, ‘It should be noted, though, that in the second study, the subjective flow experience was assumed to be elicited by the flow condition, but this assumption was not checked using a self-report flow scale.’; in line 544, either say ‘once again’ or refer to the other studies; in line 491, ‘, indicating less self-related processing,’; in lines 556-560, ‘Chanel et al. (2011) tried to classify their three different challenge-skill conditions in a game of Tetris according to EEG signals. Even though their results indicated distinct theta power between conditions in some electrodes, no precise link to states of boredom, flow, and anxiety could be obtained.’; In line 843, I guess you mean the ‘flow channel model’; in line 856, leave out ‘would’ and go on to say ‘FPSs are three-dimensional games, in which spatial navigation is crucial, since at any given time, ….’ and delete the sentence (line 860) which merely repeats the part about spatial navigation; in line 868-869, since you give a recommendation, say ‘The subjective experience of flow in the flow condition should be assessed using self-report flow scales in future studies, to determine whether the participants were able to enter a full flow state or not.’.
5.	I noticed that there is some repetition in the text (for instance, it is stated on multiple occasions that a flow condition does not guarantee a flow experience). Moreover, when describing a study, there is often a more general sentence first (e.g., line 412, ‘playing a video game’), followed by a more specific sentence (e.g., line 413 ‘while playing Tetris); this information could be presented in a more concise form in just one sentence. Finally, brackets are often used to insert full sentences (e.g., line 431-432); however, for fluent reading it is advisable to use brackets only to give short key words and to use a subordinate clause when more text is needed. Please revise the text once more according to these opportunities for improvement.
Validity of the findings: I am confident that the revised, more in-depth discussion of the findings together with explicit recommendations for future study designs makes this literature review an interesting read for PeerJ’s readership and clearly shows its added value to the field. In addition to some minor language- and grammar-related issues I have already brought up in the other sections of the review, my only remark here is, whether the ‘joyous state of focused attention’ should not be re-named as a ‘subjectively effortless state of focused attention’ in order to set it apart from a ‘state of positive valence and heightened arousal’. Other than that, I find the discussion section very well thought-out!
Additional comments: At this point, I have to stress the importance of proof-reading a manuscript multiple times to ensure a consistent and correct style; I myself have experienced that a manuscript can get rejected due to formal mistakes. I have put a lot of effort in trying to find these mistakes for you, but I do not claim to have found all of them, so please check again. A good example for persistent inconsistencies and formal mistakes are the tables:
1.	For ‘Experimental type’, you write either ‘FPS Game/game:’ or ‘Game’ with no colon. Similarly, for ‘Design’, you write either ’40 minutes gameplay’, ’10 minutes’, or ‘3 minutes blocks of gameplay’. Stick to one way of reporting. I would suggest ‘(FPS) Game:’ and ‘Boredom/Flow/Anxiety, 10 minutes gameplay’.
2.	For ‘Measures’, it happens quite often that the ‘&’ is in the beginning of a line or a comma is missing; to avoid these mistakes, I would suggest simply enumerating all indicators with commas (e.g., ‘EDA, HRV, fEMG’ instead of ‘EDA, HRV, & fEMG’). Same for multiple games under ‘Experimental Design’ – here, only for the dual tasks the ‘&’ should be used.
3.	Still, some commas are missing when three or more items are enumerated throughout the tables. In the last column, I would also suggest to only use the ‘&’ when indicators are enumerated, but not for results – in this case, use ‘;’ (e.g., Table 1 ‘Inverted U-shaped relationship between LF-HRV & cortisol level with self-reported flow; positive linear relationship between parasympathetic activation & self-reported flow).
4.	Some formal mistakes remain: in Table 1, for Chanel et al. the s in participants is shifted to the next line, there are superfluous blanks in the lines for Leger et al. and for Harmat et al. under ‘Design’, a bracket is missing in ‘77(40f)’, and the enumeration in the last column of Leger et al. should be ‘A, B, & C’. In Table 2, there is another superfluous blank in ‘Moreno et al.   (2020)’, ‘autonomy condition’ in the last column of De Sampaio et al. should be lowercase as is flow condition in the other lines, and the enumeration in the last column of Klasen et al. should be ‘A, B, & C’. In Table 3, under ‘Design’ and DeKock et al. the font size changes. In Table 4, the ‘&’ is in the start of the line under ‘Experiment type’ and Castellar et al..
5.	Why not put ‘fEMG’ instead of ‘Facial EMG’ (of course explaining the abbreviation below)? Same for ‘RR’ and ‘Respiratory Rate’.
6.	It is important to clarify in the last column how the findings were related to flow. Sometimes you write ‘for flow’ and ‘during flow’, sometimes ‘for flow condition’, ‘during flow condition’, and ‘at flow condition’ or ‘in the flow state’, ‘with the flow experience’, and ‘during self-reported experience of flow’. This is unnecessarily confusing. I would suggest you stick to ‘in the flow condition’ whenever the analysis was based on group differences, and to ‘during self-reported flow’ whenever it was based on correlations with a flow score.
7.	‘LF-HRV’ and ‘HF-HRV’ should consistently be spelled with the hyphen.
8.	In Table 2, please put ‘Increased activity in the left IFG, left putamen, & posterior cortical regions during self-reported flow; decreased activity in MPFC, PCC, & AMY during self-reported flow’.


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: ARCHOSAURIFORM FOOTPRINTS IN THE LOWER TRIASSIC OF WESTERN ALPS AND THEIR ROLE IN UNDERSTANDING THE EFFECTS OF THE PERMIAN-TRIASSIC HYPERTHERMAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment (see note to editor).
Experimental design: No comment (see note to editor).
Validity of the findings: No comment (see note to editor).
Additional comments: Porto Alegre, August 20, 2020

PeerJ
Dear authors

REFEREE REPORT

The manuscript entitled “Archosauriform footprints in the Lower Triassic of Western Alps and their role in understanding the effects of the Permian-Triassic hyperthermal” (ID: 51782) and authored by Fabio M. Petti, Heinz Furrer, Enrico Collo, Edoardo Martinetto, Massimo Bernardi, Massimo Delfino, Marco Romano and Michele Piazza was completely revised by me.
In this manuscript, the authors described a new occurrence of fossil tracks (Chirotherium and Isochirotherium) assigned to archosauriforms from the Lower Triassic deposits of the Gardetta Plateau of NW Italy. A new ichnospecies of Isochirotherium was erected (I. gardettae isp. nov.) and a discussion on the distribution of tetrapods on low latitudes during the Early Triassic was made.
The length and structure of the manuscript is good, as well the number (11) and quality of the figures. The authors cited both classic and up-to-date papers on the manuscript. Because I am not an English native-speaker, I was not able to evaluate the idiom, but the manuscript seems to be very coherent and readable. Other punctual suggestions and corrections were made directly on the manuscript file that I send to you.
The only point I think can be better explored is the differences on manual dactyly between the Isochirotherium ichnospecies. The authors used this character to differentiate the materials and erect the new isp. However, there are no comments made on a potential preservation bias on it, because it is not unlikely pentadactyl tetrapod can produce tetra- or tridactyl manual footprints due the substrate conditions and variations on the weigh center and hand kinematics of the producers (see, for example, the works of Peter Falkingham on the “Goldilocks Effect”).
Based on what I mentioned above, I consider that the manuscript likely publishable in PeerJ after pass by minor modifications (minor revision request).
I am available for any clarification you may want.

Sincerely yours,
Dr. Heitor Francischini
Universidade Federal do Rio Grande do Sul
heitorfrancischini@hotmail.com / heitor.francischini@ufrgs.br
ORCID: 0000-0001-9809-7784


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: ARCHOSAURIFORM FOOTPRINTS IN THE LOWER TRIASSIC OF WESTERN ALPS AND THEIR ROLE IN UNDERSTANDING THE EFFECTS OF THE PERMIAN-TRIASSIC HYPERTHERMAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English grammar used through the manuscript is clear and professional.
The background is well presented and completed with ichnological, taxonomical, and geological actualized literature. I have not cross-checked the reference list.
The figures and tables are well executed and are all necessary to support the results presented in the paper. The structure is correct for this kind of paper.
Experimental design: The research is original, with analysis of primary and bibliographic data.
The technical methods used to analyze the data are modern, adequate, and well described for replication.
Research questions are clearly stated, relevant, and meaningful, and are followed throughout the manuscript.
Validity of the findings: The manuscript is a good example of how to analyze in detail the ichnological record and used this information for an ichnotaxonomical, taxonomical, paleobiogeografical and biochronological studies.
The results are robust and the conclusions relevant.
Additional comments: The authors propose a compressive manuscript about the relationship among the Early Triassic ichnofauna found in the North of Italy, the Permo-Triassic Mass Extinction, and the paleobiogeographical bias. Based on geologic and biochronologic information, they pointed out that vertebrate tracks are probably late Olenekian in age. The authors concluded that the ichnological record is a useful tool to study the presence of archosauriformes at low latitudes during the Early Triassic epoch.
I have added some comments in the attached pdf about the ichnotaxonomy of Isochirotherium and the choice of useful ichnotaxobases.
On the other hand, I wonder why the bone vertebrate record is scarce in the Early Triassic in the equatorial zone, but there are abundant vertebrate tracks. Maybe taphonomical biases?


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: ARCHOSAURIFORM FOOTPRINTS IN THE LOWER TRIASSIC OF WESTERN ALPS AND THEIR ROLE IN UNDERSTANDING THE EFFECTS OF THE PERMIAN-TRIASSIC HYPERTHERMAL
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is quite well prepared with excellent illustrations. However,  there are many small errors of English grammar: see edited PDF.  Please make agreement between plural and singular subjects and verbs.
    I have doubts about the validity of erecting a new ichnospecies of Isochirotherium because the new ichnospecies is only briefly compared with I. soergeli (the type). Ideally the new ichnospecies should have a clear comparative diagnosis.  Authors should explain how they determine whether the tetradactyl manus is a preservational (extramorphological) phenomenon, or evidence of front limb posture.  The authors "open the door" to discussing this problem after ichnotaxonomy section  but do not adequately relate problem 'back to' ichnotaxonomy afterwards.

There is also the problem that the quality of preservation is not addressed.  Recently it has become fashionable to refer to the quality of preservation scale of Belvedere and Farlow (2016) and Marchetti et al. (2019). These scales do not need to be followed religiously, but they should be mentioned. This is easily done
Experimental design: no comment
Validity of the findings: The use of the term "trackmaker identification" should be introduced more cautiously.  It is rarely possible to identify the trackmaker precisely at the species or genus level. SO THE TRUTH IS THIS IS AN EXERCISE IN "INFERRED TRACKMAKER IDENTIFICATION." The paper proves this by suggesting that  Chirotherium and Isochirotherium can only  tentatively be "correlated" with trackmakers  at the family level.  There are 7-8 named Isochirotherium ichnospecies, and we cannot match each with a trackmaker taxon with any confidence.   I recommend that the authors make this uncertainly clear.  (However, ichnotaxa are clearly useful in providing paleoecological information, especially when body fossils are incomplete, for example with no feet. !!

The discussion and conclusions are a little speculative, but acceptable because the ideas are interesting and provocative and it seems the PTME  and aftermath have become a subject of repeated discussion by many authors.

OK
Additional comments: Interesting paper. Minor to very  moderate revision suggested
Please pay attention to my comments about:
English grammar
meaning of "inferred trackmaker identification"
"Quality of preservation"
and rigorous criteria for naming new ichnospecies


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: ARCHOSAURIFORM FOOTPRINTS IN THE LOWER TRIASSIC OF WESTERN ALPS AND THEIR ROLE IN UNDERSTANDING THE EFFECTS OF THE PERMIAN-TRIASSIC HYPERTHERMAL
Review round: 2
Reviewer: 1

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK
Additional comments: After reviewing this paper a second time,  and the rebuttal comments,  I think it can be published without further revision. However, I defer to the editors and other reviewers to see if they have any further suggestions.
    I note however that I  was not the only reviewer to ask whether the trackmaker had a truly tetradactyl manus and not a pentadactyl manus that was incompletely preserved.
   This will be something to consider in future studies. Chirotheres are sometimes categorized as small manus and large manus.


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 P53 SIGNALING PATHWAY OF THE LARGE YELLOW CROAKER (LARIMICHTHYS CROCEA) RESPONDS TO ACUTE COLD STRESS: EVIDENCE VIA SPATIOTEMPORAL EXPRESSION ANALYSIS OF P53, P21, MDM2, IGF-1, GADD45, FAS, AND AKT
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are two main issues to consider. The first being that there are 65 figures showing RT-cPCR data on different tissues at different time points following drop in temperature. The authors need to come up with a better way to present their data.   It is not possible for the reader to go through these figures.
Secondly, all data are interpreted such that changes in levels of mRNAs are due to p53. But it has to be considered that also other mechanisms can control these genes. In some instances the correlation to p53 mRNA levels are poor. In this way, the different models proposed are quite complicated.
Experimental design: This seems to be ok. However, in this study they subject the animals to cold shock whereas in the sea the change in temperature is likely to be slow. This should be discussed.
Validity of the findings: The data look fine but the interpretations might be wrong.
Additional comments: Most important is to find a better way to present the data.


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 P53 SIGNALING PATHWAY OF THE LARGE YELLOW CROAKER (LARIMICHTHYS CROCEA) RESPONDS TO ACUTE COLD STRESS: EVIDENCE VIA SPATIOTEMPORAL EXPRESSION ANALYSIS OF P53, P21, MDM2, IGF-1, GADD45, FAS, AND AKT
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1.	There is little grammatical mistakes. Data should be latest so it should be better to use recent references at lines 45 and 46 to provide latest justification for your study. There is also need to state scientific hypothesis. It should be influential to give a clear idea, why the research was carried out and the novelty of the manuscript.
2.	Figures are relevant and well labelled but Author should cross check the graphs as graphical presentation of 3a1-7 and 3b (muscle), p53 and Gadd45 mRNA expression level at 3 h were not consistent. Similarly, recheck graphical presentation of MDM2 and Gadd45 (Fig. 4a1-7, b) in brain tissue as well as in gill tissues (6a1-7 and 6b) recheck p53, MDM2 and Akt mRNA expression levels.
3.	Author should explain how the altered expression of genes play role in activation of p53 signaling pathways at lines 214 and 215.
4.	Author should mention the reason behind the inhibited p53 expression in the liver at specific time points at lines 234 and 235.
5.	From the perspective of relationship between p53 and MDM2, it is suggested that author should also explain the effect of IGF-1 in p53 signaling pathways?  How it play role in acute cold stress?


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 P53 SIGNALING PATHWAY OF THE LARGE YELLOW CROAKER (LARIMICHTHYS CROCEA) RESPONDS TO ACUTE COLD STRESS: EVIDENCE VIA SPATIOTEMPORAL EXPRESSION ANALYSIS OF P53, P21, MDM2, IGF-1, GADD45, FAS, AND AKT
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: Stress play key regulation of various metabolic process including DNA damaging and cell cycle progression.  The paper my Qian et al describe the effect of cold induced stress on large yellow croakers which is economically important marine fish in specially china and around. The author previously reports the cold stress on p53 signaling and continued the study on gene network.

Qian et al., in present study report on upregulation and down regulation of various genes involved in cold stress, the studied by qRT-PCR analysis which gives additional evidence on cold induced stress studied before, The paper is clear and written nicely

Although expression levels were elevated and reported using qRT-QPCR, It would be great if additional study included, like- is the expression levels were also observed in protein level by doing western blotting on some on the key genes (p53 and MDM2!) regulation.

This experiments may be mostly suggestion- if authors are interested in understanding expression of many genes involved, they should perform microarray on samples, this gives clear regulatory pathway involved in cold stress.

Author did not provide explanation…why there is sudden decrease and increase in the level of expression (between 3- 6 hr) qPCR analysis of Akt in liver tissue.

MDM2 is ubiquitin ligase and regulates activity of p53, in a high expression of MDM2 why decrease in p53 activity was not see, is author role out possibility of other biological path way ?

why there is sudden increase in qPCR analysis of p21 in the muscle, whereas early and later time point show no significance difference (Fig 13)

legends reading show 9 fig by data presents 65 figures this need to be fixed
and this is confessing

the conclusive model needed for putative gene network in combined study

Thanks


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 P53 SIGNALING PATHWAY OF THE LARGE YELLOW CROAKER (LARIMICHTHYS CROCEA) RESPONDS TO ACUTE COLD STRESS: EVIDENCE VIA SPATIOTEMPORAL EXPRESSION ANALYSIS OF P53, P21, MDM2, IGF-1, GADD45, FAS, AND AKT
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: Qian et al., in the revised version responded well to prior critiques and manuscript improved lot for readability and clarity specially figures. I would expect future finding from this group as they promised in the rebuttal letter.


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

Input:
Title: INDIVIDUAL DIFFERENCES SHOW THAT ONLY SOME BATS CAN COPE WITH NOISE-INDUCED MASKING AND DISTRACTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: -The manuscript is generally well written and the authors are generally clear in communicating their thoughts. However, throughout the manuscript there are some run on sentences that are long winded that I believe would be clearer if broken into multiple sentences, as well as a few points where grammar needs to be check or more clarity added. As such the manuscript should be carefully edited. Some examples of these occur at lines:
•	Line 47-51: provides examples of where individual differences are documented than later states “this” is often overlooked. Clearly state “this” as individual differences. And I assume this is true although you just provided a handful of citations contradictory to this statement?
•	Line 74: more clearly state what is meant by “tracking efforts and sensory strategies”
•	Line 74: unclear at first if author is trying to improve bat perception relatively easy, or how bats improve their perception with ease.
•	Line 75: I feel like this line clearly states what is in the sentence before. Just state what you mean, no need to ramble for multiple sentences 
•	Line 83-83: “increasing difficulty”. Not clear at time how you increased difficulty.
•	Line 94-95: State the opposites as opposed to just saying the opposite would be true in masking.

-The introduction briefly describes the background of noise disturbances in animals and quickly gets into the details of auditory mechanisms that may be causing this disruption. Various aspects of noise disruptions (masking, distraction, etc) are well described and hypotheses clearly stated.

-While I appreciate the brevity of the intro, I would like to see more details on some past animal studies with noise.
•	I appreciate the general emphasis in intro/discussion on importance of individual differences and not just group means
•	Line45 “Yet it is not often understood what mechanisms drive these changes”. In the few studies that do get to understand the mechanisms, what do the show? Or do NONE test mechanisms?
•	Line 40: Authors discuss anthropogenic noise. Do any studies compare the frequency distributions of anthropogenic noises in cities, parks, nature areas and at what frequency’s the maximum energy occur. Are these anthropogenic noises within the bats echolocation range? Are there measurements of anthropogenic noise increases in areas over decades or years to show the increase? These may guide the hypothesis of distraction vs masking, and provide more details to the context of anthropogenic noise disturbance to bats in particular.

-Discussion brings up windmills and bat ecology. Add a sentence explaining why this is an issue for non-bat scientists.

-Figures are informative and related to main data discussed in manuscript. I put for the following suggestions for increase clarity:
•	Ensure the use of colour-blind friendly colour palette
•	I suggest dotted or broken lines, or use of squares/circles/etc so figures are clear for individuals printing in greyscale (yes, those who print still exist). Would solve above issue with colour-blind palette.
•	Figure captions are clear but I recommend stating what each graph represents, what boxplots are, and any described patterns by bats prior to stating the asterisks denote significance
•	I assume statistical significance in figure descriptions is p<0.05, clearly state
•	Fig2 – “Ripple Height” on X-axis appears partially cut off. If legend is to be within an animal panel I would suggest Bat A (top, left panel) as opposed to Bat B.
•	Fig1- Is it possible to put a real picture of the apparatus in addition or in lieu of panel A?

-Raw data is provided and data measurements conform to those of the field.
Experimental design: -The authors present an original study with well defined questions, predictions, and aimed to fill a specific gap in the scientific literature. All methods are ethical and had ethics approval.

-The mushroom maze is established (Baier 2019) but not common in the field for perception studies, especially compared to standard y-maze platforms.
•	Objective decision measurements are good and give animals room to explore. Did animals ever not trigger the sensor but appear to roost above it and behaviourally make a decisions?
•	Consider adding a brief statement regarding echolocating through mesh or possible disruption between mesh/ripple depth when echolocating for behavioural and non-auditory audience

-Authors should include details regarding animals used in the experiment and selection criteria. Considering 4/9 were able to be trained reliably where these individuals older or have previous training for other experiments, from wild populations and not bred in captivity, etc. As a reader I immediately wonder if age or past experience facilitate learning and real world acoustic accommodations vs a juvenile with less experience or born in captivity.

-Authors provide sufficient details regarding experimental methodologies, statistics, etc. as well as ample reasoning as to the methods used. (ex. Statistical modelling can be subjective and the authors include why they deemed factors like length of day in experience to be important).

-Lines 193-194: I understand all trials of one condition were completed prior to the next auditory stimulus likely for ease of experimenter, but over time with the same stimuli could individuals start to “tune out” the smooth/sparse/non-overlapping noise? Similar to how over time humans “tune out” traffic or background noise. Could this impact results? Statement to why this procedural decision was made would be appreciated.

-Lines 199-202: Is it standard to start with easiest discrimination and move to hardest? Could there be animal learning during this time? Was animal previously trained to leave through the exit door is this just innate behaviour where animals tried to escape? What were protocols to determine animal was satiated (ex. 3 consecutive trials without eating the mealworm? Or randomly determined).

-Line 213: clarify whether 4s was recorded prior to decision or if posthoc a longer recording was cut to only include 4s prior to decision.

-Line 238: I do not believe the parentheses describe both highest and lowest frequency

-Excellent details on lighting and past visual aspects of bat vision, as well as how specific factors were decided upon to be placed into the model and why others were not included.
Validity of the findings: -Data are provided, statistics are sound, and experiments test the hypotheses provided.

-Authors are clear when speculating on any results, and clearly state whether their hypotheses are supported.

-Descriptions of results are appropriate
Additional comments: The authors have presented a study that is of importance to understanding bat auditory perception with future ecological relevance. This manuscript read clearly and logically, and the experimental design was well thought out with the appropriate measurements evaluated. It was a pleasure to read this manuscript.

I commend the authors on this extensive and time intense study. The amount of work in this study is huge. Kudos to you! My condolences on the passing of your mentor and friend. I’m sure you have made them proud with the work you have presented here.


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

Input:
Title: INDIVIDUAL DIFFERENCES SHOW THAT ONLY SOME BATS CAN COPE WITH NOISE-INDUCED MASKING AND DISTRACTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The purpose of this manuscript was to investigate how acoustic noise influences behavior and auditory perception in individual echolocating pale spear-nosed bats (Phyllostomus discolor). Bats were tested in the lab and trained on a psychoacoustical discrimination task in a variation of a Y-maze or T-maze that allowed animals to crawl toward a rewarded stimulus (i.e. a smooth disk) in a 2-alternative forced choice (2-AFC) paradigm. In the maze bats were tasked to discriminate the trained rewarded stimulus (flat disk) from an unrewarded stimuli (i.e. one of seven types concentric rippled disks all of the same spatial frequency but with differing ripple amplitudes). During testing, the performance of four trained bats was tested in silence (i.e. no acoustic playback) and with three types of noise via acoustic playback. The results showed that all four bats were able to complete the 2-AFC task but to vary degrees as the psychoacoustic threshold of 70% correct response varied for selecting the smooth disk versus a rippled disk with various ripple amplitudes. In short, the behavioural performance of two bats (A&B) seemed to be largely unaffected by noise playback whereas two other bats (C&D) had much higher (worse) ripple thresholds. As expected, all bats increased the amplitude of their echolocation calls in one or more trials during acoustic playback of noise; however, other echolocation call parameter changes shown by each individual were rather small (i.e. call duration, peak echolocation frequency) and the authors concluded that such differences were unlikely to explain overall differences observed in the behavioural performance of bats A&B compared to bats C&D. Moreover, trial duration and the proportion of aborted trials did not see to correlate with the behavioural performance of the specific four individual bats (out of nine) that managed to complete the study. The manuscript demonstrates there was high individual variability in response to noise treatments but the data do not show a clear pattern with respect to behavior and neurobiological mechanisms that could explain the results.
Experimental design: Overall, I found the science in this manuscript to be interesting and the Methods appropriate. The study was fairly well designed and carefully conducted as was the data analysis. I also found the manuscript to be well-written and easy to read. All of my suggestions below are intended to help improve the manuscript.
Validity of the findings: N/A
Additional comments: SPECIFIC COMMENTS

1.	One shortcoming of the manuscript is that at least three important citations were not included. The studies below were also conducted in the laboratory, albeit on a different species of echolocating bat, and demonstrate that some bats are unaffected by exposure to various types of noise. I mention this upfront because the authors seem to be unaware of these reports, which are directly related and highly relevant to their study.

Simmons AM, Hom KN, Warnecke M, Simmons JA (2016). Broadband noise exposure does not affect hearing sensitivity in big brown bats (Eptesicus fuscus). The Journal of Experimental Biology, 219(7):1031-1040.

Simmons AM, Hom KN, Simmons JA (2017) Big brown bats (Eptesicus fuscus) maintain hearing sensitivity after exposure to intense band-limited noise. The Journal of the Acoustical Society of America, 141(3):1481-1489.

Simmons AM, Ertman A, Hom KN, Simmons JA (2018) Big brown bats (Eptesicus fuscus) successfully navigate through clutter after exposure to intense band-limited sound. Scientific Reports 10, 8(1):1-3.

2.	(lines 47-51)  Individual differences in response to noise has also been document in bats (see point 1).

3.	(lines 51-52)  I agree with this point; however, I am still unclear as to how the mechanisms of “masking” can be independently dissociated from the other suggested perceptual mechanisms (?) of noise disturbance such as distraction and misleading (also, the term misleading as an independent mechanism from distraction may itself be misleading). For example, both masking and distraction have physiological and attentional components that may not necessarily be mutually exclusive from each other when measured with behavior. This could also be true for stress, fear, and avoidance.

4.	(line 70)  Major points. This sentence may be misleading. It is my opinion that the manuscript did not tease apart the relative contributions of masking and distraction as perceptual mechanisms because it is unclear that they are mutually exclusive when measured with behavior. (lines 80-81). I agree that when noise does not overlap with the bat’s echolocation calls this may result in less masking of returning echoes but even at “off-biosonar signal frequencies” masking can still occur. Moreover, playbacks of noise with spectrally overlapping and non-overlapping bandwidths (re echolocation calls) can also be attentionally distracting. Increasing task difficulty by using disks with lower ripple amplitudes decreases the available signal-to-noise ratio (SNR) in echoes and thus in the bat’s ability to make a perceptual decision, but it is unclear that this is a mechanism of distraction because when the SNR becomes too low there is no signal for the bat to detect or be distracted by. (lines 86-88) I do not completely understand the logic of this prediction. Distraction could be just as or more prominent for acoustic playbacks that spectrally overlap the bat’s own echolocation calls and thus received echoes regardless of the noise temporal structure. Also, the introduction of temporal gaps in the noise may introduces additional signal frequencies and/or a cue (i.e. they sound rougher… lines 149-150) and opportunities for detection, masking, and distraction (as suggested on lines 88-92).   (lines 92-95)  It is unclear to me that the predictions are consistent with the background knowledge presented.

5.	(lines 182-183)  Minor point. Please provide additional clarifying text. Was the entire testing arena on a rotating platform? Why did you say the disks were “swiveled” to their positions?

6.	(lines 194-195)  Perhaps I missed it, but I am unclear on this point because I did not see an explicit comparison of the bat’s performance in silence for the first test and then the re-test condition in silence. What was done to assure the reader that performance was not due to learning or other effects?

7.	(lines 207-208)  The manuscript uses the number of aborted trials as a metric to indicate the bat’s aversion to noise but this is not necessarily a good measure because all four bats aborted some trials even in the silence condition with no noise playback. At least two bats had, on average, lower numbers of abortions to a noise treatment than the silence treatment. My point is that it is very difficult to know why a bat aborts any trial and in at least two animals it appears that trials were aborted for reasons other than aversion to noise.

8.	(lines 219-232)  I am wondering if the small changes in signal duration and spectral frequency may have more to do with the impressive methods used to extraction signals from within noise and delineate the extracted calls? I don’t know. Were the same methods used to extract and delineate calls in the silence condition?

9.	(lines 244-246)  This would seem to make sense… analyze the loudest call recorded by one of the two microphones. When a call was detected on both microphones, presumably it was always louder in the microphone nearest to where the bat broke the infrared beam (i.e. the decision point)? Is this true? How often did you measure calls recorded from the microphone that was located further away and opposite to the side where the bat broke the IR beam (presumably, this did not happen very often).

10.	(lines 254-256)  Minor point. Consider moving these results to the Results section.

11.	(lines 293-295)  Because the Methods made a point of saying that the number of days that a bat was in an experiment may be an important variable to analyze, what were the Results from this analysis? Did you find that your bats learned the task or that they took longer to complete trials that you thought would be more difficult tasks?

12.	(lines 326-329)  Minor point. I’m not sure the terms “coping” and “non-coping” are the best to use to describe bats A&B from C&D. All bats had to cope with the experimental treatments. Maybe consider alternative terms and something a little less anthropomorphic?

13.	(lines 395-397; lines 402-404)  I agree because I think it is very difficult to design a task that mutually excludes mechanisms of distraction from those of masking.

14.	(lines 426-428)  An increase in trial duration could also be predicted under a mechanism of masking.

15.	(lines 450-455)  What is the evidence that the increase in echolocation call amplitude was involuntary?  (lines 461-463)  An increase in call amplitude should also result in less distraction because the amplitude of the received echo (i.e. the SNR) should also be louder.


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: MACREL: ANTIMICROBIAL PEPTIDE SCREENING IN GENOMES AND METAGENOMES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, this is a very high quality submission, with professional English used throughout. It is extremely well cited, which was important given the dizzying array of software methods used. The article is structured appropriately, and the figures are clear.

I noticed 2 typographical errors (line 56 "Hidrophobicity" and line 174 "biased amino compositions").

I do feel the article is not self-contained. The authors make an extensive set of comparisons of their tool to many others, with little explanation of the state of the field. While I think the content is well written for an expert in this subfield, I would strongly recommend devoting more space in the introductory section to bringing other secondary metabolism/natural products researchers up to speed. Perhaps at least brief explanations of the current software approaches that you'll compare against in the Results, and their strengths and weaknesses. What makes Macrel unique? Given that the actual results are not miles better than existing tools, be sure to explain why Macrel holds an important niche here (as I think it does).
Experimental design: The experimental design is excellent, and fits well within the Aims and Scope of PeerJ. The investigation is rigorous, and there were no detectable violations of standards or leading in the author's experimental work. I applaud the authors' efforts to make all data available, all code and scripts available, and clear methodology that should allow for easy reproducibility.

The only issue I had was that the manuscript does not make clear to me why this machine learning method seems to be exclusively used on metagenome sequence, especially as the metagenome sequence is first trimmed and assembled. Is there a reason why it will not or cannot work well on isolate genomes or isolate genome reads? Prediction of AMPs in well-established model genomes would provide a better avenue for confirming results biochemically. (I am not suggesting that chemical confirmatory experiments be done for this manuscript, but I do think the natural products community would be interested in this.) If there is an obvious explanation that I'm missing, I feel it would be best to articulate it more clearly in the intro and the Conclusions.
Validity of the findings: The findings are well articulated and valid. These are not high-impact results, but that is not a criteria for PeerJ, and the honest appraisal of the method is well received.
Additional comments: Overall, I think this is a well-prepared manuscript, but could perhaps be improved with the changes listed above, and I think it should be accepted pending minor revisions. These suggested revisions are:
- A bit more explanation on the state of AMP prediction (ie description of specific tools compared against in the Results section)
- An explanation of why Macrel is used on metagenomic sequence, and not isolate genomes
- Very minor typographical errors


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

Input:
Title: MACREL: ANTIMICROBIAL PEPTIDE SCREENING IN GENOMES AND METAGENOMES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: I played around with a number of lanthipeptide sequences that I had on hand, and it seems to me that they all achieve higher AMP probabilities once I manually remove the leader peptide part. This seems to match the example of microbisporicin A1 the authors use in figure 2 c, where the coordinates also seem to be for the processed lanthipeptide, not the prepropeptide. Can the authors comment a bit how this would impact the ability of MACREL to pick up on RiPPs, which usually contain a leader or tail peptide?
Additional comments: In their manuscript "MACREL: antimicrobial peptide screening in genomes and metagenomes", Dias Santos-Junior et al. describe a software pipeline to screen for antimicrobial peptides in (meta)genome data. The manuscript is well-written, the source code and training/evaluation datasets are available. Using the provided install script, the tool is very easy to install via conda. This is a nice break from many other bioinformatics tools.

The tool is straightforward to use, and comes with a user manual on ReadTheDocs. A minor comment I'd have on the user interface is that it'd be nice if --help would actually list the commands available.


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: MACREL: ANTIMICROBIAL PEPTIDE SCREENING IN GENOMES AND METAGENOMES
Review round: 2
Reviewer: 1

Output:
Basic reporting: As this is a second review, I won't go through the checklist again. No further issues.
Experimental design: No further issues
Validity of the findings: No further issues
Additional comments: I thank the authors' for their thoughtful responses to my first review, and the adjustments made to the manuscript are well-considered and quite acceptable. I recommend publication in its current form.


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

Input:
Title: MACREL: ANTIMICROBIAL PEPTIDE SCREENING IN GENOMES AND METAGENOMES
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 responded to my questions to my full satisfaction, thanks!


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: OPTIMIZING THE AMOUNT OF PIG MANURE IN THE VERMICOMPOSTING OF SPENT MUSHROOM (LENTINULA) SUBSTRATE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Language is perfect throughout the manuscript.
References should need to include.
Article structure and tables are clear but need correction in figures.
Experimental design: Modification should be needed
Validity of the findings: Modification should be needed
Additional comments: Line number 90-91: include the relevant references and discuss about the issues of other studies.
Line number 107 – 109: include the analytical method
Lin2 112 – 116 – Experimental design is confusing. Did you analyzed the C/N ratio after mixing SMS with pig manure? Or the mixing ratio is based on separately measured C/N ratio of CMS and pig manure? How the C/N ratio reduced with increasing volume of pig manure or decreasing volume of CMS?
Line 118 – 121: Juvenile or adult worms? Worm used with empty gut content? Include the average weight per worm. How to maintain 60-80% humidity, any temperature control chamber used? Add all details.
Figure 1 and 2:  Figure doesn’t mean anything without pointing. Physical characteristics means solid particles? Is that dark indicating the solid particles figure 1? Point with arrow mark in images. All images in figure 2 (A-E) is 5 µm size except 2F which is 10 µm, why?
Line 279 – 280: statement standing alone is meaningless, combined with previous line (line 277 to 280).
Correlation (ratio of feed mixture, worm growth and other compost parameters) study should be need for getting more clear conclusive evidence of the results.


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: OPTIMIZING THE AMOUNT OF PIG MANURE IN THE VERMICOMPOSTING OF SPENT MUSHROOM (LENTINULA) SUBSTRATE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript deals with the study of optimizing the ratio of pig manure addition in SMS vermicomposting based on the comprehensive consideration of physical, chemical, and biological parameters.
According to the authors, the S2 treatment showed optimal processing in SMS vermicomposting and pig manure addition through various factors which includes suitable C/N ratio, higher PPO activities and degradation rate of lignin.

There are a couple of small details that I consider should be addressed before publication:
In line 203 --> check the units.
 Fig 1 and 2 --> mention the images either in lowercase or uppercase.
Experimental design: No comment.
Validity of the findings: In fig 3 (f) you have shown the graphical representation of PPO activity. Can you explain why the S4 treatment shown a drastic decline from 42nd to 56th day.
Additional comments: Each part of the submitted manuscript: the introduction, materials and methods, results and discussion, and the conclusion are well described. The work is well designed and is well performed. The experimental results and the conclusions are pertinent and supported by the results.
However, the English should be checked again.


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: OPTIMIZING THE AMOUNT OF PIG MANURE IN THE VERMICOMPOSTING OF SPENT MUSHROOM (LENTINULA) SUBSTRATE
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: Satisfactory
Validity of the findings: Explained well
Additional comments: There is no further change required for this manuscript.


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

Input:
Title: OPTIMIZING THE AMOUNT OF PIG MANURE IN THE VERMICOMPOSTING OF SPENT MUSHROOM (LENTINULA) SUBSTRATE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Language is thorough throughout the manuscript.
The corrections made in the manuscript was content.
Experimental design: No comment.
Validity of the findings: The corrections made in the manuscript was content and clear.
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: TIME OF NIGHT AND MOONLIGHT STRUCTURE VERTICAL SPACE USE BY INSECTIVOROUS BATS IN A NEOTROPICAL RAINFOREST: AN ACOUSTIC MONITORING STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This timely article is well written but a few changes might increase its impact.
First, the authors should clearly articulate the hypothesis that guided the work. They then should identify specific predictions they will be able to test with their data.  These minor changes will enhance the readability and impact of their research.

The title and the abstract give no indication that the data base was obtained by acoustic monitoring.  This is an important omission.

Other than these two points, I enjoyed the manuscript.  The results are important and interesting. The data are well presented and analyzed.
thanks for asking me to review it.
Brock Fenton
Experimental design: see above
Validity of the findings: see above
Additional comments: No additional comments


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

Input:
Title: TIME OF NIGHT AND MOONLIGHT STRUCTURE VERTICAL SPACE USE BY INSECTIVOROUS BATS IN A NEOTROPICAL RAINFOREST: AN ACOUSTIC MONITORING STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please, see general comments for the authors.
Experimental design: Please, see general comments for the authors.
Validity of the findings: Please, see general comments for the authors.
Additional comments: The manuscript “Temporal variation in vertical stratification of neotropical bats” (#52673) evaluates bat species activity throughout the night in forest understory compared to that above/in the canopy. This is an interesting, little addressed issue, and the results bring significant novelties on the use of vertical stratum by neotropical rainforest bats. Data collection was based on passive acoustic records during nine consecutive nights using two forest towers for accessing the tall stratum, presumably in pristine Amazon forest, in French Guiana. The experimental design and analyses are well done, with a robust dataset and solid results. However, the introduction and discussion need major reviews for increasing focus and the insertion of the results into the literature, better exploring the findings within the context of the study, as I comment below along with minor appointments.

A first aspect is the lack of presentation of the forest type and description of the study site at all. Although presumably the study was in the Amazon rainforest, only in L183 (discussion) does "Amazon rainforest" appear, but even at this point it is not referring to the location of the current study. I think the title could anticipate the forest type (e.g., “Temporal use of vertical strata by neotropical rainforest bats”), and the methods must begin with the study site description: the general climate, geographical coordinates, the type of forest, conservation status, the height of the canopy and the characteristics of the understory (nearby the towers).

The introduction focuses conservation aspects (first paragraph), the appropriateness of bats as a study model, and the acoustic methods (second paragraph), but lacks expectations about the activity and use of the vertical strata by the bat groups recorded here. It can be substantially improved with the description about what we known on bat species vertical stratification, the activity and use of the strata by different bats, and accounting for the study forest types (it is not currently mentioned even for cited studies). Most of the current content could be reduced or excluded.

The objective, as described in both the abstract (L15-16) and the main text (L51-53), does not clearly present the study question, but it rather brings a description of methods, such as the use of canopy towers, what was monitored and where (above and below canopy), and how long and when (throughout nine nights in the wet season). Thus, I suggest rewriting the objective to clearly show the addressed question, what the authors asked, before presenting how, where or when it was approached.

L16-17: Use the past tense when presenting results. Change “We show that…” to “We found that…”, and the following sentence (L18) to “Overall, bats were more active above canopy, but multiple species/acoustic complexes were more active in the understory”. In this sentence, it is unclear whether “multiple species” means the same as “acoustic complexes”, or it refers to individual species plus those cases recognized as acoustic complexes. Please clarify.

In addition, the tall class of the vertical stratum is unclear as sometimes it is used “above the canopy” and in other sentences is “in the canopy”. Were the recorders installed inside the canopy (just below the taller canopies) or indeed above canopy (which means the open space above the forest)? This is important for understanding the results, because the exposure of bats in the environment (e.g., moon light), the types of resources used, and the structural/physical complexity of the environment influences the bat activity. I think that this use of ‘above’ or ‘in’ the canopy should be consistent throughout the manuscript, and precisely described in methods.

L19: Change to past tense.

L22: Data collection is restricted to nine consecutive nights only, so it seems inappropriate to address variation between seasons as part of the conclusion. The focus should be on the variation over night between the two strata, avoiding speculations out of this context, like seasonal differences, both in the abstract and the discussion.

L58: include the distance between the towers.

L63: Four recorders were used in total, correct? What is the approximate maximal distance that recorders can detect bat calls? Is it similar above and below the canopy?

L76-77: Phyllostomidae is also in Table 1.

L116: the first and second sentences are repetitive; they could be just one, e.g., “Overall bat activity was estimated to be 9.5 times higher in the canopy than in the understory.”

L119-120: change “are/aren’t” to “were/were not”

L123: This result (a positive effect of moonlight on overall bat activity) was not discussed; how moonlight affects activity below and above canopy would be additionally applicable and interesting into the focus of the manuscript.

L136-138: change “is” to “was”, “they are” to “it was”, and “has” to “had”

L140-141: change “are” to “were”, and “is” to “was”

L145-150: The beginning of the discussion looks like an introduction. I suggest starting with the main/most general findings supported by the results, and then use the literature to introduce the main general discussion.

L151: This paragraph starts saying that the greater activity in the canopy corroborates the work of Marques et al. (2016), but the following paragraph (L158) starts pointing out "some differences" with the study by Marques et al. (2016). It is unclear what these differences are, and it appears contradictory to the previous text.

L158-159: Even though Marques et al. had sampled in a different season, the current data from nine nights are no longer enough to represent one season, which makes all the following discussion difficult.

L169: At this point in the discussion, it should be fine to address which groups of species have similar and different patterns, which are possible differences that may explain the patterns (e.g., feeding habit, foraging behavior). “No clear preference for stratum” is also a pattern. It sounds to me a very interesting result that deserves a more appropriated and detailed discussion, using a richer literature.

L174-182: This part is a bit confused as only Saccopteryx spp. are used as examples for approaching a general pattern; and partition of nighttime or canopy strata is also unclear without a previous discussion on time and space use by the bat groups.

L191-194: estimating distance to the roosts is not central in the paper. Even speculative parts should be closer to the major paper’s aims.

L199-201: This sentence is too strong. Even considering variations in activity over night and strata, conclusions about habitat quality would not necessarily be erroneous. In fact, contrary to this idea, if most species use both strata, then sampling only the understory seems enough for detecting most of the bat fauna.

Figure 1: I suggest placing the species (X-axis) in decreasing or increasing order of effect size. This will allow to quickly identify which groups have similar and opposite trends.

Figure 2: I suggest the same, to order the spp. vertically according to the effect sizes, taking the values for understory (though the values for canopy will not be ordered, it will improve visualization of differences between spp. and strata).

Table 2: Do no italicize the family names, and “sp.”


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: TIME OF NIGHT AND MOONLIGHT STRUCTURE VERTICAL SPACE USE BY INSECTIVOROUS BATS IN A NEOTROPICAL RAINFOREST: AN ACOUSTIC MONITORING STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The purpose of the manuscript “Temporal variation in vertical stratification of neotropical bats” was to study the vertical space used by neotropical bats in French Guiana. The authors used GLMMs with a Bayesian approach and passive acoustic tools to achieve this goal. The calls were recorded in two localities (towers), each one sampling the two strata. The authors found that the bats were more active in the canopy than understory. With intervals of 80%, it was evidenced that six species are more active in the canopy, five in the understory, and other six without preference strata. They mention that lunar light had a positive effect on activity but that the data cannot be explored for the species. Overall bat activity decreased every hour in the canopy as the night progressed, whereas activity in the understory did not change over time. This study aims to contribute to the knowledge about the temporal and special segregation of bat communities in neotropical forests.

The literature is adequate, but I suggest strengthening the introduction and discussion, as well as including the hypotheses and predictions in the introduction, and how these will be tested.

The supplementary material data must have a more detailed description because they must be self-explanatory for whoever wants to use this information in the future. For example, in xls data, the variables are abbreviated, and it doesn't have units. What does mean x, color, number, S. Alt, M.Az, T.illm, what are the units of these variables?
Minor comments and others are in the attached file.
Experimental design: Given that the authors want to work a new statistical approach to what is commonly worked, I suggest that the authors writing why they choose this new approach and why this approach would allow us to understand the segregation processes in bats. I suggest that the methods should be rewritten, and data treatment in detail (view: Zuur and Ieno. 2016; Stanton 2017). For example, describe whether the data was transformed, how many models are tested, and what was the model selection criterion. Include the statistical output of the models is reported, or of the fixed effect (lunar luminosity).

Also, the authors need to include how the moonlight measurement was obtained in the study area. The cited article does not refer to a specific effective measurement and if to the need to have several measurement indices of this variable. So I suggest that the authors be more specific and mention how they obtained this variable. Even in the data set (supplementary material) a column with the name color (red, green) that makes me doubt if this is the variable that was used as luminosity.

Another important aspect to be included is the characterization of the habitat, since the forest cover around the sensors can influence in the recording of the species (Gibb et al. 2018). More information about the habitat would resolve this question.

In lines 151-152, 153, 155, 171-172 the statements are very general, so they are not informative. I suggest that the authors be more specific, and include the name of the species or acoustic complexes.

The discussion should be strengthened, specifically in temporal and spatial segregation in the study area, and not discuss strongly topics conservation and seasonality aspects, because you did not have data in the study to support this discussion.
Validity of the findings: The authors found differences in the use of the strata for some species. As well as temporal segregation was found for in four species of the Emballonuridae family selected for this analysis. But there are gaps in the methodology and in the statistical analysis that do not allow us to understand why the authors selected 4 species of the 19 sonotypes that they registered. The authors mention that there is a deficit in the sampling (n samples size), but I think that the data could be include, or maybe do a statistical analysis to support to discard the other species.

I suggest, that authors exploring in the discussion the presence of the species in each stratum, this related to their body morphology to explore or find resources in those environments. For example, narrow wings might move more easily on the understory than on the canopy. Another important aspect is that the authors do not mention how they obtain the luminosity measurement and this variable is included in the models, and have positive results in the activity.
Additional comments: The manuscript is interesting and highlights the importance of this study on spatial and temporal segregation in Neotropical bats. I suggest improving the methodology and statistical design.  Also, is very important to include the hypothesis and the prediction that the authors want to test. As well as take advantage of the suggested topics in the introduction and the discussion section (partition of the environment, the temporality of the resources (insects) at night, the luminosity and its influence on the activity in the bats).


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: TIME OF NIGHT AND MOONLIGHT STRUCTURE VERTICAL SPACE USE BY INSECTIVOROUS BATS IN A NEOTROPICAL RAINFOREST: AN ACOUSTIC MONITORING STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: See comments for the authors.
Experimental design: See comments for the authors.
Validity of the findings: See comments for the authors.
Additional comments: I really liked the review carried out by the authors, with energy to approach very well the points raised on the first version, incorporating modifications that bring up the main findings in more depth, and the use of appropriate literature. It was a pleasure to participate in the review, and I believe that this paper will have a great audience. My only suggestion about the content is to change the current sentence at the end of the Abstract (Discussion), as the main message is not exactly what is there, but rather the conclusions available in the two first sentences of the Discussion (and in the Conclusion) of the main text.

In addition, some typos should be corrected during the editorial process, for instance: period (L 112), commas (L 231, 243), italic/non-italic for “i.e.” and “sp.” (L 205, 242, 244), numbers up to 9 in full (L 147), and "Pteronotus" (L 240). I also suggest avoiding abbreviation of species names (genus) at the beginning of phrases (L 211, 214, 265, 280, 283). Increasing font size within figures 2 and 3 will improve visualization, mainly the titles and axes’ names for Kernel scatterplots.


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: TIME OF NIGHT AND MOONLIGHT STRUCTURE VERTICAL SPACE USE BY INSECTIVOROUS BATS IN A NEOTROPICAL RAINFOREST: AN ACOUSTIC MONITORING STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript "Time of night and moonlight structure vertical space use by insectivorous bats in a Neotropical rainforest: an acoustic monitoring study", is clear, well structured, and consistent with the scope of PeerJ.

This study aims to contribute to the knowledge about the temporal and special segregation of bat communities in neotropical forests of French Guiana.

The figures and tables are clear and appropriate.

The authors applied the suggestions of the reviewers, the adjustment of the text was assertive, allowing for a more pleasant reading without information gaps. The methods allow the replicability of the study. The cites and references are complete and adequate.
Experimental design: The methods improved a lot.

The data collection and the analysis description is good.

The statistical output of the models was reported, but I suggest it like supplemental material.

Also, I suggest adding the ethical note that is missing and move the moonlight data for the methods section (See minor comments).
Validity of the findings: This study shows pertinent results about the spatial and temporal distribution of bats in the tropical forest through passive acoustic monitoring.
Additional comments: The new manuscript is really good, and clear. The methods section improved a lot and It is now clearer for the reader.

The data collection and the description of statistical analysis are well detailed. The discussion is adequate and in accordance with the results found.

I have some minor considerations like moving the “Moonlight data collection” to the methods section, add the ethical note, and the data availability DOI or link to Zenodo (See PDF file).

Congratulations by the new version.


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

Input:
Title: SESAMOIDS IN CAUDATA AND GYMNOPHIONA (LISSAMPHIBIA): ABSENCES AND EVIDENCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript Evolution of sesamoid bones in Caudata and Gymnophiona (Lissamphibia) presents results about the presence/absence of sesamoids in selected extant amphibians.
I do not agree with the presence of sesamoids in those groups is understudied since their morphology is well known and sesamoids are not frequent or/and remarkable in those groups.
The goals are clear and unambiguous but the title of the manuscript biases the reader in the wrong direction since the exploration of a large sample has few results in order to discuss and/or interpret the evolution of these structures.
The introduction and background are disorganized to place the focus of the research. As the definition of sesamoid contains many aspects (gene expression, tissues properties, movements, ontogeny, topology) it could be necessary to explain what kind of findings the authors are expecting in Urodela and Gymnophiona (for example, sesamoid associated with skull articulations) as the most important issue and secondarily, appendicular sesamoids in Caudata.
Reports of sesamoids in the anuran skull are not frequent. The squamosal-mandibular sesamoid in Bombinatoridae (Clarke, 1987) needs to be checked because the figure of the dry skeleton in that paper lacks lower jaw The pieces attributed to the sesamoid could be part of the lower jaw. Another report of a small sesamoid in the tendon of muscle levatorae mandibulae externus is described as rare sesamoid in the lower jaw articulation of a neobatrachian frog (Fig. 16. In Fabrezi et al, 2017, J. Exp. Zool B, 328: 546–57).
About the presence of sesamoids in postaxial and appendicular skeletons in Urodela, it is necessary to justify the exploration beyond the absence of literature data.
I find valuable novel data about the variation in the presence of sesamoids in some Caudata but the discussion is based on many ideas that are not linked with few supporting results.
Experimental design: The study presents data about the presence or absence of sesamoid in cleared and stained whole mounts and dry skeletons. However, both anatomical preparations present limitations depending on the preserved specimen (decalcification for long exposition to fixative liquid, age of the individual), or loss of bones with soft tissues. Furthermore, it is necessary to provide the location of the sesamoid within a ligament because there are different muscles that open and close the mouth in the mandibular joint. Similar information should be provided for sesamoids in limbs.
Validity of the findings: Few results (observed variation in Caudata) limit the discussion. The absence of sesamoid precludes any evolutionary interpretation for Gymnophiona.
Discussion about the presence of mandibular sesamoid in some species of Ambystomatidae, Salamandridae, Plethodontidae, Proteidae and Sirenidae should be related to results that are novel contributions and opposed to features that are already known and/or not derived from results.
Diet, biomechanical interpretations, and fossil data to discuss the mandibular sesamoid and early limb development (ectodermal apical ridge) to discuss appendicular sesamoids are not providing developmental/ecological/evolutionary arguments as the title suggests.
Additional comments: The authors must consider that morphological variation and morphological evolution are not synonymous.


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: SESAMOIDS IN CAUDATA AND GYMNOPHIONA (LISSAMPHIBIA): ABSENCES AND EVIDENCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic Reporting
The body of the text and approach lacks a coherent series of tests and criteria necessary to evaluate homology of sesamoids, particularly between amphibian ‘mandibular sesamoids’ and those sesamoids found in other lineages of tetrapods. The illustrations and photographs do not offer enough anatomical details for the reader to adequate assess the assertions the authors make regarding the positions, composition, and topology of the sesamoids under review. The submitted manuscript requires more attention to some aspects of the English. There are several instances of grammatical errors (e.g., pronouns) that affect the interpretation of the anatomical descriptions and interpretations.
Experimental design: Experimental Design
It is unclear what criteria the authors are using to define what a sesamoid is. Descriptions and prose suggest they occur in any number of tissues such as ligament AND muscle as well as anywhere else, but other accepted definitions of sesamoids (sensu Benjamin & McGonagle https://doi.org/10.1007/978-1-4419-0298-6_4,; Bengamin and Ralphs https://doi.org/10.1046/j.1469-7580.1998.19340481.x) are quite precise in that sesamoids are intratendinous nodules that often have trochlear systems associated with them, all of which arise epigenetically due to compressive forces acting about wrapping muscle tissues. Thus, describing the ‘mandibular sesamoid’ of amphibians as lying within a ‘ligament’ between the quadrate and prearticular bones goes against the above definition. Arguments regarding these conflicting definitions are welcome, however the authors here do not provide clarity or precision through descriptive text or figures to this purpose. For example, the presence of a nodule within ‘ligament’ within the jaw joint in the amphibian taxa discussed here suggests that an acceptable, and testable hypothesis is that this is a mineralization of Meckel’s cartilage or a rudiment of an ‘articular’ bone, rather than an intramuscular nodule (or sesamoid sensu Haines, Benjamin & Ralphs). But the authors do not provide the readers any evidence to evaluate their case, whether it be histology of the mineralized tissues and their surroundings, imaging showing soft tissue topologies or other data. The photos provided are interesting, but lack clear positional data and magnification for the readers to truly see the work.
This lack of clarity extends into the authors interpretations of function and homology in the Discussion. They seem to homologize all ‘sesamoids’ in the adductor chamber of reptiles as ‘mandibular sesamoids’ sensu the structure in the amphibian jaw joint. But the cartilagos transiliens of turtles and crocodiles have no associations with the jaw joint (i.e., quadratoarticular joint) and have clearly been shown to be intramuscular/intratendinous sesamoids, rather than intercalary, ligamentous, articular nodules akin to the amphibian ‘mandibular sesamoid’. They go on to suggest the amphibian mandibular sesamoid serves a jaw locking function akin to the crocodilian pterygoid flange & sesamoid system. But they do not offer any description of the biomechanical structures and phenomena that facilitate this behavior. I think in general, if these authors refer to the work and exposition of Montero et al., 2017 study of nodules in the otic joint of reptiles, they will find an example of a rich and concise exploration of sesamoids, and sesamoid-like structures in at least cranial skeletal tissues.
Finally, I am unable to evaluate the distribution of sesamoids in the limbs of amphibians, but I suggest the authors take care in their comparisons and homologies between appendicular and cranial sesamoids and sesamoid-like structures.
Validity of the findings: Validity of Findings
As discussed above, it is challenging to evaluate the validity of findings about phylogeny or function for example, because the authors do not offer enough precise details of morphology in their system of interest or clarity of hypotheses of homology being tested.
Additional comments: Overall, new data on the diversity and distribution and tissue biology of sesamoids are very much. More clarity on the distribution and diversity of ‘sesamoids’ is welcome in vertebrate evolution and skeletal tissue biology. However, several fundamental issues with the approach in this paper hamper its effectiveness.  It has potential to be a welcome contribution, but in its current form, it lacks the evidence and exposition necessary for robusticit in the scientific literature.


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: SESAMOIDS IN CAUDATA AND GYMNOPHIONA (LISSAMPHIBIA): ABSENCES AND EVIDENCE
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1.	¿Is the argument logical?

Yes

2.	Are the methods suitable and results plausible?

Yes

3.	Are the findings adequately described and discussed?

Yes

4.	Is the interpretation of the data appropriate in light of available theory?

Yes

4. Are key papers in the field cited?

Yes.

The authors respond to the quiestion posed in the paper. However, this is an atypical paper, because it is a good example of what we could call as "negative" results since they did not find what they were looking for, which makes it very interesting because it shows that we have to do enough research to be able to draw powerful conclusions. Hypotheses scientific research are usually raised to search for “positive” results, and if the opposite is found, it is considered that it is not worth presenting them to the community. In this case, the authors dare to do it, which is very important for us, researchers in vertebrate morphology, because they save us an important step in the search, in this case, for sesamoid elements in Caudata and Gymnophiona. This being the case, it is difficult to evaluate this paper:  what to say about something that does not exist, as in the case of the Cecilias, or that is in very few, as in the case of salamanders? In this situation, the authors take the only path left to them, and that is to find out what is the probable evolution of these structures in current and fossil groups, including even the other groups of tetrapods, all this using the bibliography they have by hand.
Experimental design: •	There is not experimental design. I suppose the tha authors used material already cleared and stained because they do not say anything about the protocol they used for these.
Validity of the findings: •	Considering the amount of species and specimens they observed, I think their findings are valid.
Additional comments: I have some  comments:

1. About the references: Transfer the reference from line 416 to line 411.
Change Vera et al. 2013 to Vera et al. 2014, or viceversa

2. About the homology:

The authors claimed that  (lines 300-302) “Under this premise, we propose the primary  homology of most mandibular sesamoids in tetrapods, since all of them are embedded or related to the ligaments linking the skull and the mandible”.

But, if they proposed a topology (phylogeny?) including their results, why do they keep calling these relationships as primary homology? This one is based on position and similarity of forms, prior to the phylogenetic analysis, but when characters are already included as part of a phylogeny, they should be called secondary homologies. In fact, it is clear that the trees show that these sesamoids would not be homologous since they appear in trees that the taxa have polyphyletic relationships, at least among the salamander species studied.

3. Because the conclusions must be inferred from the discussion, it would be worthwhile leaving them rather explicitly at the end of the 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: SESAMOIDS IN CAUDATA AND GYMNOPHIONA (LISSAMPHIBIA): ABSENCES AND EVIDENCE
Review round: 3
Reviewer: 1

Output:
Basic reporting: Please find all of my comments in one section
Experimental design: Please find all of my comments in one section
Validity of the findings: Please find all of my comments in one section
Additional comments: Dear Authors,
Thank you for your careful inclusion of comments and your discussion and clarification of patterns of sesamoids in the heads of amphibians. I remain confident that this submission is a worthy contribution. Please excuse my delay in the review.

Perhaps it is a philosophical difference in approach, but I remain skeptical that it is correct or wise to synonymize all sesamoids in the head as the same sesamoid (i.e., the mandibular sesamoid). Given than many of the sesamoids presented here lie on the jaw opening side of the jaw joint, rather than the jaw closing side of the head (where other sesamoids can occur), these sesamoids differ greatly in their topological position and developmental position (e.g., pharyngeal arch 1 vs 2) compared to sesamoids in the jaw adductor muscles. This alone suggests nonhomology. I also disagree with employing Diogo et al’s 2015 overly broad position on what serves as homology, particularly in this study on structures in the head. Applying findings from limbs, which develop from arguably a more simple anlagen of layers, to that of the tetrapod skull, which has numerous different cell populations (e.g., neural crest), ossification patterns (membrane vs endochondral) and quite specific domains of differently-innervated musculature, seems overly superficial and lacks the attention to detail many other authors have clarified. Even in the limbs, I cannot fathom how sesamoids on the flexor side of a limb could possibly be considered 'the same' as sesamoids on the extensor side of a limb.  I do agree that the identity of some neighboring bony structures may not always be significant compared to the position of sesamoids in clearly homologous muscles, for example the arrangement of post-dentary elements in different lineages of tetrapods is somewhat independent of sesamoids in the Bodenaponeurosis of Sauropsids. Though I wholly disagree with the finding of Montero et al 2017 that the surangular bone has anything to do with the jaw muscle, sesamoid, tendon relationships in crocodilians, but that is only part of our conversation here and not part of the paper.

Ln 292: these sesamoids are not ‘within jaw bones’ they are between or among them. ‘Within’ would mean they were somehow inside the elements.

Here it is important to say that there remains a number of errors in the writing that can greatly affect description and interpretation of position. I absolutely understand the authors’ challenge in the expectation of writing in English for these journals and I appreciate my privilege in not having this challenge. I certainly could not write a paper in Spanish that is remotely as clear as this one, even if I still see issues with clarity. I leave this up to the editor to help shepherd.

Ln 246 The discovery that ‘sesamoids’ may merge with bones plastically, or developmentally/evolutionarily while under different mechanical loads has a much deeper history than Abdala’s 2yr old paper. Please see Barnett and Lewis 1958 and references therein about traction epiphyses and apophyses. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1244993/?page=10.
 There is also a vibrant literature on traction epiphyses in the modern medical and orthopedic literature.