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: EFFECTS OF SELF-ISOLATION AND QUARANTINE ON LOOT BOX SPENDING AND EXCESSIVE GAMING—RESULTS OF A NATURAL EXPERIMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: I found the manuscript to be basically well written and well referenced.
As a comment on the introduction, I felt the authors tried to contextualize their study with regard to the controversy around the Internet Gaming Disorder diagnosis. E.g. line 58 “despite having codified gaming disorder (in the ICD-11)”, line 61 “significant disagreement”, and in particular, lines 64-67 that they are examining the effects of the pandemic on excessive gameplay “given the scientific debate about the potential for excessive video gameplay to have maladaptive consequences”. This needs to be handled quite carefully. Prima facie, it’s not clear to me why the effects of the pandemic on video gaming says anything about the IGD controversy (unless they are relying heavily on COVID-related contamination fears causing an increase in gaming, see comment in Validity). Second, the authors should pay careful attention to exact wording here, e.g. on line 65, for many academics, video gaming is only considered excessive if it has maladaptive consequences, so this line as worded is a tautology.
The study is pre-registered and the pre-reg hypotheses are presented on lines 94-123. I found it confusing that the results does not adhere to the same order of hypotheses. Either section could be re-organized but it would help the reader if they were aligned or at least cross-referenced.
I appreciate the dataset is open, but there is little reporting of descriptive stats other than in Figure 1. E.g. for interpreting the K-10 difference as ‘negligible’ (line 200 and 221) it would be great to see the means / SDs.
The authors present Fig 1 for the effects of self-isolation by PGSI group status. This analysis does not show a significant interaction. They do not show the corresponding figure for the PGSI continuous analysis that yields the significant interaction effect. One issue here is about the basic reporting, that is makes sense to graph the more interesting effect (or show both). There are related issues here that are perhaps more relevant to design and validity. First, in the pre-reg hypotheses, H3 is really the same hypothesis as H1, just tested with a categorical rather than continuous model. Likewise, H4 is the categorical version of H2. I'm not sure what to recommend here because these were pre-registered; but in both cases it is the same hypothesis tested in two ways. Second, the authors see an interaction (difference in correlation coefficients) in the continuous model (H2) but not the categorical model (H4). There is a speculative interpretation on line 243 about differences in the number of problem gamblers rather than how much they are spending, but the basic issue is that these 'discrepant' analyses are being conducted on the same data. It is more likely that this reflects either the thresholding of the PGSI (e.g. Currie et al thresholds vs the original Ferris & Wynne thresholds) or the relative statistical power of the two models. Inherently, a continuous model makes better use of the full data than any model that relies on binning scores together.
For PeerJ, the consent form should be uploaded with the Supp; the authors have confirmed this but I did not see it.
The raw data are available via an OSF link but there is no readme file on the variable annotations. With extensive reference to their pre-reg materials, I was able to find the geographical variable (see my comments on Design), but I would encourage the authors to prepare a document on the variable definitions.
Experimental design: This manuscript reports an online survey on Prolific of gaming behaviour during the early stage of the COVID pandemic. The focus on loot boxes (both expenditure and the Risky Loot Box index) and excessive video gaming provides important data for dissemination, and the design includes problem gambling (PGSI), distress (K-10) and contamination fears (Padua) as further covariates. The sample size is fairly large (n=1144) from US, New Zealand and Australia. A key finding is that the relationship between loot box spending and problem gambling is stronger in the group who describe themselves as self-isolating. This has implications for the public health discussion around the pandemic response, as well as wider implications for effect sizes in post-COVID gaming /gambling research.
I did have some concerns about the independent variable that forms the basis for the ‘natural experiment’ here. Participants were categorised as self-isolating or quarantining, versus not. A parallel model of lockdown (yes/no) was abandoned as too few participants endorsed being not in lockdown. Some basic points: 1) could the authors clearly state the date(s) on which the survey was run, perhaps in relation to important pandemic dates (e.g. declared state of emergency) in those jurisdictions, 2) can the authors add descriptives split by the 3 jurisdictions? 3) in the supp, can the authors state the number of participants who were in lockdown?
Currently, the analysis plan simply collapses by region. If for example NZ had a more restrictive ‘lockdown’ than the US, is it possible that their independent variable (self-isolation Yes/No) simply reflects a cross-jurisdictional effect? Second, the analysis plan considers the i.v. as ‘veridical’. Early in the pandemic there seemed to be public confusion about the terms ‘lockdown’ and ‘self-isolating’ (vs social distancing) (and again, the level of confusion may have varied by jurisdiction). The pre-reg materials do not indicate that definitions were provided to participants, which would be a limitation. Moreover, as 95% of participants were in lockdown, to what extent is ‘self-isolation’ within lockdown a subjective or objective status? (again I'm aware there are now clear jurisdictional definitions about these terms, but my point is whether the participants were thinking in these terms or not). This is quite important because subjective self-isolation (or conversely a subjective rejection of the local public health guidance) could be related to contamination fears in particular.

Other
Prolific survey: 54 participants did not play video games. How were the survey advertised on Prolific. As a prevalence rate, this seems high but it may reflect the general characteristics of Prolific participants. Please also add Age data to the Methods.
Line 170: why was the loot box outlier cut-off of 3.29 SD used?  The authors state that this was a pre-registered threshold but it seems an unusual number.
Validity of the findings: The authors included measures of distress and contamination fears. The authors allude in several places to the debate about whether gaming causes ‘psychopathology’ or is used to copy with negative states, and their distress and contamination measures appear to be interpreted as speaking to this e.g. lines 42 and 44 in abstract. This interpretation seems to warrant some discussion as to whether these constructs are state or trait related. The K-10 is past month, so presumably state, but the Padua contamination scale could be viewed as a stable trait. The questionnaire did not appear to ask whether the items had changed at all in relation the pandemic to the pandemic. Similarly in discussion line 223 “isolation requirements have resulted in increased excessive gameplay or expenditure” – the verb “increased” here implies some longitudinal component or at least a retrospective judgment as to whether one’s activities have changed (i.e. under COVID). Their design does not speak to this.
Line 207 “small but important contributor” – how do Ferguson’s criteria establish that a small effect size is important?
Additional comments: no further comments


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

Input:
Title: EFFECTS OF SELF-ISOLATION AND QUARANTINE ON LOOT BOX SPENDING AND EXCESSIVE GAMING—RESULTS OF A NATURAL EXPERIMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: Minor changes as indicated below
Experimental design: Issues addressed in revision
Validity of the findings: Issues addressed in revision
Additional comments: This is a thorough and well thought out revision. The rationale for the paper is much clearer in this revised version.

I found a couple of sentences to be a bit awkward:

"Thus it appears that spending by problem gamblers may be specifically impacted by the presence of loot boxes in video games while playing"

Comment: The structure of the sentence does not quite work and it's a key point. It needs to be something like:

Something like: "Problem gamblers who play games might be more likely to increase their spending on gambling-like features such as loot-boxes during the pandemic."  ?

More generally, the results suggest that social isolation during the pandemic may inflate some pathological gaming effects

Comment: "pathological gaming effects"  (odd expression).  What is this effect? An increase in loot box expenditure in problem gamblers? An increase in the magnitude of the slope or strength of the relationship between PG and loot box spending? Need to make this a bit clearer.


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: EFFECTS OF SELF-ISOLATION AND QUARANTINE ON LOOT BOX SPENDING AND EXCESSIVE GAMING—RESULTS OF A NATURAL EXPERIMENT
Review round: 2
Reviewer: 2

Output:
Basic reporting: basic reporting is sound
Experimental design: I appreciate the authors' thorough response to the reviews. The comments on design and validity have been satisfactorily addressed.
Validity of the findings: See above.  I have checked the new data dictionary on the OSF and I thank the authors for adding this document.
Additional comments: I have two remaining minor comments, both on the abstract
Abstract line 31 “…Australian, Aotearoa New Zealand, and US residents who were quarantined or self-isolating (n = 447) or not (n = 619)…” I would encourage the authors to be very clear here that participants were self-reporting as quarantining/self-isolating or not.
Also for the abstract line 44-45, I would question whether the sentence “These relationships may represent temporary coping mechanisms which abate when COVID-19 ends” is grounded in data from this study, and it seems at odds with the paragraph on line 327 of discussion. This sentence could be re-worded as "It is unclear whether these relationships..."


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: A NOVEL BICYCLIC 2,4-DIAMINOPYRIMIDINE INHIBITOR OF STREPTOCOCCUS SUIS DIHYDROFOLATE REDUCTASE
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this study, the authors screened the open-source Pathogen Box compound library for new drug candidate against Streptococcus suis. They found a potential compound MMV675968 and tried to improve that it targets SsDHFR. The paper is clearly written and professional English language is used throughout. The structure conforms to PeerJ standards, and raw data are supplied. However, the background should be improved to show the study context better, and the Figures should also be improved.
For background:
1.	In Abstract, the authors mentioned “S. suis is an emerging zoonotic pathogen” (line 21), which I agree, but in Introduction (line 46-49), it hard to tell the description is for human infection. Please clarify.
2.	In Abstract, the authors said “it has become increasingly resistant to multiple classes of antibiotics” (line 22), but this statement lacks supporting materials throughout the article. Detailed evidences about “resistant to multiple classes of antibiotics” should be added somewhere around line 51 in Introduction.
For Figures:
1.	The overall resolution should be improved, now both the Figure 1 and Figure 2 seem a little blurry.
2.	Figure 1D, I think the title of the Y axis is not “percent growth”.
3.	When you denotes the statistical significance with “*”, it is better to indicate which two sets of data you are compared.
Experimental design: The study is original primary research within Scope of the journal, most of the methods are described with sufficient detail & information to replicate, partial of the research question is well defined, relevant and meaningful, and some of the investigation are performed to a high technical & ethical standard. However, major improvements are needed.
1.	The authors’ most important issue. You can not say the MMV675968 TARGETs SsDHFR without ruling out the possibility that the inhibition of S. suis growth is resulted from the inhibition of other important target by MMV675968. Thus, as you do for E. coli surrogate, at least you should make sure that the S. suis growth inhibition by MMV675968 can also be reversed in the presence of thymidine supplement. Only after confirmation of this, you can  say MMV675968 targets SsDHFR, and then you can discuss about the permeability of DHFR inhibitors (in Discussion, line 229-234).
2.	Minor questions: 1) Line 94, even you cited the E. coli surrogate you used in your study, it is better to shortly describe why both DHFR and TS enzymes were deleted; 2) Like you define the percent growth in line 80, you should also define the percent activity of DHFR in line 116; 3) Line 127, there are inhibitory activities of at least 3 compounds (No. 123, 269 and 383 in Table S1) are not 90% or greater inhibition of growth; 4) Line 148, from Figure 1B, the inhibition is not “completely”; 5) Line 163, where are the eight DHFR inhibitors from? If they are from Pathogen Box, please indicate their numbers; 6) Line 177 and line 179, please use different color in Table S1 to separately indicate the “eight” and “26” hits.
Validity of the findings: 1.	The novelty of the findings is not very convincing. The authors said MMV675968 is a novel inhibitor of S. suis dihydrofolate reductase. As we can see from the discussion, the authors has already found MMV675968 is a inhibitor for A. baumannii DHFR, is there significant difference between the DHFRs from S. suis and A. baumannii, or between DHFRs from gram positive and negative bacteria? If there is, please discuss. If there isn’t, I don’t think it is a NOVEL inhibitor for DHFR just because the bacterium is different.
2.	In line 237-239, “can serve as broad-spectrum antibiotic candidate” “can serve as an antibiotic candidate against Gram-positive pathogens” are speculations but not conclusions, please change the tone correspondingly, at least do not be so affirmative.
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: A NOVEL BICYCLIC 2,4-DIAMINOPYRIMIDINE INHIBITOR OF STREPTOCOCCUS SUIS DIHYDROFOLATE REDUCTASE
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1)	In the introduction section the Authors have also to describe the role of DHFR as main target of different classes of compounds (i.e. antimalarial, antibacterial and antineoplastic agents [Targeting dihydrofolate reductase: Design, synthesis and biological evaluation of novel 6-substituted pyrrolo[2,3-d]pyrimidines as nonclassical antifolates and as potential antitumor agents. Eur J Med Chem 2019, 178, 329-340]).
2)	They have also to cite the more recent role of host DHFR for anti-influenza drug development [Tonelli M., Naesens L., Gazzarrini S., Santucci M., Cichero E., Tasso B., Moroni A., Costi MP, Loddo R. Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus. Eur. J. Med. Chem. 2017, 135, 467-478].
3)	In the title and also in the paper main text modify “2, 4 diaminopyrimidine” with “2,4- diaminopyrimidine”.
4)	Besides citation 30 and 31 (row 210) add the previously indicated citation related to cycloguanil as antiviral agent [Tonelli M., Naesens L., Gazzarrini S., Santucci M., Cichero E., Tasso B., Moroni A., Costi MP, Loddo R. Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus. Eur. J. Med. Chem. 2017, 135, 467-478]
5)	In the conclusion, row 236:  modify “MMV675968, a bicyclic 2, 4 diaminopyrimidines” in ““MMV675968, a bicyclic 2,4-diaminopyrimidine”
6)	Conclusions are too short, they should be more detailed.
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: The manuscript describes the discovery of a novel 2,4-diaminopyrimidine inhibitor, namely MMV675968, from a screening of the open-source Pathogen Box compound library against Streptococcus suis.
This compound have been evaluated in enzyme inhibition assays on the S. Suis DHFR and also in cell-based assays to assess growth inhibition of two S. suis isolates. Reversal effect on antibacterial activity has been demonstrated in S. suis-infected E. coli PA414 cells exposed to compound MMV675968 in combination with supplement of thymidine.
MMV675968 proved to be effective in both two in vitro assays, comparing favorably with methotrexate for inhibitory potency. Additionally, MMV675968 demonstrates a better selectivity profile for SsDHR than human DHFR, thus showing an improved safety profile with respect to methotrexate.
On the whole, the biological data look solid and significant.
The manucript is interesting and references are adequate and updated.


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: A NOVEL BICYCLIC 2,4-DIAMINOPYRIMIDINE INHIBITOR OF STREPTOCOCCUS SUIS DIHYDROFOLATE REDUCTASE
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript from Songsungthong shows the inhibitor of the dihydrofolate reductase from Streptococcus suis by a 2,4-diaminopyrimidine from the pathogen box of MMV and attend the criteria of PeerJ judgment.
Experimental design: Although the results are interesting, in my point of view, other experiments could bring a more robust work to be published and cited. I am quite concerned about the methods used for in vitro activity of SsDHFR. Although the group has published other manuscripts using this protocol, I wonder why they did not perform the protein purification of the enzyme since they Ahave it already expressing in E. coli. I think more details bout the enzymatic assay should be add in methods since it is also not clear and I am assuming they are working with the absorbance of NADPH consume. If this is the case, even with the low chance, it could have the interference of other enzymes from E. coli to have some background effect as NADPH/NADP+ is a universal coenzyme and used for a number of different enzymatic systems. So in the way it the result is present could have a chance of the results to be misinterpreted. So, I strongly suggest that the authors use a pure enzyme instead of a cellular lysate.
In addition, although the authors suggest that MMV675968 is a “strong” inhibitor, I believe it could be considered a moderate inhibitor of the enzyme since they reported an inhibition at 10 µM. This although seems to be higher than TMP and other non-classic antifolates, in my opinion, is not a strong inhibitor.
Also, although the MMV has reported that these compounds are non-toxic, it should be interesting to have a toxicity experiment of  MMV675968 against human cell lines or alternatively against the human enzyme to indicate the selectivity of the compound.
Finally, I also suggest using modeling tools to try to predict how this compound could bind in the active site of the protein. The DHFR from S. pneumoniae has about 54% of identity to S. suis and could be used even as a model to perform some molecular modeling of the enzyme and as well as docking simulation. A comparison between the active site could bring a plus to the manuscript.
Validity of the findings: Since the compound MMV675968 has a similar or even higher inhibition than other nonclassic antifolates, the findings are valid and interesting.
Additional comments: Interesting work, but quite preliminary and more experiments should be necessary to bring an advance in the field.


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: A NOVEL BICYCLIC 2,4-DIAMINOPYRIMIDINE INHIBITOR OF STREPTOCOCCUS SUIS DIHYDROFOLATE REDUCTASE
Review round: 2
Reviewer: 1

Output:
Basic reporting: In this study, the authors found a potential compound MMV675968 and proved that it targets SsDHFR. Now the manucript has been greatly improved by modifing the background and Figures, and adding more necessary data. The paper is clearly written and professional English language is used throughout.
Experimental design: The research is within Aims and Scope of Peer J, and raw data are supplied. Research question is well defined, relevant and meaningful.
Validity of the findings: All underlying data have been provided. They are statiscally sound and controlled.
Additional comments: My comments are minor.
Line 144, for the definition of percent SsDHFR activity, it is better to use “A340 reduction” than “A340 change” to clarify better that you mean A340 reduction. Even it is reduction, the numbers still should be positive, which I noticed that you calculated as negetive numbers in Raw Data tables (1D and 2B), you just need to calculate reversely. Furthermore, I don’t think the calculted “A340 reduction/min” is raw data. I bring this issue up is because that the A340 reduction/min values (such as -0.08, -0.01, -0.0014) you calculated are too small, and they are even within the measurement error of a spectrophotometer. To make it more clear, you should mention the raw OD numbers in your raw data table and also mention the reaction time in your method.
Line 157, last time when I mentioned “there are inhibitory activities of at least 3 compounds (No. 123, 269 and 383 in Table S1) are not 90% or greater inhibition of growth”, I mean that even the value of percent growth is less than 10, however, it could be higher than 10 when you consider the SD, then the inhibition is less than 90% (not “90% or greater”, at least for one SS strain). Thus, its better to exclude these componds from the 34 “compounds with high inhibitory activity (with average percent inhibition of 90-100%)”.
Line 249, “DHFRs from various bacteria species do not necessarily cluster to the same clade. Consequently, even though MMV675968 is a known inhibitor of DHFRs of Gram-negative bacteria (Nelson & Rosowsky, 2001; Songsungthong et al., 2019), it cannot be assumed a priori that MMV675968 will effectively inhibit DHFR from S. suis.” Are the SsDHFR and the DHFR studied from the same clade? Which I assume not according to your description. If it is true, just clarify this and mention it is still necessary to test whether the MMV675968 is a effective inhibitor for SsDHFR.


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: A NOVEL BICYCLIC 2,4-DIAMINOPYRIMIDINE INHIBITOR OF STREPTOCOCCUS SUIS DIHYDROFOLATE REDUCTASE
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am happy with the corrections and the manuscript should be published.
Experimental design: fine
Validity of the findings: fine
Additional comments: fine


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: OFFSPRING AND ADULT CHEMOSENSORY RECOGNITION BY AN AMPHISBAENIAN REPTILE MAY ALLOW MAINTAINING FAMILIAR LINKS IN THE FOSSORIAL ENVIRONMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript does need some polishing. There are several instances where inappropriate words are used, and sentence structure is clumsy. The comments below are aimed at improving the manuscript in this regard.
There is a bit of a gap in the literature that you cite. I would include some more recent overviews such as:
While, G. M., M. G. Gardner, D. G. Chapple, and M. J. Whiting. 2019. Stable social grouping in lizards. Behavior of Lizards:321–339.
Whiting, M. J., and G. M. While. 2017. Sociality in lizards. In D. R. Rubenstein, P. Abbot (Eds.) Comparative social evolution (pp. 390–426), Cambridge University Press. Cambridge, UK.
L20: Change ‘cohesive social role in many animals’ to ‘function in maintaining cohesive social groups in animals’.
L21: Change ‘with an evident direct parental care’ to ‘with direct parental care’.
L61: Change ‘that difficult these studies’ to ‘that make these studies difficult’.
L63: This goes from singular (the species) to plural (They). I would recommend starting this sentence as ‘Individuals spend (not spent as is currently written) all their lives buried…’.
L67: Change ‘in’ to ‘on’.
L70: Change ‘mainly’ to ‘usually’.
L71: Change ‘during’ to ‘for’.
L72: Change ‘suggests’ to ‘suggest’.
L77: Change ‘or’ to ‘and’ and drop the ‘)’.
L80: I would change ‘epigeal’ to ‘terrestrial’.
L84: I would change ‘a main role’ to ‘an important function’.
L88: Singular to plural again.
L115: Change ‘We lifting stones’ to ‘We lifted stones’.
L123: I would change to ‘Groups made up 24% of records, and single adults were not collected.’
L133: I would change to ‘…on the substrate surface…’.
L142: Change ‘in’ to ‘within’.
L144: How often were individuals weighed?
L164: Change ‘able’ to ‘capable’.
L203: What do you mean by ‘counterbalanced’? Do you not mean ‘randomized’?
L237: Delete ‘than to the’.
L243: I would word this to indicate that the individuals are able to detect and discriminate – not the species.
L245: Change ‘able’ to ‘capable’.
L246: Change ‘a juvenile amphisbaenians is able to’ to ‘juvenile amphisbaenians are able to’.
L247: Change ‘with which the juvenile has been long-term grouped’ to ‘with which they have been associated in the long-term’.
L267: Change ‘like’ to ‘such as’.
L269: ffor
L301: Change ‘found’ to ‘find’.
L302: Insert ‘other’ at the start of this line.
L308: Change ‘able’ to ‘capable’.
L310: Change ‘enough different as’ to ‘different enough’.
L312: How could males be more aggressive to unfamiliar juveniles when they cannot discriminate between juveniles?
L323: Change ‘allow to determine’ to ‘reveal’.
Experimental design: Overall, the experiment design is fine and is clearly explained. The statistical analysis appears sound.
The finding that males do not discriminate between associated and non-associated juveniles is very interesting. I wonder if indeed (as you speculate in the discussion) that this may be because there is a lower probability that the male found with the female and juvenile is actually the father. If that is the case, it may be worth checking if there is a greater range in TFs between the males in comparison to the adult females. If, for example, 50% of the males were they actual fathers, those individuals may be expected to have higher TFs (if indeed fathers can recognise their offspring). It should be a very simple thing to check and if that is the case, it would make this a much more powerful study.
Validity of the findings: I think that the manuscript would be strengthened by addition of a paragraph the explicitly considers the methods used. Are differences in TF a reliable way of demonstrating recognition? For example, if a juvenile TFs had similar rates in response to the scent of two adults, one of which is the parent, does this definitely mean that the juvenile cannot distinguish between parent and non-parent? What if the juvenile TFs simply because it is trying to discriminate? And so TF rate may be also impacted by the interest of the animal to the scent presented.
Additional comments: The study reported in this manuscript tests for individual discrimination in a species of amphisbaenian. Family groups were collected from the field and tongue flick rates were used to measure recognition between adults and juveniles. Adult females appear to be able to discriminate between familiar and unfamiliar young. Juveniles appear capable of discriminating between familiar and unfamiliar adult males, but not females. It is really interesting that adult males could not discern the difference between juveniles and that juveniles could not discern between females. Although some possible explanations are provided for the surprising results, they are not entirely convincing. Overall, this manuscript reports some very interesting findings and I would like to see it published. I do think it could do with some polishing and the addition of an extra paragraph in the discussion that explicitly assesses the method (Validity of findings). I think that it would also be worth assessing the TF rates for the adult males to see if there is any pattern that could show if not all males were the actual fathers of the familiar juveniles (see experimental design).


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: OFFSPRING AND ADULT CHEMOSENSORY RECOGNITION BY AN AMPHISBAENIAN REPTILE MAY ALLOW MAINTAINING FAMILIAR LINKS IN THE FOSSORIAL ENVIRONMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, the manuscript is well written, with results that follow clear hypotheses and with a wide appreciation of literature. However, I noticed in a number of places some grammatical errors. I have tried to highlight these in my general comments that hopefully help to streamline the manuscript.
Experimental design: The research question is clearly defined, and the majority of the experimental design appears to be valid. However, the methods section lacks some detail, rationale and justification regarding some of the more critical decisions about how to collect data and subsequently handle and analyse it. As such, assessing the results is somewhat challenging given the lack of clarity. I have pointed to these in my general comments to the authors, most of which I think can probably be addressed with more information, but without which it is hard to judge whether the results are valid.
Validity of the findings: No comment.
Additional comments: In this manuscript, authors tested whether individual amphisbaenians were able to discriminate between familiar and unfamiliar individuals using chemosensory mechanisms. They conclude that there is some evidence for this, but this depends on the sex of the reciever and provider of the signal. Overall, I really enjoyed reading the manuscript, and learning about the species of which I knew nothing! My minor comments largely refer to some writing hickups throughout the ms. But, I do have a few broader comments which I think the authors should address to help the reader to interpret their results.

1. My major comment is about the measure of tongue flicks as a way of determining discrimination. I am unsure about the validity of this measure, and would suggest that the authors explain the rationale for this much more. My concern here is whether authors are actually measuring recognition, or at least the extent to which the measure reflects discrimination.

2. My other concern lies with the analysis. The section is very brief, and as such it is somewhat difficult to interpret the results. This is because it is unclear (i) how the data were treated, and (ii) how the models were constructed, (iii) how model fit was assessed. Though I think that the authors provide interesting results, it is hard to assess the reliability of these without these details.

3. As a less serious one, I would have liked more information on the species and their social organisation. It is an unfamiliar system, and I would have liked more detail to help to interpret the data and results.

line 60-61; this sentence is not clear, can you edit to clarify your meaning?
line 67; could you expand on this point a bit? For instance, can you elaborate on what sort of "area" are they relocated in, and over what temporal period? It would help to have a more detailed description of their social organisation/social structure
line 77; remove parentheses
line 79-80; to make this more accessible to broader readers, perhaps describe what "fossorial" and "epigeal" mean
line 89; do you mean to mark and identify their own home range?
Line 115; unclear what this searching method refers to. Could you please clarify?
Line 117; What is a "presumably familiar group"? Could you explain what criteria were used to determine this, and why. Also, I assume that the sample size in parantheses here is the number of groups eventually found. It might be better placed later in the manuscript
Line 121; Could you elaborate on what the SVL cut off is that you used to determine juveniles, and how this SVL was determined?
Line 125; I think that having more detailed information about the social organisation of the species earlier could be helpful in interpreting methods here. For instance, it is hard to determine if capturing only individuals that are living in groups is representative
Line 127; Edit to "..were kept together.." or something similar
Line 129 - 132; I think if I understood correctly, individuals found in a group in the field were kept together in the same terrarium. This sentence could be clearer I think.
Line 154; This seems to me a critical assumption in the study, and it would be beneficial to elaborate on the idea that rate of tongue flicks represent detection and discrimination - with discrimination being the key here.
Line 164; should read "..were capable of.."
Line 195; how were tongue flicks determined, and were they recorded as "instances" - so you count the number of TF per trial?
Line 213; what is a within factor?
Line 210; the data analysis section needs a bit more detail. It is not clear what the dependent variable is. I think it might be counts of TF which has then been log transformed. In which case you should really run this model with the raw counts and a Poisson distribution. Either way, I would suggest that the authors provide more detail about the analysis as it is hard to assess the validity of the model structure from the information that is provided.
Line 234 - 240; This is a long sentence with a lot of information and results in, which is somewhat hard to digest without looking at the figure itself. Consider revising to improve clarity.
Line 244; remove full stop
Line 245; here and elsewhere in the manuscript (I noticed quite a few places), "are able of offspring recognition" should be changed to "are capable of ..." or, "are able to recognise offspring"
Line 246; should be either "a juvenile is able to....", or "...juveniles are able to"
Line 269; "ffor" - remove f
Discussion in general; The authors provide some nice detail that could explain the slightly contradictory patterns in the results. However, I think it misses some explicit mentioning of this. For instance, authors conclude that juveniles are able to discriminate between familiar and unfamiliar males, but not females. But on the other hand, conclude that females are able to discriminate between familiar and unfamiliar juveniles. This is a somewhat unexpected pattern, and I was looking forward to the discussion explicitly addressing this. Perhaps authors could consider revising to discuss whether they believe this to be biologically meaningful, or rather some artifact arising from something in the way the data was handled.
Results in general; Could you provide results tables with the full model outputs?
Figures; I think overall these are a nice way of showing the data, but it could also be nice to see the actual spread of the data (rather that summarising in boxes)


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: OFFSPRING AND ADULT CHEMOSENSORY RECOGNITION BY AN AMPHISBAENIAN REPTILE MAY ALLOW MAINTAINING FAMILIAR LINKS IN THE FOSSORIAL ENVIRONMENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: The MS was relatively well written with a good structure, good use of references and mostly clear and unambiguous writing. I did find minor mistakes in some of the that pervaded across the MS. These should be relatively easy to fix. I detail the specifics below in the general comments section.
Experimental design: The MS reports a relatively simple experiment in which the authors provided focal lizards with cotton wool buds containing the scents of different individuals and measured their response. This experimental design is fairly standard for studies of responses to olfactory cues and appeared to be relatively well executed. These experiments were placed in the appropriate context within both the introduction and the discussion.
Validity of the findings: The authors aim was to study kin recognition in a amphisbaenian reptile which has been suggested to live in stable social groups. Such simple social systems are excellent model systems for trying to understand broader questions about the origins and evolution of social organization linked to family life. Central to understanding this is understanding how key communication traits that mediate interactions between individuals (the building blocks of such social groups) go vary with aspects of the social living. The authors do a good job of placing their research in this context and site much of the relevant literature related to this topic. The experimental design is relatively simple but appears well executed. The raw data provided looks robust with respect to the recording of tongue flick rates. I had a few queries about the ways in which the data were analyzed which I detail in the next section. The conclusions appear well stated and backed up and the authors did a good job of not taking their results too far given that lack of paternity assignment and thus knowledge of the actual relatedness between individuals (e.g., the extent to which the authors could infer kin recognition).
Additional comments: I had a number of suggestions with respect to the MS that I hope improve the strength of the paper. I detail these below.

Title: In line with your inability to assign or know parentage between the offspring and adults – should this be altered to “Offspring and Adult Chemosensory recognition…”?

Lines 47 – 48: This sentence jumps out a little – I wonder whether you need it. The link to viviparity are important in some respects (see below) but I am not sure it is important to mention up here. Furthermore, you use both viviparous and oviparous examples in the rest of the paragraph.

Lines 56 – 58: I did not get a feel for the big sell of this paper here in terms of our understanding of co-variation between social evolution and recognition. Just a sentence or two pointing out perhaps that an increased understanding of the diversity of social life in reptiles prompts deeper questions about the mechanisms by which they are maintained (one mechanism by communication).

Lines 72 – 74: It might be worth pointing out that these simple suggested forms of parent-offspring associations are similar to those identified for other lizard species, including those that live in stable family groups (e.g., Gardner et al. 2016; Halliwell et al. 2017).

Lines 94: The formation and maintenance of family groups?

Lines 127: Given you don’t know these are family groups – is there another way to articulate this – “Individuals who were found together in groups were maintained together in separate”

Line 135: Should this be thigmothermy?

Lines 202 – 203: It is not quite clear what you mean by each scent stimulus was used once – does this mean that once you used one stimulus (e.g., cotton wool bud) it was thrown away and a new one used for the next focal animal? I also assume this means that each individual was tested on subsequent days for the rest of the scent combinations – so an adult was tested 3 times and a juvenile 5 times.

Lines 211 – 214: Given that the same individual was included in the data set multiple times (e.g., each juvenile was tested five times and each adult three times) I think you might need to control for subject id in your models with a mixed modelling approach.

Discussion general: I wonder whether you can go back to some of the original points of the introduction and the links to viviparity to explain some of your results. For example, you found that females responded the same to all offspring whereas males responded more strongly to familiar conspecifics. To me this makes sense, given that females will always be present at the production of their offspring whereas males will not necessarily. This might mean that there is limited “need” for females to recognise their own offspring during these early stages of parent-offspring association – because they are always there. In contrast, the male may not be present and therefore there may have been stronger selection on males to distinguish between familiar and unfamiliar offspring. This of course requires there to be some costs of associating with offspring – but that could simply be the costs associated with not eating them if normally there is conspecific infanticide.

The same arguments could be used to explain the juvenile results. As with above, offspring are always going to be associated with their mother upon birth. Therefore, if individuals do not disperse from their natal site, they have no need to necessarily recognise their mother. The adult male however may not be their father – and thus there may be stronger selection on recognising between their own dad and another male.

This would explain both sets of results with the same mechanism. Given the points raised about viviparity and the role it plays in mediating social evolution in these taxa – this may represent a good opportunity to discuss some of the broader implications of viviparity for mediating selection on recognition mechanisms.

Lines 266 – 269: More broadly these simple recognition mechanisms may be the first steps towards more complex forms of parental care – and more complex forms of family life. This is probably a point worth making somewhere here.

Lines 271: change to “that may reduce infanticide by other individuals, such that offspring”

Lines 300 – 302: And this point is more relevant to females than males – that is they should always be found with their mothers (if their mothers give birth to them) but not necessarily with their fathers (depending on the mating season and levels of dispersal).

Lines 305 – 308: Is there a precedence for where different entities within a species differ in the variation of their chemical signals in a way that mediates the response?

List of the minor corrections I identified (this may not be exhaustive).

Line 61: change to “make these studies difficult”?

Line 63: change to “spend”

Line 68: Not sure this sentence needs “Moreover”

Line 71: changed to “maintained for several months into the next season”

Line 77: remove “)”

Line 90: change to “can discriminate”

Line 92: change to “have self-recognition abilities” or something similar.

Line 115: change to “lifted”

Line 127: change to “separate”

Line 130: change to “by keeping individuals together”

Line 142: change to “within”

Line 164: change to “display juvenile recognition”

Line 184: change to “undertaken”

Line 198: change to “had the ability to detect conspecifics using chemosensory communication”

Lines 202 – 203: How often were individuals swabbed for their scent during this time – did this overlap
with the actual tongue flick assays?

Line 244: remove “.”

Line 286: remove “On the other hand,”


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: ASSESSING THE EFFECTS OF TIME-DEPENDENT RESTRICTIONS AND CONTROL ACTIONS TO FLATTEN THE CURVE OF COVID-19 IN KAZAKHSTAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well-written, with extensive literature review. Figures and tables are sufficient to illustrate the results of this study.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: There are many similar existing studies on the topics and the current study fails to add novel insights. Following are three minor comments:
(1) Normally, \Delta is not used as a model coefficient;
(2) It would be better to explicitly indicate the dates in x-axis of Figure 1
(3) The values of incubation periods, recovery periods and time to death those values lie outside the confidence intervals predicted by most studies, which are not plausible.


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: ASSESSING THE EFFECTS OF TIME-DEPENDENT RESTRICTIONS AND CONTROL ACTIONS TO FLATTEN THE CURVE OF COVID-19 IN KAZAKHSTAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this manuscript, the authors present a SEIRD model with both time-invariant and time-varying transmission rate for the control and assessment of time-dependent restrictions put in place by governments during the COVID-19 pandemic.
The paper is well structured; the presentation of the topics is clear, and a very professional English language is used. The problem is clearly explained in the introduction where compartmental models SIR and SEIR are reported in the modelling of COVID-19 pandemics. The same, however, does not happen for the SEIRD model with constant and time-dependent parameters. Although it is difficult to follow the significant number of preprints and papers appearing about this subject, a few references are needed. SEIRD has been used in COVID-19 pandemic both with constant parameters (for example https://doi.org/10.1101/2020.05.10.20083683,   https://doi.org/10.3346/jkms.2020.35.e317) as well as time-dependent parameters, see  https://doi.org/10.1371/journal.pone.0237417 and references therein.
Moreover, while the choice of the Trust-Region Reflective method for the solution of the inverse problem (parameter estimation) is well-motivated, nothing appears, in the introduction, concerning the solution of the forward problem (ODE). A discussion about this point would improve the whole introduction.
Concerning the Mathematical modelling (section 2) the SEIRD model and reproduction number are presented for the most general case and then studied for a close population. It is advisable to state the SEIRD for a close population and carefully check the correspondence of equations (9)-(13) with the modelling simulation reported in table 6 (further discussion in the next paragraphs).
The paper presents a case study based on Kazakhstan epidemic data. The experimental section is well designed, and the Initial assumptions are reported in detail. However, the initial value of the exposed E(0)=20  I(0) appears to be entirely arbitrary. The motivation and the influence of this choice on the final results need further discussion.
The description of the parameter estimation procedure and simulation 1 (4.2) are clear and accurate. On the contrary paragraphs, 4.3 and 4.4 need improvement.
The plots in figure 4(a-c) and the data in table 6 are obtained by splitting the simulation into 14 days intervals.  Since the parameters \alpha-\beta-\gamma-\delta are constant on each interval and change from one interval to another, they are piecewise constant functions throughout the time domain. The text does not evidence this fact, which should be highlighted by reporting in a table the values of the parameters computed at each time interval.
Moreover, from the text, it is not clear whether the control actions sigma(t) are assigned/guessed or obtained through a parameter estimation procedure. This aspect should be clarified in detail by explaining how the numbers in the second column of Table 7 are obtained. Moreover, if such values are assigned, pèlease explain the reasoning behind these choices.
Table 7 is not easy to read, especially in the shaded part, the link to the four scenarios described in the text could help the reader.

Finally, the included Matlab code that computes data in Table 6 and plots Figure 4 (a),(b),(c), performs the optimization step using only Infected and Dead populations. (see runNonlinear.m at line 32)
Please amend this by correcting the code and the table/figures or writing a consistent expression in equation 20, explaining why the Recovered data should be removed.

Typos:
Ln 88: /tiem/.  /time/
Ln 248: /apparent/.  /evident/

Decision

The present manuscript tackles an actual crucial topic, and even though plenty of literature is available with the same purpose, the methodology presents a novelty aspect. The paper is well written, and it has a good structure. The results are engaging, but there are essential aspects in the reference, mathematical model and experimental section that need to be clarified before it can be accepted for publication.
Accept after revision.


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

Input:
Title: ASSESSING THE EFFECTS OF TIME-DEPENDENT RESTRICTIONS AND CONTROL ACTIONS TO FLATTEN THE CURVE OF COVID-19 IN KAZAKHSTAN
Review round: 1
Reviewer: 3

Output:
Basic reporting: “Figure 2. Block diagram of the SEIRD model used to model the dynamics of COVID-19 in Kazakhstan” is not present.

Line 23: ….."to better plan for and control of the subsequent waves of the pandemic"….
Seems “of” is extra here.

Line 26: …"which is one of the critical measurements"… measures may be better.

Line 83-85: The sentence needs to be reworded to make it clear.

Line 88: ----"tiem-related"--- must be time-related

Line 105: ----"parameters"-----change it to "parameter"

Give reference for equation (7), it can not be arrived using equation (6)

Line 130-134: Split the sentence into smaller sentences

Line 147: for fatality rates provide reference

Line 155: -----"estimates"---change it to estimate

Use passive for writing paper and avoid we, I etc.
Experimental design: For equation (14) one more assumption needs to be mentioned that is birth and death rates are almost equal in addition to being negligible (as has been mentioned).

In equation (6), the intervention parameter must always be positive and up to 1, else the transmission rate can lead to higher values in partial intervention case than in no intervention case.

Also consider adding statistical analysis to see the variation between model results and reported data.
Validity of the findings: Results in Line 213-219 difficult to justify as intervention parameter is showing negative vales.

Without statistical analysis difficult to comment on validity of results.
Additional comments: Please revise the work as per the mentioned comments.
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: ASSESSING THE EFFECTS OF TIME-DEPENDENT RESTRICTIONS AND CONTROL ACTIONS TO FLATTEN THE CURVE OF COVID-19 IN KAZAKHSTAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have correctly included all the suggested amendments. The paper is significantly improved.


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: ASSESSING THE EFFECTS OF TIME-DEPENDENT RESTRICTIONS AND CONTROL ACTIONS TO FLATTEN THE CURVE OF COVID-19 IN KAZAKHSTAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: All comments addressed
Experimental design: The revised σ(t) ∈ (−∞,1] is difficult to justify especially on the lower bound. As it will make the modified beta reaching to infinity. And such large values of beta will infect the global population within a day, which is not the characteristic of at least this COVID-19.

Moreover, the removal of control interventions should bring the transmission to natural value of beta, meaning σ should become zero. Making σ negative means that the removal of control interventions are making transmission rates increase beyond the non-intervention level.

It would be good to provide references for effective beta values going beyond non-intervention values while removing control interventions and justification for this scenario.
Validity of the findings: Depend on the validity and justification of the σ(t) ∈ (−∞,1]
Additional comments: Dear Authors,

Please address the 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: ASSESSING THE EFFECTS OF TIME-DEPENDENT RESTRICTIONS AND CONTROL ACTIONS TO FLATTEN THE CURVE OF COVID-19 IN KAZAKHSTAN
Review round: 3
Reviewer: 1

Output:
Basic reporting: All comments addressed
Experimental design: All comments addressed
Validity of the findings: All comments addressed
Additional comments: Dear Authors,

Thanks for your efforts


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: 6MA-PRED: IDENTIFYING DNA N6-METHYLADENINE SITES BASED ON DEEP LEARNING
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment.
Experimental design: no comment.
Validity of the findings: no comment.
Additional comments: In the calculation method of 6mA site recognition, deep learning is rarely applied. The paper applied the attention mechanism of deep learning to 6mA site recognition and achieved good results. The method proposed in the paper has achieved good results in the identification of 6mA site of rice, Mus musculus and human genes. The experimental methods are reasonable and the experimental conclusions are convincing. There are the following suggestions or questions.
1．The description of the model structure is a bit vague. It is recommended to add a detailed description of the model.
2．Why use kmer word segmentation and what are its advantages?
3．Why the dot product method is used when calculating the attention score？
4．What are the advantages of the attention mechanism of the paper compared with the self-attention in Transformer?
5．There are a few misspellings of words in the paper.
Finally, it is recommended to accept this paper.


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

Input:
Title: 6MA-PRED: IDENTIFYING DNA N6-METHYLADENINE SITES BASED ON DEEP LEARNING
Review round: 1
Reviewer: 2

Output:
Basic reporting: Most computing methods for 6mA site recognition are still machine learning models。At present, there are relatively few papers recognized by 6mA sites in multiple species。Using a deep learning model to solve the recognition of cross-species 6mA site recognition is indeed relatively novel. From the results, the model performs well in cross-species identification. However, there are still some doubts about the details of the paper.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: ①　Why doesn't the embedding layer adopt one-hot?
②　What are the advantages of combining KMER and embedding?
③　Does the model have any special handling in dealing with cross-species recognition?
④　How about replacing the sequence model with a convolutional neural network?


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: 6MA-PRED: IDENTIFYING DNA N6-METHYLADENINE SITES BASED ON DEEP LEARNING
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript presents a new predictor for DNA 6mA sites. I have several comments for this manuscript that need to be fixed. Please refer to the general comments.
Experimental design: The manuscript presents a new predictor for DNA 6mA sites. I have several comments for this manuscript that need to be fixed. Please refer to the general comments.
Validity of the findings: The manuscript presents a new predictor for DNA 6mA sites. I have several comments for this manuscript that need to be fixed. Please refer to the general comments.
Additional comments: The manuscript presents a new predictor for DNA 6mA sites. I have several comments for this manuscript that need to be fixed.

Major comments:
- For data preprocessing. The authors collected the dataset from different sources, and it seems they do not remove the homology sequences. Approaches such as CD-HIT should be applied with a reasonable threshold to remove the redundancy sequences in this combined dataset.

- The authors should provide a more detailed description of the datasets. How do they select the negative dataset? Is there any overlap in both positive and negative sample between the two datasets they used?

- The authors should clarify why do they use the Kmer instead of One-hot encoding? Did they compare these two encoding schemes on the same condition?

- The authors should provide the experimental results to clarify why they use k=3 in Kmer instead of others.

- The authors should also compare their method with some conventional machine learning algorithms, such as XGBoost, GBDT, SVM, Random Forest, lightGBM and logistic regression

- It would be better to develop an online webserver to facilitate the users to use their method.

- Some loosely associated citations can be further refined.


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: 6MA-PRED: IDENTIFYING DNA N6-METHYLADENINE SITES BASED ON DEEP LEARNING
Review round: 2
Reviewer: 1

Output:
Basic reporting: Identifying DNA N6-methyladenine sites
Experimental design: Deep Learning was used.
Validity of the findings: Good accuracy was obtianed.
Additional comments: The paper can be accepted.


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: 6MA-PRED: IDENTIFYING DNA N6-METHYLADENINE SITES BASED ON DEEP LEARNING
Review round: 2
Reviewer: 2

Output:
Basic reporting: none
Experimental design: none
Validity of the findings: none
Additional comments: none


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: 6MA-PRED: IDENTIFYING DNA N6-METHYLADENINE SITES BASED ON DEEP LEARNING
Review round: 2
Reviewer: 3

Output:
Basic reporting: The authors did not fully address my comments.
Experimental design: The authors did not fully address my comments.
Validity of the findings: The authors did not fully address my comments.
Additional comments: The authors did not fully address my comments.


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

Input:
Title: THE EXPRESSION CHARACTERISTICS AND PROGNOSTIC ROLES OF AUTOPHAGY-RELATED GENES IN GASTRIC CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is an interesting manuscript however, it must be improved.

ATG is not an abbreviation for "autophagy-related genes" hence using ATGs abbreviation is incorrect. Please correct it according to: Look people, “Atg” is an abbreviation for “autophagy-related.” That’s it. Daniel J. Klionsky. Autophagy. 2012 Sep 1; 8(9): 1281–1282. doi: 10.4161/auto.21812 PMCID: PMC3442874.
Moreover, all gene symbols should be italicized.
Please correct ATG8/LC3 as well.
In the introduction section lack of information about gastric cancer (GC). Please include epidemiology, risk factors, and classification of GC into the manuscript.
Line 96 „different histological types” what types were taken into consideration?
Line 160 HR please explain the abbreviation
Line 196 is:  "Adjacent" please correct to "adjacent"
Line 205 is: "Some" please correct to "some"
Line 212 is: "AMBAR1" please correct to "AMBRA1"
Line 234 with III stage but what type of cancer?
Line 237 Atg4b – what do you mean? A mouse system?


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

Input:
Title: THE EXPRESSION CHARACTERISTICS AND PROGNOSTIC ROLES OF AUTOPHAGY-RELATED GENES IN GASTRIC CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: Minor comments:
Articles must revise with grammatical and typical errors eg, line 171(-year).
Improvement in figure qualities will strength the article.
Experimental design: Title: The expression characteristics and prognostic roles of autophagy-related genes in gastric cancer

Authors characterized the expression of different genes which responsible for autophagy mechanism in gastric cancer. The study design and usage of bioinformatics tools is appropriate for this study.
Validity of the findings: The study reports the upregulation of ATG8/LC3 has direct effect on gastric cancer. Overall the study design, material and method selection is supporting the concept of study.
Additional comments: No additional comments


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

Input:
Title: THE EXPRESSION CHARACTERISTICS AND PROGNOSTIC ROLES OF AUTOPHAGY-RELATED GENES IN GASTRIC CANCER
Review round: 1
Reviewer: 3

Output:
Basic reporting: Clear outline of the paper with a sound description of aims and objectives. Citations are relevant and recent.
Experimental design: Authors have employed a reasonable experimental design. The subject selection us clear. Here are my comments on the methods section:
1) Page 90: Please cite a relevant reference for Pathvisio. Also, please mention any further details like version, URL, settings used etc.
2) Authors have cited reference for Oncomine and TCGA dataset. Please provide any relevant details like version, URL etc.
3) Lines 102-103: Authors write – “The patients’ TNM stage, T, N and M were considered as the clinical parameters”. Please explain the criteria for deciding these clinical parameters and/or cite a relevant reference.
Validity of the findings: This is an interesting and informative study; and the findings would contribute to the progression of knowledge in the field. The manuscript would gain much if authors provide any biochemical validation of the results pertaining to the differentially expressed genes in GC vs normal cells by techniques like RT-qPCR, immunoblot etc.
Additional comments: The manuscript submitted by Wang. Jing et al., presents a study on identification of the role of autophagy related genes (ATGs) in the occurrence and development of gastric cancer (GC). Using previously published datasets, authors studied the expression of ATGs in cancer and normal tissues. Authors identified several ATGs associated with either TNM stage, T stage or lymph node metastasis stage. Authors conclude that Alternations in the expression of the ubiquitin-like conjugated system in ATGs might play a key role in GC occurrence. Overall, the manuscript is well written and informative. Here are a few remarks that need to addressed.
1) Authors need to include more introductory literature on the already published literature on ATGs’ association with cancer, especially the GC cases. I would also recommend if authors include molecular details behind the association.
2) It would be helpful if authors summarize their findings in the form of a schematic model.
3) The discussion section is long and hence can be shortened.


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 EXPRESSION CHARACTERISTICS AND PROGNOSTIC ROLES OF AUTOPHAGY-RELATED GENES IN GASTRIC CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript meets basic criteria of reporting and publication.
Experimental design: Experimental design employed here is scientifically sound and the revised version provides all the relevant information on it.
Validity of the findings: The findings are novel and provide insights into the biology of autophagy-related genes in gastric cancer.
Additional comments: In the revised version, authors have addressed my concerns. I recommend this manuscript for publication in PeerJ.


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: EVALUATION OF FGFR1 AS A DIAGNOSTIC BIOMARKER FOR OVARIAN CANCER USING TCGA AND GEO DATASETS
Review round: 1
Reviewer: 1

Output:
Basic reporting: - The use of language needs to be improved. There contains some grammatical errors, as well as some jargon.
- Quality of figures need to be improved.
- The authors should provide raw data, processed data and source codes for reproducing their results
- It is important to show some literature reviews related to the relevance of EGFR1 on ovarian cancer.
Experimental design: - Research question is a bit confusing. The authors have not shown the relationships between FGFR1 and ovarian cancer in the literature review. If it is not reported in previous works, why did the authors want to perform a work with this specific gene? At least it must have some experimental evidences.
- The authors have not explained well on their methods. It is necessary to make the methodology clearly, and the readers could reproduce their results.
Validity of the findings: If the authors could find that FGFR1 is an important biomarker for ovarian cancer and it is the first study shows this, it is very impact and novel. However, the current experiments and performance results did not show enough evidences on this point. For example:
- The survival analysis is not significantly different between high and low level of FGFR1, it  cannot be convinced that EGFR1 is important in OC.
- How can we know the different distribution between training and validation cohort? The authors should perform some statistical tests on this.
- Why did the authors plot ROC curve for GEO datasets, but not in TCGA?
Additional comments: - Section 2.2, line 101 to 105, what is "(González Martín A OA)"?
- ROC curve or AUC has been used in previous works such as https://doi.org/10.1016/j.chemolab.2019.103855, https://doi.org/10.1016/j.neucom.2019.09.070, and https://doi.org/10.1186/s12859-019-2972-5. Therefore, the authors should refer more works in this description.
- Why were the normalization values similar between all samples in Fig. 3?


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

Input:
Title: EVALUATION OF FGFR1 AS A DIAGNOSTIC BIOMARKER FOR OVARIAN CANCER USING TCGA AND GEO DATASETS
Review round: 1
Reviewer: 2

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: In this manuscript “Evaluation of FGFR1 as a diagnostic biomarker for ovarian cancer using TCGA and GEO datasets “ Xiao et al. have discussed diagnostic value of FGFR expression in ovarian cancer patient cohort from TCGA and GEO datasets. Although authors have performed some bioinformatics analysis but haven’t discussed any biological insights gained from such analysis. This manuscript is very poorly written, no methodological details were provided and does not add any value to move the oncology field forward.

Please see the comments below:

1. Authors should clearly discuss the rationale of analyzing FGFR expression in ovarian cancer patients? Why FGFR1 and not FGFR2-4?

2. It is not clear how FGFR1 expression was predictive of survival. It is not shown in Figure1 of the manuscript. A quantitative way to subset patients in FGFR1 expression high or low patient groups should be used to analyze whether FGFR1 expression is predictive of survival in OV cancer patients. Does other FGFR family genes (e.g. FGFR2/FGFR3/FGFR4) are also predictive of survival?

3. Figure1 should indicate p-values and hazard ratio statistics.  This should also be validated across various ovarian cancer cohort datasets (please see cbioportal – OV data). Compare FGFR1 expression levels in OV and normal cancer patients.

4. Methods section: TCGA data- authors should clearly describe TCGA data statistics and mention how many samples were downloaded from TCGA ovarian cancer data. It is not clear what analysis was performed using FDR cutoff (Line 94). Please clearly mention the details.

5. Figure5: Please explain what forest and funnel plots are representing here? What do authors meant by “we found no significant heterogeneity by fixed-effected model “  what is publication bias?  (line 180-182). Section 3.4 describes methods and no results.

6. Section 3.2 : what does authors meant by : FGFR expression was validated in OC and normal ovary tissues in GEO dataset””. This section should be moved to methods as it doesn’t discuss any results

7. Figure2: This flowchart is not informative unless authors mention all the details. What was inclusion and exclusion criterion? What is the significance of mentioning all the GEO hits unless they were used for the data analysis.

8. Figure quality is very poor and mention statistics test used to calculate p-values.

9. Figure3: What does x and y axis represents? It is not clear how the data normalization was performed?

10. Figure 4: What is the significance of AUC curves here? It is not clear what authors wants to show here? Why this analysis was not carried out using TCGA data,

11. Figure legends are very poorly written and doesn’t describe the data shown in figures.

12. boxplots will help in understanding the variations in the clinical features as discussed in result section 3.1

13. Figure6: Mark where all the interesting genes lie.

14. Manuscript is very poorly written and has many spelling mistakes.

15. Line 115: samles ->”samples”

16. Figure 4: “Expression date” -> “Expression 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: EVALUATION OF FGFR1 AS A DIAGNOSTIC BIOMARKER FOR OVARIAN CANCER USING TCGA AND GEO DATASETS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This manuscript uses the datasets/databases for providing insights for using FGFR1 as a reliable marker for ovarian cancer. Overall the manuscript is very well written.

-Please provide more information on why FGFR linked genes were chosen for this study. This information should be included in the introduction section.

-The scientific language used to describe the work can be improved to make the statements more impactful. Some examples where the sentences can be modified include lines 44, 45, 66-70, 71-73, 77, 78, 93, 94, 139, 140.
Experimental design: - It has been mentioned in the discussion section that due to lack of control samples the statistical power of analysis was reduced. If possible, the authors should try to gain some more data for control set to strengthen the manuscript.

-The statements in “Conclusion” section overlap with the “Discussion” section. Authors should make the necessary changes.

- It is unclear what numbers (5) and (6) are used for in 106th line?

- Please remake Fig 1 and Fig 7. The figure quality is very poor and text is hardly visible.
Validity of the findings: Ovarian cancer is one of the hardest to treat cancers and the discovery of novel biomarkers will enable the development of drugs to treat cancer. Evaluation of FGFR1 as a prognostic marker in OC is important however more metadata from multiple databases are required to validate the findings of the current study. Nevertheless, the current study and data are important for the field.
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: EVALUATION OF FGFR1 AS A DIAGNOSTIC BIOMARKER FOR OVARIAN CANCER USING TCGA AND GEO DATASETS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Thanks for addressing my previous comments, but I think there are some comments that have not yet been addressed or not yet addressed well. I suggest a substantial revision on some unanswered points:
- The use of English still needs to be improved.
- More literature review should be added related to EGFR1 and ovarian cancer.
- I suggested the authors clearly revised the methodology part, but they mentioned that they revise the 'Study Characteristics' which located in "Results".
- I suggested the authors refer more works for ROC curve & AUC, but the authors might skip it. Please go back and re-check my previous comment.
- "Although FGFR1 expression is not significantly different in the survival analysis, we believed FGFR1 plays an important role in diagnosing ovarian cancer." --> this finding could not be convinced in their analyses.


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

Input:
Title: EVALUATION OF FGFR1 AS A DIAGNOSTIC BIOMARKER FOR OVARIAN CANCER USING TCGA AND GEO DATASETS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thanks for addressing the 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: CYTOCHROME P450 MONOOXYGENASE GENES IN THE WILD SILKWORM, BOMBYX MANDARINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: This manuscript describes identification of cytochrome P450 genes from draft genomic sequence of wild silkworm (Bombyx mandarina). The authors compare these gene models with those of the well-studied domestic strain Bombyx mori.

1.	One of the major claims of this manuscript is that the CYPome of B. mandarina is considerably smaller than that of B. mori (Line 24 and others). However, this claim cannot be accepted immediately. First, the presumable evolutionary time of 5000 years after branching is too short to cause such a large change in gene battery of a wild species. Second, the quality of the primary data, i.e. the assembly of B. mandarina genome, is not high enough to draw any conclusions about the proteome that encodes. Although the authors improved the initial de novo assembly by a template-guided method using B. mori genome as the reference, this attempt cannot recover missing sequences unrepresented in the initial contigs. Third, as detailed in the following item, the authors’ gene models are likely to contain an appreciable number of fusions and fissions of true genes. This increases inaccuracy in the estimated number of P450 genes.
2.	The authors use the gene models of B. mori downloaded from Silkbase as the reference. However, more than a half (44/82) of these models appear to be incorrect as Kawamoto et al (2019) reported manually modified versions of them (Table S5), including a total of nine gene models correcting for erroneous gene fusions or fissions. The reliability of the gene models of B. mandarina derived from the Refseq annotation is likely to be even worse than the Silkbase versions, considering the low quality of the genome assembly. Thus, only a very small fraction of 70-80 potential orthologous pairs between the two strains has been legitimately compared based on correct gene models of both strains. The “highly variable intron-exon structures among these genes” (Line 263) most likely reflect the inaccurate gene structure prediction of either or both CYPomes.
3.	Another major message of this manuscript is that CYP306A is a candidate gene responsible for the stronger insecticide resistance of the wild strain compared with the domestic one (Line 30 and others). However, I cannot follow the logic described in the paragraph Lines 340-374. Even though CYP306A is differentially expressed between substructures of silk gland, how that phenomenon is relevant to insecticide resistance? Obviously, silk gland is not the major organ involved in insecticide metabolism.
4.	In Table 1, the columns of Family and Subfamily are dispensable, as the gene name contains that information. Instead, this table should contain other important information, such as CDS/aa lengths, exon numbers, sequence identities between orthologous B. mandarina and Bombyx mori proteins, etc.
5.	Figure 3, Table S6, and S7 (Go and pathway analyses) are not much informative, as they represent the features common among all insects (or even arthropods).
6.	The gene structures shown in Fig. S2 are hard to interpret. Exon-intron organization of genes would be better demonstrated in a similar manor as that shown in Fig 1 of Ai et al (2011).
Additional comments: Bioinformatics approaches are valid only when the primary data are of sufficiently high quality. The present stage of the available experimental data does not reach such a standard. Better assembly of the genomic sequence of B. mandarina and more comprehensible expression analyses for various organs, developmental stages, and environmental conditions would be necessary to find any biologically significant  differences between wild-type and domestic strains.


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: CYTOCHROME P450 MONOOXYGENASE GENES IN THE WILD SILKWORM, BOMBYX MANDARINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this manuscript, the authors provided P450 monooxygenase genes in wild silkworm, Bombyx mandarina using new reference-guided genome data and RNAseq data from silk grands. They identified 68 P450 genes and determined location of each P450 gene in chromosome. Through KEGG enrichment and transcriptome analysis, they found candidate P450 genes involved in ecdysteroidogenesis and insecticide metabolism.
As the author described, P450 monooxygenase genes have multiple and important roles in biological process such as juvenile hormone biosynthesis, ecdysteroidogenesis and insecticide metabolism. The findings and topics of the manuscript are important for comparative biology and genome biology. So I think the manuscript worth to publishing for “Peer J”. However, there are many points which should be revised before the publishing.
All figure captions is too short to understand the figures. Describe more detail.
Fig. S1 is “Phylogenetic tree of cytochrome P450 genes in the wild and domestic silkworms.”. Although it is important figure, the figure is not clear. I cannot recognize ID of each gene in the figure file. The figure should be replaced to the clear one.
Experimental design: The authors performed several data analysis. The authors utilized many tools of data analysis in this study. However, each tool is not referred property. Tools used in the study should be referred with version, paper, URL of the tools and parameter when you run the tools. So Lasts (line 97), Hisat2 (line 118), Stringtile (line 120), Transdedecoder(line 123), KEGG (line 130), KoBAS (line 131), InterProscan (line 132),  MCScanX (line 139), Circos (line 141),GeneWise (line 159) and iTOL (line 165).
Validity of the findings: Authors found candidate P450 genes involved in ecdysteroidogenesis and insecticide metabolism. There are two point which should be addressed. One is to find P450 genes involved in JH synthesis. The authors described “They fulfill many important tasks, from the synthesis and degradation of ecdysteroids and juvenile hormones to insecticide metabolism (Feyereisen 1999).“ (line 316-317). However, they found candidate gene of only ecdysteroidogenesis.  Authors must add candidate P450 gene of JH synthesis as they found candidate P450 gene of ecdysteroidogenesis.
Another one point is that the authors concluded that they found candidate P450 gene involved in insecticide metabolism. I think this conclusion did not appropriate. In general, insecticide metabolism could be occurred in other tissues (e.g. fat body). If the authors want to show candidate P450 gene involved in insecticide metabolism, RNAseq data of fat body or other tissues playing insecticide metabolism must be added.
Additional comments: Minor comment
1. Correct “juvenile hormones (JHs)” (line 317)
2. Why “CYP306A1” in bold? (line 332)
3. In figure 4, why one P450 show “CYP306A1”. It makes confused and should be correct to gene ID.


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: CYTOCHROME P450 MONOOXYGENASE GENES IN THE WILD SILKWORM, BOMBYX MANDARINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors describe the difference in the numbers of P450 genes between the domesticated silkworm (Bombyx mori) and the ancestor wild silkworm (B. mandarina) in the manuscript. It is very interesting that the numbers in B. mandarina is quite different from B. mori, if it is correct, because P450 genes have highly diversified functions and are biologically very important. However, I think that the data are unclear and the discussions are insufficient. The manuscript needs major revision for publishing in this journal. The data, figures and tables should be reconsidered.
Experimental design: The degree of the improvement of the quality of the genome assembly in B. mandarina is essential in this paper. But it is difficult to understand how much the quality was improved. It would be better to summarize the differences between the new B. mandarina genome and the old one in another table (lines 191-207). Chromosomes 4, 6 and 21 on B. mandarina are half in size in comparison with B. mori, as shown in Table S2. Is it correct?

In Materials & Methods, Lastz, HiSAT2, StringTie, TransgDecorder, KEGG, KOBAS, Circos, GeneWise, HTSeq and so on need citations.

In my understanding, insecticides are metabolized mainly in midgut and fat body. RNA-seq data of midgut in B. mandarina seems available in the SilkBase. Checking the P450 genes expression in the midgut should give an important information to this paper (lines 312-).
Validity of the findings: The numbers of 68 P450 genes in B. mandarina is critical, but I am afraid that there is a possibility of missing some P450 genes, because the authors used the fragmental assembly of B. mandarina genome, few RNA-seq data, and B. mori genome as the reference. The authors should describe the manuscript with considering the possibilities of missing P450 genes. In conclusion at line 353, “B. mandarina may have lost many cytochrome P450 genes” sounds overstatement.

The authors should focus on the difference of P450 genes between B. mori and B. mandarina. P450 genes only found in B. mori are listed in Table 1 (CYP365A1, CYP6AB8, 2 CYP6AE5, CYP6AW1, CYP340A1, CYP340A5P, CYP340A6, CYP340E1, CYP341A6, CYP367A1, CYP4AX1, CYP4AX2, CYP4S6, CYP4G23, CYP4M9, CYP3un1, and CYP49A2). CYP6AE7 and CYP6AE3P are duplicated (?) in B. mandarina. However, not all of them are well described. The authors should discuss the possible function of the species-specific P450 genes. Which genes are possible “certain key genes” that are critical for insecticide resistance in B. mandarina (lines 24-25 and 247-250)?

My understanding is that molting and juvenile hormones are synthesized in prothoracic gland or corpus allatum. P450s produced in the silk gland do affect the growth and differentiation of the silk glands (lines 319-347)? CYP306A1 is Phantom, which is an important gene involved in insect hormone biosynthesis as shown in Fig. 3. Does CYP306A1 have some function in the silk gland? Can CYP306A detoxify Phoxim (at lines 340-347)? If so, it is very interesting.
Additional comments: Fig. S1 looks important. I think that this figure can be shown in the text, instead of Fig. 4. When summed up, there seem to be 85 B. mori genes in the figure. Is “KWMTBOMO11023-11024” is in Mito. Clan? or CYP3 Clan?

Figure 4 is the expression analysis of “different tissues in the silk glands”, but it is difficult to understand and not so meaningful. I recommend to improve the figure or I think the figure can be supplemental.

In Table 1, “ ‘*’ and ‘$’ have two counterparts in B. mandarina ” needs more explanation. Are the genes duplicated in B. mandarina?

In Table S1,
- NCBI RefSeq Accession: GCF_003987935.1 is of B. mandarina, not B. mori.
- http://silkbase.ab.a.u-tokyo.ac.jp/cgi-bin/download.cgi is of B. mori, not B. mandarina.

The title would be “Computational functional analysis of --” in line 291.


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: CYTOCHROME P450 MONOOXYGENASE GENES IN THE WILD SILKWORM, BOMBYX MANDARINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: I appreciate that the authors generally well responded to my and other reviewers’ criticisms and the revised manuscript, table, and figures are considerably improved in various aspects. However, I consider that the following points must be clarified before this manuscript is accepted for publication.

1.	Sentences in the following lines should be refined.
	Line 227
	Line 294
	Line 372-374
2.	Following references should be modified or completed.
	2014. Transdecoder_r20140704
	AKAi	-> Akai
	Harris R. 2007
Experimental design: No comment
Validity of the findings: 1.	I still doubt the authors’ conclusion that B. mandarina has a significantly smaller CYPome than B. mori. Nearly 5% of BUSCO entries are not found on the B. mandarina assembly, indicating that the number of missing genes is not negligible. As previously pointed out by Reviewer 3, Table S2 and Figure 3 indicate that several chromosomes of B. mandarina are significantly smaller than the counterparts of B. mori. In particular, Chromosome 21 encodes a CYP cluster that is missing in the B. mandarina assembly. The size variation represented in logarithmic scale in Table S2 is somewhat misleading; (wild - domestic) / domestic would be a more natural measure of size variation. Anyway, if these size variations are real, they would be visually detected by cytogenetic analyses. The authors should refer to his point.

2.	Table 1 and Figure S5 suggest that XP_028036989.1 (CYP9A20), XP_028036546.1 (CYP367B1), and XP_028040841.1 (CYP4M5) are mis-predicted to generate artificial fusion genes. These mis-predictions should be corrected.
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: CYTOCHROME P450 MONOOXYGENASE GENES IN THE WILD SILKWORM, BOMBYX MANDARINA
Review round: 3
Reviewer: 1

Output:
Basic reporting: Line 343:
AKAi -> Akai
Experimental design: no comment
Validity of the findings: Line 22 and others:
Disjointing three artificially fused genes would yield three more predicted genes. Table 1 suggests that at least two of the three affected genes (XP_028036546.1 and XP_028040841.1) appear to respectively correspond to two CYP genes in B. mori. The authors should reexamine all B. mandarina vs. B. mori syntenic regions where presence/absence of CYP genes is discordant.
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: CYTOCHROME P450 MONOOXYGENASE GENES IN THE WILD SILKWORM, BOMBYX MANDARINA
Review round: 4
Reviewer: 1

Output:
Basic reporting: non
Experimental design: non
Validity of the findings: The criteria for discriminating genuine and pseudo genes are not consistent. For example, XP_028042624.1 and XP_028042717.1 are respectively only 158 and 125 aa long but counted as genuine gene products. Although the lengths of the neglected genes/pseudogenes are not shown, they are likely to be longer than 200aa as judged from Figure S2 of the first submission. The gene/pseudogene discrimination should be carried out on consistent criteria that are explicitly described.
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: CYTOCHROME P450 MONOOXYGENASE GENES IN THE WILD SILKWORM, BOMBYX MANDARINA
Review round: 5
Reviewer: 1

Output:
Basic reporting: non
Experimental design: non
Validity of the findings: non
Additional comments: non


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: A METHOD TO ADJUST A PRIOR DISTRIBUTION IN BAYESIAN SECOND-LEVEL FMRI ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	The paper requires complete restructuring/reorganization. Sentences used are quite long and confusing. For example, in line number 7 to 10, the sentence is vague with sub-strings “In terms of…” used twice in one sentence. Such style makes it hard to follow the paper. There are multiple issues like this.
2.	Starting from line 13 to 15 “Such as the result from relevant previous studies…” seems to be out of context in a sentence.
3.	The paper starts with the keyword fMRI in the title itself and throughout the paper. Please add a full form of it on its first occurrence in the abstract/introduction. I believe this would increase the readability of paper for a general audience. Likewise, there are several other instances where the full form of the acronym is not present.
4.	In the same line’s introduction should start with a paragraph discussing the wider subject area.
5.	In the line 51, the first sentence of the paragraph should be supported with at least one or two citations as it claims that Bayesian analysis is implemented in a wide range of tools.
6.	In the line number 251, the last sentence at page number 7 can mislead. “Figure 3 (Left)” can be interpreted as something which is on the left side.
7.	Figure 4 covers a major part of the performance evaluation study done by the author. Results also show improvement in terms of iterate and false positive. However, there is no in detail explanation provided or all eight sub-figures (part of figure 4). This way it is all left to the reader to interpret. I strongly advise explaining quantitative and qualitative trend to show in at least two to three paragraphs.
8.	Along the same lines, explanations are needed for figure 5 and figure 6. It is even more important when these figures are referred.
9.	Section 4 (discussion section) starts with the sentence “In the present paper…”. That sentence can be framed in a better way.
10.	In the line number 410 citation is incorrectly presented.
11.	There are multiple instances of grammatical errors. For instance, Line number 456: “It may suggest that…” should be changed to “It is suggested that…”.
Experimental design: The paper proposes a method based on Cauchy prior distribution to analyse Bayesian second level fMRI images. The research area has the potential to directly impact society and therefore relevant. This is an incremental work` and performance results are promising. It would be even better if more arguments are presented to support the result obtained.
Validity of the findings: The obtained results are validated and conclusion is well stated.
Additional comments: Please make corrections as suggested.


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: A METHOD TO ADJUST A PRIOR DISTRIBUTION IN BAYESIAN SECOND-LEVEL FMRI ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Figures 5-6: The colors (red, blue, sky blue) did not show up correctly from the reviewer's side. I can see yellow and white as well as tiny dots in black or dark blue. Please make sure of this issues addressed in the revision.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The present work extends previous developed Bayes Factor-applied second-level fMRI analysis by adjusting the Cauchy prior distribution based on a priori information derived from relevant previous studies. The authors reported the improvement of the performance of proposed Bayesian second-level fMRI analysis. This is an interesting direction of increasing the validity of fMRI-based approaches. While all the tests in the present work focus on group-level characteristics, such an improvement could also be effective on individual differences. Recently, task-based fMRI has been argued with limited test-retest reliability of measurements on the inter-individual differences (PMID: 32489141). A demonstration of the improvements on the task-based fMRI reliability using this method would be highly recommended. More details of the reliability crisis in neuroscience can be found in a recent comment (PMID: 31253883).


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: A METHOD TO ADJUST A PRIOR DISTRIBUTION IN BAYESIAN SECOND-LEVEL FMRI ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author has incorporated all the suggestions in the revised paper.
Experimental design: Now improved the presentation. All suggestions have been incorporated in the revised manuscript.
Validity of the findings: Good. Revised version looks fine to me.
Additional comments: All suggestions have been incorporated in the revised manuscript.
A good work.


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: A METHOD TO ADJUST A PRIOR DISTRIBUTION IN BAYESIAN SECOND-LEVEL FMRI ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The revision has been quite addressing the issues raised.