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: CHANGES IN SPRINT PERFORMANCE AND SAGITTAL PLANE KINEMATICS AFTER HEAVY RESISTED SPRINT TRAINING IN PROFESSIONAL SOCCER PLAYERS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The writing and basic reporting is clear and unambiguous, with appropriate references and sufficient background and context provided. Overall the updated version of this manuscript reads very smoothly. The authors have made the edits that I suggested as it relates to the writing/text in the manuscript.
Experimental design: The research question is well defined, and quite important from a practical standpoint in the fields of applied biomechanics and sports performance. The manuscript clearly defines how this research fills a gap in the current literature. Although challenges exist in conducting training/intervention studies with professional sports teams, the authors have identified these limitations, and from my perspective these limitations do not outweigh the contributions of this study or detract from the impact of the findings.
Validity of the findings: In the revised version of the manuscript, the authors have revisited the statistical approach based on comments of the other reviewers. From my perspective, the current statistical analysis and reporting is robust and allows for straightforward understanding of the results. The conclusions presented in the Discussion nicely follow the results, with an appropriate amount of interpretation and speculation.
Additional comments: In this updated version of the manuscript, the authors have made the necessary modifications to my comments and suggested revisions. Overall, the revised manuscript is stronger than the originally submitted version, with important practical applications for coaches and athletes.


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: CLIMATIC NICHE COMPARISON BETWEEN CLOSELY RELATED TRANS-PALEARCTIC SPECIES OF THE GENUS ORTHOCEPHALUS (INSECTA: HETEROPTERA: MIRIDAE: ORTHOTYLINAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: I found a number of long, difficult to understand sentences sometimes completely unclear. I think the ms language needs to be improved.

Figures 7-11 is redundant in a main text. I suggest to add them as a supplementary material
Experimental design: Comparing the species distribution is an interesting subject though the research idea have to be properly derived. In the introduction, I miss the general idea. To what bases the eight species out of 23 Orthocephalus have been selected, and then why the distribution of selected species are compared to each other? Based on previous knowledge of climate niches, what was the expectation? Why the niches of transpalearctic species are expected to be more similar? ...... I suggest to rewrite introduction to develop research idea/hypothesis in a better way.

Methods: Rather comparing everything to each other and get mess, I suggest to define specific targets for comparison. For instance, the second question in introduction is relevant in this context however this question is blurred and lost subsequently. I believe a number of such question/hypothesis can be easily formulate considering the species range size and distribution patterns (including widespread vs local, geographic location), species phylogenetic/life history closeness etc
Validity of the findings: Conclusions are difficult to follow because it is not effectively related to the questions/ideas provided in the introduction. After reading the discussion I missed something basic, most important let alone the conclusion where for instance a sentence "...each of those species demonstrate a different climatic niche" is totally priceless. I suggest first to better formulate the research idea and then develop discussion accordingly.
Additional comments: The manuscript "Climatic niche comparison between closely related trans-Palearctic species from the genus Orthocephalus (Insecta: Heteroptera: Miridae: Orthotylinae)" reports a results of interesting study based on distribution modelling of members of widespread insect genus. However there are a number of shortfalls need to be addressed. I made a comments, suggestions and questions on the ms text directly in pdf form which I believe is rather easy to solve in the revised version.


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

Input:
Title: CLIMATIC NICHE COMPARISON BETWEEN CLOSELY RELATED TRANS-PALEARCTIC SPECIES OF THE GENUS ORTHOCEPHALUS (INSECTA: HETEROPTERA: MIRIDAE: ORTHOTYLINAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, the author provides the background information necessary to know that very few studies have explored climatic niches of species with trans-Palearctic distributions (especially insects) and why starting to fill this knowledge gap would be greatly beneficial for understanding the similarities/differences of the species’ distributions and the differences in climatic factors contributing to the climatic niche models. However, the introduction could use additional information about the general biology of these insects, such as similarities or differences in morphology, physiology, and/or food sources (if known) that could affect niche preferences.

The English is difficult to comprehend at times with confusing run-on sentences (e.g., lines 71-74, 76-78 202-204, etc.) along with distracting and unnecessary commas (e.g., lines 28-30, 36-39, 68-70, 103-105, etc.). This should be improved upon to ensure that readers can understand the text. I have highlighted many of these areas in the annotated pdf for clarification.

Table 1 – this table is not very intuitive. I would recommend synthesizing the material into a more readable table, potentially with one column per species (e.g., the CF model uses all variables so that column is not necessary if you instead denote PC and PI for each model with symbols and separate total areas with a comma). You could also add a description of what each bioclimatic variable is (e.g., in column 1: Bio1 – Annual Mean Temp).

Table 2 is also not intuitive. I would recommend including an additional explanation in the table description about how to interpret what the numbers mean (i.e., how to interpret significance for identity and background tests from these numbers alone). From my experience, I have usually seen niche identity and background test results depicted as graphs (e.g., Figs 1D and 2D in Warren et al. 2010), which seem much easier for readers to understand than a table. If feasible, it could be helpful to include a graph for each test comparison in the Supplemental material.

Overall, the figures are really nice (i.e., easily distinguishable colors, perfect size). However, I recommend putting either country boundaries or lat-long ranges on maps to make it easier to follow when you describe the distributions in Results. As someone who is not very familiar with that geographic area, it was a little difficult to follow at first pass. Also, I would recommend adding a scale for the suitability scores on Figs 3-6 to make it clear what colors correspond to highly suitable versus not suitable.

The Results section Comparison of the variables for the species with similar environmental niches (or at least some elements of it) seems like it should be in the Discussion section.

Other very minor points:
Line 86: change has to have

Lines 259, 286, 330, 356, 381, 401, 534, 537: you reference the wrong figures – Figure 5 references should be Figure 4 and vice versa (also highlighted in the annotated pdf).

Line 340: change to driest

Line 422 and 424: bio1 and bio7 were both labeled annual temperature range

Line 492: change to widespread
Experimental design: The author provides necessary background information for their research question and clearly defines the aims of this study. Additionally, the Materials and Methods section provides a great amount of detail for performing environmental niche modeling and niche overlap analyses. Pointing out the potential pitfalls and addressing them by comparing different models significantly strengthens the results. A researcher interested in environmental niche modeling for their study system could greatly benefit from this. Well done.

I’m still a little confused about why many records from European countries were excluded – could you expand upon why you chose to do this (was it just to decrease the likelihood of records with wrong species identifications?) and how this sampling bias could potentially affect construction of the climatic niches?

Why did you choose 5 arc-minute resolution for the bioclimatic variables (e.g., was there a trade-off between high resolution across a large geographic space and computational efficiency)?

What was the cutoff value for significantly correlated bioclimatic variables? And why/how did you choose this? For example, Jeskova et al. 2011 (http://doi.wiley.com/10.1111/j.1365-2486.2011.02508.x) considered high correlation between variables when the correlation coefficient was ≥ 0.9.

Line 206: The description for the niche identity test is not intuitive (i.e., it’s a run-on sentence and difficult to understand). I would recommend breaking this sentence up into a few, more detailed sentences to highlight the details for this test. Also, why was the identity test only run with the CF model?
Validity of the findings: As pointed out earlier, listing the potential pitfalls of environmental niche modeling and addressing them by comparing different models significantly strengthens the results. Additionally, you have developed a robust methodological framework for others to test this type of hypothesis for other taxa.

You covered background comparisons resulting in niche conservatism for both widespread and limited distributions in the discussion; however, I did not see any reference to the O. funestus vs O. proserpinae background test comparison resulting in niche divergence. I think it would be useful to devote at least a sentence or two to discuss this result and maybe include a potential hypothesis explaining this.
Additional comments: General recommendation – make sure that when you mention information relevant to a figure or table you refer to that specific figure or table. For example, in one paragraph (lines 264-272) there were several mentions of the contributions made by the bioclimatic variables for each model, yet there was no reference to Table 1 for any of these (e.g., could add (see Table 1 for summary) somewhere at the beginning to clarify where this information is coming from).


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: REGISTERED REPORT: INVESTIGATING A PREFERENCE FOR CERTAINTY IN CONVERSATION AMONG AUTISTIC ADULTS COMPARED TO DYSLEXIC ADULTS AND THE GENERAL POPULATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is very well written and easy to follow. Appropriate literature is cited. Hypotheses are clearly stated and follow logically from the introduction. Link to OSF given. My only major suggestion is to share the full set of items so that it is easier to understand what is being tested. It might also help to expand on what is proposed to be involved in processing an inference/ implicature by giving some theoretical background. Reference to relevant theoretical frameworks would be helpful as there is some debate about when inferences are and are not necessary and what they involve in different cases (e.g., Kintsch, 1998, Comprehension). Lack of a theoretical statement on this and lack of access to materials made me wonder what was in fact being tested.

Other notes:
If a value-neutral term is intended would 'preference for certainty' be better or is 'intolerance of uncertainty' preferred as a conventional expression?

The section in the intro on the inclusion of a dyslexic group - and the selection of this group rather than others - was a little vague at first but became clearer in the method around line 172. Perhaps this justification could be given earlier.
Experimental design: The proposed research is original primary research within the aims and scope of the journal. With the caveat above, the research question is well defined, the means of testing it are justified and the results are likely to advance knowledge. Methodological and analytic standards are high. Detail is sufficient to replicate with the exception of provision of key inference test materials. Unless there is a good reason not too, these materials should presumably be shared and this would be my only major request for revision. This is all the more important given how difficult it is to define inference, to come up with good tests of it and to be clear why they are a test of inference (perhaps even this is a question of individual differences to some extent, with some arriving at a given 'inference' more through spreading activation and others by making a more proactive effort after meaning). Of course this is work in progress and some of this has to be left underspecified for now. The purpose of sharing materials would not be to scrutinise every item before the test is run, but to help everyone to make sense of what is being tested and what is found.

Having said this, I had specific notes about some test items. For example, in the video about free seats, there are free seats available in the background of the picture so the answer is also available visually.

I also wondered whether there were specific reasons why people were likely to struggle with different items - for example, reasons relating to real world knowledge and ability to generate world models that would make the speech observed plausible. It appears this could relate to uncertainty in several ways. For example, someone could be uncertain because they struggled to generate plausible real world contexts that would justify the answer or because they could generate several scenarios and weren't sure which was more likely to hold  (e.g., 'I heard the police say there were a lot of trains' or 'there were so many trains, I couldn't hear what the police said').

Other notes:
Missing word on line 179   > the online platform

Perhaps clarify that for the literal items, the speaker intends to convey uncertainty. For the implicature items, the uncertainty is in the mind of the listener.
Validity of the findings: N/A
Additional comments: I look forward to hearing about the results.


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

Input:
Title: TRENDS IN SUMMER PRESENCE OF FIN WHALES IN THE WESTERN MEDITERRANEAN SEA REGION: NEW INSIGHTS FROM A LONG-TERM MONITORING PROGRAM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors present an extensive dataset on fin whales occurrence in the Western Mediterranean Sea collected from from opportunistic platforms (ferries) between 2008 and 2018. Overall, this is clearly an important effort and that there are gaps in our knowledge of how fin whales are distributed there. My feeling is that, although this is an interesting study before to be published in a peer-review journal I would suggest to correct some important issues (see below).

A short temporal variability (data collected during summer months) is a limitation for this study and more in several regions characterized by an important environmental seasonal changes. Therefore, fin whales will be present in these areas during different periods of the year, when they undertake seasonal feeding migrations into the area. It is for this reason, that authors should include environmental data in the models (SST, Chla, depth, slope, etc.). For example, information on the levels of chlorophyll-a at the date of observations and in previous dates (15 days before, one month before...). This information could help to explain the observed fine-scale differences in whales habitat use.
Experimental design: The statistical analysis, as described, is not adequate. The way the analysis is done here, the authors created one GAM in which they only included "year" as covariate, does not explain the spatio-temporal distribution of the species. Authors should include more variables within the GAMs, describe data exploration protocols to identify outliers, data variability, and study the relationships between covariates and response variable. For example, effort, zone, type of ferry, wind speed (and associated sea state) is largely related to sampling visibility and this variability could affect the observed differences between species. Why authors did not include environmental variables that could influence the presence of whales and the capacity to observe the cetaceans? Why authors did not include latitude and longitude, depth, sea state, etc as potential predictors of cetacean presence? I do not understand why authors create GAMs with only one predictor.

Another red flag of the manuscript is the the choice of statistical tests. In line 215 authors explain the use of Pearson's correlations but they did not carry out normality tests. Moreover, authors considered as correlated when Pearson's r value was > 0.5 without carrying out any kind of statistical test indicating a p value.
Validity of the findings: Authors need to further acknowledge and discuss the limitations of distance sampling techniques to estimate density (which are only mentioned in passing) and that, at times, their data and results are oversold.

The methods will need to be re-evaluated.  As it is, I am not comfortable providing additional comments regarding results and discussion as these could be biased by the non-adequate analysis.
Additional comments: Suggested references to facilitate the changes suggested in the ms:

Zuur AF, Ieno EN, Elphick CS (2010) A protocol for data exploration to avoid common statistical problems. Methods Ecol Evol 1:3–14

Hastie TJ, Tibshirani RJ (1990) Generalized additive models. Chapman and Hall, London

Díaz López, B., Methion, S. (2019). Habitat drivers of endangered rorqual whales in a highly impacted upwelling region. Ecological Indicators, 103: 610 – 616.

Virgili, A., Racine, M., Authier, M., Monestiez, P., Ridoux, V., 2017. Comparison of habitat models for scarcely detected species. Ecol. Model. 346, 88–98.


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: TRENDS IN SUMMER PRESENCE OF FIN WHALES IN THE WESTERN MEDITERRANEAN SEA REGION: NEW INSIGHTS FROM A LONG-TERM MONITORING PROGRAM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have undertaken some good work to summarise a long-term data set collected along ferry routes. Such long-term datasets are often lacking regionally and the use of ferries does facilitate collection of these data in a cost-effective way. It’s an approach that has gained considerable momentum over the last decade and it’s very positive to see this paper reporting on the valid use of these data. So I can congratulate the authors for working with these data and presenting some useful results.

The structure of the paper is generally fine although I would reorder slightly to make very clear the spatial scale of the analysis. And I suggest the authors reconsider the title of the article and some headers to remove reference to abundance – this was not calculated; it is simply density.  The background information appears complete and appropriately referenced. The figures are well presented although some suggestions in the “general comments” below to help clarify the spatial units on maps and also Table 1. The analyses and results do address the research questions set out in the introduction.

The “raw data” is shared but the files appear to be incomplete. As they currently stand, these data could not be used to reproduce the analysis. For example, in the sightings file the perpendicular distance has not been included. In the effort data, there are no covariates; those used in the analysis, such as sea state should be available. A metadata file or “READ ME” tab in the datasheets would be useful to describe each field and its units. The field “site ID” (sightings) and “group” (effort) need explaining and it is not clear how one could assign sightings to the transects.

The context of the paper is for assessment and reporting under MSFD on Good Environmental Status. However, the authors need to carefully review the wording related to MSFD in the manuscript as it has been misinterpreted and inaccurate in many places.

The English throughout needs to be reviewed; I appreciate the challenges of writing a scientific paper when English is not your first language. I have tried to make some suggestions in the commented pdf to assist with that review.
Experimental design: The authors have undertaken some good work to summarise a long-term data set collected along ferry routes  Utilising such platforms is a cost-effective means of surveying and this paper demonstrates the value in the data collected in this way. It also highlights the importance of this ferry network in the absence of designed regular surveys to monitor cetacean populations. However, the language in the paper sometimes suggests competition between platform of opportunity and dedicated surveys (e.g. aerial line transects) but instead the strengths (and weaknesses) of the different approaches should be acknowledged. The results from these different approaches can compliment each other.

A distance sampling data collection protocol has been followed. However, some concerns are raised (see general comments) with regards to the scanning area and measurement of distance and angles. The methods also needs to mention the assumptions underpinning a distance sampling analysis and whether they believe their protocol and dataset upholds them.

The research questions are clear and the approaches taken appropriate. The description of the methods used for data analysis would benefit from some further clarification. In particular, the treatment of the data needs to be more clearly written, especially with regards to the spatial stratification of the dataset (i.e. transects into transect groups and areas). Perhaps the section on geographic scale could come earlier on in the methods section. Also needs to be consistent use of area codes (e.g. PS v PEL for Pelagos Sanctuary) throughout text and figures.
Validity of the findings: The sightings data raise some concern about how they have been collected and consequently how they have been handled for fitting detection functions (see “General Comments”). The analytical approach is appropriate, although some comments are made around the choice of method; so, some additional information to justify this would be helpful and make it clearer for the reader.

The discussion and conclusions around the key questions are generally well formulated. However,  the authors need to be more precautionary when interpretating results at sub-area/basin scale when the data comes from few ferry routes (in some subareas in particular) surveyed repeatedly. Some of the shortcomings of these types of data need to be acknowledged and inference from the results not stretched. The strengths of these types of survey are in the temporal resolution and when coupled with good ferry route coverage (multiple routes spread throughout areas) can be particularly effective.  In the datasets presented here, those in the Pelagos Sanctuary, best fit this description with what appears to be reasonable spatial coverage and long-term year-round data  - this represents a good example of a cost-effective monitoring approach. Discussion on this could be enhanced. See general comments for how these data might be further utilised.
Additional comments: Smaller comments/edits are highlighted and commented in the uploaded pdf - this likely has to be viewed in Adobe Acrobat in order for those comments to be visible.

109-114   The wording of these sentences is not quite right and could be misleading. The Commission Decision 2017 (https://eur-lex.europa.eu/legal-content/EN/TXT/PDF/?uri=CELEX:32017D0848&from=EN) dictates that abundance of species and their distribution (including cetaceans) are criteria to be assessed as part of Descriptor 1 Biodiversity set out in MSFD. So "trends in species abundance" is not required by MSFD, although many Member States may choose to use as part of their national indicators with which Descriptor 1 is assessed. The evaluation of trend in abundance as an indicator would not necessarily lead to a threshold setting – arguably you would not need a threshold for this approach. However, if thresholds have not been established, trends can be used in assessments of GES; there are an allowable approach rather than one that is asked for in the legislation.

151 – 152  One of the advantages of surveying from ferries is that they offer good temporal resolution because they often travel year-round. I wonder why the authors decided not to use data outside the summer months – the “influence of seasonal variability” can be dealt with in the analysis, without excluding those data. Perhaps there were too few surveys outside summer months?

157  The Figure 1 could colour code the western Mediterranean basin area and the “ADRION” region.

160  Can more detail be given about the scan area. 130o either side is mentioned but is this from the bow (transect line) abeam? Is there cross over of search area from observers on the port/starboard across the bow? Scanning area should ensure the transect line is given more search time but careful not just to scan directly ahead. Also line 175 says that the zero of the protractor was pointing to the stern of the vessel – I assume this is meant to be the bow (front) of the vessel? If observers are facing backwards then this will violate distance sampling assumptions and bring into question the validity of the analysis and results

184 The assignment of transects routes to subareas is not at all clear. The text suggest there are 2 separate transect groups (I think is a mistake in the test), yet Table  1 lists unique transect groups for each route. Figure 2 gives the impression that there are 4 subareas. The relevant table, figure and text all need revising to make it clear how the data were stratified spatially.

185 – 186 You would aim to have as much of the transect surveyed as possible, and so you have discarded those transects where surveying was carried out on less then 30% of its length. However, this does not ensure “representative’ coverage because the 30% coverage may all occur at one end. Representative coverage would be one that had some survey effort on all parts of the transect or if the study is interested in habitat associations, would have some (representative) sampling of all the different habitats along the route.

189 The analysis described is a standard line transect distance sampling analysis and not a strip transect? For strip transect, ones surveys a predetermined “strip” (e.g. 500m wide) and the assumption is that all animals in that strip are counted. So density is very easily count/area of the strip. The authors are fitting a detection function to distance sampling to account for imperfect detection of animals off the transect line – this gives an estimate of the ESW which can then be used to estimate density. Was there any truncation of the data? The assumption with this method however is that all animals on the transect line are detected with certainty. This section needs review so there is not confusion of the reader with regards the approach taken,

200 The raw sightings data raise some concerns about the degree of rounding, when radial distances and angles have been recorded (the majority of values end in “0”). The fitted perpendicular distance histograms should be examined and shown per transect group to demonstrate this is not a problem or if it is, how this has been dealt with when fitting detection functions.

207 To estimate density along a transect, were the data pooled over months and years? So data from one route were pooled, correlated transects removed, and detection functions fitted on the remainder of the transect data to derive density on each transect? A mean density was derived for transect group?

211  in the equation, rather “number of individuals sighted along the transect line” shouldn’t it be the number of sightings x mean group size? There is variation in group size as described later in the manuscript.

215 What are the variables being tested in the Pearson’s correlation coefficient test? Assume you are testing for spatial autocorrelation between density of fin whales on the repeated transects? Perhaps you could have generated a variogram?

239 Would it have been possible to include “group size” in a multi-covariate detection function? Might have been important for ESW and perhaps some subarea differences that could have been captured?

245 this section is entitled “abundance”…But abundance has not been estimated. Abundance along the ferry route could be calculated but you would need to consider how useful that it is given the limited spatial coverage of a broader basin. Arguably, in the Pelagos Sanctuary it appears that there are multiple ferry routes through the area with reasonable spatial coverage. One might consider using ferry data for that area in a spatial model to predict abundance.

256 You have estimated density per transect and a mean density per transect group. Why was a GAM not fitted using density (or N abundance along the route – estimated using an effective search area & probability of detection)? ESW could have been used as an offset. Needs further justification for the approach taken.

319 The header refers to “abundance” but this has not been estimated

322 Perhaps easier to have table of  these density results, that would include ESW too. But Figure 4 is very clearly presented.

346 – 348 Again, perhaps a table of the GAM model details would be better than text description of the number of knots etc. Summary table of the GAMs and outputs

367 Is it possible that fin whales are present but just not near enough to the ferry route? Are there data from autumn/winter/spring that have been looked at to verify the conclusion that they are “absent” . The last sentence of this paragraph provides reference to some sightings in the Adriatic so perhaps occasional or rare, rather than absent, better describes their occurrence in the Adriatic

387 The statement that interannual variability in the Western Pelagos is due to the influx of NENA fin whales is very definite but the previous line suggests they do not move further east than the Balearics. There is limited transect effort at the Balearics. The statement needs to be adjusted to reflect that it is possible that NENA fin whales are in the WP or further references given to support the statement.

401 Whilst repeated surveys along ferry routes can give an idea of distribution through time, their ability to provide robust information on distribution in space can be limited and should be interpreted with care

421 This is a very important point and the authors have here acknowledged the limitations in their analysis and the discussion/conclusions should keep this in mind.

414 Figure 2 in Morgado et al (2017) shows that 2013 was the second highest yearly mean encounter rate and so this is not different from the authors results. In fact, the GAM for PS suggest increasing density until 2012, then a slight dip to 2013 before increasing again  - the pattern up to 2013 is the same in Morgado, atleast for encounter rate. The Whale Occurrence Index gives a slightly different picture but interpretation needs to take into account how representative of the PS area the fixed route surveys are in both studies

433 -434   Care when referring to aims of the MSFD – the main aim is not to “assess trends in
population abundance” The aim is “The Marine Strategy Framework Directive aims to achieve Good Environmental Status (GES) of the EU's marine waters by 2020 and to protect the resource base upon which marine-related economic and social activities depend.” The abundance of fin whales, and trends in abundance, could be useful as indicators for assessing the biodiversity descriptor D1 – and there is a criterion for abundance. Perhaps the authors could report whether the Mediterranean countries that border the area of their research, have a “fin whale or baleen whale abundance” indicator – this would add weight to the need for these studies. Or perhaps the Pelagos Sanctuary has conservation objectives that require monitoring of fin whale abundance?

438 The authors report density, over time, along transect routes. Interpretation of these results at the wider scale (e.g. basin) need to be caveated because in the western basin in particular, there is very limited spatial coverage throughout. So a lower density on the ferry route may simply represent a redistribution of animals rather than real change in wider density / abundance.

445 With my previous point in mind, I would use the wider scale aerial surveys (e.g. Panigada et al.)  that have designed survey transects, as evidence to support your findings rather than the authors trying to explain Panigada’s findings.

469 Another MSFD point, please check and accurately state what the MSFD requirements are. Abundance of species is a criterion for descriptor 1 (see the 2017 commission decision) and so should be used in assessments of GES but "fin whale abundance" is not specified. Be careful to make a clear distinction between what MSFD says and perhaps what countries have established as indicaitors.

489  Properly designed large scale surveys provide a robust approach for estimating abundance. However, they tend to be done in a limited time window. Ferry surveys can not “correct” these surveys but they do add additional data on distribution around the surveyed routes and patterns over the entire year which are often not available from designed large scale surveys.

Table 2 Just include results for routes that were tested (leave out the empty rows and explain in text)


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: TRENDS IN SUMMER PRESENCE OF FIN WHALES IN THE WESTERN MEDITERRANEAN SEA REGION: NEW INSIGHTS FROM A LONG-TERM MONITORING PROGRAM
Review round: 2
Reviewer: 1

Output:
Basic reporting: In my previous examination of the manuscript, I suggested that major revisions and a positive re-review are required before this paper is sufficient for publication in a peer reviewed journal and join the scholarly literature. After having reviewed the manuscript and not observed any changes in certain important points I still consider that the work is not of sufficient quality to be published.

There are a number of considerations that led me to this decision. The manuscript is missing a number of relevant methodological details which would be needed to thoroughly understand and replicate this study. The authors should be aware that the manuscript should be contingent on demonstrating that their analytical approach is robust.

All the suggestions given in my previous review were made to improve the content of the manuscript and not to modify the aim of the study. The authors should consider that in order to describe a temporal trend in the presence of a given species, the effects derived from sampling variability should be ruled out.

Specifically, the manuscript lays out a description of a trend in presence of whales but then relies on many assumptions (some unrelated to the analysis). The manuscript cannot conclusively prove the existence of a trend in presence of whales, because authors did not include in their analysis the potential influence of other explanatory factors (i.e. changes in effort, sea state conditions, type of vessels used, speed of vessels, etc.) largely related to sampling visibility and this variability could affect the observed differences between years.

Without that, I do not think that the manuscript warrants publication.
Experimental design: The manuscript is missing a number of relevant methodological details which would be needed to thoroughly understand and replicate this study. The authors should be aware that the manuscript should be contingent on demonstrating that their analytical approach is robust.
Validity of the findings: The manuscript lays out a description of a trend in presence of whales but then relies on many assumptions (some unrelated to the analysis). The manuscript cannot conclusively prove the existence of a trend in presence of whales, because authors did not include in their analysis the potential influence of other explanatory factors (i.e. changes in effort, sea state conditions, type of vessels used, speed of vessels, etc.) largely related to sampling visibility and this variability could affect the observed differences between years.
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: PORTANINI (INSECTA: HEMIPTERA: CICADELLIDAE) FROM PERU: CHECKLIST WITH NEW RECORDS AND DESCRIPTIONS OF TWO NEW SPECIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Excellent.
Experimental design: Very good.
Validity of the findings: Excellent.
Additional comments: This contribution provides descriptions of two new species, new records, and illustrations of all species of Portanini known from Peru.  This will be a very useful reference for future work on the group.  The species descriptions and illustrations are excellent.  The material examined section is detailed and the appropriate data is reported.  Please see notes on the attached .pdf with suggestions for changes and some minor points to address.


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

Input:
Title: PORTANINI (INSECTA: HEMIPTERA: CICADELLIDAE) FROM PERU: CHECKLIST WITH NEW RECORDS AND DESCRIPTIONS OF TWO NEW SPECIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: It is a very valuable contribution to the knowledge of the leafhoppers from Peru. This contribution implies that another researchers can include more new taxa based in the information provides in this manuscript.
Additional comments: Undoubtedly a great contribution to the knowledge of the leafhoppers of Peru. The manuscript so designed allowes to the youngest to enter to the exciting world of taxonomy, particularly of the family Cicadellidae of the Neotropics, an underexplored region for insects, specially in the megadiverse Peru!


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: PORTANINI (INSECTA: HEMIPTERA: CICADELLIDAE) FROM PERU: CHECKLIST WITH NEW RECORDS AND DESCRIPTIONS OF TWO NEW SPECIES
Review round: 1
Reviewer: 3

Output:
Basic reporting: Some corrections in the text are necessary, which are marked up in the sent file.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The manuscript is a good contribution to the knowledge of Portanini. Descriptions are precise and illustrations have good quality. However, it is necessary a new attentive reading to correct some minor errors in the text.


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: PORTANINI (INSECTA: HEMIPTERA: CICADELLIDAE) FROM PERU: CHECKLIST WITH NEW RECORDS AND DESCRIPTIONS OF TWO NEW SPECIES
Review round: 1
Reviewer: 4

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: The ms is excellent and suitable for publication with a few minor changes as indicated in the attached revised file.


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: DRIVER VERSUS NAVIGATOR CAUSATION IN BIOLOGY: THE CASE OF INSULIN AND FASTING GLUCOSE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study by Joshi and Watve  highlights the possible misinterpretations of experimental data in biomedicine due to lack of the understanding of driver versus navigator causation.  As a case study, they analyzed the glucose-insulin relationship to provide a potential proof of concept.
Authors have systematically analyzed the published data/literature and performed the relevant experiments to revisit the glucose-insulin relationship and highlighted the previously misinterpreted and exaggerated roles of insulin in regulating blood glucose levels in humans.
Experimental design: The study is novel, rigorously performed and systematically presented. The methodology and search criteria used are relevant and the limitations are also clearly mentioned which makes the study more reliable. Sufficient evidences from the literature and the experimental data supports the claim of the study. The manuscript is written in a  lucid and comprehensive way.
Validity of the findings: However, some minor concerns must be addressed before publication.
1. References are missing at some places throughout the manuscript (for example in paragraph 246- 255, lines 471 and 473)
2. Figure No 8 and 9 are not sufficiently described and labeled.  The figure legend should be written more comprehensively. It is difficult to understand what is shown in figure from the legend. More detail should be added in figure legends for figure no. 3-7.
3. Authors claim that fasting glucose in FIRKO knockouts remain unchanged, however some studies does not support this observation. Authors should carefully review these studies in detail to find the possible reason of inconsistency towards the conclusion of their original result.
4. To generalize the concept of driver and navigator causation in biology and/or in a broader prospective, some more cases with similar observation from the literature should be added (with references) in the discussion.,
5. Authors cite one hypothetical case of body temperature in the conclusion section, but this not supported relevant references.
6. Figure is not cited in result 2.5 (line no. 576)
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: DRIVER VERSUS NAVIGATOR CAUSATION IN BIOLOGY: THE CASE OF INSULIN AND FASTING GLUCOSE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The author is trying to say there are logical traps in interventional inferences because steady state and perturbed state are different. They concluded that it is necessary to differentiate between types of causalities. To demonstrates this, they used the insulin and glucose as an example and reached the conclusion that researchers may have to carefully re-examine causal inferences from perturbation experiments and set up revised norms for experimental design for causal inference. The paper is well written and reads well, the background information is adequate. The result is clear and informative.
The figures are clear, and the subtitles are detailed. The reasonings in the paper are also clear.
However, there are some minor parts that needs to be improved.
1.	Figure 2 is a great analogy, the author explained the analogy between 2A and insulin sensitivity, it would be great if they also explain the analogy between 2B and the glucose homeostasis model
Experimental design: The experiment design is good. The question is well defined and then the author used 5 different approaches to prove the concepts.
Validity of the findings: The conclusion are well-stated. The reasoning is also reasonable and clear.
Additional comments: No additional comments


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

Input:
Title: EXOGENOUS MELATONIN IMPROVES SALT STRESS ADAPTATION OF COTTON SEEDLINGS BY REGULATING ACTIVE OXYGEN METABOLISM
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript entitled “Exogenous melatonin improves salt stress adaptation of cotton seedlings by regulating active oxygen metabolism” has been submitted to Peer J. The study has been conducted well but some concerns make me hesitant. There are some points that I think might be helpful.
The novelty and hypothesis of the study have not been defined. There are some experiments that showed the effects of melatonin as a ROS scavenger, so, please mention what can distinguish your work.
The introduction should be re-written because it emphasizes the effects of salinity and antioxidant enzyme activities which is completely clear for scientists. The most important part of your work is the application of melatonin, not salinity. What is the melatonin, mechanism of action, biosynthesis pathway and …
Why did you select 150 mM?
I think you should have had control+ 50, 100, 200 and 500 melatonin as treatments, which could have shown the effects of melatonin under normal conditions. Why did you delete these treatments?
Line 132-133 “When the cotton seedlings reached the three-true-leaf stage, the following treatments were imposed” how many days after transplanting?
The statistical design should be clarified. One-way ANOVA is not correct. Salinity and melatonin are two factors.
How did you compare means? LSD, Tukey?
Use one decimal for percentage. 37.2% instead of 37.24%
How many times did you spray MT?
The quality of figures is low, please replace them with high-quality versions.
Your work is a physiological study, so, the discussion should be explained the pathways and mechanisms of actions, therefore, please improve this part.
Line 391: “This study showed that …” please revise the sentence.
Line 419-421: “was oxidized to oxidized ascorbic acid (DHA)…” should be revised.
Line 461: “In conclusion” should be removed.
The conclusion should be re-written. No recommendation and suggestion. Please don’t repeat your results.


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

Input:
Title: EXOGENOUS MELATONIN IMPROVES SALT STRESS ADAPTATION OF COTTON SEEDLINGS BY REGULATING ACTIVE OXYGEN METABOLISM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The present manuscript explains the effect of exogenous melatonin in cotton under salt stress by measuring different parameters. The study is well-structured but some changes are needed.

First, the English language should be improved to ensure that an international audience can clearly understand your text.
Experimental design: The experimental design is correct.

Line 130-131: Use micromolar as concentration unit in micronutrients.
Line 160-164: Follow the same style indicating the assay kit reference as for soluble sugar and soluble proteins.
Line 153, 161, 167, 169: change to "by using ...".
Validity of the findings: The results part could be improved on the result presentation as there are many data (so many percentages, which can be confused). A possibility is to add a PCA analysis to show how diferent parameters are affected by melatonin addition as general vision of melatonin addition under salt stress.

Discussion part need to be re-structure as the authors presented results as in the Result part and then, they explained effects of melatonin or salt stress in other plants. It could be better if they explain both together. Justification of results need to be improved.
Also, some sentences need a reference (ex. line 441).

Line 177-178: This text has no sense. Re-write.
Line 197-199: Add reference.
Line 201: Use past simple.
Line 240-242: Add reference.
Line 316-318: Add reference.
Additional comments: The article need to change some aspects before acceptacion.


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: EXOGENOUS MELATONIN IMPROVES SALT STRESS ADAPTATION OF COTTON SEEDLINGS BY REGULATING ACTIVE OXYGEN METABOLISM
Review round: 1
Reviewer: 3

Output:
Basic reporting: The role of secondary metabolites are well known in improving plant resistance to abiotic stresses. The functional role of melatonin in stress regulation is less known and seldom studied. In this perspective, the present study is important. The contents of the paper are quite well structured and nicely presented. Results are no doubt important to understand the stress responses and to evaluate the role of melatonin in stress regulation. However, the conclusion is drawn on the basis of basic experimental findings and such approach have been reported in plants under stress. The work is nice, but lacks novelty and individuality.
Experimental design: We designed but lacks novel experimental approach.
Validity of the findings: The biochemical datasets depicts the role of melatonin in controlling salinity stress in cotton. However, only biochemical datasets cannot be decisive in concluding that melatonic controls the redox regulation. Other more precise approaches could have been adopted to come up with a concrete conclusion.
Additional comments: 1. The paper lack novelty from experimental approach point of view.
2. The authors may use other approaches such as antioxidant gene expression profiles, redox proteomics and metabolomics approach supported by biochemical analysis.


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

Input:
Title: EXOGENOUS MELATONIN IMPROVES SALT STRESS ADAPTATION OF COTTON SEEDLINGS BY REGULATING ACTIVE OXYGEN METABOLISM
Review round: 2
Reviewer: 1

Output:
Basic reporting: The study conducted well, and the manuscript has been written in a good shape, especially after revision. English is at a standard level for publication.
Experimental design: Materials and methods have been significantly improved.
Validity of the findings: My biggest concern about this study is the novelty; there are several papers that evaluated the effects of melatonin as a salt alleviator.

The conclusion needs more improvements. You should present suggestions and recommendations to researchers or drow a clear picture of future studies.
Additional comments: After revision, the manuscript has been improved significantly. The goals and hypotheses have been mentioned clearly. All comments have been addressed completely.


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: DETECTION AND ESTIMATING THE BLOOD ACCUMULATION VOLUME OF BRAIN HEMORRHAGE IN A HUMAN ANATOMICAL SKULL USING A RF SINGLE COIL
Review round: 1
Reviewer: 1

Output:
Basic reporting: This research investigates the use of an RF coil to measure changes in the tissue/fluid volume ratio in a head phantom, simulating an intracranial hemorrhage.

The paper is well written and presents an interesting method for detection of intracranial hemorrhage.  The literature review is lacking a few key studies, but is sufficient.

The article is well structured with appropriate figures and tables.
Experimental design: The research experimental design is well structured with useful and supporting methods to investigate the hypothesis.   Overall the research is well designed.

Minor concerns:
An actual image of the sensing inductive coil is missing.
What is the permittivity of the phantom skull and how is it different to an actual bone?
The model does not take into account the properties of actual skull bone and skin layers.
The model does not take into account other biofluids which may change the effective permittivity such as cerebral spinal fluid shifts.

How do the investigators ensure that the changes in signal reading were not due to changes in the relative placement of the faraday cage.

The single coil will be sensitive to motion artifacts as well if the spatial symmetry surrounding the head is not maintained.

Line 246: Change "let define" to "let us define"

It would be helpful to present an S11 graph frequency sweep of the entire frequency range so that the resonant frequency response and peaks can be seen.
Validity of the findings: Volume is not being estimated, instead, the authors are only measuring change in volume.  As such, the title of the paper should be reconsidered to not include volume estimation.  The authors incorrectly assume the initial blood volume of the head is zero.  While this may be correct in their phantom, the tissue/fluid ratio is not.  Figure 3, Figure 5, Figure 7, and Figure 8 should all be revised to indicate that it is a change in blood volume and not an absolute volumetric measurement or estimation.
Additional comments: A vector network analyzer is expensive as well.  It is not clear how this technology meets the primary rationale for this work to develop a low cost simple to use diagnostic tool.

Line 61: Please revise comment that the head is a closed "box" to something more anatomically correct.


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: DETECTION AND ESTIMATING THE BLOOD ACCUMULATION VOLUME OF BRAIN HEMORRHAGE IN A HUMAN ANATOMICAL SKULL USING A RF SINGLE COIL
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an interesting study. In the study, you tried to prove the efficacy of your designed measurement system in detecting intracranial hemorrhage in a simulating model. The English of the manuscript is easy to understand. The citations of literature are proper. Photos of the experimental setup and brain model provided serve as intuitive visual evidence for readers to understand the study method.

In the conclusion, line 523, I suggest rephrasing “which may reduce the deterioration” to “which may help physicians initiate early intervention to prevent further deterioration” to make sense.
Experimental design: The use of a simple in vitro brain model with calf brain tissue, chicken blood, and anatomical skull simulating human intracranial hemorrhage is quite unique. However, in the discussion section, you need to justify the efficacy of using such an in vitro model. How much does it differ from real live brain tissue in vivo? As live brain activities generate electrical signals, this auto-generated electroencephalography interference will most likely compromise the proposed detection method.
Validity of the findings: The data and algorithm provided are robust in terms of the accuracy of such a model to detect bleeding. The goal of building such an inexpensive and safe device that can detect early stroke is of significant clinical importance.
Additional comments: I commend the authors for their unique experimental design.
If the author can justify their use of an in vitro calf brain that is devoid of electrical activities in the discussion section, the rationale of the experiment design could be further 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: DETECTION AND ESTIMATING THE BLOOD ACCUMULATION VOLUME OF BRAIN HEMORRHAGE IN A HUMAN ANATOMICAL SKULL USING A RF SINGLE COIL
Review round: 2
Reviewer: 1

Output:
Basic reporting: Changes were made based on the previous comments. It looks better now.
Experimental design: The chapter of 'The Phantom as a Human Head Model' attempted to justify the use of the phantom. I see it was moved to the Discussion section which makes sense now.

The added paragraph explaining the difference in the frequency ranges between the electrical activity in the brain and that of the operating system does sound logical.
Validity of the findings: Data and algorithm provided are robust.
Additional comments: The manuscript is improved. Good.


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: MULTI-YEAR PAIR-BONDING IN MURRAY COD (MACCULLOCHELLA PEELII)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study did not clearly specify hypotheses, presumably because it was more of an exploratory study on mating systems in this species. However, given the range of genetic and other variables measured in the stufy in their estimation of mating systems, a set of clearly defined predictions somewhere at the end of the Intro regarding what would be expected under different types of potential mating systems (e.g. monogamy vs polygamy) would have been helpful to process the results that were actually obtained.

I also felt that the Introduction focused too heavily on the biases in literature/studies conducted on freshwater versus marine fishes in terms of mating systems. This study doesn't compare the two. Instead, more effort should be put into describing what IS currently known about the mating systems of freshwater fishes, and then discussing how we can use genetic techniques to indirectly infer mating systems (in addition to directly inferring based on parentage or observations). Currently the Intro lacking in information on genetic techniques employed in the study, and their relative effectiveness.

I also suggest cutting paragraphs on parental care (starting lines 54 and 60), because while technically correct, they are not relevant to the topic of the current study.

Line 67: Neolamprologus pulcher has been shown to be monogamous as well as polygamous, and this has been reported in the literature (Desjardins et al 2006 and Wong et al 2008)
Experimental design: No comment
Validity of the findings: Impact and novelty well discussed especially in light of management of freshwater fish. Data seems robust and well-analysed.
Conclusions regarding type of mating system not overstated and need for further verification is highlighted.
Additional comments: Thank you for your attempt to elucidate a tricky aspect of their reproductive behaviour.


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: MULTI-YEAR PAIR-BONDING IN MURRAY COD (MACCULLOCHELLA PEELII)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Although this paper is basically well writen, there are many serious flaws in the figure legends, and in many cases it is insufficient to explain.
Fig. 2: It is unknown what each numerical value indicates and what "normal" means.
Fig. 3: It does not exaplain what the difference in color of the point is indicating (I think that it is the year of sampling...).
Fig.6: There is no explanation about the color and numerical value of each plot. I can not find a reson why you made a decision to attach numbers and mather's names only to some plots. How is the explanation of the results of lines 257-259 in the maintext shown in this figure?
Experimental design: I think that you should explain in more detail in the introduction section about the SNPs, and the application of it to parentage analyses.
Validity of the findings: no comment
Additional comments: I listed specific comments below.
1) L30: What does "good" mating strategy mean?
2) L32: Kvarnemo et al (2000) reported monogamy in H. subelongathus, not H. whitei.
3) L39-46 & L54-66: I do not think the information in these paragraphs are necessary for your study.
4) L29 & L72: under-represent or underrepresent
5) L79-82: References are required.
6) L95 All organisms live in competitive environment.
7) L97: Refereces are required.
8) L100 & 107: SNPs?
9) L135-145:More detailed explanation of reproductive biology of this fish is required. Is this fish not only to care eggs but also larvae?
10) L148: Abbreviation "DoY" is not defined before.
11) L188: "15" and "13" should be superscript.
12) L199: DArTseqs?
13) L202 & Fig. 5-7: I cannot find a positve reason for giving a unique name to fish. Something like #1, 2, 3 is enough.
14) L234: Incomplete sentence.
15) L298-299: Incomplete sentence.
16) L314-319: unnecessary discussion, remove.
17) L329-338: uncecessary discusiion, remove or shorten.


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: MULTI-YEAR PAIR-BONDING IN MURRAY COD (MACCULLOCHELLA PEELII)
Review round: 1
Reviewer: 3

Output:
Basic reporting: Clear, unambiguous, professional English language used throughout:

Although the manuscript is generally well-written, I was missing explanations of abbreviations several times (or they came too late; e.g. lines 100, 148, 162). In a few cases, sentences were very hard to follow, as they were too long and convoluted (e.g. lines 102-104, and 321-323). I also think there is room for more explanations, like “In order to achive this, we did that”.

Intro & background to show context:

It is clear you lack some background knowledge on what is know about mating patterns in freshwater fishes. To improve your introduction, and also to nuance your conclusions, I suggest you read these the publications (and references therein):

Barlow, G. W. (1984). Patterns of monogamy among teleost fishes. Archiv für FischWissenschaft, 35, 75-123.
Barlow, G. W. (1986). A comparison of monogamy among freshwater and coral-reef fishes. In Indo-Pacific Fish Biology (Uyeno, T., Arai, R., Taniuchi, T. & Matsuura, K., eds.). Tokyo: The Ichthyological Society of Japan.
Kvarnemo, C. (2018). Why do some animals mate with one partner rather than many? A review of causes and consequences of monogamy. Biological Reviews. doi: 10.1111/brv.12421

Literature well referenced & relevant: Otherwise, yes!

Structure conforms to PeerJ standards, discipline norm, or improved for clarity: As far as I can judge, yes.

Figures are relevant, high quality, well labelled & described:

Seven figures is a lot. Most figures were informative, but the one I would delete first is Figure 3, as I didn’t see its full value. I read the MS printed in black-and-white. This exposed the fact that almost all figures were impossible to understand, without later checking the colour version on my computer. But even with colour, there is more work to do. Please use bold and plain text for inbred and outbred in figure 2, much thicker lines, with different patterns (dashes, dots, etc) in figure 4. In figure 3 and 5, I don’t think colour is needed (or unclear why it would be). For clarity, in figure 3 and 6, please use kilometers (km) as unit, instead of meters combined with K. Also please explain why the dots line up like they do. Is it an artifact of some sort or a true effect of asynchronous hatching?

Raw data supplied (PeerJ policy): I was unable to access the files. The "figshare" site did not work properly.
Experimental design: Original primary research within Scope of the journal: Yes.

Research question well defined, relevant & meaningful.

Actually, based on what it says in the discussion, the original research question was another, and the authors just stumbled on this one. But I’m fine with that. It’s honest; better than pretending they were looking for this result all along.

It is stated how the research fills an identified knowledge gap.

Yes, to some extent, but I think there are more gaps to be filled by this data set (e.g. see my comment on the introduction & background above). In addition, the authors have chosen to limit their scope to full sibs, filtering out all halfsibs. I think that’s a huge mistake. The study and the paper would be so much stronger if they also looked for halfsibs. If it feels overwhelming, maybe they could limit their search to the individuals they know have bred monogamously for 1, 2 or 3 years, to see if they practice polygyny/polyandry at the same time and/or sequentially.

Rigorous investigation performed to a high technical & ethical standard:

I admit that I’m more at ease with microsatellite data than SNPs, and that the R scripts mentioned are unfamiliar to me. But, as far as I can judge, yes.

Methods described with sufficient detail & information to replicate:

I am missing one important piece of information: How and why were the authors able to identify the maternal genotype, but not the paternal? (And why the funky names?) Have the authors taken tissue samples from females but not males, to match the offspring to, or how does this work? Needs clarification.
Validity of the findings: Impact and novelty not assessed.

The authors do try to sell their results as being the first time monogamy is found in a freshwater species of fish. Since it is not completely true (see Barlow 1984, 1986; Kvarnemo 2018 for examples), and PeerJ doesn't appreciate that kind of sales pitch, it should be tuned down/removed, and the “single example” (line 68) rephrased.

Nevertheless, Barlow’s reviews were published before easy genotyping became available, and too few genetic studies have been done since, so there is a knowledgegap to fill, especially for freshwater species (but marine species as well). Yet, largemouth bass (DeWoody et al. 2000: Proc R Soc B, 267, 2431-2437. DOI 10.1098/rspb.2000.1302), and a number of freshwater cichlids have been studied using genetic markers, but mainly for single breeding events. So, as far as I know, these genetically documented freshwater fish pairbonds lasting three years is likely to be a real novelty.

Negative/inconclusive results accepted: N/A

Meaningful replication encouraged where rationale & benefit to literature is clearly stated: N/A

Data is robust, statistically sound, & controlled: Yes.

Speculation is welcome, but should be identified as such: Some speculations in discussion, but all OK.

Conclusions are well stated, linked to original research question & limited to supporting results: See above. Should be rephrased a little.
Additional comments: Detailed comments:

Abstract:  Please mention the fact that Murray cod has paternal care in the abstract, as this is likely to be of interest to future readers of yours, especially in relation to the pattern identified by Barlow between monogamy and parental care in freshwater fishes. I therefore urge you to give more information on what is known about parental care in Murray cod in the main text (line 94).

Abstract (lines 12-15) and in methods (lines 108): Unclear why didn’t you trust your genotypic evidence of monogamy, but used isotopes as well. Please justify/motivate.

Line 21: I suggest you rephrase “particularly if improved methods for analysing SNP data for identification of siblings in the absence of parental genotypes become available.” (replace “if” with “as” or “when”, if more appropriate).

Introduction: I suggest you avoid using capitals for species names, unless its named after a person or geographial place.

Lines 24-25: Feel free to add some invertebrate groups into the animal kingdom as well.

Line 33: Kvarnemo et al. 2000 studied Hippocampus subelongatus, not whitei.

Line 61: “in various species males provide parental care”. In fact, in fish taxa that show care at all, male care is most common – more common than female care or biparental care (Gross & Sargent 1985; or Reynolds et al. 2002):

Gross, M. R. & Sargent, R. C. (1985). The evolution of male and female parental care in fishes. Am. Zool., 25, 807-822.
Reynolds, J. D., Goodwin, N. B. & Freckleton, R. P. (2002). Evolutionary transitions in parental care and live bearing in vertebrates. Phil. Trans. R. Soc. B 357, 269-281.

Lines 62-65: Hard to follow. Probably needs more detail.
Line 81: What do you mean by “meata-data”? Try to be more specific.
Line 95: What do you mean by “evolved in a competitive environment”? As opposed to what?
Line 98: Repeated matings: In what sense? Please be more specific.
Lines 102-104: Eh?
Line 156: 700 m per day: is it really that constant? Must depend on rainfall, right?
Line 178: genlight object =?
Line 197: Pew not in reference list.
Line 202: “putative mother” – or father? How would you know?
Line 220-225: I had no idea r = coefficient of relatedness can have negative values. Is that really correct?. And what is a coefficent of inbreeding?
Line 241: see previous comment on filtering out halfsibs.
Line 272: “size based” is not tested here. Please delete.
Lines 277-280: yes, but better to make one good paper than two half hearted ones.
Line 294: which risk? (pls, try to be more specific)
Line 308-313: Right. Any monogamous pair-bonding will reduce the number of available mates for unmated individuals. Then, of course, assortative mate preferences (size, condition, age, whatever) will add other restrictions on suitable mates. I think it’s likely to find mutual mate choice in long-term monogamous animals, if their fitness depends on some traits of their partner (and compensation by mating with multiple partners isn’t an option). So, some assortative mating is likely, but sure, it doesn’t need to result in very strong assortative mating (for example, see section III-6 in Kvarnemo 2018 for more on this topic).
Line 327: Please rephrase to: “dispersal, which still is an”.
Line 335: Please add “also” after “occur”.


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: DETERMINANTS OF BEHAVIOURAL AND BIOLOGICAL RISK FACTORS FOR CARDIOVASCULAR DISEASES FROM STATE LEVEL STEPS SURVEY (2017–19) IN MADHYA PRADESH
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. This is a generally well-written manuscript on an important public health issue of the current world including the Indian population.

2. The literature review and context provided are adequate

3. Data presented in a clear manner but facts need to be corrected 9see comments for Results section).
Experimental design: The methods described are inadequate. The following points need to be addressed:

1. Although the sampling procedure to recruit subjects has been cited (reference 5), there is nothing in the Methods section of this manuscript. It would be good to provide a brief description to make this article independent. Readers will be able to understand the procedure without reading the reference article;

2. the definition of diabetes in their original descriptive article (reference number 5) and the current one is different in respect to the cut-off point of blood glucose (126 or 200 mg); The two manuscripts provide two different measurement approaches, fasting and random. This will have a big implication on the results of this paper.

3. Table 2 defines hypertension as SBP>140 or DBP>140, which should be DBP>90.
Validity of the findings: The results are presented clearly. However, there are points of concern:

1. The characteristics of the study participants have been rightly given at the beginning of this section. However, the results are erroneous. All the numbers given here for age, education, and tribes are for the females given reference number 5. These should have been for both sexes. Summary information for marital status and employment could be given as has been given for age and education.

2. Subsequent description of findings is in fact directly reproduced from Table 4 of reference number 5. Hardly there is any description of risk factors presented on the concerned table here (Table 1). Please see the lines 86 to 93.

3. Table 3 is redundant of Figures 1 and 2. Table 3 could be easily avoided.
Additional comments: Considering the journal's readership and similarity of population characteristics, it would be good to have a discussion of similar articles from neighboring countries, Bangladesh, Nepal, Myanmar, Sri Lanka, and the Maldives.


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: DETERMINANTS OF BEHAVIOURAL AND BIOLOGICAL RISK FACTORS FOR CARDIOVASCULAR DISEASES FROM STATE LEVEL STEPS SURVEY (2017–19) IN MADHYA PRADESH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The STEPS survey is designed for NCD surveillance for comparison globally and within the country. This study used data from STEP wise approach survey conducted. It is suggested to change the title as “Determinants of behavioural and biological risk factors for cardiovascular diseases in Madhya Pradesh, India. A WHO STEP wise approach”.

Line 20:  termed as high epidemiological transition states (ETLs)- This should be Epidemiological Transition Level states
“Line 42 We conducted this study to understand socio-demographic determinants of CVD risk.” The objective of STEPS may be to identify the risk factors on NCD and not to understand the determinants however, this scientific paper aimed to analyse the determinants.  Therefore, need to rewrite the sentence.
It is suggested to use smokeless tobacco in place of oral tobacco users as this will confuse the readers. Similarly, change DRANK ALCHOL to excessive use of alcohol or alcohol use whichever is appropriate.
Language editing is critical in accepting the paper.
Experimental design: It is appropriate to include the detailed methodology such as sampling design, selection of the respondents etc to make it reader friendly. It is also suggested to provide operational definition of all terms used in this paper.
“Line 58: individuals (STEP-2); and laboratory testing for blood glucose and cholesterol were done in 4698”. Globally, STEPS following point of care instruments for all biometrics however, in your study it was mentioned that laboratory testing.  This needs to be explained, that includes collection, storage and transportation of blood samples etc.. In addition, what are the methods used for measuring both blood glucose and lipid profile.  Also suggested to include rationale for choosing this method. It is also suggested to include the rational for choosing this method for biometric in the methodology session.
Validity of the findings: “Line 167 Current study provides a unique opportunity to ascertain if risk factors in scheduled tribes of
Line “168 Madhya Pradesh are different as compared to other tribal groups in the country.”

The above statement by the author needs to be re-written as this is not an unique opportunity to ascertain the risk factors in scheduled tribes.  This is applicable in all population.

Age classification needs to be revised to make it a standard by making same intervals and inclusive.

Suggested to use WHO nomenclature for risk factors as the study followed WHO STEPS protocol.

Under the education category one of the categories “not formally educated” this needs to be clarified.  Are they literate or illiterate?  A state like MP which is low in education indicators there needs to be a category named illiterate.

All tables should be incorporated with sample size (n).

When we consider the biological risk factors only age and gender are major determinants.  Other social factors are less likely to influence the biological risk factors.  The author needs to re-consider the analysis.

It is suggested use similar terms- like biological risk factors and behavioural risk factors across the paper. Some places it was mentioned that clinical risk factors.

The author tried to capture the determinants of risk factors for CVD however, for the programmatic/policy point of view there needs to be clearly indicating the need for improvement in certain factors.  Therefore, it is suggested to segregate the analysis by modifiable and non-modifiable risk factors that will provide proper guidance to policy makers. To be more precise, if the paper focused more on modifiable risk factors that would through light in providing appropriate health promotion interventions in the state to improve the health of the people.
Conclusions and recommendations should be based on the findings and provide appropriate suggestions to policy improvements.  It is proposed to review the current government interventions towards NCDs in the country, especially in MP.  The government initiative focused on NCDs namely “Health and Wellness Centres” providing multiple services to address the modifiable risk factors.  The author needs to review this and provide suggestion to improve the activities of centres.
Additional comments: A good attempt in finding out the factors associated with NCD risk factors among tribes in India, a has relevance in the present context.  Appreciate the authors in selecting the policy relevance topic for the research.


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: DETERMINANTS OF BEHAVIOURAL AND BIOLOGICAL RISK FACTORS FOR CARDIOVASCULAR DISEASES FROM STATE LEVEL STEPS SURVEY (2017–19) IN MADHYA PRADESH
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overall it is an interesting dataset and analysis. Write up is clear but descriptive. Perhaps authors could use multivariate analyses to combine domains to show which are more prominent factors in the study population.
Experimental design: Overall experimental design is good but Hypotheses could be written more clearly so that readers are able to see what is being tested.
Validity of the findings: Generally good details of the analyses carried out and results are presented in figures and table. Authors should make clear in their write up which categories are reference categories for odds  ratios.
Additional comments: Overall a good write up, please make hypotheses more explicit and discussion should more focused to the hypotheses.


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: IDENTIFICATION OF BIOMARKERS ASSOCIATED WITH CLINICAL SEVERITY OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The present work is to the greatest extant comprehensible written and well structured.

The literature, especially in the discusion part should be extended:
In the discussion the findings should be set in relationship to other studies investigating biomarkers for COPD severity and exacerbation. For example:
a.	Work of Singh et al. Source Paper – Plos ONE 2014
b.	Rogers, 2019, PlosONE
c.	Ect.

The article is well structured, however there are some missing parts:
Gene clustering analysis (Figure 1): Cluster 7-10 are missing in the figure.

Dataset of the GEO Omnibus: please add link in method section.

Please find further details in general comments.
Experimental design: The methodical setup to analyze the data sets sounds solid. However, a graphical analysis pipeline should be added to improve the clarity of work flow.

Precise description of patient cohorts are missing (the own and GEO database)

A link to the GEO Databaseset should be added

Please find further details in general comments.
Validity of the findings: Conclusion should be edited: tha analysis demonstrate markers for clinical severity of COPD but not exacerbation.

The discussion part should contain the discussion with other works analyzing biomarkers for COPD.

The final analysis of TLR2 expression in own clinical samples is not completely meet the demands that TLR2 is a marker for GOLD III/IV, since no differences to healthy smokers are observeable.

Please find further details in general comments.
Additional comments: Data analyzed in the present work based on a microarray data set (GSE54837) published by Singh et al. 2014 (PLOS ONE). In this work Singh et. al analyzed genes associated with COPD exacerbation in 138 sputum and blood samples.
In the present study Zhang et. al. used the microarray data set (received from the GEO database) to analyzes differential regulated genes in blood samples of 226 patients which were staged based on their lung function parameters to GOLD I (n=90), II (n=58), III (n=55) and IV (n=13). Using data preprocessing and cluster analyses they identified different set of clusters up or down regulated from GOLD I to GOLD IV. Using functional enrichment analyses they could demonstrate, that up-regulated genes were associated with defense, inflammation or immune responses, whereas down-regulated genes were associated with cell activation. Further network analyses based on data received from protein-protein interaction analyses and miRNA-target gene regulatory relation analysis revealed five nodes associated with upregulated genes (TLR2, IL-10, MMP9, HMOX1 and CCR1) and two nodes associated with down-regulated genes  (CD79A and PLCG1). Analyzing blood samples from an own clinical cohort the group demonstrated that TLR-2 mRNA expression levels are increased on PBMC of GOLD III/IV COPD patients in comparison to GOLD I/II patients and that TLR-2 expression correlated with serum levels of inflammatory mediators (IL-6, IL-8, TNF-a and IFNy).

The present work is to the greatest extent comprehensible written and well structured.

There are several points which should be clarified before considering the manuscript for publication:

1.	The work want to identify biomarkers associated with COPD exacerbation, an objective also the publication which was source of the data set was aiming for.
However, different from the original article the present manuscript did not differentiate patients based on exacerbations per year but on degree of disease severity derived from the lung function parameter FEV1 and staged the patient from GOLD I to GOLD IV.
So that the present markers are associated with the severity of the disease (clinical grade) but not with the susceptibility to develop exacerbations.

2.	Beside the description of the own patient cohort also the cohort of the original study should be described and at least classification of patients in subgroups should be explained.

3.	A detailed information on the own patient cohort is missing. Information like number of subjects, disease state, age, sex ect. should be added.

4.	TLR-2 was chosen to demonstrate the clinical importance as a possible biomarker in an own clinical cohort. Unfortunately, there seem to be no differences in the expression between GOLD IV patients and healthy smokers.
    a.	 Give the other top up- or down regulated marker better results?
    b.	How were the correlations of TLR-2 to the inflammatory cytokines performed? Were all samples taken or just within the subgroups.

5.	How is the sensitivity and specificity of the identified marker?

6.	Can you confirm the results with other free data sets?
  a.	Especially the subject number in the GOLD IV group is quite low and should be increased.

7.	In the discussion the findings should be set in relationship to other studies investigating
biomarkers for COPD severity and exacerbation. For example:
 a.	Work of Singh et al. Source Paper – Plos ONE 2014
 b.	Rogers, 2019, PlosONE
 c.	Ect.

8.	Discussion:
 a.	Please edit Line 271-282, this part is quite confusing because lower expression in COPD of TLR2 and IL-10 in other works are described, you demonstrate higher levels but do not discuss the differences.
 b.	283-294: You describe that lymphocytes like CD8 and B cells are increased in COPD and that the number of lymphocytes are associated with COPD, however, CD79A was downregulated. Please discuss this observation.

9.	Gene clustering analysis (Figure 1): Cluster 7-10 are missing in the figure.

10.	The methodical setup to analyze the data sets sounds solid. However, a graphical analysis pipeline should be added to improve the clarity of work flow.

11.	Dataset of the GEO Omnibus: please add link in method section.

12.	Advantages and disadvantages of the present study should be described. Please explain the advantage of the biomarkers to identify the clinical phenotype in comparison to the standard method, the assessment of lung function and number of exacerbations.

13.	There are some minor typos which should be corrected. For example: line 114 molecular functions (MF), and pathways..


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: IDENTIFICATION OF BIOMARKERS ASSOCIATED WITH CLINICAL SEVERITY OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript entitled “Identification of biomarkers associated with chronic obstructive pulmonary disease exacerbation from mild to severe” by Zhang et al. studies gene expression profiles in blood samples from COPD patients in order to identify biomarkers associated with COPD. The authors used Gene Expression Omnibus Database to obtain gene expression profiles of 226 blood samples. Thereafter, they performed gene clustering analysis followed by pathway enrichment analysis. Based on the obtained results, the miRNA of genes with PPI relations were predicted. The identified biomarkers were TLR2 and CD79A where the relationship between TLR2 and the inflammatory markers from the clinical samples of COPD patients was verified.

1. The manuscript is well written. The analyses are appropriate and statistics are well used.
2. The abstract has to be rewritten according to the flow of the manuscript (line 30, 'finally....' should be at the end of the abstract).
3. Experimental design is optimal. Nevertheless, in the description for Fig 1 (line 177-178 and 180), authors mention 10 clusters that were chosen for further analysis. However, there are only 6 clusters in the figure; clusters 7, 8, 9 and 10 are missing.
4. Please provide the sequence of the primer used.
5. The authors suggest that TLR2 and CD79A can be used as independent biomarkers for clinical COPD classification, therefore, it would be interesting to see the relationship between CD79A and inflammatory factors as well (the authors have only provided the PCR and ELISA results for TLR2).
6. Including more speculations about significance of the findings in the discussion section will add more value to the text.


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: IDENTIFICATION OF BIOMARKERS ASSOCIATED WITH CLINICAL SEVERITY OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Pleas find specific information in General Comments

Please check orthography, and typos, there are still sentences and sections which are hard to understand.

Figure legends should be extendend.

Some methodical descriptions should be extended.

Results have to be added to improve the confirmation of the hypothesis.
Experimental design: Some methodical descriptions should be extended.
Validity of the findings: I have still the feeling that the discussion part is incomplete. Here own results should be set in relationship with findings of others.

What is already known about biomarkers of COPD severity and exacerbation, how fit the new detected biomarkers in the present picture. Where are similarities and differences.

Still a critical dispute with the own work are missing. What are downsides and benefits of analyzing potential biomarkers via micro assay data of blood.

Please state helpfulness of biomarkers analysis beside classical classification of the disease state.
Additional comments: In the present work a data set generated by Singh et al. 2014 (Plos One) was used to identify biomarkers associated with the severity of COPD.
Here, TLR-2, IL-10 and CD79A were highlighted as potential serum biomarkers for COPD severity.
The group tried to confirm differentiated expression of TLR-2 in sera of patients and healthy volunteers of an own COPD cohort.
Here they demonstrate that TLR-2 expression is increased in GOLD III-IV COPD patients. And that TLR-2 expression is positive correlated with inflammation markers like IL-6, IL-8, TNFa and IFNy.
Unfortunately, several improvement suggestions of the reviewers in the first phase of the process were not or incompletely answered.
Here, important information is still missing:

1.	Reviewer 1: Comment 4:

TLR-2 was chosen to demonstrate the clinical importance as a possible biomarker in an own clinical cohort. Unfortunately, there seem to be no differences in the expression between GOLD IV patients and healthy smokers.
a.	Give the other top up- or down regulated marker better results?
b.	How were the correlations of TLR-2 to the inflammatory cytokines performed? Were all samples taken or just within the subgroups.
Response: Thank you for your constructive comments. We have added some disscussions about the results. And the pearson correlation analysis was used to investigate the correlations of TLR-2 to the inflammatory cytokines. We have added it in the methods part.

Reviewer Response:
There are still no information given if the TLR2 expression is significantly different between GOLDIII/VI and healthy smokers. There is also no statistically comparison of the other inflammatory marker between the both groups.
The group did not answer the question if correlations were performed with all samples of all patients and healthy volunteers or within each subgroup (healthy, healthy smoker, COPD I/II, COPD III/IV).

2.	Reviewer 2: Comment 5.
The authors suggest that TLR2 and CD79A can be used as independent biomarkers for clinical COPD classification, therefore, it would be interesting to see the relationship between CD79A and inflammatory factors as well (the authors have only provided the PCR and ELISA results for TLR2).
Response: Thank you very much for your comments. The hub protein CD79A was enriched in the function of lymphocyte activation. CD79A has been demonstrated to play diverse roles in the development and function of B lymphocytes. The relationship between CA79A and COPD is not well understood until now. Importantly, our results showed that CD79A was negatively correlated with the clinical classification of COPD. However, the relationship between immunity and inflammation is complex. In the whole immune system, CD79A is not a key marker at the core position, and the simple expression level of CD79A is hard to explain anything. Based on this, we did not study the expression relationship between CD79A and inflammatory factors furtherly.

Reviewer Response:
The authors answer that it is not meaning full to relate CD79A expression to inflammatory markers.
Since CD79A is one of their top Biomarkers I would recommend that comparable to TLR-2 the negative association of this marker and also IL-10 should be demonstrated in their cohort. These results will strengthen the importance of their observations.

3.	Reviewer 1: Comment 5.
The methodical setup to analyze the data sets sounds solid. However, a graphical analysis pipeline should be added to improve the clarity of work flow.
Response: Thank you very much for your comments. We have added some contents in figure 3. but due to the different trends and directions of this study, it is difficult for us to change the table into an appropriate picture for display in the results of bioinformatics analysis.

Reviewer Response:
I do not understand why the author is not able to add a graphical work flow how the micro-array data sets were analyzed. These work flow are common in studies re-analyzing micro array data and should be demonstrated to estimate quality of the analyses.
I can´t detect anything in figure 3 which is associated with such anwork flow overview.

4.	Reviewer 1: Comment 8.

a.	Please edit Line 271-282, this part is quite confusing because lower expression in COPD of TLR2 and IL-10 in other works are described, you demonstrate higher levels but do not discuss the differences.
Response: Thank you for your valuable comments. We have discussed the difference which was highlighted in red in the discussion part.
Line 316-321 (track changed manuscript):
Most of studies showed that the decreased IL-10 level in airways is related to the pathogenesis of chronic airway inflammation in COPD (Takanashi et al. 1999). Lower IL-10 level was reported to be associated with a higher frequency and severity of COPD(Sun et al. 2013b). The present study about IL-10 in COPD was different. We are confusing that the results showed the IL-10 expression level a rising trends from stage I to IV.

Reviewer Response:
Here the improvements of the authors are quite sparse, do you have any speculations why IL-10 is downregulated? For example, what are differences in the methodical setup between the works?

Minor:
1.	Please explain how the TLR2 Kit works.
a.	How do you detect TLR2 on the surface of monocytes using a realtime PCR (Line 183)
b.	Please describe precisely how the differences in expression levels were detected.
2.	Information given in the figure legends are sparse and should be extended.
3.	Please check orthography, there are still sentences and sections which are hard to understand.


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: IDENTIFICATION OF BIOMARKERS ASSOCIATED WITH CLINICAL SEVERITY OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors addressed all concerns raised by the reviewers and the manuscript has been significantly improved. It is suitable for publication in PeerJ.
Experimental design: NA
Validity of the findings: NA
Additional comments: NA