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: NO ISLAND-EFFECT ON GLUCOCORTICOID LEVELS FOR A RODENT FROM A NEAR-SHORE ARCHIPELAGO
Review round: 2
Reviewer: 2

Output:
Basic reporting: In general, basic reporting is done to a high standard although I have some smaller points that I address in specific comments to the authors below.  Revisions have addressed reviewers’ requests for additional background information in specific areas to aid in understanding the context of the study and interpretation of the results. Figures are clear (except see questions about figure 2) and raw data is shared.
Experimental design: Revisions have been made that address concerns raised by original reviewers about experimental design and methodology. These changes explain why methodological choices were made based on precedent in the literature and logistical constraint (e.g. why these islands were chosen for the study when findings reveal they don’t appear to exhibit island syndrome) and provide more detail about how certain procedures were done (e.g. assay methodology, statistical analyses). While I still find some parts of the reports on statistical methods to be difficult to follow at times, I find this section improved over the previous draft and have provided some additional suggestions on wording that may clarify lingering questions
Validity of the findings: Revisions have made interpretation of findings more clear. I still have one comment on statements comparing changes in abundance over time between mainland and island sites which I highlight below.
Additional comments: Line 64: I find the term matrices surprising in this context.  Perhaps just “materials.”

Line 136: I am assuming that females can rear multiple litters over the course of the summer?  Specifying this may aid in interpretation of female GC levels.

Line 148: Consistency in what?

Lines 232- 260.  I appreciate the revisions that you have done to clarify your models- this section is easier to follow.  However, I still get lost in some of the details and can’t keep track of what terms go in what model easily. I think it would be much easier if for each of the 3 general model types you identify (line 235) you just spell out exactly what terms were used in the full model. I imagine this looking something like “We tested our outcomes of CPUE, GCs … in three different model types: A,B, and C.  For analyses testing differences between mainland/ island sites, full models included random effect A and fixed effects for X, Y,Z and Y *X.”  It might take a little more space, but I think it will help your readers understand exactly what is happening. Then you can just report in your results section “in our final reduced model X significantly predicted abundance (describe direction here). Y, Z, and their interaction were not significant in the initial full models and were excluded from the final reduced model.” This way you’re spared reporting what got dropped from what subset of models in your methods section, which I think can get confusing.  You seem to have done this in some sections of the results.

Section starting at Line 328 and Line 349: While I think it is good to spell out what terms are in and out of your final models, this section gets a little bit confusing because it reports results, but doesn’t spell out for every result whether the p-values come from full or reduced models. This is especially confusing because presumably the p-values for non-significant terms shifted a little every time you did a single deletion of one variable and re-ran the model, so the reader can’t tell whether the p-values you’re reporting for non-significant terms come from a maximal model, or a partially reduced but not final model. To me it makes sense to only report p-values for final reduced models, but to also say that variables x, y, and were non-significant in full models and were deleted from the final reduced model.

Line 373-Line 374:  This figure shows a correlation in trapping of sites between the two years.  It is not clear how this figure shows a decrease in abundance that is greater in island than mainland sites. To do so, we’d need to have a best fit line showing the correlation between island sites and a second line show the correlation in trapping results between mainland sites so that there was some way to see a difference between the two. This could also be enhanced by a caption indicating that results above the 1:1 line show increase in abundance and results below the 1:1 line show a decrease in abundance across time. However, I'm not convinced that this is the best way to show the results--- you could also report in a bar graph. More importantly, in your results for your abundance analysis (Table 1), you do not report a significant interaction between habitat type and year, so I don’t understand how you have the support to make this claim that there is a greater decrease in abundance in one habitat type than the other.

Line 440: So implicit in this is the idea that raccoons are more likely to trip traps on island sites than on mainland sites. Do you know anything about raccoons on the mainland- do think it’s fair to say they may be at lower density than on islands or have different behavioral patterns?

Line 457: Word missing.

Line 470:  Do you know anything about hair turn-over outside of molt?  Is it conceivable that animals shed so much hair between molts that this could be the case?  Part of assessing the likelihood of this may be knowing if animals molt multiple times a year or just one time a year.

Figure 2:  This figure should have an R2 value on it? Also see previous comment on interpretation of this figure in the discussion.


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: FASCIOLA GIGANTICA, F. HEPATICA AND FASCIOLA INTERMEDIATE FORMS: GEOMETRIC MORPHOMETRICS AND AN ARTIFICIAL NEURAL NETWORK TO HELP MORPHOLOGICAL IDENTIFICATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are numerous grammatical errors throughout the text that require thorough revision, preferably by a native English speaker. While these errors do not impede the understanding of the paper’s content, they greatly affect the professional presentation of the study and require further revision.

The introduction provides a well referenced contextualisation of this study, especially from a biological standpoint, yet regarding the field of geometric morphometrics, a number of terminological components should be revised. These include (in no particular order of importance):

Between lines 97 and 103 the authors mention the geometric and mathematical problems presented by the variable size when considering traditional metric approaches in biological studies, yet do not mention the terminological differentiation between methods that exclude size from those that include this variable. I recommended that the authors clarify the difference between shape (which is correctly mentioned) and form (which is not mentioned at any point within the text) to help construct a stronger argument within this paragraph. For this I recommend the authors consult the work of Jungers, Falsetti and Wall (1995) with their paper titled Shape, Relative Size, and Size-Adjustments in Morphometrics in the Yearbook of Physical Anthropology, volume 38, pages 137-161.

A similar terminological issue can be found in line 110, where the authors mention Rohlf and Marcus’s methods for “visually representing shape”. It is important to point out that this technique has a specific name that should be mentioned and was in fact developed prior to Rohlf and Marcus’ work. I recommend that the authors consult the ample bibliography regarding Deformation Grids and Thin Plate Splines while also encouraging the authors to use these terms within their own work.

The authors frequently make reference to “outline-based” approaches. Once again I encourage that the authors use the correct terminology here. Throughout the methods, results and other parts of the text, the authors make reference to the “Outline Data” and “Pseudolandmarks”; the correct term the authors should be using is semilandmarks. For the differentiation between landmark types I recommend the authors consult the works of Dryden and Mardia (1988) in their book titled Statistical Shape Analysis. As for the terminological definition and developed use of semilandmarks the authors are encouraged to consult the work of Dr. Philip Gunz in collaboration with P. Mitteroecker and F.L. Bookstein, especially their 2004 book chapter titled Semilandmarks in Three Dimensions from D.E. Slice’s (Ed.) Modern Morphometrics in Physical Anthropology (pages 73-98). As far as I am aware, Gunz et al.’s book chapter is available online via Research Gate.

On line 257 the authors make reference to: “final outputs were the “weights””. This use of the term “weights” is quite confusing especially when referred to as a product of Neural Networks. Machine and Deep Learning models use weights to obtain the outputs. The whole process of training a model is to find the optimum combination of weights throughout the model that best map out the relationships between inputs x and outputs y (at least in the case of supervised learning). The outputs in themselves are not the weights of the model. The authors are therefore required to clarify what they refer to by the term weights? I suggest the authors either use a different term for the outputs or revise this sentence entirely to clarify what they actually mean. The presentation of this particular statement currently generates quite a lot of confusion.

In line 261 it is not entirely apparent as to what the authors refer to by using the terms “testing” and “training”. Good practice in Machine and Deep Learning require that testing and training sets be separated prior to training. This is performed so as to ensure the model is unbiased when presented with new data, thus providing an efficient means of evaluating model performance. Within this paragraph the authors talk about random subdivisions throughout each iterative process, therefore I think the authors are actually referring to training and validation sets. In different types of cross-validation techniques this is the correct term that should be used. I recommend that the authors revise this statement to ensure they are not confusing the term testing with validation.

While the figures and tables presented are of great value and help contribute towards the detailed description of the results, the authors are encouraged to revise the titles and descriptions provided for each. In table 2 the authors use superscript letters to indicate statistical differences according to p values, however at no point mention what a, b, c or a combination of these letters actually means. Is each letter an indicator of the degree of statistical significance? If so is "a" more significant than "c"? Therefore what does the combination of "a" and "b" mean? In table 3 a slightly better description of these superscript letters is provided, however it is still unclear as to what the authors are referring to. Therefore (1) would it not be better to directly include the p values (highly recommended) and (2) why is this description provided for table 3 and not for table 2? I suggest the authors review each of their table and figure descriptions in detail to improve the presentation of their work.

On a positive note, I think the supplemental materials and raw data supplied are of value to the scientific community and may help authors in the future when performing similar studies.

As far as I can tell, the reference list is well structured, complete and all citations mentioned within the reference list are indeed included within the text.
Experimental design: The use of Artificial Neural Networks within this study requires more details, not only in able to support the validity of results obtained but also to ensure that other authors are able to replicate these results.

The authors mention they used a single hidden layer composed of three neurons after a process of trial-and-error. In order to properly evaluate the performance of artificial networks in the processing of data of this nature much more information is needed regarding the configuration of the model. How was the model trained? Which optimisation formula was used? Were any further hyperparameters tested and if so which parameters were changed? Considering this, the authors are encouraged to provide much more data regarding the training of their neural network, which could easily be provided if necessary as an additional supplementary file.

In addition to this, the authors mention firstly that the neural network was only able to achieve 64% in one of the cases, while tables also demonstrate how the neural network performed poorly in other cases. This to me does not seem to be an issue with the use of neural networks in these type of studies, but more to do with the configuration of the network and/or the quality of input data.

While Deep Learning was not the primary objective of this paper it is useful to comment that a more detailed study into the architecture of the model, the correct configuration and hyperparameter optimisation may be the best means of significantly improving the results. Along these lines I encourage that the readers consider this concept further and comment within the discussion of their paper the possibilities this experimental factor may have on their result. Please consult, for example the works of Wolpert (1996) The Existence of a Priori Distinctions between Learning Algorithms.

Why were only 8 PC scores used? How many PC scores in total were produced, and why were only these selected for classification? Did the authors perform any study into the value and weight each PC score had on the quality of the results and efficiency of the models?

Turning to the Geometric Morphometrics a number of important issues have to be questioned:

As before I strongly suggest the authors justify their use of only 8 PC scores.

How many semilandmarks were used for the study of “Outline Data”? Why this number? Where other configurations tried and tested? Why were they not combined with the fixed landmark data? Consulting traditional geometric morphometric literature, most authors do not perform their analyses solely using fixed landmarks or solely using semilandmarks, yet choose to combine the different types of configurations so as to maximise resolution and accuracy. If the authors used a model that contained both the fixed landmarks and the semilandmarks describing the contour, they may have a better means of defining morphological variations within their samples.
Validity of the findings: The results within this study appear conclusive, however a number of important concepts have to be confronted in order to improve the presentation of the authors’ results.

The act of basing one's arguments solely on a given p value is not necessarily good practice within applied statistics and has been the topic of heated debates for quite some time. The authors are thus encouraged to support their results with additional statistical metrics that can support their claims. For example,

In ANOVA testing and other univariate or multivariate tests should be accompanied either by data regarding residuals or the F statistic, all of which are useful for supporting results rather than relying solely on a given p value.

Mahalanobis distances – The authors mention briefly the significance of mahalanobis distances obtained, yet make no reference as to the precise value of these distances themselves. This can neatly be summarised in a table containing the mahalanobis distance between each group and their corresponding p value of statistical significance.

The authors when referring to the classification results only make reference to the accuracy. This is a poor means of summarising the performance of a model. First of all, is this a balanced accuracy from the validation technique employed, or is this the accuracy observed when tested on the test set? How was this value obtained? Neural Networks are stochastic in nature, different training sessions are likely to produce different results: have the authors taken this into consideration? Examples of other model evaluation metrics that should be considered are specificity and sensitivity values obtained through the calculation of confusion matrices. Furthermore, what was the overall confidence of the classifications? It is not the same if a model classifies an individual correctly with 51% confidence as opposed to a model that correctly classifies an individual with 99% confidence. This can be consulted via each model/test’s loss when making overall predictions.

Why did the authors choose to use Mahalanobis distance calculations as opposed to Procrustes distance calculations? Mahalanobis distances are well known for being affected by sample size. This is especially important considering the issue of sample size is one that is mentioned by the authors themselves on a number of occasions.

Along these lines, the authors mention that 36 complete specimens were selected for the study (lines 187-188), yet previously mention that around 90 worms were collected in one of the samples (line 125). Why were 36 only used at this later stage? Could the authors please simply clarify where these numbers have come from?

In addition, why choose 36? Is this number statistically significant? How did the authors ensure this? Were statistical power tests performed to confirm 36 as a statistically significant value?

Regarding the conclusions, in lines 421-422 the authors state that “landmark data did not allow us to recommend this morphometric technique for identification purpose”. I have to disagree with this statement and ask that the authors revise. In this particular study the landmark model was not as successful but this is not to say that if another landmark configuration is used other authors may not conclude differently. The quality of these results may vary depending on how the data is processed (consider previous comments regarding the ANN) and the combination of landmark models used (as previously stated in other comments). The authors should refrain from rejecting landmark based models considering how another configuration may more useful when combining both semi and fixed landmark data.

In lines 389 the authors mention that “the landmark based approach require a little bit more knowledge about the internal anatomy of the parasites…”. Have the authors considered possible statistical noise product of inter-analyst errors? The value of some landmarks can be assessed on the reproducibility of the landmark model.
Additional comments: The study presented by Sumruayphol, Siribat and colleagues demonstrates how multiple statistical methods can be used to identify different, with the use of both traditional metric techniques, geometric morphometric techniques as well as numerous statistical and artificially intelligent means of processing these different datasets. The ideas presented within this paper are interesting while their results are also valuable, nevertheless, there are elements within the methods and results that require further development in order to provide a more complete and precise presentation of their results. Likewise some methodological questions need to be clarified to justify their use of the specific techniques employed within this paper. This could greatly contribute towards the value of their study. Under this premise I recommend this paper undergo major revisions before it be considered for publication.


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

Input:
Title: FASCIOLA GIGANTICA, F. HEPATICA AND FASCIOLA INTERMEDIATE FORMS: GEOMETRIC MORPHOMETRICS AND AN ARTIFICIAL NEURAL NETWORK TO HELP MORPHOLOGICAL IDENTIFICATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear English used throughout, literature references properly cited, raw data shared.
Experimental design: Methods described with sufficient detail and information to replicate.
Validity of the findings: All underlying data have been provided; they are robust and statistically sound.
Additional comments: This manuscript is informative about characterization and identification of Fasciola gigantica, F. hepatica and Fasciola intermediate forms. It is an interesting study that would be useful for improve the identification and, in my opinion, scientifically sounds. The authors present their data and associated analyses in a clear and coherent manner. I believe that the conclusions drawn are well-supported by the data included.

Below authors will find some suggestions/questions:

Is the ethics committee's certificate available regarding the use of animals in this study?

Line 54 – typo “Mas-Coma, Bargues &Valero, 2005”. Please check other typos throughout the manuscript.

Line 69 – “...has been used to help Fasciola species identification” insert some references here.

Line 80 – I don't think "Amer" should be italicized here.

Line 81 – When you cite the acronym for the first time please explain what it means (just in the first time).

Line 88 – The acronym ITS1 and ITS2 has already been cited above and should be explained just for the first time in the text. Here one should only refer to the acronym.

Line 86 – This paragraph is similar to the previous one, with many repeated information. It would be better to restructure both.

Line 94 – “(Periago et al., 2006; Valero, Marcos & Mas-Coma, 1996; Valero, Panova & Mas-Coma, 2005; Ashrafi et al., 2006; Afshan et al., 2014)” Should these references be in alphabetical or chronological order? Because neither is being followed. Check this for the other text references.

The authors should make explicit their hypotheses at the end of the Introduction section.

Materials and Methods:

Line 141: Regarding specimens obtained from the Liverpool School of Tropical Medicine (England): Do the authors know how this material was prepared? Could a procedure increase or decrease its size or change its shape in relation to specimens collected in the field? The time (1993) could not change the specimens?

Line 187: “We selected 36 complete specimens”, but you collected 90 specimens, right? Make it clear why you didn't use them all.

Line 202: check the citation of Valero et al and the following references.

Line 255: I think the correct citation of “Camila, Antonio & Lincoin, 2015” actually is “Lorenz, Ferraudo & Suesdek, 2015”.

Line 280: Is this molecular identification method 100% accurate? Or is there any overlap between the identifications?

Line 305: “Fasciola intermediate forms” letter S is blue.


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

Input:
Title: FASCIOLA GIGANTICA, F. HEPATICA AND FASCIOLA INTERMEDIATE FORMS: GEOMETRIC MORPHOMETRICS AND AN ARTIFICIAL NEURAL NETWORK TO HELP MORPHOLOGICAL IDENTIFICATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The overall presentation of the paper has improved significantly. The presentation of both tables and figures has also improved, however figures 2 needs a label for the axis represented. I would also suggest including the units of measurement in said label to facilitate the reading of the graph. While it is understandable what figures 3 and 4 represent, I would also suggest labelling these axes and including the percentage of variance represented in each PC score.
Experimental design: While the inclusion of supplementary files and expansion of the methods is an important improvement to the quality of the paper, there are still a number of issues that have to be addressed to ensure reproducibility. In my previous review I recommended that the authors describe the hyperparameters used in their artificial neural network. While many of my doubts have initially been clarified, the authors are still missing some details. It is important that the authors at least describe the optimization algorithm used. The authors are also required to state which activation function is used in the single hidden layer as well as the activation function used to produce the output. The importance of these three details (at least) is found in how any analyst who wishes to replicate this study using a different software would need to know how to configure and train the classification model. This is a vital piece of information that any user of python or R (such as myself) would require in order to construct the neural network and replicate these methods.
Validity of the findings: In my previous review, I asked the authors to justify their reasons for selecting their number of PC scores. This comment simply required the authors state the reason behind their use of this specific number of PC scores. The authors’ choice of wording however raises more questions than it does answers, with their stress on the use of the word ‘ “rule” ‘. Why is “rule” in quotation marks? If the authors wish to state that they followed a ‘ “rule” ‘ in statistical multivariate analysis, could they please cite an author who states this ‘ “rule” ‘ in order to justify their choice in phrasing. Multivariate statistics is a very large field of research and no single ‘ “rule” ‘ exists. Otherwise I think that simply removing this part of the sentence would help avoid issues. They could simply state “This specific number of PC scores was selected so as to use a number of variables that does not exceed the number of individuals in the smallest sample” or a phrase along these lines.
A small note: while the inclusion of the mean and standard deviation of 30 iterations of the Neural Network are a valuable inclusion, could the author please specify whether the sd value is the first deviation from the mean (68% of the distribution) or otherwise (2sd = 95% distribution, 3sd = +99% distribution).
Additional comments: The quality of the paper has improved significantly and I thank the authors to take the time to explain each of the questions/revision comments raised. These minor revisions are relatively easy to rectify and each can be corrected with the addition of a few words that clarify the respected sections of the paper. Upon clarification of these minor points I feel this paper would be ready for publication.


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

Input:
Title: INJURIES AMONG ADOLESCENTS IN GREENLAND: BEHAVIOURAL AND SOCIO-ECONOMIC CORRELATES AMONG A NATIONALLY REPRESENTATIVE SAMPLE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The submission is written in clear unambiguous and technically correct English. However, the intro and background can be improved, as well as the structure of the text.
Experimental design: The research is conducted in conformity of the ethical standers, but the experimental design can be improved: Research questions and/or hypothesis and relevance of the study are missing, and methods should be described with sufficient information, since reproduction is not possible with the information provided.
Validity of the findings: The data are robust and statistically sound, but they are not up to date. That is not a necessity for all studies, for example to investigate theoretically based research questions, but for a study investigating the prevalence of phenomena and their determinants it is necessary. Speculations and conclusions can be improved by linking them to research questions and results of the study.
Additional comments: See the attachment


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: INJURIES AMONG ADOLESCENTS IN GREENLAND: BEHAVIOURAL AND SOCIO-ECONOMIC CORRELATES AMONG A NATIONALLY REPRESENTATIVE SAMPLE
Review round: 1
Reviewer: 2

Output:
Basic reporting: I find the language fully acceptable – but I am not a native English speaker. The structure seems to confirm to the standard of the journal.

The tables are relevant. the data are robust, the statistics are excellent, the subject is very relevant and is a useful contribution to the knowledge about injuries in Greenlandic adolescents – which as stated is very sparse.
Experimental design: Fully acceptable
Validity of the findings: Se below
Additional comments: I find the language fully acceptable – but I am not a native English speaker. The structure seems to confirm to the standard of the journal.

The tables are relevant. the data are robust, the statistics are excellent, the subject is very relevant and is a useful contribution to the knowledge about injuries in Greenlandic adolescents – which as stated is very sparse.

Despite this, the paper needs a major revision due to serious limitations.

The study has a serious limitation: The authors have a total lack of knowledge about the context the data has been gathered in.

They also seems to assume that the ways of living are the same all over the Arctic region and therefor mainly use US or Canadian literature on areas where Greenlandic literature can be found rather easy.

This lack of local knowledge have the result that most of the discussion is pure speculations For some of the speculations the authors draw conclusions that are not only wrong, but unacceptable wrong.

Specific comments
Line 59 - 61. Population data should be updated
Line 68-69 Data on suicides should be updates, use examples data from the office og the Chief Medical Officer or Statistics Greenland.
Line 86 Either exclude Greenland in the sentence or include a Greenlandic reference.
Line 92 It I correct that no other publications in English exist, still grey literature such as the national reports from the HBSC study are published.
Line 143: Is the selection of cut-points according to the literature or how were they selected?
Line 191. The International data from the HBSC study only include the agegroups 11, 13, 15.years.
Line 193 “thrice” – is the word really used in ordinary language?
Line 200 There are healthcare providers in all Greenlandic towns and villages, although not doctors in some smaller towns and in villages.
Line 202-205 This is pure speculation – can the authors find any documentation. Half of the year it is daylight 24/7 – doesn’t that count as well? May be the lack of road accidents is due to lack of cars in many villages!
Line 213-214 .. despite that Greenlandic adolescents are binge drinking – as in the other Nordic countries.
Line 220-223 The speculation could be checked by consulting the international HBSC report from the 2005/2006 study.
Line 241 Please reality check the statement about the suicide rate as a cause of decreased fatherhood involvement in Greenlandic fathers – it is not correct.
Line 243 There are numerous Greenlandic articles about suicide why not use a Greenlandic reference.
Line 250-261 this is completely wrong. Canadian ways to look at education and at the school system cannot be applied to Greenland. And the words are not in Greenlandic but in the language used by Canadian Inuits. The Greenlandic school system and ways of thinking about education is very highly influenced by Danish and Nordic traditions which and is very different from the Canadian ways.
Line 261-264 wrong again. Please 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: INJURIES AMONG ADOLESCENTS IN GREENLAND: BEHAVIOURAL AND SOCIO-ECONOMIC CORRELATES AMONG A NATIONALLY REPRESENTATIVE SAMPLE
Review round: 2
Reviewer: 1

Output:
Basic reporting: See pdf and below
Experimental design: see pdf and below
Validity of the findings: see pdf and below
Additional comments: Review of the revised manuscript “Injuries among adolescents in Greenland: behavioural and socio-economic correlates among a nationally representative sample”

I thank the authors for their rebuttal letter, which is very clear. I also thank them for the revision of their manuscript on injuries among adolescents. I must say the revision is a serious improvement. Congratulations for that. I have some minor comments, some recommendations and some questions.

Introduction
The authors provide a clear purpose of the study: investigating the socioeconomic and behavioural correlates associated with injury occurrence. However, I wish to provide three recommendations.
1.	A difference between intentional and unintentional injuries are provided, but it is not mentioned whether both kinds of injury are under investigation, or only one of them. This is important for understanding the discussion.
2.	In the abstract it is mentioned that the primary outcome is measuring the experience of injury. This does not match with the newly formulated purpose in the introduction.
3.	The introduction is on violence and injury. At the end of the introduction they refer to Schnohr and Niclasen who found an increase on bullying. This term is not mentioned earlier. Although bullying can be perceived as a behavioural correlate associated with injury, the authors should provide a link to injury and violence on the one hand, and bullying on the other.

Materials and methods
I understand the argument of the authors concerning the time limitation of the data. And I agree with them, concerning the purpose of the research. Most comments on the measurement part are not relevant anymore. Here I have four recommendations and one question.
1.	Although there is a link to the website for more information, it is convenient to provide some information on the data collection methods, for example the situation in which the questionnaire was completed.
2.	The cut points for the independent variable is mentioned twice: under the measurements as well as under the statistical analysis. Since in the latter part the base for this choice for these cut points is provided, they can be deleted in the measurement part.
3.	The first part of the statistical analysis concerns the measurements. This part should be moved the description of the measurements.
4.	As is mentioned in the comments in the rebuttal letter, injury is the dependent variable and all the others are the independent variables. However, ‘Significant differences between each category and independent variables were explored using … ANOVA for the continuous variable age”. I don’t understand how the ANOVA is conducted. This sentence suggests that in this analysis a continuous variable (age) is the independent variable and a categorical variable (injury) is the dependent one. In ANOVA the independent variable should be the categorical and the dependent should be the continuous one.
5.	Since for the measurement of the independent variables the authors refer to a website, and no information is provided about the answering categories of these variables, it is more convenient to mention there that these variables are categorical and to provide some examples.

Results
Two recommendations on the results:
1.	Some more frequencies are reported, but they are not completely clear. It is mentioned that parent socio-economic status and self-assessed wealth are independent variables, but frequencies are provided for mothers’ SES, for fathers’ SES and for families’ SES. And I don’t understand the frequencies for ‘living with parents’: of the participating adolescents, 78% lived with their mother and 60% lived with their father. Together that’s 138%. Also, frequencies for physical activity (VPA) and VPA (outside school hours) are missing.
2.	Table 1 is very clear. Except for the living circumstances. An extra line for adolescent who live with both parents makes it complete.

Discussion
The discussion is seriously improved. I have one question and one suggestion.
1.	As mentioned above, it is not clear whether the authors measured intendent or unintended injuries, or both. For the lower prevalence, they provide the explanation concerning transportation in Canada. Since my problem concerning the definition of HBSC is cleared in this revision, I don’t understand why the authors deleted the explanation concerning difficulties seeing a healthcare provider (and the explanation concerning time spending indoors).
There is a lot of literature on parenting style and difference between mothers and fathers. These studies mostly suggest that mothers are more protective than fathers. That may be an explanation for the finding that living without a mother increases injuries, whereas living without a father does not.


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: INJURIES AMONG ADOLESCENTS IN GREENLAND: BEHAVIOURAL AND SOCIO-ECONOMIC CORRELATES AMONG A NATIONALLY REPRESENTATIVE SAMPLE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Regarding "Injuries among adolescents in Greenland: behavioural and socio-economic correlates among a nationally representative sample" is changes to be much more basis on Greenlandic realities and research and not NorthAmerican making it much more reliable and interesting.

There are still som minor changes needed:

Line 213 ff: The sentences about inclusion I not correct as is can be read at the international homepage. All schools in Greenland is invited to participate. The parents do not give informed consent. The school board decide if the school want to participate.

Comments to the result section: In Greenland two peoples and to major languages is used a relevant item to look at I violence in different population groups, either using “Where is your father/mother born”, perceived ethnicity or language performance.

After these revisssions it is my view that it can be published and that it actually can contribute to the sparse research on the topic in Greenlandic adolescents.
Experimental design: See above
Validity of the findings: See above
Additional comments: Se above


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

Input:
Title: INJURIES AMONG ADOLESCENTS IN GREENLAND: BEHAVIOURAL AND SOCIO-ECONOMIC CORRELATES AMONG A NATIONALLY REPRESENTATIVE SAMPLE
Review round: 3
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: I wish to thank the authors for the rebuttal letter and the improvements of their paper.

In the second review I wrote that the first part of the statistical analysis concerns the measurements, and that this part should be moved the description of the measurements. The authors reply with the remark that it is changed. The statistical analyses descriptition however still contains remarks about the measurement, which have to be part of the measurement ( ‘The question ‘During the past 12 months, how many times have you been injured?’ had five response options……. While both intentional and unintentional injuries were included’.)

In the second review I also wrote that percentages in the results section are not clear:   of the participating adolescents, 78% lived with their mother and 60% lived
with their father. Together that’s 138%. The authors mention that they are not to be understood as cumulative percentages. But then they have to reformulate the text, since now it seems like a typo.

In the second review I asked for an extra line in Table 1 for adolescents who live with both parents. This extra line would make it complete. The authors indeed placed this extra line, but now the percentages for no injuries are not correct: 19.9 is living without mother, 39.5 is living without father, 13.2% is living without both parents and 53.4% is living with both parents. This counts up to 126%. The same for 1-2  injuries and 3+ injuries. So somewhere the percentages are wrong, or the categories are wrong, because an overlap in these categories is not possible.

It have noticed that the concepts in the text are different from the concepts in the table. For example, in the text it is called ‘maternal socioeconomic status and in the table it is called ‘’ job mother (skilled job)’. The same for father’s SES and family wealth with below and above average (in the table self-assessed wealth with well-off, average and not well-off).


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: CO-EXPRESSION NETWORK ANALYSIS REVEALS THE PIVOTAL ROLE OF MITOCHONDRIAL DYSFUNCTION AND INTERFERON SIGNATURE IN JUVENILE DERMATOMYOSITIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is quite well written, has a good structure. English is good, despite a few minor typos. Below I list a few minor concerns:

Referring to module colours in the abstract can be confusing. Similarily across the manuscript - referring to module colour seems unnatural. Maybe it would be worth to handle modules in another way? Besides information on module colour, no other data on the particular module's structure is available directly from the manuscript.

Line 117: It is hard to note those 12 modules in the picture - are there really 12 colours but mixed together?

Urgent: The figures lack readability. Fonts are too small and impossible to read. Figure fonts are also inconsistent across the manuscript.

Line 133: Misspelling: Go -> GO

Line 134: Biological process instead of BP would be more informative

Fig 4 should be moved to supplementary data in this form. Otherwise, the authors need to try to show it in a more feasible way suitable for the manuscript.

Line 86: Missing citation for KEGG

Fig 2A - The figure would benefit much from aligning tree's leaves with heatmap.

The paragraph starting at 132 - the long lists of GO terms are redundant with the figure. After tweak readability of the figure, the paragraph can be cleaned from redundant information.

What is the colouring scheme in Suppl fig 3?

Drug screening is missing from the Methods section. The reader would find it helpful to have a screening method underlying the cited database explained in a few sentences.

The paragraph starting at line 210: How do these drugs' mechanisms of action relate to the identified hub genes? Can authors at least try to rationalize why these drugs were chosen in the context of functional analysis of hub genes?
Experimental design: The reported study is well designed.

I'd like to ask the authors why only the GSE3307 dataset was used? Was that the only dataset (besides GSE11971, of course) with JDM data?

Also, did you compare obtained results to other dermatomyositis (not only juvenile) GEO data, which are available? Finding similarities/differences could be informative. Of course, this concern goes beyond the immediate scope of this study but maybe inspire the authors.
Validity of the findings: The findings seem to be sound in the light of performed analyses.

However, I miss the link between drugs' list and identified hub genes. Which of those genes are targeted by the drugs? How does the targeting affect them? Do we target up-regulated gene products? What are the mechanisms of proposed drugs' actions? I'd much appreciate some discussion on this.
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: CO-EXPRESSION NETWORK ANALYSIS REVEALS THE PIVOTAL ROLE OF MITOCHONDRIAL DYSFUNCTION AND INTERFERON SIGNATURE IN JUVENILE DERMATOMYOSITIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript by Zhong et al. is an example of in-depth in silco study using gene expression data available in public repositories, in this case of patients suffering from juvenile dermatomyositis. Such studies are well within the scope of PeerJ, and the reviewed manuscript has no fundamental flaws in methodology or interpretation of results. I do, however, have some significant concerns about the structure and language of the manuscript, that need to be addressed by an extensive rewriting before acceptance.
In general, the entire manuscript should be edited by a native speaker of English or a professional editing service, as it contains many examples of awkward phrasing and terminology, and incorrect grammar. I will list the most obvious language problems below, but they are too numerous to mention here.
Some sections of the manuscript should also be restructured and/or expanded, as explained below and in the subsequent sections of the review. Numbers refer to lines in the manuscript file

A. Language problems.
2. I have doubts about the word "signature" in the title. Did the authors mean "signalling"?
25. One does not screen a drug for genes, it's the gene products that are screened for potential small molecule inhibitors. Also, this sentence implies that the authors performed actual drug screening, while what they in fact did was search the database of known inhibitors using the genes identified in their study. There's nothing wrong with this, but it should be made clear in the text from the beginning.
61. "should contain" - did it, or did it not?
61-62. "specimens at least three biological replicates" - incorrect grammar/syntax
62. "package of limma" shold be "the limma package"
63. "The specific platform" - what platform? This isn't explained anywhere.
84. One does not use a database to upload genes. What the authors did was to search the database using the genes they found.
116. "equal" not "equals"
124-125. Awkward repetition of "independent"
133. "GO" not "Go"
162-163 and 187-189. The word "including" should not be used when all the genes are listed in the sentence.
169. "to for"?
172-173. Drugs don't "show negative correlation" with a disease. Meaning unclear.

B. Structure and completeness
16-18. This is not background. Background section of the abstract should summarize the introduction, i.e. explain the problem (JDM).
23. Don't put detailed methods (like the information that MCODE is a Cytoscape plugin) in the Abstract, just name the main methods used.
25-26. The colors assigned to the modules are arbitrary, here they are out of context. Use something like "Three key modules were identified".
29. See comment for lines 172-173 above.
58-66. What is described here is the critical stage in a gene expression analysis - identification of differentially expressed genes (DEGs).  This should be divided into two sections: "Datasets" and "Normalization and DEG analysis". The "Dataset" section should contain the GEO IDs of the datasets with the number of JDM and healthy control samples in each (no need to list each sample in a dataset, this is correctly presented as supplemental data). Information about the platform used to obtain the data should also be included. Providing this information as a concise table would be optimal for legibility. Also, the normalization of data and DEG identification should be described more clearly. Was between array or within array normalization performed (or, preferably, both?), and was limma used for all the normalization steps (sva is often used for normalization prior to DEG analysis in limma)?
68-69 and 113. The list of top DEGs should be provided as a supplemental file.
106-111. This information should be in the first section of "Materials and methods", preferably in a table form (see comments for 58-66 above), and only briefly referenced here.
123-167. It would be good to provide lists of GO terms and KEGG pathways for identified modules (JDM and control), as well as a list of hub genes. In general - all the lists identified in the study should be made available as supplemental information.
168-173. See comment in section A - explain what is the correlation for the three compounds and how they are different from the remaining 8 in Table 2 with respect to their action on the identified hub gene products.
176-182. Two unrelated statements (a description of JDM and a description of WGCNA algorithm) should not form a single paragraph. Also, this information belongs in the Introduction, rather than Discussion.
183. See comment for lines 25-26. The discussion should be readable without going back to figures or results, and the colors are meaningless out of context.
187-190. This is an exacct copy of the information already presented in lines 161-165 and in Table 1, a reference to Table 1 would be sufficient.
232. A description of author contributions is customarily provided here.
Experimental design: This research is within the aims and scope of PeerJ. Its strengths include a rich dataset and in-depth statistical analysis. The use of DEG co-expression networks combined with knowledge contained in GO and KEGG databases is a routine method that often yields significant insights. This study is no exception, and the obtained results provide insights that were not apparent when the original datasets were published. It is therefore an excellent example of the possibilities afforded by using modern bioinformatic and statistical tools with the wealth of data contained in public repositories. The biomedical problem selected for the study is well defined and relevant, and the study is performed to a sufficiently high technical standard.
The methods section should be expanded. In addition to comments provided in the previous section of the review, I also believe that it would be beneficial to provide snippets of R code used to perform the analyses in supplemental files.
Validity of the findings: I believe the data used in this study are robust and adhere to the standards used in the fiels. In the comments contained in the first section of the review I stated what data should be additionally included as supplemental files.
The discussion is brief and to the point, I would even encourage some more speculation and exploration. For example, the authors link the mitochondrial respiratory chain genes identified in the study to ROS production. Do they believe that mitochondrial dysfunction is among the causes of JDM, or is it rather a result of the JDM pathology? Is the ROS hypothesis supported by the data, are there any genes related to oxidative stress in the lists identified in the study?
Additional comments: The negative comments are generally related not to the methods ad results of the study, but rather to the way it is presented and described.
A recent study published in PeerJ from the same institution (Chen S, Yang D, Lei C, Li Y, Sun X, Chen M, Wu X, Zheng Y. 2019. Identification of crucial genes in abdominal aortic aneurysm by WGCNA. PeerJ 7:e7873 https://doi.org/10.7717/peerj.7873) could serve as a model to show how the majority of my concerns could be addressed, and what methods and data should be included in supplemental fles. If there is a significant overlap in the methods used in these two studies, a reference to the published methods could replace some information in your methods section (something like "array data normalization was performed as in Chen et al. 2019" if applicable),


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: CO-EXPRESSION NETWORK ANALYSIS REVEALS THE PIVOTAL ROLE OF MITOCHONDRIAL DYSFUNCTION AND INTERFERON SIGNATURE IN JUVENILE DERMATOMYOSITIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I'd like to thank the authors for significantly improving the manuscript, especially for adding the paragraphs on biological interpretation. I found however few very minor issues, which could be addressed before final accepting the manuscript. (I include also typos and small editorial issues I found in order to help a little bit).

Lines 32-34 (abstract) and one more in the manuscrpit: what is the difference between the potential to perturb and providing therapeutic goals? These two categories contain different substances but I cannot get the difference.

Line 51: JDM children - shouldn't be JDM in children? Besides, JDM means juvenile so why children?

Line 57: Missing whitespace before Adaptative

Line 61: method that mines (the s form)

Line 139: Please define DEG once more - not everyone (including me) reads methods section.

Lines 139-140: based on [...] 0.05, - these detailes should be placed in the methods section rather than results...

Line 143: We input - OK, but input where?

Line 148 and following: could that be possible to put the numbers into the figure? The paragraph looks awkward in this form...

Line 226: missing 'e' in suggested

Line 250: used the databse TO predict

Line 253: according to literature - please provide some refs then.

Table 1: why keeping so many decimals for VDAC1 and SP110 while not for e.g. TPI1? I'd suggest rounding to the first decimal. Also round the numbers for DDX60L to the 3rd?

Table 2: I'd enjoyed this table much more knowing what those columns mean. It was explained in the methods, but the reader would benefint greatly if the caption carried some brief information, e.g. "Mean in the range xxx-yyy mean that the target is ...", N and P also look abstract.

Figure 4: Please consider dragging and dropping the objects, especially in the triangle-including part. Circle-like representation is quite confusing and is isn't imposed by the data type. After a little bit of focus the reader will find the denser clusters himself, but why not helping him a little? Let the clusters form clusters - Cytoscape allows for moving objects.

Figure 2: While studying this figure I thought in that in the tree maybe instead of colour names the real colours could be used? Or you could simply skip tree leaf names and moved the color legend in the matrix below from the below to the above to serve as legend for two figures at once?

Figure 1: leaf names are unreadable in the tree.

REMARK ON COLOURS: First of all - you know which clusters are chosen and presented individually on further figures. Why not choosing more discerning colour for those instead of blue, lightgreen and midnightblue - all of them similar in fact? Maybe orange, teal (of some pastel flavour) and light green - they separate visually? You could easily use those colours across the figures and the data would be much more readable. The rest of the clusters also looks quite dull, but they are rather for informative purposes as they are not chosen further.

Overall - good job!
Experimental design: No comments for now.
Validity of the findings: No comments for now.
Additional comments: I'm giving 'minor revision' to give the authors a chance to tweak the manuscript a little. Yet I'm satisfied with the revision.


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

Input:
Title: CO-EXPRESSION NETWORK ANALYSIS REVEALS THE PIVOTAL ROLE OF MITOCHONDRIAL DYSFUNCTION AND INTERFERON SIGNATURE IN JUVENILE DERMATOMYOSITIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The revised manuscript is a significant improvement of the original submission. It is now structured in a way that is acceptable for publication.
Experimental design: The revision improved the description of methods and results, and is now sufficient to warrant publication.
Validity of the findings: The revision does not change my initial favourable opinion on the validity of findings.
Additional comments: I believe the paper is significantly improved in this revision and can be accepted for publication in PeerJ.


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

Input:
Title: DISNET: A FRAMEWORK FOR EXTRACTING PHENOTYPIC DISEASE INFORMATION FROM PUBLIC SOURCES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper presents a framework named DISNET to extract information from diseases and their signs, symptoms, and diagnostic tests from public data sources. The vast amount of digital data about diseases demands new methods and tools to structure and make sense of them. DISNET is a new approach that tries to address these challenges on textual data, based on a combination of rich data sources, text mining, NLP, and modern Web technologies.

The topic is relevant. The paper is clear, well structured, and easy to understand. The Introduction provides a good description of the current landscape and numerous references to previous works. It appears that the raw data used to build the system is not still available (the authors explain that “access to the data will be enabled once the paper is published”), but users can already perform various queries on the data using the DISNET API.

The figures and tables are relevant according to the paper content, but their legends are not clear enough. They should be self-contained; that is, the content of the table or figure should be understandable without reading the text of the manuscript. Also, the font size used in some figures is too small (e.g., Figure 6, Figure 10). Please, increase the font size to make it more readable.

The paper contains some minor grammar mistakes and typos (I have listed some of them in the “General comments for the author” section), and it would benefit from some closer proofreading.
Experimental design: The authors present a validation of the information extraction process and show how the system can be used to perform queries in two very simple scenarios. In future works, the authors should perform a more robust evaluation of the system, focused on assessing the usefulness and usability of the system in a real setting.
Validity of the findings: The authors adequately present the methods used to build the system and show that (and how) it can be used to retrieve information about diseases via the REST API. My main concern in relation with the validity of the findings is the claim that DISNET “is good enough to be used to extract diseases and diagnostically-relevant terms.” The authors should clarify what the meaning of “good enough” is. How can the authors claim that the system is good at performing a task without conducting a comprehensive evaluation with real users? I strongly encourage the authors to clarify or remove any subjective statements such as that one and limit their claims to the results obtained during their validation process.
Additional comments: 1. Integrating information from heterogeneous data sources is a very challenging task. However, the authors state that “thanks to its flexibility, new sources could (and will) be incorporated in the future.” Could you please elaborate on (1) what makes the system flexible; (2) what would be the steps needed to add a new data source to DISNET?
2. How are discrepancies or conflicts between data sources solved? For example, suppose that the symptoms for the disease D1 are S1 and S2 according to one source, but S1 and S3, according to a different source. How would users take advantage of contradictory information in these cases?
3. The authors explain that one of the advantages of their work is that Wikipedia is used as the primary source of knowledge. My concern is that some of the information on Wikipedia may be inaccurate or wrong. Could you please explain in more detail why using Wikipedia over other more formal and curated sources is an advantage and not a disadvantage?
4. Even though I do not consider it essential for publication, the paper would substantially benefit from a structured comparison between DISNET and existing approaches. I suggest that the authors include a table comparing DISNET to other existing systems. This table will help the reader get a better picture of the current state of the art and to understand the advantages of DISNET. The current Introduction section contains an extensive list of references to existing works with no explanation for many of them (e.g., lines 75-85, 95-98). Either using a comparison table or a textual analysis, the authors should summarize existing work and clarify how DISNET is different. For example, the authors mention (see lines 154-157) that having a method for information sharing, such as an API, is not common in existing systems. It would be beneficial to know precisely the systems that have/do not have this capability.
5. A structured comparison between different candidate data sources would enrich the paper as well, and it would help the authors to support their choice. However, again, I don't consider this comparison essential for publication.
6. Abstract - Background: What do the authors mean by “customizable disease networks”?
7. Abstract - Methods: “…extracted from Wikipedia and PubMed websites.” Using the term “websites” imposes a limitation on the scope of the work. Consider removing that term.
8. Queries that return a large number of results (e.g., http://disnet.ctb.upm.es/api/disnet/query/diseaseList) need to support pagination to decrease the response time and unnecessary network traffic.
9. L435: Who has performed the manual analysis?
10. By looking at the DISNET queries presented on the use case, it seems that DISNET is limited to free-text queries. Does the system support ontology-based queries?
11. The DISNET queries presented use the parameter matchExactName. Does the system support any other matching methods?

Grammar and typos (this list may not be complete):
L71: facilitate -> facilitated
L76: system -> systems
L141: recovery -> retrieval
L151: encyclopaedia
L215: “…to include the following three web sites…” -> However, the authors only mention i) Wikipedia, and ii) PubMed. What about the third system?
L244: Virtuous -> Virtuoso
L246: Reference error.
L486: Reference error.
L516: Reference error.


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: DISNET: A FRAMEWORK FOR EXTRACTING PHENOTYPIC DISEASE INFORMATION FROM PUBLIC SOURCES
Review round: 1
Reviewer: 2

Output:
Basic reporting: Relative to the basic reporting standards of PeerJ, this manuscript is fully compliant and moreover, high quality in its scholarship. Ample and appropriate references will facilitate contextualization by the intended audience of readers, and facilitate appropriate linking of citations. The English language is excellent, clear, professional, and needs no improvement.
Experimental design: The research presented is within the Aims and Scope of PeerJ, to the best of my understanding, as it concerns biomedical research informatics, and proposes a novel methodology, data workflow and resource. Methods are described in detail and well documented, such as Metamap configuration details at http://disnet.ctb.upm.es/apis/disnet. Source code is apparently not shared, however, the API Is well documented, and includes example queries and other data via the group GitLab repo at https://midas.ctb.upm.es/gitlab/disnet/paperdisnet.  Regarding the online resource, an API but without GUI, when I have tried to "Sign Up" the following notice appears: "Registration is temporarily disabled. If you have any question please contact with the administrator" However, I was able to register, obtain a key and use the API, so apparently the notice was spurious.
Validity of the findings: The work described, DISNET, is an ambitious project toward an important goal reflecting high levels of knowledge, skill and effort suited to this task. The title and abstract make clear that the goal is "extracting phenotypic disease information from public sources" which differentiates this project from ontology projects which focus on expert curation of disease knowledge. For the intended audience, the focus on the framework and shared methodology is quite significant, and differentiates this work from contributions comprising databases which may have validity and value worthy of publication, but often lack sustainability and reusability. The authors recognize in the introduction the critical importance of sharability, and go on to further emphasize the relationships among diseases as a critical focus of DISNET, and cite the PubMed-based HSDN as a previous effort along these lines. Five advantages over previous research are claimed, and I agree with all. The strongest points in my view are the use of both structured and unstructured data (and semi-structured, the Wikipedia sections), harmonized systematically from heterogeneous sources, all shared effectively via documented API, in short, adherence to FAIR principles.

My biggest concern about this project and paper relates to the semantic difficulties of the concepts "disease", "phenotype", "symptom", and others. This problem is a chronic condition and limits the rigor of biomedical informatics, and particularly the accuracy of mappings among heterogeneous sources. "Knowledge extraction" depends on strong metadata, ontology and semantics. I expect the authors understand this well, and for example the issue of what is or is not a disease.  Is "hypertension" a disease? Or symptom? ICD-9 includes "Unspecified essential hypertension" (code 401.9). Diseases are defined in various ways, for various reasons, by different sources. Likewise for symptoms and phenotypes, etc., what is and is not a phenotypic trait or symptom will depend on definitions which can vary among sources. And, the relationships can vary. A symptom may be a diagnostic criterion, thus its presence is somewhat definitional and tautological (e.g. gastritis ⇔ inflammation). A trait could precede and possibly cause disease onset (e.g. hypertension => heart attack), or be a consequence, possibly a complication or another disease (e.g. diabetes => diabetic neuropathy). I am not suggesting any major revision to this manuscript, however, only that these challenges and limitations and understandings be noted, and thereby inform and guide the readers. I am fully in agreement with the use of UMLS and Metamap by the authors in addressing these challenges. I am unfamiliar with TVP and unable to comment without access to the 2015 book and conference paper cited ("Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases").
Additional comments: Congratulations and thank you for the hard work and considerable expertise in producing this resource. In addition to the main concern described, I did experience some timeout errors when using the API (/diseaseList?source=wikipedia&version=2019-10-15). Perhaps this is due to lack of response pagination, as a diseaseList?source=pubmed returns 10+MB and apparently all 2355 diseases.  If the goal is to maximize impact and benefit to the community, you might consider allowing downloads, and/or Docker images. Likewise, open source, while not obligatory, may increase use and impact.


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: INCREASED ABSORPTION IN AUTONOMOUS SENSORY MERIDIAN RESPONSE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The standard of this manuscript is high, and I have no concerns with the quality of the writing, of the visual elements, or the overall structure.
Experimental design: I have no concerns with the experimental design. However I have a (completely unsupported) suspicion that everyone is potentially an ASMR-experiencer, so in that sense there is no control group. However I like the use of a questionnaire to classify people.
Validity of the findings: No problem here (but see next section for comments).
Additional comments: 1. Line 117. How were the included participants selected? Was this random? Have the authors tried the analysis without dropping some participants, and if so did it change the findings?
2. Line 142. The flow questionnaire in use here is different to the one used by Barratt & Davis (2015). Why the difference? Barratt & Davis did not spend long looking for appropriate scales for that paper, so it would be useful to know if the FES is a better instrument.
3. Line 185. The relationship between ASMR and the personality measures is presented here as a table (Table 2). It would aid interpretation if these were also presented as a scatter plot, since that would reveal possible non-linear structure in the data.
4. Line 203. Although the authors should not feel the need to cite it, Barratt, Spence & Davis (2017) PeerJ 5:e3846, found that the sorts of video features that trigger ASMR accord well with the list provided here. The surprise (to the authors) in that work was that background music is highly distracting for ASMR.
5. Line 230. 'AMR' should be 'ASMR'.
6. Line 243. The inconsistency with the Fredborg work is very interesting. I wonder if ASMR is not a form of mindfulness at all, as there is a clear, external stimulus to focus on (my understanding of mindfulness is that the focus is internal). I agree with the authors that more work is needed, as the two constructs are often linked in the popular media.


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: INCREASED ABSORPTION IN AUTONOMOUS SENSORY MERIDIAN RESPONSE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper reports the results of a single study investigating the role of absorption, flow, and mindfulness in Autonomous Sensory Meridian Response (ASMR). A questionnaire was administered to participants who experience ASMR, as well as those that do not. The primary measures were absorption, mindfulness, and flow. The results showed that the groups differed on the measure of absorption, but not flow or mindfulness. The main implication is that it is the passive ability of absorption that contributes to the ASMR experience, compared to more ‘active’ elements of flow or mindfulness. The paper contributes to the growing literature on ASMR and possible causes of the phenomenon.

The reporting of the study is good, the article is clearly structured and well written overall. There is sufficient background information about ASMR, and the logical structure of the introduction is good: the purpose of the research is clear and well-justified, and the paper presents the results of a clear ‘self-contained’ which sets out a clear research question and answers it. Raw data is available and clearly labelled.

Although the authors have done a reasonable job of explaining flow, mindfulness, and absorption, I didn’t feel confident understanding the differences between the constructs after reading the article. I think more clarity throughout on both (a) the differences between the constructs, and (b) the measurement of these constructs, would improve the piece and really help the explanation of the work.

For example, when flow is introduced in the introduction, the current explanation leaves several things unclear. Is “flow” a state or a trait? does it describe a singular experience or a trait like individual difference? it is unclear what scoring “high on flow” (line 74) really means – people are more susceptible to flow? Or they experience it more often? What is the distinction between a regular measure of flow and a “global measure of flow” (line 83)? Considering the conclusions of the research concern the differences between constructs which are at face value very similar, it is important to clearly describe and explain the differences between the constructs and their measurements in the introduction.

This issue particularly applies to the construct of mindfulness, which has been criticized for being particularly nebulous and multifaceted, and sometimes even meaning completely contradictory things! A useful paper for the authors to use to help define mindfulness in their introduction is:

Van Dam, van Vugt, Vago, Schmalz… et al. (2018) Mind the Hype: A critical Evaluation and Prescriptive Agenda for Research on Mindfulness and Meditation. Perspectives on Psychological Science, 13, 36-61. https://doi.org/10.1177/1745691617709589

A clear definition of mindfulness would also help with justifying the study. I liked the explanation at the end of the introduction indicating the incompatibility of previous results, and explaining how investigating the role of absorption would elucidate this. I think with clearer definitions of flow and mindfulness this would be improved further.
 The definition of absorption is clear, and it was helpful to me when you described it as a “stable personality trait”. The structure of this section could be improved in to more clearly indicate that absorption is a facet of flow and clarify the relationship between flow and absorption.

This extra clarity provided in the introduction regarding the concepts of flow, absorption and mindfulness and their relationship can also be carried over into the discussion when explaining the findings (e.g. lines 242-243; 251-259). On reading the article, it was only when I got to this section (e.g. lines 256-258) that I began to understand the relationships between the variables, and I think moving this clarity into the introduction would help.

Regarding other reporting, There are no statistical errors in the reporting of the inferential statistics, as determined by http://statcheck.io . The descriptive statistics in Table 1, however, do not correspond to those reported in the results section. For example, SD for absorption in ASMR participants is 23.81 in the text, and 23.80 in the table. Mindfulness mean/SD for ASMR participants is 3.21/.81 in the text, 3.20/.80 in the table. For flow, mean for ASMR is 36.49 in text and 36.5 in the table; and 38.16 in the text and 38.09 in the table for controls. These are just the errors I noticed, Please can the authors double check all  numbers in all tables to ensure consistency with the text, and the statistics calculated from the uploaded raw data.

Regarding reporting style of statistics, the authors should use a consistent reporting style. In some places, p values are reported as <.05 (e.g. line 188), in others they are reported in full (e.g. line 182). Likewise, in some places they are reported to 2 decimal places (line 177) and in others 3 (line 179). I would suggest the authors follow APA style, which dictates that all p values are reported in full to 3 decimal places, the only exception being very small p values reported as <.001. Please can the authors go through the manuscript and change the reporting for all these statistics.

Another (pedantic) point regarding reporting statistics: APA style recommends that leading zeros be used when reporting statistics that can feasibly be larger than 1, but not for statistics that cannot (see https://blog.apastyle.org/apastyle/2010/07/a-post-about-nothing.html). Therefore, the SD’s reported in table 1 (and in the results section, e.g. line 178), and the Cohen’s D values reported in the results section (e.g. line 175) should have leading zeroes (e.g. 0.81 rather than .81), as the values can potentially exceed 1.

Finally a few bits of language I found awkward/misleading/debatable:

Abstract: “intentionally created ASMR Youtube videos” – Whilst most ASMR videos are created intentionally, there is also a large number that trigger ASMR incidentally (e.g. Bob Ross videos) so I think this is misleading.

Intro, lines 62-65: Whilst I agree that there is an element of focus in experiencing ASMR, the description that it is necessary to focus on certain triggers to experience it doesn’t sit well with the “autonomous” description of the sensation, and I’m not sure whether it is maybe a bit misleading to say that one needs to focus on the triggers in order to experience it. E.g. experiencing it in everyday life – one does not need to prepare to focus on a trigger in order to subsequently experience ASMR, - it may just happen autonomously in response to triggers – although I do agree that subsequent focusing may prolong and intensify the sensation. So perhaps this could be reworded to just clarify that one does not have to choose to focus on the triggers in order to experience it at all.

Line 84 – I would like a comma after the (Thienot et al., 2014) reference
Line 95 – missing “the” before “immersive nature of ASMR”
Experimental design: The study reports original primary research within the scope of the journal. The research question is well defined, relevant, and meaningful, and the paper makes an excellent contribution to the growing literature on ASMR.

Enough information is included to replicate the study, and the methods are described with good detail. My only comment echoes the one in section 1 regarding clarifying the concepts of flow and mindfulness and their measurement, which has impacts for understanding the purpose of the study, the findings, and the methodology with regards to the constructs being measured. The following paper gives advice about reporting measurement and the relationship between constructs which the authors might find useful, e.g:

https://psyarxiv.com/hs7wm/
Validity of the findings: The statistical tests performed are appropriate, and replicable using the dataset provided.

One interesting question concerns the incongruence of the present findings and Fredborg et als (2017). I was intrigued by this, especially as both studies used the same measure of mindfulness. There appears to be no obvious difference between the sampling method, and both studies were adequately powered, as discussed by the authors.

However, the descriptive statistics might give us a clue. The means for mindfulness in ASMR participants in both studies are actually very similar: 3.34 (SD= 0.75) in the Fredborg data, and 3.21 (SD = 0.81) in the current data. It is the difference in the control participants that is more obvious. In the Fredborg study, the control participants had a mindfulness score of 3.02 (SD = 1.17) -  but in the present study, the control participants had a score of 3.28 (SD = 0.79). Investigating the raw data, I created histograms of the four distributions using the original data. (e.g. ASMR and control participants, for both studies, attached as a supporting document).

It seems that in the Fredborg study, the control group sampled a particularly high number of people with low MAAS scores (indicated by the positively skewed distribution), whereas in the present study, the control participant data appears to be slightly negatively skewed (indicating more controls reporting higher mindfulness scores, and very few controls reporting low mindfulness scores). The distributions for ASMR participants in both studies are normally-distributed.

It seems to me that the difference in the means and distributions of the control participant scores could explain the discrepant findings between the present research and Fredborgs, and (if the authors agree!) this could be presented as a potential explanation.
I agree with the recommendation to encourage further research on this question.

A second point I would like to see slightly more discussion of in the discussion is Flow, and its measurement. It was interesting to see that only 43% of participants reported Flow. Is this normal? How does this compare to other studies that have used this measure of flow? Have they also found similarly low percentage of people reporting it? If the amount is not similar to those reported in previous research, are there any reasons for this? A brief discussion on this would be helpful for other researchers reading the paper who may be interested in researching the relationship between ASMR and flow.
Additional comments: Overall the study makes an excellent contribution to the growing literature on ASMR, and the finding that absorption is a key element of the ASMR experience. In order of priority, the main suggestions to improve the manuscript would be:

1.	To employ a clearer definition of the construct of mindfuless in the introduction, and clearer discussion about how this construct (in the particular way the authors are conceptualizing it and measuring it with the MAAS) is related to flow and absorption. The paper by Van Dam et al (2018) will hopefully be of use.
2.	To clarify the definition of ‘flow’ and its measurement.
3.	To continue this conceptual clarification of the constructs in the discussion and conclusion section when interpreting the results and summarizing the findings.
4.	To fix the consistency of the statistical reporting.
5.	To consider the explanation of control group differences to explain the difference between the current findings and Fredborg et al.s, and include this if the authors agree.
6.	To add a bit of extra discussion regarding the measurement of flow, and whether 43% of people reporting it is consistent with other literature (and if not, suggest possible theoretical or methodological reasons why).


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: INCREASED ABSORPTION IN AUTONOMOUS SENSORY MERIDIAN RESPONSE
Review round: 1
Reviewer: 3

Output:
Basic reporting: Please see my comments regarding extra literature, framing of the paper, and other comments in  'General Comments for the Author'.
Experimental design: Please see my comments on extra methodological details required in 'General Comments for the Author'.
Validity of the findings: Please see my suggestions for statistical analyses, as well as interpretation, discussion of the limitations of the study in 'General Comments for the Author'.
Additional comments: This paper reports the results of an online survey examining the relationships between absorption, flow, and mindfulness in ASMR. When compared to control participants, ASMR sensitive participants reported significantly higher rates of trait absorption but not flow or mindfulness (although ASMR participants were significantly more likely to have experienced flow). Additionally, the intensity of ASMR experience was positive correlated with trait absorption, suggesting that those with more intense ASMR triggers are also more likely to become highly absorbed more generally (this is a particularly nice finding that I think could be emphasised more in the discussion).

There is a lot to like about this paper: it is well written, suitably conducted, and reveals interesting and important results with regards to both differences between ASMR and non-ASMR participants but also individual differences within the ASMR sensitive population. I especially appreciate the distinction made between flow and ASMR and between mindfulness and ASMR because these concepts have been conflated in previous work (despite anecdotal reports that ASMR is different from both mindfulness and flow). This paper helps to make clear the connection between these experiences may be their underlying association with the trait of absorption.

I have no hesitation in recommending this paper for publication following a few revisions which I outline below. Overall, this is an excellent paper and a pleasure to review – thank you for contributing to our growing knowledge of this exciting experience!

1) Unnecessary removal of data points.

The rationale for reducing the number of data points in the analyses (which is such a waste of valuable data from willing participants!) is not clearly justified. The group size imbalance is not substantial (59% ASMR) and it is not clear how such an imbalance would adversely affect the validity of results or the conclusions drawn. The approach used would make sense if the number of participants was specified a priori and once that number of ASMR participants were recruited then data collection stopped. However, to remove valuable data after collection simply to ensure that the numbers of participants in each group are equal is unnecessary at best.

It also is not clear how participant groups were matched according to age and gender (i.e., the procedure for this – was it done randomly?) - so that would need to be clarified if the authors choose to keep the analyses with the subsample of the data. If age and gender are factors of concern then why not include them as covariates in an analysis rather than deleting data to ensure that the control group are age and gender matched? Or at least demonstrate in advance that age and gender are related in a meaningful way either to the experience of ASMR or to the dependent variables (through appropriate statistical analyses).

The authors should re-run their analyses using the full data set and report these in the text in addition to, or instead of, what is currently reported. If age and gender are of concern then I would suggest demonstrating this through statistical means and including them as covariates in an ANOVA. At the very least I would want to know that the results remain the same whether the full or reduced data set is used.

2) Citing previous literature.

Given that ASMR is such a small field it is important to fully present all the existing evidence related to the subject matter of the paper. I would therefore suggest including reference to other aspects of personality related to ASMR (e.g., link to neuroticism – Fredborg et al., 2017 – Frontiers and Poerio et al., 2018 PloS ONE supplementary materials). Another substantial oversight is a paper by Roberts et al., (2018, Psychology of Consciousness) which directly examined the relationship between ASMR, absorption and flow. These results should be included in both the introduction and discussion sections.

3) Framing of investigation and ASMR.

The objective of the study should be more clearly and accurately defined throughout the paper. In the introduction it is framed as an investigation into what underpins the ability to experience ASMR and its psychophysiological benefits. However, in the first line of the discussion it is framed as elucidating whether ASMR is associated with an atypical personality profile. I don’t think the paper does either of these things conclusively so perhaps the study is better framed as an investigation into personality differences between ASMR experiencers and non-experiencers?

I also question the use of the phrase ‘atypical’ in the sense that ASMR is referred to as being linked to an atypical personality profile – why is the term ‘atypical’ used? This could be a bit misleading for readers. I would suggest more neutral phrasing like: ‘Trait ASMR has been consistently associated with a number of personality traits including…’.

4) Consideration of Limitations.

There should be a discussion of the paper’s limitations for readers to appreciate. Three obvious limitations spring to mind but there may be others.

1) Causality – due to the correlational nature of the research it isn’t possible to conclude that the trait of absorption predisposes people to experience ASMR or that it underpins the experience of ASMR. The results could reflect third variable explanations as well as reverse causality (e.g., the ability to experience ASMR makes people more likely to get fully immersed in other experiences; both absorption and the ASMR trait are underlined by another variable such as openness to experience or dissociation)

2) Self-selection – recruited participants are likely to have known about the ASMR community in advance and likely to watch ASMR videos. Perhaps these people are more likely than non-video watchers to be high in trait absorption? In the methods section the ASMR questionnaire asks whether participants watch videos online but the results are not reported (or I could have missed them – but please report % if they haven’t been included).

Because you have data on whether participants watch ASMR videos or not I’d be really interested to see whether there is a difference between these two groups in terms of absorption – if there isn’t that might go some way towards allaying the self-selection concern.

3) Verification of ASMR status. A common criticism of ASMR research is the self-verification of ASMR status. This paper (line 110) notes that additional questions were asked of ASMR respondents but it isn’t clear what these questions were or how they were used to filter out people who may not truly experience ASMR (did you remove any participants after examining the responses to these questions?).

Please could these be described in the paper in full (as it will be useful for other researchers)? It may also be helpful to refer to methodological recommendations on recruitment for trait ASMR research (see Hostler et al., 2019, Peer J).

5) More minor points.

-	Line 55: how does the atypical personality profile facilitate ASMR?
-	In the introduction it would be helpful to describe common triggers earlier on for readers who are unfamiliar with ASMR.
-	Either use ‘such as’ or e.g. but not both (this is in several places in the manuscript) e.g. line 70 and frequently in the methods section when describing example scale items.
-	Consistency: the paper flips between US and UK English spelling.
-	A parallel structure in the order of the results presented in text and Table 1 would be helpful for readers.
-	In the results section it would make sense to have the descriptive data described first (i.e. response to the ASMR questionnaire).
-	Please report exact p-values and 95%CI for effects.
-	Calculation of ASMR intensity score needs to be clearer: does it take into account number of triggers and intensity or just intensity of selected triggers? For example if I have 2 triggers which are very intense (rated 6) would my average be 6 or would the average include 0 for all the other triggers that don’t induce my ASMR? Variety of triggers and intensity of triggers seem like two separate measures so perhaps keeping them separate would add more to our existing knowledge of individual differences in the ASMR experience? Could the authors please clarify their method of calculating intensity (perhaps intensity isn’t the best description for this measure if it also includes a measure of number of triggers?)?


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: INCREASED ABSORPTION IN AUTONOMOUS SENSORY MERIDIAN RESPONSE
Review round: 2
Reviewer: 1

Output:
Basic reporting: No problem.
Experimental design: No problem.
Validity of the findings: No problem.
Additional comments: I am grateful to the authors for responding fully to my comments. The manuscript reads very well now, especially in light of the responses to the other expert reviewers.


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: INCREASED ABSORPTION IN AUTONOMOUS SENSORY MERIDIAN RESPONSE
Review round: 2
Reviewer: 2

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
Additional comments: The authors have done an excellent job of responding well to the points raised in my first review – thank you. As an exception they have not fully addressed the point regarding how the study is able to able to shed light on the mechanisms of ASMR/the framing of the paper. This has much to do with how some (minor) sections of the paper have been written which set up incorrect expectations about the inferences that can be drawn from the methods used.

The introduction is set up as trying to understand mechanisms but the nature of the study (correlation) can’t answer these questions. I appreciate that the point about correlation as a limitation is now mentioned but I think there needs to be greater clarity about what the paper is able to achieve from the outset.

In the introduction the following statement is made:
“However, it remains to be established what underpins the ability to experience ASMR and its psychophysiological benefits. One line of evidence suggests that ASMR-experiencers show a specific personality profile which may facilitate ASMR.”

It still isn’t clear what it is about personality that facilitates ASMR. I suggest removing these sentences and replacing with something like ‘Previous research suggests that there are personality differences between people who experience ASMR and those who do not’. That way the reader isn't being led to believe that the paper will be able to answer questions about mechanisms.

It would also help to avoid confusion for readers if there was a distinction between state and trait ASMR. The phrase ‘ability to experience ASMR’ is used a lot through the manuscript but it isn’t clear whether this is meant in state or trait terms (or both?). It would help to make this clear in the paper in case readers thought that the paper sheds light on why some people experience ASMR and others don’t.

At the end of the discussion the following statement is made:
“In summary, our findings contribute to the existing literature documenting individual differences underpinning ASMR by showing that absorption proneness may be an important factor contributing to the ability to experience ASMR and its therapeutic benefits.”

This sounds good but it is slightly misleading. The word underpinning and general phrasing are suggestive of a mechanistic understanding of ASMR which is not possible from the methods used. It is also not possible to make any conclusions about the therapeutic benefits of ASMR as this was not assessed. It would help to reword so that the contribution is not overstated and suggestive of a mechanistic understanding of ASMR.

I say all of this because the paper is likely to be read by the general public/media as well as scientists due to the popularity of ASMR. It is therefore important not to overstate the potential of the methods for answering big mechanistic questions like ‘why do some people experience ASMR and others don’t?’ in case the results are taken out of context.


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: INVESTIGATING THE POTENTIAL USE OF SENTINEL-1 DATA FOR MONITORING WETLAND WATER LEVEL CHANGES IN CHINA’S MOMOGE NATIONAL NATURE RESERVE
Review round: 1
Reviewer: 1

Output:
Basic reporting: One important point on this paper:
Although the paper is acceptable to publish in journal but I am not sure it fall within the scope of Peerj journal. In my idea it is suitable for a journal with remote sensing scope.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Although the paper is acceptable to publish in journal but I am not sure it fall within the scope of Peerj journal. In my idea it is suitable for a journal with remote sensing scope. But if editor believes it falls within the scope it is with minor revision accept.

The paper entitled “Investigating the potential use of Sentinel-1 data for monitoring wetland water level changes in China’s Momoge National Nature Reserve”  aims to systematically investigate the potential of using Sentinel-1 C-VV data to change detection of water level. The paper is presented in a good structure and it described the method and results clearly. Although with some more discussion it would be complete.

In addition some corrections are required as follow:
Introduction:
Although introduction provides valuable information for readers but it’s too long. Please shorten this section
Line 12-19: Please remove the repeated words same as: Wdowinski et al. (Wdowinski et al. 2004; Wdowinski et al. 2008)
Data
Line 131-134: Remove these lines, the OLI is known by readers.
Method
Line 168: Please remove “The method of selection of training samples was similar to that published in literature”. The refrence “(Jia et al. 2014) “ is enough.
Line 175: although MLC is most widely adopted parametric classification but it is old method, and in the recent papers the methos same as SVM, ANN and … are popular. Please remove lines 174-176.
Line 188-190: The references are old . In addition, 9 references are not required to describe these popular terms. Two references are enough.
Line 247: 2.4.5. Best-fit Analysis : please provide more information about Best-fit Analysis
Figures: Please increase the quality of figures. Some figures are not readable same as figure 11