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: LOCAL-SCALE DETERMINANTS OF ARBOREAL SPIDER BETA DIVERSITY IN A TEMPERATE FOREST: ROLES OF TREE ARCHITECTURE, SPATIAL DISTANCE, AND DISPERSAL CAPACITY
Review round: 2
Reviewer: 2

Output:
Basic reporting: This is the second time that I have reviewed this paper and upon reading it again, I still admire the robust statistical approaches the authors took to addressing spider beta diversity within this forest.  However, many of the same issues I had in my first review remain and new issues are now apparent with the addition of the map provided in the response to reviewers.  The specific details are outlined below:

Major Concerns
The overall structure of the paper fails to present the information in a clear and concise manner.  Within the response to reviewers, the authors provided very clear predictions with a very clear outline of how every test in the methods relates to a specific prediction.  This should serve as a template for be how the manuscript should be reformatted.

Additionally, it is unclear why spider vagility cannot be described in terms of dispersal, allowing for the paper to be framed within a larger ecological content rather than a spider-centric focus.

Finally, the discussion still unnecessarily reiterates results rather than focusing on the implications of the results. Ultimately, the length of the discussion can still be reduced by about 25% as it is the exact same size as it was in the first submission.
Experimental design: Both reviewers point out that the addition of three forest stands, for the purpose of expanding the variation in tree architecture, also introduces a confounding variable of stand age.  It is insufficient to assume that differences in tree architecture is the best explanation for differences in spider beta diversity considering the wide array of differences in forests of different ages.  Additionally, the map provided in the response to reviewers also makes it clear that these stands are spatially distinct confounding measures of tree architecture with not only stand age but also physical location.  Further consideration needs to be given to the role of stand age and the physical separation among these distinct forest stands before this manuscript is ready for publication.
Validity of the findings: No comment
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: LOCAL-SCALE DETERMINANTS OF ARBOREAL SPIDER BETA DIVERSITY IN A TEMPERATE FOREST: ROLES OF TREE ARCHITECTURE, SPATIAL DISTANCE, AND DISPERSAL CAPACITY
Review round: 3
Reviewer: 1

Output:
Basic reporting: The current version of the manuscript has been greatly improved. I am happy with the revision. I think that it is ready to publish.
Experimental design: No comments.
Validity of the findings: No comments.
Additional comments: No comments.


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

Input:
Title: NATURAL HISTORY AND MOLECULAR EVOLUTION OF DEMERSAL MEDITERRANEAN SHARKS AND SKATES INFERRED BY COMPARATIVE PHYLOGEOGRAPHIC AND DEMOGRAPHIC ANALYSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: - language very good throughout the manuscript
- background information includes relevant literature
- figures are all relevant and look appropriate
- the hypothesis can be tested using the applied analyses
Experimental design: - the research question is well defined, whether there is a phylogeographic pattern in four elasmobranch species across the Mediterrenean and if the Sicilian Channel provides a strong biogegraphical barrier
- the study is based on a very dense sampling studying a high number of individuals and 3 mitochondrial markers
- methods are explained in detail, but some of those are, in my opinion, not required to test the hypothesis and should be considered with caution (e.g., BSP; see comments in the attached PDF)
Validity of the findings: - the results are robust and are partly congruent with former published studies
- conclusions could be improved, more discussion is needed why the present results differ from other studies on the same species
Additional comments: See attached PDF


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: NATURAL HISTORY AND MOLECULAR EVOLUTION OF DEMERSAL MEDITERRANEAN SHARKS AND SKATES INFERRED BY COMPARATIVE PHYLOGEOGRAPHIC AND DEMOGRAPHIC ANALYSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this article, the authors perform a comparative phylogeographic analysis on two pairs of closely related elasmobranch demersal species (two skates and two catsharks) in the Mediterranean Sea and adjacent Atlantic, by using sequences of three mitochondrial DNA gene fragments. Although the study is quite interesting and new knowledge is presented, the paper has several flaws that need to be addressed.

The English language of the text, although generally good, should be improved and the manuscript would benefit if proofread by a professional. There are several points where the phrasing seems incorrect: for example in line 46 “paired phylogenetically and ecologically related species” sounds somehow incomprehensible (do you mean “pairs of”?); in line 228 you probably mean “few”=a small number and not “a few”=some; in line 300-301 “the events that overturned the planet” sounds as if an asteroid hit the planet and turned it upside down.

The introduction lacks clear scope, is not coherent and the first part as well as lines 32-37 are quite general and not directly related to the findings. I suggest, after you clearly define the aim of the study (see comments on the next section), to rewrite the introduction in order to better justify your study and to give more details on the previous knowledge directly related to your study (e.g. previous findings on elasmonbranch phylogeography, phylogeographic barriers in the Mediterranean). The authors state in lines 43-44 that “the role of the Sicilian Channel as a partial barrier to elasmobranch dispersal rather than a transition/genetic admixture area is still under debate”, without providing any literature. There are also references, like Tsigenopoulos et al. (2003) (line 26), which deal with freshwater fishes and not marines ones, as it is stated in the introduction.

The structure of the article seems to conform to an acceptable format. Figures are relevant to the content of the article, of sufficient resolution, and appropriately described and labelled,although they contain few grammatical errors in the labels (e.g. in Fig2-5, you should write “haplotypes” (in plural), the “Blue dashes” are actually “Blue dots”, and “relative” seems superfluous).
In Fig.1 you should include on the map the names of the sea regions mentioned in the manuscript. In table 2, the geographic area of the south-western Mediterranean (N. African coast) is not the Alboran Sea. The Alboran Sea is between the Straits of Gibraltar and the Almeria-Oran front. Please correct throughout the text and tables. Moreover, in the Adriatic Sea it is included a sample from the NW Ionian Sea.

The raw data (DNA sequences) have been deposited in GenBank (accession numbers are provided in Table 1) and they are already publicly available. However, they do not contain any metadata (sampling site, collection date), are practically useless for other scientists and cannot be used for checking the results. The authors should provide a supplementary table with the metadata of the sequences (species, sample name, sampling site with coordinates if possible, collection date and accession numbers for each gene) and it would be desirable to put this information in GenBank as well.
Experimental design: The research question (i.e. the aim of the study) is not clearly defined, nor the knowledge gap being investigated is clearly described. As a consequence, the aim of the study, as described in the introduction, is not fully concordant with the analysis followed and the discussion. The authors state that their aim is “to assess phylogeographic structures, infer demographic patterns, and testing for common natural histories and environmental/climatic factors driving their evolution” (L59-71). Regarding the first aim, what they actually do is to focus almost exclusively on whether the Sicilian Channel is a barrier to gene flow for these species (absolute, partial?), ignoring other potential barriers, such as the Almeria-Oran front and the hydrographic isolation of the Adriatic Sea. The AMOVA analysis focuses on the East/West subdivision,while no pairwise comparisons (e.g Φsts) are performed. If this is actually their aim, it should be clearly described and explained in the Introduction, although it would limit the scope of the article. Otherwise, they should examine more thoroughly the genetic structure/differentiation of the species and compare the observed patterns.
Regarding the last aim (“testing for common natural histories and environmental/climatic factors driving their evolution”), this is not sufficiently addressed.

The investigation seems rigorous and performed to a high technical & ethical standard, although the sampling scheme misses some areas of the Mediterranean Sea, like the Aegean Sea and the sample sizes are rather small.
Validity of the findings: The Discussion is not well written, the interpretation of the results is sometimes confusing and not very convincing.
More specifically, the results of the phylogeographic analysis sometimes seem not to be properly interpreted and not to be concordant with previous studies on the same species. Especially for S. canicula, the results contradict previous findings (Gubili et al. 2014, Kousteni et al. 2015), which demonstrated strong genetic structure, but the authors do not try to explain this discrepancy (different sampling scheme, inadequate sample size?). Moreover, all haplotypes of S. canicula but one in the current study are region-private, which is an indication of strong genetic differentiation, but it is also quite peculiar and it should be explained (biased sampling scheme, higher resolution of the marker?). The authors should also take into account that they lack samples from the Aegean Sea, which are genetically quite distinct from that of W. Mediterranean.
For R. clavata, the authors claim that their findings are “somehow unexpected since previous studies revealed a relict and unique cytochrome b Mediterranean haplotype (Chevolot et al., 2006)”, without elaborating further. However, the current findings seem to be concordant with that of Chevolot et al. (2006). The only difference is that given the higher variability of the marker used and the more extensive sampling in the Mediterranean, the authors were able get higher resolution and to reveal more, closely-related haplotypes and a couple of small differentiated clades.
In line 277, the authors claim that “rajid skates exhibited sharply different phylogeographical patterns” compared to catsharks. However, R. clavata did not exhibit any strong phylogeographical pattern unlike R. miraletus and the partitioning of variation according to AMOVA was similar to that of S. canicula.
Overall, the authors should re-examine the interpretation of their results and take into account previous findings.

There are points in the discussion that are rather confusing and not very meaningful. In lines 223-226, you refer to dispersal of catcharks “between the northern (larger) or southern (narrower and steeper) coastal shelves of the Mediterranean” which “contribute to the admixture of both catshark populations”. Do you mean populations of both catshark species? Otherwise, which two populations do your refer to and what do you try to explain here?
In lines 251-261, you try to explain why for some teleosts the Sicilian Channel is an effective barrier and not for the four elasmobranch species studied, by implicating seawater temperature and salinity discontinuities that affect the dispersal of early-life stages in bony fish. However, for the great majority of the teleosts of the Mediterranean, the Sicilian Channel is not an effective barrier as well. The few bony fish species that exhibit this east/west divide are mostly benthic (e.g. flat fish), or have relict distribution in the northern parts of the Mediterranean (sprat).
In lines 262-265 you try to relate the discordant phylogeographic patterns of the studied species with the recent phylogenetic origin of catsharks (in which way? Do you also have any evidence for the phylogenetic origin of the two skates? ).

The final conclusions are too vague.
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: NATURAL HISTORY AND MOLECULAR EVOLUTION OF DEMERSAL MEDITERRANEAN SHARKS AND SKATES INFERRED BY COMPARATIVE PHYLOGEOGRAPHIC AND DEMOGRAPHIC ANALYSES
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This is a very well written and well organized paper. The language is professional and clear throughout. The introduction gives sufficient background and references are appropriate. The structure and length of the paper is adequate for the subject matter and there are relevant hypotheses relating to environmental conditions over time and the phylogeography and historical demography of four target demersal elasmobranch species.
The study is original, the questions are well defined and answered, the methods are appropriate and well described. The data analysis is robust and well presented and the conclusions are well supported by the results.
Overall this paper was a pleasure to read I have nothing to add that would make it better.


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: NATURAL HISTORY AND MOLECULAR EVOLUTION OF DEMERSAL MEDITERRANEAN SHARKS AND SKATES INFERRED BY COMPARATIVE PHYLOGEOGRAPHIC AND DEMOGRAPHIC ANALYSES
Review round: 2
Reviewer: 1

Output:
Basic reporting: See "General comments for the author"
Experimental design: No changes
Validity of the findings: No changes
Additional comments: I appreciate the effort that went into the Discussion to better compare and discuss the present findings with the results found in the literature. However, I also find that the authors included so many examples and got lost in many details, for example, identifying particular Aegean haplotypes in specific species, that are not relevant for the overall discussion. This makes it a little bit difficult to read and it is not all needed to discuss the role of the Sicilian Channel. Also, and unfortunately, I had to invest much more time in understanding and rephrasing the Discussion section as the English was not as Professional as in the previous manuscript (see my comments in the attached PDF).


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: NATURAL HISTORY AND MOLECULAR EVOLUTION OF DEMERSAL MEDITERRANEAN SHARKS AND SKATES INFERRED BY COMPARATIVE PHYLOGEOGRAPHIC AND DEMOGRAPHIC ANALYSES
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Thanks for the revision, looks fine to me now!


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: 60S DYNAMIC STATE OF BACTERIAL RIBOSOME IS FIXED BY YEAST MITOCHONDRIAL INITIATION FACTOR 3
Review round: 1
Reviewer: 1

Output:
Basic reporting: The language needs substantial improvement, the citations are sufficient.
Experimental design: The rational for the experiments are not well-elaborated and the physiological significance is unclear. The experimental design is poor and lacks obvious controls.
Validity of the findings: The manuscript revolves around two sets of experiments that are not vaildated by additional, well-approachable experiments to determine kinetics of subunit dissociation. Data are therefore not robust and do not support the conclusion or the proposed model.
Additional comments: More work will be required to elaborate the findings of this manuscript. Standard methodology can be applied.


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: 60S DYNAMIC STATE OF BACTERIAL RIBOSOME IS FIXED BY YEAST MITOCHONDRIAL INITIATION FACTOR 3
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is written with clarity with appropriate structure and context and the article meets the requirements for providing raw data for PeerJ.
The authors provide a series of experiments including bacterial growth curves, ribosome profiles augmented with recombinant proteins and molecular modelling. For the most part the figures are clear and easy to follow.
Experimental design: The original aims are clear - the authors wished to see if a yeast mitochondrial factor can complement for a bacterial initiation factor by analogy to a related study where this was done with a mammalian factor.  The study runs a risk of being phenomenological, as it is not clear that the entity they describe has any relation to physiological complexes that might actually form.

Issues related to technical rigour and description of methods are as follows:

1.	Growth curves for bacterial cells do not appear to have error bars or they might not be very large. The raw data suggest that a number of technical replicates were made but it is not clear how this relates to the data in the graph – were mean values and standard deviations calculated? And plotted?

2.	The western blot in Fig. 2B is used as evidence that Aim23deltaNdeltaC cannot bind to the ribosomal subunits. These data are incomplete. The authors need to show the input samples as well as the samples taken from the gradient, particularly as they only sample two peaks. How are we to know that the researcher who carried out the experiment didn’t simply forget to add the reagent to those samples?
Validity of the findings: On the basis of their data, the authors conclude conclude that the yeast mitochondrial initiation factor is stabilizing a new “60S” form of the ribosome that is locked in pre-dissociated state. There are some issues with this interpretation, mainly because it relies on just a few observations from one kind of experiment and there are no orthogonal methods to support these data. It is important that the authors tone down their claims as the language used is far too strong.

1.	It is not clear what the molecular modelling brings to the study as the proposed model has not been validated experimentally. The authors should avoid discussing the model as if it has high precision e.g.

Line 357-9 ‘This has been confirmed by the molecular modelling … terminal extensions of Aim 23p … have been shown to interact directly with the core protein part which probably makes Aim32P “fixed” on the small subunit.’

2.	The observation that a 60S particle is formed is based on the ribosome profiling curves presented in figure 2. The apparent 60S peak might really be the sum of the 50S and 70S curves, suggesting that it is not a new entity that is being formed, but rather Aim23p is inefficient at subunit dissociation. For a 60S particle to form it suggests that the ribosome would become more compact compared to the 70S to have a smaller hydrodynamic radius. It is hard to imagine how this would occur in the context of all of the structural data available for ribosome particles. Furthermore, if Aim23p were stabilising a dissociation complex, one might expect that it would act as a dominant negative in cells, yet this is contrary to what the authors observe [line 371-2 ‘… the presence of even large amount of Aim23p in E. coli cells with physiological amount of the cognate IF3 has no effect on bacterial viability…’]. One would also expect to see more 60S at higher concentrations of Aim23p and again this is contrary to what the authors observe (Fig 2B).

Unless there are orthogonal data to support the existence of the 60S particle directly, it is not appropriate to state that:

Line 209 ‘…we have to hypothesize that Aim23p somehow affects the whole ribosome structure…’
Line 248-9 ‘The only possible explanation of this phenomenon is that “60S state” is indeed subjected to dissociation easier than the normal 70S state.’
Line 354 ‘…the 60S intermediate dissociation state has been for the very first time fixed by adding a protein to the ribosomes…’

These statements should be toned down to give a more nuanced interpretation.
Additional comments: no comment


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

Input:
Title: INSOMNIA AND INTELLECT MASK THE POSITIVE LINK BETWEEN SCHIZOTYPAL TRAITS AND CREATIVITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The current manuscript reports on a study that investigates whether creative ability is explained by variation in schizotypy and schizotypy-related health observations (general health complaints, insomnia). This study question is to me exciting, and I was very pleased to be invited reviewing this manuscript. The authors observed that indeed the link between creativity and schizotypy was moderated by insomnia and general health, but not always in the expected direction. Thinking as to how and why these results have occurred, I stopped reading focussing on the first sections instead. I feel there is too much to be tested, verified and calculated before going to a discussion.

To reiterate, the study question is interesting. I am also not worried about the methodology. I am equally pleased about the sample size. I have theoretical and data processing suggestions I strongly advice the authors to take into consideration.

The introduction would profit from some more rigorous implementations of the previous literature. When reading this section, I had the impression the authors are rather informed on sleep but less so on schizotypy. They used the o-life questionnaire, in the abstract they refer to the impulsive component, which is, however, missing in the result section. If they include the impulsive component, they should have a good think in which theoretical concept they consider it. Indeed, many schizotypy researchers would consider the impulsive non-conformity component not to be representative of schizotypy but to rather reflect borderline tendencies or also hypomanic ones. Also, cognitive disorganisation is often thought to largely reflect social anxiety / Neuroticism. The authors cited our study (Mohr and Claridge). In the same issue, we published our contribution the authors can find many important other ones that summarize the latest trends and considerations in the schizotypy literature.

Having said so, if the authors take our contribution serious (Mohr and Claridge), they should have tested for a much different assumption, i.e. that positive schizotypy alone is linked to creativity. If so, they should have selected participants who are high in positive schizotypy and relatively low in the other dimensions. One could then also assume that these sub-group should have lower insomnia and health complains problems, because they have less cognitive disorganisation and introvertive anhedonia. The reasoning, the theoretical part of the introduction could be turned into a much more literature driven development of interesting research questions the authors can tackle. Indeed, approaching the data the way suggested here would allow them arguing that previous studies were heterogeneous because this reasoning was not considered. In general, I would have liked to see more recent studies on schizotypy and creativity, and also more on health related issues. I consider it appropriate to refer to the work by Kerry Schofield and Gordon Claridge. I also feel the recent work by Maggie Webb could be accounted for, Andreas Fink is always active in the domain of creativity. A deeper digging into the literature on creativity and schizotypy would profit this interesting study, polishing the reasoning and shaping a priori predictions.
Experimental design: no comment
Validity of the findings: The data and analysis approach: I consider regressions a good choice. Personally, I do not find it always the easiest choice to decide which type of regression to use. The current authors chose a step-wise hierarchical regression. I am not too sure why they chose this version and not one in which all variables were entered at the same time. Spontaneously, I would have expected them to add “confounds” to the first step to continue working on the variance in the second step when the contribution of the variables in the first step have been eliminated. Now, I am not sure whether they consider the schizotypy and health related information to be equally important or whether it would be better to think again in a stepwise fashion (the authors might have wanted to achieve so, they report on step 2a and 2b). Is it the case that they wanted now to first account for the variance explained by schizotypy and then the other variables or vice versa? What would be the logical reasoning? Was collinearity accounted for? Where is the information on the skewedness of the variables? Also, I got very confused about the presentation of the 3-way interaction of the variables in e.g. Figure 3. I would consider it more appropriate to present the data along the x-y-z axes. Yet, the results as presented do not indicate that there is a 3-way interaction. I doubt that the current treatment of the results is appropriate. Yet, I do not claim to be a statistical expert and would advise the authors to consider the advice of a statistician. But before doing so, I consider it more important to be sure about the previous literature and the precise study question. Knowing this will allow the choice of statistical analysis.

At this point, the authors would also change Figure 1 into a Table. Ideally, one would see the correlation coefficients and the respective p-values, e.g indicated by stars. The colour coding does not seem very pertinent to me. Likewise, I found it difficult to see the relevance of the results shown e.g. in Figure 4. A more informative table on the regression results would be more comprehensive to me.

A very important point to me is the lack of expected findings. One can look for the significant ones and explain them, but in my view, one should equally look at those who were not significant. For instance, one should have expected a relationship between positive schizotypy and divergent thinking as well as the remote associates tasks. Yet, no such result was observed. Why not? How does the current study diverge from studies that found such links? Moreover, where relationships were found, we were mainly dealing with self-report measures. Are the current results a response biases finding? Here studies on schizotypy and signal detection theory are informative. Schizotypes not being higher in one thing or another, but being “simply” more inclined to say “yes”. Thus, not a higher d-prime, but a lower response criterion.

Some “minor” observations.
1)	In the first paragraph, it would be appropriate to also cite some seminal studies here. Ettinger’s study is more about cognitive functioning. When it comes to the concept of schizotypy other references are more appropriate, either the classical ones by Meehl or Claridge, but also overview and theoretical studies on the construct(s), e.g. by Tom Kwapil or also Lenzenweger.
2)	The study by Acar and Sen seems very critical to the current study and some more information what was actually found by these authors would be perfect to learn about. I cannot imagine that the study had not more crucial findings that are relevant to the current study.
3)	Data clearning under participant section would better go to the data analysis section. Using age in the regression analysis in a first step would also mean that no participant needs to be excluded for age.
4)	The authors have an excellent distribution of gender. Gender differences are known for schizotypy, and thus, it should be added to the regression analysis.
5)	I am not sure what the two forms of the verbal divergent thinking mean. If the outcome of the coding was not so good for form 2, why using the data of this form?
6)	Control fluency for total number of ideas. In the case of the current measures, “creative” ideas might be higher because people created more ideas, or even better, they provided a higher number of mainly creative ideas. Thus, when calculating the number of original ideas as a function of the overall output, the proportion is a more meaningful variable.
7)	How was the study introduced?
8)	What else was assessed in this study? Probably the current reasoning would profit from controlling for other variables the authors have assessed. Do the authors have former drug use (e.g. alcohol, cannabis, nicotine – for which we found a role on the link between schizotypy and cognition).
9)	For the sleep analysis, did the authors assess objective measures of sleep? Is it not the case that the subjective sleep appreciation and actual sleep measures frequently deviate substantially?
Additional comments: I hope my observations will help the authors to further work on their manuscript.
Christine Mohr


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: INSOMNIA AND INTELLECT MASK THE POSITIVE LINK BETWEEN SCHIZOTYPAL TRAITS AND CREATIVITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Article raises and reports on an important consideration in creativity/schizotypy research: that of the effect of sleep disorder on cognitive control, and thus the role that impacted control might have for creativity and schizotypy.

***INTRODUCTION***

1) schizotypy as a multi-dimensional construct that is dimensionally associated with creativity
2) creativity as a multi-dimensional construct which is impacted by cognitive control
3) Link between schizotypy/ sleep/ cognitive control/creativity

Consider:
- Insert a paragraph on link between schizotypy and creativity through cognitive control before the paragraph on sleep. This will enable a stronger rationale for sleep/creativity/schizotypy through cognitive control.
Paragraph 3 currently has unclear logic. It outlines the link between sleep disorders and schizotypy, and states "therefore, we can assume" an averse effect of sleep on creativity. Clarifying the role of cognitive control may attenuate this.
The following paper may help in elucidating here: Carson, S. H., Peterson, J. B., & Higgins, D. M. (2003). Decreased latent inhibition is associated with increased creative achievement in high-functioning individuals. Journal of Personality and Social Psychology, 85(3), 499–506. https://doi.org/10.1037/0022-3514.85.3.499

- Consider differentiating the type of creativity that sleep disorder is likely to affect (e.g., do you expect the same or different effects of schizotypy/sleep on convergent vs. divergent thinking? (i.e., arguably CRAs vs. DT)

(METHOD and RESULTS dealt with in Experimental design and Validity)

** DISCUSSION **
1) Reports results:
positive schizotypy associated with CAQ, when controlling for general mental health.
disorganised schizotypy positively predicts remote association problem solving performance, if insomnia partialled out.
no dimension of schizotypy  associated with fluency and creativity of divergent thinking, not even when the effect of general mental health or insomnia was statistically controlled.

2) Support for positive schizotypy & CAQ - Rawlings and Nelson; Holt.
Consider also including discussion of the role of intelligence in creative achievement - as you note there may be buffers for sleep deprivation (e.g., Jauk et al. 2014 - included below)

3) Positive association between disorganised schizotypy and CRAs.
The speculation underlying why this might be the case is reasonable (i.e., controlling for negative effect of lack of sleep enables a facilitative effect of disorganised schizotypy through an extended semantic search). This is an interesting and possibly very important finding. However, as noted by the authors, this finding is inconsistent with a meta-analysis conducted by Acar and Sen (2013). It is also inconsistent with more recent findings (e.g.,  Webb, Little, Cropper and Roze, 2017 - included below). Given the evidence to the contrary, the likelihood that this is a statistical artefact seems quite possible, and replication is definitely required before strong claims can be made.

4) No association between schizotypy and DT.
Reviewer speculation: Evidence indicates that unusual ideas (originality) is most consistently associated with psychoticism (e.g., Acar & Runco, 2010), which is associated with positive schizotypy (as Acar and Sen state in their 2013 meta-analysis). Is it possible that, because uniqueness of ideas is not being scored in this study, this is the reason that there is no observed relationship between schizotypy and DT? Re-scoring the data according to fluency, flexibility, and originality may change the results - would perhaps be interesting to compare.

Further research to consider:

Acar, S., & Runco, M. A. (2012). Psychoticism and Creativity: A Meta-analytic Review. Psychology of Aesthetics, Creativity, and the Arts, 6(4), 341–350. https://doi.org/10.1037/a0027497

Burch, G. S. J., Pavelis, C., Hemsley, D. R., & Corr, P. J. (2006). Schizotypy and creativity in visual artists. British Journal of Psychology, 97(2), 177–190. https://doi.org/10.1348/000712605X60030

Fink, A., Slamar-Halbedl, M., Unterrainer, H. F., & Weiss, E. M. (2012). Creativity: Genius, madness, or a combination of both? Psychology of Aesthetics, Creativity, and the Arts, 6(1), 11–18. https://doi.org/10.1037/a0024874

Jauk, E., Benedek, M., & Neubauer, A. C. (2014). The road to creative achievement: A latent variable model of ability and personality predictors. European Journal of Personality, 28(1), 95–105. https://doi.org/10.1002/per.1941

LeBoutillier, N., Barry, R., & Westley, D. (2014). The Role of Schizotypy in Predicting Performance on Figural and Verbal Imagery-Based Measures of Creativity. Creativity Research Journal, 26(4), 461–467. https://doi.org/10.1080/10400419.2014.961778

Webb, M. E., Little, D. R., Cropper, S. J., & Roze, K. (2017). The contributions of convergent thinking, divergent thinking, and schizotypy to solving insight and non-insight problems. Thinking & Reasoning.

Zabelina, D. L., Condon, D., & Beeman, M. (2014). Do dimensional psychopathology measures relate to creative achievement or divergent thinking? Frontiers in Psychology, 5(SEP), 1–11. https://doi.org/10.3389/fpsyg.2014.01029

** GENERAL WRITING **
Writing is generally clear and concise. A few instances in which statements could be made clearer still. Please see the following for persnickety corrections:

Line 53: If the claim is "often regarded", consider including more than one study that uses it as such.

Line 59  the grammar within the phrase "loosened thinking, speech, and inadequate emotional reactions" does not make clear that disorganised speech is part of loosened thinking - consider "loosened thinking and speech" to clarify.

Line 75: "Although positive schizotypal traits may have benefits in the non-clinical population, some of the individuals with high schizotypal traits face with subclinical mental-health problems (e.g., anxiety, insomnia, depression, diffuse somatic complaints)" - this seems a little strong. Consider revising as "are associated with subclinical mental health problems", and note studies in which this is the case.

APA errors (e.g., citations not listed in reference list author within brackets/ use of & outside of brackets)
89, 93, 156, 268, 272,
Experimental design: Research questions:
Well defined, relevant, meaningful

**METHOD**

Generally well written and clear, but would appreciate clarification of the following:

== Divergent thinking measures:
Given only two forms of Just Suppose test are implemented, it would be nice to know what the two questions were.

Line 143: Authors report selecting 10-10% of ideas - is this the true range?

== CRAs:
Who developed the Hungarian form of the CRAs? (Bowden and Jung-Beeman provide an English test)

== Sleep measure:
Would be nice to have an explanation for why a sleep *questionnaire* used, when the rationale for investigating sleep was built regarding physiological measures. Might a questionnaire produce a different effect/relationships compared to physiological indicators?
Validity of the findings: Standards of PeerJ generally met.

**RESULTS**

Decisions regarding missing/filtered data are clearly set out. Data analysed in a fitting manner.

Request for further information regarding analysis of compound remote associates: what was done with time-outs vs. incorrect responses? Loose-associative thinking, perhaps exacerbated by lack of cognitive control, could lead to inaccuracies in CRAs.
Additional comments: This study has clear implications for the literature. It would be nice if there was a replication included in this, and if there were intelligence measures/other convergent thinking tasks to compare with the CRAs and DT measure. However, that seems a task for future research, which I for one will be excited to read.


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: METABOLIC MARKER GENE MINING PROVIDES INSIGHT IN GLOBAL MCRA DIVERSITY AND, COUPLED WITH TARGETED GENOME RECONSTRUCTION, SHEDS FURTHER LIGHT ON METABOLIC POTENTIAL OF THE METHANOMASSILIICOCCALES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is very clearly formulated, logically structured, well-referenced, and uses figures of good quality. It is therefore easy to follow.
Experimental design: The experimental design is excellent and outlined in a detailed manner that will be helpful to researchers performing similar metagenomic-marker gene based analyses in the future. The importance and advantage of the proposed approach over computationally even more intensive screening methods are clear.
Validity of the findings: The findings are valid, and the authors do not overstate the importance of their findings.
Additional comments: Title:
The term "metabolic versatility" in the title suggests to this reader the ability to catabolize a wide spectrum of substrates or perform active metabolism under a wide range of environmental conditions, neither of which were reflected in the findings. I suggest replacing "metabolic versatility" witha more neutral term, e.g. "metabolism".

Abstract:
The abstract is almost exclusively focused on the method and its potential applications. Since the entire Discussion is devoted to the analysis of metabolic capability and the title also points out the important role of metabolic reconstruction in this manuscript, I suggest adding 2-3 sentences on inferred/potential metabolic traits here. This should include a cautious mentioning of the presence of genes that could enable aceticlastic methanogenesis, since this is an important finding even though physiological studies are necessary to demonstrate this form of catabolism in the actual organism. In turn, other parts in the abstract, e.g. the introduction of the method, details on the methodology, could be made more concise or streamlined to only feature information that is essential for a general understanding of the approach used.

L. 12 in Abstract: unclear what is meant with "understudied". Please use a more precise term.

Introduction:
L. 65-66: this sentence is too strong. mcrA genes are excellently suited for the reconstruction of taxonomic affiliations except in highly divergent phylogenetic clusters since mcrA has never been laterally transferred (as far as we know), there is a vast database of mcrA genes that have been taxonomically assigned, and methane-cycling Archaea are among the best physiologically and metagenomically characterized groups of anaerobic microorganisms. This sentence generally applies to many less-studied, less-conserved, and more frequently laterally transferred metabolic marker genes, but not necessarily to mcrA.

L. 91: again, unclear what is meant with "understudied". I suggest using a more objective and precise term, e.g. "physiologically unexplored" or simply "uncultivated".

Results:
L. 253-267: this literature review belongs into the Introduction, e.g a new paragraph inserted before the final paragraph of the Introduction.

Discussion:
This reads largely like a mixture of results and interpretation (discussion). I therefore suggest merging the Results and the Discussion into Results & Discussion, if this is allowed in PeerJ. Alternatively, all descriptive parts of the current Discussion can be separated from the more interpretive parts (e.g. concerning metabolic capabilities) and moved into the Results section.


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: METABOLIC MARKER GENE MINING PROVIDES INSIGHT IN GLOBAL MCRA DIVERSITY AND, COUPLED WITH TARGETED GENOME RECONSTRUCTION, SHEDS FURTHER LIGHT ON METABOLIC POTENTIAL OF THE METHANOMASSILIICOCCALES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript “Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds light on metabolic versatility of the Methanomassiliicoccales” by Daan Speth and Victoria Orphan deals with the directed mining of public databases for mcrA genes in order to investigate the global importance of methanogenesis. Apart from some minor questions, I find the manuscript technically sound and the results justify the authors’ conclusions. The results are of substantial novelty, particularly, as the authors additionally recovered a previously unknown genome from the order of the Methanomassiliicocci and provide insight into its metabolism. Their findings highlight differences in previously described genomes and expand the known metabolic versatility of Methanomassiliicocci with the potential for aceticlastic methanogenesis. My major criticism is related to the citation of original literature in the introduction and the structuring of Results and Discussion section. I recommend a combined “Results and Discussion” section for this manuscript, if this is possible according to the journal style. Apart from these issues and the specific comments listed below I enjoyed reading this manuscript and congratulate the authors on this nice piece of research.
Experimental design: The experimental design is - apart from a few issues stated in the detailed comments below - state-of-the-art.
Validity of the findings: The data is robust. Particularly the fact, that the authors reconstructed full genomes to underpin their novel, gene-based findings is laudable.
Additional comments: Specific comments:
L 35: Please add a citation for genome-resolved metagenomics: Tyson et al., 2004 Nature.
L 38: This reference seems out of place; moreover, it is a review. Would be good to cite the original paper that performed metabolic predictions from reconstructed genomes from metagenomes (Tyson et al., 2004).
L 51: please specify if these genomes were redundant, i.e. from samples from the same environment. Would be good to give the number of different Methanomassiliicocci genomes.
L 59: Thomas et al. were not the first to describe binning of genomes. Other examples are Dick et al., 2009 in Genome Biology, in which scientists around Jill Banfield described k-mer based genome binning.
L 62: Delmont et al. were not the first to state that genome-resolved metagenomics necessitates manual curation. Please update citation.
L 58-66: The authors should also here (or elsewhere) discuss the disadvantage of their approach. For instance, the presented technique is limited to one specific gene and its diversity in public databases that provide the seed for the searches.
L 72-74: A citation for this statement is needed. Experience showed that genomes from metagenomes can be assembled and binned if they have at least an average coverage of ~7x, in some instance genomes with an average coverage of ~4x was successful. If a gene is recovered with a coverage <4x, how reliable is the reconstruction?
L 83: Scheller et al were probably not the first to describe that mcr gene products catalyze the last step in methanogenesis. Please provide a (better) reference here in addition to the citation for the initial step in ANMEs.
L 90: in L 86 the authors state that a substantial part of the diversity of mcr genes has been overlooked since multiple new organism groups have recently been discovered. So why do the authors restrict their analysis to the clade of Methanmassillicocci? That group is already known and has cultivated representatives. The point that I’m trying to make is, that the statement in L 86 might be a little bit too enthusiastic compared to the results that the authors got.
L 129: The authors state that it took 4 months to process the data. In the following sentence, they state how they sped up the process. How much time did it take after improving the scripts?
L 129: The authors only use the forward sequence for their analyses. However, they claim (L 72-74) that their process is able to detect functional genes of low abundance. This might actually not be possible by discarding 50% of the information available.
L 133: Why do the authors use DIAMOND? It is by far the fastest blast search tool when searching large datasets, but there are tools that use Hidden Markov Models to search read databases and they are tremendously fast. Example: “Short-Pair” in BMC Bioinformatics. 2017; 18(Suppl 12): 414. That process also uses paired-read information.
L 146: Why did the authors use IDBA_UD? Apart from the fact that it generally necessitates a tremendous amount of RAM, it is also very slow. The only advantage over very fast contigers like megahit is, that IDBA_UD is a scaffolder. But scaffolding is not useful for the approach the authors have chosen, since they specifically look for a fully assembled metabolic gene (mrcA). In contrast, the authors use Megahit for assembly of the draft genome, which could substantially benefit from scaffolding. It is recommended that the authors revisit the bioinformatics process as it is described in the paper.
L 147: Please indicate which mode you used for Prodigal (meta?).
L 150: Why were the mcrA genes of Syntrophoarchaeum not added in to the original database since it might have enhanced the detection of organisms related to those?
L 152: Please provide information on which model you have used for your ML tree. Was bootstrapping performed?
L 170: Please specify parameters for RAxML. Additionally, please justify the models that you used for the ML algorithm.
L 189-195: Please provide detailed information on the parameters used for each bioinformatics tool. Generally, the documentation of the different bioinformatics tools used in this manuscript is poorly described.
L 195: Please provide detailed information on how you curated the genome annotation.
L 196: please submit the genome to a public database. Your research benefits from public databases so it would be great to have your genome also in these databases for other researchers.
L 214: Here is the explanation for the question I asked for L 150. Maybe also explain in L 150?
L 202-219: This seems rather a discussion than a results section and it is also quite repetitive regarding the introduction.
L 265: How did you assess the environmental origin of your samples? Did you use a computational method?
L 283ff: The Discussion section rather seems to be a Results section since most of the text states new results on the MALP genome analysis.
L 348-349: please add citation for membrane complexes.
L 349-350: partial sentence, please rephrase.

Figure 1:
Please add commas to the value “12005048” to improve readability.

Figure 2:
Some sequences have zero sequences from PCR and zero sequences from metagenomes. How is this possible? Were they only represented by a genome sequence from an isolate? Please explain in the text.
C: Please specify abundance of sequences based on PCR. Is this from amplicon surveys? During Sanger times, people sometimes only submitted one representative sequence per cluster. Since I guess this has not been taken into account, the authors should spend a few more words on what this abundance actually means and what type of data is the basis for their analysis.


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

Input:
Title: METABOLIC MARKER GENE MINING PROVIDES INSIGHT IN GLOBAL MCRA DIVERSITY AND, COUPLED WITH TARGETED GENOME RECONSTRUCTION, SHEDS FURTHER LIGHT ON METABOLIC POTENTIAL OF THE METHANOMASSILIICOCCALES
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment.
Validity of the findings: no comment.
Additional comments: This work was to develop a gene-mining method to uncover the function-oriented unknown organisms from public metagenome database. The gene encoding the alpha subunit of methyl-coenzyme M reductase of methanogens was used as an example to illustrate how this new approach works. Over eighteen thousands of metagenomes available in public database were screened for the presence of mcrA and the obtained mcrA dataset was then used to assess the diversity and distribution of the Methanomassiliicoccales, the 7th order of methanogens which have remained largely unclear in terms of ecology and physiology. Furthermore, a draft genome related to the ‘Lake Pavin cluster’ within this group of methanogens was reconstructed. The data mining technique developed in this work appears very efficient. Firstly, mcrA sequences were obtained from the Pfam database and these were used to retrieve sequences available in NCBI-nr database. BLAST score method was used to eliminate the false positive hits. The mcrA dataset obtained had a much wider coverage to the known McrA sequences. Scripts were developed to perform DIAMOND search of mcrA sequences among over eighteen thousand metagenomes datasets. A stricter BSR method was used to screen the mcrA hits. Finally 1460 high quality near full length mcrA sequences were obtained. An in-depth research was conducted on the Methanomassiliicoccales-related mcrA sequences which showed the highest number of novel sequences retrieved from the multiple databases. A further effort was to reconstruct the genome of a Lake Pavin cluster Methanomassiliicoccales. The work was labor-demanding but well done and the technique developed shall be deemed to be very useful given the rocket growth of metagenome database. Following are a few minor comments.

Line 76, where not were.
Line 206, add ‘of’ between oxidation and methane.
Line 283 and below: it seem weird to separate Results and Discussion. Combination will be better.
Line 329, what do you mean ‘the second to last step of the methanogenic pathway’?
Lines 336-338, was methyltetrahydrofolate present in MALP?
Line 341, in line 336 it states that THMPT is likely absence. But here you thought THMPT can be a product of acetyl-CoA disproportionation?
Line 361, what other hydrogenases are predicted in MALP genome?
Line 408, delete ‘it’.


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

Input:
Title: EFFECTS OF INCOME AND RESIDENTIAL AREA ON SURVIVAL OF PATIENTS WITH HEAD AND NECK CANCERS FOLLOWING RADIOTHERAPY: WORKING AGE INDIVIDUALS IN TAIWAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study is well written, adequately referenced, and the figures and tables appropriate.

I have a few minor suggestions related to technical details which I will put in the comments section below.

It was nice to include the raw data, but in SPSS format, it is unreadable to anyone who does not have SPSS (including this reviewer).
Experimental design: In the first sentence of the abstract it is unclear what the range 35-89% refers to (I assumed countries, but it turned out to be prior studies). Perhaps the number of studies considering survival after RT has been limited, but part of the reason may be that this is information that cancer registries collect (at least in the US). If I wanted to know five-year HNC survival after RT, I would not consult the literature; I would consult the SEER database, where I would get a definitive number that was population-based. If Taiwan lacks a cancer surveillance system where it is easy to find this information, then this paper serves a useful purpose in that regard.
Validity of the findings: The authors have identified significant independent effects of region and income on HNC survival in Taiwan, as well as effects related to treatment type. The data are robust and the statistical methods valid. The magnitude of the effects is rather large and would seem to lend itself to some potential intervention.

The authors suggest that the male-female differences may be related to betel nut use, but they do not say whether betel nut use varies by region or income level - it would seem to.

In the concluding paragraph, it would be useful not to simply restate the findings, but to address what, if anything, could or should be done to reduce the large disparities that were identified.
Additional comments: There is a strong effect of receiving chemotherapy having a higher mortality rate. This is counterintuitive as chemotherapy is supposed to be beneficial. The authors need to say something about this finding in the discussion.

Line 48-51: % higher risk of mortality and hazard ratios  are redundant; either will suffice.

Line 71: The basis for the list of cancers being compared is unclear. There are other relatively common cancers for which HNC survival is better - why only list those for which it is worse? Maybe this sentence does not need to be here at all?

Line 72: see comment in box 2 above

Line 88: "However, only a limited number..."

Materials and Methods section: The definition of the four regions is never given. A map would be useful, but at a minimum there should be a citation.

line 98: It is unclear what exactly is meant by "unclear data".

line 99: These procedure codes are not from ICD9. A search for these codes yielded only other Taiwanese papers, so maybe this is a coding system specific to Taiwan? Please clarify.

Is 100 doses of radiation in 75 days considered the minimum standard?

line 107: If US dollar equivalents are given, the date on which this conversion was made should be listed, since it is variable - although it's not clear that it is even necessary to do this, since this is not a US-based journal nor is the readership US-based.

line 182-183: The reason for limiting the age to 65 should be moved to the methods. Same for the listing of which sites are considered part of oral cavity and which are not (lines 224-227) and the reason for the RT date cutoff of 2009 (line 240-241).

line 201: "access other hospitals"


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

Input:
Title: EFFECTS OF INCOME AND RESIDENTIAL AREA ON SURVIVAL OF PATIENTS WITH HEAD AND NECK CANCERS FOLLOWING RADIOTHERAPY: WORKING AGE INDIVIDUALS IN TAIWAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: Well-written throughout.
However, "survival" is at times 5-year (when other work is reported), and at times just "survival". It is not clear if it is 5-year survival that the authors are referring to, e.g.:
(lines 48-50): Patients with moderate income levels had a 36.9% higher risk of mortality as compared with patients with high income levels (hazard ratio (HR) = 1.369; p < 0.001). Patients with low income levels had a 51.4% greater risk of mortality than patients with high income levels (HR = 1.514, p < 0.001).
or whether it is "median survival" (e.g. lines 145 -- in which case the difference in survival should be reported in months or days, not %).
Similarly, this part is also confusing:
172 Males had a 104.9% greater risk of mortality than females (HR = 2.049, 95% CI
173 =1.943–2.162, p < 0.001).

It is not clear whether it was 5-year mortality or not.
Experimental design: Generally sound, national registry retrospective cohort design.
However, it is not reported whether Cox proportionate assumptions were met, and the lack of TNM staging, or even information whether the RT was with palliative or curative intent, is a serious limitation (i.e. we do not know if poorer patients are less compliant, have poorer nutrition that increases complications, or simply present late), a limitation which the authors themselves acknowledge.
Is the intent of RT (palliative vs curative) not present in the registry? If not, it should be stated. If it is, it should be in the model.
Validity of the findings: As mentioned above, the lack of TNM staging, or even information whether the RT was with palliative or curative intent, is a serious limitation (i.e. we do not know if poorer patients are less compliant, have poorer nutrition that increases complications, or simply present late), a limitation which the authors themselves acknowledge.
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: EFFECTS OF INCOME AND RESIDENTIAL AREA ON SURVIVAL OF PATIENTS WITH HEAD AND NECK CANCERS FOLLOWING RADIOTHERAPY: WORKING AGE INDIVIDUALS IN TAIWAN
Review round: 1
Reviewer: 3

Output:
Basic reporting: According to me this manuscript in its current form  only partially passes the last bullet of this section (Self contained with relevant results to hypothesis). Specific suggestions are below:

1.	Line 63: ‘as a result of this condition’ instead of ‘due to this disease’
2.	Sentence beginning line 64 does not  make complete sense. ‘Although’ part of the sentence should be followed by a counter part. do you just want to say that RT is associated with several complications, that impair quality of life? you can certainly structure this sentence much better and easier to read.
3.	Line 65: ‘common’ word is not appropriate here. common in what context? in the general population? obviously No.. you could say frequently observed complications among patients receiving RT
4.	in first paragraph, you should also give stats in the country of your study sample- since geography is one of your predictor variables
5.	lines 74 to 81; it might be better if you reference each study next to the factor they studied or found to be associated with survival- it is hard to know go back to the study with all being listed together.
6.	line 82, line 137: add “patients” after HNC- check throughout the paper
7.	lines 81 to 88: are you repeating what you write in lines 74 to 81? why?
8.	line 89: replace “determined” with examined
9.	Restructure sentence- “therefore in the present study we examined the survival rate of HNC patients following RT among working age individuals in Taiwan, and assessed the influence of income and residential area on the association”
10.	Please reword title of Figure 1- add patients, RT, in instead of with, area groups, comma to N
11.	correct typos in title of figure 2- please check them all
12.	line 180, 182- you should add this info about age and follow-up in results- typically not a part of Discussion section
13.	line 181- correct to HNC patients
14.	need to work on Discussion section – you do not add figure or table #s, CI, SDs in Discussion – they should be in results- only add those data from study that are necessary to make a point and keep the flow
15.	Need to work a lot on Discussion section- besides language, you need to add literature in support and against your findings- how does your study fit in existing literature- why this study is relevant in Taiwanese population if earlier studies have shown similar results
16.	It seems your Discussion is very much focused on sharing what you found- while you do that interpretation of your results in Discussion section, it has to be in done in the context of literature- what are the possible reasons for your findings, mechanisms, solutions, other factors- I don’t think you have to talk so much in length to describe what you found- it has to be an interpretation of results- eg lines 202 to 208- you mention all what you found in different ways- this should be in results- Discussion section is meant to provide an interpretation and what did you add to knowledge, acknowledging the limitations and future research agendas.
17.	lines 217-220- again all this data should not be in this section
18.	line 217- reframe- correct grammar
19.	line 209- among male HNC patients- use appropriate language
20.	lines 198 to 202- reference? need to restructure, correct grammar
21.	lines 221-223- should be in results
22.	lines 223- 228- should be in methods- discussion is not where you tell this
23.	lines 228- talk in flow- you mentioned about males and females in lines 213 -215 above
24.	lines 231- 236- it seems that you wanted to tell factors why HR was higher in your study, but the factors you say there are not the ones who looked into. are you simply stating the reasons why survival might be lower in males than females? if so, please clarify the language and words you use
Experimental design: According to me this manuscript in its current form only passes the first, partially second and third bullets of this section. Specific suggestions are below (some of them might be in Basic Reporting section above):

1.	Line 97: explain more about the dataset- how do patients make into this database? collected from hospitals? voluntary reporting or mandated? repeat visits? how you accessed data? how are ICD9 codes assigned? is this administrative dataset for billing? how are income and geographic are and other variables recorded- self reported ..etc
2.	Line 98: what do you mean by “unclear data”?
3.	why did you exclude the ages you did? reference for definition of working class age groups? you could structure this better- why write >=20 years in line 95 and >=65 years in line 98?
4.	usually you would begin by explaining the data set – what sample size you began with and then what were your exclusions (and why)- and how many you excluded for each reason- so readers know exactly the flow of how you zeroed down to the final analytic sample from your 66,626 patients. See flow-charts for trials- something on those lines should be used. your sample selection is unclear as of now.
5.	line 99: explain what are these procedure codes, what do you mean by <100 times? what is the rationale and why you are excluding them
6.	line 100- follow a pattern of writing numbers – 40,985- add comma; also line 133; check throughout the paper
7.	line 103: explain ICD in full form
8.	lines 103 to 105-include in your flow chart- how many had code for HNC and from that how many received RT and then your exclusions one by one
9.	line 104- I think you should explain the cancers you included and not just the codes.. just say we included patients with cancer of tip of tongue (ICD9 code xx), floor of mouth (ICD9 code yyy)………. etc..  it is good for reproducibility of study
10.	also for flow of the paper- these codes should come earlier in the beginning of flow chart- definitions in terms of codes of HNC, RT

11.	line 107: “categorized” instead of ‘defined”
a.	add colon after name of each category- it is confusing to read otherwise
i.	eg- low income: USD 547 per month; moderate income: uSD 547-781 per month…………. etc
12.	line 113- what is the rationale behind 2009 for date of RT administration
13.	line 123- for consistence add the continuous variables in parenthesis

14.	you don’t describe the start and end periods of follow-up for survival analysis- they should be made more explicit in methods section

15.	line 124: you should state how the underlying assumptions for the test are met- if you checked them or not to determine appropriateness of test
16.	line 129: what were the adjusting variables- indicate here for clarity

17.	Figure 1- what test did you use? I am guessing it is chi square test within the specific population groups- eg. among all in northern region, tabulating survival and income- so you would get 1 p value for that statistic- I don’t get how you have small brackets for specific income groups? Eg. p value for distribution of survival across income levels among people in Northern region was <0.05, but what does the small arrow on medium and high income there refers to?
18.	Figure  1- second graph- did you mean p<0.05 or >0.05 for #

19.	line 140- figure 1 does not give the overall survival in each group- it breaks up data by income and geographic region- if you want to say ‘as shown in fig 1’- add overall survival rate in each group in table maybe- row and column total

20.	line 152- why do you say <65 years again- you have defined your sample population- saying some of them again makes it confusing- for eg here it seems that you have included all those who are <65 years- did you include those <20 years for this analysis?
21.	need to correct sentence framing
22.	line 156- it is not logistic regression
23.	line 174, 176- compared to what? always mention comparison group even though it is in tables

24.	lines 232- what do you mean by greater significance? Significance is either yes or no based on your p value- did you mean to say higher HR?
25.	line 240- I think this should go in methods- why you selected that cutoff- also dis VMAT completely replace other modalities after 2009, so you are confident that those who received after 2009 will have received VMAT?- if not, there is a bias and assumption which should either be addressed (if you can identify what treatment was given) or acknowledged as a limitation
Validity of the findings: According to me this manuscript in its current form  only partially passes second bullet (Data is not adequately controlled) and third bullet. Specific suggestions are below:

1.	Racial disparities in survival of HNC patients are well known- did you account for that?
2.	Age group should also be adjusted for
3.	line 180- you never mentioned about universal insurance system before this point- should explain this in Methods- if it is universal insurance why do you see income based differences? Did you look at other SES factors- education, occupation etc?
4.	line 183- I think you included those <65 years, did you include those 65 years as well- be specific about exclusions – was it <65 years or <=65 years?
5.	line 210-211- how did they define “deprived areas”. you say in live 216 that you found associations in deprived areas- what was your definition?
6.	lines 209 to 216- but you did not stratify by gender- if you are stating this paper it seems that gender specific associations might have been helpful.
7.	VMAT introduction date makes me question the validity- are we sure that all patients who received treatment after  2009 got VMAT? if not there is a significant bias there.
8.	also it is possible that “deprived” areas like eastern were slower to get VMAT- it was not that common in those areas as compared to Northern- and that is why risk of mortality is higher in those regions. how do you account for that? I do not think stratifying by 2009 date of treatment will take care of that noise if it was not a complete replacement by VMAT after 2009. There is an important confounding in that case.
9.	you need to elaborate your limitations – there are several other limitations and assumptions as mentioned above in  my comments, and they should be acknowledged here – they can significantly affect the results and their interpretations
10.	if you do not have data on HPV, at least talk about it in Discussion or limitations , as HPV is becoming a significant risk factor for HNC especially oro-pharyngeal cancers and HPV positive tumors are directly related to prognosis- they have better survival
Additional comments: 1.	OVERALL- there is a lot of scope to improve language all over the paper- regarding selection of words and connectors. I have also made some suggestions, but authors should read through the paper carefully to improve the language-  correct gramma and typos
2.	Make sentences consistent- comma  for numbers, etc.- have mentioned examples in comments above
3.	figures do not seem to be of adequate resolution


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

Input:
Title: EFFECTS OF INCOME AND RESIDENTIAL AREA ON SURVIVAL OF PATIENTS WITH HEAD AND NECK CANCERS FOLLOWING RADIOTHERAPY: WORKING AGE INDIVIDUALS IN TAIWAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is a second review of a paper I previously reviewed. I am placing all of my comments in the general comments box below.
Experimental design: This is a second review of a paper I previously reviewed. I am placing all of my comments in the general comments box below.
Validity of the findings: This is a second review of a paper I previously reviewed. I am placing all of my comments in the general comments box below.
Additional comments: The authors have adequately responded to each of my comments. (I was unaware that SEER*Stat stopped including radiation data in its public-use database in 2016; they do offer it in a supplemental database, but that detail is not important for this paper).

While the quality of the English in the original submission was adequate, with the need for minor corrections noted by the reviewers, the quality of the new text (in red) is more of a problem. Sentences are poorly constructed and do not always follow logically from one to the other and there are many typos. For example, line 189 "according", line 225 "medical", line 251 "squamous". This requires attention before 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: EFFECTS OF INCOME AND RESIDENTIAL AREA ON SURVIVAL OF PATIENTS WITH HEAD AND NECK CANCERS FOLLOWING RADIOTHERAPY: WORKING AGE INDIVIDUALS IN TAIWAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: Generally good writing, with some typos, e.g.:
"although this large deviation may result from" (suggest "variation" rather than "deviation")
"differences in study design" (remove the "s" in designs)
"Accorind to " ("According to")
"It's generally agreed that HNC pateints "
"This may result from that patients with higher income level "
Also, since the patients were not enrolled in the study, but registry data was used, suggest not to use the word enrolled.
Experimental design: Generally much improved. However, suggest the following:
1. Time from RT, rather than time from diagnosis, is used; there is nothing to tell us if
a. the time was not available (in which case, it should be mentioned as a limitation);
b. the time was available but not examined (for what reason);

2. There should be an attempt (e.g. sensitivity analysis) to explore the following interactions statistically:
a. socioeconomic level and geographic region
b. socioeconomic level and other modalities of treatment (chemotherapy, surgery), since the data is available

and whether these change the findings should be reported
Validity of the findings: Generally valid for the specific population studied.
Additional comments: Suggest highlight in the discussion that radiotherapy and chemotherapy, unlike surgery, require a protracted period of compliance throughout the outpatient treatment (please confirm that in Taiwan, radiotherapy and chemotherapy are indeed outpatient treatments where the patient stays at home), and the presence of young or invalid dependents (children or patients'' parents) and working-age caregivers (spouses) may worsen the compliance.


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

Input:
Title: EFFECTS OF INCOME AND RESIDENTIAL AREA ON SURVIVAL OF PATIENTS WITH HEAD AND NECK CANCERS FOLLOWING RADIOTHERAPY: WORKING AGE INDIVIDUALS IN TAIWAN
Review round: 2
Reviewer: 3

Output:
Basic reporting: There are multiple typos and grammatical errors in the correct text.
I still think Limitations section needs more insight- please see attached for details.
Experimental design: please see attached for details
Validity of the findings: please see attached for details
Additional comments: No additional comments


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

Input:
Title: THE INFLUENCE OF SAMPLE DISTRIBUTION ON GROWTH MODEL OUTPUT FOR A HIGHLY-EXPLOITED MARINE FISH, THE GULF CORVINA (CYNOSCION OTHONOPTERUS)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is very well written. The Introduction is very clear, the background is carefully documented with relevant and well referenced literature. Perhaps the Introduction is too long (it seems a small review around this topic), but it could be very useful for readers.
Experimental design: The protocol used to fit the different growth models and to compare them is also sound, very well explained and robust. The parallel usage of simulation and experimental data is the best way to evaluate the different aspects and drawbacks of each model.
Validity of the findings: The results and the related discussion are also clear and coherent. I didn’t find weakness or inconsistencies in the approach. However, the only weakness of the paper is represented by the lack of the originality of the finding and of the related “message” of the paper. As the authors honestly declared in the abstract, “Our results serve as a reminder of the importance of complete sampling of all size and age classes” and, unfortunately, it is hard to find more than a reminder in the contribute of this paper to the relative field of work. Other sentence that definitively allows assessing the relevance of the paper are present in the discussion. Ex. Lines 346-348: “Similarly biased fishery-dependent data have been the only data available for age and growth studies with Gulf Corvina, and previous studies have taken markedly different approaches to dealing with its limitations” or Lines  375-378: “The results of our study reinforce the well-established principle that each size and age 376 class must be sufficiently represented for growth modelling to produce biologically reasonable 377 results (Cailliet et al., 1986; Cailliet and Tanaka, 1990; Francis and Francis, 1992; Cailliet and 378 Goldman, 2004)”. Yes, I strongly agree with the authors, but then why the readers should be interested in this paper? I’m sorry for this comment.
Additional comments: What I would like to suggest to the authors is one between two options: 1) rewrite some parts of the paper to stress the originality of the finding. Perhaps the authors could explore the cascade issues linked to the usage of wrong growth estimates in the stock assessment models? 2) transform the paper into a small review around this topic. At the present stage the paper is more interesting as a source of reference and as an historical reconstruction of this research framework.


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

Input:
Title: THE INFLUENCE OF SAMPLE DISTRIBUTION ON GROWTH MODEL OUTPUT FOR A HIGHLY-EXPLOITED MARINE FISH, THE GULF CORVINA (CYNOSCION OTHONOPTERUS)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The text is overwritten -especially in the Introduction and the Discusssion should be better organized.  See general comments
Experimental design: The issues re; interpretation of groeth models in fish--Are we seeking to ek
lucidate the biology or are seeking to provide a description of the sample population and thus assess the impacts of fishing are important issues and should be spelt out more explicitly
Validity of the findings: The data presented are fine but would be greatly improved by some fishery independent sampling of small individuals
Additional comments: Bolser et al Review
General
At first sight, this paper deals with a number of issues that appear repetitively in the field of fisheries management, the treatment of which become technical and doctrinaire. However there are some important issues that are canvassed in this study and it emerges as something more than just another debate about the best way to model size at age data. As the authors point out under-representation of the maximum size and ages that the population members can achieve leads to underestimates of generation time and  turnover rates. Agreed. They make the point if one does not ensure adequate representation of all age classes (read here, especially the large old fish) then “published growth models ---may not be representing biology but rather the influence of exploitation.” There are however likely to be a number of fisheries biologists, conservationists etc who would argue that measuring the influence of exploitation is exactly what is needed.
The Discussion that deals with this raises a number of important issues. Considerable variation occurs in the age structure of fish populations for a number of reasons; variation in recruitment success and the year class phenomenon, consistent selection of size and age classes by fisheries are the obvious ones. The authors commendably call for data sets that will result in the generation of demographic parameters that represent that true biological status of the population. This usually means capturing the influence of larger older members on generation times and mortality rates. The importance of this depends on the rate at which parameters are modified in a Darwinian sense—the salmonid people suggest this can be rapid.  A better understanding of biology of the fished species requires information on possible increases in initial growth rates and reduction of the age at maturity.  Selection imposed by the removal of the most fecund members of the population might be driving the age at maturity downwards. Is adding additional older individuals when analyzing such a population going to be realistic? We don’t know, but the point is worth debating.  I think the authors handle these aspects fairly well but they need to be clearer about the alternative views as they have different consequences for fisheries management—and will likely attract some rebuttals.
If you want biological realism, you are not going to get it without fisher- independent sampling. In the present case, the focus should be on sub-adults, especially those that have not recruited into the fishery. There are two reasons for this. If there is going to be a response to fishing then this is where you will find it. Secondly getting better representation of the very early age classes is the best way to get realistic values of K (see below).
Government regulations usually require evaluations of the sustainability of fished stocks. This places a heavy responsibility on the development of fisheries models that estimate rate processes especially growth and mortality by methods where you don’t have actual age estimates.  This study through comprehensive analysis of otoliths gets us past that point.  However to do this properly you also require fishery-independent data, not simply balancing up the year classes by age-class information derived from the fishery (see line 106).

Specific

Lines 40-45. Introduction. This is overwritten and over-referenced. The intro could start at line 45.
 Figs 4 & 5 Line 72. Are the authors happy with the use of K as a rate? K is a reciprocal of
time with units of time-1 (not length.time-1 as would be expected for a growth rate). Rather,
K varies with the age at which the growth trajectory reaches (or would reach) asymptotic
length L∞, and is a measure of the curvature of a growth trajectory. This point has been debated but much of the fisheries literature uses K as a measure of growth. So be it. However, there is an empirical point that is clear from Figs 4 and 5. The value of k is very sensitive to the distribution of size at age estimates of younger fish. If you miss these then the backward projection of the growth curve gives untenable estimates of to. Inclusion of smaller individuals usually increases K as does constraining the curve to a realistic settlement size. Many people don’t want to do this but if you don’t it is incumbent to have better representation of the younger age classes.
Lines 53, 77,381,392. Data-poor fisheries. Suggesting data poor fisheries will deliver poor service because they may use inaccurate estimates of L∞, K and other parameters is naïve. The problem with using data poor-estimates (especially in the Prince Hordyk papers)  is that high levels of localized spatial variation occur in fish demographic parameters and are not taken into account. The consequent fisheries tools are used in areas where the demographic parameters are more biased than anything discussed in this paper. There are also major episodes of temporal variation due to climate forcing that reduce the value of estimates from data-poor models many of which use related species as proxies. The data sets in Figs 4 and 5 with high variances in size for each age class must reflect some of this. It is necessary to specify the spatial location of the sampling. With respect to temporal variation, the otoliths of this species would certainly allow the type of back calculation used by Black to take the impact of location-specific climatic variation (ENSO) into account.
Figs 4 & 5. The distribution of values for year classes 2 and 3 suggests the authors would do well to read Mulligan TJ, Leaman BM (1992) Length-at-age analysis: Can you get what you see? Can J Fish Aquat Sci 49:632–643.
There is now increasing evidence that populations at any given time may contain rapid and slow growing cohorts. Fast growing individuals will be very large at intermediate ages but do not survive. The older individuals may comprise members of the slow growing cohort. Back calculation to check on the growth rates with an age classes can sort this out.

In general the authors need a  more explicit treatment of the alternatives—Do you want accurate  age parameters in order to present a biologically realistic description of the population (achieved by ensuring better representation of each age class) or do you want models that reflect the impact of the fishery. At present, these tend to be buried in the Discussion. They need a clearer treatment as alternatives as they lead on to some important issues, the critical need for fishery-independent sampling, the need to get younger individuals for better estimates of K. Moreover, while they argue that we should be getter parameters that are biologically realistic, the selection imposed by fishing modifying age and reproductive schedules may be important aspects of the biology of the species in areas where fishing occurs.
They also need a better treatment of data-poor fisheries. Reading the discussion one gets the impression that the main problem is that they can generate inaccurate parameter estimates. This is not the case. What compromises data-poor estimates (even the better ones that don’t use other species as proxies) is that they ignore localized spatial variation and the temporal climate-driven impacts on growth rates. As the authors are seeking to make a general case for demographic sampling, they need to be more up front about the distorting impacts of spatial and temporal variation. My reading of the ms tells me that they have raised some interesting issues but need to improve the platform on which they are presented.


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

Input:
Title: THE INFLUENCE OF SAMPLE DISTRIBUTION ON GROWTH MODEL OUTPUT FOR A HIGHLY-EXPLOITED MARINE FISH, THE GULF CORVINA (CYNOSCION OTHONOPTERUS)
Review round: 2
Reviewer: 1

Output:
Basic reporting: I confirm that the paper is very well written and organized. The authors did a remarkable effort to improve some issues of the manuscript. I am satisfied of this new version and of the replies to my comments. I think the paper is now worth of publication.
Experimental design: The experimental design is sound, well presented and support by data.
Validity of the findings: The findings are valid and useful to promote better researches in this framework
Additional comments: I appreciated the author replies and I agree with them.


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

Input:
Title: THE INFLUENCE OF SAMPLE DISTRIBUTION ON GROWTH MODEL OUTPUT FOR A HIGHLY-EXPLOITED MARINE FISH, THE GULF CORVINA (CYNOSCION OTHONOPTERUS)
Review round: 2
Reviewer: 2

Output:
Basic reporting: The Introduction and Discussion are now more succinct and readable.
Experimental design: No further criticisms
Validity of the findings: Worthy of publication in the fisheries literature.
Additional comments: My congratulations to the authors on a detailed and balanced response to the critiques outlined in my review.

My support for the value of this ms is that the literature is now replete with examples that fit various growth models to data as an end in themselves and do not explore basic biological properties that may modify or drive model parameters in unexpected ways.


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: NONSPECIFIC STRESS RESPONSE TO TEMPERATURE INCREASE IN GAMMARUS LACUSTRIS SARS WITH RESPECT TO OXYGEN-LIMITED THERMAL TOLERANCE CONCEPT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The investigation is a clear contribution to knowledge on the impact of climate change, which is also included in the guidelines of the journal. The expression of the text is simple, concise and scientific. The research has been carried out with ethics, especially taking into account the use of other species of minor evolutionary scale.

The introduction needs more detail. I suggest to improve the defense of the use of the biomarker and its description, in addition, it should specify other factors that influence even if they will not be analyzed at a later time and why he chose precisely the factor temperature for the study, the goals are not ben defined although the objectives and finally would have to endorse this type of studies with a database of legislation (EPA UNITED NATIONS OECD...) to provide additional justification.
In discussion would have to introduce the application of the biosensor shallow way

Specific Comments

64 to 74 lines Within the methodology it is convenient to remove them and carry the information of the biomarker to introduction
(materials must refer exclusively to the objects used to perform the job, only put the animals that are used, its origin and type of sampling)
66 line: enter if the zooplankton or benthic species is
94 line: why this age , this age are more sensitive?
96-97-98 lines:  Why it chose this range of temperatutas
184 line: Appoint Representative species
Experimental design: The research question is well determined, the experimental design is appropriate and modern, however in the statistical analysis, the sample of 3 individuals is low and the repetition of the bioassay should be adjusted to a minimum of n= 6-8  for a good statistic
Validity of the findings: The work complies with the objectives and in any case with the premises, assumptions and arguments raised, the results are clear, concise and sufficient appropriate measurements
Additional comments: The article has good quality but requires certain minor changes to improve the introduction
The article are not defined the goals, although if the objectives
Check the match or contrast with more papers published by other authors even comparing with other bioindicators.
In addition to the conclusions derived directly from the conduct of the investigation should include any alternative interpretation that is discarded during the work.
It should reflect more closely the innovations found.