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: INCREASING EVIDENCE THAT BATS ACTIVELY FORAGE AT WIND TURBINES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: The statement in the discussion “Our study provides strong support for the hypothesis that bats are using wind turbines as a foraging resource” can be interpreted in two ways: 1) bats forage around turbines; 2) turbines affect bat behavior and/or resources such that the area is preferred or used more than other areas without turbines.

The correspondence between insect composition in light traps and those in bat stomachs and pellets is very suggestive that bats forage in and around wind turbines.  It is also certainly possible that turbines can attract insects which in turn attract bats.  Alternatively, the correspondence may simply reflect a situation where bats are foraging on available insects (both near and far from turbines) and the turbines do not affect this relationship in any meaningful way.  That is, while the study does show that interpretation 1 is valid, it is harder for this reviewer to feel that a strong case has been made for interpretation 2.  Foraging behavior at turbines has been observed both visually and acoustically in other studies, and Foo et al. contribute additional evidence that this activity is also prevalent in their study area.  (The statement that eastern red bats were likely roosting on the turbine structures after foraging nearby is a particularly noteworthy observation.)  However, the study was not designed to falsify the hypothesis that turbines serve as a focal resource (although they may well be).  To accomplish this, it would be necessary to sample both bat activity and insect prevalence at sites distant from turbines, and perhaps also assess fecal pellets obtained from bats captured at these locations with those collected at turbines.  From this a comparison of the proportion of bat calls with approach and terminal phase components recorded at locations distant could be made with those sampled close to turbines.  If proportions were similar, it would indicate that turbines are not necessarily attracting bats and they simply encounter these features as they are foraging across a landscape; that is, foraging activity is similar.  A study that applied this method to acoustic samples is Jameson and Willis (2014) who observed “a smaller proportion of feeding buzzes at [meteorological] towers compared to woodlots during all study periods despite the dramatic increase in overall activity at towers during autumn” and concluded that bat presence was likely associated with visual attraction to tall structures for purposes of social interactions.

I applaud authors for a solid study showing that there is, as stated in the manuscript title “increasing evidence that bats actively forage at wind turbines”.  However, the authors may wish to consider tempering statements such as “abundant foraging opportunities continue to attract migrating bats to wind turbines” with a caveat that “attraction”, that is, relatively greater foraging use of turbine areas was not experimentally determined nor specifically the focus of the study.
Additional comments: It would be useful to see the night-to-night correspondence in stomach samples relative to insect trapping.  High correspondence would indicate that utilization matched availability (at least for certain orders), and provide strong evidence of prey capture at or near the wind site.  Low correspondence would indicate prey capture at a distance from a site, or perhaps a low within-night match of utilization-availability.  These results could be added to the supplementary materials.


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: INCREASING EVIDENCE THAT BATS ACTIVELY FORAGE AT WIND TURBINES
Review round: 2
Reviewer: 1

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
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: INCREASING EVIDENCE THAT BATS ACTIVELY FORAGE AT WIND TURBINES
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: The primary concern this reviewer had with the initial ms was that the authors were making too strong a claim that bats are attracted to turbines for foraging.  In the revised ms and response the authors acknowledge this and have made changes to the text that temper this claim while still indicating that it remains a phenomenon that needs further investigation.  The authors did demonstrate that foraging does occur at turbines, and correctly conclude  that foraging opportunities may be one reason that bats are active at those locations.
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: NEW SPECIES OF THE ENDEMIC NEOTROPICAL CADDISFLY GENUS CONTULMA FROM THE ANDES OF ECUADOR (TRICHOPTERA: ANOMALOPSYCHIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English used throughout the manuscript is sound and there are only a few minor typing mistakes. The literature is up to date and all important references are cited in the text. I suggest the addition of a few authorship references along the text. The manuscript has a coherent structure with no misplacement of text in wrong sections. The authors correctly present background information for the reader in the Introduction section and state their hypothesis. The results are new and relevant to science and in accordance with the issues stated in the introduction. The figures are well drawn and present clear information of the necessary issues.
Experimental design: The research presented is within the aims and scope of PeerJ. The methods used by the authors are those mostly used by the entomologists and suit correctly the aim of the manuscript. The methods are described in sufficient detail and references correctly cited.
The research question helps filling a biodiversity gap extant in caddisfly studies, especially in the still poorly known Andean area.
Validity of the findings: The species presented by the authors are undoubtedly new to science and are presented in a clear way with sufficient illustrations to support their asserts. The additional distributional data the authors provide are meaningful and help us to better understand the biodiversity and distribution of organisms. The authors propose a species synonym, which seems to be correctly stated based on the knowledge and material available. The argumentation they provide for the synonym is logic and the evidences provided are sufficient to lead to this conclusion.
Additional comments: The authors present three new species of the high altitude caddisfly genus Contulma. Based on the descriptions and illustrations provided, the species are definitely new and represent a significant contribution to caddisfly knowledge. They also present new records and an identification key of males of Contulma, which is a relevant contribution to science, especially taxonomy and ecology of aquatic insects. The manuscript is well written and contains only some minor issues that should be addressed, such as citation of figures and rearrangement of a few sentences. All those issues are marked in an annotated 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: NEW SPECIES OF THE ENDEMIC NEOTROPICAL CADDISFLY GENUS CONTULMA FROM THE ANDES OF ECUADOR (TRICHOPTERA: ANOMALOPSYCHIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper is well-written.  The figures are very good, and the literature matches with the call-outs in the text.  A good contribution to our knowledge of this genus.  Some minor corrections are suggested in the PDF.
Experimental design: This paper falls within the Aims and Scope of the journal and meets all other stated objectives.
Validity of the findings: no comment
Additional comments: Please see yellow highlighted areas for minor suggested improvements.  A table with all of the known species, their authorities, and country distribution would improve the overall value of this paper.  This manuscript was also reviewed by Tatiana I. Arefina-Armitage.


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: NEW SPECIES OF THE ENDEMIC NEOTROPICAL CADDISFLY GENUS CONTULMA FROM THE ANDES OF ECUADOR (TRICHOPTERA: ANOMALOPSYCHIDAE)
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper is clear and well written.  The authors present an excellent overview of the current state of Trichoptera taxonomy in the Neotropics and ample background information on the distribution, habitat, and previous work of the genus.  The illustrations are superb and expertly done.   Relevant collection, specimen, and database information are provided.
Experimental design: This original taxonomic research is within the scope of PeerJ and fills an important knowledge gap for Neotropical taxonomy. The work meets the highest technical and ethical standards in taxonomy. The methods are described in great detail and in such as way to facilitate replication by another investigator.
Validity of the findings: The superb illustrations, detailed diagnoses and descriptions, and identification key will prove to be valuable resources for future workers of this group.  The authors present ample evidence for the designation of these new species.  The authors explain their rationale for the synonymization of C. duffi with C. penai.
Additional comments: Thank you for the opportunity to review this manuscript.

This original taxonomic research is within the scope of the journal and appropriate for publication in PeerJ.  The importance of describing rare, highly endemic new species, such as these new Contulma from the Andean region of Ecuador, cannot be overstated. This work is an excellent contribution to our overall knowledge of Trichoptera taxonomy and distribution, and provides a rare glimpse into the remarkable diversity of these little known organisms.  Climate change, land-use changes, and other threats to high altitude glacial streams and inter-Andean valleys all underscore the critical need to document this diversity.

The paper is clear and well written.  The authors present an excellent overview of the current state of Trichoptera taxonomy in the Neotropics and ample background information on the distribution, habitat, and previous work of the genus.  Methods are clearly described, and include valuable information regarding databases and adherence to ICZN standards. The illustrations are superb and expertly done.  The diagnoses and descriptions are detailed and clear.  The synonymization of C. duffi with C. penai is well explained and justified.  The inclusion of references to previously published illustrations, will make the identification key an especially valuable resource for future workers.  I was unable to test the key using actual specimens, but based on previously published illustrations, it worked perfectly.

I offer a few very minor changes below as suggestions for improvement.  I have also listed some very minor edits (mostly typographical errors).  All of these are meant as suggestions to improve the paper and should be left to the authors as to whether or not they are needed.

1.)	Please check for consistency in formatting for in-text citations.  For example, on line 33, Holzenthal 1988 is written without a comma, however on line 48 Holzenthal and Río-Touma, 2012, the comma is included.  I leave it to the PeerJ editors to confirm the proper final formatting.
2.)	Lines 45-49:  The authors explain that these species are rarely collected using standard light trap techniques and that most specimens are hand netted during the day or collected by Malaise traps, especially at high altitude.  They go on to state that infrequency of collection does not equate to rarity in nature.  Although not explicitly stated, the authors seem to imply that this may be a reflection of minimal collection efforts or perhaps low temperatures.  Although admittedly speculative, perhaps a sentence to this effect would help to clarify.
3.)	Line 97: Author & year not listed for first mention of C. paluguillensis.
4.)	Lines 99-100: First mention of species listed do not cite authors & years.  Are these also described by Holzenthal and Flint 1995?
5.)	Line 194: Author & year not listed for first mention of C. lanceolate.
6.)	While not critical to the paper, readers might appreciate a short recap of what is known regarding the phylogeny and species relationships of the genus.  The authors cite Holzenthal and Flint’s (1995) comprehensive revision of Contulma, yet they make no mention of species groups, although they are somewhat alluded to in some of the diagnoses (e.g., lines 99-101, 152-153, Footnote 2 of key). I recognize a phylogenetic analysis is certainly outside the scope of this paper, but a broader discussion of morphology, species relationships, and how these new species might be placed, would add valuable context.
7.)	Line 203: There is an extra “s” in the word process.
8.)	Footnote 1 of Key: Robertson is incorrectly spelled.
9.)	Line 249: posteromesal is incorrectly spelled.
10.)	Line 384: setose protuberances (needs space).
11.)	It is unclear why each of the figure legends begins with “Catalog of the Neotropical Trichoptera (Caddisflies)”.  Typographical error?

In summary, I recommend this manuscript for publication with very minor revisions.  It is an excellent work!


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

Input:
Title: COMPARATIVE ANALYSIS OF THE MICRORNA TRANSCRIPTOME BETWEEN YAK AND CATTLE PROVIDES INSIGHT INTO HIGH-ALTITUDE ADAPTATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: In general, the manuscript is well written. However, the following issues should be addressed.

The growing environment of the experiment animals should be provided, especially the altitude. The altitude could potentially affect the overall result. In the section of differential expression of microRNA, more detail on how to normalize read counts should be provided. The method of FDR calculation is also needed.

In Result section,
Line 120, it is hard to interpret (88.86±4.87%).
Lline 131, it is not traditional way to use correlation coefficient to measure experimental confidence, what is the method to calculate the correlation coefficient: Pearson or Spearman’s?
Line 166~169, how the Pearson’s correlation of family, cluster and background are calculated is not clear, between yak and cattle or between tissues? If it is between yak and cattle, how are tissues treated in the calculation. More details are needed to interpret the result.

Figure1. ‘coserved’ should be ‘conserved’
Figure 2. The color scale for the heatmap is too wide.
Figure 3. Legend does not match the figure. There are 5 panels in the figure, while there are only A to C in legend.
Figure 4. p-value should use –log10 instead of –log2. Fold change in p value does not make sense and is hard to interpret.
Table S1: Format the spreadsheet to show all numbers.
Table S2: Round or format the numbers to an easily reading format.
Table S5: Does ‘genomeID’ represent chromosome?
 All the supplementary tables need to be reformatted to a readable and scientifically meaningful format.
 All supplementary figures should have figure legends.
Experimental design: no comment
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: COMPARATIVE ANALYSIS OF THE MICRORNA TRANSCRIPTOME BETWEEN YAK AND CATTLE PROVIDES INSIGHT INTO HIGH-ALTITUDE ADAPTATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript presents the findings from miRNA profiling study of Yak and Cattle. It is well written with a professional article structure. The findings sound interesting to relevant research community.
Experimental design: No comments
Validity of the findings: Some minor comments on the data analysis

In the method section of data analysis for small RNA sequencing, the author wrote "Given the reliability of analysis results, reads with a copy number larger than three were retained for subsequently analysis. Comparable amount of miRNAs were identified for using bovine genome or yak genome (data not shown), we selected bovine genome as the reference genome in this study."  More details need to be added here. For example, does the "copy number" mean "read count"? need to be greater than three in all samples or at least one sample? Regarding miRNAs identified with bovine and yak genome, the number of miRNAs might be similar, how about their expression level? If the expression level is not similar, the results from yak genome will have to be used.

In the section for identifying miRNA targets, how are the ortholgous human miRNAs identified for bovin miRNAs, by comparing sequence similarity or simply by matching the names?
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: COMPARATIVE ANALYSIS OF THE MICRORNA TRANSCRIPTOME BETWEEN YAK AND CATTLE PROVIDES INSIGHT INTO HIGH-ALTITUDE ADAPTATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: Revision by a native English speaking colleague or editing services is required.

The introduction would benefit from some discussion of the evolutionary relationship between yak and cattle. Related to this point, the introduction should provide some justification for using cattle as the comparison species in this study.

The legend for Figure 4 requires additional details for panel D.

Figure 4 panel D contains text that has been resized such that the aspect ratio is incorrect.

The legend for Figure 4 includes the statement "miRNAs in red indicated upregulated in heart, miRNAs in black indicated downregulated in yak". This color scheme appears inadequate as the two possibilities are not mutually exclusive.

The data from this study is available through NCBI GEO under the accession number GSE87833. The GEO record for this study contains errors that should be corrected. For example, the methods section contains information from a different study: "Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice". The GEO summary also includes the word "epigenetic": "we illustrated the epigenetic differences in the microRNA transcriptomes level for heart and lung between yak and cattle". It isn't clear to me why the term "epigenetic" is used in this context--the authors have not demonstrated that these expression differences arise from epigenetic mechanisms as opposed to DNA sequence differences.
Experimental design: The sample size is small but appears suitable for interspecies comparisons. However, more information on the animals is needed. Specifically, were they maintained at high or low elevations?

The section "Data analysis of small RNA sequencing" contains some confusing and inconsistent statements. First, the statement "Given the reliability of analysis
results, reads with a copy number larger than three were retained for subsequently analysis" is unclear. What is the "analysis results" referring to? Also, what does it mean for a read to have "a copy number larger than three"? Does this refer instead to a miRNA with support from more than three reads? Second, the statement "Comparable amount of miRNAs were identified for using bovine genome or yak genome (data not shown), we selected bovine genome as the reference genome in this study." The section up to this point makes no mention of using a reference genome--instead reads are mapped to bovine and other mammalian pre-miRNAs. Thus the meaning of this statement is not clear.

The section "Data analysis of small RNA sequencing" refers to a database as "NCBI". A more specific name for this database is needed.
Validity of the findings: In general the results are interesting but do not, in my mind, convincingly indicate that the miRNA expression differences between cattle and yak relate to high altitude adaptation. A more convincing study would have incorporated mRNA expression, such that the differences in miRNA expression could be linked to target gene expression differences. In general the language used to describe the conclusions needs to be adjusted to better convey the indirect nature of the findings. For example, the conclusion "revealed extensive roles of miRNAs in high altitude adaptation" could be "suggest extensive roles of miRNAs in high altitude adaptation."

The paper does not include a discussion section. A discussion section should be added and should include a discussion of the limitations of this work, including the limitations of miRNA target prediction.

The discussions of the implications of the miRNA expression differences do not seem to note which miRNAs are expressed more highly in yak and which are expressed more highly in cattle. Figure 4 does not clearly convey this information. This information should be included this in the discussions and in figure 4. For the miRNA differential expression results to support the hypothesis that miRNA expression is involved in high altitude adaptation it is important that the direction of the expression differences be discussed.
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: COMPARATIVE ANALYSIS OF THE MICRORNA TRANSCRIPTOME BETWEEN YAK AND CATTLE PROVIDES INSIGHT INTO HIGH-ALTITUDE ADAPTATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The issues raised in last review have been taken care of. No further comment
Experimental design: The experimental design meets the journal standard. No further comment.
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: COMPARATIVE ANALYSIS OF THE MICRORNA TRANSCRIPTOME BETWEEN YAK AND CATTLE PROVIDES INSIGHT INTO HIGH-ALTITUDE ADAPTATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: Basic reporting
---------------
1. The authors indicate that an editing service has been used. However, the writing does not seem to have improved in quality and thus still requires extensive editing and is not suitable for publication in its current form.

2. The figures still contain text shown at incorrect aspect ratios.

3. The legend for Figure 4 still requires information describing panel D.

4. "reads mapping to bovine or other mammalian miRNAs were defined as conserved miRNAs": based on this statement, reads mapping only to bovine would be classified as "conserved", which doesn't make sense.

5. "reads with a read count larger than three" is unclear. I assume the authors mean "miRNAs  supported by three or more reads".

6. line 122: "Given the reliability of analysis results"--In the revised version it is still not clear to me what this statement refers to.

7. line 124" "Comparable amount of miRNAs" should be "Comparable numbers of miRNA species"

8. lines 130 and 131: the normalization methods and FDR methods should be stated rather than just referring, for example, to a "default" method.

9. the discussion includes results that are not presented in the results section, for example "we identified 784 and 807 miRNAs using yak and cattle genome, respectively". The discussion should not present new results.
Experimental design: Experimental design:
--------------------

10. Based on the miRBase information on microRNA nomenclature, orthology should not be inferred by name alone:

http://www.mirbase.org/help/nomenclature.shtml

"The numbering of miRNA genes is simply sequential. For instance, at the time of writing the last published miRNA was mouse mir-352. The next novel published miRNA will get the number 353. However, if you submit an Xenopus miRNA that is identical to human mir-121 for example, we will suggest you also name your sequence mir-121."

"Please note that miRNA names are able to convey only limited information, and are entirely unsuitable to encode information about complex sequence relationships. You should not therefore rely on the name to tell you all you need to know about the sequence. Sensible database approaches should instead use dedicated fields and annotation to describe such relationships, such as the "family" data provided here."

Based on the author's response to reviewer 2 and on the methods of the paper, the authors have not used a suitable, sequence-based approach to confirm that they have identified the appropriate human ortholog miRNAs for inferring mRNA targets. This raises questions about the validity of all the downstream functional analysis. The authors need to apply a more rigorous ortholog detection procedure, and they need to clearly describe this procedure in the methods.
Validity of the findings: I have concerns about the validity of the findings given the issue with the miRNA ortholog identification described under Experimental design.
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: GENOME-WIDE ASSOCIATION STUDY OF PIGMENTARY TRAITS (SKIN AND IRIS COLOR) IN INDIVIDUALS OF EAST ASIAN ANCESTRY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a important piece of work and well investigated. I have only minor points that should be adressed. Unfortunately due to the relatively small sample size no, so far unknown variants, showed significant association with eye and skin colour. I would, however encourage the authors to investiage ZNF804B in more details and in larger datasets if possible.The level of the English throughout the manuscript is very high and, therefore the manuscript is easy to read and well structured. The figures and tables in the manus are overall of high scientific quality and support the content of the manus nicely, however the graphic overall quality of the figures is low and eg. the abscissa in Figure 1 and 2 is inadequate.
The use of literature is satisfying, but should be supplemented with more literature. Lines 48-52: Andersen et al. 2013 (Forensic Sci Int Genet. 2013 Sep;7(5):508-15. doi: 10.1016/j.fsigen.2013.05.003).
Experimental design: I like the overall study design with a study population and follow up population to replicate the skin pigmentation findings. The statistical analyses are wisely choosen and performed in a very nice way.
I see some challenges with the measurements of skin pigmentation and the use of imputatation. The authors have obtained buttock pigmentation measurements for the study population, but not for all of the follow up populations. It is well known that buttock levels resemble the constitutive pigmentation levels, whereas arm levels may be influenced by environmental factors (UVR) (eg. Johansen et al. 2013, PLoS One. 2016 Mar 3;11(3):e0150381. doi: 10.1371/journal.pone.0150381). I find it problematic to compare these two areas of measurements without any further discussion. This should be adressed in the discussion section. Also a better discription upon the sample collection for the follow-up samples is needed. Much could be learned from the very nice description of the study population "Measurement of pigmentary traits". Eg. how many replicates were taken and did the authors use the median of the replicates if any?
I would also appreciate a discussion about the use of imputation.
Validity of the findings: The outsome of the study is important for research within the field of pigmentation genetics. The East Asians is a neclegted population groups. It is not surprising that no variants show significant association with skin colour as the variation within the investigated group is minor. A the authors also describes, the number of samples needs to be increased in order to find variants with minor effects.
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: GENOME-WIDE ASSOCIATION STUDY OF PIGMENTARY TRAITS (SKIN AND IRIS COLOR) IN INDIVIDUALS OF EAST ASIAN ANCESTRY
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript reported a GWAS on pigmentation in Asian populations. Such study is much needed. The strength of this study included instrument-based pigmentation phenotype measurement. The reviewer only has two suggestive comments.
1. The authors did not report meta analysis of the discovery set and replication set. Any reason for it?
2. It would be helpful to list the results of all the pigmentation loci previously identified in white populations. It is important to compare the beta estimates between the two racial groups. Of course this study has a much smaller sample size so that P value is not comparable.


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: MECHANISMS OF OAT (AVENA SATIVA L.) ACCLIMATION TO PHOSPHATE DEFICIENCY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript reports the mechanisms of oat acclimation to phosphate deficiency. The major findings include the capacity of oats to use organic phosphate (phytate) as a source of phosphorus and the role of different pools of acid phosphatases in acquiring phosphorus from soil. The paper is prepared professionally, minor language editing is recommended (e.g. "another enzymes" in the abstract, line 57, etc.). The statement that acclimation of cereals to phosphate deficiency remains undiscovered sounds a bit too strong. There are many publications in this field, and the authors cite the most important papers in their manuscript. The manuscript contains valuable sets of data that can be useful for agronomists and plant physiologists involved in the problem of phosphate deficiency in cereals and in oat in particular.
Experimental design: The experimental design is acceptable. Four cultivars have been used. The parameters studied mostly refer to the general classical physiology. The biochemical characterization of isoforms of acid phosphatases adds an important information to this study. The methods are described with sufficient detail. This research fills some existing knowledge gaps in phosphorus acquisition in cereal plants.
Validity of the findings: The major findings in this study are valuable. They include the capacity of oats to use organic phosphate (phytate) as a source of phosphorus and the role of different pools of acid phosphatases in acquiring phosphorus from soil.
Additional comments: In general, this manuscript contains important sets of data on phosphorus acquisition by oat plants. The study has a value for practical applications. It is useful for the agronomists that face the problems of phosphate deficiency in their field practice.


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: MECHANISMS OF OAT (AVENA SATIVA L.) ACCLIMATION TO PHOSPHATE DEFICIENCY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The topic of the article is interesting and it is suitable for publishing in Peer J.
The presented studies concern on growth parameters and physiological adaptations which enable four commercial cultivars of oat to grow under Pi deficiency. The authors postulated that extracellular phosphatases play significant role in acclimation of oat plants to low Pi regime.
Although the method of acid phosphatases assays is quite old-fashion, the concept and results are valuable and might be good base for application in agriculture. A better understanding of the mechanisms of plants responses to Pi deficiency is essential to develop strategies to increase crop yield. It would be worth to carry out some genetics approaches to elucidate mechanism of oat responses to Pi starvation at molecular level (i.e. identification of AP sequences in oat’s genome, analyses of AP genes expression in different Pi nutrition, Western Blot to determine AP proteins in more quantitative way).
The introduction is written well and purpose of the study is clearly presented. Also results were analyzed properly with adequate statistical methods. The discussion was based on updated literature and supports the research hypothesis.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Minor changes have been suggested:
Line 198-200: Please explain why you used different concentrations of inorganic (1 mM KH2PO4) and organic (0,1 mM phytic acid) as a P source? Is 1 mM concentration of Pi enough optimal for crops?
Line 425: “…oat cultivars could effectively utilized phytates, organic P forms generally not easily available to other plants”. This sentence should be rewritten. It seems that only oat might use phytates as a P source? Are there any specific phytases from oat that mobilize organic P reserves in soil? A reference is needed.
Line 613: Abbrevations:
PN – is missing
PM – is missing
PAM- is missing


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: CAN 9Q34.2 RS633862 POLYMORPHISM PREDICT SURVIVAL IN EPITHELIAL OVARIAN CANCER?
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall several parts of the manuscript- especially the introduction and discussion section needs to be rewritten to address several grammatical and punctuation errors. Several aspects needs to be rewritten to address the technical aspects and to ensure the right rationale and message is getting across

The results need to be addressed again to ensure the statistics used are well explained and the correlation is well described
Experimental design: Line 141- p value – report the exact p value form the gtex
Kindly expand on the results obtained from SNPinfo

Kindly expand on the overall follow up time line.

Detailed clinical and pathological information was retrieved for all the patients however, no information is provided. Including a demographics table including all this information is pertinent

For the multivariate analysis- kindly mention in the methods exactly which covariates have been included in the analysis including if continuous or catergorical

How was the bioinformatics analysis done to determine that the SNP was a TFBS. Also kindly expand on the actual bioinformatics analysis done vs. information look up using databases such as GTEx and UCSC genome browser. Along the same lines “Genotype-phenotype correlation analysis” is merely looking up the expression on the GTEX database or was any further analysis using the samples in the study done?

The gene-expression of the ABO bases on the genotyped should be determined (if samples permit) in the study samples itself to check the correlation with
Validity of the findings: Rationale for picking ABO vs others reported in the previous paper by the authors should be expanded upon

Conclusion/Discussion needs more clear writing to tease apart the message

Lack of greater follow up time was reported as one of the short comings of the paper. However no details on the actual follow up done was provided

Some kind of replication is warranted especially for the gene expression reported usingGTEX

Further information is needed regarding the SNP in question - rs633862
 - minor allele frequency especially in the Han chinese population
 - rationale for the grouping of the SNP - AA+AG vs GG instead of carriers vs. non-carriers of the SNP
Additional comments: The paper needs to address some big questions and several parts need to be readdressed to make it clear  and lucid. More elaboration is needed on the SNP itself and the reason for not addressing the gene dosage effect and grouping both carriers and non carriers together. If G allele is being purported as the protective allele then additional analysis with just the GG genotype is needed to support this claim.


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: CAN 9Q34.2 RS633862 POLYMORPHISM PREDICT SURVIVAL IN EPITHELIAL OVARIAN CANCER?
Review round: 1
Reviewer: 2

Output:
Basic reporting: Literature references, sufficient field background/context provided
Data missing for study group as detailed below
Experimental design: Study group design-
1. Separating loss of follow-up and death from the disease may better clarify survival analysis

2. Time at enrollment is not stated. Importance arises weather neoadjuvant chemotherapy was introduced to advanced stage disease at time of enrollment. The same pitfall for discussing survival analysis is also true for treatment with Bevacizumab as it is a factor for prolonged survival in a subgroup of ovarian cancer patients. If so, this needs to be discussed as an optional explanation for survival difference.

3. There is a need for sub classifying EOC by histological subtypes as the prognosis is different. HGSOC comprised 71% of EOC in this study. Are the results true for other subtypes of EOC apart from HGSOC?

4. There is missing data regarding how many patients had reached to follow up and was there a difference between the groups in that matter?
Validity of the findings: See above
Additional comments: Research question well defined, relevant & meaningful dealing with front research in oncology

In summary, representing the study group by histologic subtype, number of patients reaching to follow-up, stage of the disease and novel treatments relevant for accepted treatment of ovarian cancer today my explain survival difference ruling out the hypothesis of this study


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: CAN 9Q34.2 RS633862 POLYMORPHISM PREDICT SURVIVAL IN EPITHELIAL OVARIAN CANCER?
Review round: 1
Reviewer: 3

Output:
Basic reporting: The report is clear and well written and professional English is used through out . References are  up to date and relevant. There is a few typos to be corrected in subediting. Reference 1 Angelov et al. should be 2014 not 1900.

Tables and figures are relevant and clear.
Experimental design: The research question is well defined, relevant and original.
Methods appear to be well decribed.
Validity of the findings: The data is well presented and appear statistically sound. Limits of the applicability are acknowledged.
Additional comments: Congratulations on an excellent paper. I support the publication this manuscript.


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

Input:
Title: CAN 9Q34.2 RS633862 POLYMORPHISM PREDICT SURVIVAL IN EPITHELIAL OVARIAN CANCER?
Review round: 2
Reviewer: 1

Output:
Basic reporting: Several grammatical and spelling errors need to be rectified in the manuscript.
Experimental design: Comments have been addressed
Validity of the findings: Comments have been addressed
Additional comments: The authors need to address the discrepancy regarding the expression data. In the manuscript text they report that AA genotype has increased mRNA expression whereas the Gtex data (figure 2) states that GG genotype has increased mRNA expression.
Also, in the text they report "rs633862 G→A variant may regulate ABO expression" whereas it technically should be A->G since

All other comments have been addressed.


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: WATER ABSORPTION THROUGH SALIVARY GLAND TYPE I ACINI IN THE BLACKLEGGED TICK, IXODES SCAPULARIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please see comments to author.  Minor adjustments are needed.
Experimental design: No Comments
Validity of the findings: Please see comments to author.  Minor adjustments are needed.
Additional comments: Reviewer comments to the submitted manuscript entitled, “Water absorption through salivary gland type I acini 1 in the blacklegged tick, Ixodes scapularis” by D Kim and colleagues.
In the present study, the authors perform a number of molecular and physiological analyses to demonstrate the mechanisms of water absorption and rehydration through the tick salivary gland. The authors go on to suggest that type 1 acini are responsible for water balance, which is a nice addition to Y. Park’s previous work focused on the neuroendocrinology of tick salivation.  The authors suggest the Na+-K+-ATPase protein may represent a target site for tick control, but this reviewer thinks the potential for exploiting this target as a site of control is limited. This reviewer does not see any glaring errors in the research design or the presentation of the data.

The manuscript is well written with very few grammatical errors, repetitions, or incorrectly cited references.  The data are clearly presented.  There are a few minor revisions that are suggested:

1.	Previous work by D Kim and Y Park has shown evidence that the Na+-K+-ATPase pump is involved in ion secretion rates.  It is likely that the water secretion is due to the development of an osmotic gradient that is derived from an electrochemical gradient that facilitates the transport of anions.  However, the authors show the Na+-K+-ATPase is expressed in the type II and III cells for ion secretion whereas this study suggests the Na+-K+-ATPase is responsible for water balance in type 1 cells.  This reviewer suggests discussing the expression patterns of Na+-K+-ATPase and the potential implications for osmotic regulation and maintenance.
2.	  Line 85: This reviewer suggests including the final concentration of rhodamine in the feeding studies versus the volume and starting concentration.
3.	Line 117: was this water labeled with Rho123?
4.	Methods: It would be beneficial to include a statistics section that highlights the number of replicates, statistical analyses used, etc
5.	The data presented in lines 174-184 assume that oaubain is inhibiting a membrane expressed Na+-K+-ATPase pump.  However, this molecule is not completely specific for Na+-K+-ATPase and has been shown to alter calcium cycling, mitochondria functioning, etc.  Either of these will most certainly alter the function of the salivary gland acini and should be addressed with additional studies or, at a minimum, a more thorough discussion.
6.	Lines 231-240: Historically, RNAi has had difficulties penetrating through the basement membrane of tick salivary glands and has been shown to be marginally effective at reducing mRNA constructs.  Therefore, the assumption that the inability to reduce Na+-K+-ATPase mRNA due to a long half-life is a large assumption and should be softened.   Also, it would be of great benefit to include a figure showing the RNAi knockdown in the synganglion lading to reduced feeding.


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: WATER ABSORPTION THROUGH SALIVARY GLAND TYPE I ACINI IN THE BLACKLEGGED TICK, IXODES SCAPULARIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript by Kim et al., "Water absorption through salivary gland type I acini in the blacklegged tick, Ixodes scapularis" is well written and addresses an important topic, water balance in ticks. This work builds on these authors previous studies. However there are concerns to this current version.

The general concern is that its unclear in this manuscript why this was conducted. Authors should clearly state the objectives of this study, how data in the manuscript accomplished these objectives. What is the implication or contribution of these data to tick physiology?

Some specific objectives include
1. Explain the formula that was used to calculate the volume of water that was imbibed by ticks.
2. Clearly state controls
3. Results section lines 195-199 did not make sense, what does natural behaviors in drinking water?
Experimental design: Experiments not well described, please explain your controls
Validity of the findings: Difficult to determine in absence of well explained controls
Additional comments: Explain objectives and how data here met those objectives


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: WATER ABSORPTION THROUGH SALIVARY GLAND TYPE I ACINI IN THE BLACKLEGGED TICK, IXODES SCAPULARIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: This research is properly designed and described
Validity of the findings: Conclusions are well stated otherwise I have no comments
Additional comments: An important contribution to the literature on salivary glands of ixodid ticks. The only error I could find is the incorrect authorship for a cited paper which should read as follows:
Needham G, Rosell R. Greenwald L. and Coons, LB


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: LAND SNAILS OF LEPTOPOMA PFEIFFER, 1847 IN SABAH, NORTHERN BORNEO (CAENOGASTROPODA: CYCLOPHORIDAE): AN ANALYSIS OF MOLECULAR PHYLOGENY AND GEOGRAPHICAL VARIATIONS IN SHELL FORM
Review round: 1
Reviewer: 1

Output:
Basic reporting: This preliminary study of Leptopoma from Sabah is interesting and important because:
a)	because studies on the molecular systematics of Cyclophoroideans and the Familt Cyclophoridae are few and far between and this study is the first of its kind for the genus Leptopoma and
b)	 because it seeks to explore the utility of traditional shell-based taxonomic characters in a quantitative way.

Overall it meets all 5 of the basic reporting requirements, but I recommend that the following changes should be made:
-	The sampling for the molecular component of their study is limited so they need to state in the discussion that this is a preliminary study looking at a small individuals at a small number of sites and adapt their discussion accordingly
- e.g. clearly highlight the localities sampled in the phylogeny on the map in Figure 1 so that readers can differentiate those localities from all other sites.
- 	Avoid repetition – don’t repeat what has been said in the introduction in the  discussion and conclusions
-	Standardise and explain/refine terminology and use it in a consistent way.
- e.g. Explain what is meant by shell form right at the beginning of the article by stating that it  includes all shell morphological characters (shape, colour pattern, ornamentation). Actually, I would avoid using the word ‘form’ in this context because it often implies shape/size or colour pattern. Instead I would use shell morphology here and use form in the context of the 8 colour patterns - you can refer to these as colour forms. In this way you avoid confusion with your other use of shell colour pattern (i.e. one of the 3 characters used to define the 8 colour forms)
- e.g. replace the term ‘apertural ring band’ with ‘apertural ring’ or ‘apertural band’
- e.g. Don’t use alternative terms such as characters/traits – stick to one option – seeing as this is a taxonomic paper I would use characters and drop the use of traits.
Experimental design: Overall it meets all 5 of the experimental design requirements

Obviously a lot of thought has gone into the experimental design and an attempt has been made to use some very recently developed tools/ approaches – that’s very commendable as is the effort that has been made to explore morphological variation in a quantitative way – the authors are really trying to tackle a difficult problem boldly. That said, they shouldn’t overemphasise the broader relevance of their findings, but more on this below.
Validity of the findings: While the authors’ data/results do support their conclusions, they shouldn’t overemphasise the generality of their results. There are three issues here:
1)	Having only sampled 4 of the c. 100 species in the genus they shouldn’t conclude that their results are generally applicable to the whole genus. Clearly their findings indicate that there may be a wider problem, but this issue has still to be investigated.
2)	Nowhere is it made clear what the global ranges of the 4 Leptoma species. Are these species endemic to Sabah? Or are these species more widely distributed? I think it is important to provide a little information on this in the methods or even in the intro. e.g. Species X has a range encompassing the Malay Peninsula, and the islands of Borneo and Sumatra. Provide references as appropriate/if available. If most of what is currently known is largely based on the BORNEENSIS dataset the authors should make this clear.
3)	As with 2), it is not clear how representative this study is in terms of the overall species richness of Leptopoma in Sabah. What proportion of Sabah’s Leptoma species are included in this study?

In the discussion the authors need to briefly lay out what they would do to improve the design so that they can improve their understanding of the Sabah Leptopoma and broaden the relevance of their findings e.g. improved sampling from across the ranges of the 4 species, improved population sampling.
Additional comments: I have made lots of suggestions directly on the pdf of the MS - please have alook at these. Please also re-write the abstract to reflect the changes I have suggested. Make it clear in the abstract that the study is based on a new/recently gnerated datatset, that your study deals with the taxonomy of 3 species in Sabah and that your findings necessarly reflect this - i.e. avoid extrapolating from your study to the whole genus.

I look forwad to seeing more from the authors on this very interesting and intriguing system and it is great that they are trying to quantify shell characters even though it is an extremely challenging thing to do.


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: LAND SNAILS OF LEPTOPOMA PFEIFFER, 1847 IN SABAH, NORTHERN BORNEO (CAENOGASTROPODA: CYCLOPHORIDAE): AN ANALYSIS OF MOLECULAR PHYLOGENY AND GEOGRAPHICAL VARIATIONS IN SHELL FORM
Review round: 1
Reviewer: 2

Output:
Basic reporting: Species delimitation is known to be problematic in the genus Leptopoma, which is traditionally classified based solely on shell morphology. This is an interesting study to investigate the molecular phylogeny of similar-looking species in Sabah, and examines the reliability and suitability of some conchological characters for species delimitation in two polymorphic species that occur sympatrically. The figures and tables are clear, and as a whole, the manuscript is well structured. Nevertheless a slight change in the title is suggested because there is insufficient evidence to suggest that the variations are due to geography.
Experimental design: Adequate and methodical.
Validity of the findings: The findings are sound. The unreliability of certain characters, notably shell colour and patterns, used in shell morphology based taxonomy are well elucidated by the results.
Additional comments: I suggest that the introduction include a little explanation regarding the presence of a “dark ring band” in the aperture of some specimens of both Leptopoma pellucidum and L. sericatum.  It is not apparent whether this character is only found in the Kinabatangan population and nowhere else. Is this found only in gerontic shells with a much thickened outer lip? As the authors have mentioned in the discussion, this interesting character has not been noted in other works. Hence some details will be informative.

The problem of species delimitation with intermediate shell forms has not been properly treated? Were intermediates sequenced or included in this study? I would be interested to know the status of these intermediates.

Most experienced taxonomists are well aware of the limitations of using shell colour and patterns for species identification. For example many fossils and subfossils, especially of extant species, without discernible colour can usually be quite easily identified by the relevant experts. Students however, often use colour and patterns in their initial attempts at classification. Perhaps a sentence could be added in the conclusion to emphasize the reliability of the ‘hard’ characters such as shell surface sculpture, spire profile, and shape, over colour and patterns.

Overall, the MS is clear and well written. However the language still requires a bit of attention. This is nevertheless a very minor issue and does not affect the quality of the study. I have made some slight edits on the marked PDF attached.


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: PROTEOMICS RESEARCH AND RELATED FUNCTIONAL CLASSIFICATION OF LIQUID SCLEROTIAL EXUDATES OF  SCLEROTINIA GINSENG
Review round: 1
Reviewer: 1

Output:
Basic reporting: I found that the manuscript had a large number of sentences that need to be rewritten in clear and unambiguous English, and would recommend that the authors get some help in writing the manuscript.   Some of the sentences that I found to be unclear can be found on lines 38, 121,123, 150, 174, 190, 276, and 290.

I found that the materials and methods section was very difficulty to follow.  In multiple instances important information was lacking.   For example, it's unclear whether multiple gel slices were used for the proteomic analysis or if the entire protein mixture was included in a single analysis.  Items like the composition of Buffer B (line 150) or what's in the solutions 1, 2 and extraction buffer (lines 139 - 145) need to be added.   To summarize, the entire materials and methods section needs to be rewritten.

The authors did not include all of the references from the text in the References.  For example they cite an article from Georgios et al, 2012 (lines 254 and 315) on Neurospora chitinases, and don't include the reference in their references cited.  In line 315 the reference is given as evidence that the chitinases are used during sclerotia formation.  While I don't doubt that chitinases are expressed during sclerotia formation, the reference is for Neurospora crassa, which does not make sclerotia - the reference doesn't apply to the statement being made and should be deleted from line 315.

I would also strongly request that the authors include a figure of the gel electrophoresis.  This is a vital piece of data that needs to be included.

Another very important element that is lacking is a much more detailed analysis and discussion of how their results for S. ginseng exudates compares to analysis of Liang et al on the proteins in S. sclerotiorum exudates.  The authors practically ignore the excellent proteomic analysis for S. sclerotiorum exudates even though they are using the S. sclerotiorum genome as their basis for identifying their proteins.  A close examination of the Liang et al paper will be instructive to the authors on how they need to present their findings.   My examination of their findings would indicate they haven't found anything new or novel.

I also think that the authors need to re-examine their discussion section and the references they are using to make sure they more accurately present the research literature and how the findings add to that literature.  For example, the work of Colotelo and it's relationship to their work would be a good topic to discuss.
Experimental design: It is difficult to assess the experimental design for the proteomic analysis because the materials and methods section lacks key information about how the experiments were conducted.   The basic approach is sound and the type of information they obtained seems to be what one would expect.  The research question is well defined but a more rigorous comparison with what is known about exudates in other Sclerotinia species would be helpful.  One major flaw in the analysis is that the S. ginseng genome is not available and so the S. sclerotiourm data-base was used.   Although I understand that they couldn't use the data-base for the organism being studied, the problems with using another data-base are not discussed or addressed in any way.
Validity of the findings: The data does seem to be robust and statistically sound.
Additional comments: Although I think a proteomic analysis of Sclerotina exudates is a good research project, I can not recommend that the article be published.   I would recommend a total rewriting of the article with the inclusion of key information that is currently lacking (like the gel picture, and a comparison to other exudates).  I think the materials and methods section needs to be completely rewritten to include a clearer narrative of how the experiments were performed.   The current discussion section is lacking key analyses.   As mentioned above, the Liang et al article covers the same type of analysis and would be a good model for the authors to follow.


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: PROTEOMICS RESEARCH AND RELATED FUNCTIONAL CLASSIFICATION OF LIQUID SCLEROTIAL EXUDATES OF  SCLEROTINIA GINSENG
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is sufficiently concise and well-written, and provides necessary background an experimental details.

The raw data has not been shared.  At a minimum, the peptide sequences should be made available for the matched peptides.
Experimental design: Experimental design is acceptable.  Although there are no independent replicates, the objective is merely to identify proteins present, not quantify them.  Exudates from >600 plates were collected, so this provides some pseudoreplication that is sufficient for this purpose.
Validity of the findings: Findings are valid and sound, except as noted in the General comments for the author (below).
Additional comments: If the journal format allows it, the Results & Discussion sections should be combined.

In any case, most of the Discussion is not relevant, and does not draw on or reference the Results.  For example, lines 300-311 (about the droplet morphology) are in fact new results that were not presented in the results section.  Regardless, the information lines 300-311 is not particularly useful or relevant, or well-supported and thus should be removed.  Lines 287-293 provide very general information about proteins and could also be deleted.

A list of peptide sequence for the identified peptides should be provided, if not the raw spectra.


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: PROTEOMICS RESEARCH AND RELATED FUNCTIONAL CLASSIFICATION OF LIQUID SCLEROTIAL EXUDATES OF  SCLEROTINIA GINSENG
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript has been greatly improved.   I find the English and the referencing of the research literature to be acceptable.
Experimental design: The revised Material and Methods section has been rewritten and is much improved.  The only comment I have is that the authors used a Bradford assay to determine the protein concentration in their concentrated exudate sample (line 118), which contained 2% SDS.  Generally the Bradford is not used for protein determination with SDS containing samples since SDS affects the assay.  However, they might have used the Bradford assay and included SDS in their standard curve.  I would simply ask the authors to double check whether they used the Bradford or some other assay for protein determination and if the Bradford assay was done and the standard curve was generated in an SDS solution to state that this was the case.
Validity of the findings: The data presented clearly identifies a number of proteins in the S. ginseng exudate.   Since a similar study with S. sclerotiorum exudates has been done, I do not see their findings as being especially novel, but their report does add to the information about fungal exudates.   Their conclusions are well stated and supported.
Additional comments: The manuscript has been substantially improved by the rewriting process.


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: PROTEOMICS RESEARCH AND RELATED FUNCTIONAL CLASSIFICATION OF LIQUID SCLEROTIAL EXUDATES OF  SCLEROTINIA GINSENG
Review round: 2
Reviewer: 2

Output:
Basic reporting: Revised manuscript is now acceptable.
Experimental design: Revised manuscript is now acceptable.
Validity of the findings: Revised manuscript is now acceptable.
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: RECORD BREAKING ACHIEVEMENTS BY SPIDERS AND THE SCIENTISTS WHO STUDY THEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, the paper is clearly innovative and has the potential to provide valuable contribution to the field of arachnology.

However I believe that its main focus can become ambiguous, since some of central terminology used can be misinterpreted. Particularly the term "record", which in arachnological research is often linked to geographical occurrences of species.
(eg.
Estol, N. and RODRIGUES, E.N.L., 2017. A new species and a new RECORD of the spider genus Nesticus (Araneae, Nesticidae) from southern Brazil. Zootaxa, 4231(4), pp.564-566.

 Malamel, J.J. and Ambalaparambil, S., 2017. First RECORD of Epidius parvati Benjamin, 2000 (Araneae: Thomisidae) from Pathiramanal Island, India. Check List, 13(3), p.2114.

DEMİR, H., SEYYAR, O. and NAJİM, S.A., 2017. Thomisus citrinellus Simon 1875 is a new RECORD (Araneae: Thomisidae) for spider fauna of Iraq.
)

 This does not mean the title should loose it's outreach message, or its focus towards reaching and engaging with a broader audience. In fact the title can be rewritten to reinforce this objective, while making it clear what "record" means in this context (eg. Record breaking achievements by some of the world's smallest champions: A scientific frame work for the first database of World Record Holding Spiders).

The title section "a resource for using organismal biology as a hook for science learning" is neither intuitive to understand (e.g. organismal biology), nor a part of the publication analysis.

I don't disagree with the statement, and potential areas towards which the publication can be impactful should be mentioned, but since they were not a part of the analysis, it is my personal opinion that they should not be referred in the title.

Literature references provide a good background in the context of this research, but were neither exhaustive, not systematic. It is perhaps impossible, or unfeasible to produce on a comprehensive scale, but it would be clearly valuable to produce a systematic one (I mention this approach in more detail at the "validity of the findings" section).
Experimental design: The primary research fits well within the area of "Literature Review Articles"and this was how I accessed it's scientific and methodological merit.

The work is relevant and meaningful, but I don't  believe the research question was well defined, and it doesn't state clearly how it fills and identifies knowledge gaps. I believe this is mostly due to to a lack of a rigorous approach, and a lack of information on how to replicate the study.

Although this was not (neither can it realistically be) a comprehensive review of spider record holding achievements published in the literature, it is my opinion that the authors should:
a) have built a structured scientific framework for the set of traits that can be measured or analysed in a standard way, and b) attempt to produce a comprehensive or representative systematic bibliographic review. An approach which would not only enhance the manuscript but also allow for it's reproducibility.

Therefore, I would strongly encourage the authors to use their "Brief Introduction to Spiders", as base point to define which metrics can be considered for record achievement (including the ones which were considered but no scientific data was found). Generating a framework that methodically revises the current knowledge and pinpoints unstudied fields of research, allowing other arachnologists to built upon it.

In practice, I am suggesting revising the proposed "four general categories" in a methodical manner.
(E.g.
 Category II - Morphology
      Section a - Prossoma
           Characters 1 - external;
                  Traits: Overall traits (biggest/smallest; proportionally larger/smaller; flattest/tallest carapace, most/least colourful...)
                            Eyes (largest/smallest; proportionally larger/smaller...; for best eyesight see cat.III physiology)
                            Chelicerae/fangs (longest/shortest; proportionally larger/smaller; wider/thinner...; for venom toxicity or wider opening angle see cat.III physiology; for quicker closing time see cat. IV behaviour)
                            Ornaments (hairiest/baldest; most cuticular spines - Aphantauchilus...

            Characters 2 - internal;
                  Traits: Venom gland (smallest/biggest; proportionally larger/smaller; etc...; for venom toxicity see cat.III physiology)
                             Brain (smallest/biggest; proportionally larger/smaller; ... for best memory see Portia fimbriata cat IV behaviour)

      Section b - Opistossoma
          Characters 1 - external;
                 Traits: etc...
)

This sort of methodically approach (eg. comprehensively listing all morphological traits that can be feasibly measured) would facilitate the analysis of the database, and the detection of unstudied/unrecorded areas, and when broadly applied to all the categories explored would not only include more physiological traits (eg. longest/largest/smallest male/female reproductive organs), but also:

- more environmental features (e.g.  the hottest/coldest habitat dweller);
- more behavioural traits (eg. the loudest spider, see  Allard, 1936, Davis, 1904; Edwards, 1981, Lahee, 1904; Prell, 1916; Rovner, 1980; Uetz& Stratton, 1982);
- physiological achievements (eg. longest period under freezing temperatures, longest time under water, see Pétillon et al. 2009)
- more behavioural achievements (eg. organic projectiles other than silk, since spiders are able to project venom - Scytodes, or excrete liquid from their anus - Hummidia, to considerable distances);
- other traits (eg. best body mimic: of leafs -Arachnura, of toads - Poecilopachys australasia; of ants - Aphantauchilus; most realist body double - Cyclosa sp.; etc...)

All of which clearly fit the publication premise but were not assessed, potentially because these traits were not researched methodically, but rather collected out of availability.

No such list can ever be truly comprehensive, but I believe this approach, even if it generates multiple unknown record holding positions, would clearly allow for gaps to be made clearer, and incentivise other to either provide information about those gaps, or  research those fields.

Another way to tackle large data gaps, might also be the analysis of local record holders (eg. the most venomous spider in Europe, or the most venomous in the US).

Besides producing a rigorous analysis of traits, I would also suggest the authors to perform a systematic bibliographic review on all, or at least on one of the category keywords (as a sampled approach). Using a reference-based search strategy, which would be both reproducible and insure that all the bibliography currently available (in the selected database) was comprehensively revised.

As a guideline I recommend analysing the methods used in:

Savilaakso, S., Garcia, C., Garcia-Ulloa, J., Ghazoul, J., Groom, M., Guariguata, M.R., Laumonier, Y., Nasi, R., Petrokofsky, G., Snaddon, J. and Zrust, M., 2014. Systematic review of effects on biodiversity from oil palm production. Environmental Evidence, 3(1), p.4.

Reed, J., van Vianen, J., Foli, S., Clendenning, J., Yang, K., MacDonald, M., Petrokofsky, G., Padoch, C. and Sunderland, T., 2017. Trees for life: the ecosystem service contribution of trees to food production and livelihoods in the tropics. Forest Policy and Economics.
Validity of the findings: As it stands the results can be considered inconclusive, however the suggestions made above should allow the publication to obtain robust data that provides statistically sound conclusions on which specific areas or research fields have been the most, and the least investigated in arachnological literature.
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: RECORD BREAKING ACHIEVEMENTS BY SPIDERS AND THE SCIENTISTS WHO STUDY THEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper does not necessarily take a form of hypothesis-test setting. Various interesting records about spider are presented, but these records are not related to each other, and are not well integrated in discussion. Therefore, I feel that this paper was somewhat descriptive and distracting. In review thesis, the authors should find new perspectives from heterogeneous findings and phenomena.
Experimental design: No comment.
Validity of the findings: This is a very useful review that allows ordinary people to access interesting records of spiders. However, as it is a list of known facts, it seemed that there is lack of heuristic elements. I felt that it is necessary to find synergistic findings obtained by gathering various records of spiders. As the authors say, it would be better to provide examples of creative discussion (L.708-709).
Additional comments: This paper is an article that summarizes interesting records of spiders with World Record format, based on academically correct information to remove the misunderstanding concerning spiders. Because it is an unprecedented type of paper which is different from the typical review article, it is very difficult to evaluate, but I felt that it could be useful literature to inform the spider world. On the other hand, from the viewpoint of academic novelty, I felt this paper is somewhat descriptive, and the new perspective obtained by gathering many records is unclear. Also, from the viewpoint of generality, since this paper only focuses on the spider topic, I got a somewhat specific impression. In order to emphasize “spider’s greatness”, I think that it would be better to have a comparison with world records of other taxonomic group such as insects. I think that this paper does not necessarily need to be published in the general science journal, and recommend submission in another journal dealing more specifically with entomological or arachnological issues.


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: RECORD BREAKING ACHIEVEMENTS BY SPIDERS AND THE SCIENTISTS WHO STUDY THEM
Review round: 1
Reviewer: 3

Output:
Basic reporting: Review of Peer J #18552
This is an interesting paper that brings together information about spider biology and taxonomy with the intend to inspire the public and educators to engage with the natural world. I agree that spiders have a privileged position as most people have some opinion about spiders and often react positively when provided with more information.
Overall, I believe this paper will make an interesting contribution and only have  few comments to make about its readability.

Writing style – overall the paper is very well written and entertaining to read. My comments are:
The terminology used throughout the paper is confusing and makes it unclear who the intended readership is. Is it biologists? Is it lay-people? If it is the later, then terms need to be explained.

Throughout (e.g. 60, 62) phrases are placed in parentheses, but they do not have to.
75-76: sentence too long and convoluted – please rephrase
Overall the introduction is quite lengthy and could be shortened and sharpened. Eg. Is 87-92 necessary?
106: Here we build on records from the scientific…
140: The body of a spider is divided….
140 and onwards – please refer to Fig 1
146 & 147 & 149: ‘behind’…some of the terminology used in this paper is quite sophisticated, so I do not see why the term ‘posterior’ cannot be used instead of ‘behind’
152: from the ophistosoma
156: terminology already explained earlier
162: remove ‘so called’
163: explain terminology earlier
174: why what?
177: use the term ‘collaboratively’
178-181: repetitive
187-190: repetitive
223: First and last listed spider
238: what do the terms in the parentheses mean?
237-239: sentence complex and convoluted, please rephrase
244-245: please explain these obscure terms (nomen dubia; synonymized)
313: explain GB
340: explain holotype
375: the least number…
376: explain anophthalmic
384: capable of spinning…
386: ‘dimension’ – do you mean ‘diameter’?
394: explain MJ
397: explain GPa
418: why ‘sic’
419: explain hypogean
426: greatest longevity
482: in what year?
547: what do you mean by conscious?
581: a small number…
620: plant products
688: I found the discussion quite repetitive, with arguments that have already been presented in earlier sections.
Rather than repeat this information, maybe the discussion could provide some examples of how educators might utilise this information
Experimental design: no applicable
Validity of the findings: not applicable
Additional comments: The idea of this paper is great, I really like it and it almost works, but for the Discussion which needs some work.


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

Input:
Title: RECORD BREAKING ACHIEVEMENTS BY SPIDERS AND THE SCIENTISTS WHO STUDY THEM
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revision of the Discussion section by the authors seems to solve the problems I was concered about in the previous review. English expression and cited references are also appropriate.
Experimental design: no comment
Validity of the findings: I think that the purpose and perspective of this paper became clear by the revision of the Discussion section. No problem.
Additional comments: In the previous review, I was concerned about whether this MS fits the concept of the "PeerJ", but  I changed my mind that there is no problem with this point after reading the author's response. In my country, there were no such literature which summarizes interesting records of spiders, so it seems very useful for widely communicating the attractiveness of spiders to people. Additionally, I think that this review is meaningful in presenting a new framework of the review paper. I judge that this paper is worth publishing.


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: RECORD BREAKING ACHIEVEMENTS BY SPIDERS AND THE SCIENTISTS WHO STUDY THEM
Review round: 2
Reviewer: 2

Output:
Basic reporting: Review Peerj-18552

I have seen the original version of this manuscript and the authors have addressed my concerns. In particular, the discussion is much improved. I only have picked up a few minor items.
Line 61-62: remove – unsubstantiated claim
333: the term ‘orb-web spider’ is more accurate. Spiders don’t weave
361: are fangs different from chelicerae? Please check terminology
402: so there are no species that have lost the venom gland? Can you clarify this point? See line 454
466: there are plenty of original papers that attest to the visual acuity of jumping spiders (e.g. work by Zurek)
499: eggs and sperm
Experimental design: no applicable
Validity of the findings: not applicable
Additional comments: Review Peerj-18552

I have seen the original version of this manuscript and the authors have addressed my concerns. In particular, the discussion is much improved. I only have picked up a few minor items.
Line 61-62: remove – unsubstantiated claim
333: the term ‘orb-web spider’ is more accurate. Spiders don’t weave
361: are fangs different from chelicerae? Please check terminology
402: so there are no species that have lost the venom gland? Can you clarify this point? See line 454
466: there are plenty of original papers that attest to the visual acuity of jumping spiders (e.g. work by Zurek)
499: eggs and sperm


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: COMPARATIVE GENOMIC ANALYSIS OF THE PKS GENES IN FIVE SPECIES AND EXPRESSION ANALYSIS IN UPLAND COTTON
Review round: 1
Reviewer: 1

Output:
Basic reporting: The MS (##18119) reported the PKS genes and its expression profile in upland cotton. The results are overall interesting and could be published. However, the MS is poor prepared. Please see my comments and suggestions below!

Overall,  I think there are three major problems should be addressed.
1. The PKS genes were found in many plants. why are the PKS genes selected from these species (Populus tremula, Vitis vinifera, Malus domestica, and Arabidopsis thaliana) compared with cotton PKS genes?
2. Most figures are too small to see clearly.
3. There are many mistakes in the MS, including abbreviations, spaces between words, singular and plural, etc. The English language should be improved. I suggest that you have a native English speaker review your manuscript.
Experimental design: no comment
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: COMPARATIVE GENOMIC ANALYSIS OF THE PKS GENES IN FIVE SPECIES AND EXPRESSION ANALYSIS IN UPLAND COTTON
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript needs extensive editing to improve its language and grammar. For example, the first abstract seems to be less well edited and states “Plant type III polyketide synthase can catalyze into a series of secondary metabolites …”. I believe the authors meant to write that PKS can catalyze reactions forming secondary metabolites. Line 25 should read “ … candidate genes involved in brown cotton fiber synthesis …” rather than ““ … candidate genes involving in brown cotton fiber synthesis …”. I think that the column heading in Table S2 should read “No. of exons” rather than “No. of extrons”. There are other sentences throughout the manuscript that need to be edited.

The introduction should lead the reader to understand why the problem is important and why certain genes are studied. The article aims to study the plant polyketide synthase genes in upland cotton and compare them to other plant species. This is a valid and appropriate question but the introduction could be improved to state any specific and additional reasons as to why this question is important. For example, is the pigmentation of brown cotton fibers of great commercial importance because it commands a higher price? Is the study of PKS genes in upland cotton also important because PKS genes might be implicated in stress response and tolerance, thus helping to produce sturdier versions of a very widely grown crop?

All acronyms should first be introduced with their full names and then used thereafter. For example, CHS is first used in line 41, and the reader is only introduced to the full term in line 60. Also, it is initially unclear why CHS is discussed until about lines 70-80 where it is explained that CHS is an important PKS gene involved in many processes including the regulation of pigmentation.

All previous results and data mentioned in the manuscript should refer to the appropriate publications. For example, line 83 mentions that the upland cotton genome has been sequenced and assembled but no citation is given. In addition, appropriate scientific names/accession names of the upland cotton and brown cotton lines.

All the software tools mentioned such as DNATOOLS, MEGA, Plantcare etc.  should also be accompanied by the citations of any respective publications. For some of the previous results mentioned, it is not clear which publication is the relevant citation. For example, two papers are simultaneously cited in line 197, but it is not clear whether they both mention the increase in chalcone synthase activity or if one of them is about the four PKS genes mentioned next.

Some of the figures are too small to be legible. Specifically, Figures 4, 5, and S1 are not legible in the current resolution and size.

Line 342 mentions Li T 2012 but this publication is not listed in the references.
On line 411, Cao et al., 2016 is cited for the discussion of comparative tandem duplication and fragment duplication evolution rates. Is this the first or most prominent publication finding this result?

Figures 5 and 6 represent the experimental data generated in this manuscript, and the raw data for these figures has been provided.
Experimental design: I do not have any major objection to the scientific validity of the methodology of the experiments and the bioinformatics analyses carried out by the authors. This review is not supposed to judge the impact or novelty of the results and findings. However, it will be very useful to the reader that the results presented here are discussed to illuminate the broader scientific questions they answer or raise. For example, line 234 makes a broad statement that the different motifs found in the different sub-families may be important for the different functional roles performed by the proteins. This seems like a truism, and I suggest the authors try to discuss whether anything is known about the functional role of the motifs they find in the PKS genes studied. Currently, all that the manuscript mentions is that the motif annotations were taken from SMART and Pfam databases. The division into general and specific motifs is due to their abundance in the genes studied, but Cao YP, 2016. I believe the same paper is elsewhere cited as Cao et al., 2016. Is this the same paper? Why is this relevant to the differentiation between general and specific motifs?

The method used to differentiate between tandem and fragment duplication should be clearly mentioned.

The authors discuss the relevance of the Phe sites in the PKS genes, and line 258-260 mentions that these sites are related to the decarboxylation reaction of malonyl CoA. Please provide a reference for this statement. Subsequently, it is mentioned that the second Phe is substituted by Tyr in certain genes and Thr, Gly, and Ser are also replaced in some genes. For these and other substitution sites, is it possible to differentiate between highly conserved sites, background drift, and positive selection? Can the authors calculate site-specific substitution rates or use some other appropriate method to comment on this?
Validity of the findings: As mentioned earlier, I would strongly suggest the authors to discuss the broader scientific context of the specific and quantitative results presented. For example, what is the importance of studying the chromosomal locations of the PKS genes? Is this used to identify the genes as the result of tandem and fragment duplication?

I do not have any major objection to the data quality and the conclusions drawn.
Additional comments: Overall, the manuscript uses appropriate experimental and analytical tools for the questions it studies. The study of genes involved in pigmentation in brown cotton fibers and the PKS genes in upland cotton have scientific and commercial importance.

The manuscript needs major editing for language and presentation. In addition to correcting grammar, some paragraphs, especially in the introduction should be rearranged for better logical flow. This will help the reader and also allow for a better peer review once any ambiguities and distracting language problems are removed.

I have suggested one additional analysis: assigning the site substitutions discussed in the manuscript as conservatory, neutral or positively selected. If the authors feel this should not be done, please mention why it is so.


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: COMPARATIVE GENOMIC ANALYSIS OF THE PKS GENES IN FIVE SPECIES AND EXPRESSION ANALYSIS IN UPLAND COTTON
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper has a clear structure, sufficient field background, and professional figures and tables.

1. The English writing needs to improve. For example,

line 222-224, "in addition to GhPKS3 lack of motifs6,7 and GhPKS1 lack of motifs6 almost all PKS family members include motifs1,2,3,4,5,6,7 these 7 motifs." in addition to sth -> in spite of sth.
line 224-225, two predicates in "this is less Chal_sti_synt_N and Chal_sti_synt_C domain part of the phenomenon is very obvious."
line 272-273, no predicate in "In upland cotton, PKS gene distribution in A2_chr6
273 (1), A2_chr8 (2), A2_chr9 (1), At_chr11 (1), Dt_chr8 (1), Dt_chr10 (1), Dt_chr11 (4)."

2. For some unknown reason, in many sentences, two individual words are concatenated without spaces in between, making the sentences difficult to understand. For example,

line 37, PKSIand PKSIIonly -> PKS I and PKS II only
line 41, for examplechalcone -> for example, chalcone,
line 110, domainswas -> domains was
line 116, weightof -> weight of
line 113, thalianawere -> thaliana were
line 139, databaseof -> database of
line 187, anddivided -> and divided
line 307, geneswere -> genes were
line 318, functionand -> function and
line 348, onlyexists -> only exists

3. Some abbreviations are not defined. For example,

line 47, CHSL is not defined.
line 81, Proanthocyanidins should occur before PA.
Experimental design: The research fills the knowledge gap of the PKS genes in upland cotton. Some analysis needs to describe in details.

1. For example, it is not clear how did the authors derived the conclusion that no direct homologous genes between the species in line 200-201. Is there any p-value or hypothesis testing that support this conclusion?

2. The authors claimed that "gene duplication is the main driving force of the amplification of PKS III gene family" in line 447-449. However, it is not clear how the conclusion was derived based on the facts that (1) "10 gene replication events were identified in the 52 genes" in line 283, and (2) Ka/Ks<0.4 indicates negative selection in line 292. Is 10/52 significantly high? How is negative selection associated with amplification of PKS gene?
Validity of the findings: In this paper, the authors identified 11 PKS genes in the genomes of upland cotton species. The 11 PKS genes in cotton were compared with PKS genes in other plants.
The expression of the PKS genes was quantitatively measured at various growth stages and tissues. The data is solid and the analysis is sound.
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: COMPARATIVE GENOMIC ANALYSIS OF THE PKS GENES IN FIVE SPECIES AND EXPRESSION ANALYSIS IN UPLAND COTTON
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been edited and the language has improved greatly. Line 19 reads “(a)ccording to phylogenetic tree, a total of 52 PKS genes …”, which should be “according to the phylogenetic tree, a total of 52 PKS genes …” or “according to the constructed phylogenetic tree, a total of 52 PKS genes …”.

The supplementary tables S1-S5 reported in the Excel file do not have column headers.

On line 333 it says“(f)our pairs of duplicated genes belonged to tandem duplication and seven pairs of duplicated genes belonged to fragment duplication”. I understand that these genes can be identified from the figure showing the chromosomal locations of the genes, but it would be helpful if a table lists which genes result from tandem duplication and which genes result from fragment duplication.
Experimental design: Concerns raised in the review have been addressed.
Validity of the findings: Concerns raised in the review have been addressed.
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: EARLY SKIN-TO-SKIN CONTACT BETWEEN HEALTHY LATE PRETERM INFANTS AND THEIR PARENTS: AN OBSERVATIONAL COHORT STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: please see attached report.
Experimental design: Please see attached report.
Validity of the findings: please see attached report
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: EARLY SKIN-TO-SKIN CONTACT BETWEEN HEALTHY LATE PRETERM INFANTS AND THEIR PARENTS: AN OBSERVATIONAL COHORT STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: pass. see comments below
Experimental design: pass see below
Validity of the findings: pass see below
Additional comments: Thank you for allowing me to review this very well written manuscript on a population that is often ignored but have significant morbidity.  Some minor editing is needed.
I have questions and concerns related to the retrospective nature of data collection during the first 24 hours. Additional information is needed regarding the retrospective data – how was it obtained, from where and by whom. It appears that you are comparing two different data sets (first 24 hours – retrospectively collected) and (2nd 24 hours prospectively collected by a parent diary). Please clarify and discuss what the problem with this may be (needs to be in the limitation section) and also included in the discussion section.
The discussion also needs to include possible reasons why BW only a predictor for SKS care in mothers and fathers during the 2nd day as well as why primiparity may affect the amount of SSC the father participates in.
Please include a limitation section which should included lack of data concerning other comorbidities that may affect lactation (ie pregnancy induced hypertension, diabetes etc)
Clarify why you consider the sample size to be satisfactory (line 297). Was a power analysis performed?
Line 28: I suggest using a different word than advice (perhaps recommend?)
Line 74: add the word “during” after respectively.
Line 79: I suggest using a more traditional description of the study design
Line 82: it would be more appropriate to report the number of LPI infants born at this hospital
Line 84: Define assistant nurse and midwifery care
Line 88: who offered the individualized support?
Line 91: please clarify whether placing infants STS immediately after birth was part of the research protocol or a standard of care. How did you verify this occurred? What if there were no father or partner? Was data collected regarding how soon after delivery SSC began?
Line 103: I would change twins for multiples to include triplets ect
Line 128-130: this is confusing and needs clarification
Information regarding consent and approval by the ethical review board needs to be presented earlier in the methodology
Line 151: define threatening fetal asphyxia
Line 178 to 180 is confusing and needs to be rewritten for clarity
Line 244: a definition of SUPC is needed
Line 277: “facilitated” should be substituted for another word


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: EARLY SKIN-TO-SKIN CONTACT BETWEEN HEALTHY LATE PRETERM INFANTS AND THEIR PARENTS: AN OBSERVATIONAL COHORT STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thank you for the opportunity to review the manuscript entitled: Early skin-to-skin contact between healthy late preterm infants and their parents: An observational cohort study.

I commend the authors for the improved clarity of the manuscript presented.

Abstract Background; the term breastfeeding you could quantify this for the reader as you report exclusive breastfeeding in the conclusion. I perhaps would add :
“its associations with breastfeeding (exclusive and any) ….

Results section Abstract; I suggest that the authors: use confidence intervals (CI) and not p values in the abstract. If using p values report with up to 2 significant digits and a maximum of 3 ( p=0.12, p=0.001) see:  Lydersen, S. (2014). Statistical review: frequently given comments. Annals of the rheumatic diseases.

Abbreviate the term standard deviation (SD).

Results section Abstract:  it is quite difficult to make sense of so I would suggest that it is rewritten perhaps something like this;
 Sixty-four mothers spent a mean 14.7 hours,  5.6, standard deviation (SD), during the first 24 hours after birth. While Fathers (n=64) experienced a mean of 9.2 hours  3.3 (SD) ….

Conclusion: line 53. Replace the word ‘it’ with SSC
Perhaps leave the reader with an important message about SSC and the timing of it and the importance of fathers and mothers both participating rather than restating the key results.
What should be done next?

Main text
Line 211- 214 – reference needed for the statistical methods used
line 215- please state if you adjusted for confounding factors/covariants and if so which ones and why?

Results
Tables: table 1 is not clear.
 I suggest you combine table 1 (demographics) with 2 and 3 respectively. This will make it easier for the reader.
P values - report with up to 2 significant digits and a maximum of 3 (p=0.12, p=0.001)

 Day
Variable
n (%)
Mean (SD)
Unadjusted
 95% CI
Pvalue
Full model
 95% CI
pvalue
Trimmed
 95% CI
pvalue

Conclusions
A take home message is needed rather than just repeating the key results
What are the implications to practice / policy
Experimental design: no comment
Validity of the findings: Please review the conclusion; a take home statement is needed
what is the significance of the results -clinically and to policy?
Additional comments: No additional comments