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: LINKED WITHIN-HOST AND BETWEEN-HOST MODELS AND DATA FOR INFECTIOUS DISEASES: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 3

Output:
Basic reporting: In general, I really appreciate the theoretical and applied motivation for this study. I also feel that the study is timely and holds potential for applied applications of the questions raised in the paper. The paper is overall well written, thoughtfully constructed, and addresses important questions. I think the paper would benefit enormously from only a few very minor modifications.

The paper is well written, thoughtfully constructed, addresses an important question, and yields interesting and timely results. I provide a few comments and suggestions, I hope that they will prove constructive.
Experimental design: Lines 76-77: I appreciate the rigorous approach taken in the systematic review. I can’t help but wonder if your review would be expanded if the following search terms were included: cross-scale models, nested models (e.g., Gilcrest was an early proponent of these models and he uses the term nested models), in-host, among-host. In addition, I am assuming that the studies covered in the previous reviews on this topic that you mentioned were also included in your study (i.e., even if they did not appear in your Web of Science search)? For example, Hite and Cressler 2018 and Greenspoon et al., 2018, Smith and Mideo 2016 are a few examples that I do not see included in your reference list (i.e., in any of the main text or online supplementary information). I understand that this may seem like harping on a few studies not being included and I do not mean to do that. It’s just that a large portion of the current manuscript is devoted to describing the search terms. Given this emphasis, I just wonder if more studies would be included in the search terms were expanded.
Validity of the findings: In this manuscript, the authors conduct a systematic review of the literature to examine the current state of cross-scale models that integrate data into the theoretical analyses. They provide a detailed overview of the specific types of models, host-parasite systems, linking mechanisms, and sub-fields addressing these questions. Their review illustrates that despite repeated calls for data-theory integration, few studies currently meet these demands.

This study reports valid findings that appear quite timely and useful across multiple fields.
Additional comments: Lines 54-55: Are there references supporting the relationship between vial load and transmission? I know these relationships are quite difficult to obtain empirically and while this relationship is often assumed, I was not aware that there are many empirical studies that explicitly quantify this relationship. If so, providing those references would be quite useful. If not, maybe revise the sentence?


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: HOW GLYPHOSATE AND ITS ASSOCIATED ACIDITY AFFECT EARLY DEVELOPMENT IN ZEBRAFISH (DANIO RERIO)
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is a well designed study that addresses the question of the degree to which acidification plays a role in glyphosate's toxicity to zebrafish.  The results are sound and interesting, and the paper is definitely worthy of publication.

I only have a few minor comments.

ll 84-87:
"In the aquatic environment, where glyphosate is degraded to CO2 and aminomethylphosphonic acid (AMPA), which, in turn, is degraded to inorganic phosphate, ammonium and CO2, glyphosate’s half-life is estimated between 4.2 and 14 days (Giesy, Dobson & Solomon 2000, 87 Vera et al. 2010)."

It is not the case that it always degrades very quickly. Glyphosate can persist up to a year in seawater. See:

Mercurio P, Flores F, Mueller JF, Carter S, Negri AP. Glyphosate persistence in seawater. Mar Pollut Bull. 2014 Aug 30;85(2):385-90.

ll 240-241: "a lack of somite formation and eye development was not detected."

This is confusing. Somite formation was missing and eye development was not detected? Please rephrase for clarity.

l. 243
"Yet, even the embryos in glyphosate treatments that lacked tail detachment were able to move, albeit to a limited extent."
Is this a clear abnormality? Able to move prior to tail detachment?

ll. 282-283:
"around a third of the larvae did not hatch prior to 96 hpf and about 15% remained unhatched at that time point."
In other words, 33% remained unhatched at the previous time sample point?

Since the primary target of glyphosate is absent in metazoans, the toxic side-effects of

ll 437-440:
"Since the primary target of glyphosate is absent in metazoans, the toxic side-effects of glyphosate may be caused either by secondary target sites or indirectly by inhibition of the shikimate pathway in the associated microbiome of the tested animals (Samsel & Seneff 2013, Motta, Raymann & Moran 2018)."

You should reference this paper which shows that glyphosate has many off-target effects in Roundup-Ready soybean plants:

Luiz Henrique Saes Zobiole et al. Effects of glyphosate on symbiotic N2 fixation and nickel concentration in glyphosate-resistant soybeans. Appl Soil Ecol 2010; 44: 176-80.
These effects can not be due to the shikimate pathway since the plants have been engineered to be protected from EPSPS synthase inhibition.

Additional potential references:

A paper published in 2016 by Swanson et al. suggested that metabolic acidosis might be a significant contributor to glyphosate's toxicity to humans. It would be appropriate for you to reference this paper during the discussion section.

Swanson NL, Hoy, J, Seneff S. Evidence that glyphosate is a causative agent in chronic sub-clinical metabolic acidosis and mitochondrial dysfunction.  Int J Hum Nutr Funct Med 2016; 4:32-52.

The recent paper below by Ehrl et al. shows that glyphosate crosses lipid membranes much more readily under acidic conditions compared to basic conditions.  This would be a good reference for you to add as supporting evidence of increased toxicity under acid conditions.

Ehrl BN, Mogusu EO, Kim K, Hofstetter H, Pedersen JA, Elsner M. High Permeation Rates in Liposome Systems Explain Rapid Glyphosate Biodegradation Associated with Strong Isotope Fractionation. Environ Sci Technol 2018; 52(13): 7259-7268.
doi: 10.1021/acs.est.8b01004. Epub 2018 Jun 19.


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: HOW GLYPHOSATE AND ITS ASSOCIATED ACIDITY AFFECT EARLY DEVELOPMENT IN ZEBRAFISH (DANIO RERIO)
Review round: 1
Reviewer: 2

Output:
Basic reporting: "No comment"
Experimental design: "No comment"
Validity of the findings: "No comment"
Additional comments: The introduction is consistent with the proposal developed throughout the text; however, it is necessary to better describe the reason for the pH variations used in the study. It is important to include the possible consequences of pH variation at individual and population level and in which cases this happens in the environment.

It is also necessary to mention the sources of direct and indirect pollution by which pesticides come into contact with non-target organisms besides those included in the text, such as incorrect disposal of packaging and direct application (line 81). What is the pH variation that glyphosate causes in its solutions? Include reference (Line 103).

Include the reference for mortality of zebrafish with temperature variation (Line 344).

With regard to the discussions, it would be interesting to first describe the main findings in the research, and from this to align with the literature. It is also important to emphasize the importance of the parameters evaluated for the development of the embryos, when the fish suffer these changes demonstrated in the results, which can lead to adult life. In the environment, what are the consequences of animals with these deformations?

The idea of using the new herbicide is innovative. It is important to demonstrate that these new compounds do not affect biodiversity and it is possible to produce food organically with quality and quantity.


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: HOW GLYPHOSATE AND ITS ASSOCIATED ACIDITY AFFECT EARLY DEVELOPMENT IN ZEBRAFISH (DANIO RERIO)
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors contribute to the understanding of glyphosate's influence on zebrafish, an important vertebrate species, at both neutral and low pH. They also compare glyphosate's action on the zebrafish to a novel (to science), natural substance (7dSh) that also interferes with the shikimate pathway, advancing our understanding of both glyphosate and 7dSh. I recommend this paper for publication.

I have the following suggestions.

Line 96. The authors state "it could be conceivable to develop ecologically sound alternatives that can potentially substitute for glyphosate." Because the authors are familiar with the work of Brilisauer et al. at Tübingen University, and worked with the cyanobacteria antimetabolite 7dSh in this study, showing that "it neither lowers pH nor induces severe effects in zebrafish embryos (Line 465), the authors might consider reworking Line 96. For example, "it could be conceivable to develop the cyanobacteria antimetabolite 7dSh to substitute for glyphosate." I suggest the authors either say this or acknowledge that there are already ecologically sound alternatives to glyphosate for weed control and that 7dSh might be an important addition to these technologies and methods (such as those practiced in organic agriculture).  For example:

Dayan, Franck E., and Stephen O. Duke. “Natural Compounds as Next-Generation Herbicides.” Plant Physiology, vol. 166, no. 3, 2014, pp. 1090–1105. JSTOR, www.jstor.org/stable/43191531.

Line 66. Help the reader understand which list glyphosate tops (ie, sales or usage).

Line 70. The IARC's designation of glyphosate as a probable carcinogen is important to note, but consider adding citations that expand the reader's understanding of other possible adverse effects on human health from glyphosate exposure. Such as:

Swanson NL, Leu A, Abrahamson J, Wallet B. Genetically engineered crops, glyphosate and the deterioration of health in the United States of America. J. Organic Systems 2014; 9: 6-37.

Samsel, A., Seneff, S. Glyphosates suppression of cytochrome P450 enzymes and amino acid biosynthesis by the gut microbiome: pathways to modern diseases. Entropy 2013; 15(4): 1416-1463. (Which is referenced elsewhere in the paper.)

Line 78. Reference to microbial degradation of glyphosate is from 1977. Is there more current research available for citation?

Line 80. Perhaps here is a place to insert a sentence or two about the surfactants and adjuvants used with glyphosate, that have their own toxicity issues. Glyphosate is never used alone for agricultural applications. Adverse effects from spray drift and runoff are impacted by the addition of these chemical components in glyphosate formulations. Such as:

Tush, D., Loftin, K.A., and Meyer, M.T., 2013, Characterization of polyoxyethylene tallow amine surfactants in technical mixtures and glyphosate formulations using ultra-high performance liquid chromatography and triple quadrupole mass spectrometry: Journal of Chromatography A, v. 1319, p. 80-87, doi:10.1016/j.chroma.2013.10.032.

"We demonstrate that non-target effects below toxicity thresholds are not due to the declared active ingredient G but undoubtedly to the formulants alone and in formulations, as previously documented for some instances. Their endocrine-disrupting action can be explained by the membrane disruptions, where the steroidogenic enzyme aromatase is located in the endoplasmic reticulum, but may also be due to possible direct enzymatic interactions that could be synergistic with heavy metals (see below). The endocrine disruption by GBH has been observed in vivo by our group in several instances, on the androgen/estrogen balance that aromatase controls, after short-term Roundup treatment and after long-term exposure."(Tush et al. 2013)

The paper can stand alone without references to adjuvants in glyphosate formulations, but because scientific experiments and observations have shown membrane disruptions and other endocrine-disrupting action by commercial formulations, it may strengthen the impact of the authors' results that show that glyphosate alone can also cause sublethal adverse events.
Experimental design: No comment.
Validity of the findings: Results are thorough and informative, as is the data and conclusions.

Line 254. It would be helpful if it was more clearly stated that 7dSh did not induce mortality or malformations at any of the pH levels tested.

Line 369-375. Discussion of the elevated ROS is an important issue. Some discussion of elevated ROS disrupting enzymes and the importance of this would be welcome, but not necessary.

I look forward to seeing this paper published in PEERJ.
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: EFFECT OF INSECTICIDE FORMULATION AND ADJUVANT COMBINATION ON AGRICULTURAL SPRAY DRIFT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper “Effect of insecticide formulation and adjuvant combination on agricultural spray drift” focuses on the role of some adjuvants as contributing factor to reduce the drift of sprayed insecticides. The topic is relevant and interesting, and the study contributes to the knowledge of the drift phenomenon. Results are clearly reported and coherently discussed. The text is clear and well understandable. In general, the paper is relevant for its publication on PeerJ.
Some minor changes for “Material and methods” and “Discussion” chapters and for the Figures are suggested to the Authors.
Experimental design: Experimental design, mainly based on Standard protocols, is accurately described and the statistical analysis of data seems correct. However, I need to clarify some points about the experimental methods. I am adding some comments for the Authors.
Validity of the findings: In general, the results mainly confirm previous findings on this topic; however, Authors clearly discuss both the points of novelty and of weakness of their work, coherently with the data obtained in the experiments.
Additional comments: •	To improve the clarity of the paper, I suggest dividing the “Material and Methods” chapter (that is very long) in sub-paragraphs (for example: 1- field trial, 2 – ground deposition; 3- vertical deposition up to n – statistical methods).
•	Some abbreviations have to be explained when they appear for the first time in the text (i.e. CI for Confidence Interval).
•	Please, check superscript and subscript numbers in formulae and equations (H2O, cm2, etc).
•	I think that the “Discussion” part can be partly reorganized, starting from some general statements about the work to more specific comments. Please, consider moving the lines 456-464 to the beginning of the “Discussion” section.
•	Figures 2 and 3 are not very readable: it was difficult for me to distinguish the single curves and the grey area of the confidence interval make the lines less clear. I suggest trying to redesign the curves, for example plotting the CI with a fine bar than with an area.
•	In Figure 1, I don’t find the black rectangles mentioned in the caption.
•	In the Abstract (line 26) you mentioned that “the drift was reduced by as much as 37% by formulation type alone and reached 63% by incorporating certain spray adjuvant”. Firstly, I didn’t find the data of 37% reduction along the text. Please, could you put this finding more evident in the text or in a table that includes a summary of the relative effects (in %) of the treatments on the drift reduction? Then, I think that this sentence is clearer by dividing the effects of adjuvants on the drift from the intrinsic value of drift of each formulation type (it is a given characteristic of the formulation itself).
•	Line 472: is it correctly placed?
•	Line 151: what is a size of 50 mesh for the nozzle?
•	Lines 182-184: is the area of each sampling point calculated according to a Standard protocol? Why the sampling points does not fall in the center of the range shown in Table 1? (I am sorry for the last dumb question, probably it depends from the fact that I didn’t catch perfectly the sampling scheme).
•	Lines 263-269: in the efficacy test, you used a parametric method (ANOVA) to analyze the data of insect mortality. To me, it appears very improbable that this kind of data meet the assumption of normality. Please, check the data distribution normality and, if necessary, consider a non-parametric method to analyze data.


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

Input:
Title: EFFECT OF INSECTICIDE FORMULATION AND ADJUVANT COMBINATION ON AGRICULTURAL SPRAY DRIFT
Review round: 1
Reviewer: 2

Output:
Basic reporting: This submission meets all basic reporting criteria. It is especially well written and clear. The article includes sufficient introduction, however, the introductory paragraphs summarize a  lot of detailed information that are not common knowledge for most readers, so a few more citations would be useful here.
Experimental design: This is a good piece of original research. The research rational, hypotheses and experimental approach are clearly detailed.

The methods are described in especially good detail and are very unambiguous. But here are a few points of clarification that would be useful.

First, lines 99-100 mention subsamples were averaged. Just to be clear, subsamples were not analyzed as part of the model? And why not if subsampling was used as part of the design?

Beginning line 164, please clarify timing of fluorometer measurements post-sampling and/or correction of results for degradation that may have occurred prior to analysis.

Log transformation for analysis and then reporting results for the untransformed finding are always problematic in terms of interpretation, especially when continuous findings are reported. For instance, line 306 and figure 2 are summarizing predicted trends in deposition as a function of distance – both were log transformed for analysis, so do the trends still hold as presented when untransformed? Similarly, the regression equation is developed for log VMD and results are reported for change in VMD as a function of RH (line 370) and windspeed (Figure 3) – how was transformation and back transformation of analysis handled? Some clarification in the methods or results would be useful.
Validity of the findings: There are no issues with the findings. The data are robust, statistically sound (see possible exception above), and controlled.
Additional comments: Nice piece of work. A lot of good deal of effort went into these results. I addition to comments here, the annotated manuscript points out a few minor things.


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: FUZZYSPLIT: DEMULTIPLEXING AND TRIMMING SEQUENCED DNA WITH A DECLARATIVE LANGUAGE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is generally well written, and presents an interesting approach to the problem area. That said, I have some suggestions for improvements:

1 - In the FuzzySplit section, the 'Interval-length wildcard patterns' concept, needs a little more detail, in particular why such a concept is needed.

2- There is no real description of the "template language" in the manuscript, beyond the subset which is used in the Example section. This could either be done as an extra section before or after the example.

3 - At the end of the Example section, it briefly mentions paired-end support as being 'easy' - I would not expect most readers to have sufficient understanding of the tool to achieve this, and thus would suggest expanding this section to cover this.

4 - I'm somewhat confused by the multithreading explanation - given that the read structure seems to depend on the template file, how is it possible to 'batch reads' before matching them against the template?

5 - Missing 'were' in the last line of the Result section, Demultiplexing paragraph.

6 - The figure legends are missing information to help interpret the figures (it's in the main text nearby, but the legends themselves should be more informative). For Figure 1, the baseline should also be plotted, and the figure legend describe the key parameters (threads, ngrams etc).

7 - The figures lack x-axis values, and the provided percentages, for figures 1 and 2, are relative values and thus not useful for estimating how long another data set may require to process.

8 - In the case of figure 3, it would be useful to know whether the errors were false positives or false negatives. Given the random sequence generation approach, one would expect some false positives, but false negatives would be more concerning
Experimental design: It would be beneficial to have some concrete example scenarios which motivated the high-flexibility approach chosen.
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: FUZZYSPLIT: DEMULTIPLEXING AND TRIMMING SEQUENCED DNA WITH A DECLARATIVE LANGUAGE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English is clear. There is some ambiguity in the mathematical notation that should be fixed to improve clarity. Some nonstandard terminology was used.

The section “Matching Multiple Interval-Length Wildcard Patterns” is hard to follow. It should clearly state what the problem is and what the used mathematical symbols mean. Perhaps adding a drawing would be a good idea?

Data availability: Evaluations were done on simulated data only, which is sufficient for this type of problem, but the scripts should be made available. It appears as if they are in the GitHub repository; this could just be mentioned in the manuscript.

The program is missing a license. I would suggest an Open-Source license to match the spirit of PeerJ. The chosen license should be mentioned in the manuscript.
Experimental design: The introduction aims to advertise usage of a new domain-specific language for preprocessing of sequencing reads. The major advantages given is the greater flexibility of such an approach. However, the only example given is that of parsing and demultiplexing FASTQ files, which is not compelling enough of itself.

I would suggest to give at least one more example here (best would a problem that other tools cannot solve easily because of their inflexibility, a contrived example would be ok), but also to shift emphasis in the introduction towards the actual knowledge gap this paper addresses, which is (roughly) how to write an efficient interpreter for a pattern-matching domain-specific language (DSL).
Validity of the findings: The idea of using a DSL for sequencing data preprocessing is a nice one, but I would also like to see a discussion of the limitations of the approach. I can imagine some disadvantages:

* Error messages could become cryptic: “Pattern abc incomplete at line xyz” vs. “The FASTQ record is missing quality values"

* Yet another language to learn (a small one, but nonetheless)

* Every user has to re-implement a FASTQ/FASTA parser

* I guess handling SAM files becomes complicated (does it?)

* Binary files (BAM files) cannot be handled (or can they?)
Additional comments: Major comments

1. What is proposed is a so-called “Domain-Specific Language (DSL)” and this should be mentioned somewhere.

2. As stated above, the section “Matching Multiple Interval-Length Wildcard Patterns” is somewhat hard to follow. What actually *is* a wildcard pattern P_j, and what does it mean that “characters are allowed by a pattern”?

For example, with the chosen notation, I would immediately expect that both T and P are strings, but only T actually is. P is some kind of sequence of patterns P_j, but what these individual P_j are is undefined.

Giving examples for the three types of patterns on page 2 would probably already help a lot, but also a mathematical definition is needed.

(With that improvement, it should also become clear whether “fixed-length wildcard patterns” are a special case of “interval-length wildcard patterns”, but it would not hurt to state this explicitly.)

Regarding “the formula assumes”: This anthropomorphism should be removed (the formula itself does not assume).

Second bullet point on the page: The notation {x...y} is not explained.

3. There seems to be a connection to regular expressions. A multiple-length interval pattern appears to be the same as a regular expression with length restrictions such as [a-z]{3,7} (3 to 7 occurrences of one of the characters a, ..., z). If this is correct, I suggest to mention this connection. Optional: Have you compared runtime of your implementation to grep, which can also deal with this type of expression?

Minor comments

* (Introduction) “The searching algorithms must also be fuzzy”: As can be seen from the paper titles in the list of references, the standard term to describe this type of string search would be “approximate pattern matching”, “approximate string matching” or similar. The “fuzzy” adjective is nonstandard, and mentioning the standard term would help to clear any confusion with fuzzy logic (only reading the title, this was my first thought).

* Paragraph: “We aim to streamline the development ...” Here, you give as reason for using a DSL that the tool itself does not need to be changed if requirements change. But the actual reason for using a DSL is that it is more expressive than a general-purpose programming language. Otherwise, one would not gain anything because modification of some kind of source code is still necessary. Also, in a language that is already very expressive itself (I state this coming from Python), the advantages of a DSL may not be as clear-cut as implied here!

* (page 4, fuzzy patterns) “As each fuzzy pattern may have multiple subpatterns, ...”: Using the term “subpattern” here and subsequently was confusing to me as I would have initially expected a subpattern to be a part of a pattern, like a substring is part of a string (for example, the pattern contains 20 characters, but you can split it up into two 10-character subpatterns). Why not use the term “pattern” only? Then also all the subsequent descriptions are in line with terminology in the literature, a “fuzzy pattern” could then be defined to be a set of patterns. And the \rho notation could be replaced with P, as one would expect.

* “Fuzzysplit splits each subpattern into location-agnostic n-grams.” Are the n-grams overlapping or non-overlapping? Also, an n-gram by itself is location-agnostic by default – no need to mention this.

* How would the DSL handle FASTA files, where the sequence is split over multiple lines? How to do this is not obvious from the given example.

Software suggestion

* To simplify usage, you could create a wrapper script so that the program can be run directly with 'fuzzysplit input.fastq ...' instead of 'java -jar fuzzysplit.jar input.fastq ...'. That the tool is written in Java could be considered an implementation detail and as a user, I shouldn’t have to care about it.

Spelling, grammar, style

* fasta or fastq formats -> please use uppercase “FASTA” and “FASTQ” (multiple occurrences)

* demultiplexing reads by a barcodes/indexes -> remove the "a"

* an required pattern -> a required pattern

* we use a fixed-length wildcard pattern can match any character -> ... pattern that can match ...

* the matching locations of all subpattern -> ... of all subpatterns

* Ukonnen’s cutoff heuristic -> Ukkonen

* as a recursion function -> as a recursive function

* GBSX ... is much less accurate than either tools: I suggest to tone this down by removing "much"

* evaluates to 1 for some expression F iff F is true: Use a normal “if”. The next sentence already specifies what happens when F is false.

* Some incorrect lowercase occurs in the references: gbs -> GBS, Gbsx -> GBSX, illumina -> Illumina, BMC bioinformatics -> BMC Bioinformatics, etc. They get lowercased by the BibTeX style. To prevent this, ensure that you enclose the words you want to protect in curly braces (in your .bib file). For example: “A robust, simple genotyping-by-sequencing ({GBS}) approach for high diversity species”


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: FUZZYSPLIT: DEMULTIPLEXING AND TRIMMING SEQUENCED DNA WITH A DECLARATIVE LANGUAGE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Most of my concerns from the initial review seem to have been addressed.

I am still concerned by one point however, regarding the identification of individual reads when using multi-threading. Given that the template seems to define the record structure (e.g. 4 lines of template, matching the length of a FASTQ record), how can the boundaries of each read be found without applying (to at least some extent) the template in the 'main' thread? This seems even more difficult if applied to a format with a variable number of lines per record, such as FASTA. On the other hand, if partial use of the template is required during this partitioning process, which is by definition single-threaded, it would seem to represent a real scalability bottleneck.
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: FUZZYSPLIT: DEMULTIPLEXING AND TRIMMING SEQUENCED DNA WITH A DECLARATIVE LANGUAGE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Most of my minor concerns have been addressed, but in my opinion, two major ones were not that need some work.

I realize that when I suggested to write something "clearer" in my initial review, it may not have been obvious to the author what I meant. I have taken the liberty here of writing out entire suggested sentences, but this is in no way intended to mean that they should be transferred literally into the manuscript. Instead, I use this as a way of giving very concrete examples of what I mean.

1. From the rebuttal:

>> As stated above, the section “Matching Multiple Interval-Length Wildcard Patterns” is
>> somewhat hard to follow. What actually *is* a wildcard pattern P_j, and what does it mean that
>> “characters are allowed by a pattern”?
> I have clarified this by defining the problem better in the section.
>> Giving examples for the three types of patterns on page 2 would probably already help a lot, but
>> also a mathematical definition is needed.
> I have not added any examples, since I have made the mathematical notation more clear.

I’ll take the definition of a fixed-length wildcard pattern as an example to illustrate what I meant. Here is how one could write it:

A fixed-length wildcard pattern is a tuple (C, n), where C is a set of characters and n is a nonzero length. A fixed-length wildcard pattern \emph{matches} a text T at position i if T_j\in C for j=i,...,i+n-1. An example is ({G, C}, 5), which matches any substring of length 5 that consists only of G or C.

Or with more prose:

A fixed-length wildcard pattern consists of an allowed set of characters and a length. It is said to match a text at position $i$ if the substring of length $n$ of the text starting at position $i$ uses no other characters than the allowed ones.

I’m not asking for these exact definitions to be added to the manuscript, but the ambiguity in the current definition on page 2 needs to be resolved. In particular, the given definition is unclear about whether there is a single set of allowed characters or whether there is a set for each position. I realize that it becomes clearer later on during the description of the algorithm, but the reader should not have to guess.

>> For example, with the chosen notation, I would immediately expect that both T and P are strings,
>> but only T actually is. P is some kind of sequence of patterns P_j, but what these individual P_j
>> are is undefined.
> I have clarified that P_j is an object that represents an interval-length wildcard pattern in the
> implementation.

Another, earlier sentence that you added already defines what P_j is ("Each interval-length wildcard pattern P_j matches only ..."), so this sentence can be removed again. That P_j is implemented as an object is not important here.
Experimental design: 2. From the rebuttal:

>> I would suggest to [...] to shift emphasis in the introduction towards the actual knowledge gap this paper addresses, which is (roughly) how to write an >> efficient interpreter for a pattern-matching domain-specific language (DSL).
> I have added another example for paired-end demultiplexing to better explain the DSL aspect of
> the tool. However, I have not included an example that is exclusive to this tool. The main goal is
> to introduce the idea of applying DSLs to demultiplexing and adapter matching.

My suggestion of changing the introduction has not been addressed.

The current introduction focuses on Fuzzysplit as a tool, which sets the expectations too high: A new tool is usually expected to have more features, be faster or use less memory as the existing ones, which isn’t the case here. The manuscript emphasizes the flexibility of the tool, but what the concrete advantages of this are is unclear. This is not a problem – novelty is not a requirement for publication in PeerJ, so the tool not being better than others is fine. However, you do need to address a "knowledge gap". Here, the knowledge gap is not the tool itself, but the idea of using a DSL, which is what the introduction should focus on.

I think just rearranging a couple of sentences would be enough. For example, instead of saying "In this paper, we introduce our novel Fuzzysplit tool, ...", you could say: "In this paper, we introduce the idea of [using a DSL], and also describe the algorithms to efficiently match [certain types of patterns], which we have implemented in our novel Fuzzysplit tool." That is, just change the framing slightly.
Validity of the findings: no comment
Additional comments: Most of my minor concerns have been addressed, but in my opinion, two major ones were not that need some work. These are listed first below.

I realize that when I suggested to write something "clearer" in my initial review, it may not have been obvious to the author what I meant. I have taken the liberty here of writing out entire suggested sentences, but this is in no way intended to mean that they should be transferred literally into the manuscript. Instead, I use this as a way of giving very concrete examples of what I mean.

- Thank you for listing some of the limitations of the approach, but doing so at the end of the conclusion makes the manuscript end on quite a negative note! I suggest to move those to a separate "Limitations" section before the conclusion. And/or you can turn some of the limitations into "Future work" or "Open questions" items to make them sound less negative. (Declaring something as future work does not meany you yourself promise to work on it.)

- It appears Reviewer 1’s point 4 about splitting the input into chunks for multithreading has not been addressed: For splitting, the position at which to split needs to be known. For example, for FASTQ, valid splitting positions would be after every four lines, but with flexible templates, how is this done without fully parsing the file beforehand?

- From the rebuttal:

>>The notation {x...y} is not explained.
>It indicates an interval.

I have not seen this before. Why not use the standard [x, y] notation? No special explanation would then be necessary.

- "Fuzzysplit splits each subpattern into location-agnostic n-grams that may overlap." Adding the "may overlap" in this revision made the sentence less clear because "may" can be understood to mean that they sometimes overlap and sometimes don’t (which I believe is not correct). Why not simply: "Fuzzysplit splits each subpattern into overlapping n-grams." And as I stated previously, n-grams are "location-agnostic" by nature since they are just strings of length n. If you leave this in, readers like me may start to wonder whether your idea of what an n-gram is is different from theirs.


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: BACTERIAL AND ARCHAEAL SPATIAL DISTRIBUTION AND ITS ENVIRONMENTAL DRIVERS IN AN EXTREMELY HALOALKALINE SOIL AT THE LANDSCAPE SCALE
Review round: 1
Reviewer: 1

Output:
Basic reporting: One of the barriers to smooth reading of the manuscript was incorrect grammar throughout. The authors should ensure they have a fluent English speaker read over and edit their manuscript.

Overall, there were sufficient literature references and background provided to set up the stage of the research.

The outline of the manuscript follows an acceptable format. The authors should ensure that for each figure and table, any abbreviations used are defined. There are several figures/tables where this wasn't done, including the supplemental figures/tables and Table 5. Additionally, several figures have incorrect legends including Figs. 3 and 7. The authors did submit raw sequence data to a public depository.

The authors presented an objective rather than a hypothesis. The results were relevant to this objective, however, presenting a hypothesis could make the paper stronger, more convincing, and provide a framework in which to focus on in the paper.
Experimental design: The authors do present original primary research on an objective that is stated at the end of the introduction. The authors present several research gaps such as a lack of information related to Archaea in hypersaline soil environments and a lack of examination of microbial communities and phsicochemical properties at their specific research site. The manuscript could be improved  if the authors could better address why understanding Archaea distribution in hypersaline soils is important.

The experimental design overall seems okay, however, there were some shortcomings. First,  I was left unconvinced as to why and how adding the geospatial analysis was beneficial to the study. When looking at a transect, it seems correlation analysis/CCA would be sufficient. Geospatial analysis would be more useful when looking at a study site with 2d collection sites. Second, the description of the methods could be improved in that even steps that are given a reference could be briefly spelled out. Also, the section describing three DNA extraction methods includes no description as to what those methods were or justification for why three methods were used (lines 104-120).
Validity of the findings: The sequence data for the research project were submitted to the NCBI's SRA for public access. The quality of the data I'm sure is relatively robust. An n=13 is not a huge sample size, but sufficient to draw useful results from.

The results of the study need to be refined and presented in a clearer matter. It was difficult to read through. Perhaps ordering the results into the specific pysicochemical parameters would be useful to organize ideas more efficiently. Similarly, the discussion needs to be improved to convey the most important findings from the results. Focusing on maybe just a few patterns would be very helpful in leaving the reader with a clear understanding of the take home message of the research project, and what the next steps are.
Additional comments: The authors have chosen an interesting project to work on, however, the manuscript itself needs a lot of improvement in order to be of publication quality. In general terms, the writing quality, both in terms of grammar and English usage, needs improvement in order to flow better. Also, abbreviations need to be used consistently throughout the manuscript and figures/tables. Regarding specific issues to be addressed, my suggestions have been annotated in the PDF of the manuscript, and stated above.


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

Input:
Title: BACTERIAL AND ARCHAEAL SPATIAL DISTRIBUTION AND ITS ENVIRONMENTAL DRIVERS IN AN EXTREMELY HALOALKALINE SOIL AT THE LANDSCAPE SCALE
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are a number of issues with the basic reporting or the results.  A number of the problems are listed below, but the authors need to do a thorough and careful revision to be sure they have located all of the errors in the text. Also the legends on all Figures and Tables need to be checked for accuracy and should include the units in all cases.  See specific comments below.
Results
Figure 2: should the last column be water content or water holding capacity (WC)? All the data is reported as WC
Line 219-221 What is the r-value for this negative correlation?
Line 246: reported Chao 1 values are incorrect according to the data in Table 3
Line 247 PD values are also reported incorrectly (range is 4.97-7.37)
Line247 –What do you mean by “taxa diversity” – be more specific. Is this species richness?
Table 3 and lines 245-249: Can you explain why your 4 alpha diversity metrics (OTU richness, Chao, Ace and PD) show different relative relationships among your samples for species richness?
Figure 3: the relative abundance key in your heat map appears to be backwards – red should be the most abundant not the least.
Lines 255-256 – what correlations were used here (Spearman’s?) and please designate the r or rho values so the strength of the correlation is indicated.
Figure 5 Clarify figure so the strength of correlations is understood (r or rho value) and whether correlations are positive or negative.
Line 256 Spirochaetes is positievely correlated with what?
Line 257: The statement that WC is significantly correlated with “most bacterial phyla” does not correspond to the data - only significantly correlated with 5 phyla which is less than half of those listed
Line 257-258: Clarify correlations of Chorobi with soil properties (<50% of those listed)
Line 262 Silt content of TX 010 higher than that of TX008. Check your analyses against your data. There are many statments in the Results section that do not correspond to the data presented in your figures and tables.  A more careful analysis of your data is required before this work can be published
Lines 265 -266: this statement is not supported by the heat map in Figure 5A for Chlorobi, WS2 and OD1
Lines 275-279 Please define the sill/nugget ratio and the significance of the high and medium rankings.
Line 281 A pH of 10.2 may be lower than the narrow pH range of 10.3 to 10.6, but it is hard to believe that this difference would make a significant impact on relative abundances of taxa.  Are you sure that pH is not conflated with something else?
Line 285  Check the easting values for the low predicted EC.  These values do not correspond to figure 7
Lines 299-300 Where is the Shannon ratio of Bacteria:Archaea presented in the results?
Line 304: As stated above, the pH range is very narrow and it is hard to believe it would affect the relative abundance of Thaumarcheota.  They also appear correlated with lower EC values
Lines 305-311.  Please put labels for the observed values on the kriging plots so that the reader can follow this discussion.
Figures 8 and 9: for Kriging figures please clarify the units of observed values
Experimental design: Specific Comments
Introduction
Line 41: grammar correction. Soil is spatially and temporally the most heterogeneous environment on earth
Lines 44-45: Do you mean the “weather forms the soil” or do you mean to say that – at a global scale, weather determines soil diversity.  Please clarify this sentence
Line 53: grammar correction: change to geochemical contribution to microorganism distribution.
Line 55-56 change to, the determination of … and their relationship to
Line 64 change to, can grow
Line 72 change to, make
Lines 74-77 remove italics for cited authors not in parentheses

Methods
The experimental design of this research is good.
Lines 99-100: EC is typically determined from the supernatant not a saturated soil extract, but pH can be determined from a saturated extract. Is this reported correctly?
Line 124: don’t you mean that sequences <290 nt and >530 nt were removed. It doesn’t make sense as written. Same for archaea
Line 134 assignment was determined using
Line 139 change assignations to assignments throughout paper
Line 143 these sequence numbers are extremely low. Please explain
Validity of the findings: Specific Comments

Discussion
Line 324-326 Why was organic C not mentioned in Lines 280-290 of the results where it is stated “other measured factors were more homogeneous – other than pH, EC and WC?
Lines 340-345 As stated earlier, your alpha diversity metrics are inconsistent.  Tx008 and Tx012 have low Shannon and Chao 1 values but high observed richness (OTUs). Also there is quite a range of Chao 1 values.  I would not call this “similar species richness and diversity in most samples”. You should explore differences between richness and evenness to explain the different patterns.
Line 348-349: Figure 2 shows a correlation of Cenarchaeum with sand and silt but not clay and it is not clear from the heat map whether this correlation is negative or positive.
Line 358-359: Which diversity metric are you using to show that Archaeal diversity correlates with WC, total C and inorganic C? Table S1 cites pH, WC, EC and clay.  Your use of multiple analysis tools and the errors in some of the presentation of results as outlined above make it difficult to follow your conclusions. A careful revision is needed to correct errors in this manuscript and label the figures as directed above so that correlations can be more easily followed.
Line 369 – what about Gemmatimonadetes (Figure 3). This phylum appears more abundant or as abundant as Bacteroidetes.
Line 391 -396 Again, you have to point out that your site does not have a pH gradient.  10.3 – 10.6 is not a gradient
Lines 398-414: while it is relevant to explain how these organisms can survive under these extreme conditions, the authors also need to explain their didtribution across the transect since that it is the objective of this manuscript.
Line 415 Which diversity metrics are you using to support this statement. As stated above you need to discuss richness and evenness (OTUs, Chao vs Shannon). In a few sites Archaea diversity was higher for some metrics.
Lines 422-431 – this section should discuss the correlation between the spatially heterogeneous environmental parameters such as EC, WC, and orgC and the respective distribution of bacterial or archael phylotypes

Conclusion
Line 441-443: The statement that bacteria have a more homogeneous distribution along the sampling transect due to patterns for Proteobacteria and Actinobacteria is an unfortunate focus since Chlorobi and Firmicutes are highly variable in relative abundance (Figure3) ranging from 0.01 to 25%. The variability appears high for Firmicutes in Figure 9.
Additional comments: The objective of this study was to examine environmental drivers influencing the spatial variability of microbial populations along a 211 m transect through former Lake Texcoco in Mexico.  The transect included significant variability in EC, water content (WC) and org C. Efforts to model the spatial heterogeneity of microbial communities within a limited area are valuable because microbes operate at a pore scale and thus can be influenced by pore-scale variations in soil physicochemical properties. The authors used an interesting combination of statistical tools to correlate the variability in bacterial and archaeal relative abundances with variations in soil properties. They also used Kirging to try and predict the observed variation. While the Methods used in this manuscript are good, the reporting of results is poor because there are a number of statements in the Results section that do not correspond correctly to the data presented in the figures and tables as described under specific comments.  In addition, there are errors in the figures as described below.  Finally, the authors do not do a good job in the Discussion of synthesizing the patterns revealed by each of the analysis tools, thus it is difficult to follow such comments in the discussion as the statement in lines 358-359 that Archaeal diversity corresponds with water content. The research has merit because the experimental design is good and the data generated appear to reveal some interesting patterns, however a major revision is needed to correct all of the errors, improve the figures and write a more focused discussion to indicate how all the different analyses can be integrated to explain the observed herterogeneity in the distribution of bacterial and archaeal relative abundances.


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: BACTERIAL AND ARCHAEAL SPATIAL DISTRIBUTION AND ITS ENVIRONMENTAL DRIVERS IN AN EXTREMELY HALOALKALINE SOIL AT THE LANDSCAPE SCALE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have submitted a "major revision" of a previously submitted manuscript. Overall, the authors have addressed most of the suggestions.

The English has been improved in this revision of the manuscript, however, there were still some errors, some of which have been corrected in the annotated manuscript I am attaching.

The results are relevant to the hypothesis (lines 89-91). However, the term "great spatial variability in physicochemical characteristics" (pH, EC) is misleading because the pH only varies from 10.3 - 10.9.  Perhaps this should be discussed in the introduction. Furthermore, microbial community structure should be expanded to include diversity.

Consistent use of abbreviations is suggested. Often the authors go back and forth between water content and WC, or phylogenetic diversity and PD. Please see lines 444, 285-286, and 515.

Some sentences are confusing or out of place. The sentence in lines 481-483 seems out of place and does not fit in with the rest of the paragraph. The sentence in lines 491-492 is confusing and should be reworded. The legends in Fig 1 - 3  are confusing and should be reworded for clarity. For example, Fig 2 A) does not just show significant correlations, it shows all correlations. It is suggested that either the authors only show the phyla/genera that have significant correlations with physicochemical properties, or that it be reworded to, for example, "spearman correlations between a) phyla or b) genera. Significant correlations are displayed as red (negative) or blue (positive) (p<0.05)".

For Fig. 3, the A and B should be A and C, and the C and D should be B and D. Please ensure that all Figures and references to the Figures are correct.
Experimental design: The experimental design is sound. The authors have added more detail and explanations as suggested after first review.
Validity of the findings: For the discussion, rather than starting with the "soil characteristics", which is basically a repeat of the results (lines 380-389), it would be more beneficial to begin with a paragraph presenting the major findings to help guide the reader and provide a focus.

The paragraph starting on line 408 should be more specific as to which soil property affects which soil microbial communities. Also, the term "A lot of" is not very professional. Also in this paragraph, ammonium oxidzation is introduced, without a discussion of how this function relates to this environment, or why it would dominate in areas with lower pH and EC. (Also, saying lower pH is misleading because there really is no pH gradient).

In lines 446 - 452, microbial activity is introduced, however, this is not a focus of the paper.

In lines 453-454, does WC "control" the microbial community? Or is there just a correlation? A

The paragraph in lines 491 - 499 is out of place in the discussion, and should be moved to the results. Also, I think the purpose of this paragraph is to explain why there are low sequence counts, however, this needs to be more explicit.  Also, lines 496-498 do not support why there would be low sequence counts in the extreme hi saline soil of this study, since in the referenced study there are high sequence counts.
Additional comments: Overall, the experimental design and the results presented seem robust, however, the discussion of them still needs great improvement. As it is now, it is hard to read through the discussion because there is
a lack of order and flow. Furthermore, the overall conclusion needs to be more focused so that the reader comes away with the main take-home points of the paper.

Please see some minor comments in the attached pdf  as well.


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: DISCOVERY OF PLASMA MESSENGER RNA AS NOVEL BIOMARKER FOR GASTRIC CANCER IDENTIFIED THROUGH BIOINFORMATICS ANALYSIS AND CLINICAL VALIDATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article explored further putative biomarkers for gastric cancer disease. The article is well organized and comprehensive. However, the following notes need to be adjusted.

Abstract
Results: rephrase the results of association with clinicopathological features to be more concise with clear language.
Conclusion: were >>> could be putative
Experimental design: Methodology
304 GC cancer: different number of samples are noted in the Figures
Line 84: available from each study >>> available for each study
Validity of the findings: Results
Could you explain how you combine ROC curve by log regression analysis? To have at the end a value higher than a single value and not the mean of the three values?

Figures
Unify font size of p values in Fig. 2
Fig 2 is box plot not scatter plot
Set cutoff values, sensitivity and specificity in Fig. 3
Unify format of ROC in Fig 3 and 4
Write more labels on Fig. 4
Additional comments: Discussion
Further addition enrichment analysis to identify putative function of the three significant genes is warranted.


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: DISCOVERY OF PLASMA MESSENGER RNA AS NOVEL BIOMARKER FOR GASTRIC CANCER IDENTIFIED THROUGH BIOINFORMATICS ANALYSIS AND CLINICAL VALIDATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is easy to follow, not complicated, even pedagogical. In few words, it is even too simple and it is not simple for the reader to know if she/he believed in the results or she/he thank that she/he believed in the results. Some parts must be more detailed to have a better view of the experiment.
Experimental design: it is properly done in the way that it is explained, but there is a break with the results. Reader expect a large number of complicated cases… and it is directly restricted. Similarly, it is not clear how the different types of adenocarcinoma
are treated. Is the merging of adenocarcinoma
correct ?
Validity of the findings: As said before, it is easy to follow, but how is done the reduction of the selected genes? How is it sensitive? More details must be provided. And more analyses must be done. Is their some co-regulation? Some proteins implicated in similar pathways, same pathways. In few words, it is a bit too short. For instance, some p-values are not so high, aren’t they?
As said in PeerJ ‘Speculation is welcome, but should be identified as such.’
Additional comments: I like the idea and design, but cannot say if I think/believe it is properly done at this level.


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: DISCOVERY OF PLASMA MESSENGER RNA AS NOVEL BIOMARKER FOR GASTRIC CANCER IDENTIFIED THROUGH BIOINFORMATICS ANALYSIS AND CLINICAL VALIDATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overall, the study has merit and the technical approach is valid, however, It appears that this manuscript is not carefully revised. The manuscript requires improvement in several concerns which will be written in details in the comments for the authors' section.
Experimental design: - The comments will be written in details in the comments for the authors' section.
Validity of the findings: - The comments will be written in details in the comments for the authors' section.
Additional comments: The manuscript requires improvement in the following concerns:

- The authors are advised to copyedit the manuscript: a native English speaking colleague could help them with this issue, if possible, or they may need to use a professional language editing service.

- Authors are advised to revise all the manuscript to ensure that all abbreviations have been written in their long name at their first mention in the text, tables, and figures, especially the gene names.

-Authors are advised to revise all the manuscript to ensure that all gene names are written in italic font, especially (only for example) lines: 147-149, in the tables and figures.

Abstract:
- Lines 38, 39: The authors mentioned that “expression levels of COL6A3, SERPINH1 and PLEKHG1 were significantly downregulated in GC plasmas” Are these genes upregulated or downregulated?

Methods:
- Why did the authors select this specific type of database? It is better to give the readers a concise hint about its advantages relative to other online databases.

- The characteristics of the dataset used in the current study should be presented in a table for better clarification and readability (even if supplied as suppl. materials)

- The authors did not mention how they selected the study data and the outcomes of the database, the filtration process, the quality control measures they follow in their work on Oncomine database to facilitate the replication of their work by interested future researchers.

- The authors validated their findings on 56 GC patients and 14 healthy subjects. On what basis they selected their controls (inclusion and exclusion criteria) and how they knew they are healthy subjects?

- What is the reference they follow or their institute follows to diagnose gastric cancer? This answer will help readers to some extent to follow the authors and understand the clinicopathological presentation/association tables (1 and 2).

- It was not clear why did the authors did two consecutive centrifugation steps at two different speed for the collected samples. Please clarify.

- Please add the characteristics of the included controls to Table (1). Why did the authors do the RT in triplicate meanwhile they did the qPCR in duplicate? In other words what was the aim of the former biological replicates?, each RNA sample yield 3 tubes included cDNA then what the further processing steps with these 3 replicates. Please clarify to the readers.

- Thanks to the authors for providing the primer sequences in a suppl. table. Are these primers self-designed or derived from other published work? If the former, please provide the name of the software you applied in its formal citation in the text, or provide the citations you follow if they were derived from other publications.

- I advise the authors to read and refer to the MIQE (minimum information for publication of quantitative real-time PCR experiments) guidelines ( PMID: 19246619) for reporting their qPCR methodology.  Although they explain the extraction step in details, the methodology of their quantitative PCR needs more elaboration about the type of the syber green mix they used the amount/concentrations they applied for the samples before mention of the PCR programming.

- In suppl. table for the primers sequences, the melting temp. for the primers was 59°C, why did the authors run their PCR at 58°C?

Statistical analysis:
- Please update your reference of the SPSS program as it is related to “IBM SPSS” co.

References:
- Lines 337, 364: Please provide the volume/page range and/or the DOI of the specified references.

Figures and Tables
- Each figure and table should be self-exploratory; all mentioned abbreviations either included on the figure/table or its legend should be written in details in the legend.
- In addition to the above related general comment, more specifically:
A- Figure 1: Are the P values mentioned in the heat Map corrected ones? What about the false discovery rate, why did not the authors apply?
B- Figure 2: please mention the statistical test applied for this comparison.
C- Figure 3: the authors should correct the gene name of (C) as it is PLEKHG1 not GPT2, list the abbreviations mentioned in the figure as recommended above and indicate the value at which the P is significant.
D- Table 1: The authors should add the control group characteristics.
What is meant by (59±26) in the 2nd raw?
Please add in the table footnote how are the data presented? The stage of cancer classified on which basis (provide the reference the authors followed), Why did the authors apply the value of 15 for lymph node metastasis classification?
Please revise the total of the stage (I+II+III: 37) + (IV: 18) = 55 and the total GC patients wear 56?!
The number of L.N metastasis (31+7) involved which stages? Please clarify for the readers.
Why did according to the differentiation classification of the patients, the total are (19+11) = 30?
Please all these issues should be clarified in the table footnote

E- Table 2: it needs an extensive revision
- Add “circulating” after “expression of” in the table title
- Add to the footnote the type of data presented in the table, the abbreviations, the type of statistical test applied and what “*” and “**” did mean?
- Add the total number (n =  ) for each column to facilitate following the results.
- Why did for each gene the total of stages (I+II+III) and (IV) is less than the total number of patients by one?
- Please replace the terminology “under moderately” by an appropriate one. Pay attention to be consistent for the applied terminology all over the manuscript to avoid confusion of the readers.

Discussion:
It is concise and related to the study findings, just the authors should provide the study limitation(s) by the end of the discussion.

Minor comments:
- Line 60: the terminology “recently” is not appropriate as the cited reference was 2015.
- Line 82: p-value≤10-4 let the “-4” superscript.
- Line 113: –ΔCT should be superscript.
- Line 149: add “, respectively” after the closing bracket.


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: DISCOVERY OF PLASMA MESSENGER RNA AS NOVEL BIOMARKER FOR GASTRIC CANCER IDENTIFIED THROUGH BIOINFORMATICS ANALYSIS AND CLINICAL VALIDATION
Review round: 1
Reviewer: 4

Output:
Basic reporting: English requires general adjustments (e.g. inappropriate use of definite articles).
Experimental design: Given the heterogeneity of gastric cancer, sub-analyses have to be provided for different biological and histopathological entities. In general, it does not appear to make sense to include mesenchymal tumours like GIST and gastric tumours "other" that could possibly be also lymphoma or carcinoid, i.e. non-carcinomatous entities in the same analyses.

Fig. 1: It is unclear what "12 analyses from 5 included studies" really means. What kind of studies? What kind of analyses? As it stands, it is not possible to understand what these data really mean and which cancer subtypes were included. Furthermore, why are all cells in Fig. 1B for analyses 1-3 grey?
A comprehensive data file on the primary analyses should be provided as a supplement.

The type of GC (histological/biological sub-type) of the patients included are not stated. Furthermore, the ratio of cases to samples is skewed about 4-fold towards cases. It would make statistically a lot more sense to reverse this ratio, i.e. include around 250 controls. At least, a 1-to-1 ratio has to be provided before results can be trusted. This is also important to interpret the ROC analyses.
Validity of the findings: Crucially, no survival analysis nor mRNA data on the tumour specimens has been provided for the patient cohort investigated. Hence, it is completely unclear whether plasma mRNA and cancer mRNA levels show any relevant correlation.

Costs for radiological and endoscopic procedures are NO argument for PCR-based diagnostics of gastric cancer. These techniques have to be performed if GC is suspected. Furthermore, given the sensitivity and specificity results, the suggested qPCR-based biomarkers are likely not suited for a screening of GC - this has to be discussed. Furthermore, it is not stated what the possible purpose of the biomarker would be - secondary prevention? Biological dignity? Diagnostic?
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: DISCOVERY OF PLASMA MESSENGER RNA AS NOVEL BIOMARKER FOR GASTRIC CANCER IDENTIFIED THROUGH BIOINFORMATICS ANALYSIS AND CLINICAL VALIDATION
Review round: 1
Reviewer: 5

Output:
Basic reporting: Nothing
Experimental design: Nothing
Validity of the findings: Nothing
Additional comments: This study identified three serum mRNAs, COL6A3, SERPINH1 and PLEKHG1, as unfavarite prognostic factors in gastric cancer, using Oncomine database.  The authors evaluated the usefulness of the three mRNA, using 56 gastric cancer patients and 14 healthy subjects. The authors concluded that these three mRNA are useful biomarker in gastric cancer patients. This study may be a promising. However, there are some drawbacks.

Major1. The study compared serum of gastric cancer patients with healthy subjects, but did not compare gastric cancer with other cancers such as colon cancers, pancreatic cancer, and lung cancers. That is why the specificity of these biomarkers for gastric cancers may be relatively low. These biomarkers are specific for gastric cancer?

Major 2. Are there any differences in outcomes between gastric cancer patients with positivity of three biomarkers and with positivity of one or two biomarkers.

Major 3. Table 1. The cut off levels of lymphatic metastasis is 15. How was the cut of level of lymphatic metastasis determined? Is there any difference in outcomes of patients?

Minor1. In Abstract, line 38-39, PLEKHG1 were significantly downregulated……
Is this description true? Probably, upregulated?


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: DISCOVERY OF PLASMA MESSENGER RNA AS NOVEL BIOMARKER FOR GASTRIC CANCER IDENTIFIED THROUGH BIOINFORMATICS ANALYSIS AND CLINICAL VALIDATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have properly answered my questions.
Experimental design: Authors have explained more precisely their hypotheses.
Validity of the findings: It is a scientific paper with a correct design.
Additional comments: Authors have properly answered my questions.


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: DISCOVERY OF PLASMA MESSENGER RNA AS NOVEL BIOMARKER FOR GASTRIC CANCER IDENTIFIED THROUGH BIOINFORMATICS ANALYSIS AND CLINICAL VALIDATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: All the required concerns have been done.
Experimental design: All the required concerns have been done.
Validity of the findings: All the required concerns have been done.
Additional comments: The authors have responded to all concerns raised previously by the referee. Thanks


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

Input:
Title: DISCOVERY OF PLASMA MESSENGER RNA AS NOVEL BIOMARKER FOR GASTRIC CANCER IDENTIFIED THROUGH BIOINFORMATICS ANALYSIS AND CLINICAL VALIDATION
Review round: 2
Reviewer: 3

Output:
Basic reporting: I will only respond to the rebuttal concerning the issues I raised with the previous version:

Effort was made to improve language.
Experimental design: I will only respond to the rebuttal concerning the issues I raised with the previous version:

The authors did not care to take out non-adenocarcinoma of in silico analyses. Why?
Validity of the findings: I will only respond to the rebuttal concerning the issues I raised with the previous version:

I was not suggesting to increase the case number - but the control number, which should easily be doable. The reluctance of the authors to provide any further experimental data does not seem plausible. Do they consider a power below 90% to be sufficient for biomarker discovery studies?

The authors did not add data on mRNA expression of their biomarker candidates from primary cancer tissue - which has to be provided if claiming any relevance of biomarker.
Additional comments: I will only respond to the rebuttal concerning the issues I raised with the previous version:

The authors still vastly overstate the potential role of a qPCR-based biomarker approach. Their gross misjudgement of the role of endoscopy for evaluation of gastric cancer casts serious doubts on their understanding of the role of biomarkers for the diagnosis of cancer. They were given the opportunity to elaborate on this - but did not do so. In particular, no considerations of false-positive results and what to possibly do with these are made. This kind of scientific reasoning is dangerous and might have detrimental effects on health care.


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: EXPANDING GLOBAL COMMODITIES TRADE AND CONSUMPTION PLACE THE WORLD’S PRIMATES AT RISK OF EXTINCTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript of Estrada et al. presents an assessment of the threat to primates as a result of the advance of international trade in commodities in 75 countries that hold the highest diversity for the group. Agricultural commodities (soy, rubber, livestock and vegetable oil) and non-agricultural commodities (oil and ore) were selected, with assessments being made for countries in the Neotropical region, Africa and Madagascar, South and Southeast Asia. The authors compiled data on the loss of forest cover between 2001 and 2015, data on international trade in commodities for the years 2000 and 2016, data on the Gross Domestic Product for the countries involved. Primates, used here as a response group, were evaluated by the number of currently threatened species and habitat loss scenarios associated with six different RCPs (Representative Concentration Pathway) for the years 2050 and 2100. Based on an equation of species-area relationship, the authors estimated the number of species that will be extinct in the future for each of the RCPs.
Experimental design: In general, the manuscript is very interesting, well written and with many relevant data on the dynamics of the world trade of commodities. My main point concerning the study was the weak association between commodity production and threats to primates, as suggested by the title of the manuscript. It is quite intuitive to assume that species of primates present in commodity-producing countries, whose activities demand more and more areas, would be increasingly threatened. But the authors failed to show this relationship. All the dynamics of the trade and expansion of commodities were well demonstrated, but it was not demonstrated if the conservation status of the primates was changed during the considered period. This relationship could indicate whether the expansion of commodity production would actually pose a more significant threat to primates. The ideal would be to demonstrate the variation of the conservation status of the species within the analyzed period for the change of the commodities. Perhaps the calculation of the Red List Index variation (Bubb et al. 2009) is a good way to indicate if the conservation status of species has changed along with the loss of forest cover and commodity expansion. Thus, a simple graph showing in the Y-axis the variation of the RLI between 2000 and 2016 and in the X-axis the variation of the commodity production for each primate-range country would give an idea of this relation.

The main point raised by the authors is that international trade in commodities generates large environmental impacts in exporting countries. The use of the primate group as an example is only circumstantial since virtually any taxonomic group could be used in this context. So my recommendation would be to change the order of subjects in the introduction so that the text begins by talking about commodities, the characteristics of primate-range countries and then about the expected impacts on primates.

Another critical issue is that some regions of Brazil, such as the Atlantic Forest, are not producing commodities for export, but they have many species of primates, including endangered species. In the opposite direction, there is the Cerrado, which has low primate diversity but is the main export region of agricultural commodities in the country. Argentina would be the equivalent of the Cerrado, that is, it has a low diversity of primates (only 6 species) and high production of commodities. Thus subregional situations may mask the results, and this should be better discussed in the text.
Analysis of future scenarios for primates is unclear or not adequately presented. The authors used land use projections in different climatic scenarios to indicate the area available for primate occurrence. The result of the analysis suggests that there may be a significant increase in the number of endangered species, but a species-area relationship would indicate the number of extinct species, i.e., the difference between current and future species richness.  Nevertheless, the authors indicated in Table S8 that 100% of all primates would be threatened with extinction in most of the scenarios. Does it mean that the species-area equation did not indicate any extinction? In my opinion, the table should show the number of species that might be extinct in the future due to land-change and climate change.
Based on the results, the authors suggest some measures that could be taken to mitigate the impacts. Some of the proposals (eg, "sustainable intensification," "reduce greenhouse gas emissions" or "protect natural biodiversity") are very generic and could be applied to any taxonomic group that is being impacted by the production of commodities. The most relevant would be to point out specific actions for species of primates that may disappear shortly.

Some specific remarks:

The introduction presented is quite similar to the introduction of Estrada et al. (2017), which, in my opinion, represent a self-plagiarism.

•	“Nonhuman primates (primates from here on), our closest biological relatives, are an essential component of tropical biodiversity, contributing to forest regeneration and ecosystem health. Primates play important roles in the livelihoods, cultures, and religions of many societies and offer unique insights into human evolution, biology, behavior, and the threat of emerging diseases.” (lines 47-51)

•	“Nonhuman primates (primates hereafter) are of central importance to tropical biodiversity and to many ecosystem functions, processes, and services. They are our closest living biological relatives, offering critical insights into human evolution, biology, and behavior and playing important roles in the livelihoods, cultures, and religions of many societies.” (Estrada et al. 2017).

The authors should re-write this part, and also avoiding the exceeding self-citation. I counted 23 times that Estrada et al. 2017 and Estrada et al. 2018 were cited in the text. Citations of papers from the second author (Chaudhary & Brooks, 2017 and Chaudhary & Mooers, 2018)  sums 11 times. Altogether, the 34 citations of paper from the authors are 11 times more frequent than the citation of other papers.

Still talking about citations and references, there are several errors along the manuscript that should be corrected. Here is a list of the mistakes:

Line 54 . IUCN Red List would be a better source to be cited here, since the organization is the one responsible for the definition of threatened status of the species.
Line 92 – Check the citation format of Henders, Persson & Kastnter 2015. Should be the same of Henders et al. 2015, as in Line 72.
Line 140 – Missing reference: Clapp 2016 and FAO 2015.
Line 140 – Which FAO 2018 is this? 2018a or 2018b?
Line 277 – Please correct Chaudhary and Brookes, 2017 to Chaudhary and Brooks, 2017
Line 315 – Keep the consistency along the text: either cite 3 authors or use et al. (as in Henders et al. 2015 or Lanjouw et al. 2015)
Line 318 – Missing reference: IUCN 2018 (Is this Grasp & IUCN 2018?).
Line 441 – Lewis, Edwards & Galbraith 2015: keep the consistency along the text: either cite 3 authors or use et al. (as in Henders et al. 2015 or Lanjouw et al. 2015)
Line 535 – Change Nomuh Forbanka 2018 to Nomuh 2018.
Line 725 – Missing reference: FAO, IFAD & WFP 2015.
Line 751 – Is this Porter-Bolland et al. 2016 or 2012, as in the reference list?
Line 784 – Which FAO 2018 is this? 2018a or 2018b?
Line 791 – Missing reference: World Bank 2018.
Line 14 (Table 1) – Missing reference: Curtis et al. 2015.
Line 866 - Please check the reference Ahrends et al. 2015, which is not cited in the text.
Line 898 - Please check the reference Barrett et al. 2013, which is not cited on the text.
Line 938 – Put Clapp 2019 after Clapp 2017.
Line 948 - Please check the reference Cottrell et al. 2019, which is not cited in the text.
Line 968 - Please check the reference Diesmos et al. 2014, which is not cited in the text.
Line 1083 - Please check the reference Harfoot et al. 2017, which is not cited in the text.
Line 1108 – Put IUCN 2019 after IUCN 2015.
Line 1108 – Please check the reference IUCN 2019, which is not cited in the text. Is this IUCN Redlist 2019 cited in Figure 1?
Line 1126 - Please check the reference Kok et al. 2017, which is not cited in the text.
Line 1173 – Reference duplicated (the same as in line 1165)
Line 1178 - Please check the reference Liu et al. 2019, which is not cited in the text.
Line 1191 – Incomplete reference? It is apparently cited as Mazumder et al. 2014 in line 371.
Line 1203 - Please check the reference Meyfroidt et al. 2013, which is not cited in the text.
Line 1225 - Please check the reference Nantha & Tisdell 2009, which is not cited in the text.
Line 1228 - Please check the reference Nepstad et al 2006, which is not cited on the text.
Line 1264 - Please check the reference Ranganathan et al. 2016, which is not cited in the text.
Line 1280 - Please check the reference Seto et al. 2012, which is not cited in the text.
Line 1362 - Please check the reference Zalles et al. 2019, which is not cited in the text.

Table 2. Please choose a column to order the data. I suggest ordering descending by # of species.
Validity of the findings: Please see the previous item.
Additional comments: Please see the previous item.


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: EXPANDING GLOBAL COMMODITIES TRADE AND CONSUMPTION PLACE THE WORLD’S PRIMATES AT RISK OF EXTINCTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an excellent and much needed analysis of how commodities production, trade, and consumption patterns need to change in order to prevent the extinction of primates and their habitats. The analysis is rigorous and relevant and it is clear that the authors have produced a publication-ready manuscript and I thank the authors for working so hard on that. Overall, I think this is a critically important manuscript to be published at this time and I believe your journal should do whatever you can to promote the piece once it is published.

I have just a couple of comments for the authors to consider for this and future articles.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: These are those two things to consider:

1)	I know that we primatologists like to think in the four-five region system for grouping data. Lately, I have been wondering how useful this grouping process is for understanding patterns. I refer to the region designations: Neotropical, Africa, South Asia, and SE Asia. I know these terms come from tradition and the desire for standardization and gross categories. First, I don’t know that the categories really tell us anything. Second, I am learning from our students that the term New World and Neotropical (because it is the same thing) is offensive because it erases indigenous history in the Americas. Third, the comparisons are uneven. In one terms, we are using a forest/vegetation term and in the others, continent terms. If you are stuck on the four big categories, perhaps the Americas. I, however, believe the countries are much more important for the actual outcomes here.
2)	Figure 17 is important. I wonder if there is a way to do this in a more meaningful way to address how individual consumption and behavior influences larger-scale systems. I believe the bottom boxes could be more creatively integrated to influence greater impact. Perhaps bring in the local, regional, global scale here.

Here are some minor things:

Line 78: what are some examples of the negative conservation consequences?
Line 87: perhaps define forest-risk commodities. Examples are provided but what places something in this category? Large scale monoculture?
Line 135: Was 2016 used as most recent example with relatively complete data? What were 2000 and 2016 chosen? I think I know why but it might good to be explicit.
Line 232: Change ‘amount’ to ‘degree’
Line 271: Add comma after SE Asia and change ‘he’ to ‘the’. This sentence is a little awkward with the ‘also…’
Line 316: Make soybeans(s) plural to be consistent with use in other places.
Line 750: Are primate-range and primate-habitat interchangeable? I noticed range used in other areas. I know that they are interchangeable but do you want to use them both?
Line 792: What is a native forest and why is it important?


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: EXPANDING GLOBAL COMMODITIES TRADE AND CONSUMPTION PLACE THE WORLD’S PRIMATES AT RISK OF EXTINCTION
Review round: 2
Reviewer: 1

Output:
Basic reporting: After reading the new version of the manuscript, I am quite confident that the text is now in shape to be published. The authors had revised all critical points raised on the first revision. Therefore, I have no objection to its publication.
Experimental design: See above.
Validity of the findings: See above.
Additional comments: See above.


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

Input:
Title: REPEATEDLY ADOPTING POWER POSTURES DOES NOT AFFECT HORMONAL CORRELATES OF DOMINANCE AND AFFILIATIVE BEHAVIOR
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is well written. I only have a few minor comments. Once addressed, the paper will be ready for publication, and will make a nice contribution to the literature.
Experimental design: Rigorous investigation performed to a high technical & ethical standard.
Methods described with sufficient detail & information to replicate.
Validity of the findings: Data is robust, statistically sound, & controlled.
Conclusion are well stated, linked to original research question & limited to supporting results.
Additional comments: The paper is well written, and reports a well-designed experiment.
I only have a few minor comments. Once addressed, the paper will be ready for publication, and will make a nice contribution to the literature.

While the association between cortisol and stress is well established, I would use more tentative language when discussing the the status / affiliative effects of testosterone and progesterone, as they are based on early findings.

The reference below should be added when discussing the association between testosterone and status (as far as I know it is the only study that directly tested the hypothesis in a causal fashion).

Nave, Gideon, et al. "Single-dose testosterone administration increases men’s preference for status goods." Nature communications 9.1 (2018): 2433.

The p-curve analysis of Cuddy, Schultz & Fosse, 2018 was flawed, see http://datacolada.org/66 -- I would add a footnote about this issue and refer to the blog post.

I suspect that the bars are hiding some of the dots in Fig. 2 – this should be fixed.

Can you explain what “We used a well-established “number estimation style” procedure to induce minimal group membership, assigning participants to either the group of over- or under-estimators”: mean, and add a relevant reference?

What does “see Dotsch & Todorov, 2012 for an example of the noisy stimuli used for reverse correlation of mental representations)” mean? This seems out of place.

When reporting the results, please include 95% confidence intervals of the effects (this is especially important for a null result). Please indicate if the point estimates from Cuddy et al. (2010) lie outside the confidence intervals.


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: REPEATEDLY ADOPTING POWER POSTURES DOES NOT AFFECT HORMONAL CORRELATES OF DOMINANCE AND AFFILIATIVE BEHAVIOR
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is clear and data are provided with analytic scripts.

The authors might find the special pre-registered issue on power poses in Comprehensive Results in Social Psychology (Vol 2, 2017) to be especially useful for finding additional studies that have examined the effects of power poses on a variety of outcomes for their references.

The authors should highlight the novel aspect of their work (the examination of progesterone on affiliation motives) more in their abstract and manuscript.
Experimental design: The experimental design is appropriate. However, the authors should provide less methodological details in the introduction, as this is redundant with their methods sections.

Descriptions of the timeline of the study and the power poses should be split into two figures and presented much earlier in the methods section to allow the reader to understand the study design. The authors can substantially cut their description of the poses by referencing the figure of the poses.

Results: Given that the effects of power poses are most robust on feelings of power, did the authors collect evidence of feelings of power? Did they collect any behavioral measures related to power? If so, they should be reported.

Results: I commend the authors on their open data and analytic scripts. The authors could comment their scripts more fully, though. This will help researchers who are unfamiliar with R.

Results: The authors should clarify what eta-squared G is.
Validity of the findings: My major comment has to deal with the robustness of the data (see below):

Absence of Evidence is Not Evidence of Absence:

The authors’ find no evidence that physical poses have any impact on hormone levels, regardless of the “dose” of those poses. They interpret this as evidence that poses do not impact hormone levels. For example, they state (in the discussion):

“While effects on other outcome variables described as promising by Cuddy et al. (2018) might be reproducible, the available evidence against an effect on hormone samples begins to CLEARLY outweigh evidence for such an effect.” (emphasis added)

However, the frequentist hypothesis-testing framework does not allow this conclusion. If the authors want to make this strong conclusion they need to use a statistical approach that can determine equivalences (e.g., equivalence testing; Lakens, 2017) or use a Bayesian approach.

This is particularly important because the authors likely do not have the data necessary to conclusively argue that poses do not impact hormone levels. With only 82 participants, the precision in their estimates in hormone levels is low, which will render such results inconclusive. I do not think that the authors need to show conclusively that the data are more likely under a null model (e.g., the Bayesian approach). Rather, I think they should be more circumspect in their conclusions.

This is related to the authors’ power analysis. They note that they based their sample size off the smaller effect size from Carney et al. (r = .34; 2010). According to this benchmark, their sample of 82 would have 90% power to detect this effect. However, r = .34 is a relatively large effect size for social/personality psychology. My expectation is that if physical poses impact hormonal correlates of power, that the effect would be quite small, say, r = .10. This more conservative estimate would be more in line with the effects of the most robust effect of physical poses—on feelings of power. Using this benchmark, the authors only have 15% power to detect this effect. This level of power is far too low to argue that their null results are evidence for the absence of an effect. I would like them to recalculate their power analysis based on an estimate lower level of power, and then to discuss the limitations of their study for detecting small effects.
Additional comments: The authors present a single study testing the effects of physical poses on hormone levels. This study attempts to replicate, improve, and extend the results of Carney, Cuddy, and Yap (2010). The authors find no evidence that poses impact levels of cortisol, testosterone, or progesterone. These results contribute to the growing body of evidence that does not support the conclusion that hormonal changes drive the effects of physical poses on feelings or behavior. The paper is well written and I commend the authors for providing their data and analytic scripts.


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: MIR-421 IN PLASMA AS A POTENTIAL DIAGNOSTIC BIOMARKER FOR PRECANCEROUS GASTRIC LESIONS AND EARLY GASTRIC CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: Authors should check their references. there are so many reviews as references which is not suitable. original authors must be mentioned rather than reviewers.

miRNA expression details should be given.
Experimental design: no comment
Validity of the findings: Raw Cts' extended over 30 cycles which is not acceptable for a valid PCR result. RNA quality and quantity (semi) and the PCR procedures, like if there is any preamplification step carried out or not should be given in details.
Additional comments: Authors referred some reviews that actually don’t carry out the study of relevant findings. If authors want to add a review to the article they should add it as an advisory or as a recommendation not as a reference. So Authors must check the references and find the original articles instead of reviews.  Two of them are;
a)	Leung et al 2008
b)	Park & Kim 2015

Reference for miRNA definition is not suitable as every researcher in this field knows that Victor Ambros (2001) must be referred for that definition.

The sentence starting in line 46 does not need a reference and moreover reference given for the sentence is not suitable.

The sentence starting with at present in line 49 does not need a reference rather it is a conclusion sentence completing the previous sentences. Also both references are reviews.

In line 101 Union of “International Control Cancer” should be “Union of International Cancer Control”.
 For delta delta Ct method Pan et al is not the reference (Pan et al, 2018) to be used as the mentioned author didn’t generated the formula.

Authors should specify the brand with catalog number of the Helicobacter Pylori assay.

Did authors measured RNA quantity after RNA isolation (via nanodrop ie)?

Authors should give the details of Quantitaion of miRNAs. And specify if there is any preamp step, cDNA step and which chemistry used for monitoring PCR products like sybergreen taqman scorpion probes.

What was the threshold for non-specific PCR products. In figure 1a GC miR-16 raw Cts’ showed a wide range of threshold and looks like authors didn’t rule out any PCR products over any threshold (SD extended over 30 cycles). Authors should check real time PCR graphs if there are any false positive results. and there should be a limit for Ct values for being accepted as it worked.

Authors used miR-16 as a reference for comparison. In figure 1a raw Ct of GC patients are wider. Did authors checked if those samples have any problems due to any procedure problems or maybe an overlooked patient with any contributing health problem.