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: INDIVIDUALS WITH FIBROMYALGIA HAVE A DIFFERENT GAIT PATTERN AND A REDUCED WALK FUNCTIONAL CAPACITY: A SYSTEMATIC REVIEW WITH META-ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: - First of all, I think there are some formal flaws in the wording of the manuscript. Some sentences should be clearer. I recommend authors to request a language editing service to improve these aspects.

- The beginning of the introduction is adequate, but I believe that it does not sufficiently address the knowledge and relevance of this topic. The main point of this manuscript is gait in patients with FM, but they only mention this aspect superficially in lines 69-74. Furthermore, they refer to an opinion editorial (reference 14) on central sensitization syndromes that is not directly related to the main interest of this review.

- In addition, it would be interesting to comment on previous literature in this field.

- It is necessary to improve the resolution of Figure 1, since it is not possible to see the content in detail.
Experimental design: - Objective: Should be better written (to assess the impact of fibromyalgia on FM patients?).

- It would be interesting to describe in detail the search strategy (line 100)

- Why was the year 2000 used as a selection criterion? Similarly, why was the BMI cut-off point set at 35 and not others?

- An important methodological limitation of this review is the lack of risk of bias assessment of the included articles. I suggest that the authors use some appropriate scale for this purpose, such as the Newcastle-Ottawa modified quality assessment scale (NOS). In the same way, the certainty or quality of the evidence found should be evaluated.

- Throughout the manuscript, and specifically in lines 134-137, it is described that a meta-analysis of the 6MWT variable was performed. However, it is not described how the statistical analysis was performed. Was a statistical aggregation of the data actually performed or were they only collected? I do not know if this should be called meta-analysis.

- Another of my main concerns is that only 9 compared the outcomes of FM patients with healthy subjects. The main objective of this review is to quantitatively and qualitatively assess the gait of FM patients, but this is not possible without adequate comparison groups.
Validity of the findings: - The validity of the findings is totally influenced by the methodological limitations of this review.

- I do not think it is possible to draw general conclusions from the results obtained.
Additional comments: In general terms, I think the article can be interesting and add some value in this field of knowledge.

However, I suggest to the authors to totally revise and improve the methodology used. It is necessary to perform meta-analyses that really evaluate the presence of gait disturbances in these patients, to consider whether it is relevant to include studies that do not present a control group and to assess the methodological quality of the included studies.


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: INDIVIDUALS WITH FIBROMYALGIA HAVE A DIFFERENT GAIT PATTERN AND A REDUCED WALK FUNCTIONAL CAPACITY: A SYSTEMATIC REVIEW WITH META-ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: - This manuscript has clear and unambiguous, professional English used throughout.
- The literature references, sufficient field background/context are provided.
- It presents Professional article structure, figures, tables. However, the figures present poor quality (very hard to read). Finally, the raw data was not shared.
- Self-contained with relevant results to hypotheses. However, there are aspects in the methods that should be improved.
Experimental design: - The manuscript presents original research within the aims and scope of this journal.
- The research question is well defined, relevant & meaningful. This manuscript is clear on how the research fills an identified knowledge gap.
- A rigorous investigation is performed to a high technical & ethical standard. However, there are aspects in the methods that should be improved.
- The methods are described in detail, but there is not enough information to replicate at the current state.
Validity of the findings: - The rationale & benefit to literature is well written. However, some concepts and definitions should be revised.
- The analysis needs more clarification in order to be robust, statistically sound, & controlled.
- Conclusions need more clarification while linking to the research question and supporting the results.
- The discussion is well based on the literature and brings explanations related to mechanisms that could explain some of the findings.
Additional comments: 1.	Thank you for allowing me to review this interesting and timely work. It is a very interesting systematic review about fibromyalgia and altered gait and walking performance. However, there are a few points that the authors should address. Please take a look at my specific comments below (attached).
2.	The state aim "was to verify qualitatively and quantitatively the impact of fibromyalgia on the gait pattern of patients with FM". However, the objective state here does not align with the further described statistical analysis. My understanding (after reviewing this SR) is that the goal "was to perform a systematic review and meta-analyses comparing walking test performance and gait pattern between individuals with and without fibromyalgia”.
3.	I suggest the search be more cohesive by having a search strategy focused on combining three conceptual groups of terms: (1) fibromyalgia; (2) walk (performance) tests; and (3) gait analysis.
4.	I also suggest clarification about the difference between walking test performance and gait pattern analysis.


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

Input:
Title: INDIVIDUALS WITH FIBROMYALGIA HAVE A DIFFERENT GAIT PATTERN AND A REDUCED WALK FUNCTIONAL CAPACITY: A SYSTEMATIC REVIEW WITH META-ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: in discussion I would suggest to deepen the part between:
- speed and fatigue
- cognitive function and gait cycle
If possible, in the results part, also reporting in a separate table, if in the various articles analyzed specific data and scales are reported to measure fatigue and cognitive function.
Experimental design: no comments
Validity of the findings: I suggest to report, please, the quality level of the papers analyzed according to the scales most convenient for you (for example PEDRO or others)
Additional comments: Dear Authors,

please,
in  discussion section I would suggest to deepen the part between:
- speed and fatigue
- cognitive function and gait cycle
If possible, in the results part, also reporting in a separate table, if in the various articles analyzed specific data and scales are reported to measure fatigue and cognitive function.

Also,
I suggest to report, the quality level of the papers analyzed according to the scales most convenient for you (for example PEDRO or others) (in Result Section)

Also,
It would be important to suggest or hypothesize the importance of your results in the light of the rehabilitation treatment or adapted physical activity (by inserting specific exercises or paths on this topic) ( at the of discussion and conclusion).

There are some studies that report a decreased proprioceptive deficit in FM patients: so, if we feel more unstable, maybe we go slower because we are afraid of falling? or to move?
if the articles you have analyzed give you this possibility, the discussion could also be enriched with these aspects


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: INDIVIDUALS WITH FIBROMYALGIA HAVE A DIFFERENT GAIT PATTERN AND A REDUCED WALK FUNCTIONAL CAPACITY: A SYSTEMATIC REVIEW WITH META-ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have significantly improved their manuscript based on the above comments. It would be interesting to include more information about how the meta-analysis was performed in the methods section.
Experimental design: Ok
Validity of the findings: Ok
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: INDIVIDUALS WITH FIBROMYALGIA HAVE A DIFFERENT GAIT PATTERN AND A REDUCED WALK FUNCTIONAL CAPACITY: A SYSTEMATIC REVIEW WITH META-ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: •	Clear, unambiguous, professional English language used throughout?
    o	Please review some paragraphs where the idea is a bit confusing (notes/comments are provided in the main track changes document)
   o	Please be consistent with the use of acronyms e.g. using FM constantly over the text instead of fibromyalgia (or vice-versa). My suggestion is to pick one.
   o	Please substitute the word “subjects’ with “individuals”, “people”, or “persons” throughout your text.
   o	Please substitute the word “healthy” with “without FM” or “control” throughout your text.
•	Literature references, sufficient field background/context provided?
   o	The article includes sufficient introduction and background to demonstrate how the work fits into the broader field of knowledge. Relevant prior literature is appropriately referenced. (specific notes/comments are provided in the main track changes document)
•	Professional article structure, figures, tables. Raw data shared?
   o	The structure of the article is in conformity to the ‘standard sections’.
   o	Most of the figures are relevant to the content of the article: Figure 2 would e more relevant with the meta-analysis results.
   o	Figures have now good resolution and are appropriately described and labelled.
   o	Tables 1: Please add information on the meaning of the numbers in the table. On the table heading, please substitute the numbers with a short expression of what is being assessed through NOS.
   o	It would be interesting to have a table with the excluded studies (as supplement material).
•	Self-contained with relevant results to hypotheses?
   o	The submission is ‘self-contained,’ represents an appropriate ‘unit of the publication’; however, it does not include all results relevant to the hypothesis. The process of how the meta-analysis was carried out is not clear. It misses important information to be able to affirm or not the hypothesis.
       - Important points to be clarified: how did you perform the meta-analysis? It is missing the description of how this statistical analysis was performed.  For example: “Did you used Hedges’ g to calculate the standardized mean difference (SMD) between individuals with and without FM using the means, standard deviations (SD) and sample sizes of both groups? If the full text did not contain SD, did you calculate SD from the reported standard error or confidence intervals (CI)? Did you use random-effects models with an inverse variance (IV) method to pool the SMD of included studies? Did you calculate the heterogeneity with I-squared (I2)? Did you estimate publication bias visually via re-displayed funnel plots? Did you use Duval and Tweedie’s Trim and Fill test to estimate the adjusted (or unbiased) pooled SMD (if the case)?
Experimental design: •	Original primary research within the scope of the journal?
    o	Yes
•	Research question well defined, relevant & meaningful. It is stated how the research fills an identified knowledge gap?
    o	The submission clearly defines the research question, which is very relevant and meaningful to the area. The knowledge gap being investigated is identified, and statements are made as to how the study contributes to filling that gap. However, I suggest including in the text the reason for not including articles before 2000 (for transparency) since the FM diagnosis was established in 1990 and possibly performance tests as the 6MWT and 8fUP could have been used in studies before 2000. An important aspect that should be included is the test Time up and go: why this test was not included? It assesses the same parameters as the 8fUP (the only difference is the distance to the cone).
•	Rigorous investigation performed to a high technical & ethical standard?
    o	The investigation can improve the statistical analysis in order to be conducted rigorously and to a high technical standard. The research was conducted in conformity with the prevailing ethical standards in the field.
•	Methods described with sufficient detail & information to replicate?
    o	Methods are Not yet described with sufficient information to be reproducible by another investigator. Details on how the Meta-analysis was performed need to be presented: how did you perform the meta-analysis? The article is missing the description of how this statistical analysis was performed. I also suggest that authors be more careful with the language used while interpreting study findings based on qualitative analysis of studies not included in the meta-analysis (when this was not possible). More details are provided in the main track changes document).
Validity of the findings: •	Impact and novelty not assessed?
    o	The impact, degree of advance, and novelty of this systematic review are of interest to multiple audiences. More information related to the meta-analysis must be provided for the study replication, and to add more value to the literature.

•	All underlying data have been provided; they are robust, statistically sound, & controlled?
    o	The data on which the conclusions are based still misses information related to the meta-analysis to be robust, statistically sound, and controlled. I also suggest that authors be more careful with the language used while interpreting study findings based on qualitative analysis of studies not included in the meta-analysis (when this was not possible). More details are provided in the main track changes document).
•	Conclusions are well stated, linked to original research question & limited to supporting results.
    o	The conclusions still need work to be better connected to the original question investigated, and should be limited to those supported by the results. The conclusions are based still misses information related to the meta-analysis
Additional comments: Additional comments are provided in the "peerj-60354-Main_Document_R1_PRS_Reviwer 3"


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: INDIVIDUALS WITH FIBROMYALGIA HAVE A DIFFERENT GAIT PATTERN AND A REDUCED WALK FUNCTIONAL CAPACITY: A SYSTEMATIC REVIEW WITH META-ANALYSIS
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: INDIVIDUALS WITH FIBROMYALGIA HAVE A DIFFERENT GAIT PATTERN AND A REDUCED WALK FUNCTIONAL CAPACITY: A SYSTEMATIC REVIEW WITH META-ANALYSIS
Review round: 3
Reviewer: 1

Output:
Basic reporting: - Literature references are provided and a sufficient field background/context is present in the text.
- Good quality figures and tables
- Relevant results to hypotheses.
Experimental design: - This review is original research within the aims and scope of the journal.
- Research question is well defined, relevant & meaningful.
- Methods described with sufficient detail & information to replicate.
A few suggestions for improvement:
- Review the section "Data Collection process": there is repetitive information between lines 137 to 146.
- Line 163: I suggest the use of the word "impact" instead of "effect" of the FM.
Validity of the findings: - In the discussion, it's needed less information already present in the results section and focus more on the "how" they add value to the literature
- In the conclusion, I suggest including information related to the quality of the studies from which the conclusions were drawn.
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: EXPLORING INTERACTIONS BETWEEN BEAUVERIA AND METARHIZIUM STRAINS THROUGH CO-INOCULATION AND RESPONSES OF PERENNIAL RYEGRASS IN A ONE-YEAR TRIAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript. by Vera et al., the researchers report the results of an intriguing experiment examining the impacts of two entomopathogenic fungi (EIPFs) on the growth of perennial ryegrass, an important forage plant for pastured livestock. The writing is clear and unambiguous in nearly all places (minor exceptions noted in detailed comments below), and the literature review and context provided are sufficient. The article structure is also clear and aligned with standard scientific expectations, and the motivating questions are clearly articulated at the end of the introduction. Nearly all the raw data are provided as supplements; if the authors can add in the results of their culturing study, this manuscript will be completely aligned with the PeerJ “basic reporting” standards.
Experimental design: In this manuscript, the authors describe a thorough study on the effect of EIPFs on ryegrass, representing original, primary research that falls well within the aims and scope of PeerJ. The research questions are well defined and focus on how well the focal strains of EIPF colonize ryegrass, how their abundance changes over time, and whether their colonization of the ryegrass affects plant biomass. To my knowledge, this is a real gap in our understanding of how plants interact with entomopathogenic endophytes, and is a valuable contribution to the field.

The experiments presented represent a rigorous approach: The authors began by collecting plant and larval material from nine sites across southern Chile and cultured the fungi they contained on fungal growth media. From these, they selected strains belonging to two entomopathogenic genera (Beauveria and Metarhizium). The authors then used these strains to inoculate ryegrass plants in a “mini-pasture” experiment, which included a water restriction treatment in the summer. The authors regularly measured aboveground biomass and measured colonization by the applied entomopathogenic fungi in roots using qPCR and microscopy throughout the nine month experiment. They found that the fungi coexisted in plant roots, and that plants in the water-restricted treatment had less variable rates of fungal colonization than the plants in the wet treatment. The applied fungi did not discernibly affect plant growth in this experiment, although dry weight was slightly greater for inoculated plants than uninoculated ones in October (prior to water restriction) and in February (only for water-restricted plants). The statistical methods employed appear to be appropriate, and the methods are almost entirely described in sufficient detail for future replication. (I have requested occasional additional details in my minor comments, below.)
Validity of the findings: Although the authors have examined the effects of only two fungal strains on their ryegrass mini-pastures, their findings strike me as both valid and interesting. They have provided the underlying data for most of their analyses, although I would love to see the data for their field sampling and culturing added to the supplemental data files. I am unfamiliar with the method these authors used to calculate the relative abundance of their fungi from the qPCR data (details in "additional comments"), but a citation with more information about the method, or a shift to a more standard ratio-based metric, would address this concern. The conclusions are clearly stated and supported by the evidence presented in the paper (although the authors seem disappointed by their interesting negative result). If the authors want to dig into the connection between EIPFs and scarabaeid herbivory of ryegrass roots, it might be worth devoting some space in the discussion to outlining the most productive future experiments that could address that question directly.
Additional comments: Overall, I found this to be an interesting and well-written paper. It is easy to follow, and I think it is valuable to know that these entomopathogenic fungi can coexist in ryegrass roots as endophytes. It is also helpful to know that these endophytes did not seem to affect ryegrass growth in the mini-pastures, although, based on the framing of the paper, this may be an unexpected negative result. I appreciated the authors’ thorough approach and illustrative figures, particularly the photos of the field site, mini-pastures, and the lovely fluorescence microscopy images of endophytic fungi in roots. If the authors are able to address the questions and concerns I articulate below, I think this will be a valuable contribution to PeerJ.

Major points:
1)	The authors describe an ambitious field sampling project to collect fungi for the mini-pasture experiment. However, in this version of the manuscript, they don’t report how many fungi they found overall and from how many different samples of the various substrates, what the diversity was like, or how many entomopathogenic strains they ended up getting. (They say these entomopathogenic fungi were relatively common, which is entirely possible, but I would love to see some kind of table summarizing how many they got across their sampling sites!) I would also like to know which sites and isolation material (larva, root, seed, etc.) provided the strains that they used for the experiment.
2)	The negative result in this paper – that the entomopathogenic fungi did not improve plant growth – is quite interesting. Do the authors have any data on whether scarabaeid larvae were present in the mini-pastures prior to fungal inoculation, and at what densities? If the larvae were absent, it is perhaps not surprising that the fungi provided no growth benefit to the plants. I think it would be valuable to spend a little bit of time in the Discussion laying out future experiments that could help determine whether these entomopathogenic fungi can actually protect ryegrass from root herbivores like the scarabaeids.
3)	The current draft of the manuscript appears to lack the required “data deposition statement” for some of the supplemental files. (It might be easiest to read if this is appended as a separate paragraph after “Conclusions,” although I believe the authors can choose to describe their data deposition strategy throughout the manuscript, as appropriate.) I appreciate the detailed information available in the supplements. The only major piece that is still missing is the results of the culturing and antagonism assays from field-collected fungi. The authors should upload those data, and also please double check that all supplemental files are mentioned and described somewhere in the manuscript, so readers can easily find them.
4)	Field permits: Were Juan Carlos Marin, Luis Toloza, and Carlos Villagra the only land managers whose properties were involved in the field sampling? If so, it seems like the permissions were appropriately acquired, which is great! Please clarify this by specifying which of the nine field sites were managed by which person.

Detailed/minor comments:

In general, this manuscript reads well and tells an interesting story about a nice experiment. I noticed several typos as I read, noted below, which should be easily corrected with the spell checking feature of any commercial word processing software (e.g. Microsoft Word). The whole document should be checked, since I probably missed some minor errors.

Abstract:
 L39: “… using a linear mixed-effects model and ANOVA statistical test.” This is more statistical detail than I usually expect to see in an abstract. (These would be critical details if they were new statistical approaches, but I think these are good, standard tests.) Feel free to omit if you need to tighten this section.
L41: “… isolated only in scarabaeid larvae…” Based on the methods section, I thought you isolated fungi from seeds, plant material, AND living and dead scarabaeid larvae. Did you use only strains from scarabaeid larvae, in the end? If so, please mention this in Methods.

Introduction:
L54-58: This short paragraph is a bit more broad than I find useful, as a reader, and I’m not sure what “broad yet limited” means with regard to our understanding of endophyte ecology. I’d recommend opening the paper by getting right into EIPFs as rapidly as possible. They’re so interesting, and there’s a lot we don’t know – maybe keep the first sentence that you have, just to introduce endophytes, and then go right into what is currently your second paragraph (“Some fungal endophytes…”).
L68-69: “… the origin, biology, and ecology of EIPFs are still poorly understood.” I’m sure this is true, but in this paper you can only really address a little bit of the biology and ecology of these organisms (and nothing about their origins, evolutionarily speaking). I think it would be clearer here to focus on the facets of EIPFs that you explore in this paper.
L71-79: Although this paragraph is interesting – I didn’t know anything about the evolutionary biology of EIPFs – it doesn’t seem too relevant to the rest of the paper, since you don’t try to clarify the evolutionary origins of these fungi yourselves, nor do you interpret your results in light of their evolutionary history. I think the introduction would be stronger if you focused just on the aspects of EIPF biology and ecology that you explore in the present study.
L86-87: “Thus, for example, they belong to the most common entomophatogenic fungi…” What does it mean to “belong to… fungi?” I would suggest rephrasing as follows (and fixing the typo): “These genera are among the most common entomopathogenic fungi in soils planted with perennial ryegrass,” (if, indeed, this statement is true – I’m not as familiar with ryegrass-associated fungi as the authors must be).
L101: “… where a substantial fraction of EIPF isolates was gathered.” What is a “substantial fraction,” here? The phrasing implies that you ALSO collected other EIPF isolates, but that most of them (a “substantial fraction”) came from the nine pastures mentioned earlier. If true, please mention where you got the other isolates at this point in the text. Otherwise, consider rephrasing “substantial fraction” to something else, like “many,” or, even better, naming the exact number of EIPFs you gathered.
L106: “growing in mini-pastures natural…” should read “growing in mini-pastures with natural…”
Methods:
L123-126: “The farmers….” This sentence would be a better fit in the acknowledgements section. I think you could remove it from the methods.
L136: Does “ended” mean “killed”?
L137: “Schock” should read “shock”
L144: “Isolates belonging to the genera Beauveria and Metarhizium were sequenced…” How did you identify the fungi in those genera? Please describe your morphological ID strategy, or cite a paper that describes it.
L149: “To remove fungal infections…” should read “To detect fungal infections” or “to extract fungal DNA.”
L165: “Antagonisn” should read “Antagonism”
L166: This line refers to “Table S1” as if it might contain data about the EIPF antagonism assays, but instead table S1 contains information about the bacterial and fungal load of ryegrass seeds tested! Could you please upload a table with the antagonism data?
L182: How did you choose the GTR+I+G model for this analysis? Please clarify in text.
L203: I appreciate the description of the soil used in the mini-pastures, but I would like to know more! What was the vegetation like in the area where the soil was collected? Did you expect the soil to contain scarabaeid larvae, and did you find any? Were soils sieved or otherwise homogenized before use in the mini-pastures?
L236-237: The sampling times, here called S1, S2, S3, S4, and S5, are never mentioned again in this paper. No need to tell us about these S labels if they don’t show up later!
L253-254: “… the raw threshold cycle values determine for each fungal consortium with their specific primer pairs were subtracted from those of the perennial ryegrass-specific primer pair…” This seems like an unusual way to standardize your qPCR data. Would it be possible to cite another paper that does it this way, so your readers can understand why you selected this analysis method? Alternatively, I think it may be more typical to use a ratio for this kind of relative abundance analysis, e.g. Ct_fungus divided by Ct_ryegrass, to give you a sense for the relative abundance of each fungal gene relative to the ryegrass gene.

Results:
L332: “There were significant differences…” Whenever I see this, I want to ALSO know both the magnitude and the direction of these differences. Was it a big or small difference? Which treatment had the higher values? Please be as specific as you can while reporting these results.
L337-339: “… colonization … by M. aff. lepidiotae… did not vary, whereas colonization by B. vermiconia… increased.” This is great! I’d love to see every result reported with this level of detail (contrast to line 332).
L348-349: “… from July to October…” I think it would help Northern Hemisphere readers if you could include here which season this is, e.g. “… from July to October (winter)…,” especially since you mention “the beginning of summer” at the end of the sentence.
L352: “… also a significant difference in fresh weight…” Once again: how large was the difference, and which group had a higher value?

Discussion:
L369-372: I think it would be more effective to open this section with a summary of your results and their potential implications, rather than with this general sentence about what EIPFs can do in other systems.
L378: “… EIPF communities are relatively frequent…” In the context of this sentence, it’s a little confusing to think about entire communities of EIPFs having different frequencies across a landscape. Might be clearer to say “… EIPFs are relatively common…”
L395-397: “Observations by Barelli… suggested that there is an initial period of colonization of the rhizosphere…” I don’t think I understand why you are including this detail here. Does this matter when we try to interpret your results? How might it change things? If not relevant, omit; if it is relevant, please describe a little more so your readers can follow your reasoning!
L403-404: “On the basis of these observations, we infer that both fungi are able to interact symbiotically with this forage plant…” I think you could omit this sentence, since a “symbiosis” means by definition that the two organisms grow together, which you just established in the preceding sentence. Do you mean that they interact in a commensal (or even slightly mutualistic) way? (You could make that argument, based on your growth data.) If so, please be specific.
L415: “… observing differences between the two seasons…” Which season was better, and is it consistent with what you would have expected?
L426-427: “… Beauveria was more severely affected than Metarhizium…” What direction was this effect? Did Beauveria experience a greater reduction in biomass during the dry season than Metarhizium? The discussion will be more illuminating the more specific you can be!
L431-432: I found myself getting confused here because two sentences begin with “However,” and it’s hard to keep track of the contrasts that are happening. Consider trying some different transitions to avoid multiple instances of “however” in a row.
L440-442: “… we postulate that these EIPFs could be efficient controllers of white grubs…” This seems very hypothetical, based on the results of this paper. I think it would help to be a little bit more cautious about this proposed connection: Perhaps this is a good place to say that the EIPFs, which you have demonstrated can coexist in ryegrass, might be useful in controlling grubs, and future experiments examining the impact of these strains on the grubs and ryegrass would be beneficial.

Figure 1 (legend): “(D) Ryegrass pasture effected…” should read “(D) Ryegrass pasture affected…”
Figure 3:
-	How did you select the root whose images you present in this figure? Was it representative of most of the roots you looked at, or was it an especially well colonized root? Which moisture treatment was this sample from? These details could go in methods, and/or be mentioned here in the legend.
-	What are the units on the y axis? Is this… the ratio of (Ct_fungus/Ct_ryegrass)? Or maybe (Ct_fungus – Ct_ryegrass)? Please label specifically.

Supplements:
-	I can’t find a mention of Supplemental Figure 1 in the main text. Could you please mention it, where appropriate, so interested readers know to look for it?
-	All supplemental tables: It would be helpful to have some kind of header or brief description of the table’s contents in each supplemental file.
-	Table S2 may have a typographic error: pH (in water) is listed as 60. Should this read 6,0?
-	Table S3: What does the asterisk mean after the header “Larvae”? Please clarify in the legend.
-	Table S4: Column D header should probably read “Efficiency,” rather than “Efficience.”


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: EXPLORING INTERACTIONS BETWEEN BEAUVERIA AND METARHIZIUM STRAINS THROUGH CO-INOCULATION AND RESPONSES OF PERENNIAL RYEGRASS IN A ONE-YEAR TRIAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: Line 101: Change “was” to “were” because the word “isolates” is plural.

Line 103: This study did not explore how EIPF strains can act as a biological control of white grubs. Please remove the last phrase.

Line 137: Change “schock” to “shock”.

Line 163: There is a missing period.

Line 165:  “Antagonism” is spelled incorrectly.

Line 166: The first two columns in Table S1 are confusing. What do the codes under “Seeds” and “Endophyte” mean? Please remember that readers are not familiar with the codes you assigned during your experimental design. Please re-name or reformat this table to be more intuitive. Perhaps you could list locations that correspond to the map in Figure 1 where you collected the seeds and fungi.

Line 298: Please provide more information on the linear mixed model. What were the fixed effects? What were the random effects? How did you choose among statistical models (e.g., AIC)? How did you check that the assumptions of the model were met (e.g., residuals normally distributed, etc.)?

Line 201-203: Readers not based at your university do not know what “local climatic conditions present in the EEAA belonging to the Universidad Austral de Chile located in sector Cabo Blanco” are. Please report the actual values for precipitation, temperature, etc.

Line 326: It is not clear from Tabe S4 which samples were inoculated vs. uninoculated, especially for readers that are not familiar with reading qPCR values. Could the authors add an extra column to clarify?

Comments related to Figure 3: There is no Figure 3C. It skips from 3B to 3D. Please re-format. What is the y-axis labeled “Relative Colonisation Rate”? Is this different from “Relative Abundance” in Table S4? Rate implies a unit per unit time, but the x-axis is categorical for a given month. How can you have a “rate” from one qPCR abundance reading? Was it based on the change from the previous month? Why aren’t there statistical codes above each bar - why are some blank?

Figure 3A-B: “Different letters indicate significant differences among treatment groups”. I’m confused. What is the treatment group for 3A? Are you referring to month or fungal taxon? For 3B, I’m confused because the term “treatment group” seems to imply 80-85% FC vs. 40-45% FC but the statistical codes don’t seem to match drought treatment. For example in 3B, “c” is the same for fungal taxa WITHIN but not among drought treatments whereas “a” vs. “b” seems to signify differences between the abundance of two fungal taxa WITHIN but not among a drought treatment. Please clarify what the statistical codes are referring to.

Line 332: There is a missing comma between “June” and “August”.

Figure 4: Again, I’m confused why there aren’t statistical codes above each bar. Some are blank.

Line 350: Is the Tukey test a pairwise comparison between July and October? You mention a decrease towards the beginning of summer at the end of the sentence, so it’s not clear which two months you’re comparing.

Line 350: Usage of “however” means that you’re contradicting the preceding sentence. Differences in dry weight in October do not contradict fresh weight findings in the previous sentence. These are two different findings that are not directly comparable.

Line 355: “was not significantly so under optimal soil moisture conditions” Could the authors rephrase this? I’m not sure what “not significantly so” means.

Line 364: Replace the comma with a period.

Line 365: What are those three p-values comparing? Is it control vs. inoculated per month? If so, why are there only three p-values? I’m confused why Figure 4E is cited… there is no water stress treatment in 4E.

Lines 389-392: These sentences are not particularly helpful for a reader. Please explain what mechanisms of root colonization or plant-endophyte interactions are relevant to the findings you discuss in Lines 392-399. How do these cited works contextualize your findings?

Line 432: Avoid using “however” as a transition for successive sentences.
Experimental design: Line 150: I’m a bit confused about the sequencing of the ryegrass seeds. The authors extracted total genomic DNA from seeds and used fungal-specific primers to amplify the ITS region with PCR. The “automated genetic analyzer” sounds like Sanger sequencing technology, unless I am mistaken? How can you Sanger sequence when amplifying from total genomic DNA? Couldn’t there be multiple fungi living within the seeds?

There’s no rationale for why these plants were co-inoculated rather than separately inoculated with each endophytic strain. I understand that the qPCR method allowed the authors to quantify the abundance of each fungal strain but it seems odd to not have treatments where plants were inoculated with just one strain. The authors state that they were unable to isolate these fungal genera from ryegrass roots and seeds, so I’m wondering why they assumed that fungal co-occurrence on plant roots was more important to explore than separate inoculation.
Validity of the findings: The two main response variables in this study, fungal abundance and aboveground biomass, were quantified with sound methods.
Additional comments: I appreciate the work undertaken by these authors. This field experiment tested how fungal abundance and drought stress affected plant growth. The results showed interesting temporal patterns in fungal abundance for two understudied fungal endophyte species and how changes in fungal abundance correlated with plant growth traits that further our understanding of the ecology of these fungal taxa. However, I have numerous questions and concerns that should be addressed before this article can be published that I discuss in the various sections of this review.

The effect of drought on ryegrass is introduced rather abruptly at the end of the introduction. What is it about this system that makes understanding drought important? For example, are plants typically drought stressed during certain seasons (e.g., summer) and did that inform the experimental design? Do these plants have adaptations for drought stress? Is there evidence in the literature that drought stress has impacted the population dynamics for this plant species or that EIPF can mitigate drought stress for plants? While the importance of drought to ryegrass may be obvious for the authors, it is not obvious for the readers. Please explain and build a case for why your study explored drought in the context of EIPF interactions.

Why were there no measurements of belowground plant biomass? EIPF likely have more direct effects on roots than shoots.

I enjoyed and appreciated the microscopy images the authors provided of endophyte root colonization.


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: EXPLORING INTERACTIONS BETWEEN BEAUVERIA AND METARHIZIUM STRAINS THROUGH CO-INOCULATION AND RESPONSES OF PERENNIAL RYEGRASS IN A ONE-YEAR TRIAL
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript is greatly improved, and satisfactorily addressed my concerns from the prior review. I thank the authors for their detailed responses to my comments. The updated manuscript is much clearer, and will be an interesting publication. There are still occasional typographic errors, but I suspect those will be easy to take care of in the final formatting stages. I only have a couple of additional minor comments which I think will improve the manuscript.

L23: “most of such pastures” should be changed to “most such pastures.”
L138: I am still kind of confused by the use of the word “remove” here. Does this mean that you sterilized the seeds before grinding, in order to remove all fungal infections throughout the seed? (But -- you wanted to preserve endophytic infections, right?) Or were you sterilizing just to remove fungi on the outsides of the seeds? I think this would be clear by adding a comma: “To remove external fungal infections on ryegrass seeds, 1g of seeds were surface sterilized as described above, and then ground under liquid nitrogen as with the mycelium.” Or something like that? If I still have not managed to capture your meaning here, I would request some kind of rephrasing, if possible, just so it’s a little clearer for future readers.
Table S1: Thank you for adding these data to your submission! Would it be possible to add one more column to this table, indicating which of these strains you identified as EIPFs? This is not strictly required, but I suspect some readers may find it helpful.
Table S3: Please add column headers to this table. Additionally, the first pH entry still reads “60.” Please change to the correct value (likely 6,0).
Experimental design: As before, the experimental design seems appropriate to me, and relevant to the Aims and Scope of PeerJ. This is an interesting study that addresses a relevant knowledge gap.
Validity of the findings: The findings presented here appear to be valid and the conclusions seem justified based on the data.
Additional comments: The authors have done a very nice job revising this paper. Every section has been improved since the last version -- I commend their efforts! I think this paper will be a useful reference for future researchers.


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: STRUCTURAL ANALYSIS OF M1AP VARIANTS ASSOCIATED WITH SEVERELY IMPAIRED SPERMATOGENESIS CAUSING MALE INFERTILITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Good English, Sufficient literature provided, Professional article and row data sharing.
The article is well witten and coclusions supported by data analysis
Experimental design: Thde paper is well conceived, interesting and conclusion are supported by investigations
Validity of the findings: Results will add the the knowledge in the field. One major comment is whether the authors can reinforce final conclusions possibly adding referring to experimental findings even by other researchers, if any.

Data are mainly computational and conclusions are mainly derived from theoretical observations.
Additional comments: One general  comment is whether the authors can reinforce final conclusions possibly referring to experimental findings even by other researchers, if any.


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: STRUCTURAL ANALYSIS OF M1AP VARIANTS ASSOCIATED WITH SEVERELY IMPAIRED SPERMATOGENESIS CAUSING MALE INFERTILITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1) The manuscript has a significant amount of typos and redaction flaws and the English language needs to be improved to ensure that the readers can clearly understand your work. For example, in lines 93-94:
“MethodsA comprehensive whole exome sequencing and variant prioritization study (Wyrwoll et al., 2020) have firstly shown that the biallelic missense...”
A line break is missing after “Methods” and “has previously” would be more appropriate than “have firstly”.
The manuscript would greatly benefit from being reviewed by someone who is proficient in English and familiarized with your research subject, like a colleague or a professional editing service.

2) In Methods the authors list in Table 1 the five missense variants individually. According to  Wyrwoll et al., 2020, the different individuals with infertility presented the following bi-allelic variants:
p.Ser50Pro and p.Leu430Pro, in compound-heterozygosity
p.Gly317Arg in compound-heterozygosity with a loss-of-function variant p.Trp226LeufsTer4 reported as pathogenic when homozygous
p.Arg266Gln in compound-heterozygosity with a loss-of-function variant p.Trp226LeufsTer4 reported as pathogenic when homozygous
p.Pro389Leu as homozygous in an infertile individual, and as heterozygous in his fertile brother.
In order to avoid confusions about the bi-allelic combinations of these varians, I suggest the authors consider presenting this information about the zygosity of the five VUS, either in Table 1 or in the Introduction section. I also suggest to add the scores of the  In Silico Predictions (PolyPhen-2/SIFT/MutationTaster) assessed by  Wyrwoll et al., 2020

3) Since the pathogenicity of these five variants has still not been confirmed by functional experiments, and four of them are biallelic with other Pathogenic variants, I would like to suggest to avoid using the term “mutation”. Use instead “variant” or “change”, as recommended by the Human Genome Variation Society (HGVS) http://varnomen.hgvs.org/bg-material/basics/. However, this is subject to the preferences of the Journal.

4) I appreciate the effort of the authors in preparing the figures and providing all the supplemental information, however I find some of the figures and tables are hard to follow, inappropriate resolution and their legends do not provide enough explanation. For the supplementary figures, I could not find any legends.

To mention some things that could be improved in figures:

-Figure 2:
In panels (B) and (D) the text is hard to read. Is always better to avoid superimposing text over the structures as much as possible, prefer to place text outside and point to the amino acids with arrows. The sticks of the lateral chains are barely distinguishable from the cartoon representation. It is neither clear where the variants are in the predicted secondary structures in (B) nor if they are part of or close to the putative cleft in (C).

-Figures 3-6 should ideally have consistent start-end values in the Y axes of their panels.

-Figure 8:
The text is too small, the residue indexes can not be read. It is not clear to me what is the meaning of  “Percentage of secondary structure of the residues near each mutation site..”. Does it refer to the percentage of the total time of simulation during which the amino acids were adopting each one of the secondary structure conformations?

-Figure_S1:
It is not clear to me which models are being aligned in each panel, do the colours have a meaning?. Also, changing the point of view of the structures between the panels is visually quite disorienting. It is better if the same view is consistently used in all the panels, unless the authors were trying to show different aspects, in which case it should be explained in a figure legend.

-Figure_S2:
For a more clear identification of where the variants are in the multiple sequence alignment in Figure_S2, the corresponding positions should be highlighted. This could be done   with a symbol on top of it or a box enclosing the column, for example.

-Supplementary material 2
It is not clear what is the meaning of the different colours

5) For a better narrative in concordance with the order of the sections in Methods, I recommend starting the Results with the “Evolutionary conservation” section in first place, and then move on to the structural analysis.

6) The abbreviations used in the manuscript should be introduced on first usage in the Abstract, and again if/when they appear in the main body of the document. Please, explain NOA also in the introduction.

7) The reference for UniProtKB (lines 108-109) should be introduced instead in the “Evolutionary conservations” section, where it is first mentioned.
Experimental design: Five variants were previously observed in bi-allelic combinations in male individuals diagnosed with infertility and reported as variants of uncertain significance (VUS) for this phenotype (Wyrwoll et al., 2020).
In the present work, the possible impact of these five missense variants, observed in the Meiosis 1-Associated Protein (M1AP), is being investigated using protein structure homology modelling followed by molecular dynamics simulations.

I would like to mention three key points that need to be addressed in the experimental design of this work.

1) According to what Wyrwoll et al., 2020 mention in their report:
To gain insight into the function of M1AP and better assess the relevance of identified variants, we pursued two strategies. First, we attempted to model M1AP’s 3D structure. However, because of the lack of information on M1AP and comparable 3D structures, it was not possible to achieve a reliable prediction (BLAST results for sequence of UniProt: Q8TC57 are below 30% sequence identity to known protein structures, details in Supplemental Methods).

In the present work, the Table 2 in “Results” lists the experimentally determined structures selected as temples by the modelling programs, as described in the “Molecular modelling and validation” section. However, the sequence identity between the target sequence and this structures, along with the experimental methodology (X-ray, NMR, cryo-EM) and quality (i.e. RMSD, R-factors when applicable) of these structures are not being provided. This information is crucial when performing homology modelling, as it determines, along with the model quality assessment, to which extent the final models can be trusted with enough level of detail for further computational analysis. Particularly the calculations of stability, amino acid contacts, surface cavities and molecular dynamics, like the ones performed afterwards by the authors, require as input high quality structures (in general atomic resolution with values <3Å) as their estimations are very sensible to lateral chains orientations and interactions.
The authors should properly describe all this information of the experimental structures chosen as start templates along with the regions of the target sequence effectively covered by the templates and  their oligomeric state, paying particular attention to coverage and similarity/identity of the positions affected by the missense variants and its surroundings.

I recommend the authors to go through this recent very comprehensive and clear review for good practises in protein modelling:
Haddad Y, Adam V, Heger Z (2020) Ten quick tips for homology modeling of high-resolution protein 3D structures. PLoS Comput Biol 16(4): e1007449. https://doi.org/10.1371/journal.pcbi.1007449

2) In the “Molecular modelling and validation” section, it is not clear how the model for the structures with the variants were generated and validated. Accompanied by this, in the Results sections there is no mention of the quality assessment of these variant models.

3) In the “System preparation section”, some of the key parameters for a molecular dynamics simulation are not mentioned:
-Neither the barometer nor the Gamma parameter from the Langevin thermometer are provided.
-The criteria adopted to decide when the system was equilibrated and ready for the production MD is not clear.  Did the energy of the system improve after the relaxation?
-The xyz dimensions  (line 128) of the system box lack a unit of measure.
Validity of the findings: I acknowledge the huge work that the authors have done for obtaining the model structures and in performing  subsequent molecular dynamics simulations. However, there are multiple weak points where the authors fail in supporting the validity of their findings:

1) In Results, “Molecular modeling and validation” section, lines 206-208, the authors say:
“Although PROCHECK and WHATCHECK scores of this final model were slightly decreased, the VERIFY3D, ERRAT and PROVE scores were significantly improved after the 100 ns MD simulations as shown in Table 3”.

It is true that VERIFY3D, ERRAT and PROVE scores have improved for the model after the MD simulations, but still:
a) ERRAT AOQF of 86.99% is lower than 91% (bad quality),
b) PROVE BOPA 6.5%  is higher than 5% (bad quality),
c) PROCHEK and WHATCHECK  give bad scores to the GalaxyWeb model and to the model after the MD simulations

The authors are giving a final assessment of “Good” to the “improved” model, based only in one of the five scores (VERIFY3D), disregarding  the bad scores of the remaining four.

This lack of rigurosity, along with the absence of proper information about the PDB structures used as templates, provides a dubious support to the reliability of the models for all the further structural analysis carried out by the authors
Also, as I mentioned before, the quality assessments for the structural models with variants, are not presented.

2) In Results, “Molecular modeling and validation” section, lines 184-186, they authors say:
The multiple models generated by the same tool (i.e., GalaxyWeb, I-TASSER, PRIMO,
Robetta and Robetta-domain) were highly similar to each other (see the structural
alignments in Fig. S1).
As I mentioned before in the Basic Reporting section, Fig. S1 lacks a figure legend and is poorly informative regarding which models are being superposed in each panel. Overall, except maybe in panel (A), the structural superpositions in this figure clearly show differences between the structures, there is an abundance of loopie regions adopting multiple conformations and hence conferring  many possibilities of orientations to the alpha helices and beta strands that they connect. Nevertheless, it is not accurate to rely simply on the visual observation of the superimposed structures, the degree of structural similarity has to be properly quantified using, for example, RMSD between the aligned structures.

3) In Results, “Structural details” section, lines 213-215, the authors suggest:
“Although there is currently no known interaction in the literature, this cleft of this underrecognized protein is suitable for being a binding site for a ligand such as DNA”
The authors are being too speculative without further discussing in what evidence they base their suggestion. What made them think that the putative cleft is “suitable for being a binding site for a ligand such as DNA”?

4) The RMSD (Figure 3) , RMSF (Figure 6) and Foldx ΔG of unfolding (Figure S3) show high values and also high oscillations between the different time steps of the simulation, and between the step 1 and step 2. This tells that the structures are experiencing big movements and have high and fluctuating energies, even when only looking at the wild-type models. This could be an indicative that the structures were not correctly stabilized in the pre-production MD simulation, but also that the structural quality of the models is not good.

5) Based on their Results, the authors discuss (lines 291-293):
 “Instead of being variant of uncertain significance as previously concluded in Wyrwoll et al. (2020), our findings validated that these variants are the lead candidates for NOA”
The authors should be very cautious with the extent of support their results can give to their discussions and conclusions (lines 291-293 and 308-310). I strongly suggest reviewing this and reformulating. It is recommended that computational analysis can be used for adding support and prioritizing candidate variants and exploring possible molecular mechanisms, but in order to validate and confirm functional effect and pathogenicity, this has to be combined with functional experimental assays.

In case they have not done so, I recommend the authors to go through this two resources:
-The ACMG guidelines: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, Genet Med 17, 405–423 (2015), https://doi.org/10.1038/gim.2015.30
-Guidelines for investigating causality of sequence variants in human disease, MacArthur et al., 2014, Nature 508, 469–476 (2014), https://doi.org/10.1038/nature13127
Additional comments: I acknowledge the enormous effort the authors have invested, considering that M1AP represents a challenge, since it lacks elucidated protein structures. This is a very interesting and important protein to study, the elucidation of how the molecular mechanisms of its normal function are being altered by variants leading to male infertility, is urgently needed, as this knowledge could hopefully add valuable information for developing treatments in the future.

However, the present work lacks rigurosity and fails in key points to ensure the validity of the author’s findings: the methods are not clearly explained to ensure reproducibility and the structural models here obtained fail the quality assessments for being used in the subsequent structural analysis. Unfortunately, not accomplishing these fundamental points makes this manuscript, in its current state, not appropriate for its publication.


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

Input:
Title: THE DIRECT AND INDIRECT EFFECTS OF A GLOBAL PANDEMIC ON US FISHERS AND SEAFOOD WORKERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The paper describes covid-19 case rates for the seafood production and processing sectors in the United States collected through media reports and secondary sources and compares these to other sectors of the food system. There are several areas where I have concerns, which could be addressed with more information about the methods and additional text for the readers about uncertainty.

I am concerned about reporting case rates to readers without adequately describing the potential error and uncertainty in both the numerator and the denominator. The numerator is based on i) cases reported by the media and ii) discovered by a search engine. Leah Douglas’s award-winning journalism is remarkable and I am glad you are able to put these data to use. I think the methods section needs a longer description of her methodology particularly since so much of the findings rest on this database. For the denominator, how close is the NAICS dataset to the actual number of workers? Have you vetted these values in other ways?

As for comparisons between the seafood and non-seafood sector, I would also like to hear more about how your team supplemented the FERN data with your own searches. Are you over-representing seafood? and would that make the seafood sector look riskier than non-seafood sectors when comparing head-to-head?

The characterization of the non-seafood sector as the rest of the food system is probably an overgeneralization. After looking at the appendix it appears to be just farms, food processors and meatpacking plants.
Validity of the findings: Introduction

“While occupational health has not been as widely explored as work-related injuries have in this sector…” I’m confused by this sentence. My understanding is that work-related injuries are part of occupational health?

“An article published in the Washington Post during the pandemic reported a sales decline as high as 95% for US fisheries (Reiley,2020)” A more robust source would be NOAAs recent covid-19 Report
https://www.fisheries.noaa.gov/feature-story/covid-19-impacts-us-fishing-and-seafood-industries-show-broad-declines-2020

Abstract
“Based on news reports, seafood workers were about twice as likely to contract COVID-19 as
 workers in other parts of the overall US food system.” See comments below about concerns over this comparison.

Methods
“New articles” typo?

“This includes some articles published in the US about other countries as well as articles that might not focus on our specific topic.” I am a bit surprised that false positives were not filtered out?  Can the author explain why?

Did you distinguish fishing vs aquaculture-related cases?

What is your definition of an outbreak?

Results

“Between March 2020 and September 2021, we identified a total of 1161 US news articles that specifically 156 mentioned (COVID) AND (worker OR employee) AND (seafood OR fisheries) (Fig. 1).”   Was this from the initial 20,229 articles? In the methods it says these articles were not filtered, but it seems like they may have been. Please clarify.

“By May 2020, additional outbreaks had been reported across the country—from the Northeast to the Gulf Coast—primarily in seafood processing plants, but also at crawfish farms in Louisiana (Korban and Cherry, 2020).” The way this sentence is written, it sounds like covid cases were primarily within the seafood sector when we know they were in all aspects of society.

“Despite being a small part of the overall food system, the seafood industry accounted for 3.84% and 5.23% of all cases and outbreaks...” I am a little uncomfortable with this comparison because there may be bias.  It appears you supplemented the FERN database with your own search strategy specifically  for the seafood sector. Would that inflate the number of seafood cases relative to the denominator (total cases among farms, meatpackers and food processors)?  In addition, was the study done of the food system or just the stages mentioned above in parentheses?  It would be helpful to know what % of data points (rows) came from your search vs FERN.

“As a rough estimate, we estimated there were 65 COVID-19 cases 203 per 1000 workers in seafood versus 31 cases per 1000 for the overall food system.” Same concern as above. Were you oversampling the seafood sector? Is the food system being conflated with the production and processing sectors?

“These numbers are difficult to compare to the general population as the cases identified here in food systems include only publicly documented cases or outbreaks for workplaces, as opposed to cases in general” yes, I agree.

Discussion
“Seafood-related COVID-19 cases occurred throughout the seafood value chain, including fishing vessels, seafood processors, and seafood distributors.” Were the boundary conditions for the seafood sector search different than for FERN? I don’t think FERN tracked food distributors but I could be wrong.

I talked with seafood plant operators in Alaska and my understanding was that the summer processing season was challenging, to write and implement new covid protocols, but was fairly successful.  It sounds like Copper River may be an exception?

Conclusions
 I think this paragraph could be condensed by removing background literature and methods.  A few sentences on the main findings and their importance is what I tend to look for.

Figure 2. what is the definition of a non-seafood case?

Table 1.  how would the case rate compare to the meatpacking sector, which seems more similar than the general category of food processing?

The supplement only reports case data. Where is the outbreak data coming from?  What is your definition of an outbreak?
Additional comments: no comments


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

Input:
Title: THE DIRECT AND INDIRECT EFFECTS OF A GLOBAL PANDEMIC ON US FISHERS AND SEAFOOD WORKERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The language was clear and concise through most of the manuscript. In a few instances, the authors could help the readers by being more specific while making their points clearer. Additionally, increased specificity could help future researchers separate this study that focuses on COVID-19’s impact on the US seafood sector from the pandemic’s impact on the global seafood industry. Some of these instances are listed below:

Lines 56-59: In line 58 you describe the estimated “fatality rate for seafood workers was” which could read more clearly if you specified ‘seafood workers in Alaska was’. I recognize that you set the context and draw the conclusion in the first and last line, but this could be made clearer for a wider audience.
Lines 108-110: Despite potential repetitiveness, specifying that this manuscript focuses on the COVID-19’s impact on the American seafood sector could be accomplished by the insertion of “US” in the phrase “our goal was to document the spread of COVID-19 within the <US> seafood sector” (Line 109, suggested insertion indicated by text within <>)

Lines 114-115: “...seafood workers would be disproportionally affected by the pandemic compared to other seafood workers”. Did the authors mean ‘other food system workers’ or ‘other non-seafood workers’? Please correct this and it's recommended to double-check the manuscript for other instances where such a mix-up could impact the message of this manuscript.

Lines 126-129: The authors describe the search criteria, resultant number of articles, and caveats about some of the articles within this number. They then state that they “did not filter articles beyond this point.” For an international audience, it may be clearer to specify that articles published in the US but about other countries were filtered out, or use clearer language to describe the article filtering process.

Line 184: Given the context of this line at the start of a section on COVID-19 cases in the seafood industry, the wording “The first reported COVID-19 outbreak in the US occurred in April 2020 at a processing facility” could come across as slightly ambiguous to an international audience. Are the authors describing the first-ever reported COVID-19 outbreaks in the US? Was it at a seafood processing facility? Clarifications through more specific language could be helpful for a wider readership.

Lines 292-295: There seems to be a minor grammatical issue towards the end of this run-on sentence. This sentence could be modified to read as “... in an outbreak <where> the employers took no additional protection measures” (suggested word to be inserted in <>).

Lines 299-300: This sentence is somewhat unclear in terms of what the authors mean by ‘locally collected’ and ‘come from international countries’. The authors may want to clarify this statement.
Alongside the above instances requiring additional clarification and/or specification, the authors have done a commendable job in clearly describing additional details and caveats to their findings. Examples of these include lines 148-151 and 203-205.

The literature in this manuscript is current and well referenced. I particularly appreciated the literature described in the Introduction highlighting the dangerous working conditions of seafood workers, which were re-examined in the Discussion.

The tables and figures included in the manuscript are of professional quality. Code used to generate the figures and tables has been included and the data availability has been clearly described. A minor suggestion concerning Figure 2 is to change the faceting or plotting order of the plots so that the number of cases and outbreaks are represented as columns rather than rows. This would help readers track trends related to COVID-19 in seafood and non-seafood over time, as the different scales between the two systems don’t assist the comparison.

The article adheres to a standard manuscript structure. The inclusions of the case study comparisons and mention of additional hypotheses in the Discussion were effective.

The manuscript serves as a self-contained unit of publication where the goals and aims are clearly stated and concisely examined. The inclusion of additional questions for future studies to consider was beneficial to the manuscript's goals in highlighting considerations required for the wellbeing of workers in seafood systems.
Experimental design: This study attempted to document the spread of COVID-19 within the US seafood sector and also highlight the indirect effects of the pandemic. The authors examined news reports and covid case data in the US seafood industry to understand the geographic and temporal trends in cases, the indirect and direct effects of the pandemic, and how the US seafood sector compared to other US food sectors.

The knowledge gap concerning the health and working conditions of seafood workers during disease outbreaks and other diseases is described well in the Introduction, as are the replicable methods to address this gap. The use of secondary data and sensitive reporting of labor demographics and working conditions by the authors are at a high technical and ethical standard.
Validity of the findings: This manuscript’s reporting on the impacts of COVID-19 on the US seafood sector is timely and effective. The findings provided and additional questions to be asked are beneficial to fisheries socio-economic literature. Throughout the manuscript, the authors make the case for additional research attention on seafood workers and support these claims through background contexts, rigorously analyzed data, and logical conclusions. Caveats and additional details about the context and assumptions made by the author are made throughout the paper. In some instances, these could be more clearly specified (as has been discussed in detail under Basic Reporting). In summary, the conclusions are well stated, linked to the original research questions, and no new data or suppositions have been included.
Additional comments: No additional comments. Please refer to detailed comments in previous sections.


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

Input:
Title: THE DIRECT AND INDIRECT EFFECTS OF A GLOBAL PANDEMIC ON US FISHERS AND SEAFOOD WORKERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: the authors have addressed all of my concerns.
Experimental design: the authors have addressed all of my concerns.
Validity of the findings: the authors have addressed all of my concerns.
Additional comments: the authors have addressed all of my concerns.


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: FOCUS ON POLISH NURSES’ HEALTH CONDITION: A CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: In the introduction, many health problems experienced by nurses and related factors (time, physical, chemical, biological, infectious, etc.) are mentioned. However, it is necessary to create a transition between paragraphs. First of all, explaining the health problems related to occupational working conditions (such as shift work, long work and intensive work), then physical, chemical and biological etc. Indication of health problems that arise due to reasons can provide an integrity. Thus, it is thought that a better transition between sentences can be created.

What do the abbreviations D, H, HCh in Figure 1 mean? "Welling"?
Line 150. Typo. Parenthesis is not closed.
In order to accurately diagnose the health status of nurses; For each measurement parameter (blood pressure, height measurement, BMD etc.) and laboratory tests, it is recommended to indicate internationally valid reference ranges/cut-off points, with a bibliography.
Discussion part started with lifestyle perpectives of nurses.  However, there is no such "subject" in the research questions or findings. It is recommended to write an introduction directly related to the findings. Otherwise, it is recommended to start the discussion on Line 293.
There is repeated informations about the findings of the research  in the discussion. (lines 306-315). A specific discussion of the research findings is suggested.
Line 285-293: It can be moved to ıntro. It loks like associated with the importance of the subject.
Experimental design: In the method, the power of the sample to represent the universe should be explained by specifying the power analysis and accessibility ratio.
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: FOCUS ON POLISH NURSES’ HEALTH CONDITION: A CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The research project is interesting and deals with important issues for the nursing profession. The work has a chance to be published, however, it requires improvement.
Experimental design: Table 3 requires a bit more description in the text of the work.
Validity of the findings: Only 153 nurses were included in the study. Therefore, it cannot be concluded that "... study shows the poor health condition of Polish nurses, especially those over 50", because the obtained results concern only a selected group of Polish nurses.
Additional comments: I propose to update the literature. Perhaps it is worth replacing older literature with more recent ones, especially on the health condition of Polish nurses. I present several possibilities:

The effect of subjective perception of work in relation to occupational and demographic factors on the mental health of Polish nurses. Frontiers in Psychiatry.

Working excessively and burnout among nurses in the context of sick leaves. Frontiers in Psychology.

Factors determining work arduousness levels among nurses: using the example of surgical, medical treatment, and emergency wards. BioMed Research International


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: A MACHINE LEARNING APPROACH FOR IDENTIFICATION OF GASTROINTESTINAL PREDICTORS FOR THE RISK OF COVID-19 RELATED HOSPITALIZATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: Rephrasing of the sentences needed in several places
e.g. line 96 - "2 distinct kinds of population had been considered for this study. First group consist of..." could be "Two distinct populations were considered for this study. The first group consisted of..."
Experimental design: Methods are not described with sufficient detail & information to replicate.
This reviewer found two main issues
1. The choice of machine learning before considering classical statistical models.
Although the authors correctly state that " Machine learning helps to quickly identify patterns and trends of the large volume of data, that are difficult for humans to recognize". However it seems that the number of variables and observations in the study are small enough for statistical models or the more interpretable machine learning approaches like lasso, ridge regression or other penalized approaches. Statistical models would also have helped in judging the direction, magnitude and significance of the effects.
It is understandable that various machine learning algorithms have been implemented in this field but we also need to justify the choice of the less interpretable models before proceeding to apply them.

2. It is not clear which specific variables were used for each of the analytical and visualisation approaches in the  methods section "Data analysis". The reader cannot also clearly make a connection between each of the methods and variables in the results section. For instance, which variables were involved in the Chi-squared and Fisher test? Which null hypothesis and which of the factors were tested?
Which variables were tested using the multiple comparisons with the Benjamini Hochberg adjustment? Which variables were used in the contingency table, which continuous variables were tested
using the Kruskal Wallis test?
Rephrase the two-way ANOVA description (lines 139-141): the sentence is confusing and it is not clear which two factors and which interactions because multiple factors are mentioned here.

What were the predictors used for the machine learning models, 2D representation of the data by PCA?

Though this reviewer is conversant with R and could dig for this information in the supplementary files provided, readers not conversant with this analytical tool cannot relate to the analysis and results of this study in the absence of a clear connection between the variables and the analysis methods. This also applies for which methods were used to obtain which conclusions in the results section.
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, & controlled
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: A MACHINE LEARNING APPROACH FOR IDENTIFICATION OF GASTROINTESTINAL PREDICTORS FOR THE RISK OF COVID-19 RELATED HOSPITALIZATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript needs major polishing in terms of spelling, grammar, formatting and overall use of language. The presentation has some flaws in these aspects.
Experimental design: The experimental design is acceptable. The authors have used both statistical analysis and machine learning ( Random Forest ).

However, the authors may want to add other measure to test the accuracy of the model, compared to just ROC.

Also, the authors may want to compare the results using other machine learning algorithms such as decision tree, neural networks, extreme boost, logistic regression, and support vector machine.
At least the accuracy can be compared.
Validity of the findings: The findings seems fine.

An additional figure for Variable Importance would have been valuable.
Authors may also want to add a table containing all the variables with description.
Additional comments: In Discussion ( line 258 onwards ) seems more like Introduction. In Discussion, authors should compare their results with other related studies.


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: A MACHINE LEARNING APPROACH FOR IDENTIFICATION OF GASTROINTESTINAL PREDICTORS FOR THE RISK OF COVID-19 RELATED HOSPITALIZATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is aimed to explain the SARS-Cov-2 predictive factors considering gastrointestinal and liver problems as symptoms for the hospitalizations. The paper is written in a clear and correct language. However, there are fundamental problems as explained below.
Experimental design: no comment
Validity of the findings: 1)  It is not wise to factor out a dominant predictor. Clustering the factors, for example, considering two or more factors together in different combinations may provide better results than factoring out a single dominant predictor. Plus, the difference of the ROC obtained is, as outlined in lines 188-190,  only 3%, which is very small to arrive at such bold conclusion.
2) The difference in patients admitted to hospital and discharged home for AST is 0.74 – 0.56 = 0.18, for ALT, it is 0.61-0.48 = 0.13. This implies the mean values are almost equal showing that AST is not conclusive enough to factor it as an important predictor than ALT.
2) Most of these symptoms are also dependent on other environmental and epidemiological factors unique to a specific type of patient. So, there is no preferred predictor for this specific type of disease.
3) Some of the points that are inconclusive based on available data but mentioned in the paper. For example, on Line 161, and Table 1 the total number of female and male patients considered is 347 as opposed to 352 as explained in the “detailed comments” section below.
Additional comments: Considering, the above concerns and the following detailed comments, the paper needs to carefully address these issues before it is considered for publication.

Detailed comments:

Line 96: “2 distinct …” may be re-written as “Two distinct…”. Starting sentences with numbers may create confusion since the authors also used numbers for citations.

Table 1: In the “Gender” row and “Outpatient test center: SARS-CoV-2 negative” category, the number of female, 206 and male, 141 add up to 347 but the number, n of the total negative outpatient number is 352. What is the reason for this discrepancy?
Line 161: “There were no significant differences based on sex.” The data isn’t shown for the gender category. So,  how do we know this?

Lines 166-168: “Comparing SARS-Cov-2 negative and SARS-CoV-2 positive participants the presence of these symptoms has been more than three times higher in the positive group than in the negative one.” This sentence doesn’t seem to be supported by data. According to Table 1: The number of positive group, who are presented with the symptoms are 122 and the negative 101. They are almost equal and the difference is NOT a multiple of three.

Lines 188-190: The AUC values for the two curves is 0.799 and 0.76, the difference of which is 0.033 = 3%. So, can these be conclusive enough to quantify the dominance of the liver enzymes?  Also as explained here,
Lines 59 – 61: “Furthermore, using machine learning random forest algorithm, we have identified elevated AST as the most important predictor for COVID-19 related hospitalizations.”


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: A MACHINE LEARNING APPROACH FOR IDENTIFICATION OF GASTROINTESTINAL PREDICTORS FOR THE RISK OF COVID-19 RELATED HOSPITALIZATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Authors have adequately addressed issues raised during the first review


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: A MACHINE LEARNING APPROACH FOR IDENTIFICATION OF GASTROINTESTINAL PREDICTORS FOR THE RISK OF COVID-19 RELATED HOSPITALIZATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: The ms is now much better compared to the first draft.
Experimental design: Acceptable
Validity of the findings: Acceptable
Additional comments: The authors addressed the comments that were raised.


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: A MACHINE LEARNING APPROACH FOR IDENTIFICATION OF GASTROINTESTINAL PREDICTORS FOR THE RISK OF COVID-19 RELATED HOSPITALIZATION
Review round: 2
Reviewer: 3

Output:
Basic reporting: In this revision, the authors tried to incorporate some of the comments and provided rebuttal for questions that required explanations. This revised version is better than the original article but there are still some problems. Such as, (a) language, abbreviation usage, and punctuation still require editing, (b) the graphs occupied unnecessarily large spaces and on two pages. These figures can be minimized to occupy a single page,, (c ) the Figure captions are not explanatory enough as explained in the detailed comments below, and (d) the comments mentioned in the detailed comments below need attention.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Lines 176-177: “...O2 saturation, CRP, GMT, AST, Bilirubin…). The abbreviations are mentioned for the first time. These have to be interpreted.
Line 180: ATB is mentioned for the first time without interpretation.
Line 200: “ 30 patients were …” Starting sentences with numbers are still present in the manuscript even though the authors corrected some of the paragraphs in the introduction.
Line 227: “... wasalso …” is written as one word. Consider correcting it.
Lines 227-231: The figures for ALS and AST are separate and it is difficult to compare. Perhaps combining the  two graphs may provide clear information. Plus there is no figure for Bilirubin but in the statement, “ There is no statistically significant difference in the levels of ALT(Figure 2) and Bilirubin.”
Lines 247-252: Figure 5 has two dimensions dim1 (~14%) and dim2(~10%). These are to indicate the first pca and second pca respectively. Neither the explanation nor the Figure captions has sufficient explanation about the PCA values.


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: A MACHINE LEARNING APPROACH FOR IDENTIFICATION OF GASTROINTESTINAL PREDICTORS FOR THE RISK OF COVID-19 RELATED HOSPITALIZATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Almost all the comments were addressed.


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

Input:
Title: AN ISSUE OF CONCERN: UNIQUE TRUNCATED ORF8 PROTEIN VARIANTS OF SARS-COV-2
Review round: 1
Reviewer: 1

Output:
Basic reporting: Long sentences in the discussion part. Spelling mistakes of ORF8 in the discussion.
Experimental design: Authors should provide detail about identification of T-ORF8 and matlab programs.
Validity of the findings: Discussion needs to be modified with more clarity.
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: AN ISSUE OF CONCERN: UNIQUE TRUNCATED ORF8 PROTEIN VARIANTS OF SARS-COV-2
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comments
Validity of the findings: No comments
Additional comments: The hypothesis and conclusions were clearly identified and the importance of the study was stated making it easier to follow the authors' experimental design. Well laid out schematics and tables were also appreciated.


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: AN ISSUE OF CONCERN: UNIQUE TRUNCATED ORF8 PROTEIN VARIANTS OF SARS-COV-2
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript writing and data organization is poorly organized. The concept of unique T-ORF8s has to be better explained.
Experimental design: The analysis of variants within USA is not relevant, and other factors may be analyses together with geography. Manuscript organization is confusing with unnecessary tables and figures that distract the reading.
Validity of the findings: The work requires a deep phylogenetic analysis to support major claims, which is lacking.
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: AN ISSUE OF CONCERN: UNIQUE TRUNCATED ORF8 PROTEIN VARIANTS OF SARS-COV-2
Review round: 1
Reviewer: 4

Output:
Basic reporting: The paper reports the role of mutation in ORF8 of SARS CoV2 leads to second wave in several countries. the authors have done significant in silico analysis of orf8 from different regions.
Experimental design: experimental designing is very well planned. but there is a small suggestion if anything related to structure can be included it will be good and further enrich the manuscript.
Validity of the findings: the findings requires a experimental validation. but the in silico analysis has significant impact.
Additional comments: no comments


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

Input:
Title: STATE OF BIODIVERSITY DOCUMENTATION IN THE PHILIPPINES: METADATA GAPS, TAXONOMIC BIASES, AND SPATIAL BIASES IN THE DNA BARCODE DATA OF ANIMAL AND PLANT TAXA IN THE CONTEXT OF SPECIES OCCURRENCE DATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: ok
Experimental design: Ok
Validity of the findings: ok
Additional comments: The paper is very interesting and enlightening. It has identified the gaps and clearly led readers and workers on the field the rigt research direction to take. I recommend to publish the paper as it is now.


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

Input:
Title: STATE OF BIODIVERSITY DOCUMENTATION IN THE PHILIPPINES: METADATA GAPS, TAXONOMIC BIASES, AND SPATIAL BIASES IN THE DNA BARCODE DATA OF ANIMAL AND PLANT TAXA IN THE CONTEXT OF SPECIES OCCURRENCE DATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a well-written review paper about the current state of the biodiversity documentation in the Philippines.   However, I have some minor comments on the manuscript:

Lines 39-152: There was no mention regarding to the estimated number of species of plants and animals in the Philippines. I think there is a need to mention about this in the introduction as baseline information. The authors may add references about the richness of the flora and fauna in the Philippines.

Line 226: “data on Homo sapiens and Homo luzonensis” change to “data on Homo sapiens and H. luzonensis”
Experimental design: This paper utilizes the available data from the different online data-bases and it was properly acknowledged.
Validity of the findings: The results are well supported by the presented data.

Figures are clear and well-prepared.

Lines 337-338- The data on the coordinates are not usually indicated in the publication (for plants) because of some conservation issues. You may cite references about these issues, like it will encourage the poachers to collect the specimens etc.
Additional comments: This paper focuses on the review about the state of biodiversity documentation in the Philippines. However, this paper did not mention anything about the background on the biodiversity of the Philippines. The authors can check the book of Catibog-Sinha and Heaney (2013). It is a very important reference about the biodiversity researches in the Philippines. I suggest that the authors should consider citing Catibog-Sinha and Heaney (2013).


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: STATE OF BIODIVERSITY DOCUMENTATION IN THE PHILIPPINES: METADATA GAPS, TAXONOMIC BIASES, AND SPATIAL BIASES IN THE DNA BARCODE DATA OF ANIMAL AND PLANT TAXA IN THE CONTEXT OF SPECIES OCCURRENCE DATA
Review round: 1
Reviewer: 3

Output:
Basic reporting: This research work is interesting and can be seen as a contribution particularly in this so-called time of "big data".

The language in some parts of the manuscript can be improved with a bit of a technical tone, and by making the sentences more concise, non-repetitive, and lessening the use of conjunctions, or compound/complex sentences. Examples are: Lines 41-46, paragraph 2 of the Introduction.

For the reporting of the results and its discussion, the authors gave more emphasis/examples on animal taxa, while for floristic groups it is more in passing. Also, take note of the names of taxonomic groups: Marchantiophyta, while Tracheophyta is not a phylum. The presentation of the results, particularly in the section Initial processing of biodiversity data, will be better if the authors provided a Table instead of a histogram to show details of taxonomic groups (higher level), number of taxa, genetic marker, number of records, etc. to really show the available data. As it is not unfamiliar to barcoders, that COI is mostly utilized for animal groups, while matK and rbcL are for plants, and one can assume that the reported frequency for COI is just because of the high number of available barcodes for animals that were used for this study. See Lines 326-327. For figures, take into consideration the readers who are not from the Philippines (Fig 6A), what does ca and mm mean?
Experimental design: Is this considered a systematic review, or falls under meta-analysis?

Although the need situation is well elucidated, the gaps presented are not new nor exclusive to the Philippines (e.g.: over-representation of taxa, concerns on spatial data, incomplete metadata of barcodes), as these are "personally" well-noted by most workers dealing with genetic/barcode data. To add novelty and relevance to this paper, I suggest that the authors provide/suggest a well-thought system/tool that workers can use/adopt when handling metadata prior to their submission of sequences to different databases.

The protocols presented in the Materials and Methods portion are repeatable. However, in my opinion, it is better to present the protocols with a scientific tone rather than "everyday written English".
Validity of the findings: As mentioned above, the results may not be novel anymore, or it appears that it was just repackaged as "in the Philippine setting", as the points being raised are already recognized by the community (but not often in written form). The presentation of figures/graphs is insightful in some aspects to give points to the arguments/discussion, but there are things that the authors should have considered before comparing/ coming up with "conclusions". Examples: Taxonomic biases in Philippine barcode data= In lines 375-377 it was mentioned that barcode records are related to the taxonomic diversity of a group. Definitely, taxa with a high number of representatives will really have a high barcode record compared with taxa with a low number of species just like what was mentioned in line 382 (phylum Marchantiophyta). In addition, one of the goals of barcoding is to unravel the diversity (incl. taxonomic diversity) within a group of organisms, and large taxa receive greater attention when it comes to DNA barcoding than smaller groups as the circumscription of taxa in the latter group is more often clear-cut. For spatial biases in Philippine barcode data, does the location/accessibility to these provinces play a factor, as well as forest cover when it comes to terrestrial organisms? For Barcode data favoring commonly documented taxa, is it only the level of endemism that plays a factor, or does it include the number of Philippine workers who deal with these taxa? There are a lot of points that the authors should consider when it comes to discussing their results, as the findings raised key points that have multiple root cause; hence, should be viewed with different lenses and supported by literature.

The conclusion part (lines 625-627) claimed that the study elucidated that incomplete metadata of barcodes can limit its useability, but this was not well discussed in the text. Also, some parts of the conclusion appeared like raising a note for action, it might be better to provide a system/tool/pipeline on how Philippine workers can mitigate the problem, as the authors mentioned in the text big data can be a tedious
Additional comments: NA