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 NOVEL CURATION SYSTEM TO FACILITATE DATA INTEGRATION ACROSS REGIONAL CITIZEN SCIENCE SURVEY PROGRAMS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study undertakes to resolve an ongoing limitation facing those looking to integrate datasets from different sources. I think that the manuscript introduces the reason why this can be a challenge, and workable way to overcome this.

1.	The manuscript would benefit from being tighter and more succinct.
I think that all the information is in here, but there is repetition and a bit jumbled, mainly in the introduction.

I am not a programmer, but I have a background in taxonomy and recording and felt that the information up to line 159 could be condensed. At present, the introduction mentions concept relating to recording and the integration of data, then explains how programmes have dealt with this within the same paragraph. I think that the information would be better split between taxonomy and programming. For example, you could start with a brief overview of how data from citizen science (CS) programmes are used, the challenges of nomenclature, and how this causes problems in data aggregation. This could be followed by how others have tried to resolve this generally (e.g. from line 124), the paucity of integrated models (e.g. from line 101), the specific difficulty & example (e.g. from line 141), before introducing how you tackle these challenges in this study.

2.	Further explanation of taxonomic procedures
Given the open and interdisciplinary nature of PeerJ, I believe that a few well-placed sentences regarding taxonomy might help. It’s alluded to in lines 65-70, but I think a few lines on taxonomic processes might help others understand why species names can be different but not ‘wrong’, as well as species names changing over time (especially as splitting/lumping mentioned later on). For example, a short explanation on how species are described through published papers, and that the community are not obliged to use binomial signed in reclassifications and reference an example (e.g. “Description of a new genus for Euptychia hilara (C. Felder & R. Felder, 1867) (Lepidoptera: Nymphalidae: Satyrinae)” Zootaxa 4012 (3): 525–541). Also a note of synonymy, which is mentioned later, but is still quite esoteric.

Additionally
-	The abstract should be condensed into one paragraph. The second paragraph contains a lot description that is in the manuscript and not required at this point (e.g. lines 44-51 could be reduced to saying what you did rather than explaining how).
-	The first paragraph of the discussion could be absorbed into the introduction.
-	Try to avoid colloquial terms. For example line 384 “On the other hand” (perhaps “Conversely”?) and line 574 “can’t afford to”.
-	Line 33 – does ‘long legacy of data’ mean historical records?
-	Line 73 – mention GBIF for the first time, yet introduce the abbreviation in line 127.
-	Line 73 – What do you mean by ‘associated’ with a voucher specimen? Validated?
-	Line 75 – by ‘only taxonomic names’ you mean Latin binomials rather than common names, or names rather than individual organisms?
-	Line 143 -Does usage refer to which species name is given to an organism, or grammar related difference (e.g. hyphen used between double barrelled names instead of a space)?
-	Line 176 – Is there a reference for butterflies being second most monitored group? Is this globally?
-	Line 299 – What is meant by ‘species concept’? I’m assuming that you are referring to a taxonomic unit rather than a biological species concept? Is it the same as ‘taxonomic concept’ on line 317?
-	Supplemental Article S1 – I couldn’t see any explanation for colours and initials in the spreadsheet. I think that these would be well placed next to the totals so that this could read as a stand alone document.
The discussion nicely explains how this programme has the potential to be  adapted in taxa and scale. The figures and tables really are really helpful in visualising the text, and the raw data provides opportunity for further exploration by the reader.
Experimental design: I have no experience of programming, but the method looks like it could be easily replicated or adapted for other taxa or by other citizen science programmes. I’m very pleased that you consulted the program leaders, which I think will add some gravity to the study (lines 284-290). I’ve seen too many programmes designed without consulting the end user, and species identification is rarely straightforward.

I do think that the method would allow a recorder with an interest in programming to give it a go themselves.
Validity of the findings: I applaud the authors for tackling an ongoing issue in the use data from recording schemes. The reasons why a single list of species names is not used universally used can be tricky to explain in an academic paper (I find that it often relates to personalities), as tactfully noted in lines 329-331.

The authors have outlined why this area requires more attention and how integrated data can be widely used in decision making processes.

I think that this will be an iterative process and the programme refined over time, but I think that making this available to the community will stimulate the attention it deserves.
Additional comments: I see that programme managers have been involved, but have you approached any checklist authors? This is only out of interest, as I noticed Dick Vane-Wright’s name on the NABA checklist, and wondered if anyone else had commented on how this might transfer internationally.


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 NOVEL CURATION SYSTEM TO FACILITATE DATA INTEGRATION ACROSS REGIONAL CITIZEN SCIENCE SURVEY PROGRAMS
Review round: 1
Reviewer: 3

Output:
Basic reporting: a) clearly written
b) intro does not show context as well as it could because it does not describe how  scientists resolve taxonomic conflicts (more comments below).  The approach in the paper starts to solve the problem they have identified using  NA butterfly survey data but it does not help the reader know if the method that is developed will be widely applicable or not. For instance perhaps this was the state of bird taxonomic 100 years ago or it is the current state of dragonfly taxonomy. For other vertebrates there are competing sites that try to keep track of taxonomic advancements and provide a standard.   I am not sure about the taxonomy of other groups. Plants taxonomists are slowly working on standards.

c) structure is good
d) figures seem clear
e) raw data has been supplied
Experimental design: a) research is original
b) it is clear the research is filling in a gap but it is not clear if the approach will have wide use. It think the paper is very important in tackling a problem that the taxonomic community has not tried to solve systematically but one that needs to be solved for the rest of biological studies

c) methods are rigorous and generally well explained but  I am not clear about how this research relates to ontological research generally and how resolution methods work for other kinds of ontological work. This is a lack of my expertise
Validity of the findings: a) the paper is novelty but I cannot tell about its impact
b) The conclusion section are about providing context for the work and about what they plan to do than about their results
Additional comments: The authors have tackled a difficult and fundamental problem in biology, namely resolving taxonomic name differences across different taxonomic systems. This problem has challenged biologists across the globe with the creation of systems such as ITIS and GBIF, and the desires of biologists to solve taxonomic problems and to do larger scale spatial analyses.

The linking of common and scientific names to taxonomic concepts and the resolution of differences across names and concepts is a problem that taxonomists as a community have not addressed.  These authors are trying to address the problem

I see this paper as a case study that systematically resolves differences among local butterfly checklists by using multiple authoritative accounts and working closely with citizen science groups who collect and manage their local data while using   different authorities.

The scientists appeared to be are motived to do these project because the survey  groups share a common survey method (Pollard Walks) making the data of high value to ecologists because of the structured nature of the method that includes repeated surveys of the same areas and records search effort and contrasts with the more common analyses of presence only data. The first three paragraphs of the introduction devote lots of words to the value of these kind of survey data but this point does not seem central to the point of the paper.  My sense of the central point is that it is independent of what one does with the data. Understanding taxonomic differences is a problem whenever one is trying to work with a group of species. Given that taxonomists do not have a system in place to provide a community vision of species concepts and names, the paper is supplying a solution.  In that regard I think other scientists also need to resolve local taxonomic lists but may not be motived by doing it for the same reasons the authors are.  I suggest saving the first three paragraphs for a paper that analyzes Pollard walk data. I think  readers will be more interested in the how’s and the generality of the approach than a specific application. This is not to say that as a case studies that integration of Pollard survey is in any way inappropriate. I think is makes a nice example.

How does the method described here compare with efforts by other North American groups that have butterfly data across the continent such as NatureServe, BugGuide, BAMONA, iNaturalist and NABA? As I recall NatureServe used a human curation system, iNaturalist started with the NatureServe Standard and now lets users curate the taxonomy to some extent.  NABA uses a board of experts who periodically review the literature I think.

How much of your method requires human curation and how much can be done by machines?  As taxonomy research advances. how are updates made?

The paper has two empirical results.

1) It does a good job of describing and quantifying the differences found across lists (Tables 1 -).
4
It would be important to know if these categories of differences the same as found in other groups.  Are there any comparison data around?  If not, it would be good to say so.

2) It describes a method to reconcile the differences between the groups.

I am not sure why Ytow et all 2001 (a Ebbe Neilsen prize winner) is not discussed or cited

Ytow, N., Morse, D.R. and Roberts, D.M., 2001. Nomencurator: a nomenclatural history model to handle multiple taxonomic views. Biological journal of the Linnean Society, 73(1), pp.81-98.

Lines 347-349: this was disappointing to read because I agree that 3rd  party resolution is a most important case, at least for synthesis projects.  Could you take a stab at this so people could than make use of the butterfly data for other analyses?

Line 438:  Tool is not meant to stand alone  Glad to know this but it means there is not a tool for other use

I think the paper has value because it systematically identifies taxonomic issues about differences among authorities. This can channel actions that need to be resolved by the taxonomists.  This value is not explicitly stated.


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 NOVEL CURATION SYSTEM TO FACILITATE DATA INTEGRATION ACROSS REGIONAL CITIZEN SCIENCE SURVEY PROGRAMS
Review round: 2
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: This manuscript is much improved. However, in many places the writing can be clarified or streamlined, and in a few instances somewhat defensive language could be toned down. Also, it’s fine to briefly mention a planned extension of work presented in a manuscript, but extensive description of plans (e.g., lines 875-898) is not convincing. All of us would like to do a lot of things that may or may not happen, sometimes for reasons beyond our control.

line 32. Change “interpretations” to “identifications” or “names”

line 33. “coercing” is a rather loaded word. Change to “encouraging”, and, to avoid repeating the same word, remove the “encouraging” after “While”.

line 39. Again, “interpretation” doesn’t seem accurate

line 41. “curate the term” is not clear

line 45. “scaffolding” is unclear

line 254. What’s a “truly” integrated analysis?

line 257. Change “between” to “among”

line 258. This might be a trend in citizen science, but not in data collection by trained lepidopterists.

line 263. And with names only, especially when data collectors are not experts, it’s less certain whether the identifications are correct.

line 292. The relationship between the concept and the taxa? Not clear.

line 294. Not really reinterprets, although there are reclassifications on the basis of morphology, genetics, life history, and other types of data.

line 300. Why is unstable in quotation marks? Do you not actually mean unstable? Same with line 304 (what do you actually mean?) and elsewhere (line 357, 545, 554, 698, 752, 792)

line 307. What do you mean by “taxonomic interpretation of the data source”?

line 314. What do you mean by reanalysis of names? “inscribe” is not the correct word.

line 315. Remove “event”

line 328. What is a “system of web-services”?

line 399. Change “demonstrating” to “testing”

line 411. “thus far unanimously agreed”—this is vague. Which programs have agreed?

line 462. Clearer to say “at the genus or family level”

line 465. As opposed to inappropriately combined? Sufficient to simply say “can be combined”

line 470. Should be evaluating, not demonstrating.

line 514. Taxonomic, not biodiversity. Biodiversity is a far more comprehensive term; it is not synonymous with species or other levels of orgainzation.

line 521. Either explain “official” or delete.

line 524. “Opler and Warren” is short. Throughout the manuscript, spell out rather than abbreviating. Same for species (line 600 and elsewhere), receiver (line 642 and elsewhere), and donor (line 643 and elsewhere).

line 549. Change “must” to “would”

line 550. “personal” not “personnel”. How many is “all”?

line 551. Delete “Conveniently”

line 679. Delete “exactly”

line 698. bi-directionally nonidentical really is a mouthful and not easily understood. Please work to find a clearer term.

line 893. Not clear. Do you mean different taxonomic levels?

line 910. Delete “100% of”

line 928. Conclusions are unnecessary. Delete any material covered above, and integrate any novel material into the discussion.


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

Input:
Title: A NOVEL CURATION SYSTEM TO FACILITATE DATA INTEGRATION ACROSS REGIONAL CITIZEN SCIENCE SURVEY PROGRAMS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been much improved and reads in an easy to follow manner
Experimental design: Integrating such data is as much about the data as it is the data providers, and this is handled sensitively in trying to achieve the main outcomes. Even if all parties agreed, taxonomic classification is dynamic, and this has been accounted for.
Validity of the findings: The program is very targeted, but consequently a great opportunity to trial within a specific taxon group and geographic area. I imagine that tweaks will be required once the programme is widely used, and I get the impression that the authors would welcome the opportunity to increase usability where required.
Additional comments: I found the revised manuscript easier to follow and understand. Good luck with everything!


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 NOVEL CURATION SYSTEM TO FACILITATE DATA INTEGRATION ACROSS REGIONAL CITIZEN SCIENCE SURVEY PROGRAMS
Review round: 2
Reviewer: 3

Output:
Basic reporting: The revisions improve the manuscript. The authors had good responses to the reviewers questions and comments
Experimental design: OK
Validity of the findings: It is an old problem in biodiversity informatics.  Different  solutions have been proposed. This is a novel one
Additional comments: The revision improve the manuscript. I think you illustrate a method that can be developed into a tool.

Some comments

1) Title
Is it a system or a method?

2) Abstract

First sentence addition “Integrative modeling methods, such as niche modeling,”

Last sentence to add? “After integration, these taxonomically standardize datasets can subsequently be used as input for many kinds of biodiversity analyses.

3) line 346  This was well before the current global explosion of citizen science monitoring programs ( see Pocock et al 2015 for development in Great Britain) ,

Pocock, M.J., Roy, H.E., Preston, C.D. and Roy, D.B., 2015. The Biological Records Centre: a pioneer of citizen science. Biological Journal of the Linnean Society, 115(3), pp.475-493)

4) line 501-506 can delete the word “Objective”

5) line 601 Comment For phylogenetic comparisons, these issues would be good to resolve.


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: EVALUATION OF KNOWLEDGE, ATTITUDES, AND CLINICAL EDUCATION OF DENTAL STUDENTS ABOUT COVID-19 PANDEMIC
Review round: 1
Reviewer: 1

Output:
Basic reporting: - The introduction needs more details about COVID-19. There are reports about four different types of coronavírus, some infect humans and mammals and others, only birds. SARS and MERS viruses have caused serious respiratory diseases. SARS-CoV2 has a membranous structure of protein spines and penetrates cells through ACE2 cell receptors. Bats and humans are believed to be hosts of the virus and is speculated the presence of an intermediate host called pangolim(squamous anteater) mammal that inhabits tropical areas of Asia and Africa.

- The English language should be improved in all document.
Experimental design: - Methods are simple but well described
Validity of the findings: - Tables and graphics can be improved, considering aesthetic aspects
Additional comments: - I suggest that on the topic “discussion” the authors:
* explain the difference between surgical masks and N95 respirators.  Also on this topic, they should enfasize the use of rubber dam in endodontics, which can minimize the spraid of virus.
*Talk about preventive measures to control and minimize infection in dental pratice

- The bibliografic references should be reviewed and padronized


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: EVALUATION OF KNOWLEDGE, ATTITUDES, AND CLINICAL EDUCATION OF DENTAL STUDENTS ABOUT COVID-19 PANDEMIC
Review round: 1
Reviewer: 2

Output:
Basic reporting: •Basic reporting needs to improve as there are grammatical errors throughout the manuscript. It is advised to do a grammar check before submitting revision.

•In the structured abstract background could be improved as to why your team is doing this study? Background should be focused on the importance of dental students equipping themselves with COVID-19 practice guidelines and precautions. Objective can be added as heading or modify the objective to be a continuation of the background. Results section in abstract can be concised, avoid percentages and statistically significant reporting with p value.

•Structuring of results could be improved by creating sections.  In the questionnaire report knowledge questions first, then attitude and then practice. Follow the same in the results. Discussion could also be structured better a paragraph should address one issue and everything related can be clubbed in that.

•For the figures please add horizontal and vertical axis titles. Refrain from using words like our students in the figure titles.
Experimental design: •The article is a cross-sectional study within the scope of journal. The gap in knowledge is addressed, but the rationale for gender comparison is unclear.

•The methods are described clearly with appropriate statistical tests application.

•Replace participation rate with response rate as it is more ideal for online surveys. Avoid terms like negative response as this can confuse readers.

•The question of antibiotics usage is not appropriate as the disease in question is a virus and antibiotics are only advised for co-infections. Justify why there is a need to include benefits of antibiotics in the questionnaire.
Validity of the findings: •	The study validity can be improved by providing the current status of dental students, whether they are suspended temporarily during the outbreak or are currently working as per the government regulations in Turkey. The study results can be useful to similar dental institutions.
Additional comments: •The study could be added to the evidence base and is likely to get citations. But grammatical errors and structuring of manuscript needs to be improved


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: EVALUATION OF KNOWLEDGE, ATTITUDES, AND CLINICAL EDUCATION OF DENTAL STUDENTS ABOUT COVID-19 PANDEMIC
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors did the review properly and the paper can be published.
Experimental design: The authors did the review properly and the paper can be published.
Validity of the findings: The authors did the review properly and the paper can be published.
Additional comments: The authors did the review properly and the paper can be published.


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: EVALUATION OF KNOWLEDGE, ATTITUDES, AND CLINICAL EDUCATION OF DENTAL STUDENTS ABOUT COVID-19 PANDEMIC
Review round: 2
Reviewer: 2

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


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

Input:
Title: ALTERED GUT MICROBIOTA ASSOCIATED WITH SYMPTOM SEVERITY IN SCHIZOPHRENIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: No comments
Additional comments: Li et al used 16S rRNA sequencing technology to analyze the gut microbial composition of patients with schizophrenia in South China with a relatively large sample size and an effective method. Reliable statistical methods were used to demonstrate differences in gut microbiota between patients and healthy controls. In addition, the authors analyzed the correlation and symptom severity between the  genera of microbiota and significant changes in the relative abundance of the patients, and initially identified three genera related to the development of schizophrenia. However, some contents are insufficiently specified.

1) Why should the residuals of the relative abundance of the altered microbiota be used to calculate the correlation between the relative abundance and the severity of the symptom group?

2) Why was the p value used for calculating the relative number of phyla and genera of microbiota differences, but not the other p values?

3) The p-value in "Relationship with Clinical characteristics" should be clearly displayed, not just using values below 0.05.


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: ALTERED GUT MICROBIOTA ASSOCIATED WITH SYMPTOM SEVERITY IN SCHIZOPHRENIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Abstract:
1. In line 38-39” 82 SZ patients and 80 demographically matched normal controls (NCs)”. Demographic data included many variables, please point out which variables were matched in this study and you are supposed to describe in the method.
2. I wonder the reason that there was missing the conclusions and keyword in the abstract.

Introduction
1. The pathway of gut microbiota influence schizophrenia should be further discussed, especially inflammatory and metabolic pathways.
Experimental design: Method
1. Please describe the source of participants in normal control group. Additionally, the start time and end time of this study should be reported.
2. The “BMI:18-35 kg/m2” in the inclusion of normal control group was not appropriate. This item indicate that obesity participants would include the normal control group. But obesity participants would influence the characterization of gut microbiota in normal control group.
3. Constipation is a common symptom in patients with schizophrenia and common adverse event by using antipsychotics. So it should be addressed both in the exclusion of NCs and patients with schizophrenia.
Validity of the findings: Result
1. Though the mean levels of cholesterol, triglyceride and glucose in the SZ group were normal, it did’t mean all of included patients with schizophrenia were normal. So I wanted to know were there any metabolic abnormalities in included schizophrenia patients. If there were, it should be reported analysed. If there weren’t, the SZ sample of this study lack of representation. Because previous studies suggest that about 50% of patients treated
with APs develop metabolic complications.

Discussion
1. Antipsychotics are the cornerstone in the schizophrenia. In addition, antipsychotics–especially the second-generation, or "atypical" antipsychotics – can cause severe metabolic side effects such as obesity, dyslipidemia, and type 2 diabetes. And gut microbiota may act via metabolic pathway to influence the MGBs. Hence, the influence of the drug use between gut microbiota and schizophrenia should be discussed.
Additional comments: Table 1.
1.Please provide the data of history of taking medicine,  history of smoking and drinking as the method described.


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: ALTERED GUT MICROBIOTA ASSOCIATED WITH SYMPTOM SEVERITY IN SCHIZOPHRENIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: The authors have responsed to the comments/suggestions of the reviewers well.


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

Input:
Title: ALTERED GUT MICROBIOTA ASSOCIATED WITH SYMPTOM SEVERITY IN SCHIZOPHRENIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: None.
Experimental design: None
Validity of the findings: None
Additional comments: None


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 DIET OF OTTERS (LUTRA LUTRA) ON THE AGRI RIVER SYSTEM, ONE OF THE MOST IMPORTANT PRESENCE SITES IN ITALY: A MOLECULAR APPROACH
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English used throughout.

The majority of the manuscript is well written und easy to understand, however, the authors fail to define some of the metrics they use such as „frequency of occurrence“ or „relative presence“ these might not be common knowledge for all potential readers. Additionally, the English is sometimes flawed. I tried to point out some errors and minor comments below, but would advise the authors to seek the help of a native speaker for proof reading.
Lines 64-65: “please rephrase “deserving of conservation actions”
Line 69: please rephrase “basic for”
Line 105: please rephrase “full of”
Line 113: please rephrase “aged”
Line 114: please remove “been”
Line 116: 0°C is a very unusual temperature for preservation, please explain
Line 129: please add “gene” at the end of the heading
Line 145: how were the 50ng of DNA measured? Was 3each sample run on a Qbit or nanodrop before? Please explain.
Line 152: please rephrase “amplification” (probably to plate?)
Line 154: please explain if the full 25µl were combined and replace “in” with “of”
Line 157: please consider replacing “hunting booty” with prey (spectrum)
Line 159: please rephrase “flowing upstream”
Lines 182-183: please rephrase “making”
Lines 208-209: Please explain in detail how the negative controls were handled during and after sequencing regarding the equimolar pooling and how it was determined, that they do not contain contamination.
Line 220: please rephrase “but there are not necessarily these”
Line 239: please rephrase “most indigenous species”

Literature references, sufficient field background/context provided.

Regarding the cited references I have two major concerns: First, the literature references regarding the molecular analyses seem a bit dated and I would strongly advise the authors to have a look at Deagle et al. 2019 (Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?) as it not only provides a great literature summary, but also input for improvements of the analysis of the present manuscript. Additionally, the used statistics software was not named.
Second, the main focus of this manuscript is otter diet. However, the introduction primarily focuses on otter distribution and contains only little information on the available prey species in the study region. It would be a great improvement of the manuscript if the reader is presented with this information in the introduction instead of learning about it bit by bit in the results and discussion.
A third concern is, that the authors do not reference other (molecular) Eurasian otter studies carried out in other countries (e.g. Hong et al 2019, Lanski et al 2008, 2010 or Carss et al 1995, 1996)) and do not provide information on the otter population in the study area. An approximate individual count or territory count would be beneficial to the present manuscript.

Professional article structure, figures, tables. Raw data shared.

I found the structure of the article conform to the usual standards. However, there is an imbalance between the different sections: whilst the introduction is missing critical background information, parts of the Materials and Methods could be omitted. This concerns the description of the local flora and the river structure outside of the study area (lines 90-97). Additionally, the last part of the result section is rather repetitive and could be condensed considerably. The Materials and Methods section does not have a heading but is otherwise informative and well written.
The figures are well connected to the manuscript, but their resolution is rather low. In Fig. 1 the Caolo river is not named. For Fig. 2 and 3 a lot of information is missing in the caption and in Fig. 3 some text is overlapping with a line.
Regarding the Tables, I would suggest to either remove Table 1 and include the information on spraint counts in the text or remove the respective paragraph in the main text and add this information to the figure. The Caption of Table2 should include definitions of the used abbreviations.
I found the raw data accessible and sufficiently described.

Self-contained with relevant results to hypotheses.

The fact that the authors include a sentence on the amplification of invertebrate DNA from the samples in the abstract and this is never mentioned in the main text of the manuscript has me doubting if the manuscript is self-contained. Unfortunately, the authors do also not state any hypotheses. Nevertheless, I do think the work represents an appropriate “unit of publication”.
Experimental design: Original primary research within Aims and Scope of the journal.

The current manuscript fits well into the Scope of the Journal.

Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.

The authors clearly state the usefulness of the presented work and that the molecular analysis of otter spraints can help with the clarification of prey species identity of taxa which are not easy to identify with morphological methods. As a reviewer is was, however difficult to assess if and how the study contributed to adding to the knowledge on otter diet in the study area, as the manuscript at the moment does not contain a description of the available prey items, and species, which are difficult to distinguish morphologically.

Rigorous investigation performed to a high technical & ethical standard.

There is one aspect of the present manuscript for which the presented information is not sufficient to determine of this criterion was met: the results of the NCBI blast search matching the obtained sequences to species or higher taxonomic entities. The Blast search is a key aspect for the whole manuscript and the validity of the results. Without knowledge on
•	the locally available prey species,
•	how many of them have 16S sequences published on Genbank,
•	the suitability of the chosen target fragment to distinguish between all of them
it is impossible to judge the quality of the presented results. I would strongly suggest the authors to add a list of potential prey species and an alignment of their 16S sequences to the paper. This could also explain why certain sequences can only be assigned to genus or family. In case most of the local prey species have publicly available 16S sequences, blasting against a custom and well curated reference sequence database might improve the taxonomic resolution of the results substantially.

Additionally, the use of read counts as a measure of ingested biomass remains highly controversial in the field (e.g. Deagle et al 2019) and certain prerequisites should be fulfilled before doing so (e.g. primer matches equally well to all targeted species). It would be good to include some of this background information in the manuscript or put more focus on prey information obtained at the spraint level. Especially since the authors seem to use read counts as an equivalent to ingested prey biomass across different taxa (e.g. sentence in abstract) and a multitude of studies to this date show, that this is often not the case (e.g. Thomas et al 2014 and 2015).

Methods described with sufficient detail & information to replicate.

The description of the used methods is well comprehensible. For clarification purpose it should be mentioned if the morphological analysis was done before or after DNA extraction and if whole or parts of the spraints were extracted and how the laboratory was organized regarding measures against contamination.
Validity of the findings: Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.

As summarized above, the presented study shows enough levels of novelty and importance. To ensure the validity of the findings, I suggest adding the information proposed above. In my opinion this is crucial for this manuscript as the authors stress that this is not a proof of concept study, but that the data should inform conservation and management measures in the future.

All underlying data have been provided; they are robust, statistically sound, & controlled.

The raw data are available on Figshare and the step by step processing of the reads is sufficiently described.

Conclusions are well stated, linked to original research question & limited to supporting results.

The presented conclusions fit to the obtained results; however, several aspects of the paper warrant additional discussion: for instance, the size of the fish prey, life stage of the otter, and prey abundance could have a large influence on the frequency with which a certain taxon is consumed. Depending on the number of otters present at each of the five sampling sites, the detected prey taxa could even indicate individual preferences. Therefore, the authors should discuss the influence of elevation above sea level onto the consumption of amphibians with caution. In case morphological analysis did not only target crustacean remains, these data could be useful for the interpretation of the obtained molecular results (see papers by Carss et al.).
Additional comments: The manuscript shows nicely, how non-invasive sampling and the identification of prey species can help with the conservation and management of endangered species and it was an enjoyable read. Unfortunately, I can not recommend it for publication in its present state because the authors do not provide all necessary information to confirm the validity of their results and do not include crucial background information on the study system, related studies, and the used statistical metrics.


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 DIET OF OTTERS (LUTRA LUTRA) ON THE AGRI RIVER SYSTEM, ONE OF THE MOST IMPORTANT PRESENCE SITES IN ITALY: A MOLECULAR APPROACH
Review round: 1
Reviewer: 2

Output:
Basic reporting: Language quality is OK.
Literature references must be updated: there are two prior papers on the subject, while the authors claim to be the first ones.
The manuscript needs a better focus. A mere description of the diet of otters does not suffice. Actually, I think that changing the angle of the ms having a hypothesis/question to be addressed by knowledge of the diet of otters will help the authors to write a better structured discussion (and conclusions).

See suggestions in section: General comments for the authors.
Experimental design: Study within the aims and scope of the journal.
Clarification is needed with regard to the selection of primers, absence of mock communities and if chimera removal was performed or not.
I am not expert in the bioinformatic analysis, so I cannot evaluate if methods are described with enough detail to be replicated, but my feeling is that they are.

See suggestions in section: General comments for the authors.
Validity of the findings: In the preset state, I would not consider the ms as novel. Should the authors change the focus, it might increase impact dramatically!
No problem with data.
Conclusions need to be rewritten.
No problem with speculation.

See suggestions in section: General comments for the authors.
Additional comments: The manuscript by Buglione et al. describes the diet of the Eurasian otter (Lutra lutra) in ITaly, where the species is endangered. The focus of this research is on the use of DNA metabarcoding.

Unfortunatly, I cannot recommend the publication of this manuscript in its current form, but I hope that the following comments will be useful to improve the work.

1.	Lines 1 an 28. This is not the first use of DNA metabarcoding to study the diet of otters. Kumari et al. (2019) and Martínez-Abraín et al. (2020) used DNA metabarcoding with spraints of Lutra lutra. THe former worked with otters from South Korea and “targeted 12S rRNA gene region for vertebrates, 16S rRNA gene region for invertebrates, and cytochrome c oxidase 1 (COI) gene region for fishes”. The latter used a fragment of the 12S rRNA as it focused on fish diet of otters inhabiting a Spanish reservoir.
2.	Abstract: line 20. Consider using “in the area between Naples and the Ionian Sea” as many readers will be unfamiliar with the terms “Basilicata” and “Campania”.
3.	Line 34: change “analyzes” to “analyses”.
4.	LInes 35-40. It is not clear why you write here about the crustaceans and then about the additional universal set of primers. From the previous lines, I had understood that your focus was on the vertebrates… so these lines here are puzzling. Actually, as the introduction of your abstract deals with conservation, I would expect here a couple of lines describing the ecological/conservation implications of your work. Current lines 40-42 are a mere wish, so I suggest you to link your results with putative actions to be undertaken. See comment number 7 below.
5.	Introduction: please show the current distribution of the species in Italy by means of a map.
6.	Line 64. Please elaborate on the official category of threat at national and regional level.
7.	Lines 66-74. The authors should illustrate the use of knowledge about the diet of composition for conservation purposes with at least one example. The current writing seems a bit a vague with regard to the usefulness of their work. You need to better justify your investigation on the diet of otters in Campania. A mere description is not enough for a journal such as PEERJ. It could be that you expect a different diet because of whatever reason, or you might be intrigued by a putative competition between otters and anglers for the same species, or might even investigate the role of native versus exotic species in the diet of your otters…
8.	Lines 130-134. It could be useful for readers unfamiliar with the ecology of otters in the study area to specify that low importance of crustaceans. For instance, Procambarus clarkii is really important for the diet of Iberian otters.
9.	Section Sample collection: is there any record of how many individuals may form the population for each sampled area?
10.	Section Sample collection. Please indicate here that you collected 51 samples. Readers will have to wait otherwise until line 199 as one cannot precisely tell from Figure 1.
11.	Lines 146-148. Please write the PCR recipe indicating the final concentration of each reagent, rather that indicating the volume taken from the concentration of the product you purchased.
12.	At least two mock communities should have been analysed. Mock communities are highly recommended to calibrate the filtering settings to be applied during the bioinformatic analysis in order to eliminate erroneous OTU assignments (Bokulich et al. 2013). This is especially important as you write in lines 202-204 that the scope of your ms is to introduce genetic analysis as a method for developing qualitative and quantitative comparisons of the otter diet
13.	More about quantitative comparisons. You write in lines 237-240 that “the average percentage presence of the different animal species in the food of the otter…” which is a misleading sentence. As you are perfectly aware of, OTU relative abundance is defined as the number of reads assigned to that OTU divided by the total number of reads. At sample level, it might be that those “highly represented species” simply amplified better. For instance, if SPECIES A is represented by the 30 % of the sequences in spraint 1 and SPECIES B is represented by the 60 % of the sequences in the same spraint, we cannot reliably conclude that there was more SPECIES B DNA in spraint 1. Having said this, WITHIN THE SAME STUDY, the PCR bias should go in the same direction, so you may compare how the abundance of a given taxon changes. For example, if SPECIES A is represented by the 40 % of the sequences in spraint 1 and by the 15 % in spraint 2, we can conclude that there was less SPECIES A DNA in spraint 2 (Schloss et al. 2012; Geisen et al. 2015, Matesanz et al. 2019). I think this kind of explanation is needed in a journal such as PEERJ, where many readers will be not experts in metabarcoding.
14.	Have I missed how did you detect and remove chimeras from your data? Please, clarify. IF you haven’t done it, the bioinformatic analysis should be repeated including this step.
15.	Lines 216-223. If your focus was simply on Pisces and Amphibia, wouldn’t be better to have designed primers specific for these two taxonomic groups? Messing around with mammal and bird sequences does not seem a very efficient approach, does it not? I see that specific primers for fish and amphibians exist (Ac16S or the L2513/H2714 primer sets, Evans et al. 2015), so please justify the use of primers 16s mam1 and 16s mam2 in your work.
16.	Lines 247-252. Please quantify the species richness and provide statistical support for the statement of change of diet of otters according to the structure of the watercourse. You might take a look to the approach taken by Martínez-Abraín et al. (2020).
17.	Unfortunately, I cannot praise the Discussion of the current manuscript. In my opinion, it is redundant with some issues explained in Results, and difficult to read. I am sure that if you change the focus of the manuscript (from a mere description of diet to how that description solves a biological question), the discussion will be much easier to write. I also recommend to use sub-sections so that the reader goes from topic to topic smoothly. Your finding of species not previously recorded in the area (Ballerus sapa, Aspius aspius and Blicca bjoerkna) and the lowest diversity in the lower reach of the river with the dam as threshold are extremely interesting. But I would not spend so many lines emphasising that you are testing the method: DNA metabarcoding is well known to have better taxonomic precision than morphological analyses and it is already a well-established methodology, with two published papers in otters.
18.	The section CONCLUSIONS has to be completely rewritten as well. Again, once a proper focus is addressed, it will be easier to write. Just an example, the use of blocking primers was never mentioned before (nor the problem of not using them…) and appears in these very last lines. The conclusion needs first a proper question to be answered; find it and you will have a fine ms.
19.	Lines 439. It should read “Acknowledgments”.
20.	able 3: use only two decimals.
21.	All through the manuscript: when writing a genus name (e.g. Carassius) and  “sp.”, “sp.” Should not go in italics.
22.	Line 383. It should read “prove”.

References:
Bokulich et al. (2013) DOI: 10.1038/nmeth.2276.
Evans et al. (2015) DOI: 10.1111/1755-0998.12433
Geisen et al. (2015) https://doi.org/10.1111/mec.13238
Kumari et al. (2019) https://doi.org/10.1371/journal.pone.0226253
Martínez-Abraín et al. (2020) https://doi.org/10.1007/s10750-020-04208-y
Matesanz et al. (2019) https://doi.org/10.1111/1755-0998.13049
Schloss et al. (2011) https://doi.org/10.1371/journal.pone.0027310


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: METAGENOMIC NEXT-GENERATION SEQUENCING FOR THE CLINICAL DIAGNOSIS AND PROGNOSIS OF ACUTE RESPIRATORY DISTRESS SYNDROME CAUSED BY SEVERE PNEUMONIA: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this manuscript, Zhang et al investigate the value of metagenomic next-generation sequencing (mNGS) in acute respiratory distress syndrome (ARDS) caused by severe pneumonia. The present study included 42 patients using mNGS method (NGS group) and 53 patients undergoing conventional microbiological tests (no-NGS group) with ARDS caused by severe pneumonia. They found that the mortality was significantly lower and the 28-day survival rate was higher in NGS group than that of in the no-NGS group. Furthermore, mNGS was incredibly reliable for detecting special pathogens and patients with co-infections compared with conventional microbiological tests. The authors demonstrated that mNGS provide more evidence for diagnosis and guidance for treatment. In general, the study is well designed and the results are convincing. The manuscript is well written and the data are presented in an appropriate way. So, I think it is suitable for publication with some modification in writing.


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: METAGENOMIC NEXT-GENERATION SEQUENCING FOR THE CLINICAL DIAGNOSIS AND PROGNOSIS OF ACUTE RESPIRATORY DISTRESS SYNDROME CAUSED BY SEVERE PNEUMONIA: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this study entitled "Value of metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia", the authors investigated that mNGS is a valuable diagnostic tool to detect a broad range of pathogens, especially in detecting co-infection for patients with ARDS caused by severe pneumonia in ICU. The whole study might provide some important significance to clinical diagnosis and even treatment for patients with ARDS caused by severe pneumonia. However, I have a few specific comments that should be addressed to improve the manuscript:
1. Line 248, “The positive rate virus and bacterial identification by mNGS was 3 times greater than routine methods.” This is obviously confused from the results represented in Table 6. The author should illustrate it.
2. The result of this article showed that mNGS could detect more microorganisms compared with other methods, which may be the reason of better prognosis. The author considered a test is more reliable and better when the positive rate is higher. However, a higher positive rate does not always mean better. Could the author provide some evidence or reference about false positive, false negative on sensitivity and specificity for mNGS as well as for other methods?
3. Writing of this article should be further modified.


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: METAGENOMIC NEXT-GENERATION SEQUENCING FOR THE CLINICAL DIAGNOSIS AND PROGNOSIS OF ACUTE RESPIRATORY DISTRESS SYNDROME CAUSED BY SEVERE PNEUMONIA: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: well done
Validity of the findings: well
Additional comments: General comments:
This research article entitled “Value of metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia”, the authors by Peng Zhang, Yan Chen, Shuyun Li, Chaoliang Li, Shuang Zhang, Weihao Zheng, Yantang Chen, Jie Ma, Xin Zhang, Yanming Huang and Shengming Liu, extensively and detailed investigate the diagnostic and prognostic values of metagenomics next generation sequencing (mNGS) in evere acute respiratory distress syndrome (ARDS) characterized by alveolar collapse, pulmonary edema and elevated epithelial permeability, finally resulting in hypoxia and subsequent deterioration of pulmonary function. Although great advance in the diagnosis and therapy of ARDS over the last decades, the motality in ARDS patients remain higher than 30%. Therefore, accumulating attention has been made to identify the early diagnosis and targeted medicine against ARDS. mNGS is a kind of novel detection technique, which study the DNA and RNA information of microorganism in specific scenario. Importantly, this technique is extensively reported to be applied in detecting blood flow, respiratory tract, CNS disease and abscess. In the current study, the author reported, for the first time, the diagnostic and prognostic values of metagenomics next generation sequencing (mNGS) in evere acute respiratory distress syndrome (ARDS) and concluded that mNGS can be used an important avenue to improve the precision for diagnosis and prognosis of severe pneumonia-induced ARDS, which is beneficial for clinical guide for the treatment of ARDS. Overall, this study is well design and performed, and the manuscript is well written. However, several issues need to be addressed before consideration of acceptance of publication:

Major concerns:
1. The main results of the current study were not clearly shown in the Abstract. Please re-write the corresponding contents.

2. What did “positive rate” stand for in the Abstract? Furthermore, the positive rate in NGS group seemed not to be higher than the sum of other two values. Please clarify.

3. In the manuscript title, the prognosis was mentioned. However, there was deficient of relevant contents in the main text. Please correct.

4. In the introduction section: omission of several important literatures regarding the application of mNGS in the diagnosis of ARDS was a drawback of the current MS. Please correct.

5. In the introduction section: the introduction about the therapy of ADRS could be shortened, cuz the topic of this study focused on the the diagnostic and prognostic values of metagenomics next generation sequencing (mNGS) in evere acute respiratory distress syndrome (ARDS).

6. In the introduction section: a summary of this study should be provided, including the study aim and contents.

7. In methods: what is the metagenomics? Please provide the relevant method or reference.

8. In methods: Please provide the relevant method or reference about the BALF.

9. In resuts: the information in the figure was not matched with the description in the main text, for example, Fig. 1and Figure 2. In table 4, the statictical method used for primary outcome was chi-square test，but the secondary outcome was T-test, not the chi-square test. Please correct.

10. The introduction or discussion should not be mentioned in the Results section, for example when comparing the results of mNGS and culture.

11. In the discussion: 1. What the cause for the differential motality of ARDS patients in ICU? They have the similar ICU duration, expense and ventilation duration. 2. In the immunocompromised patients, They have the different ICU duration, expense and ventilation duration, but did not have statistical significance between them. Why?

12. In the discussion: the paragraph of limitation regarding the mNGS should be shortened.

Minor comments:
1. There were multiple language issues existing in the current study, including:
（1）Line 47: a negative sputum culture，“a” should be deleted
（2）Line 52: mNGS is valuable tool，chaned to“mNGS is a valuable tool”；
（3）Line 74: is chaned to are；
（4）Line 83: next chaned to next-；
（5）Line 117,118: Community and Hospital chaned to Community-和Hospital- ；
（6）Line 133: from chaned to of；
（7）Line 137: the second was chaned to were；
（8）Line 193: than no-NGS group chaned to than the no-NGS group；
（9）Line 243: a virus infection, “a” should be deleted

2. In figure 3: empirical antibiotics should be indicated in the image.

3. In figure 4: noNGS in figure, but no-NGS in the main text. Please keep the form in consistence.


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: METAGENOMIC NEXT-GENERATION SEQUENCING FOR THE CLINICAL DIAGNOSIS AND PROGNOSIS OF ACUTE RESPIRATORY DISTRESS SYNDROME CAUSED BY SEVERE PNEUMONIA: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 4

Output:
Basic reporting: The study is the description of use for mNGS identification Data (etiological agents) as of value for accurate cause-effect establishment of ARDS.  Paper states that mNGS information is valuable for subsequent disease management including pathogen-specific treatment and prognosis. Amid respiratory diseases, severe pneumonia can get complicated to ARDS depending on a number of factors from Host and from pathogens, and the study analyzed if mNGS data could make a difference in the management of these kind of illness.

Text of the manuscript is in need for some checks for proper English grammar and syntaxes. Please refer to annotated copy of the manuscript. i.e. Line 40: To use immunosuppressed patients (past tense), instead of immunosuppressive. See also lines 60, 95, etc.

-Lack of definition for some abbreviated terms (i.e. line 152. HR = Hazard Ratio).

-Lack of reference for valuable information (line 129: Cox regression analysis).

-Lines 59-67 could be re-phrased to better describe the context of the study. Please refer to annotated copy for details.

-Lines 76-77. It is widely accepted that pathogen isolation is critically dependent on pathogen load in the clinical specimen. Authors stated the opposite. Please support with references.

-Hard to find agreement if BALF clinical specimens are tested for mNGS, while for microbiological method the specimen is Sputum. Specimen are expected to be exactly the same for side-by-side comparison. Otherwise, some annotations are needed in order to better compare differences in specimens.

-Sensitivity of Sputum culture method is higher than  ¨Serological antibody test plus PCR¨ method. This is hard to explain. Please consider contamination of specimens used for culturing during handling and testing…please see next comment:

 -Line 78: Expected is 15-25 % detection  rate using Sputum culture. So, why in this study the detection rate was 62,2 % ??. This point has to be explained in detail. There is no antecedent of such high detection rates.

-In case.control studies the methods have to be exactly the same and tested identically, otherwise wrong conclusions coul be made. Were serological-PCR methods tested for all potential bacteria and other microbes as causes of ARDS ?

-Line 80: Please rephrase: pathogenic MICROBES…or delete pathogenic, or use a different wording to avoid confusions.

-Lines 81-82: Please provide reference. Respiratory pathogens use to be the main focus of development for diagnostic routines using NAT-based reagents, and serological approaches as well. Please better support statement.

-Line 105. Please rephrase: Clinical specimens FOR MICROBIAL CULTURING TESTING.

-Line 120: Anti MICROBIAL (including anti-fungi )

-Revise match between references and cites in text. Example citation of ref 18, line 244. It does not match.

Raw data findings:
-Data from subject80 (P76) must be corrected in excel table, column ARDS degree. Value of OI is higher than 200, thus is mild, not moderated as stated in the database.

-Column ¨Serological antibody  test plus PCR¨ only shows a few results (8) in group nonNGS. It would be convenient to disclose (materials and methods) which specific PCR tests were performed in order to better appreciate this specific result.

-Column ¨Serological antibody  test plus PCR¨ shows 13 agents detected in group NGS. 12 results are Influenza, none detected in NGS group ?). Authors disclosed that the NGS analysis were focused on DNA viruses, however there are a number of RNA viruses causing respiratory illness, this specific topic has to be better clarified in experimental design.

-The only one results matching between ¨NGS¨ and ¨Serological antibody test plus PCR¨ is M. pneumoniae (subject 24, P22). It would be useful to detail the protocols used for the molecular/PCR diagnostic routines.
Experimental design: -Hard to find agreement if BALF clinical specimens are tested for mNGS, while for microbiological method the specimen is Sputum. Specimen are expected to be exactly the same for side-by-side comparison. Otherwise, some annotations are needed in order to better compare differences in specimens.

-Sensitivity of Sputum culture method is higher than  ¨Serological antibody test plus PCR¨ method. This is hard to explain. Please consider contamination of specimens used for culturing during handling and testing…please see next comment:

Line 78: Expected is 15-25 % detection  rate using Sputum culture. So, why in this study the detection rate was 62,2 % ??. This point has to be explained in detail. There is no antecedent of such high detection rates.

-In case.control studies the methods have to be exactly the same and tested identically, otherwise wrong conclusions could be made. Were serological-PCR methods tested for all potential bacteria and other microbes as causes of ARDS ?
Validity of the findings: Tables and figures are well designed, and self-contained. Statistical analysis is a plus in achieving conclusions.

Conclusions are properly linked to the results and analysis conducted.
Additional comments: Study is properly planned, rigorously conducted, and convincingly analyzed. A few observations have been included within this review in order to avoid confusions for readers, and to improve the presentation of data. Data will be of value for readers provided than minor adjustments will be done on the manuscript.


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

Input:
Title: METAGENOMIC NEXT-GENERATION SEQUENCING FOR THE CLINICAL DIAGNOSIS AND PROGNOSIS OF ACUTE RESPIRATORY DISTRESS SYNDROME CAUSED BY SEVERE PNEUMONIA: A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Well
Experimental design: Well
Validity of the findings: Well
Additional comments: All the concerns have been addressed in the current version of manuscript. Recommend acceptance at this point.


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: METAGENOMIC NEXT-GENERATION SEQUENCING FOR THE CLINICAL DIAGNOSIS AND PROGNOSIS OF ACUTE RESPIRATORY DISTRESS SYNDROME CAUSED BY SEVERE PNEUMONIA: A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Manuscript PeerJ reviewing Manuscript 45653v2: ¨Value of metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia in retrospective study¨.

The study is the description of use for mNGS identification Data (etiological agents) as of value for accurate cause-effect establishment of ARDS.  Paper states that mNGS information is valuable for subsequent disease management including pathogen-specific treatment and prognosis.

Minor comments:

-Text of the manuscript is in need for some checks for proper English grammar and syntaxes. For instance, spaces before and after parenthesis: lines 69, 72, 75, 78, 80, 83, 85, 89, 94, 97, 114, 125, etc.

-Line 81: Please rephrase as ..serological antibody detection (antibody testing)….

-Error entry for references from databases is included in line 140.

-Line 147: Please rephrase as …..adjusted case-by-case according to mNGS results….

-Line 202: Please consider to rephrase.

-Line 223: Please consider to rephrase.

-Lines 224-225: Please consider to rephrase.

-Lines 249250: Please consider to rephrase.

-Line 253: Please complete word, or define abbreviation.

-Line 264: Please consider to rephrase.

-Line 302: Please consider to rephrase.

-Lines 326- 327: Please consider to rephrase.

-Title of tables 4, 5. Please modify title to better represent information contained in the tables.

-Title of table 6. Please amend title to fit English grammar.

-Title for figures 2, 3. Please consider to modify to increase self-explanatory content.

-Figure legends for figures 4, 5. Please consider to rephrase to increase auto containment.
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: METAGENOMIC NEXT-GENERATION SEQUENCING FOR THE CLINICAL DIAGNOSIS AND PROGNOSIS OF ACUTE RESPIRATORY DISTRESS SYNDROME CAUSED BY SEVERE PNEUMONIA: A RETROSPECTIVE STUDY
Review round: 3
Reviewer: 1

Output:
Basic reporting: Manuscript (#45653):
Metagenomic next-generation sequencing for the 1 clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study. Previous comments/suggestions were properly followed up.

Manuscript will be a valuable contribution to the field. It has many strengths both conceptual, and methodologically.
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: FIVE GENES INFLUENCED BY OBESITY MAY CONTRIBUTE TO THE DEVELOPMENT OF THYROID CANCER THROUGH THE REGULATION OF INSULIN LEVELS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This study employed large-scale literature data and meta-analysis to explore novel connections to explain the fact that obesity could increase the risk of thyroid cancer (TC). Their approach identified five genes (i.g., FABP4, CFD, GHR, TNFRSF11B, and LTF) that were significantly down-regulated in the case of TC, and these genes have been shown to be regulated by obesity but have not been implicated with TC, which makes the finding novel and thus important to the field of study. However, I do have several suggestions and concerns, as listed as follows.

It seems that the authors conducted a systematic literature data mining to extract genes that were implicated with TC and also influenced by obesity (176 genes). A total number of 1036 genes were identified to be associated with TC, and 534 are downstream targets of obesity. This is valuable information. However, how they did the data mining and what rules are applied to define an ‘association’ is not clearly described. How to qualify the data? Is there any confidence score for the identified genes?
Regarding the mega-analysis, the selection of the dataset is ok. However, I wonder why the authors use the term mega-analysis instead of meta-analysis? This is not clear to me.
Regarding the criteria for selecting significant genes from mega-analysis, p-value<10-7, and LFC>1 were used. While this criterion is reasonable, there should be more ‘less’ significant genes that should be addressed in the discussion. I see that the authors listed this as a limitation of the study. However, I suggest the author gives more statistical description of the mega-analysis results. For example, with abs(LFC)>1, how many were with p-value<0.05, how many with p-value<0.001, and so on. This will give the audience a better picture of the expression data for the mega-analysis results.
Regarding the pathway (Figure 1), I cannot find the reference information for LTF->INS in the supplementary material (Obesity_TC), while I see this one in the figure. And it seems that this relation is the only one with no polarity, please explain and provide corresponding information in the supplementary materials.
The author concluded that (in the Abstract as well as the Conclusion Sections) ‘Obesity may influence the pathologic development of TC through the regulation of the upstream regulators of TC.’ This statement, especially in the Abstract, seems redundant with other statements and suggest to remove it.

Minor points:
1.      Please add references for the statement given in the lines 246 to 248: ‘the reduced TGF-beta Type-II receptor (TGFBR2) mRNA was shown to play a role in the pathogenesis of papillary TC, while LTF interacts with TGFBR2 to activate TGF-β signaling and initiates the formation of TbRIII:TbRII:TbRI complex. ‘


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: FIVE GENES INFLUENCED BY OBESITY MAY CONTRIBUTE TO THE DEVELOPMENT OF THYROID CANCER THROUGH THE REGULATION OF INSULIN LEVELS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper was clear and concise, and it fits to the basic reporting criteria. Literature was well referenced & relevant with the context. You might want to talk more about mega-analysis and why you chose this method instead of other methods in the literature. Figures are relevant but, if you can, you should increase the resolution on Figure 2 for the actual publication.
In line 159, you mentioned “About 67.04% of the obesity-genes (358 out of 534 genes) have not been reported to have an association with TC. Thus, we tested the expression changes of these 358 genes in the case of TC.” You might want to talk more in detail about how you obtained these numbers (I am assuming you used Pathway Studio.)
Experimental design: I have found no problems with your study design, but I have some concerns about background correction for the different datasets you used. Did you take any measures to nullify the effects of different studies introducing noise to your findings? You might want to talk about this issue in your discussions to make a stronger point and prove the validity of your findings.
Validity of the findings: The comments and validity of findings are in the pdf file
Additional comments: Overall, a great paper. Just needs some clarifications. I have made extra suggestions for Discussion through navigating another database i have experience working with. I wish you good luck for the future work and publications.


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: FIVE GENES INFLUENCED BY OBESITY MAY CONTRIBUTE TO THE DEVELOPMENT OF THYROID CANCER THROUGH THE REGULATION OF INSULIN LEVELS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors answered all my questions that I make during last review, and make changes accordingly. I have no further questions.
Experimental design: Good in its current form.
Validity of the findings: Good in its current form.
Additional comments: The authors answered all my questions that I make during last review, and make changes accordingly. I have no further questions.


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

Input:
Title: MEDITERRANEAN SWORDFISH (XIPHIAS GLADIUS LINNAEUS, 1758) POPULATION STRUCTURE REVEALED BY MICROSATELLITE DNA: GENETIC DIVERSITY MASKED BY POPULATION MIXING IN SHARED AREAS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Revision of the manuscript entitled “Mediterranean swordfish (Xiphias gladius Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas” by Righi et al

The manuscript asses the genetic population structure of swordfish from 6 locations within the Mediterranean and one location in the Atlantic (west Atlantic, Canadian coast) This is probably the most exhaustive analysis of this species in this Sea, analyzing up to 300 individuals with 20 microsatellite loci. The manuscript is well written, although I am not an English native speaker, the English sounds good to me.
Literature references are up to date, and the article has a correct structure.

The main finding of the manuscript is the possible evidence of population structure within the Mediterranean. However, this genetic structure has not any geographical nor biological basis. Thus, the authors should implement several improvements before publication.

1.- My major concern is about the detection of the genetic structure, based on the DAPC results, with the presence of three genetic clusters.  These clusters are not related to any geographical nor biological trait. The authors hypothesize the relation of these genetic clusters to a behavior of homing towards breeding areas. However, the sampling scheme used in this study is not compatible for evaluating this hypothesis. Some specification of the sampling used is needed. For instance, are some of the locations sampled correspond to spawning or feeding grounds. Are the individual’s juveniles or adults? It can be understood that the availability of samples is not always the desired, but better sampling description and a discussion of results based on the current sampling should be done.
2.- Clear genetic differentiation is observed between Canadian location and the Mediterranean. This is not surprising, similar results have been published in multiples studies of swordfish. I wonder, about the distribution of locations in each DAPC cluster. For instance, one question interesting to ask, is the level of admixture in the feeding locations, which can be probably higher than the spawning locations. But, without accurate sampling descriptions very difficult to answer these questions.
3.- Better discussion, some authors using a similar sampling revealed an incipient genetic differentiation within the Mediterranean. A better description of this fact with the comparisons with the current results would improve the manuscript.

3.- Several minor comments:
Abstract.
Line 28. “for the first time” this is not accurate. At least one previous study of Microsatellite in the Mediterranean is already published (Kotoulas 2007).
Materia and methods.
Line 168 to 198. These two paragraphs should be reordered. Please first specify all the parameters and software used for STRCUTURE analysis. Then the parameters and specifications of DAPC analysis.
Table 1. better description of the sampling with possible identification of samples from breeding and spawning areas. Please consider to include a Map.
Table 2. Could you provide the range size of each loci.
Table 3 and 4. have you done multiple test correction?
Figure 2C. I believe that the last location should be labelled as CAN.
Experimental design: As mentioned before, the main problem of this study is that the sampling design is no adequate for the testing the hypothesis of admixture within the Mediterranean. There are no basal populations and, thus, very difficult to describe the admixture between possible different populations. At least a better description of the sampling should be included
Validity of the findings: It is difficult to validate the results since the sampling is adequate. Under my point of view the authors should be more restricted about their conclusions of admixture within the Mediterranean.
Additional comments: All general comments are already include int he first part of the revision.


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

Input:
Title: MEDITERRANEAN SWORDFISH (XIPHIAS GLADIUS LINNAEUS, 1758) POPULATION STRUCTURE REVEALED BY MICROSATELLITE DNA: GENETIC DIVERSITY MASKED BY POPULATION MIXING IN SHARED AREAS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a quite interesting work, that try to fill the gap about this species in the Mediterranean Sea.
The authors followed the PeerJ instructions for authors, but the manuscript need for a revision of the English (both typos and structure). The English language should be improved to ensure that an
international audience can clearly understand your text. The figures, especially the barplots are not of high quality. It’s difficult to read the population names. Also, in the Fig 2C there is a labelling error with two groups labelled as ADR of which one should be CAN. Some references are not in alphabetical order, and a revision of this part is needed (please see comments). RAW data are supplied and clear.
Experimental design: The experimental design of this work is what worry me the most. The questions are clear and well defined in the text, but the sampling design is not really clear, and also some methods need to be revised. It is not mentioned the stage (or size, or sex stage) of the specimens used for the analyses, and this is of vital importance for similar works on pelagic species. The authors used to sample just during the spawning months, and apparently, not juveniles were used for this analysis. I think this is a critical point, since the species is well known to be extremely vagile among spawning areas. The research is very useful to better investigate the Mediterranean-Atlantic genetic structure of this species, but the flaws on the sampling design and "consequently" methods are preventing a reliable final result.
Validity of the findings: I would say that the findings are useful, but clarifications about the sampling design and some analysis (mainly the DAPC and related Fst) are needed before Acceptance (see comments). This is very critic. I think this is the weakest part of the work, which generally I found very useful.
Additional comments: Abstract:

Your methods in the abstract needs to be restructured in order to be more concise and without general information about the utility of the microsatellite, which is not requested here. Try to change in something like:
“For the first time, microsatellite DNA was used to investigate fine-scale population structuring of swordfish from six main fishing areas of the Mediterranean Sea, in order to test the uncertainty of the stock delineation of the species in this area.”

Introduction:

Line 40-41: change “Sustainability in harvesting fish stocks to avoid their depletion and to guarantee survival and long-term production is one of the primary objectives of fishery management (Cochrane, 2002).” to “Sustainability in harvesting fish stocks, to avoid their depletion and to guarantee survival and long-term production, is one of the primary objectives of fishery management (Cochrane, 2002).”

Line 42: More than “isolated” they are “structured”. Not necessarily isolated.

Line 49: Delete “commercial”

Line 54-59: This part needs to be restructured. It seems you are talking about your results, and not the results from cited works.

Line 63-64: The Reference for this is incomplete. Please use the correct IUCN reference: “Collette, B., Acero, A., Amorim, A.F., Bizsel, K., Boustany, A., Canales Ramirez, C., Cardenas, G., Carpenter, K.E., de Oliveira Leite Jr., N., Di Natale, A., Die, D., Fox, W., Fredou, F.L., Graves, J., Guzman-Mora, A., Viera Hazin, F.H., Hinton, M., Juan Jorda, M., Minte Vera, C., Miyabe, N., Montano Cruz, R., Masuti, E., Nelson, R., Oxenford, H., Restrepo, V., Salas, E., Schaefer, K., Schratwieser, J., Serra, R., Sun, C., Teixeira Lessa, R.P., Pires Ferreira Travassos, P.E., Uozumi, Y. & Yanez, E. 2011. Xiphias gladius (errata version published in 2016). The IUCN Red List of Threatened Species 2011: e.T23148A88828055. https://dx.doi.org/10.2305/IUCN.UK.2011-2.RLTS.T23148A9422329.en. Downloaded on XXX”

Line 90-92: Smith et al. (2015) (https://doi.org/10.1371/journal.pone.0127979) have shown, even if very low, a level of gene flow between North Atlantic and the Mediterranean Sea.

Line 108-109: I would suggest to remove “for the first time”. Despite the larger number of microsatellites used in the present study, it seems that a multilocus approach have already been used, even if with just 4 microsatellites (Kotoulas et al., 2007).

MATERIALS & METHODS

Line 121: The samples were collected between May and October, during the intensive spawning for this species in the Mediterranean. The spawning seems to be unrecorded during December and January, a period rich in Juveniles. I’m wondering how much this sampling design may have masked a potential genetic structure, masked by the genetic characterization of large and migratory adults, rather than genotype less vagile juveniles. Also, I don’t see any information about the size of the specimen sampled. Were they all adults or both adults and juveniles?

Line 123: Remove “was”

Line 124: Change “for accordance” into “in accordance”.

Line 127: Change “following its specific protocol” into “following the manufacturers' protocols.”

Line 130: Change “Microsatellite amplification and genotyping and diversity analysis” into “Microsatellite amplification, genotyping and diversity analysis”.

Line 135: Change “PCA amplifications” into “The PCR amplifications”.

Line 136: Change “PCA amplifications” into “The PCR amplifications”.

Line 139: How was the amount of DNA measured?

Line 144: Change “appropriate” into “specific”

Line 153-155: This is not very clear to me. I would suggest to specify better this step, avoiding colloquial words such “other errors”.

Line 172: Change “employed” into “used”

Line 168-177: I would focus more on the different approach of both methods. For example, the DAPC doesn’t rely on a priori population assignment, but it would ideally need an a priori number of clusters.

Line 179-180: Change “and hierarchical population structure (Evanno, Regnaut & Goudet,
2005) and correct allocation…” into “and hierarchical population structure (Evanno, Regnaut & Goudet, 2005), and correct allocation…”.

Line 181-184: I would suggest to better explain this in the STRUCTURE and DAPC paragraph, explaining why (different models and math behind).

Line 191: The R package should be mentioned above, in the clustering method paragraph.

RESULTS
Line 219-220: I would like to suggest the reading of this manuscript about the effect of NA on the estimation of differentiation https://doi.org/10.1093/molbev/msl191

Line 231-232: This is a bit in contrast with the effect of NA on the Fst, for which when a strong Fst is observed, the effect of NA on the Fst values is heavier.  https://doi.org/10.1093/molbev/msl191
How the authors explain that?

Line 234: Change "The lowest and no statistically significant" into "Low and statistically not significant".

Line 236: Change "highest" into "higher".

Line 246-250: This additional analysis is not mentioned in the Methods. Why?

DISCUSSIONS:

Line 266-268: I think a citation is missing here. Improved how and compared to what?

Line 269-270: I’m not sure the analyses are suggesting three genetic groups. The problem is on the definition of cluster during the analysis (especially the pre-DAPC). Looking at the DAPC plot, the clusters within the Mediterranean are just two. Even the authors of the method (DAPC) suggest caution on this.

Line 294-297: I would focus also on the different nature of the analysis. It is more about the choose of clusters to use in the analysis of DAPC.

Line 297-299: The authors highlighted that the clusters found are not separated geographically, so I think this is not the case. Also, I think this is more related to the stage of individuals. Are all migrant adults? This may explain some of the results. I think the authors should consider this. I’m still wondering how the sampling design affected the results (adult spawners vs. juveniles).

Line 299-302: I suggest the authors to be cautious about that.

Line 371-371: This assumption needs more analysis, since the formation of more than 1 cluster within the Mediterranean have been observed mainly on the assumptions of the best K methods used, which are very sensitive to bias.

Line 381-383: I would suggest the authors to avoid to consider the genetic clusters observed here as “discrete populations”.

Line 386-388: This is the only clue about the use or not of juveniles.

Line 389: I wouldn’t use to collect just during spawning. It causes mixing situation.

REFERENCES:
Please check carefully that everything is correct and in line with the instructions for authors. I’ve noticed some weird non-alphabetically order in the references. E.g: Kasapidis et al. between two Kotoulas et al.

Kotoulas G, Magoulas A. 2007. Genetic structure of the swordfish (Xiphias gladius) stocks in the Atlantic using microsatellite DNA analysis. Collect. Vol. Sci. Pap. ICCAT 61:89–98.

Kasapidis P, Pakaki V, Kotoulas G, Magoulas A. 2009. Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius. Molecular ecology resources 9:1383–1386.

Kotoulas G, Magoulas A, Tsimenides N, Zouros E. 1995. Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius. Molecular Ecology 4:473–482.

Kotoulas G, Mejuto J, Antoniou A, Kasapidis P, Tserpes G, Piccinetti C, Peristeraki P, Garcia-Cortes B, Oikonomaki K, De la Serna JM. 2007. Global genetic structure of swordfish (Xiphias gladius) as revealed by microsatellite DNA markers. ICCAT Coll Vol Sci Pap 61:79–88.


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: PREDATORY FUNCTIONAL RESPONSE AND FITNESS PARAMETERS OF ORIUS STRIGICOLLIS POPPIUS WHEN FED BEMISIA TABACI AND TRIALEURODES VAPORARIORUM AS DETERMINED BY AGE-STAGE, TWO-SEX LIFE TABLE
Review round: 1
Reviewer: 1

Output:
Basic reporting: comments inside in the document
Experimental design: comments inside in the document
Validity of the findings: comments inside in the document
Additional comments: This manuscript dealt with an interesting research topic, which the potential of using biological control
agents in the management of Bemisia tabaci and Trialeurodes vaporariorum with predator Orius similis. This will be of great interest for the readers of PeerJ journal. However, there are some concerns that need to be addressed before it gets the acceptance level.


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

Input:
Title: PREDATORY FUNCTIONAL RESPONSE AND FITNESS PARAMETERS OF ORIUS STRIGICOLLIS POPPIUS WHEN FED BEMISIA TABACI AND TRIALEURODES VAPORARIORUM AS DETERMINED BY AGE-STAGE, TWO-SEX LIFE TABLE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Included in the attached document.
Experimental design: Included in the attached document.
Validity of the findings: Included in the attached document.
Additional comments: Included in the attached document.


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: PREDATORY FUNCTIONAL RESPONSE AND FITNESS PARAMETERS OF ORIUS STRIGICOLLIS POPPIUS WHEN FED BEMISIA TABACI AND TRIALEURODES VAPORARIORUM AS DETERMINED BY AGE-STAGE, TWO-SEX LIFE TABLE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors answered the suggestions; the manuscript has improved a lot. congratulations; minor changes are inserted in the document
Experimental design: The authors answered the suggestions; the manuscript has improved a lot. congratulations
Validity of the findings: The authors answered the suggestions; the manuscript has improved a lot. congratulations
Additional comments: Dear author

Congratulations; the manuscript is of high quality; minor changes are inserted in the document (word)


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

Input:
Title: PREDATORY FUNCTIONAL RESPONSE AND FITNESS PARAMETERS OF ORIUS STRIGICOLLIS POPPIUS WHEN FED BEMISIA TABACI AND TRIALEURODES VAPORARIORUM AS DETERMINED BY AGE-STAGE, TWO-SEX LIFE TABLE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper has a clear aim, and part of comments suggested on the first review were incorporated in the new version. The proposal manuscript has merit to be published, however, some questions still arising through methodology and results that should be clarified. All questions were described in details in the following sections.
Experimental design: i) In the first submission I asked about: i) how the authors did the model selection?, ii) How they check model assumptions?, and iii) It will be important at least include a half-normal plot of the residuals. The answer addressed to my question was:
"Dear sir as we used polynomial logistic regression for proportion of prey killed/ consumed so the errors associated with such as variable are likely to be distributed binomially. "

I disagree with the authors, and I am still concerned about goodness-of-fit of their model.  Proportion data may present overdispersion, i.e., greater variability than expected by the binomial models.  A possible solution to check the goodness-of-fit and verify the assumptions of this model can be addressed through half-normal plots with a simulated envelope. Please, included the half-normal plot as supplementary material to certify that the model is well fitted to the data. See reference bellow:

Half-Normal Plots and Overdispersed Models in R : The hnp Package. DOI: 10.18637/jss.v081.i10.

ii) The authors reported that who attached, as supplementary material, a plot of residuals versus fitted values, a Q-Q plot of empirical cumulative distribution function of a data set and a specified theoretical cumulative distribution function (probably normal distribution). However, these documents were not attached in the supplementary material. Please, supply them.
Validity of the findings: i) Table 1 shows there are no reasons to include more than an intercept parameter to explain T. vaporariorum. Hence, how the author could explain the inclusion of linear, quadratic, and cubic effects? It should be proper remove those effects as p-value is much higher than the confidence level adopted. Furthermore, they should update results and discussion after model selection.

ii) Why the Adult attack rate was zero when fed with 14 prey?

iii) Lines 376-377 Authors could discuss in more details results about searching time demonstrating how their findings is related to recent research and why this variable has a practical value.
Additional comments: i) I recommend to the authors include a smaller size of points in the Figures 2, 4, and 5 in order to facilitate the visualization of them.


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

Input:
Title: PREDATORY FUNCTIONAL RESPONSE AND FITNESS PARAMETERS OF ORIUS STRIGICOLLIS POPPIUS WHEN FED BEMISIA TABACI AND TRIALEURODES VAPORARIORUM AS DETERMINED BY AGE-STAGE, TWO-SEX LIFE TABLE
Review round: 3
Reviewer: 1

Output:
Basic reporting: See General comments
Experimental design: See General comments
Validity of the findings: see General comments
Additional comments: Authors reviewed and included all diagnostic plots, and they addressed the statistical issues as recommended. They have done a great job and I fully accept their paper.


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

Input:
Title: COMPARATIVE PROTEOME ANALYSIS REVEALS VPS28 REGULATES MILK FAT SYNTHESIS THROUGH UBIQUITYLATION IN BOVINE MAMMARY EPITHELIAL CELLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Line 30: enrich：enriched.
Line 33: Abbreviations TG should be explained on their first appearance both in abstract and in the main text.
Line 60: to better understanding: to better understand.
Line 65: these pathways: which pathways?  Just saw‘milk fat synthesis’ was mentioned before in main body, ‘these pathways’is not clear.
Line 67:  ‘it’ is ambiguous here. Authors should name it clearly, such as: this study or our results, etc.
Line 70: Cells culture should be written as Cell culture.
Line 88-89: It’s not clear for ‘foe mRNA’, please correct or clarify it.
Line 131, 140, 156: These lines were not indented as others. Please check and keep consistent through your manuscript according to PeerJ guidelines.
Line 133: ‘Bos Taurus’here should be written as Bos taurus and italic.
Line 134: ‘identified’ is repeated here.
Line 137-138: The abbreviation for molecular function is missed here.
Line 159: ‘the method described previously’,  authors didn’t describe them before, alternatively, literature(s) could be provided.
Line 216: qRT-PCR in heading line has different format from others (RT-qPCR) in Methods, Table 3 and main body (Line 220). Please check all similar words through your manuscript completely if needed.
Line 221: ‘As shown in Fig.3’, put Table 3 behind Fig.3. Fig 3 could not explain the relative expression of selected genes from one group as shown in Fig 3, while Table 3 has the relative expression.  Or provide relative expression of genes in two groups, not one.
Line 310: Please check the format of all references carefully.
Figure 2 legend：arethe,  please check the grammar.
Finally, professional English speaker is needed to polish the manuscript.
Experimental design: No.
Validity of the findings: No.
Additional comments: The manuscript describes a meaningful study for investigating proteins related to milk fat synthesis, which might be useful and important in dairy production. However, mistakes which needed to be clarified or corrected in this manuscript mean authors should take it seriously.


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

Input:
Title: COMPARATIVE PROTEOME ANALYSIS REVEALS VPS28 REGULATES MILK FAT SYNTHESIS THROUGH UBIQUITYLATION IN BOVINE MAMMARY EPITHELIAL CELLS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors compared the proteome in BMECs before and after knocking down VPS28, and found 203 proteins were screened as significantly down- (111) and up- (92) regulated in VPS28 knockdown BMECs, which were enrich in the “proteasome”, “ubiquitylation”, “metabolism of fatty acids”, “phosphorylation”, and “ribosome”. A series of genes associated with milk fat synthesis, ubiquitylation and proteasome pathways were analyzed by qRT-PCR. The results were interesting and provided information of the role of VPS28-associated ubiquitylation in milk fat synthesis, however, there are some issues that need to be revised.
Major comments:
1) Why only by 26% was VPS28 expression in BMEC down-regulated with tandem constructs? Generally knockdown efficiency should reach 80%.
2) Figure3, provide the SEM of the mean.
Minor comments:
1) L91, change “BEMCs” to “BMECs”
2) L169, delete “and”
3) L237, change “VPS28 was a subunit of ESCRTs played a” to “VPS28 was a subunit of ESCRTs that played a”
4) L259, after what treatment was ubiquitinated CD36 level increased significantly?
5) L278, are fatty acids activated to produce palmitate? What do you mean “fatty acids are activated”?
6) L325, 327, and 330, supply the information of doi.