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: IN VITRO EFFECT OF RESIN INFILTRANT ON RESISTANCE OF SOUND ENAMEL SURFACES IN PERMANENT TEETH TO DEMINERALIZATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: - English remains a concern. See, for example, "experimental group were treated (...)". Must read "the experimental group was treated (...)". Authors are encouraged to search help from a native speaker experienced with scientific English (or, alternatively, use a professional editing service).
- A thorough revision of numbers and units would seem mandatory.
- Literature has been partially ignored, and relevant papers are missing. Background must be elaborated more clearly, along with adequate references, thus leading to the aims. Remember that your rationale remains unclear, so elaborate more clearly your innovative impact.
- Article structure would seem acceptable. Raw data shared.
Experimental design: - This is an original research, but not a primary one.
- Rationale remains unclear. Both aims and objectives must be clearly elaborated.
- Investigation would seem acceptable.
- Several details on methodology would seem missing/are considered perfectible.
Validity of the findings: - Outcome would seem sound.
- Underlying data provided, and considered reasonable.
- Conclusions section would seem perfectible/in need in a thorough revision.
Additional comments: Abstract
- "Healthy premolars were selected (...)." How many premolars have been used?
- "Specimens with baseline surface microhardness (MH) values of 310-370 (g/um2) selected, (...)." Please revise for immediate understanding. Use complete sentences, and stick to clear, unambiguous, technically and grammatically correct English throughout you text.
- "experimental group were treated with resin infiltrant" - this was done WITHOUT prior etching? Please clarify.
- Do not be spuriously accurate, and separate numbers and (correct) units. "266.041±34.484g/um2" must read "266.0 (±34.5) g/µm²".
- What is "um"? Do you mean "µm"?
- What means "more severely destroyed"? Be as precise as possible here. Provide complete results, and add exact P values.
- With your conclusions, do not simply repeat your results. Instead, provide a reasonable extension of your outcome.

Introduction
- With every fact stated, please provide adequate references.
- See, for example, "Resin infiltrant is a low-viscosity, light-cured resin with high penetration ability." To guide the future readers into the right perspective on the development, the authors are strongly encouraged to refer to the introductory papers of the resin infiltration concept, see  https://pubmed.ncbi.nlm.nih.gov/19639091/, and https://pubmed.ncbi.nlm.nih.gov/17586715/.
- "(...) resin infiltrant has achieved excellent clinical results." References missing. See, for example, https://pubmed.ncbi.nlm.nih.gov/32901234/, and discuss.
- Same with "And resin infiltration is a non-invasive treatment option that fits perfectly with the concept of minimum intervention dentistry (Lasfargues et al., 2013)." Indeed, resin infiltration is "closing the gap between oral hygiene and minimally invasive dentistry", see https://pubmed.ncbi.nlm.nih.gov/19639091/, and refer to that introductory paper.
- Same with "Previous studies on resin infiltration have mainly focused (...)." References missing.
- "In this study, in order to explore (...)." Should read "In the present study, in order to explore (...)."
- Please elaborate BOTH aims AND objectives more clearly. Clarify why this study was necessary, and what significant contributions this paper would add to the literature. Remember that infiltration effects on microhardness, penetration ability of the resin, and protective efficacy, for example, are well known from literature. These aspects would seem confirmative only. Please revise carefully, and remember to convincingly elaborate your primary aims.
- You relevant and meaningful research question must be clearly defined. Please identify the knowledge gap you are trying to fill.
- A clear and indisputable null hypothesis (this must be deducible from the foregoing thoughts) is missing.

Materials and Methods
- Number and date of your ethical approval is missing.
- "A total of 80 premolars from patients who underwent orthodontic treatment involving extraction of premolars in the Department of maxillofacial surgery of Somatological Hospital of Chongqing Medical University were selected." Please combine this information with "Oral informed consent was obtained from all subjects prior to samples collection.". Refer to Helsinki declaration.
- Why did you use 80 extracted premolars, but finally managed to stick to only 20 specimens for MH testing?
- Notwithstanding, please clarify the reasons for your ethical approval. Remember that with extracted teeth an Ethical Vote would not seem necessary, see https://pubmed.ncbi.nlm.nih.gov/31990942/, and discuss.
- With ALL materials (including chemicals) and methodologies, please use general names with your text, followed by (brand name; manufacturer, city, country) in parentheses. Stick to semicolon. Revise thoroughly.
- "(4mm×4mm×2mm)" must read "(4 × 4 × 2 mm³)".
- Same with "3 mm × 3 mm". Must read "3 × 3 mm²". Revise thoroughly throughout your text.
- Do not repeat single aspects, compare "The Stomatological Hospital of Chongqing Medical University granted Ethical approval to carry out the study within its facilities." and "Ethical approval was obtained from the Institutional Review Board of our hospital.".
- "In the experimental group, the enamel blocks were treated with resin infiltrant ((...) contain Icon-Etch (...))". Please see comments given above (Abstract section). Did you Icon-Etch? How long did you use Icon-Etch? Please clarify.
- "The specimens referring to the control group were not treated with the resin infiltrant." OK, but these specimens were neither acid-etched, right? Please clarify.
- Do not use legal terms with your text, since this is not usual with scientific reports. Delete Co., Ltd., and so on.
- Again, please separate numbers and units. "15s" must read "15 s".
- What is "mmol/L"? Do you mean liter? This would be the international symbol, and this should read "mmol/l", right?
- Same with "2ml/mm2". Should read "2 ml/mm²"? Please revise thoroughly.
- Same with "37℃". Must read "37 ℃". The unit is "°C".
- Same with "umol/L". Should read "µmol/l"?
- Please revise for uniform writing, compare "12 hours" and "10s".
- "400 × magnification" must read "400× magnification". Same with "3000×".
- Regarding acidity and abrasivity of your tooth paste, and regarding the time of your brushing procedure, please refer to https://pubmed.ncbi.nlm.nih.gov/16110209/, and discuss these aspects more thoroughly.
- "(...) the specimens were placed in artificial saliva overnight." Please add information on your artificial saliva here.
- All in all, with your revision, please ensure reproducibility of your research by providing complete information.

Results
- "(...) indicating that treatment of sound enamel surfaces with resin infiltrant did not affect the degree of mineralization." First, this is not a result, but an interpretation. Second, this interpretation would seem false. With your methodology using Icon-Etch, there surely will be some mineral loss. Please discuss.
- Same with your "indicating that the demineralization degree". This would not exactly correspond to surface MH. For further reading, you might wish to go to https://pubmed.ncbi.nlm.nih.gov/10217515/. Revise carefully.
- Please provide exact P values here. P<0.05 or P>0.05 would not seem sufficient.
- Again, please revise for your spurious accuracy. See, for example, "47.356±11.687 µm". Revise thoroughly throughout your text (including your tables), and re-edit your Discussion section accordingly.
- Meaning of "vibible"?
- Meaning of "resutls"?
- With your SEM evaluation, this aspect again would seem confirmatory only. Refer to https://pubmed.ncbi.nlm.nih.gov/19639091/, and to https://pubmed.ncbi.nlm.nih.gov/17586715/, and discuss.

Discussion
- Refer to H0 when starting this section.
- "Resin infiltration is a minimally invasive approach for treating early enamel caries (...)." Again, refer to https://pubmed.ncbi.nlm.nih.gov/19639091/. Ignoring such an landmark paper would not seem acceptable.
- The rationale for "treating sound permanent enamel surfaces with resin infiltrant" must be thoroughly discussed.
- Do not use author names with your text, unless for historical reasons. See "(...) Taher et al.(Taher et al., 2011)". Authors previous work will (and must) be acknowledged with your references. With your text, however, please stick to your main thoughts.
- "(...) and ethanol dehydration can increase the penetration ability of low viscosity resin (Yoo et al., 2019)." This would seem right. However, please remember that acids do not remove organic compounds, and de-proteinistaion will be necessary to to improve the infiltration efficacy. See https://pubmed.ncbi.nlm.nih.gov/25483122/, and go to https://pubmed.ncbi.nlm.nih.gov/31990942/ and https://pubmed.ncbi.nlm.nih.gov/32901234/, for further information on organic debris, bacteria, and yeasts having been found in the pores of (demineralized) enamel. Please address that your in vitro study did not control for these aspects, and this must be clearly elucidated, since this is a limitation. Remember to add some paragraphs discussing the strengths and limitations of your study.

Conclusions
- Please exclusively stick to your revised aims (see comments given above). Do not simply repeat your results here (this section is not called "Repetition"). Instead, please provide a reasonable extension of your outcome.
- Many thoughts given with your current conclusions would seem right, not doubt. However, these should be copied and pasted to the Discussion section. Here, again, please stick to your aims.

References
- Please revise for uniform formatting. Style must be: Full List of authors (with initials). Publication year. Full article title. Full title of the Journal (italicized), volume: page extents. DOI: number
- Please revise for complete author names, and re-edit with regard to use of capital letters with reference titles.

All in all, the authors will agree that there are numerous minor and major shortcomings with their submitted draft. No doubt, there are 5 (!) (co-)authors having read and approved this manuscript, right? This reviewer would like to remind ALL (co-)authors to consequently re-edit such a paper prior to submission. This for sure will improve the quality of such a paper, at least with regard to it's content. Further language improvement will be possible by means of an editing service, thus finally facilitating reading. Undoubtedly, these comments do not intend to blame the authors. However, please remember that external reviewers will not (co-) or (ghost-)author your manuscript, so a high initial quality would seem mandatory with any submitted paper.

Again, authors are encouraged to search help from a native speaker experienced with scientific English (or, alternatively, use a professional editing service).

In total, while the authors' findings would seem relevant, this submitted draft is not considered ready to proceed. Major revisions would seem mandatory, is re-review is strongly recommended.

This reviewer does strongly encourage the authors to carefully and thoroughly revise their draft, and this review should help to improve the quality. Good luck, and stay healthy.


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: IN VITRO EFFECT OF RESIN INFILTRANT ON RESISTANCE OF SOUND ENAMEL SURFACES IN PERMANENT TEETH TO DEMINERALIZATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: The subject is current and very discussed in the literature. The references are current, however, this paper did not insert them in the introduction, this part was poor and need to improve. In text observed some typed errors.
The title (In vitro effect of resin infiltrant on resistance of
sound enamel surfaces in permanent teeth to acid
erosion and demineralization ) described acid erosion, but this work only studied demineralization process simulation of dental caries, not dental erosion.
Figure 1–very confused–not necessary
Figure 2 unnecessary
Experimental design: Materials and methods are very confused. Suggestion inserts a figure with experimental design and draw of each phase.
The polishing  of sealant was realized after protection with nail varnish  of enamel, this procedure can be compromissed the isolation and affect the demineralization process
Why used 200gf for microhardness analysis?
The surface was analyzed not clearly, it was the enamel infiltrated or around the sealant.

The rhodamine solution stained the polymers and, this way, maybe it can false results.
What moment did you realize the toothbrushing?
As result, the n was 8 and the materials and methods were 10. Why this difference?
Need to improve de discussion and conclusion.
Validity of the findings: Based on the confusion of materials and methods is very difficult the validity of the findings.
Conclusion not clear and not restrict this research.
Additional comments: Need to improve the paper for obtain to the excellence of this journal


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: IN VITRO EFFECT OF RESIN INFILTRANT ON RESISTANCE OF SOUND ENAMEL SURFACES IN PERMANENT TEETH TO DEMINERALIZATION
Review round: 1
Reviewer: 4

Output:
Basic reporting: Intro & background to show context. Literature well referenced & relevant.
The background is not adequate. Dental caries and dental erosion are completely different lesions, in the title “In vitro effect of resin infiltrant on resistance of sound enamel surfaces in permanent teeth to acid erosion and demineralization”, it seems that the authors objective was to prevent dental erosion, however the introduction was regarding dental caries, which is wrong because the methods used and the images of SEM shows that the simulated challenge (artificial demineralization) resulted in dental erosion lesions. Therefore, the authors might introduce the justification to apply resin infiltrant to prevent dental erosion.
Please read: Lussi A, Carvalho TS. Erosive tooth wear: a multifactorial condition of growing concern and increasing knowledge. Monogr Oral Sci. 2014;25:1-15.
It is not possible to understand the raw data regarding microhardness, there is no identification regarding the groups.
Experimental design: Research question well defined, relevant & meaningful. The research question is confused, because the author described dental erosion and dental caries as similar alterations. Therefore, the research question is not well defined.
Methods described with sufficient detail & information to replicate.
Methods are not well described. Tooth brushing were performed in different specimens or the ones which were demineralized? At first 80 specimens were prepared, how much were used for erosive demineralization? 10 was used for Double-fluorescence staining. It is not clear.
Validity of the findings: In Figure 5(E) Sound enamel blocks that were not treated with resin infiltrant following 96 hours of artificial demineralization, it is clear that the artificial demineralization resulted in enamel loss (erosion) and not in a subsurface caries lesion. And on the other hand, the most adequate method to measure dental erosion is profilometry, to understand the amount of enamel lost, hardness is able to show only the characteristic of the maintained enamel.
Please read: Attin T, Wegehaupt FJ. Methods for assessment of dental erosion. Monogr Oral Sci. 2014;25:123-42.
The discussion is not adequate because authors are discussing regarding dental caries and the lesion resulted from the methods is erosion.
The conclusion might also be rewritten. Be careful with speculation in the conclusion.
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: IN VITRO EFFECT OF RESIN INFILTRANT ON RESISTANCE OF SOUND ENAMEL SURFACES IN PERMANENT TEETH TO DEMINERALIZATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: •	The submission adheres to all PeerJ policies - no, but further revisions should eliminate all shortcomings
•	Manuscript is considered clear, unambiguous, and technically correct - no, but further revisions should eliminate all shortcomings
•	The article conforms to professional standards of courtesy and expression - yes
•	The article should include sufficient introduction and background to demonstrate how the work fits into the broader field of knowledge. Relevant prior literature should be appropriately referenced - no, but further revisions should eliminate all shortcomings
•	The structure of the submitted article conforms to an acceptable format of ‘standard sections’ (see our Instructions for Authors for our suggested format) - yes
•	Figures are considered relevant to the content of the article, of sufficient resolution, and appropriately described and labeled - yes
•	The submission is considered ‘self-contained,’ represents an appropriate ‘unit of publication’, and includes all results relevant to the hypothesis - no, but further revisions should eliminate all shortcomings
Experimental design: •	The submission describes original primary research within the Aims & Scope of the Journal - yes
•	The submission clearly defines the research question, which must be relevant and meaningful. The knowledge gap being investigated has been identified, and statements have been made as to how the study contributes to filling that gap - partially, and further revisions should eliminate all shortcomings
•	The investigation has been conducted rigorously and to a high technical standard - yes
•	Methods have been described with sufficient information to be reproducible by another investigator - partially (material and methodology supplier are missing, and will be provided with the revision)
•	The research has been conducted in conformity with the prevailing ethical standards in the field - yes
Validity of the findings: •	The data are robust, statistically sound, and controlled - yes
•	The data on which the conclusions are based have been provided or made available in an acceptable discipline-specific repository - yes
•	The conclusions have been appropriately stated, are connected to the original question investigated, and are limited to those supported by the results. In particular, claims of a causative relationship are supported by a well-controlled experimental intervention - partially, and further revisions should eliminate all shortcomings
•	Speculation is welcomed, but should be identified as such - yes, there should be no problem
•	Replication experiments might be acceptable (provided the rationale for the replication, and how it adds value to the literature, is clearly described); this paper is not considered a ‘pointless’ repetition of well known, widely accepted results - yes, and further aspects have been given with this reviewer's comments (please see below)
Additional comments: Intro
- References are missing, see "(...) and dentin hypersensitivity". Please add a sound reference.
- "(...) enamel white-spot lesions (Markowitz & Carey, 2018; Silva, et al., 2018), (...)." Please add "Youssef et al., 2020", to complete this aspect.
- Please revise for better readability: "The technique is effective in preventing the progression of initial caries in primary and permanent teeth (Faghihian et al., 2019), AND treatment of early dental caries with resin infiltrant achieved excellent clinical results (Lasfargues et al., 2013; Schwendicke et al., 2014; Faghihian et al., 2019; Youssef et al., 2020)." Insert ", and", to complete this sentence.
- Referencing must be improved, see "(Oh HJ et al., 2017)" - delete "HJ".
- The thoughts "In addition, licorice extract has proved to be effective (...).  Its action on biofilm limits the drop in pH, (...). The properties of grape seed extract facilitate prevention (...)." do not guide the reader to the main topic of this paper, and would seem misleading. I recommend to summarize these aspects, thereby focussing on your main thoughts on infiltration.
- "We used resin infiltrant to treat sound enamel surfaces, performed artificial demineralization, then measured the changes in surface hardness of the enamel by micro-indentation hardness testing. The demineralization depth and degree of penetration were assessed using confocal laser scanning microscopy (CLSM). Surface morphological changes of the enamel before and after resin infiltration, artificial demineralization, and simulated toothbrushing were observed using scanning electron microscopy (SEM), and the effect of resin infiltrant on resistance of tooth enamel to acid erosion and demineralization was explored." This would seem like a summary of your methodology only. Please shorten considerably remember that these aspects must be given with your Meths section, and this would be a simple repetition. Again, please elaborate your aims more clearly - clarify WHY THIS STUDY WAS NECESSARY, and what (missing) aspects will be added to the literature.
- A clear and reasonable null hypothesis still is missing. Remember that H0 must be deducible from the forgoing thoughts.

Meths
- "The Stomatological Hospital of Chongqing Medical University granted ethical approval to carry out the study within its facilities." Again, please add number and date of approval of your Ethical Vote.
- "(...) using a hard-tissue cutting machine." Again, please add (brand name; manufacturer, city, country) in parentheses.
- Same with your "Vickers microhardness tester", "beaker",  "constant-temperature shaker", "incubator", "ImageJ software", "scanning electron microscopy", and so on (this list is not complete, so double check and revise your complete text, please).
- See, for example, "electric toothbrush (Oral-B, Braun, Germany)". This must read "electric toothbrush (please insert model name here; Braun Oral-B/Procter & Gamble, Schwalbach am Taunus, Germany)". Again, this must be followed with ALL materials (including chemicals) and methodologies (including statistical software), so please use general names with your text, followed by (brand name; manufacturer) in parentheses. Stick to semicolon. Revise thoroughly.
- Why should you do this? Remember that reproducibility is the cornerstone of scientific advancement, and note that outputs like exact methodology protocols empower researchers to go one step further in contextualizing their work to ensure it remains replicable.
- Do not use legal terms with your text. Delete "GmbH", "Corporation" (or "Inc.", "Corp.", "™", "®", and so on).
- Again, please revise for sound grammar. "Then, these specimens ultrasonically cleaned (...)" must read "Then, these specimens were ultrasonically cleaned (...)."
- Again, "(IBM SPSS 20.0 for Mac; IBM, United States)" should be perfectible. "(SPSS 20.0 for Mac; IBM Analytics, Armonk, NY, USA)" would seem right.
- As a polite and cordially remark, please note that it is not considered the task of a reviewer to co- or ghost-author your draft. This is exclusively the authors' task, please remember that all authors have "read and approved" this revised manuscript. Astonishingly, this revised and re-submitted draft still suffers from several minor and major shortcomings.

Results
- "As shown in Table 1 (Fig. 1), (...)" - please note that (with your text, your table, and your figure) your results will be tripled. This is not acceptable, please delete Table 1. All important aspects would seem covered with Fig. 1.
- "(P = 0.25), indicating" must read "(P = 0.250), indicating". Please provide exact P values, and give 3 decimal places.
- Consequently, "P = 0.0001" must read "P < 0.001".

Disc
- What about H0? Please remember that your null hypothesis can be rejected or not rejected. Please revise carefully.
- "MH can be used as a parameter to detect changes in the mineral content of dental hard tissue (Gomez et al., 2008); MH changes can reflect mineral loss or gain." Indeed, there is a strong correlation between MH and mineral content. Refer to https://pubmed.ncbi.nlm.nih.gov/10217515/ , and discuss.
- "This result is consistent with findings from studies investigating the effect of etching gel on enamel surfaces conducted by Meyer-Lueckel et al. (Meyer-Lueckel, Paris & Kielbassa, 2007; Paris, Dörfer & Meyer-Lueckel, 2010; Neuhaus et al., 2013; Arnold et al., 2015)." There are several papers cited, so this sentence must read "This result is consistent with findings from previous studies investigating the effect of etching gel on enamel surfaces (Meyer-Lueckel, Paris & Kielbassa, 2007; Paris, Dörfer & Meyer-Lueckel, 2010; Neuhaus et al., 2013; Arnold et al., 2015)."
- A paragraphs elaborating both strengths and limitations of the current paper is missing.

Concl
- With your conclusions, please stick exclusively to your revised aims. Do not simply repeat your results here. Instead, provide sound, reasonable and generalizable extensions of your outcome. The latter must be based on your results, for sure, but this section is called "Conclusions", but NOT "Repetitions".
- "Studies have shown (Costenoble et al., 2016; Gulec & Goymen, 2019) that during orthodontic bonding, bracket bonding performed immediately or shortly following treatment of demineralized enamel with resin infiltrant did not affect the bonding quality of orthodontic brackets." This might be right, and this might be given with the Disc section. However, this is not a conclusion deducible from your results.
-  "However, this was an in vitro study, so further studies are needed to confirm the feasibility of preventive using resin infiltrant to protect sound tooth enamel against erosion and demineralization." Again, this is neither considered a conclusion sticking to your aims, nor to your results. Revise carefully.

Refs
- Please revise for uniform formatting of ALL references given.

In total, this revised and re-submitted draft has been considerably improved, and still would seem interesting. However, a further round of revisions would seem mandatory, and this must stick to all the comments given above. Re-review is strongly recommended.


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: IN VITRO EFFECT OF RESIN INFILTRANT ON RESISTANCE OF SOUND ENAMEL SURFACES IN PERMANENT TEETH TO DEMINERALIZATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper was improved, and the new references were insert. Only need to improve the proposition - line 147-148 please rewritten the purpose - like abstract
Experimental design: This paper is a original research, well wrote and with  knowledge.
Only need to inser in text the experimental design, due to this part got very confused.
Validity of the findings: The findings were significative, and provide new information. However need to improve the conclusion
Lines 1077-1079 suggestion -  " This provides evidence that application of resin infiltrant on enamel surfaces before orthodontic treatment  can be promoted resistance of dental  demineralization."
Additional comments: line 147-148 please rewritten the purpose - like abstract
Vickers hardness value should normally be expressed as a number only  (e.i. 320 or 320HV) without the units (g/um2)
line 331 - why were the polished specimens  re-applied with double-layer of acid-resistant nail varnish?
It is important insert experimental design before Resin infiltration and polishing section, due to very confused in text.
In SEM, you could add the information described in text with the insertion of arrows or another way of marking the figure.


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: IN VITRO EFFECT OF RESIN INFILTRANT ON RESISTANCE OF SOUND ENAMEL SURFACES IN PERMANENT TEETH TO DEMINERALIZATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: This revised and re-submitted paper would seem satisfying.
Experimental design: This revised and re-submitted paper would seem satisfying.
Validity of the findings: This revised and re-submitted paper would seem satisfying.
Additional comments: This revised and re-submitted paper would seem satisfying, and is considered ready to proceed.

2 minor aspects are in need of revision, and this should be possible with the proofs:
- Please note that "The null hypothesis tested was that resin infiltrant can improve the ability of sound enamel surfaces to resist acid erosion and demineralization and completely penetrate an acid-etched, demineralized enamel area." must read "The null hypothesis tested was that the ability of sound enamel surfaces to resist to acid erosion and demineralization will not differ from resin infiltrated enamel previously acid-etched and demineralized."

- "Accept the null hypothesis." must read "Thus, the null hypothesis was rejected.


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: DEVELOPMENT OF A MULTIPLEX QPCR ASSAY FOR THE SIMULTANEOUS DETECTION OF MYCOPLASMA BOVIS, MYCOPLASMA SPECIES, AND ACHOLEPLASMA LAIDLAWII IN MILK
Review round: 1
Reviewer: 1

Output:
Basic reporting: Very well written and presented manuscript.
Experimental design: Clear aims
Methods are appropriate, detailed and thorough.
Validity of the findings: Conclusions are well supported by the data.
Additional comments: Reviewing Manuscript 58967v1
Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk

This manuscript describes the development and application of a multiplex PCR assay for detection of 3 target bacterial groups in milk. These include the pathogens Mycoplasma spp and Mycoplasma bovis and environmental contaminant Acholeplasma laidlawaii. qPCR optimization, efficiency and detection limits were performed and specificity with varying levels of bacterial targets was confirmed. The method was used to test a number of milk samples and shown to have very good sensitivity and specificity. The assay offers several advantages over previously developed qPCR methods, including sensitivity and usefulness of the targets detected. The manuscript is very well written and the findings are of high quality.

Specific comments:
-	Line 178 – primer and probe concentration ranges look different here compared to that in Table 2 (75-200nM)
-	Line 220 – Table number (4?) missing
-	Line 335 – (Ct ‘greater than or equal to’ symbol should be ‘less than or equal to’)
-	Table 2 – it would be good to include the full names of ‘VIC’, ‘QSY’, ‘ABY’ and ‘FAM’ in the footnote of this table


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: DEVELOPMENT OF A MULTIPLEX QPCR ASSAY FOR THE SIMULTANEOUS DETECTION OF MYCOPLASMA BOVIS, MYCOPLASMA SPECIES, AND ACHOLEPLASMA LAIDLAWII IN MILK
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are few editorial changes required better attention to details. Some examples where the text could be improved include:
Line 43-44: suggest replacing Mycoplasma bovis with M. bovis, the abbreviation was introduced on Line 30.
Line 85: suggest replacing Mycoplasma sp. with Mycoplasma spp.
Line 141, 144, 150: suggest “The gDNA”.
Line 220: A number of the table is missing.
Experimental design: This paper describes laboratory and field performance validation of a quantitative multiplex PCR assay for the detection of Mycoplasma species, Mycoplasma bovis and Acholeplasma laidlawii. Fast detection and identification of these pathogens can greatly benefit prevention and control of bovine mastitis caused by M. bovis and Mycoplasma spp. The field milk samples used for the validation was not possible to validate the test for A. laidlawii, aside for confirmation of absence.

Overall the study is well described and the manuscript generally well written. There are minor points that require clarification (listed below) and I would be grateful if the authors could consider these.

Line 212-220: The authors prepared two separate gDNA samples from raw milk of which M. bovis and A. laidlawii were separately inoculated. The two gDNAs were then mixed in equal volumes (1:1 ratios), is there a particular reason for this? To mimic a field milk sample, a mixer of milk with equal amount of both inoculated strains could be used for DNA extraction, was this considered?

Line 222-236: The paper describes testing of field milk samples by a multiplex qPCR assay compared to a reference method (cultivation). The authors could consider adding a Cohen's kappa coefficient to determine agreement between two assays.

Line 227: What is an evidence of growth? Perhaps provide a suitable detail or criteria.
Validity of the findings: Line 245: The author described “testing between 75 and 200 nM of each primer and TaqMan probe, different Taq polymerase reagents, and several annealing temperatures (data not shown)”. If the assays are important and included in the manuscript, the authors could consider adding the results. There is currently no mention of results on the different parameter tests in the manuscript. The authors should consider adding results or revise the paragraph on line 176-187.

Line 290-291: The authors reported that milk alone resulted in DNA amplification with Ct 33 to 37. Could the authors please add a comment in this regard to discussion?
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: DEVELOPMENT OF A MULTIPLEX QPCR ASSAY FOR THE SIMULTANEOUS DETECTION OF MYCOPLASMA BOVIS, MYCOPLASMA SPECIES, AND ACHOLEPLASMA LAIDLAWII IN MILK
Review round: 1
Reviewer: 3

Output:
Basic reporting: Dear Mr. Editor,

First I apologize for my delay due to several prior engagements as well as COVID 19 pandemic.

My general observations are:

Article is quite lengthy. Authors wish to say about the development of multiplex qPCR for the detection of M. bovis, Mycoplasma spp. (which they should name in Abstract as well as in Introduction) and A. laidlawii. I could not understand that when they are targeting pathogenic etiology of mollicutes for Bovine contagious mastitis (although this is not a standard terminology for Bovine mastitis), then they should exclude A. laidlawii.

Molecular detection methods always be sharply targeted for specific antigen.

The article is quite lengthy so should be re written to make it short. I feel that in spite of expressing their research work, they have rather justified their work with elaborated text.
I fear that this may cause "loosing of interest" of our valuable readers.

In title also they wrote SIMULTANEOUS DETECTION. It is well known that multiplexes are always SIMULTANIOUS, so they should remove this word from title.
Experimental design: Experimental design is Good.

Authors should tell about the superiority of this qPCR in terms of their targeted gene, in terms of COPY NUMBER of the detectable gene / CFUs.

If primers are novel then they must emphasise this somewhere in text.
Validity of the findings: They have duly validated their findings with several other bacterial / mollicutes isolates as well as standard cultures.
Additional comments: 1. Reduce the words of manuscript.
2. Remove word "simultaneous" from the title.
3. Line no. 24: name all the mycoplasma species.
4. Line 43: Remove the word "help". Be specific and sharp in your text.
5. Authors should write about the Comparison of their developed Multiplex with other PRE PUBLISHED qPCR papers, beside giving emphasis to their Diagnostic Sensitivity and Diagnostic specificity.
6. Line no. 113: replace word "from" with "of".
7. Line 139: Under title "Genomic DNA extraction", give reference of gDNA extraction from milk as milk contains fatty globules and other salts, to it is always difficult to get good quantity of gDNA from milk. Readers would like to know about the reference.
8. Line 183: Remove " : " after "with".
9. Line no. 432 - 433: "In future, methods that accelerate DNA extraction .......Mycoplasma in milk"; what authors want to suggest. So rewrite the sentence or remove this. I feel that such suggestions are of INDEFINATE type and should be avoided.


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: DEVELOPMENT OF A MULTIPLEX QPCR ASSAY FOR THE SIMULTANEOUS DETECTION OF MYCOPLASMA BOVIS, MYCOPLASMA SPECIES, AND ACHOLEPLASMA LAIDLAWII IN MILK
Review round: 2
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: My suggested changes have been implemented.  The only thing I noticed was in Table 2, the concentration of primers/probe for A. laidlawii are out of alignment.


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 SURVIVAL ANALYSES AMONG CAPTIVE CHIMPANZEES (PAN TROGLODYTES) IN AMERICA AND JAPAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English was clear and professional.

In the Introduction there was extensive background source citation and context, and in the Discussion there was thoughtful interpretation and comparison with previous studies.

Figures and tables were helpful. Suggest larger font size in Fig 1 and 2 and population labels (AZA, Japan) in Fig 4.

Yes, clearly defined study with coherent results.
Experimental design: Appears within the Aims and Scope of PeerJ.

Well-defined question, relevant and meaningful to primatologists, anthropologists, demographers and, zoro managers and aging researchers. Contributes to our understanding of captive chimpanzee mortality.

Apparently technically sound, though I am not expert in all the statistics employed. No apparent ethical concerns.

Methos appear sufficient and detailed enough to replicate the study.
Validity of the findings: Individual-level data does not accompany study but the age-specific mortality rates generated by their analysis is provided for the AZA and Japan groups of zoo data.

Data appear robust and sound, having been acquired from accredited zoos.

Conclusions well-stated and possible reasons behind the patterns they observed are well-treated in the discussion, anticipating many of the questions this reader had while reading the results.

Speculation was avoided, except for tentative explanations for why certain patterns existed.
Additional comments: No additional comments


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

Input:
Title: COMPARATIVE SURVIVAL ANALYSES AMONG CAPTIVE CHIMPANZEES (PAN TROGLODYTES) IN AMERICA AND JAPAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is correctly written and easy to read, but a little bit of structure would help.  The literature references are completely adequate, but the Introduction lack of real hypothesis and predictions based on theoretical framework. Because of the high number of results presented, it is easy to get lost. The Results section would win in clarity with headings explaining the different subsection such as for the study of the general survival patterns, and then the distribution of age at death. These headings should be used in the M&M, Results and Discussion parts. Moreover, it is not clear for me what this study provides as new results. All the analyses presented here are very interesting but as no hypothesis nor predictions are presented in Introduction, it is not easy to understand if the authors try to answer to a specific question.
Experimental design: Introduction must be strengthened with clear hypotheses and predictions. Because of that, the research question seems to not fill any knowledge gap. Why comparing AZA and Japan data? Males and females? Wild- and captive-born individual survival parameters? What is the purpose of this study?
The Methods are well explained but some structure would help to better understand.
Validity of the findings: The Discussion is clearly the strength of this manuscript. Results are clearly discussed, and the authors provide interesting interpretations.
Additional comments: Abstract
Do you expect any environmental difference between these two populations? If yes which one and what impact on survival metrics?
Lines 37-39: What are the number between brackets? The range? The 95%CI? It should be precise.

Introduction
Line 76: some species such as elephant yes but more generally long-live species … such as chimpanzee according to Figure 2 from Tidière et al. 2016.
Lines 93-126: Although this information is required, I suggest putting it in the M&M and use the free space to describe more the hypothesis and the prediction expected. What is the interest to compare Japan and America data? What are you expecting from the sex differences?
Lines 134-136: Ok but why?

Material and methods
Line 167: You do not study fecundity here so why introducing it?
Lines 168-169: You have a remarkable high-quality dataset, why introducing error in the estimations attributing unsexed individuals half to males and half to females instead of removing these 4 individuals from the analysis?
Line 179-180: Based on which criteria?

Results
As said in the general comments, the Results would win in clarity with sub-headings introducing the different analyses done.

Discussion
Lines 317-319: This sentence is the same sentence used in Introduction, what is the new point?

Figure 1
Why the wild population chosen is Gombe? As you present different studies in Table 1 maybe you can explain why you chose the Gombe population to compare and not another one?
I found the Figure 1 not very informative as we cannot compare the survival patterns of males and females on a same site. Having clear hypotheses and prediction would help to provide adapted figures that show the answer to the hypothesis.

Figure 4
Rather than indicating in the legend the season maybe it could be easier to visualize if indicated in the figure directly?

Table 1
I am not sure to understand the criteria explaining which studies can be in this table and which cannot. For instance, why Bronikowski et al 2016 and Bronikowski et al 2011 are not in the table 1?

Table 3
According to this table there is difference between sexes, between periods and between wild- and captive born in the two datasets.
The problem of this table is that it gives comparison between females in early period and captive-born, and all others combinations. It is not easy to compare the two male populations for instance (captive- vs wild-born or early vs late period).


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 SURVIVAL ANALYSES AMONG CAPTIVE CHIMPANZEES (PAN TROGLODYTES) IN AMERICA AND JAPAN
Review round: 1
Reviewer: 3

Output:
Basic reporting: This paper uses an impressive dataset for such a long lived animal to give a clear overview of life history patterns in two captive populations. Generally the merits of the study are well explained and justified as well as honestly outlining the limitations. The results of the study are clearly explained, including some very complicated interactions. However, the authors should provide clearer explanations and clarifications in a few areas such as in describing the study population and the statistics used. Although the raw data of the life tables were provided, data needed for other analyses seem to be lacking and the authors should consider uploading R script code as well as data for full reproducibility.

For example, the description of the two study populations in the introduction (lines 102-113) needs to be clearer, more similar for example to how they are summarised in the discussion (lines 286-303). A couple of things which are not clear at the moment:
1) Are the 1302 chimps (line 110) historic and alive? If so, from what time frame?
2) There are 260 chimpanzees alive in AZA zoos, and 1395 were alive from all settings, is this latter number currently alive or in total? This is also a bit misleading as it sounds like the study will include both the AZA chimps and those in other environments, whereas it actually only includes those in AZA environments- you should either remove mention of the other institutions or make it clear that you are only studying the AZA subset.
This section could generally be made clearer by simplifying and structuring the information, for example:
"A total of n chimpanzees have been recorded in the USA between the years nnnn-nnnn. n have lived in accredited zoos, recorded into the North American Regional Studbook (nnnn-nnnn), and n in other settings, recorded by the Lincoln Park zoo project (nnnn-nnnn). This study includes only the n chimpanzees from AZA accredited zoos...." It is not clear at the moment from the introduction which chimpanzees mentioned were included in the study and the numbers given in the introduction (1302 line 110/ 1395 line 113) do not seem to correspond to the total of 1390 given in the methods/discussion (line 305).

The methods should also include a breakdown of the sample sizes for relevant variables across the two populations: e.g. alive/dead animals, captive/wild born, numbers in different institutions, early/recent time periods etc. In general, the methods would also benefit from being split into more sections for structure, eg. data selection, life tables, statistical analyses etc.

Abstract: It would help readers interpret the study to give sample sizes already in the abstract, as one of the advantages to the study is the number of individuals involved.

Line 139: Please give the reference to this previous study- Havercamp et al 2019?

Figure S1: This figure should have a legend explaining what the left and right figures are showing, and the line for Japan Captive F in the left plot is not visible (is it hidden under another line?).

There were a few cases of sentences which could be written more clearly and generally the manuscript could use a thorough proofread with some specific examples given here:

Line 65 should be “a captive population”
Line 105 should this be in the past tense- “there was”?
Line 128- It would be informative to give the sample size of the dataset here.
Line 131- the explanation of the AZA abbreviation should be given at this first mention (currently given later at line 144)
Line 132-  If “American population” is used, should it be “Japanese population” rather than "Japan population" for consistency? Same for all other instances throughout the paper
Line 168- “unknown sex individuals” should be reworded to “individuals of unknown sex”
Line 175 “differences among” should be “differences between”
Line 191 “birthdate” should be “birthday”. Same for line 199 and other instances.
Line 205- needs rewording “surviving to estimated age 79” doesn’t sound right - "an estimated age of 79"?
Line 223- be consistent with the tenses, if it is “differed” should it also be “included/excluded”
Line 250: should have “chimpanzees” or “individuals” after captive-born
Table 1: Be consistent with using abbreviation for life expectancy (LE)- only used in final column and not necessary in that column as it is the column title. Also in Hill et al 2001: "Mahale: K group 1966 (M group 1979)-1988" it is not clear what K and M refer to and are the parantheses necessary?
Table 2 legend- "AZA SSP"- this is the first mention as far as I can tell of SSP -what does it stand for and is it necessary?
Figure 3 legend “data currentness date” should be reworded
Figure 4 key labels could be improved by including a space in "AllDeaths" and changing "DeathAfter1" to "Deaths after age 1".
Table 3- could estimate column in japan section be changed to one line? Please be consistent in how you write the p value (e-n or E-n).
The sentence line 308-311 is unclear, please rephrase it – five sites where? Is the Ngogo chimp population distinct from the Kanyawara population?
Line 343- should be “explained by” rather than “explained to”
Line 374 “in context to the fact” should be “in context of the fact”
Line 424- missing “for males” after 30.1
Experimental design: The methods require more information on the packages used for each statistical analyses including citations (lines 174/188/197), and how statistical significance was determined for each. The results were generally very clear with the complicated interactions well explained.

Line 166 onwards- Although a lot of these abbreviations are standard for life tables, and many have been defined, it could aid a general audience to explain all the terms in the life tables (Tables S1&S2), either in the text in this paragraph, or within the Tables.

Line 168 Please explain why individuals with unknown sex were retained and assigned 50/50 to males and females, rather than excluding these individuals as would be considered more standard protocol. It should also be considered that if you include imputed sexes for these individuals, it would be more appropriate to base them on the sex ratio of your sample, which is female biased, rather than 50:50.

Line 196- Please give some information about how the 4 seasons compare in timing and severity between the US and Japan.

Line 188 please specify what is meant by “poisson regression” – what type of model is this, a generalised linear regression model? If so, explain this and cite the package used. More information is also needed about the response variable- is it a count of individuals that have died at each age? Similarly when reporting the results of this model (line 232 onwards), no test statistics are given for different terms, only those in the table. The authors should consider using likelihood ratio tests or similar to assess the significance of terms (comparing models with and without the term of interest), rather than simply reporting the model output.

Line 242- This isn’t necessarily the case – when there are significant interactions, then it changes how you should interpret the main effects – actually all 3 predictors have an effect they are just all in interaction with eachother, same for line 257.

Lines 315 “we also found support for this pattern” – Although you explained this comparison in the methods, it is not mentioned in the results and it seems strange to mention it for the first time in the discussion -  this should be included in the results when referring to Fig 1.

Line 376- Further to this, selective disappearance could apply here and it would be an interesting point to discuss; the capture process could have selected for only the “good quality” individuals to survive.
Validity of the findings: The authors do a very good job of explaining the limitations of their study as well as the merits. Paragraph lines 342-365 for example is a very interesting discussion of their  findings and 381-403 gives an honest overview of the limitations to the dataset.

Paragraph lines 405-417: For the interpretation of this paragraph, it would be useful to know the number of different institutions sampled from across the two different regions (suggested in an earlier comment for the methods section)- would it be possible to look at different regions within the two different countries?

The underlying data have been provided for the life tables, although not all corresponding data is included for all the analysis to be replicated as far as I can tell (for example, information on time period collected/ birth origin/ season). The authors should also consider providing the R code associated with the analyses to ensure full reproducibility.
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: DEVELOPMENT AND VALIDATION OF A NOVEL SURVIVAL MODEL FOR ACUTE MYELOID LEUKEMIA BASED ON AUTOPHAGY-RELATED GENES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: It's an interesting paper based on bioinformatics analysis. I have several suggestions to improve the paper.
1. What's the c-index of the signature? Please provide it in the revision.
2. The signature performed well in the training set, however, in the validation it didn't work as well. It's better to randomly divide the training set as inner training and inner validation set, or use the 10-fold cross-validation in the training set to construct the signature, which may achieve a better c-index.


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: DEVELOPMENT AND VALIDATION OF A NOVEL SURVIVAL MODEL FOR ACUTE MYELOID LEUKEMIA BASED ON AUTOPHAGY-RELATED GENES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English writing needs to be polished for the wording is inaccurate. For example, in the abstract ,"The results showed that the high-risk subgroup was prone to the poor prognosis of the training TCGA-LAML cohort and the validation GSE37642 cohort." the word prone is misused.
Picture pixels are very low.
Experimental design: The author needed to clarify the details how they merged two datasets GSE37642-GPL96 and GSE37642 GPL570 for they were from the different platform.
Validity of the findings: The prediction accuracy is low in validation dataset and more datasets are needed to validate this signature.
Additional comments: 1、There is great difference in prediction accuracy in prediction and validation dataset for the auc is above 0.8 in construction dataset but the auc is above  0.5 in construction dataset. This is due to overftting effect in the construction dataset. More datasets are needed to validate this signature.

2.The author chose cutoff value using the median value and please use another way to choose cutoff value.

3. Nomogram is often included clinicopathologic parameters. And it seems unnecessary since there are very few clinicopathologic parameters in both datasets. What is the prediction accuracy of the nomogram compared with the signature?

4.The author needed to clarify the details how they merged two datasets GSE37642-GPL96 and GSE37642 GPL570 for they were from the different platform.


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: DEVELOPMENT AND VALIDATION OF A NOVEL SURVIVAL MODEL FOR ACUTE MYELOID LEUKEMIA BASED ON AUTOPHAGY-RELATED GENES
Review round: 1
Reviewer: 3

Output:
Basic reporting: I have listed a few minor format issues that need to be addressed or clarified.
1. Please add LAML, LASSO, TCGA to the abbreviation.
2. In Line 128, please specify if you use a two-sided test or a one-sided test.
3. In Line 97, it misses a multiplication sign between the expression level and the beta coefficients. Please specify the right form of the expression level (linear scale or log-transformed scale?).
4. What causes NRG2 to have such a high HR compared to others in Fig 1A?
5. The label of the x-axis is missing in Fig. 1E.
6. Please specify the variance explained by both two components in Fig 6A.
7. Please explain why a cutoff of 65 years old is used in Fig. 6D?
8. Please make sure that Fig. 6B and 6F are consistent in the confidence interval band and the location of p values.
Experimental design: Most of the comments are related to the statistical analyses performed to train the 10-gene signature for reproducibility proposes.
1. To facilitate reproducibility, it is highly recommended to share your R code used in the analysis.
2. In Line 71, how did you identify these 35 autophagy genes? Is it from a database, a published article, or software?
3. In Line 86, please provide the selection criteria in texts or a diagram on how to retrieve 173 samples. Currently, the TCGA website shows 200 samples available.
4. Please cite all the R packages used in Section 2 Materials and Methods including glmnet, survminer and etc.
5. The sample size in Fig. 2A is 140 while it says 173 in Line 86. Please explain the inconsistency.
6. In Section 3.3 Clinical correlation analysis, why are only age and gender fitted in the multivariate analysis? How about other available clinical variables in the TCGA-LAML cohort? The same question is applied to the GSE3642 cohort.
7. In Line 123, please specify the number of folds used in the cross-validation, and the criteria used to identify the optimum parameter lambda.
Validity of the findings: 1. Please include a table to compare the detailed clinical baseline characteristics between the training set and the validation set (TCGA and GEO datasets).
2. Is it possible that we can compare this 10-gene risk model with other published models?
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: DEVELOPMENT AND VALIDATION OF A NOVEL SURVIVAL MODEL FOR ACUTE MYELOID LEUKEMIA BASED ON AUTOPHAGY-RELATED GENES
Review round: 1
Reviewer: 4

Output:
Basic reporting: There are grammatical errors and typos in this manuscript for example:
- Specifically, high risk subgroup were likely to have a worse survival.
- Last, the distinct drug sensitivity between patients with high- or low-risk provide further information for precise treatment for different groups .
- These findings can provide new insights for the ...

More literature review should be added in terms of related works on bioinformatics analysis.

Quallity of figures should be improved.
Experimental design: - The authors merged 2 different datasets without concern about batch effect removal.

- ROC curve has been used in previous bioinformatics studies such as PMID: 33260643, PMID: 31987913, and PMID: 33539511. Therefore, the authors are suggested to refer to more works in this description to attract a broader readership.

- Why did the authors need to run to 1000 fold CV?

- Source codes should be provided for replicating the methods.
Validity of the findings: - The authors mentioned "However, this study has some limitations", but they only showed a limitation as "Our analysis results have not been verified by in vitro or in vivo experiments". Thus, what are the other limitations?
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: DEVELOPMENT AND VALIDATION OF A NOVEL SURVIVAL MODEL FOR ACUTE MYELOID LEUKEMIA BASED ON AUTOPHAGY-RELATED GENES
Review round: 2
Reviewer: 1

Output:
Basic reporting: For some reason, all the newly added figures and tables are uploaded but not the revised figures mentioned in the rebuttal letter. Could you make sure those are uploaded to the revision submission?

1. The label of the x-axis is still missing in Fig. 1E.
2. Please specify the variance explained by both two components in Fig 6A. Please note this comment is not about the legend. But the variance explained by the PCA component.
3. Please make sure that Fig. 6B and 6F are consistent in the confidence interval band and the location of p values. Again, I don't see any confidence interval bands are added.
Experimental design: Thank you for uploading the R code.

1. The number of folds is 10 not 1000 given the code provided.
fit <- glmnet(x, y, family = "cox", maxit = 1000)
maxit is the maximum number of iteration not the number of folds.
Validity of the findings: no comment
Additional comments: Thank you for addressing all my 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: DEVELOPMENT AND VALIDATION OF A NOVEL SURVIVAL MODEL FOR ACUTE MYELOID LEUKEMIA BASED ON AUTOPHAGY-RELATED GENES
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: My previous comments have been addressed 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: MUVI SCHMALLENBERGI GEN. NOV., SP. NOV. (CRUSTACEA, TANAIDACEA) FROM THE SOUTHEAST AUSTRALIAN COAST, WITH COMMENTS ON THE DISTRIBUTION AND HABITAT PREFERENCES OF CHONDROPODINAE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript (ms) describes an undescribed new genus and new species of Tanaidacea from  Australia. Which well-deserved to be published. Overall, this manuscript is well-writing and well-structured; however, this ms needs to be amended and improved before its publication, since there are several things, according to my opinion, that needs to be addresses as:

It would be nice to see at least a dorsal drawing of the habitus because the body description was based on a photo.

It would also be nice to have a drawing showing the coxal process/apophysis of pereopod-1.

I would like suggest adding a more detailed description of the pereopods; especially, when the authors are referring to the setation. Because they use very often the phrase “other setation as figured”.

The authors need to review carefully the distribution maps. Because there are several inconsistencies and there are geographical errors at the moment to locate several species.
Experimental design: The paper presents an original study, which will be very useful and will increase the diversity and knowledge of the Tanaidacea fauna from Australia.
Validity of the findings: This is a very useful ms describing a new genus and species of metapseudid. This contribution will increase our knowledge of the Tanaidacea diversity and distribution in Australia waters and worldwide.
Additional comments: Some references are missing and some references included in the text do not match with the reference list or vice-versa.

There are several mistakes/inconsistencies and several points need to be addressed. Please, see attached a revised version of the manuscript (i.e., PDF) with comments, suggestions, and corrections to consider.


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: MUVI SCHMALLENBERGI GEN. NOV., SP. NOV. (CRUSTACEA, TANAIDACEA) FROM THE SOUTHEAST AUSTRALIAN COAST, WITH COMMENTS ON THE DISTRIBUTION AND HABITAT PREFERENCES OF CHONDROPODINAE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript has been well prepared in its general form, with excellent drawings and competent and thorough taxonomic text and description.

It is well-referenced and the inclusion of a summary of metapseudid sediment "preferences" is a thoughtful and useful contribution.

A key to the genera is useful.

The text (apart from the taxonomic section) is let down by inadequate English grammar and this could be improved, with help from annotations in the returned PDF. It is sometimes too flowery or over-indulgent.

Overall, the hypothesis of a new genus stands up well in the m/s as presented.
Experimental design: The research is well founded and fits within the general aim of defining and enumerating the complex Australian tanaidacean fauna. This is a major expertise of the two authors.

Technically, it is performed to the usual high standards of the authors, combining photographic and graphic methods to interrogate the new taxon. The drawings themselves are of a very high standard and somehow manage to combine good artistry with accurate representation.

A possible addition to the text to improve its clarity and usefulness in interpreting the taxonomy/classification of the new genus would be a Diagnosis of the subfamily Chondropodinae and its relationship/distinction within the family Metapseudidae.
Validity of the findings: This manuscript does provide good evidence for the establishment of a new genus and species within the tanaidacean family Metapseudidae.

I am not convinced by the need for background on the Australian tanaid fauna as a whole in the Introduction, and even here it is not presented in a consistent manner. I think this is covered by other papers and the emphasis should on on the family/subfamily dealt with here.

In a similar way, I think much of the Discussion about tanaid origins (re Arctic/Antarctic and historic patterns) strays too far away from the main thrust of the manuscript, is covered elsewhere and possibly has little relevance to the family discussed. It could be looked at again and revised.
Additional comments: Much of what has been said in the previous review sections does not need to be repeated here, but any revision of the manuscript should concentrate on:

improving the English text

considering the validity and necessity of sections in the Introduction and Discussion

inclusion of a diagnosis for the subfamily (and even family for context).

Otherwise, it is very nice contribution to the inventory of apseudomorphan tanaids and yet another genus to look out for in neighbouring regions such as the eastern IndoPacific/Polynesia and New Zealand.


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: MUVI SCHMALLENBERGI GEN. NOV., SP. NOV. (CRUSTACEA, TANAIDACEA) FROM THE SOUTHEAST AUSTRALIAN COAST, WITH COMMENTS ON THE DISTRIBUTION AND HABITAT PREFERENCES OF CHONDROPODINAE
Review round: 1
Reviewer: 3

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: See attachment.


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: MUVI SCHMALLENBERGI GEN. NOV., SP. NOV. (CRUSTACEA, TANAIDACEA) FROM THE SOUTHEAST AUSTRALIAN COAST, WITH COMMENTS ON THE DISTRIBUTION AND HABITAT PREFERENCES OF CHONDROPODINAE
Review round: 2
Reviewer: 1

Output:
Basic reporting: No commnet
Experimental design: No comment
Validity of the findings: No commnet
Additional comments: The last name of one author cited in the text and Table is misspelled.

There are few mistakes/inconsistencies that needed to be addressed. Please, see attached a detailed revised version of the manuscript (PDF) with comments, suggestions, and corrections to consider.


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: MUVI SCHMALLENBERGI GEN. NOV., SP. NOV. (CRUSTACEA, TANAIDACEA) FROM THE SOUTHEAST AUSTRALIAN COAST, WITH COMMENTS ON THE DISTRIBUTION AND HABITAT PREFERENCES OF CHONDROPODINAE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The revised manuscript is sound according to the criteria set out here.
Experimental design: The revised manuscript is sound according to the criteria set out here.
Validity of the findings: The manuscript provides a good summary of the interesting subfamily Chondropodinae and should provide a clearer basis for other researchers having to deal with the group.

The discussion about historical and current zoogeography remains, unsurprisingly, highly speculative and difficult to avoid circular augments but is still a valid hypothesis.
Additional comments: The authors have made some attempt to pare down the, perhaps, overblown discussion about Antarctic faunas etc in relation to the subfamily Chondropodinae, but the paper can just about accommodate what remains.

The English text still needs some attention and this is indicated in the returned 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: MORPHOMETRIC AND MICROSATELLITE-BASED COMPARATIVE GENETIC DIVERSITY ANALYSIS IN BUBALUS BUBALIS FROM NORTH INDIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Line 21: Please, add "the" before "prevailing".
Line 23: Replace "analysed" with "analyzed".
Line 25: Replace "size" with "sizes" or with "sizes for each breed".
Line 27: Replace "population" with "populations". Also, replace "Bayesian" with "The Bayesian".
Line 28: Add "the" before "Murrah". Also, replace "population" with "populations".
Line 32: Replace "Microsatellite Repeats" with "Microsatellite markers" or just "Microsatellite"
Line 40: Replace "includes" with "include".
Line 41: Remove "a" before "dominating".
Line 42: Replace "milk producing" with "milk-producing". Also, replace "the need of" with "the need for".
Line 45: Add "a" before "semi-migratory".
Line 46: Replace "requires" with "require".
Line 61: Remove "but" and add a comma (,) after "isolation".
Line 63: Replace "areas" with "area". Also, remove "as".
Line 66 and 71: Change to "well-recognized" and "region-specific".
Line 69: Remove "the" before "future".
Line 80: Figures should be self-informative and can be understood without referring to the main text. In Fig. 1, states are not mentioned, also colors for each breed are not clear enough to distinguish.
Line 85-86: Remove "average" and correct the sentence.
Line 95: Replace "To avoid age and sex effects" with "To avoid age effect".
Line 153: Measuring unit is not mentioned in Table 1.
Line 162: Put "Fig. 2" in parentheses. Please, do this for all other references to the pictures (e.g. lines 168, 172, 185, etc.)
Line 165: Remove "number of".
Line 168: How did you connect locus name in Fig. S1 with microsatellite names. It's not clear from the figure.
Line 173: Remove "by".
* Figures have many problems: Text in figures are not readable enough, even by zooming. Colors are not distinguishable enough. Almost all pictures have a lot of white space that should be cropped. Lacking adequate resolution.
* Tables are not uniform.
Experimental design: Experimental design sounds correct.
Line 86: How you investigated that the samples are unrelated?
Validity of the findings: No comment.
Additional comments: The manuscript needs a review and improvement on English grammar and 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: MORPHOMETRIC AND MICROSATELLITE-BASED COMPARATIVE GENETIC DIVERSITY ANALYSIS IN BUBALUS BUBALIS FROM NORTH INDIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.The major limitation of the study is the readability of the manuscript. The authors are advised to take English language editing services or consult the native English writers to edit the manuscript.

2.The authors are advised to follow and be consistent with the journal style for citations, bibliography, figures, tables, headings and subheadings.

3.The labels of figures must explain the figure well. For instance, in figure 6, explain each of the panel for K = 2 to 4. Put K = 2 to K= 4 on the top of the panel in vertical order. Explain well what the vertical line represents and how admixture patterns can be visualized.

4. Redraw Figure 3. It is hard to see the images. Also, check whether there is other elegant way of representing heat-map.

5. Report the descriptive statistics of the microsatellite loci in the main table.
Experimental design: 1. Please mention the pedigree information of the sampled buffaloes. How many generation were those animals unrelated ?

2. Please mention- how the sampled buffaloes represent the entire breeds respectively? Given a very limited sample size collected from few regions- how can the study claim that the genetic differentiation of these sampled animals can represent the genetic differentiation of the entire breed ?

3. Please mention clearly the version control of all the softwares packages used for the analysis in this study.
Validity of the findings: no comment
Additional comments: Introduction

Line 21: remove prevailing

Line 22: I would suggest replacing distinctness with "distinct genetic entities"

Line 23-25: I would suggest changing the sentence to read: "Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.8% of the genetic variation was found among breeds that could differentiate the studied buffaloes breeds into 3 sub-populations".

Line 29; replace intermixing with admixture

Line 34: check the journal style for subheading

Line 35-37: Please edit the grammar and flow of the sentence

Line 39: I would suggest changing "significantly .... production" to "largest milk producing region in the country".

Line 40 replace "buffalo" with "buffaloes"

Line 43: replace "lesser-known" with "little-known"

Line 44: replace " which is having" by "with"

Line 48: remove "the"

Line 48: add "and" before genetic

Line 62-65: Please edit the grammar and flow of the sentence. Take help of native english writer or english language editing services, if needed.

Line 65:  I would suggest changing the sentence to read as "The present study was performed to assess the levels of genetic diversity, and population structure among three buffalo breeds of North India".

Line 69: replace "can reduce the" with "reducing"

Materials and Methods

Line 72: check the journal style for subheading

Line 75: remove comma (,)

Line 75-76: replace "While the sampling for" with " , and samples for Nili-Ravi buffaloes were collected from Punjab state ( 28° 17' to 32° 17' N and 74° to 76° 41' E).

Line 77: remove "a" before smaller

Line 79: replace "thus" with ", and hence"

Line 82-83:  Please edit the grammar and flow of the sentence. Take help of native english writer or english language editing services, if needed.

Line 84: replace "experimentation" with "studies"

Line88: Please mention- how the sampled buffaloes represent the breeds respectively?

Line 90. Please check the text citations.

Line 91-92: Please edit the grammar of the sentence. Take help of native english writer or english language editing services, if needed.

Line 96: Add comma after effects

Line 103: check the citation style of the journal

Line 107: replace 'sizing' with 'length'

Line 118: replace 'sizing' with 'length'

Line 121: Check the journal citation style

Line 121: replace 'sizing' with 'length'

Line 126: Check the journal citation style

Line 127: add "and" before allowing

Line 131: Remove comma before SPSS

Results

Line 151: check the journal style for subheading

Line 152: I would suggest changing the sentence to read as "The means and standard deviation, coefficient of variations and comparison of mean difference between population for each trait across population is listed ..."

Line 154-155: remove " of studied populations"

Line 156: Add % after 66.7

Line 162: remove comma and add parentheses for Fig. 2. . Check the journal style

Line 168: Check the journal style for inserting figure in the text

Line 171 to 172: Please edit the grammar of the sentence

Line 172: Check the journal style for inserting figure in the text

Line 172: Define θH before using the abbreviation. Do not start a sentence with an abbreviation.

Line 185-186: Check the journal style for inserting figure in the text

Line 188: replace clubbed with clustered; replace outgroup with "distinct group"

Line 188: Please edit the grammar and flow of the sentence

Line 193: check the grammar and flow of the sentence

Line 202: Report clustering of the bovine breeds obtained by STRUCTURE analyses in the main table

Discussion

Line 203: check the journal style for subheading

Line 204: remove available

Line 206: replace buffalo with buffaloes

Line 206: replace presently with currently

Line 208-210:  Please edit the grammar of the sentence. Sentence construct is poor. Take help of native english writer or english language editing services, if needed.

Line 215: remove " extant ... till primarily"

Line 217: replace among with across

Line 220: Do not start a sentence with abbreviation

Line 221: replace varied with vary

Line 224: add of after average

Line 228: Do not start a sentence with abbreviation

Line 258: Check the journal format for inserting equation

Line 281: Check the journal style for inserting figure in the text

Line 289: replace clubbed with clustered

Line 297: Check the grammar and flow of the sentence

Line 298:check the journal style for subheading

Line 301:  Check the journal style for inserting figure in the text

Line 304:  remove comma and replace while with whereas

Line 308: remove of

Line 309: replace Still with "However,"

Conclusion

Line 319: check the journal style for subheading

Line 323: Please edit the grammar of the sentence

Line 324: replace creates with provides

Line 329: remove ", in a better perspective".


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: MORPHOMETRIC AND MICROSATELLITE-BASED COMPARATIVE GENETIC DIVERSITY ANALYSIS IN BUBALUS BUBALIS FROM NORTH INDIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
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: TRANSPORT OF BIODEPOSITS AND BENTHIC FOOTPRINT AROUND AN OYSTER FARM, DAMARISCOTTA ESTUARY, MAINE
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is well organized and generally well-written.  There were no substantive issues with presentation of the data.  I think they set up the problem quite well and incorporate a useful subset of the literature in this area.  Figure are fine, data sharing is fine, they state and test their ideas/hypotheses.
Experimental design: This is indeed "original" research within the scope of the journal.  The key question is whether one can define the "footprint" of oyster aquaculture effects.  This is one of the key concepts in defining the effect of suspended bivalve aquaculture on the benthic environment, with most studies poorly identifying sites with minimal and maximal footprint signatures.  For every study that shows large export (i.e. Testa), there are studies (Higgins) in areas with poor flushing that suggest poor sediment conditions under floats.

This study includes most of the elements one would incorporate into the program - flow, resuspension, biodeposit deposition, benthic fluxes; while I have some methodological questions, the study design is a model for this kind of work.  Key limitations are 1) it is a "snapshot" with no temporal coverage and 2) benthic fluxes were conducted without an illuminated part of the incubation.  Limitation 1 is a minimal issue, this amount of work is sufficient for a short contribution like this.  The presence of benthic "mats" suggest that although the authors want to remove the confounding effect of benthic photosynthesis, it is indeed very important and may have a number of effects.  However, such photosynthesis likely does not change the main conclusions.  (I'll address this again later).

The authors fairly present their data, it's wonderful to see the spreadsheets, and it is very easy for a practitioner to follow what they have done.  I'll address some minor/modest issues below, but the authors clearly meet the journal's standards.
Validity of the findings: The transport and fate of aquaculture biodeposits is a topic of great interest both for basic science reasons, but also it has great value in considering the "nutrient ecosystem services" rendered by such aquaculture.  Benthic systems and material fluxes in aquaculture have considerable variability in this study and virtually all others, more replication likely could not strengthen or change the conclusions.

The overall rates of O2 or DIC fluxes are really quite high for a shallow water system, but it does not seem at all clear that biodeposits account for all of the metabolism.  Systems with high benthic algal production also can have such high rates without the subsidy from aquaculture.  The control may indeed have minimal aquaculture effects (as was hoped) and the biodeposits may be spread so widely as to not have an effect in the area within the aquaculture facility, much less beyond this.  It would be good to consider a broader range of possibilities.  Either way, the aquaculture facility does not appear to create problematic environmental conditions in this macrotidal ecosystem.
Additional comments: I deferred a more detailed discussion of the benthic flux work to this section;  I'll discuss this here and add some (much) smaller line by line comments.  I have more than a general idea of benthic fluxes in aquaculture, I participated in a Roger Newell study in the Damariscotta River focused on mussel rafts, but with a small side effort at the same sites this study used.  The flow/resuspension/sedimentation work was limited to the mussels, but fluxes were carried out at the oyster site.  Our dark fluxes inside and outside the Mook facility are quite similar to this study's.  We also did denitrification and it was negligible.  Our illuminated incubations were 4.6 x lower for NH4 flux and our O2 fluxes showed high rates of gross photosynthesis (3.4 mmol m-2 h-1), consistent with your mat observations.  The sediments were autotrophic so your observations of resuspension and export are the only way to sustain such high rates.  The main observations in this manuscript are not altered by our more detailed fluxes however.  The comprehensive approach to the problem shown in this manuscript make it a valuable contribution.

Smaller comments:

Line 305-307  I would agree if the background respiration rates were very low, they are not.
Line 309-311 I don't think the algae are really confounding effects, they may increase respiration in the dark by providing more fuel.
Line 435  Is the C:N ratio mass or molar?
Line 436-440  Areal rates are chla are more useful when considering them relative to observed rates.  I don't know if you can make that switch, but it minimizes your depth of collection as an issue.
Line 502  ingestion or filtration?
Line 526-530  I think you hedged this just enough....
Line 553-556 Low O2 relative to DIC occurs in systems with iron sulfide burial, methane production, and benthic algal photosynthesis.  Newell at al. 2002 showed this with biodeposit addition studies with illumination.  Newell, R. I. E., M. S. Owens and J. C. Cornwell, 2002. Influence of simulated bivalve biodeposition and microphytobenthos on sediment nitrogen dynamics. Limnology and Oceanography 47:1367-1369.

Overall, this is a nice study.


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

Input:
Title: TRANSPORT OF BIODEPOSITS AND BENTHIC FOOTPRINT AROUND AN OYSTER FARM, DAMARISCOTTA ESTUARY, MAINE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, with good introduction and background sections, excellent referencing, and generally good, high quality figures.  The raw data are supplied and accessible.  A few comments under this heading:
1.  In Figure 1, please provide a distance scale bar for panel C.
2. In figure 3, please indicate the velocity and distance sign conventions.
3. In Figure 6, the legend duplicates “Farm replicate” and “Away replicate” is missing
4. In Figure 7, please state the location and sign convention of the observations in the caption.
5. Please provide captions/descriptions with the raw data files, and please be sure to identify units for all quantities.
Experimental design: The paper fits well with the aims and scope of PeerJ.  The research questions are well-defined and meaningful.  The study was well-designed (given the geographical constraints), carried out professionally, and reported clearly and completely.  There is one major omission in the experimental design and there are several minor clarifications/corrections/additions needed in the Methods, however:
6. The major omission is that the material in the sediment traps was not characterized or compared, other than by mass to determine apparent settling flux.  There appears (?) to be an implicit assumption that all materials caught in all sediment traps were biodeposits, but this was not tested in any way for comparison between trap replicates, trap locations, or bottom sediments.  This assumption seems reasonable for the traps immediately beneath the cages, but not the near-bottom traps.  Simple measurements such as grain size distribution and organic content might have sufficient; additional measurements such as Chl a and nutrient content would have been even better.  Combined with the sediment trap conceptual data interpretation error described below, this results in significant uncertainty in the primary finding about the extent of the farm “footprint”.
7. In eq 2 on line (l) 199, shouldn’t it be us(t) as well as h(t)?
8. The authors describe 3 different methods of estimating bottom shear velocity and state that all three methods produced similar results (l 225).  Then in the results they choose one without sufficient justification and show that the 3 estimates differ by as much as a factor of 2.5 (Figure 5), which is as much as a factor of 6 difference in bottom shear stress. It would be much better to focus on the one method that is arguably most reliable and to state clear reasons for adopting it.
9. In the description of the erosion experiments, please state the source of the replacement water used and whether it contributed to any of the variability between experiments.
10. In l 280, “along-shelf” should be replaced by “axial” or “longitudinal”.
11. In l 287, how were the sediment samples treated before grain size distribution measurements?
Validity of the findings: The primary finding that the downstream out-of-farm location was within the footprint of the farm is not well-supported.  It is a reasonable supposition, but there are in fact equally likely explanations of the data that cannot be ruled out, at least without additional analysis and/or interpretation.  The authors have convincingly shown that the in-farm and downstream locations are quite similar geochemically, but there are several important ways in which the sites are slightly different and the reasons for their geochemical similarity are ambiguous.
12. There is a major conceptual error in comparing the sediment trap data below the cages to the sediment trap data just above the bottom.  While it is likely that the cage traps are good estimates of the biodeposit flux below the cages, the cages occupy only a small fraction of the total surface area of the farm.  To represent the true farm-area-averaged biodeposit settling flux, the cage trap estimates need to be adjusted to account for the empty space between the cages (e.g., as in Testa et al 2015).  The near-bottom traps, however, are arguably reasonable estimates of the area averaged near-bottom settling flux because of particle dispersion.  For example, suppose that the cages occupied 40% of the surface area of the farm.  Then a below-cage trap estimate of 500 g/m2/d would translate to a farm-area-averaged estimate of 200 g/m2/d, considerably less than the near bottom trap flux measured at either location.
    The higher near-bottom flux numbers might be due to resuspension or to another source of settling material.  This is where characterization of the material caught in the different traps might help to identify and compare source(s).  It is not valid to assume that all trapped particles are biodeposits (as in lines 375-380) except directly beneath the cages.
13. I do not agree with the settling velocity fit shown in Figure 4.  It would have made much more sense to fit a line forced through (0,0).  It is not reasonable that a biodeposit with 0 surface area would have a settling velocity other than 0.  Indeed, without the 4 apparent outliers in the lower right of Figure 4, a linear fit forced through (0,0) might be a good description.  Given an approximately constant particle aspect ratio, it is reasonable to expect an approximately linear fit between particle surface area and settling velocity.  It is also reasonable to hypothesize that the scatter of the results might be due to variable particle densities, as the authors have done.
14. Again, the justification for choosing to use the covariance method for estimating shear velocity (lines 399-400 and Figure 5) is unconvincing and the wide difference between the different methods does not promote confidence.  Can a better justification be given (e.g., comparing to the equivalent drag coefficient referenced to 1 m above bottom)?  And once a decision is reached, there is no need to show all three estimates.
15. The statement on l 405-406 that there was only slightly more eroded mass under the farm than at the Away site understates the factor of two difference observed.  One might expect that the bottom under the farm has more fresh biodeposits that are more easily eroded, and the erosion test results support that inference.  Even if the Away site is in the footprint of the farm, it is on the outer fringe and not subject to the same rates of biodeposition as under the farm.
16. I would describe the accumulation of a mound of dislodged biodeposits in the center of the microcosm as evidence of bedload transport rather than evidence of erosion, but this may be just semantics.
17. Reference to the tidal velocity and turbidity record from the LOBO buoy is informative and its use to extrapolate to more erosive conditions under spring tide is quite reasonable.  I think it would add significantly to the presentation to show a comparison between the LOBO velocity and turbidity to the ADV velocity over the period of ADV observations only, perhaps as an addition to Figure 3?  I suspect this would also show that tidal resuspension at the LOBO site during neap tide is not absent, but certainly is weaker than during spring tide.
18. Figure 8 provides evidence that the Away site is a bit different from the Farm site, and in a direction not consistent with expectation for a site less impacted by biodeposition.  The surface sediments at the Away site are clearly both finer and more organic than at the Farm site.  This is counter to expectation as expressed in the Introduction (lines 85-87) and indicates either that expectations were wrong or that some other factor is promoting greater accumulation of organic fines at the Away site.
19. The lack of clear biological and geochemical flux differences between the Farm and Away sites does not necessarily mean that the Away site is within the footprint of the Farm.  This is acknowledged by the authors on lines 528-530.  However, on lines 635-636 of the Conclusions, this lack of inter-site difference is described as supporting the idea that the Away site is in the footprint of the farm, with no caveats.
   I think it far more likely that the alternate possibility on lines 528-530 is a better explanation – “that biodeposition is not a major influence on flux rates, i.e., that the Away site was beyond the footprint of the farm, but the deposition was small enough to have minimal impact.”  In fact, there were apparent inter-site differences in the sediment erosion experiments and in the surface sediment composition, but the erosion rates were very low and the fine, organic sediment fractions were very low at both sites.  A stronger conclusion of this study is that there was no evidence of harmful impact due to biodeposition, either under the farm or at a similar site slightly downstream.  The evidence supports the finding that biodeposition is not a dominant source of organic sediment loading in this energetic estuary under this farming intensity, but not that the Away site is reliably in the footprint of the Farm.
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: TRANSPORT OF BIODEPOSITS AND BENTHIC FOOTPRINT AROUND AN OYSTER FARM, DAMARISCOTTA ESTUARY, MAINE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is well written, with good introduction and background sections, excellent referencing, and generally good, high quality figures.  The raw data are supplied and accessible.  All my previous suggestions have been addressed.
Experimental design: The paper fits well with the aims and scope of PeerJ.  The research questions are well-defined and meaningful.  The study was well-designed (given the geographical constraints), carried out professionally, and reported clearly and completely.  All of my previous comments have been addressed.
Validity of the findings: All of my previous comments and suggestions have been satisfactorily addressed, with 2 minor exceptions:
1. The abstract still states that the authors found “similar erosion rates at the farm and away sites”, whereas the revised text acknowledges that erosion rates at the farm site tended to be about twice as high as at the away site.  I suggest that the abstract text be modified slightly to say something like “found slightly higher erosion rates at the farm than at the away site.”
2. In addition, the text under the Flow and Deposition section of the results still uses the term “biodeposition” for sedimentation rates in the traps not immediately under the oyster floats, at both the farm and away sites.  This should be changed to “deposition”, since the bio contribution is unknown.
Additional comments: No additional comments