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

Input:
Title: A PREVALENCE OF ARTHROPTERYGIUS (ICHTHYOSAURIA: OPHTHALMOSAURIDAE) IN THE LATE JURASSIC—EARLIEST CRETACEOUS OF THE BOREAL REALM
Review round: 2
Reviewer: 1

Output:
Basic reporting: The structuration of the paper is still problematic, see general section below.
Experimental design: All good here, but all methods should be put a Methods section (and all results should be the Results section).
Validity of the findings: Nothing major here; see general section .
Additional comments: Dear editor, dear authors,

First of all, let me apologize for the 2 days delay in sending my review!

The authors have made substantial modifications to the paper and have answered many of my comments. I still have some concerns about the organization of the paper. I suggest acceptation after a minor revision.

Main concerns:

L72-79. The ventral skew. This is interesting and indeed quite easy to recognize. However, the universality of this feature as an indicator of Arthropterygius is puzzling, as it is also found in a series of specimens that have been linked to the poorly known taxon Macropterygius trigonus (e.g. Lydekker 1889), which do not have a facet for an AAE element at all (or extremely reduced; e.g. Lydekker 1889; Sauvage 1912), which strongly differs from the condition seen in Arthropterygius.

L195. This addition was made to reply to a series of points raised by reviewers bit I think it appears a bit dodgy and mixed-up. What I suggested in the previous round was to describe the new remains, describe the re-interpretations of existing specimens (using their specimen numbers and mentioning holotype of, say, Palvennia hoybergeti). And only after that, discuss the similar and finally propose a new taxonomic scheme. Here, we actually get the exact opposite, starting the results by a very technical discussion of detailed features, with quotes etc. that comes before the description of the new data. I might be because the authors prefer a different structure, but the current result is still quite complex to understand. So, I propose here two different plans to make the paper clearer:

Option 1:

A. Introduction
B. Material
C. Methods (including phylogenetics and PCA)
D. Results
	D.1. Comparative description of the novel remains
	D.2. Comparative redescription of Palvennia
	D.3. Comparative redescription of Janusaurus
	D.4. Comparative redescription of Keilhauia
	D.5. Phylogenetic analyses
D.6. PCA Analyses
E. Discussion
	E.1. A wider concept of Arthropterygius (should contain all your arguments, including most of what is written in the “Anticipatory” section)
	E.2. Systematic palaeontology
	E.3. PCA, ontogenetic changes
	E.4. Palaeobiogeograhy
F. Conclusions

Option 2 (closer to what you have now):

A. Introduction
B. Material
C. Methods (including phylogenetics and PCA)
D. Results
	D.1. Preliminary paragraph briefly indicating in a couple of sentences which are synonymised etc.
	D.2. Systematic Palaeontology
	D.3. Systematic description of
		D.3.1. Arthropterygius chrisorum
		D.3.2. Arthropterygius hoybergeti
		D.3.3. Arthropterygius lundi
		Etc.
	D.4. Phylogeny
	D.5. PCA
E. Discussion
	E.1. A wider concept of Arthropterygius (should contain all your arguments, including most of what is written in the “Anticipatory” section)
	E.2. PCA, ontogenetic changes
	E.4. Palaeobiogeograhy
F. Conclusions

I would also like to comment the response to my previous comment:

Authors replied: It is more about that, in our opinion, no robust arguments for Janusaurus and Palvennia representing distinct genera, from each other, and from Arthropterygius, was provided in previous works. That the burden of proving this is on our side now is a pity. The retention of all the species as valid based on “rather minute differences” is sort a tribute to previous research.

I think there is no need to blame previous authors; either you have new data and novel interpretations suggesting this and that, either you don’t and so the knowledge remains similar to what has been published in the past. What you can do is to say that differences warrant specific but not generic recognition. But again, it comes back to my original comment asking to provide more arguments on why some features are dismissed right away as variable while others are retained without question. I just want you to pay attention to circular reasoning.

L225. I do not understand the argument on the basioccipital peg. It is said to be a vestige of the peg, but that the feature should not be scored as homologous to a peg. That is a bit weird. Either it is homologous (even if different in shape) and scored accordingly (I.e. peg present), either it is a structure with a distinct evolutionary origin and thus scored as absent.

PCA: could you explain why the figure has been modified? You seem to have increased sample size for Ophthalmosaurus as well. Also, you represent both axes with the same unit length? It is a bit strange to have the data points spread along the second axis, while obviously the first axis represents a larger chunk of the total variance.

Minor points:
L32-33. Consider replacing “most well-“ by “best-“
L62-64. Please considered deleting that new sentence, which appears as a judgment of value. The sentence starting by “Recently” is fine.
L67. […] in the present contribution […]
L71; L210 and throughout. Latin names cannot be used as adjectives ideally (exceptions are made for biostratigraphic zones).

REFS:
Lydekker R. 1889. Catalogue of the fossil Reptilia and Amphibia in British Museum (Natural History). Part II. containing the orders Ichthyopterygia and Sauropterygia. London, Printed by Orders of the Trustees of the British Museum, London, 307pp
Sauvage H-E. 1912. Les Ichthyosauriens des Formations Jurassiques du Boulonnais. Bulletin de la Société Académique du Boulonnais, 9 424-443.

All the best,

Valentin Fischer


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

Input:
Title: A PREVALENCE OF ARTHROPTERYGIUS (ICHTHYOSAURIA: OPHTHALMOSAURIDAE) IN THE LATE JURASSIC—EARLIEST CRETACEOUS OF THE BOREAL REALM
Review round: 2
Reviewer: 2

Output:
Basic reporting: Dear Editor and Authors,

I have reviewed this manuscript in the first round, and I am pleased to notice that the authors have addressed a substantial number of the requested changes.
Overall, I believe that the text flows better now, and the authors have effectively replaced numerous issues with more informative/precise/correct sentences. The addition of the new table (the specimens table) helps to keep track of the numerous specimens that are mentioned in the manuscript.
Notably many of my concerns and clarifications I asked have been addressed after the publication of Zverkov and Efimov 2019 manuscript that was in press during the first round of reviews. The publication of that paper has given further context to some of the comparisons that were not particularly clear before.
From a stylistic point of view, I particularly appreciated the rewriting of some parts that in the previous version of the manuscript read overly critical to previous authors; the expansion on the Geological Settings section and reorganization of the manuscript “Anticipatory clarification of taxonomic decisions” in its current form.
The scientific side of the manuscript was also strengthened by the reviews, particularly the modifications to the Description and Discussion are more focused and precise.
There are however some issues that still need to be addressed (see below).
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Although the general tone of the manuscript has considerably improved, there still are a handful of sentences that should be revised or better supported. One example is line 231: “Furthermore, the value of this character (i.e. presence/absence of the anterior notochordal) is somewhat uncertain.” The other reviewers and I pointed out that this kind of statement should be better supported by hard evidence or overall avoided. The authors are free to acknowledge that some characters are more useful than others, but they should clear provide evidence when their characters’ interpretation goes against previous workers interpretations. This issue has been largely addressed from the previous version of the manuscript, but still persists in some parts. Please revise the text or tone down these sentences (e.g. “based on XXXXX we believe that the value of this character is uncertain”).

I do not fully understand why the “Anticipatory clarification of taxonomic decisions” section is placed BEFORE the description of the new material. As Reviewer 1 suggested, I would think that a better place for a summarising section like this would be the discussion, or anyway a place after the descriptions. Indeed, this is the central part of the discussion and main take-away message of the manuscript. As thus, a clarification of taxonomic decision should be the main part of the Discussion pulling together the descriptions but also the results of the PCA (especially in absence of a Conclusion section). I advise the author to revise this section and re-formulate their case for the taxonomic decisions using both morphological descriptions and the PCA results.

Still, concerning this section, I am also sorry to insist on the table/figure point. In different forms all 3 reviewers asked for clarifications and recommended additions to the text: I suggested a comparative figure – which I would argue is still needed (even if time-consuming) at least as supplementary figure; R1 argued for a table “including different features and their presence/absence/NA in the species merged into Arthropterygius”; and R2 asked for clarifications too. These would be a great aid to the reader. I think that in addition to the re-writing at very least a table [and/or comparative plate (if not both]) should be added. Do not get me wrong, I do appreciate the efforts of the authors to craft the new section. This helps a lot, but I feel that a table alongside it would summarise these reasonings in a very immediate way, and it is an easy task for the authors to produce it.
Additional issues:
-	As R1 I think that comparisons with other ophthalmosaurids would be beneficial to the manuscript, and the additional references to key taxa to compare systematically important features would not significantly increase the manuscript length. I am aware and recognise that there are extensive comparisons with these taxa in previous papers. However, AT VERY LEAST the authors should mention other ophthalmosaurids when explaining: 1) previously misunderstood features; 2) diagnostic and taxonomically important features (genus defining and group defining characters). The reason for this is that the authors' new taxonomy hypothesis may have changed the distribution of some key characters in the family tree. Thus, explicitly discussing these characters in a broader context and would be an aid for future studies (as much as the authors have benefited from previous extensive comparisons in previous papers).
-	I do not see a stratigraphic log of the new localities even if the authors said they added one did the authors uploaded a wrong version of figure 1?
-	Genera and species names in italicised quotations should not be italicised too (see: “Anticipatory clarification of taxonomic decisions” section) [lines 212 to 218]
-	I do appreciate the work done to revise the diagnosis and I think the authors did a great job to clarify in which specimen the characters are visible. However, I would also rather know which of these features are shared with which other taxa.

I would be favorable to be directly contacted by email (d.foffa@nms.ac.uk) in case the authors wished further clarifications.
Many thanks and congratulations for the work done so far.
Kind regards,
Dr. Davide Foffa


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: INTEGRATED ANALYSIS REVEALS FIVE POTENTIAL CERNA BIOMARKERS IN HUMAN LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: Speculation is welcome, but should be identified by molecular biology experiments, at least real-time fluorescent quantitative PCR
Additional comments: Authors identified differentially expressed (DE) mRNAs, lncRNAs and miRNAs at different tumor stages based on TCGA database, and then constructed a lncRNA-miRNA-mRNA network based on ceRNA hypothesis.They found five potential ceRNA biomarkers in human lung adenocarcinoma. Further confirmation was performed based GEO database. These results were meaningful, however some questions need to be answered.
1. In the legend of Figure 5, yellow represents down-regulated genes?
2. For survival analysis in Figure 6, which RNA (mRNA, lncRNA or hsa-mir-196b) expression was cut off based on median value?
3. The manuscript needs language polishing.


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: INTEGRATED ANALYSIS REVEALS FIVE POTENTIAL CERNA BIOMARKERS IN HUMAN LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this manuscript, Liy et al., aim to characterize the expression of competing endogenous RNAs (ceRNAs) in lung adenocarcinoma (LUAD). Overall, the manuscript is well constructed. However, there are a few instances where precise experimental details are not clearly presented . A few minor revisions could help strengthen the quality of the manuscript:
Experimental design: 1) In figure 6, the authors should clarify the nature of the two arms of each of the Kaplan-Meier curves. Firstly, do “low-” and “high-risk” refer to the expression of the miRNA-mRNA combinations? Secondly, it is unclear what exactly each “ceRNA pair” in this experiment refers to. Are the expressions of each of 3 RNA molecules in each “pair” correlated?

2) Related to the above, in the discussion, the authors note that low expression of FENDRR has been associated with shorter overall survival and progression free survival in breast cancer. Was a similar correlation observed by the authors in this study? Figure 6B suggests the opposite might be the case in LUAD

3) The presence of a consensus motif for genes co-expressed with EPAS1 (figure 7) is intriguing. It would be curious if the existence of such a motif has been previously documented in the literature.

4) It is unclear what is meant in line 198, where the authors state, FENDRR is a lncRNA which showed the highest “degree”. Does this refer to the level of differential expression, or the level of inter-connectivity with other differentially expressed genes?
Validity of the findings: For the most part, global gene expression analysis as conducted in this study can be an extremely helpful resource. However, an issue in this manuscript is the over-interpretation of these results. As such, I would urge the authors refrain from making broad conclusive statements. For example, in line 219, they claim “these results suggested that these ceRNAs likely play an important role during lung cancer development”. Similarly, in line 302 “our study indicates that lncRNA related ceRNAs and TFs play important roles in LUAD”. Such sweeping conclusions without any functional data are a stretch and should be avoided.
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: INTEGRATED ANALYSIS REVEALS FIVE POTENTIAL CERNA BIOMARKERS IN HUMAN LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The work presented is a leading bioinformatics work that honours a peer-reviewed journal like Peer J. Based on a classic approach, but innovative when targeted molecules, the authors do a remarkable job. One of the difficulties of in silico approaches is to see the limitations of approaches and analyses. Here, there are no such problems.
The state of the art is necessary and sufficient, without articles in excess for convenience. The whole process is well brought into context.
The figures could be improved; some require too much zoom to be readable.
The ms. is self-contained with relevancy results to hypotheses.
Experimental design: The design is rigorous and well balanced.
Research is well defined, relevant & meaningful. It would be difficult to ask for additional work, as it is already quite complete.
Methods are described with sufficient detail, and could be replicate.
My only minor question can be if the ceRNA network constructed from DEGs is not too dependent of some hubs.
Validity of the findings: The design is simple and strict, so the results are of similar quality. The Conclusion are well stated, linked to original research question & limited to supporting results.
Additional comments: a simple and pleasant article to read. Well detailed and rigorous.


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: INTEGRATED ANALYSIS REVEALS FIVE POTENTIAL CERNA BIOMARKERS IN HUMAN LUNG ADENOCARCINOMA
Review round: 1
Reviewer: 4

Output:
Basic reporting: No  Comments
Experimental design: NO comments
Validity of the findings: No comments
Additional comments: The manuscript by Liu et al titled "Integrated analysis reveals five potential ceRNA biomarkers in human lung adenocarcinoma uses online available datasets and online tools to find differentially expressed mRNAs, lncRNA and miRNA at different stages of lung cancer. The paper is very very preliminary and does not present any thing significant which can published in scientific journal. I do not recommend its publication.


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

Input:
Title: INTEGRATED ANALYSIS REVEALS FIVE POTENTIAL CERNA BIOMARKERS IN HUMAN LUNG ADENOCARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author's have addressed comments from my prior review. I have no further comments
Experimental design: The author's have addressed comments from my prior review. I have no further comments
Validity of the findings: The author's have addressed comments from my prior review. I have no further 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: INTEGRATED ANALYSIS REVEALS FIVE POTENTIAL CERNA BIOMARKERS IN HUMAN LUNG ADENOCARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper is well written and pleasant to read. The state of the art is present and educational.
Experimental design: The design is well explained and simple to follow. The necessary details are present and correspond to the request of the scientific community.
Validity of the findings: Results and conclusion are strong and accurate
Additional comments: When reading the answers to all the reviewers, we can see that the authors have done a lot of work.


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

Input:
Title: SHARED GENOMIC OUTLIERS ACROSS TWO DIVERGENT POPULATION CLUSTERS OF A HIGHLY THREATENED SEAGRASS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. Not all citations, e.g. Knapp et al. 2016, are in the references this needs to be double checked and addressed. Also, the reference for Widmer and Lexer 2001 is not cited in the paper. As a result, I couldn’t easily check on the method by Knapp et al. 2016 - presumably one of the authors?
2. Lines 13-15 “However, how patterns of natural variation and population genomic structure are shaped by adaptive processes remains unknown.” and the statement on lines 61 – 63 about studying spatial variation of outliers needs to be toned down quite a bit or reworded because the likely intended meaning did not come through. This is very close to what the entire field of landscape and ecological genomics are attempting to do. There are a lot of papers on using SNP data and environmental variables to look at landscape level variation, adaptation, and even susceptibility to disease. For example, the R package LEA and the lfmm function within LEA (https://doi.org/10.1111/2041-210X.12382) or studies of environmental association. Indeed, the RDA, BayeScan, BayeScEnv, and PCAdapt analysis that the authors use has been used similarly in other plant species. Perhaps the authors meant that it hasn’t been done frequently in pooled ezRAD studies or studies of seagrasses and the like?
3. I would like to see some form of Fig. S2 in the paper instead of the supplements. It is an important enough visualization of the data that it should be part of the main body.
4. Line 169, please provide a URL for the GeOMe website.
5. On line 56 when the authors start talking about RAD-seq as a technique to gather genetic data the flow of the introduction might be improved by adding a paragraph here. The beginning of the introduction is very dense with a lot of long, run-on sentences that can fatigue the reader. The reasoning and flow are good, but readability would be improved by shortening some of the sentences.
Experimental design: 1. Within the methods I would like to know which samples were pooled? It isn’t clear until the results when Table 3 is presented that the samples were likely pooled by location. This needs to be more transparent in the methods.
2. I would like to see a contingency table analysis done and a table added to the supplements for the outlier loci to statistically support the claim that the frequency of outliers is different between the two groups (method: Slatkin M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics. 139: 457–462; recent application of: Gaither et al. 2018. Genomics of habitat choice and adaptive evolution in a deep-sea fish. Nature Ecol & Evol 2(4): 680.)
3. I can’t evaluate the method used to generate the values in supplementary Table S3 because the script was not provided. Scripts really should be submitted to a data archive such as GitHub or whatever is the authors favorite repository to ensure that experiments, including the bioinformatics, can be duplicated.
Validity of the findings: The study was well designed and the interpretation of results was clear and accurate.
Additional comments: Summary: The authors are providing valuable data about the genomic variation within a vulnerable, clonal seagrass species suffering from population declines and habitat loss/degradation. The authors are characterizing the standing genetic variation and adaptation potential of the species and have hypothesized that environment and distance will be equally important drivers of population differentiation and diversity. They collected a reasonable number of samples and cites. The use of pooled data seems to save on upfront costs of adapters/indexes necessary for NGS and is appropriate for the question being addressed. They found two distinct “population” clusters generated by differences in outlier frequency rather than private alleles. The authors did find support, although not strong, for their hypothesis that IBD and IBE are equally important in structuring the population. The management implications (naming two areas to concentrate on for preservation) and future directions (i.e. common garden experiments) were clear and well said.

General note: The number of compound and run-on sentences, especially in the introduction, reduces the readability of the paper. I suggest going through and shortening some sentences to improve this.


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: SHARED GENOMIC OUTLIERS ACROSS TWO DIVERGENT POPULATION CLUSTERS OF A HIGHLY THREATENED SEAGRASS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an extremely well written paper, well referenced and has a big message for seagrass researchers. The lack of genomic variation across southern Africa is an unexpected outcome as is the lack of IBD signal.

The pooling of individuals at the location scale concerned me and the effect of pooling needed to be discussed a little in the discussion. I was very confused about how Fis can be calculated from pooled samples - this is probably my ignorance. Clearly Fis values of 1 indicate extreme levels of inbreeding. Is this a product of the low sample size combined with the pooling of these samples?

Clearly by reducing individual variation you have reduced contemporary signatures of genomic variation. Can you discuss this further?
Experimental design: The design of collections was confused - I was not sure about whether the 3 sites at each location were all pooled or whether only samples from sites were pooled. Overall, it is hard to reconstruct the sampling design. I recommend expanding this. The table indicates most locations have 30 samples - no details of sampling distances?
Validity of the findings: Other than my own confusion about the design and methods above - this is a robust analysis and should be published
I would like some more discussion on outlier SNPs separating out populations on west and east coasts of southern Africa but also more details of the isolation by environment patterns seem among estuaries.
Additional comments: I commend the authors on an excellent and careful analysis and a clearly written 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: SEED SURVIVAL OF AUSTRALIAN ACACIA IN THE WESTERN CAPE OF SOUTH AFRICA IN THE PRESENCE OF BIOLOGICAL CONTROL AGENTS AND GIVEN ENVIRONMENTAL VARIATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: See my general comment
Experimental design: Hard to follow:
I find the manuscript hard to follow especially the methods. Perhaps this is a bit hard to change given the nature of the experiment, but I think the authors should improve the readability and make details more accessible to the readers to the extent possible in the revision.
Validity of the findings: See my general comment
Additional comments: The paper is not well written and has potential conflict with the Author's previous publication. (See Strydom, Matthys, et al. "Invasive Australian Acacia seed banks: Size and relationship with stem diameter in the presence of gall-forming biological control agents." PloS one 12.8 (2017): e0181763.)

I had invested time to review the manuscript and had piled a good number of issues regarding difficulty in understanding the methods in relation to the postulated hypothesis.

Unfortunately, I stopped reviewing the manuscript after reading a paragraph that is potentially plagiarized from the 2017 Plos One paper).
Line 291 to 305 in this manuscript was copied and pasted from page 3 of  Strydom et al., 2017.

Similar issues can be seen in other parts of the manuscript.

This being said, I decided to keep my comments on other sections.


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

Input:
Title: SEED SURVIVAL OF AUSTRALIAN ACACIA IN THE WESTERN CAPE OF SOUTH AFRICA IN THE PRESENCE OF BIOLOGICAL CONTROL AGENTS AND GIVEN ENVIRONMENTAL VARIATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are some grammatical issues and also redundant or extraneous material in places that need to be cleaned up but overall the paper is well written and structured.
Experimental design: Design is sufficient though there is scope for additional data analyses. These are noted in my attached comments.
Validity of the findings: Findings are valid though introduction could be edited to support the conclusions better.
Additional comments: I enjoyed your paper and commend you on the detailed work that was undertaken.  I have provided comments on the attached PDF. I do think there is scope for additional statistical analyses and also the need for more information in the introduction on acacia seed ecology/ ecology. Also I think you can highlight the importance of vital rates (through the lens of reproduction and seed bank dynamics) on pop dynamics in the introduction and tie this to biological control.


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: SEED SURVIVAL OF AUSTRALIAN ACACIA IN THE WESTERN CAPE OF SOUTH AFRICA IN THE PRESENCE OF BIOLOGICAL CONTROL AGENTS AND GIVEN ENVIRONMENTAL VARIATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: No Comment
Experimental design: No  Comment
Validity of the findings: No Comment
Additional comments: Congratulations on your paper. I think it is a great piece of research.  I have made some very minor suggestions (see attached PDF) to address in the proofs stage.


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: PROLONGED PITUITARY DOWN-REGULATION WITH FULL-DOSE OF GONADOTROPIN-RELEASING HORMONE AGONIST IN DIFFERENT MENSTRUAL CYCLES: A RETROSPECTIVE COHORT STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: 1. The manner of patient assignment is unknwon.  Because a retrospective study may be skewed by various confoundering factors and selection biases, knowning how the patietns were assigned to different treatment is important to understand the study.
2. Patients with PCOS and/or endometriosis were included. Because these conditions were well known to affect the IVF outcomes, the proportions of patients with PCOS and endometriosis should be given in Table 1.
3. The authors may mentioned the dosage and timing of the use of recombinant LH.
4. The authors mentioned that embryos were transferred 3-6 days after OPU. It means that patietns  would recive either blastocyst transfer or cleavage stage transfer. For comparting the IVF outcomes following a single transfer, knowing the number of embryos transferred, the stage of embryos transferred and the quality of embryos transferred is important.
Validity of the findings: 1. The study used only univariate analyses when the patients` characteristics and treatment outcomes were compared between different groups. Some of the results seems to be marginal. For instance, the P value for day 3 FSH was 0.085. It may imply that the significance would reach the criteria if the sample size was enlarged. It was also supported by the a difference in AFC (P<0.001). Taken together, it may suggest that patients in Group2 have a lower ovarian reserve thatn those in Group1. Considering the potential difference between Groups,  mulivairate analyses should be taken.
2. Other factors that related to the IVF outcomes should be considered. The outcomes should be adjusted for the factors such as the number of embryos transferred.
3.  The author may reorganized the iterm "IVF testifies" to yiel meaningful information. For instance, the term "femal infertility" may include tubal infertility or PCOS patients, but infertile patients with different etiologies may have different prognosis with regard to IVF outcomes.
Additional comments: In their  retrospective cohort study, the authors compared the cinical and laboratory outcomes beween 320 patients received a prolonged pituitary down-regulated full-dose (3.75mg) of triptorelin in the early follicular phase and 160 patients received the same full-dose of triptorelin during the mid-luteal phase.
Although the outcomes of long luteal and long follicular phase GnRH agonist protocols have been investigated, less is knwon in patients reciveing prolonged prolonged pituitary down-regulation with full-dose GnRH agonist. The study highlighted the difference in cyst formation rate, but was limited by its sample size and retrospective nature.


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: PROLONGED PITUITARY DOWN-REGULATION WITH FULL-DOSE OF GONADOTROPIN-RELEASING HORMONE AGONIST IN DIFFERENT MENSTRUAL CYCLES: A RETROSPECTIVE COHORT STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study retrospectively investigated the clinical pregnancy outcome of a total of 480 subjects who underwent long GnRH-a downregulation at different time for IVF/ICSI treatment. The study design was clear and the data presented were reasonable. However most of the references were out of date, with only 2 papers (out of 32 papers in total) were published within 3 recent years. I recommend the authors should update their references as so many new papers published each year in reproductive area.
Experimental design: This was a retrospective study, however, the authors did not clarify the study period clearly in the materials part.
Validity of the findings: The findings that the pregnancy outcomes had no significant difference between women starting long GnRHa downregulation since early follicular phase and women starting long GnRHa downregulation since mid-luteal phase, did provide a certain useful information for clinical doctors and researchers.
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: PROLONGED PITUITARY DOWN-REGULATION WITH FULL-DOSE OF GONADOTROPIN-RELEASING HORMONE AGONIST IN DIFFERENT MENSTRUAL CYCLES: A RETROSPECTIVE COHORT STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: Need to further justify why any clinic would choose to use a long acting GnRHa in late lutela phase. The rationale for conducting the study is not justified adequately.
Experimental design: Upon going through the study design and the process of conduct including the ethics committee approval and prospectively taking informed consent, this appears to be a prospective study however the title mentions it as retrospective analysis.

Figure 3 which describes the stimulation protocol with group 2 started on GnRHa in mid lutes phase shows that patients had periods. Either it’s a misrepresentation or needs explanation.

Details on the number of embryos transferred not mentioned and also feta love reduction if any.
Validity of the findings: Does the data include subjects who experienced OHSS? Was that early or late?
I do not see them accounted for in the total sample size and drop outs/exclusion.
Additional comments: no description of the number of embryos transferred


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: PROLONGED PITUITARY DOWN-REGULATION WITH FULL-DOSE OF GONADOTROPIN-RELEASING HORMONE AGONIST IN DIFFERENT MENSTRUAL CYCLES: A RETROSPECTIVE COHORT STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The basic reporting has been improved by adding detailed information.
Experimental design: The methology has been improved following revision.
Validity of the findings: In the revison, the authors provided further information to support their conclusion.
Additional comments: The manuscript has been revised according to Reviewer`s input.


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: PROLONGED PITUITARY DOWN-REGULATION WITH FULL-DOSE OF GONADOTROPIN-RELEASING HORMONE AGONIST IN DIFFERENT MENSTRUAL CYCLES: A RETROSPECTIVE COHORT STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The changes are well incorporated. No more comments
Experimental design: No more comments
Validity of the findings: No more comments
Additional comments: No more 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: PROLONGED PITUITARY DOWN-REGULATION WITH FULL-DOSE OF GONADOTROPIN-RELEASING HORMONE AGONIST IN DIFFERENT MENSTRUAL CYCLES: A RETROSPECTIVE COHORT STUDY
Review round: 2
Reviewer: 3

Output:
Basic reporting: This manuscript did a retrospective controlled study to investigate the efficiency of an injection of GnRH agonist in the early follicular phase versus that in the mid-luteal phase for ART cycles. The topic is interesting for clinical practice. However, most references focused on patients with endometriosis, not for general infertile couples. The authors should make this point clearly in the manuscript.
Experimental design: This is a retrospective controlled study to compare a full dose of GnRH agonist injection at early follicular phase with that at mid-luteal phase. Since the basic characteristics (antral follicle count) between the two groups. The choice or assignment of the two protocol might be clarified in the section of material and method.
Validity of the findings: The statistics regarding comparison between the two groups is sound. However, the conclusion is beyond the data analysis. The analysis only showed a full-dose of GnRH agonist injection at the early follicular phase is as effective as that in mid-luteal phase. I did not see any data about these two protocols are better than other protocols in terms of ongoing pregann. The authors may have to clarify the startment,
Additional comments: This manuscript did a retrospective controlled study to investigate the efficiency of an injection of GnRH agonist in the early follicular phase versus that in the mid-luteal phase for ART cycles.

1.	In the abstract, this was a retrospective cohort study. However, the title described a retrospective controlled study. Please clarify it and keep in consistency.
2.	In the abstract, authors declared that prolonged pituitary down regulation in early follicular or mid-luteal phase can “improve” ongoing pregnancy rate and live-birth rate. The data and design of this study couldn’t support the conclusion. Is this the authors’ speculation?

Introduction:
1.	Line 61: The benefit of GnRH agonist for IVF cycles exhibited mainly for patients with endometriosis. Please state clearly in the related references (Surrey, 2015; Tanbo & Fedorcsak, 2017). The reference (Surrey, 2002) is also focused on patients with endometriosis. The studied population in this manuscript is not limited in patients with endometriosis. The references here might not justify for the use of prolonged pituitary down regulation for most infertile couples.

Materials and methods:
1.	How to assign the patients into group 1 or group 2? Who will receive early follicular phase injection? Who will receive mid-luteal phase injection? The antral follicle count (ovarian reserve) is significantly higher in group 1 than group 2.
2.	Line 135: How much is the dose of micronized progesterone per day? 200mg per day or more?

Results:
1.	Please add the percentage data into the flow chart (Figure 1) to make it more clearly and easily for reading.
2.	The period in Figure 3 is strange. Do you mean that the period is on day 21 or on the 21 st day from period?

Discussion:
1.	Line 203: Again, all the references (Tanbo & Fedorcsak, 2017; Surrey et al., 2002; Soritsa et al., 2015) here are works on patients with endometriosis. The population in this manuscript is more general infertile couples, which may be not comparable with the patients with endometriosis. In addition, the first paragraph in the section of Discussion may be more suitable in the section of Introduction.
2.	Line 252: In general, the oocyte or granulosa cells in the primordial follicles have no FSH or LH receptors. How can the primordial follicle be responsive to GnRH-a or gonadotropin stimulation? Please explain or give a reference for this point.

Conclusion
1.	Line 277-278: The authors said, “In conclusion, our data suggested that prolonged pituitary down-regulation in the early follicular phase or in mid-luteal phase of the cycle can achieve higher rates of ongoing pregnancy and live birth, with low early abortion rates in fresh IVF/ICSI-ET cycles.” What does that statement “..higher rates of ongoing pregnancy….” mean? Higher than what protocol? The data in this manuscript did not support such conclusion.


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: PROLONGED PITUITARY DOWN-REGULATION WITH FULL-DOSE OF GONADOTROPIN-RELEASING HORMONE AGONIST IN DIFFERENT MENSTRUAL CYCLES: A RETROSPECTIVE COHORT STUDY
Review round: 3
Reviewer: 1

Output:
Basic reporting: The English in this manuscript is poor. Several grammar or spelling errors are noted. The followings are part of them:
Line 68：typing error “reported” instead “reproted”
Line 78: typing error “beginning” instead “begnning”
Line 80, 81: typing error “menstrual” instead “menstral”
Line179； typing error “cryopreservation” instead “cytopreservation”.
Experimental design: Line 63-67：The sentence and concept repeated in this section. Please correct it. The new added reference is not able to declare the “increased clinical pregnancy rate”. Please modify your description about the benefit of GnRH agonist long protocol and further define the purpose of this study to compare the full dose of GnRH agonist injection at follicular phase with that at the mid-luteal phase.
Validity of the findings: No comments.
Additional comments: No comments.


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

Input:
Title: MAINTAINING FIXATION DOES NOT INCREASE DEMANDS ON WORKING MEMORY RELATIVE TO FREE VIEWING
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is well written overall. In order to increase its readership, the paper would benefit enlarging the focus of the introduction (and discussion of the current results) by including reference to a growing body of evidence showing that the frequency of fixational eye movements during prolonged fixation is strongly influenced by tasks involving working memory to different degrees (e.g., Dalmaso et al., 2007; Gao et al., 2015; Siegenthaler et al., 2014).

Here are the references of the papers:
Dalmaso, M., Castelli, L., Scatturin, P., & Galfano, G. (2017). Working memory load modulates microsaccadic rate. Journal of Vision, 17(3):6, 1–12, doi:10.1167/17.3.6.
Gao, X., Yan, H., & Sun, H.-J. (2015). Modulation of microsaccade rate by task difficulty revealed through between- and within-trial comparisons. Journal of Vision, 15(3):3, 1–15, doi:10.1167/15.3.3.
Siegenthaler, E., Costela, F. M., McCamy, M. B., Di Stasi, L. L., Otero-Millan, J., Sonderegger, A., . . .Martinez-Conde, S. (2014). Task difficulty in mental arithmetic affects microsaccadic rates and magnitudes. European Journal of Neuroscience, 39, 287–294.

In the first sentence of the abstract, I would suggest deleting "eye movements and". I think the sentence is misleading as it stands. The comparison is between memory performance under different viewing conditions, not between eye movements.
Experimental design: The question addressed in the manuscript is well defined and important for clarifying different accounts in the literature. The dual task methodology adopted in the experiment seems appropriate and the overall methods are sound. That said, my first point is that the inclusion of a secondary task (finger tapping, see text in lines 92-93) able to modulate the auditory n-back task does not eliminate the possibility that a lack of difference in primary task performance as a function of free viewing vs. fixation may reflect a lack of sensitivity of the primary task. In addition, and more critically with respect to the experiment, I am not really convinced that keeping the eyes within a 400x400 window can be considered as strict fixation. This, in turn, casts serious doubts about the possibility that the two eye-related secondary tasks were really different (the presence of a main effect in the number of fixations does not rule out this possibility). The authors should address this issue very carefully. Put it more explicitly, I wonder what would happen to memory performance by using more demanding fixation constraints (e.g., those used in studies on fixational eye movements).
Validity of the findings: The dual task paradigm implemented by the authors is informative but potentially weak within a pure Null Hypothesis Significance Testing framework. I strongly suggest the authors to complement the current analyses with other analyses using a Bayesian approach which can deal with the problem of accepting the null hypothesis (lack of difference in memory performance between free viewing and "fixation") more appropriately (e.g., Masson, 2011; Rouder et al., 2017).
Here are the references of the papers:
Masson, M. E. J. (2011). A tutorial on a practical Bayesian alternative to null-hypothesis significance testing. Behavior Research Methods, 43, 679-690.
Rouder, J. N., Morey, R. D., Verhagen, A. J., Swagman, A. R., & Wagenmakers, E.-J. (2017). Bayesian analysis of factorial designs. Psychological Methods, 22, 304-321.
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: MAINTAINING FIXATION DOES NOT INCREASE DEMANDS ON WORKING MEMORY RELATIVE TO FREE VIEWING
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript is well-written. Literature review is sufficient. Of general interest may be to include comparisons with the results found in Siegenthaler et al. (2014) where they did find effect on saccade amplitude during a cognitive workload task.

Hypotheses are well addressed.

Figures are suitable but a few changes would make them better:
- Since the 4 figures share the same format, I would merge figures 1 and 2 in the same panel, and figures 3 and 4 in another one, saving space in the figure legends.
- Figure 3 does not show error bars so that text should be removed from the corresponding legend.
- The colors of the dots appear the same when printed in a B&W version, so authors could change the colors of the 3 n-back load tasks.
- Crosses should cover (bring to the front) the cloud of dots and not otherwise.
Experimental design: Methods need additional detail to understand the experimental design - How many practice trials did participant complete? How many blocks in total? How long were the trials? Was there a time limit after showing each letter for the participant to say yes? What happened if participants failed to tap the pattern correctly? and what was the distribution of repeated letters per trials (i.e. what was the percentage of required 'yes' per trial?).

Section 'Computers' does not add to the manuscript and it could be omitted.

Two first sentences in paragraph 'Software' are long and tedious to read. Simplify.

line 193 - Missing right parenthesis. Not clear what 'out of lure' means.

line 209 - Additional space

lines 231-237 - This belongs to Introduction

line 345 - Authors repeat sentence from 342 but replacing "spatial information" with the unclear "object and/or verbal information". Define exactly what object means or remove sentence.

line 361 - Remove 'our' at the end of the line
Validity of the findings: Armson, Ryan, and Levine found no evidence that fixed viewing interfered with working memory performance as measured by the n-back task, when compared to the free viewing condition. These findings fail to support a hypothesis of increased working memory load during fixation but rule out general attentional effects in the process, bringing new insights into the field. The results are conclusive. Data analysis was robust.
Additional comments: Minor edits:
line 81 - "top-Down"
line 99 - This sentence is odd - probably remove "in and of"
line 108 - Approval number is not necessary


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: MAINTAINING FIXATION DOES NOT INCREASE DEMANDS ON WORKING MEMORY RELATIVE TO FREE VIEWING
Review round: 1
Reviewer: 3

Output:
Basic reporting: Different effects of eye movements in free and fixed viewing conditions on memory encoding and retrieval has been reported. But the mechanism of the memory reduction during fixed viewing is still unclear. The present study using a working memory task – an auditory n-back task. They asked the participants to perform this task during free and fixed viewing, as well as a repetitive finger tapping. The authors reported there was no significant interactions in fixed viewing with n-back performance relative to free viewing, which failed to support a hypothesis of increased working memory load during fixation.
Experimental design: The research question seems timely and the approach reasonable. However, some crucial information is missing from the manuscript that would be necessary to fully assess the soundness of the work. For example, although the auditory n-back task has been used in several previous studies, it is still necessary to demonstrate the experimental floe chart as figure in the manuscript.
Validity of the findings: Additionally, I do not find the authors state explicitly how to measure of the number of fixations. As they reported, even during the fixed viewing condition, the number of fixations was still about 113. My main concern is that the authors did not analyze and interpret their results in depth. Since there was no requirement of eye movement during the free viewing condition, participants might still fixated at the corner of the monitor while they were doing the main n-back task.
Additional comments: Whilst not being a native English speaker, I still found some grammatical issues, typos etc., and therefore suggests additional efforts in language editing. Some specific typos to be modified:
-	P 1, Line 37: double ‘in’
-	p 6, Line 247: 11.94
-	P 9, Line 362: needless ‘the’

Overall, the manuscript is well-written, the Introduction and Discussion sections are sound. It is of potential interest to readers in this field, but I cannot recommend publication in its current form. Moderate revisions are necessary, in my opinion.


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: MAINTAINING FIXATION DOES NOT INCREASE DEMANDS ON WORKING MEMORY RELATIVE TO FREE VIEWING
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have done a very nice job in addressing my previous concerns. I have no further 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: MAINTAINING FIXATION DOES NOT INCREASE DEMANDS ON WORKING MEMORY RELATIVE TO FREE VIEWING
Review round: 2
Reviewer: 2

Output:
Basic reporting: This manuscript is well-written. Literature review has been improved. Figures have been successfully modified as requested.
Experimental design: Hypotheses are well addressed. Methods are easier to read now.
Validity of the findings: No comment
Additional comments: The authors have successfully addressed my concerns.


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

Input:
Title: MAINTAINING FIXATION DOES NOT INCREASE DEMANDS ON WORKING MEMORY RELATIVE TO FREE VIEWING
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have largely improved their manuscript. This is now a clear and interesting paper. I recommend publication in its current form.


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: EFFECTS OF THERMAL STRESS ON AMOUNT, COMPOSITION, AND ANTIBACTERIAL PROPERTIES OF CORAL MUCUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript by Wright et al. addresses the topic of coral mucus production and composition under heat stress, a current threat to coral reefs worldwide. The authors find that mucus of stressed corals has higher lipids and protein content as well as more Symbiodinium and coral cell-free DNA. The authors also find that mucus released by stress corals has unexpected higher anti-microbial activity against E. coli K-12 compared to the mucus released by healthy corals. The manuscript contains interesting and valuable for the field of coral microbiology, but few minor clarifications and comments are required to verify the validity of the findings and improve the presentation of the results.
Experimental design: For instance, the estimate of anti-microbial activity was done by inoculating mucus samples with E. coli cells that were previously grown, but how do you know that bacterial grow measurements correspond to E. coli and not mucus-associated bacteria? Did you filter mucus samples?
Validity of the findings: no comment
Additional comments: In line with your results, I would argue that the increased anti-microbial activity could potentially be explained as a mechanism to further prevent bacterial colonization triggered by increased protein and lipid contents?

Figure 4. Could you add absorbance values on the y-axis? Why did you only show 5 if the experiment was done over 12 hours?

Figure 5. Do “counts” refer to gene copy number?

L187: Once you set your tolerance level, the result is either significant or it isn’t. Avoid “marginally significant increase”, if p-value>0.05

L198: Maybe “marker gene copies” instead of “DNA sequences”?
More lipids, more proteins more antimicrobial activity

L203: Can you indicate how many gene copies you found in both conditions? “Few” gene copies is not correct.

L209: please indicate what the numbers refer to, e.g. means of untreated corals.

L212: Again, what does the 46.8±13.2 refer to? If that refers to the percentage of mucus produced versus the original mucus volume, don’t you think it will be more informative to add the mean volume produced?


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: EFFECTS OF THERMAL STRESS ON AMOUNT, COMPOSITION, AND ANTIBACTERIAL PROPERTIES OF CORAL MUCUS
Review round: 1
Reviewer: 2

Output:
Basic reporting: -	Language:
o	Clear and unambiguous language is used. Current phrasing could be improved in lines 214-216, 246-251 (clarify references), 267-270 (simplify). Further suggestions on language are:
o	Lines 31, 87: meteorological parameters (here:  temperature) are used in singular (e.g. “Summer/water temperature…reaches…”)
o	Lines 76 (°C), 76 (h), 82 (°C), …, 87 (hours), 92 (°C, hours), …, 209 (±), 212 (%) and some more. I recommend to increase consistency in the use of units (h, hours) and spaces in front of units/symbols (currently: °C no space, mL space, = space, ± no space).
o	119/120: dry mass instead of dry weight
o	Lines 48/49: double ((
o	Line 132: introduce LB
o	Line 236: of
o	Line 148: Winter (2017)

-	Intro and background:
o	Important literature such as “Niggl, W., Glas, M., Laforsch, C., Mayr, C., & Wild, C. (2009) First evidence of coral bleaching stimulating organic matter release by reef corals.” is missing so far and should thus be considered. Also, reference “Wild C, Woyt H, Huettel M (2005) Influence of coral mucus on nutrient fluxes in carbonate sediments. Marine Ecology Progress Series 287: 87-98” and “Wild C, Naumann MS, Niggl W, Haas AF (2010) Carbohydrate composition of mucus released by scleractinian warm and cold water reef corals. Aquatic Biology 10: 41-45” should be considered in introduction and discussion, because in these publications compositional analyses of coral mucus are provided. For the discussion about antibacterial properties of corals mucus it would  be beneficial to compare findings of this study with findings of “Allers E, Niesner C, Wild C, Pernthaler J (2008) Microbes enriched in seawater after the addition of coral mucus. Applied and Environmental Microbiology 74(10): 3274-3278” and “Wild C, Rasheed MY, Werner U, Franke U, Johnstone R, Huettel M (2004) Degradation and mineralization of coral mucus in reef environments. Marine Ecology Progress Series 267: 159-171”.
o	Potentially also helpful: “Lee, S. T., Davy, S. K., Tang, S. L., Fan, T. Y., & Kench, P. S. (2015). Successive shifts in the microbial community of the surface mucus layer and tissues of the coral Acropora muricata under thermal stress.”
o	Additional references would be useful in lines 44/45, 60/61, 62 in order to provide more profound background.
o	Lines 54/55: As they are a major component of the further analysis and discussion, a more profound introduction of the nutritional composition and antibacterial properties of mucus would be helpful.
o	Lines 23, 33: When referring to ecosystem functions, it would be great to go into more detail what this means – a) L. 23: what does bleaching mean for the system? and b) L. 33: which ecosystem functions are affected by (expelled) nutrient composition? Therefore, shift lines 32/33 (“highlighting…..they support”) towards the end of this paragraph. There, it is possible to provide more detail on the (above mentioned) affected ecosystem functions. Authors state a need to understand impacts of bleaching on coral communities (L. 33), but name “numerous studies” showing them (mortality on community structure (L. 39/40)).
o	Lines 17-21: The beginning of the abstract could be shortened. More emphasis should be put on the justification of study and the gaps of knowledge.
o	Lines 23-25: This section of the abstract should be enlarged and underlined by some numbers that illustrate key results.

-	Structure and standards:
Overall structure conforms to PeerJ standards.
 “&” could be used in more than one authored references as suggested in PeerJ Standards.
-	Figures:
Consistency in color use and style is generally good, but legends (branches with “healthy” and “pale”) are questionable because
-	general terms healthy and pale (see general comments)
-	term varies regarding the statistical compartment. There, the heat stress effect was called treatment. In the legend it is called “healthy” and “pale”.  But in the end, it is thermal stress. So maybe refer to it as treated/untreated or heat stressed/control. Also see Fig. 3.
-	Coral shape not needed for legend
o	Figure 2:
Better not use “weight”. Is it dry mass?
Please mention the colors and their meaning in the description
o	Figure 3:
The A section of the graph should be separated from the remaining compartments. The measure of heat stress is the fundamental distinction/treatment in this study (“healthy” and “pale”). Accordingly, it is not a comparable response parameter on the same level as the others. It should be presented in the beginning of the results section, potentially related with Fig. 1. So far, it appears inconsistent to use color change as a result of thermal stress, while differentiating all graphs according to coloration.
o	Figure 4:
What do the bars represent? Please specify in the description.
Time in h
Specify the scale. Does not the relative absorbance have a unit?
Raw data: is provided with files and Rscript. Thanks for having that all in good structure.
Experimental design: -	The scope of PeerJ seems to be met.
-	The research questions should be more sharply defined. Lines 65-67: More detail on the measures used and the relation to previously mentioned gaps of knowledge, as well as the potentially outlined ecosystem functions/implications would be beneficial. This can be a brief repetition of previously mentioned gaps in knowledge, but helps to justify study. Also, it would smoothen the path coming from the Acropora topic.
-	The investigation appears of high technical and ethical standard.
-	Methods are overall described with sufficient detail. More information should be added in lines 100/101, 111/112, 114/115, 128 to better understand the procedure and allow for replication.
Lines 165-168 should include a general sentence on model assumptions and what statistical approach was used (repeated measures anova?)
Lines 153/154 belongs to statistical analysis
Background information on nutrient conditions of the incubations/ASW would be very useful here.
Validity of the findings: Even though not including all relevant literature (e.g. Niggl et al. 2009), this work provides very interesting results.
Line 260: Towards the end of the discussion a short outlook referring to the ecosystem implications would be great. The reader may be interested to know what results could mean for the ecosystem, as ecosystem function is mentioned in abstract, e.g. short-term increase / release of more protein and lipid components – who could benefit from that?
Line 268: Please mention that this influence on the reefs nutrient cycle is at least short-term – because discussion highlights that it could be linked to the zooxanthellae expelled.
Further references should be given in 213-218, 255/256 to relate findings to current knowledge and underline what findings could mean.
Line 221: Each section of the discussion should begin with a short reminder what the key related study results according to the specific topic of interest / research question were. Accordingly, lines 221-223 should be placed at the end of line 226.
Line 242: “Surprisingly” suggests that there was an expectation beforehand – but there was no clearly stated hypothesis about that. This also refers to being a bit more detailed in the research question.
Line 185: “although” sounds like contradicting to an expectation, which should be discussed later and not in the results.
Additional comments: This is a solid and interesting study that deserves publication. However, the manuscript would highly benefit from a thorough overview of relevant literature.
Also, it appears inconsistent to use a response parameter (color) to differentiate between treatments. There are not many physiological measurements that confirm that control corals were “healthy”. They were not under thermal stress. If using that term, it would be better to define them as healthy according to Winters et al. (2009). The pale “treatment” individuals can be stated like this, but only when separated from the remaining response parameters and shown in the beginning of the results section. As the title of the study is “the effects of thermal stress”, it is certainly more appropriate to remain the color as a response parameter (also in Figure 3), but refer to the treatment as heat stress/thermally stressed and controls/unstressed.
Furthermore, some more detail in abstract, a more clear formulation of research questions, and provision of background on ecosystem implications would make the study more useful for the reader.


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: EFFECTS OF THERMAL STRESS ON AMOUNT, COMPOSITION, AND ANTIBACTERIAL PROPERTIES OF CORAL MUCUS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no additional comments
Experimental design: The authors have clarified methodological concerns raised on the first version of the manuscript as well as improved the narrative and presentation of the results.
Validity of the findings: no additional 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: EFFECTS OF THERMAL STRESS ON AMOUNT, COMPOSITION, AND ANTIBACTERIAL PROPERTIES OF CORAL MUCUS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Much better now.
Experimental design: No comment.
Validity of the findings: Much better now.
Additional comments: The authors have addressed all my previous comments sufficiently so that I can recommend acceptance of this manuscript.


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

Input:
Title: A COMBINATION OF CURCUMIN, VORINOSTAT AND SILIBININ REVERSES AΒ-INDUCED NERVE CELL TOXICITY VIA ACTIVATION OF AKT-MDM2-P53 PATHWAY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1) The authors use a clear and adequate English language throughout the manuscript;
2) The intro & background presented are well referenced and relevant to the context;
3) The manuscript structure follows the PeerJ standards;
4) The figures are relevant, well labelled and described. However, I may have some suggestions to improve their quality:
a) I suggest authors remove the frames on the top and right of figures… it will make a better presentation to the audience;
b) The most important issue lies in Figure 3C. The actin band does not appear to be homogeneous, which may indicate errors in sample concentration. This is an essential condition to calculate the real value of proteins. Therefore, errors in protein content can display false-positive results. This important issue should be fixed, as the results are not reliable.
Experimental design: 1) The authors present original primary research related to a well defined, relevant and meaningful question, which fills an identified knowledge gap.
2) The investigation was performed according to a high technical and ethical standard, describing methods with enough detail and information to replicate.
Validity of the findings: 1) The authors present meaningful findings, statistically sound and controlled. However, the description written in the manuscript’s “Discussion” section is not informative to properly interpret the obtained data. The authors repeat their results throughout the discussion, instead of providing the proper mechanisms by which the CVS combination activates AKT-MDM2-p53 pathway.
2) The conclusions are well stated, linked to the original research question and limited to supporting results. Yet, the authors state that the CVS combination has potential as prophylaxis for AD treatment, but they only performed in vitro assays, which can seem as a speculative approach. Maybe authors could consider stating it as a first step, which leads to further investigations using animal models (as mentioned in line 280-281 of the manuscript).
Additional comments: The manuscript presents a promising work which provides interesting approaches to the search for new therapeutic options in the different phases of AD. The authors suggest that the curcumin, vorinostat and silibinin combination protects PC12 cells from Aβ25-35-induced toxicity through modulation of AKT/MDM2/p53 pathway. However, some accuracies are necessary to make clear some issues.


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

Input:
Title: A COMBINATION OF CURCUMIN, VORINOSTAT AND SILIBININ REVERSES AΒ-INDUCED NERVE CELL TOXICITY VIA ACTIVATION OF AKT-MDM2-P53 PATHWAY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is very well written and the English is clear.

However, the Introduction needs more detail. There was no discussion of why beta-amyloid 25-35 was selected to stress the cells, nor did it clearly describe the author’s previous work with this compound in the cultured cell model. Adding this detail would enhance the paper and it needs to be included in order for the paper to be published.
Experimental design: The methods are well described. The inclusion of proper control groups is a concern, as noted below under validity.
Validity of the findings: The findings appear valid, but the results and figures need to be more clearly presented.
1. Figure 1 needs additional explanation. In the figure, a control and then A is shown, and then the effects of 9 potentially protective compounds. Is this in the presence of the compound plus A or the compound alone. In part B of the figure, there is the same issue. Also, what is the effect of curcumin, voinostat and silibinin alone? Those are the proper controls, which are not shown.
2. The Results section has similar issues, and needs to be more clear about what was tested and what were the results with the compounds alone.
3. The same issues apply to Figures 2, 3 and 4. While the reader can figure out what the authors mean, it should be clear in the Results section and in the figure legends.
Additional comments: This is a very interesting paper, but it would benefit from increased clarity of the experimental design and results. It discusses a novel approach to Alzheimer's disease that should be pursued.


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

Input:
Title: A COMBINATION OF CURCUMIN, VORINOSTAT AND SILIBININ REVERSES AΒ-INDUCED NERVE CELL TOXICITY VIA ACTIVATION OF AKT-MDM2-P53 PATHWAY
Review round: 1
Reviewer: 3

Output:
Basic reporting: - There are some grammatical and typographical mistakes along the manuscript which should be corrected. In many instances throughout the manuscript, it was difficult to understand what the authors were trying to convey.
- The abstract should be rewritten. The abstract must state the hypothesis and objective for the research and contain the experimental procedure briefly.
- The introduction needs more detail. I suggest that you improve the description at lines 39-50 to provide more justification for your study bringing current data on the number of people with AD worldwide and not just in some countries.
- Some references are not formatted correctly. Authors should review this section.
Experimental design: - The authors do not provide references in the methods section. Authors should review and revise this section.
- It is not clear in the methodology because the authors used the combination with CVS as pretreatment. They should explain why choosing the pretreatment protocol. Why did not they use the combination of CVS as treatment after stimulation by Aβ25–35.
Validity of the findings: - The work presented by the authors is not mechanistic and it is not novel. Why is the study important?
- No differences were observed between the control group and the curcumin-vorinostat-silibinin (CVS) group with regard to either CASP3 expression or the percentage of TUNEL positive cells. How do the authors explain this results?
- Authors should explain the applicability of the results found.
- The authors investigated whether the addition of silibinin could act synergistically with curcumin and vorinostat to alleviate amyloid beta (Aβ)-induced nerve cell toxicity. From the results obtained, it was evident that the combination showed positive effects on the parameters analyzed in the study, however the discussion is very poor and needs to be rewritten in more detail. It is necessary that the authors discuss in depth the results of the study and propose a possible mechanism to explain the benefits of curcumin, vorinostat and silibinin.
Additional comments: No additional comments


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

Input:
Title: A COMBINATION OF CURCUMIN, VORINOSTAT AND SILIBININ REVERSES AΒ-INDUCED NERVE CELL TOXICITY VIA ACTIVATION OF AKT-MDM2-P53 PATHWAY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have revised the manuscript and answered the reviewers criticisms.
Experimental design: The authors have answered the reviewers concerns and revised the figures to reflect these.
Validity of the findings: No comment.
Additional comments: The authors have made a strong attempt to reply to the reviewers concerns.


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

Input:
Title: A COMBINATION OF CURCUMIN, VORINOSTAT AND SILIBININ REVERSES AΒ-INDUCED NERVE CELL TOXICITY VIA ACTIVATION OF AKT-MDM2-P53 PATHWAY
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have replied in a satisfactory manner. According to this reviewer, the article can be accepted for publication.


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

Input:
Title: OSTEOPOROSATLAS: A HUMAN OSTEOPOROSIS-RELATED GENE DATABASE
Review round: 1
Reviewer: 1

Output:
Basic reporting: OsteoporosAtlas: a human osteoporosis-related genes database by Wang et al. is a comprehensive database of 617 osteoporosis-related genes and 131 osteoporosis regulated miRNAs. It provides a research resource for the pathogenesis of the disease for individual cases, the discovery of drug target, biomarkers and individual treatment methods and medication. I commend the authors for building such an extensive database. In addition, the manuscript is clearly written in professional, unambiguous language. Having said that, I feel the authors did not cover the existing literature well enough and this should be improved before acceptance. I have these suggestions that may help to improve this issue.
1.	Here the description and characteristics of osteoporosis have been oversimplified. It is a complex polygenic disease and genetic as well as environmental factors contribute to the cause of this disease. For more details, authors may follow these articles Huang QY et al. Osteoporos Int. 2003 and Cummings SR et al. Lancet. 2002.
2.	Authors in line 38-39 categorized the cause of the disease into three types, however, they only described the primary type in the manuscript. Authors should also provide a brief description of the secondary and idiopathic types as well.
3.	Line 47 is not clear to me, please elaborated with some evidence.
4.	Authors should mention in detail how the present study will help to improve the understanding of the genetic background of this disease and how it fills the existing knowledge gap. I think including the genome-wide association study in understanding the genetics of osteoporosis will help to make a bridge between the existing knowledge and what this study offers to understand the disease.
5.	Please provide a reference for the sentence in the line 166-167.
Experimental design: Relevance: Of sufficient interest
Originality: Moderately original
Clarity: Clear enough
Validity of the findings: Technical Correctness: Probably correct
Experimental Validation: Sufficient validation
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: OSTEOPOROSATLAS: A HUMAN OSTEOPOROSIS-RELATED GENE DATABASE
Review round: 1
Reviewer: 2

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
Additional comments: The manuscript describes a database resource for osteoporosis related genes and microRNAs, collected using a text mining approach. The database has a very specific application and may be suitable for specific readership concerned about the particular disease. The database functionalities are not working now, please check all the links. Also, in the manuscript Results section, please add few example case studies from the database on both genes and microRNAs related to osteoporosis.


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: OSTEOPOROSATLAS: A HUMAN OSTEOPOROSIS-RELATED GENE DATABASE
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is very well written. Some minor corrections are suggested as follows:
1.	Line 42: “issue” instead of “issues”; “brings” instead of “bring”
2.	Line 46, 63,93: Avoid sentence start with “And”
3.	Line 48: “Lots of studies have shown that many encoding genes’ deficiency or
 overexpression in mice cause the inhibition or promotion of osteoporosis”- confusing, consider re-write
4.	Line 63: “plays” instead of “play”
5.	Line 69: “increasing” instead of “increasingly”
6.	Line 71: “aggravates” instead of “aggravate”
7.	 Line 77: “associated” not “associate”
8.	Lines 82:  “…which makes it difficult…” instead of “which is the difficulty”
9.	Line 84: “contains” not “contain”
10.	Line 113: What is the GOA database? Other abbreviations are defined
11.	Line 158: “OsteoporosAtlas 1.0 also of the function of community curation”-meaning not clear , re-write
12.	Line 163-164: “….the osteoporosis drugs promoting…” instead of “…the osteoporosis drugs by promoting bone…”
13.	 Also check spacing between words and brackets.

Comments about figures and supplemental files:
1.	Figure 1A, 2, 3A: Font is very small.
2.	No description of supplemental files in the text. Readers will not be aware of the existence of these files.
3.	peerj-32180-Osteoporosis_gene.txt – check column alignment
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: OSTEOPOROSATLAS: A HUMAN OSTEOPOROSIS-RELATED GENE DATABASE
Review round: 1
Reviewer: 4

Output:
Basic reporting: The manuscript entitled “OsteoporosAtlas: a human osteoporosis-related gene database” reports the first osteoporosis database that catalogs the genes known to be associated with osteoporosis, a common bone disease. This database provides easy access to the information on osteoporosis-related genes to the scientific researchers and clinicians.
The article structure is appropriate according to the journal. However, authors fail to introduce the research problem to the broad readers for a clear understanding of their work.
Also, the manuscript is poorly-written and I strongly recommend the authors to take help from professional English language editors.
Experimental design: In the study, the authors used appropriate experimental strategy for the extraction of the data from the biomedical literature, however, the authors did not provide a complete detail description of the methods in the manuscript which needs to be addressed for better understanding to broad interest readers.
Validity of the findings: No comment
Additional comments: 1.	Please re-write the abstract section especially background and results section. In the background section, the research problem is not presented clearly. In the results section, highlight the fact that it is a first specialized database for the easy access of relevant information such as osteoporosis-related genes and miRNAs.
2.	I suggest to re-write the introduction section of the manuscript. As it stands now, it reads poor and is difficult to follow. It should be clear and more general; discuss different causes of osteoporosis, its pathophysiology and role of miRNAs rather than including examples of different genes and miRNAs.
3.	In materials and methods section, the authors did not introduce the terms such as whose precision, F-measure and recall against the CRAFT corpus for protein ontology-based gene/protein conformation for the readers to understand them clearly. Also, please explain the methods in detail.
4.	Throughout the manuscript, I observed lot of grammatical errors, wrong usage of punctuations which makes it difficult for reader to interpret the actual meaning of the sentence.
5.	In the results section, line 166-169 seems to be irrelevant. Also, the authors did not cite any references.
6.	Specific remarks:
line 37-38: Re-write. Same as line 20-21 in the background section;
line 43: Include 2-3 sentences to mention the reasons why women are more prone to osteoporosis;
line 48-49: Rephrase the sentence, not clear;
line 77: change “associate” to “associated”;
line 81-82: Rephrase the sentence, difficult to interpret;
line 87: write “precision” instead of “precise”;
line 102-103: Rephrase;
line 106: change “finally” into “In summary, our database consists of”;
line 121: Remove “comma” from the text “their, functional”;
line 122-123: merge the two sentences;
line129: Rephrase the text from “after clicking the button of search,” to “after clicking the “search” button,”


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: OSTEOPOROSATLAS: A HUMAN OSTEOPOROSIS-RELATED GENE DATABASE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is written in clear and unambiguous manner.
Experimental design: Original primary research within Aims and Scope of the journal.
Validity of the findings: Conclusions are well stated, linked to original research question & limited to supporting results.
Additional comments: I find the revised manuscript is suitable for publication in PEER J.


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: OSTEOPOROSATLAS: A HUMAN OSTEOPOROSIS-RELATED GENE DATABASE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed all of my concerns. I am happy with their answers. I strongly recommend this article to publish.
Experimental design: N/A
Validity of the findings: N/A
Additional comments: The authors have addressed all of my concerns. I am happy with their answers. I strongly recommend this article to publish.


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: IDENTIFICATION OF CANDIDATE REFERENCE GENES FOR QRT-PCR NORMALIZATION STUDIES OF SALINITY STRESS AND INJURY IN ONCHIDIUM REEVESII
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English used in this manuscript is extremely poor and I am afraid that it requires comprehensive editing by a native English speaker.
The general structure of the paper is good and the literature references in the introduction are sufficient. However, the discussion is quite short and has a mere three references. Admittedly, I am not familiar enough with the cited literature and to what extent there are further such studies (Assessing the suitability of appropriate house-keeping genes for qPCR in general, and more specifically, under varying stress/physiological conditions), however I think this section should be far more comprehensive.

The figures and tables are good with a few minor corrections which I have noted in the attached file. All the relevant raw data appears to be available.

The article is self-contained with relevant results to hypotheses except for one issue.
In the methods section (line 38) it is stated that the animals were collected and maintained according to Shen’s method (ref. 18). This paper has an English abstract, however the main text is in Chinese. I think that in such a case the relevant methodology should be provided here in English, however I leave this matter for the editor to weigh in on.
Experimental design: Everything appears to be fine with the experimental design, research questions and methodology employed. A sufficient number of genes were assessed and all the appropriate analyses conducted.
Validity of the findings: I have one suggestion to make here. There is one important (perhaps very important) “take home message” from this paper which is not highlighted sufficiently by the authors and is of potential wide-ranging implication (outside the Onchidium community). That is, that one cannot assume that a particular “housekeeping gene” which was found to be good (i.e. stable) in one series of experiments on a particular organism will still be relevant for standardization in other experiments (and certainly not in other organisms). The notion that stress induced by extreme environmental conditions (such as salinity) may alter the expression pattern of “putative” housekeeping genes is not apparent and should be highlighted. I suspect this will make the paper more appealing to a broader audience. I am not sure but this finding may even warrant changing the title of the paper accordingly because at the moment the title speaks to a very very small niche group of interest.
Additional comments: Please see the attached file with some initial English corrections I made along the way (I am afraid that there are many more), as well as further matters which need to be clarified before publication.


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

Input:
Title: IDENTIFICATION OF CANDIDATE REFERENCE GENES FOR QRT-PCR NORMALIZATION STUDIES OF SALINITY STRESS AND INJURY IN ONCHIDIUM REEVESII
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have studied seven potential housekeeping genes as a candidates foe reference genes to be used in qRT-PCR in the sea slug Onchidium struma and ranked them under salinity, injury treatments, and size (weight).
The study as a practical value in the use of O. struma as a model study animal, and therefore the work publishable.  However, I found the manuscript poorly written and unsatisfactorily structured. I will not specify the grammar or spelling mistakes as they are numerous but indicate about structure:
In the abstract – not clear what is the meaning of “qRT-PCR was used to assess the expression levels of…”
Last part of the introduction should indicate the aim of the study. Instead the authors placed it in the abstract.
Line 44 – not clear what the meaning of bait.
Line 45 – What is control environmental temperature means
Line 50 – not clear what is the meaning of “After treatment”
Line 51 – not clear what is the meaning of “also tissue of dorsal skin”
Line 68-73 – paragraph is too long and should be break into several sentances
Line 125 – what is SD?
Line 221 – not clear what is the meaning of “reasonable reference genes should to be able to use for the detection of any gene of interest.”
Experimental design: It is not clear why the authors chose the salinity and injury treatments.

Shen's method (line 38) should be elaborated.

in general the M&M is not clear and should be edited and re-written.

Line 62 - SYBR qPCR SuperMix is not a solution for reverse transcription of RNA.

In figure 2, the letter for each graph should be positioned inside the graph box.
Validity of the findings: The data is robust and well analyzed.
Conclusion are stated and linked to the original research question and to the aim of the study. However it seems that the authors have not elaborated about the fact that in each treatment or treatment range, results showed a different outcomes.
Additional comments: I strongly suggest that the manuscript will be edited and proofed by an English native speaker.
In addition the Discussion and Conclusion parts should be elaborated as indicated above.


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

Input:
Title: IDENTIFICATION OF CANDIDATE REFERENCE GENES FOR QRT-PCR NORMALIZATION STUDIES OF SALINITY STRESS AND INJURY IN ONCHIDIUM REEVESII
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been improved greatly from the initial submission. I have made some minor English corrections throughout the manuscript in the tracked changes file. That said, I still feel that it could be better and recommend that the authors/English editor go over it one more time before its final submission.

There is one figure in the supplement called - Leicester approval. As far as I can see this document is not referenced in the manuscript and the document is entirely in Mandarin Chinese. Please refer to this document if relevant and also I recommend that it be translated or at least have another document clarifying its purpose.
Experimental design: No comment.
Validity of the findings: No Comment.
Additional comments: I am very glad to see that this manuscript has been thoroughly revised and that overall the English is of a suitable level for publication. The various technical issues which were raised in the previous submission have also been addressed adequately.


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: IDENTIFICATION OF CANDIDATE REFERENCE GENES FOR QRT-PCR NORMALIZATION STUDIES OF SALINITY STRESS AND INJURY IN ONCHIDIUM REEVESII
Review round: 2
Reviewer: 2

Output:
Basic reporting: Dear Yang et al.
I found the manuscript to be improved based on the manuscript writing and sentence structures. However there are some weak sentences that need to be addressed. In addition - in order to strengthen the conclusions section I suggest delivering the manuscript massages in a “bulleted list”.

Introduction
Lines 34-37
“However, there inevitably are always a number of influencing factors that affect the efficiency of these reactions, such as ….”
Please rephrase the sentence

Lines 58-60
“O. reevesii has been investigated with regard to morphological, physiological and active substance perspectives, and…”
Please rephrase the sentence

Materials and methods
Lines 76-77
“The water used in the experiment was saline, and the volume of water used ensured that all the samples were retained.”
Please rephrase the sentence

Line 115
Authors indicate that PCR products were visualized in 1% agarose gel. Such percentage is best for fragments of 500 to 10,000bp , while qRT-PCR products are smaller.
Please correct

Line 122
Correct “20-ul” to “20 ul”

Discusion
Lines 261-263
“The most suitable internal reference genes in different tissues of Haliotis rufescens are reportedly…”
Please rephrase the sentence

Lines 267-278
“Sun JH found that the reference genes RPL13S and RPL32S to be the most stably
277 expressed genes in contused rat skeletal muscle; however, EF1a plus TUBB constitutes…”
Please rephrase the sentence

Lines 280-281
“This is a research direction of our laboratory in the future41-43.”
Please rephrase the sentence
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: MELATONIN IMPROVES THE EFFICIENCY OF SUPER-OVULATION AND TIMED ARTIFICIAL INSEMINATION IN SHEEP
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This study provides data showing that short term of melatonin treatment during estrus improve the uterine environment of ewe and significantly increased the pregnant rate.  Data also demonstrated that melatonin administration improves the quality and quantity of embryos and this may also contribute to the increased pregnant rate.  The findings are interesting and provide strong support for the application of melatonin in sheep to improve the reproductive outcome industrially.  However, the paper is poorly written and needs significant English editing for publication.  It is recommended that the authors find an expert to correct the numerous English errors throughout the manuscript.


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

Input:
Title: MELATONIN IMPROVES THE EFFICIENCY OF SUPER-OVULATION AND TIMED ARTIFICIAL INSEMINATION IN SHEEP
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In the manuscript "Melatonin improves the efficiency of superovulation and timed artificial insemination in sheep (#34096) " by Yukun Song et al. The authors documented that the short-term effects of melatonin on ewe’s ovulation and the results showed that melatonin treatment at 36 hours after withdrawal CIDR could promote the number and quality of embryos in vivo and increased the pregnant rate and number of lambs. These results provide a support for the application of melatonin in sheep to improve the reproductive outcome industrially.
I have some minor comments that should be addressed as following:
1.	How long does a half-life of melatonin have in the ewe blood?
2.	How was the injected doses of melatonin determined?
3.	What means of 0, 5, 10 mg were? For example, 5 mg is 5 mg melatonin per ewe or is 5 mg melatonin per kg bodyweight of ewe?
4.	In line 130, “the embryos with normal morphology were transferred into the oviduct of recipients”. Please elaborate the specific process.
5.	In line 139-142, please state how to prepare semen in vitro artificial insemination? For example, semen conservation, sperm capacitation, and so on.

6.	In line154-155, why was the melatonin concentration higher in the serum of ewes in the 5 mg group, but not that of the 10 mg group?


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: MELATONIN IMPROVES THE EFFICIENCY OF SUPER-OVULATION AND TIMED ARTIFICIAL INSEMINATION IN SHEEP
Review round: 1
Reviewer: 3

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: The aim of this paper was to investigate the role of Melatonin in superovulation and timed artificial insemination in sheep. The Authors found that melatonin treatment at 36 hours after withdrawal CIDR could promote the number and quality of embryos in the in vivo condition and increased the pregnant rate and number of lambs. The article is original and the Authors purpose is interesting, however the authors must to prepare thorough correction of the whole manuscript. In the result part, why the high concentration group had higher P4 in Estrus stage and lower pregnancy rate? What's the difference between Embryos and Normal Embryos in Table 3? How are the data in tables 4 and 6 counted? There is no standard deviation. Please indicate the number of experiments. <63.4% b (12/22) b> in Table 6 needs to be revised. Please simplify the summary section. Please go deeper into the discussion section.