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

Input:
Title: AN INTEGRATED MODEL OF SEASONAL CHANGES IN STOCK COMPOSITION AND ABUNDANCE WITH AN APPLICATION TO CHINOOK SALMON
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This is a review of Freshwater et al. I found the paper to be clear and well written, and appreciated the detail of the figures and supplemental material. Minor comments below -- my only hangup was not being able to install the software package.

- line 140: In the data collection section, I think it'd be helpful to add a little more detail about the exact effort you used from each set of samples (e.g. boat days or vessels for commercial & recreational), and what was used with the First Nations fishery [edit: this is boat days on ~ line 201, but would be helpful to discuss in this section]

- line 190: perhaps add a sentence similar to the hatchery / wild comparison, that the groupings in Table 1 also are lumping stocks with different marine distributions (e.g. spring & fall, Puget Sound & WA coast)

- line 194: how are the seasonal strata defined in the spatiotemporal strata? [edit: realizing you have this on 201]

- line 200: if these are overall pretty stationary, might be useful to include an AR coefficient
- line 201: it might be interesting in future versions of this package to model the PFMA-specific smooths hierarchically (e.g. https://peerj.com/articles/6876/)

- line 208: I'm not used to seeing equation (3a) written this way and am maybe confusing myself. Might be easier to break it into 2 equations, with P ~ Multinomial(theta, N) and theta ~ Dirichlet (gamma)
- line 209: I think it'd be cool in future work to evaluate any interannual variation in the seasonal pattern (hierarchical smooths or year-specific smooths)
- line 263: I had trouble building the package across a couple computers -- there's some errors in the code that need fixing (https://api.travis-ci.org/v3/job/750093842/log.txt)

- line 268 / figure 2: One thing that's a little bit troubling is that the CPUE predictions / CIs are widest in summer months when you have the most data (though your Fig S1 shows some regions with little data in summer). I think this is an issue of the transformation from log to normal space, because Fig S3 shows that the predicted log-catch rates have symmetrical error bars
- related to previous comment, I also wonder if it isn't possible to adjust the basis functions or GAM penalties (e.g. making the PFMA specific season smooths hierarchical)? Or using seasonal ARIMA models instead of basis functions? Though I guess with the latter the CIs will be symmetric in log space.
- line 284: I wonder how much these trends for S. Strait of Georgia are affected by the PS blackmouth effect -- in winter/spring they may be one of the few stocks present, but are dominated by more migratory stocks in summer/fall [edit: I see this is in 1st discussion paragraph]. It'd be super interesting then to look at this composition over time + how it relates to Puget Sound hatchery practices

- Figs 3/4: nice work with these, I think they'll be seen as super useful

- line 478: or compare CWT distributions to GSI distributions for well-tagged stocks


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

Input:
Title: AN INTEGRATED MODEL OF SEASONAL CHANGES IN STOCK COMPOSITION AND ABUNDANCE WITH AN APPLICATION TO CHINOOK SALMON
Review round: 2
Reviewer: 1

Output:
Basic reporting: Excellent.
Experimental design: Excellent.
Validity of the findings: Excellent.
Additional comments: The combination of revisions and responses to reviewer comments leave me completely satisfied that my comments and the comments of the other reviewer were appropriately addressed.

Just to prove I read the revised manuscript, one very minor quibble concerns line 114: Certainly Satterthwaite et al. 2015, confined to California, is in an area with lower stock diversity by most any reasonable standard. Satterthwaite et al. 2013 covers a broader geographic range (including most of Oregon) but only discusses 4 tagged stocks, so characterizing it as from a less diverse region or at least providing insight into a lower diversity of stocks is entirely appropriate. However, Bellinger et al. 2015, in their Figure 4, show results for 21 different reporting units. Some of the reporting units are quite coarse and include multiple "stocks" (e.g., "Alaska") but I would say 16 or so correspond to reasonably well defined "stocks" (and arguably, the very coarse nature of some reporting groups indicates even higher diversity). This contrasts with 11 "stocks" in Figure 3 of this manuscript. So it's not clear which study area is more "diverse", though diversity may not necessarily correspond to richness and richness/diversity per unit area or length of coastline covered might also factor into such a comparison. Overall I leave it to the authors to decide if that statement needs to be qualified or revised, and it is quite minor in the grand scheme of things.


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

Input:
Title: AN INTEGRATED MODEL OF SEASONAL CHANGES IN STOCK COMPOSITION AND ABUNDANCE WITH AN APPLICATION TO CHINOOK SALMON
Review round: 2
Reviewer: 2

Output:
Basic reporting: Great - no issues
Experimental design: N/A
Validity of the findings: Great - no issues
Additional comments: I'm totally happy with all the revisions -- nice work overall with the paper!


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

Input:
Title: PREDICTION AND ANALYSIS OF NOVEL KEY GENES ITGAX, LAPTM5, SERPINE1 IN CLEAR CELL RENAL CELL CARCINOMA THROUGH BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: -	The English language should be improved in Lines 20-24 to ensure your points are clear.
-	Line 20-21: It is not explained why ROC curve is used for.
-	Line 41: position of Reference 1 is not correct.
-	Line 61-62: It is not clear how three key genes were selected out of 35 hub genes. This is important to clarify the criteria for feature selection.
-	Data processing section, Line 79-87, needs more detailed description and English language needs to be improved. It is highly recommended to add a schematic/flowchart for this section so that the pipeline is clear and easy to understand.
-	Grammar issue in Line 89: “… were used to analyze…”
-	Scientific reporting language is not used in Line 94-102 and 110-114.
-	Line 110: what are the two groups?
Experimental design: -	A key missing piece of information is how three genes were isolated from the pool of top 35 differentially expressed genes. This is significantly important to be addressed in this work to understand the motivation and whether that can justify the feature selection part of the work.
Validity of the findings: -	The findings are expected to be explored and discussed in much more depth rather than only reporting the observations. For example, in Line 131-149, only the differentially expressed genes and their GO are reported without discussing whether these observations have been reported in the literature.
Additional comments: -	This article aims to find genes with high predictive power in CCRCC patients. This is an important study, however, there are major issues that need to be addressed.
-	The results (Line 116-187) need to be explained in more details, characterized in more depth and discussed further.


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: PREDICTION AND ANALYSIS OF NOVEL KEY GENES ITGAX, LAPTM5, SERPINE1 IN CLEAR CELL RENAL CELL CARCINOMA THROUGH BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors performed bioinformatics analysis to study the key genes in clear cell renal cell carcinoma. After different analyses, they convinced the roles of ITGAX, LAPTM5, SERPINE1 in CCRCC. Although the idea and objective are reasonable, there are some major points that need to be addressed:

- There are many grammatical errors and typos in this manuscript. The authors should go through to re-check and revise carefully.

- Another concern is that the authors missed mentioning a lot of literature review that focused on the same problem (bioinformatics analysis in CCRCC). At least they need to show what are the current processes on this specific problem and what is the novelty in this study.
Experimental design: - Source codes should be released for replicating the results.

- Did the authors concern about any batch effect removal when they merged all the datasets and performed analyses?

- Data is not much to convince the significance of the findings.

- ROC curve and AUC have been used in previous bioinformatics studies such as PMID: 32613242 and PMID: 31362508. Thus the authors are suggested to refer to more references in this description.
Validity of the findings: - Are the finding genes different from all previous works on the same problem?

- Table 2 is unreasonable, it is better if the authors display it as a heatmap figure.

- The authors should compare the performance with previous works on the same dataset.
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: PREDICTION AND ANALYSIS OF NOVEL KEY GENES ITGAX, LAPTM5, SERPINE1 IN CLEAR CELL RENAL CELL CARCINOMA THROUGH BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: 1. Grammatical errors need to be rectified; some sentences need to be rephrased for easy understanding. Dangling sentences in the Methods section of the abstract. Sentences should not start with “AND.” Proofreading will help.
2. Can log2 change and multiplicity adjustments be considered?
3. The authors can explain briefly how the fold change cut-offs were chosen.
4. Comparison with previous work, limitations of the work, and future guidelines may be added.

Please address the 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: PREDICTION AND ANALYSIS OF NOVEL KEY GENES ITGAX, LAPTM5, SERPINE1 IN CLEAR CELL RENAL CELL CARCINOMA THROUGH BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: The authors have addressed the 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: ANTI-ATHEROSCLEROTIC VACCINATION AGAINST PORPHYROMONAS GINGIVALIS AS A POTENTIAL COMPARATOR OF STATIN IN MICE
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper compared the effect of vaccinatino along vs. the effect of vaccination plus statin. The author's conclusion is that vaccination itself is enough to prevent atherosclerosis.
The reporting is clear, background information is adequate.
Experimental design: The author showed very clear experiment design in figure 1.
Validity of the findings: The results for 24 weeks is clear. The conclusion would be stronger if longer time data can be available to serve as another data point
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: ANTI-ATHEROSCLEROTIC VACCINATION AGAINST PORPHYROMONAS GINGIVALIS AS A POTENTIAL COMPARATOR OF STATIN IN MICE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Unambiguous language is mostly used throughout the manuscript, through there are a few places that warrant revision:
- Line 50: "The vaccination was conducted by through...". Either delete the "by", or "through"
- Line 51: "Then, the half number of mice...". Can revise to: "Then, half the mice..."
- Line 122: "Saliva was obtained intraperitoneal...". Can revise to: "Salive was obtained by intraperitoneal..."
- Line 139: "...were subjected wester diet...". Can revise to: "...were subjected to western..."
- Line 144: "Then, the half number of mice...". Can revise to: "Then, half the number of mice..."
- Line 148: administrate can be revised to administered
- Line 228: "...p. gingivalis infection induced efficiently in collaboration with...". Can revise to: "...p. gingivalis was induced effectively by..."
- Line 233: "First, a small scale of animal experiments might affect the unclear difference...". Can revise to: "First, the small scale of the animal experiments might not provide conclusive..."
- Line 237: "wide-spreading" can be revised to "wide-spread"
- Line 243: "comparator" can be revised to "substitute"
Experimental design: Experiment is well designed, and research question is well defined, relevant and meaningful.
Validity of the findings: The result on the validation of vaccination is sound. The result and conclusion on the anti-artherosclerotic effect of vaccine, however, was not very strong. The largest factor is the result on WD+Pg. The first aorta has very large oil red staining, indicating large artherosclerotic plague, while the rest are very small. Without the result from the first aorta, the extent of plague from the rest of the aorta in the WD+Pg group will be small, and significance level of plague reduction from PTV or Pg vaccine group will be smaller. This limitation should be discussed in more detail in the discussion section.
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: ANTI-ATHEROSCLEROTIC VACCINATION AGAINST PORPHYROMONAS GINGIVALIS AS A POTENTIAL COMPARATOR OF STATIN IN MICE
Review round: 1
Reviewer: 3

Output:
Basic reporting: Peridontitis is a chronic infectious disease caused by Porphyromonas gingivalis and it acts as an independent risk factor for cardiovascular disease by triggering the formation of atherosclerotic plaques. Innate and adaptive immune response to bacterial heat shock proteins is suggested to promote the progression of atherosclerosis. Several mice studies used recombinant proteins from P. gingivalis for vaccination. Here, Ha et al., vaccinated by immunizing proteins of P. gingivalis post sonication with heating. Ha et al., used n=32 ApoE (-/-) mice in their study grouping them into four different treatment conditions for vaccination. Ha et al., for the first time looked at efficacy of vaccination in reducing atherosclerotic plaques in the presence or absence of pitavastatin (PTV), a statin that are known to prevent atherosclerosis by lowering lipids. Ha et al., determined the immune response to vaccination by measuring IgG and IgA levels by ELISA. They found significantly higher levels of IgG and IgA levels compared to controls indicating vaccination is fruitful. Ha et al., showed that atherosclerotic plaque size is reduced due to vaccination with or without PTV treatment. Ha et al., conclude that presence of PTV had no synergistic or additive effect on atheroprotective effect of vaccination. This is altogether a nice paper with carefully acquired data. It is well written, and it provides an evidence that vaccination by using sonicated P. gingivalis with heating had an atheroprotective effect that is comparable to PTV treatment.
Experimental design: It is a original work with research question well defined. Methods section described with sufficient detail.
Validity of the findings: Comments:
1.	The authors determined the HDL and LDL levels in all groups of animals in lipid analysis. I think it would be nice to plot the data and show it in the main figure and talk about why they don’t see any reduction in LDL levels in groups that are treated with vaccination in the presence or absence of PTV. For instance, in pitavastin treatment group, I expected the reduction of LDL-cholesterol level, but I don’t see any difference in their values compared to untreated animals fed with western diet. Good news is I see increase in HDL levels. The authors claim the vaccination is comparative to PTV treatment in reducing atherosclerotic plaques, but I don’t see any changes in both HDL and LDL cholesterol levels in groups vaccinated with P. gingivalis. So, they should discuss what could be the reason for reducing plaque area in vaccinated group in the presence or absence of PTV.
2.	It would also be nice if authors can measure the cytokine production and CD4+CD25+ Tregs cells and determine if they play a role in reducing atherosclerotic plaque area similar to Joo et al., 2020.
3.	In figure 2, please find a way to describe wd (western diet).
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: ANTI-ATHEROSCLEROTIC VACCINATION AGAINST PORPHYROMONAS GINGIVALIS AS A POTENTIAL COMPARATOR OF STATIN IN MICE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author has addressed comments
Experimental design: The comments was addressed by the author
Validity of the findings: The comment was addressed
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: ANTI-ATHEROSCLEROTIC VACCINATION AGAINST PORPHYROMONAS GINGIVALIS AS A POTENTIAL COMPARATOR OF STATIN IN MICE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Basic reporting is mostly clear and unambiguous. There are just a number of places that can benefit from grammatical corrections.
Experimental design: Experimental design is clear and well defined
Validity of the findings: My concerns have been addressed, and limitations are clearly written. Figure 3A seems to be missing. If the authors can add that, it will be great.
Additional comments: I think the paper is good to go with minor revision with the language and grammar.


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: ANTI-ATHEROSCLEROTIC VACCINATION AGAINST PORPHYROMONAS GINGIVALIS AS A POTENTIAL COMPARATOR OF STATIN IN MICE
Review round: 2
Reviewer: 3

Output:
Basic reporting: Ha et al., have addressed most of the concerns raised by the reviewers. It is also understandable that they couldn't perform few animal experiments because of COVID issues. I am happy with their manuscript for publication in peerJ.
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: CHARACTERISTICS OF CRANIOFACIAL MORPHOLOGY AND FACTORS AFFECTING THEM IN PATIENTS WITH ISOLATED CLEFT PALATE
Review round: 1
Reviewer: 1

Output:
Basic reporting: I commend the authors for their study. The manuscript is clearly written in professional, unambiguous language and highlights the variability of craniofacial morphology found in patients with isolated cleft palate.
I have listed a few items that require clarification in the experimental design section of this review (see below) which I feel if addressed will add strength to their paper
Experimental design: The selection of patients (36 females aged 5.36 years) requires some clarification. These children were selected over a 12 year period (approx. 3 per year) but there is no indication of what proportion of total population pool of children with ICP these selected children represent.

In addition it appears that all these girls required orthodontic intervention at 5.36 years of age (hence the need for a lateral cephalogram) This implies the sample chosen may not be representative of all the ICP population as some will not be of need for orthodontic intervention at this age.

The authors state in 141-143 that linear measurements were normalised based on UAFH and reference Yamanouchi -unfortunately I could access this reference (I suspect it is Japanese) but perhaps the authors could justify this approach - one would assume that the standardised ruler in the head positioning device on the lateral cephalostat would have enabled calibration of the lat cephalograms for all linear measurements

The authors also mention in the discussion (lines 253) that normalisation of the linear measurements was achieved by dividing the values with the anterior facial height (N-ANS), as this is a reliable measurements and remains considerably unaffected by age or growth’ - this may require further clarification as I am unsure why this was required if the linear measurements were taken from calibrated lateral cephalograms
Validity of the findings: The authors compare their lateral cephalometric findings to those of Japanese norms but it is unclear if these norms are for female at this age or whether the norms used were from combined male and female subjects
Additional comments: The authors should be congratulated in collecting the study sample, and for their cluster analysis. Clarification on sample selection and methods for calibrating the lat cephalogram linear measurements would strengthen this paper


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

Input:
Title: CHARACTERISTICS OF CRANIOFACIAL MORPHOLOGY AND FACTORS AFFECTING THEM IN PATIENTS WITH ISOLATED CLEFT PALATE
Review round: 1
Reviewer: 2

Output:
Basic reporting: I would like to thank the authors for a well written report. My suggestions are:

Introduction:
You reference Wardill and Furlow as most widely used techniques, but where and by who as these are not widely used in some countries at all
Experimental design: Suggestions:

Not clear if this a retrospecitve or prospective cohort study sample
Please explain Hellman's stage IIA for reader
Cephalogram taken on same machine to account for magnification factor?
Were the profilograms used gender specific in view of all female sample?
Figures 1 and 2 relate to Method but are not mentioned in that section
this particularly relates to method of clustering which needs clarifying
Does figure 1 need every point measured explaining?
Validity of the findings: Discussion

Suggest a section on strengths and weaknesses of the approach including gender bias, small sample, age related findings before growth complete but before intervention
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: CHARACTERISTICS OF CRANIOFACIAL MORPHOLOGY AND FACTORS AFFECTING THEM IN PATIENTS WITH ISOLATED CLEFT PALATE
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors have made a great effort in reporting their data in ICP patients. This is usually a smaller group in cleft patients and the majority craniofacial morphology is about cleft lip, cleft lip alveolus and UCLAP patients. It is interesting to see which clusters come from the analysis though I found it a difficult point of view in the beginning.

legends and tables ok. raw data shared.

the structure is sometimes confusing. The focus is not always related to the aim:
The fact that this study is about ICP should be “ sold” more. ICP and growth is first mentioned in line 99 of the introduction. That is a shame, as a reader I would like to see the importance and focus on ICP sooner. Some better focus in de the discussion would also help readability, because the focus on pierre robin is confusing. Isn’t it more logical to put line 291-296 (adapted) before the pierre robin explanation?
Experimental design: It is always a challenge to get numbers in cleft groups:Cleft palate patients appr 5y of age were taken and only girls were included, because the group of boys was too small. Do the authors expect a lot of difference in growth between boys and girls at that age? would the group be much bigger with boys included? Considering that 4 surgeons operated this group of patients, which may have an effect on the results
I unfortunately had no access to the Japanese growth study but I presume the mean numbers at the age of 5 were taken for only girls?
I found the cluster analysis difficult in the beginnen to understand and unfortunately could not access the study of Yamanouchi et al. is there a possibility for another reference?
Amount of surgeons were taken into account (maybe mention in discussion something about effect surgeon)
Measurement error: only for distances not angles.
Validity of the findings: It is nice that clusters could be found, yet the groups are rather small. Do the authors have confidence intervals next to p-value
Additional comments: please look at the structure of the article and how this is related to the findings. It will help to keep the reader focused on the aim and the results.
the problem of course is the smaller groups within the group and 4 surgeons, even though no difference was found. may be some extra explanation on this limit should be added in the discussion


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

Input:
Title: CHARACTERISTICS OF CRANIOFACIAL MORPHOLOGY AND FACTORS AFFECTING THEM IN PATIENTS WITH ISOLATED CLEFT PALATE
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Characteristics of craniofacial morphology and factors affecting them in patients with isolated cleft
palate (#52363-v1)
General comments:
Thank you for undertaking the changes previously recommended.
I am satisfied with these changes and suggest that this manuscript be accepted for publication with minor edits noted below:
Minor edits
The text which has been added on lines 136-160 – already appears within the Figure 1 legend and this duplicated text can be deleted from this section of the paper.
. N: nasion, the anterior-most point of the frontonasal suture; S: sella turcica, the estimated centre of the hypophyseal fossa; Or: orbitale, the deepest point on the infraorbital margin; Po: porion, the upper margin of the ear canal; Ba: basion, the anterior-most margin of the foramen magnum; Cd; condylion, the most supradorsal point of the condylar head; Ar: articulare, the intersection between the external contour of the cranial base and dorsal contour of the condylar head and neck; Ptm: pterygomaxillary fissure, the inferior point of the fissure; PNS: posterior nasal spine; ANS: anterior nasal spine; A: subspinale, the deepest point on the premaxilla between the ANS and prosthion in the midline; U1 (Is) and U1a : upper incisor constructed between the incisal tip of the anterior-most deciduous maxillary central incisor and its apex; Mo: mid-point of the deciduous maxillary second molar; L1 (Ii) and L1a: lower incisor constructed between the incisal tip of the most anterior deciduous mandibular central incisor and its apex; Pog: pogonion, the anterior-most point of the bony chin; B: supramentale, the posterior-most point in the concavity between the infradentale and Pog; Me: menton, the lowest point on the symphyseal shadow; Gn: gnathion, the point on the chin determined by bisecting the angle formed by the facial plane and mandibular plane; Go: gonion, the intersection between the ramus plane and the mandibular plane; A’: intersection of a perpendicular drawn from point A to the palatal plane; Ptm’: intersection of a perpendicular line from the Ptm to the palatal plane; Ms’: intersection of the perpendicular drawn from Mo to the palatal plane; U1 (Is): upper incisor constructed between the incisal tip of the most anteriorly placed deciduous maxillary central incisor; Is’: intersection of the perpendicular drawn from Is to the palatal plane; L1 (Ii): lower incisor constructed between the incisal tip of the most anteriorly placed deciduous mandibular central incisor; Ii’: intersection of the perpendicular drawn from Ii to the palatal plane; Mo: mid-point of the deciduous maxillary second molar; Ms’: intersection of the perpendicular drawn from Mo to the palatal plane; Mi’: intersection of the perpendicular drawn from Mo to the mandibular plane.
Line 172 currently states “…. size of the maxilla [point A-pterygomaxillary fissure (A’-Ptm’)], size of the mandible [condylion-gonion (Cd-Gn)],… “ the term ‘length’ would be a more appropriate descriptor of what has been measured than the term ‘size’.  …likewise on line 268
Line 220 currently states “…. exhibited a significantly larger Gn-Cd (mandibular length) and A-B plane angle than the standard…” the term ‘longer’ would be a more appropriate descriptor when referencing Gn-Cd (mandibular length) than the term ‘larger’.


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: CHARACTERISTICS OF CRANIOFACIAL MORPHOLOGY AND FACTORS AFFECTING THEM IN PATIENTS WITH ISOLATED CLEFT PALATE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Previous comments have ben dealt with satisfactorily
Experimental design: Previous comments have ben dealt with satisfactorily
Validity of the findings: Previous comments have ben dealt with satisfactorily
Additional comments: Previous comments have ben dealt with satisfactorily


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 AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript is clear and unambiguous and the literature reference is properly cited. The figures and tables are professionally generated.
Experimental design: This manuscript fits the Aims and Scope of the journal. The research question is clearly defined. Basically it stated how research fills the reported knowledge gap. The described Methods contained details to replicate.
Validity of the findings: The impact and novelty of this manuscript is limited. The data are statistically sound and the conclusions are stated.
Additional comments: In this study Jiang and colleagues investigated the pathogenesis the pregnancy-specific syndrome Preeclampsia (PE) through RNA sequencing. The authors carried out RNA-seq analysis of rRNA-depleted RNA samples derived from 20 patients and 20 normal wowen. Compared with the normal, the authors identified 151 differentially expressed circRNAs with 121 upregulated and 24 downregulated ones. Gene ontology analysis were performed and came out with several enriched biological processes and pathways in PE patients. Finally the authors constructed two ceRNA networks and found some either upregulated or downregulated miRNAs. The authors concluded their findings revealed the potential regulatory mechanisms of PE. Overall, the authors have done quite a lot of work, including both experimental and computational work. However, several issues are pending to be addressed.

1.	The results do not convincingly support the conclusion. That is, the authors claimed they revealed mechanisms of PE. How circRNAs/miRNAs identified in this study could facilitate the understanding of PE pathogenesis? It was not clearly mentioned in Results, nor in Discussion. The authors should provide more information regarding it.
2.	Line 87: the authors only described total RNA extraction, but how rRNA-depleted RNA was prepared was actually not mentioned, particularly this part was subtitled with rRNA-depleted RNA sequencing.
3.	Line106: the criteria for identifying differentially expressed circRNAs were p value threshold of 0.05 and fold change threshold equal to 2, but in line 139 they were said as adjusted p value < 0.05; fold change, > 2 or < 140 0.5. This inconsistency needed to be clarified.
4.	Line 110: ceRNA (competing endogenous RNA)，the full name of such abbreviation should be provided when it was firstly mentioned in the main text.


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 AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors identified differentially expressed circRNAs. A functional analysis of expressed circRNAs in patients with PE was performed using the Gene Ontology and KEGG databases. The authors determined the circRNA - microRNA (miRNA) interactions. Two networks were built, one containing positively and the other negatively regulated miRNAs.

No sources for 2020. Only references to the participation of circRNAs are provided without specifying the results of the cited literature. That is, the specific purpose of the study is not substantiated.
Experimental design: Results of using programs Miranda and Diana not provided. That is, there is no evidence of miRNA/circRNAs and mRNA interaction. The authors need to provide schemes for the interaction of miRNA with circRNAs and miRNA with mRNA with the application of quantitative characteristics.

The degree of suppression of expression and upregulation of circRNAs in the two groups of patients is radically different (Fig 4), which raises doubts.

The quality of the figures is poor.
Validity of the findings: There are no novelty in the manuscript. In general, the manuscript contains a set of little related results and their discussion. As a result, the conclusion does not contain the key regulatory mechanisms out of 268 (269) possible regulatory mechanisms.
Additional comments: The manuscript is not recommended 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: IDENTIFICATION AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 1
Reviewer: 3

Output:
Basic reporting: In the present manuscript, the authors identify 14,674 circRNAs in normal pregnant women and PE patients. They found the 151 differential expressed circRNAs, performed functional and pathway enrichment analysis of these circRNAs, predicted potential interactions, and constructed ceRNA networks. Additionally, they validated 7 circRNAs and their expression.

The manuscript is good with minor mistakes. Numbers should use scientific notation, repeated periods in line 199 and 252, repeated space in line 216, words with underscore 249 and 254, and so on.

The quality of the figures are poor, it is hard to get useful information from it, especially figure 2 and figure 4.
Experimental design: In the introduction, the author briefly introduced the circRNA roles in diseases and circRNA progress in PE several diseases. However, this part needs more detailed description. Besides, it is better to mention the progress of ncRNA in PE.

In the manuscript, the authors provided some details of their methods. I don’t understand why the authors use DESeq tool (usually use counts) to perform differential expression analysis, especially the expression of circRNAs is calculated by RPM algorithm.  The RPM algorithm is a normalized method which ignores transcript length, while the authors seem to have different ideas (line 98 to 99). Besides, please provide the version of CIRI.

The authors mentioned they constructed the circRNA-miRNA network based on the differentially expressed circRNAs and differentially expressed miRNAs. However, it seems no small RNA-seq in this project, how to get differentially expressed miRNAs?
Validity of the findings: no comment
Additional comments: In the Results, the authors should give the characterization of 14,674 identified circRNAs. Only comparing those circRNAs with circBase (not CircBase) can not visually display the characteristics of those 14,674 circRNAs, such as types, length, and distribution.


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 AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: This manuscript is clear and unambiguous.
Experimental design: The detailed information of rRNA depletion is still not provided.
Validity of the findings: Their findings are not very impressive. In particular, the mechanisms of PE is not well characterized.
Additional comments: The authors has partially addressed my concerns. However, the major concern in comment 1 is not clarified.


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 AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: All the comments I made to the authors were taken into account.


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 AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 2
Reviewer: 3

Output:
Basic reporting: The authors answered my prevous questions. But less improvement. the novelty is not high. The quality of the figures are still not good. and there are a number of lingustic mistakes. the references are not uniformed.
Experimental design: the authors listed a publications on ncRNA in PE. But less discussions of them comparing with this work. Again, the circRNA-miRNA network was based on the differentially expressed circRNAs and differentially expressed miRNAs. But without small RNA-seq, even not published, how can we believe the scitific correntness of your result?
Validity of the findings: NN
Additional comments: NN


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 AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The revisions look OK.


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 AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 3
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The conclusions are appropriately stated, connected to the original question investigated, and those supported by the results.


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 AND COMPARISON OF CIRCULAR RNAS IN PREECLAMPSIA
Review round: 3
Reviewer: 3

Output:
Basic reporting: the revision is fine. the quality of the figures are not good.
Experimental design: nn
Validity of the findings: nn
Additional comments: although the findings are not so significant and research originality is not high, the revision is acceptable for potential publication in PeerJ. the english and figures requires more improvement.


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: ELATOSTEMA QINZHOUENSE (URTICACEAE), A NEW SPECIES FROM LIMESTONE KARST IN GUANGXI, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	Basic reporting

The article is generally well written and the English is excellent. All together it is a very professionally prepared article. The text is self-contained with regard to presentation of background, observations, discussion and conclusions. The literature treatment is admirable. The reviewer will only make a few suggestions that may improve the text.

Abstract: The results are presented in a sequence that starts with information about the plastid genome. That is somehow surprising for the description of a new species that must initially have been identified – or suggested to be a new species - on the basis of morphological observations. In the abstract, the morphological information comes as the very last words in the abstract. The abstract would agree better with the main text of the paper if it mentioned morphological characters that initially supported the idea that the species was indeed a new species, and that this is followed by the information about the observations of the DNA. And then the abstract may conclude with information about the cytology and the phylogenetic analysis.

Introduction: In line 50 it is stated that Elatostema is one of two species-rich genera in the Urticaceae with succulent species … It would be useful if it was stated that the other must be Pilea.

In line 65-69 it is mentioned that there is a risk of over-description of new species in Elatostema. That is certainly true, and it is certainly also true that phylogenies based on DNA sequence data may help to identify closely related species. But it is not stated to what extent these phylogenies are now adequate to so to speak “weed out” over-described new species. See further under comments on the diagnosis in line 197-200 and the discussion in line 258-272.

The data deposit statements seem adequate, and the reviewer could address the plastid genome data.

In line 75-79 it is briefly described how the new species was discovered, but there is only a very short description of how it was realized that the population of sterile plants – once they flowered in the Guilin Botanical Garden – were identified as a new species and the detailed DNA sequence data was initiated. The text about the field study permits seems appropriate.

Materials & Methods: An important point about nomenclature, particularly new names published in entirely digital media, is to make sure that the digital repositories are permanent. Perhaps the relevant articles of the International Code of Nomenclature for algae, fungi and plants should be cited and the code itself referred to (https://www.iapt-taxon.org/nomen/main.php - Turland, N. J., Wiersema, J. H., Barrie, F. R., Greuter, W., Hawksworth, D. L., Herendeen, P. S., Knapp, S., Kusber, W.-H., Li, D.-Z., Marhold, K., May, T. W., McNeill, J., Monro, A. M., Prado, J., Price, M. J. & Smith, G. F. (eds.) 2018: International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Glashütten: Koeltz Botanical Books. DOI https://doi.org/10.12705/Code.2018). It is also relevant to point out whether the requests of recommendations under Article 29 are met with (Rec. 29A.2. Authors of electronic material should give preference to publications that are archived and curated, satisfying the following criteria as far as is practical (see also Rec. 29A.1): (a) The material should be placed in multiple trusted online digital repositories, e.g. an ISO-certified repository. (b) Digital repositories should be in more than one area of the world and preferably on different continents.)

Apart from this, the nomenclature seems to follow PeerJ s requirements for its new species policies, and – when the Diagnosis and Description are improved as suggested here – they will meet the requirements of the International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code).
Results / Diagnosis: It does indeed seem as the species described here is indeed new, although closely related to E. hezhouense. Line 197-200, and Discussion: Line 252-272. The morphological characters that are said to be distinctive when compared with E. hezhouense do seem small. It is stated under Materials & Methods, line 101-105 that the same criterial as with other taxonomic treatments are used. That seems all right, although the morphological characters separating the new species from E. hezhouense are apparently slight, but a short mentioning of phytogeographical facts, for example under Discussion: Line 252-272, would seem a usefull supplement. It does not seem that the subspecies concept is much used for very local Chinese taxa of Elatostema (whereas varieties are sometimes used). Could it not be worth to compare the geographical position and habitat in the localities where the new species and E. hezhouense are found? AS far as the reviewer could find out, the type locality of the new species and the type locality of E. hezhouense are more than 400 km apart. Of course, the new species can always be sunk to the level of subspecies later, should further studies suggest that this would be a suitable taxonomic conclusion.

Further about the Diagnosis (line 197-198): The wording of the diagnosis should be improved from “Most similar to Elatostema hezhouense from which it differs by the smaller leaf laminae (28-42 x 10-15 mm vs. 55-115 x 20-25 mm), …” to “Most similar to Elatostema hezhouense from which it differs by the smaller size of the major leaf laminae (28-45 x 10-15 mm vs. 55-115 x 20-25 mm), …” The current wording was not clear to the reviewer; it could superficially look as if the sizes referred to the size of the smaller laminae (in the description called “minor laminae”).

It added to the confusion that the size of the “minor laminae” are not described in the protologue of Elatostema hezhouense; are “minor laminae” not developed in Elatostema hezhouense? If so, that would add another diagnostic character? The “minor laminae” are easily seen in Fig. 4B and 4C of the new species, but “minor laminae” cannot be seen in the drawings of Elatostema hezhouense accompanying the protologue. – In addition, the width of the “major laminae” in the new species is indicated as 28-42 mm in the Diagnosis and in Table 4, but 28-45 mm in the Description.

In the Description (line 203) the text about stipules is not clear. It says: “Stipules solitary, interpetiolar, opposite the leaf at each node, …” But the “major laminae” and the “minor laminae” are not strictly opposite, so the stipules cannot be interpetiolar (meaning located between the petioles); the correct word must be intrapetiolar, which means placed in the axil between the leaf and the stem, and – if this is correct – the wording would be more clear if it is changed to: “Stipules solitary, intrapetiolar, in the leaf-axil at each node, …” The reviewer could not spot the stipules in Fig. 4.

Distribution and habitat (line 228-231): As mentioned above, it would improve the paper if the geographical positions and habitats of the new species and Elatostema hezhouense were compared.

The figures are all relevant and of adequate quality.
Experimental design: 2.	Experimental design

Strictly speaking, there is no experimental design in the paper, but the laboratory work seems to have be carried out with rigorous and careful investigations, and the methods are adequately described. The paper represents original primary research within the scope of PeerJ.

The research questions are well defined (but see the comments on several parts of the text, where it could seem as the morphological observations were used to test the DNA data, while the sequence of event would seem to have been the opposite).
A few additional comparisons of the localities and habitats of the new species and Elatostema hezhouense are proposed.

The methods are described in sufficient detail to allow replication of the study.
Validity of the findings: 3.	Validity of the findings
The findings all appear to be valid, but could in a few cases be supplemented with additional discussion (see Basic reporting).
All necessary data are well provided, but in a few places rewording of the presentation would be an improvement.
The conclusions are well stated.
Additional comments: No further comments. All is includes in 1. Basic reporting.


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: ELATOSTEMA QINZHOUENSE (URTICACEAE), A NEW SPECIES FROM LIMESTONE KARST IN GUANGXI, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well prepared in the text with sufficient literature and reasonable structure too. Some words should be modified so that the readers can get the meanings very clearly. Please see the highlighted words.
Experimental design: The methods are well designed and the original data is comprehensively analysed in the whole manuscript too.
Validity of the findings: The new finding of the new species can increase our knowledge about the biodiversity of the genus Elatostema. Authors apply integrated methods to elucidate the new taxa and its phylogenetic relationship, which provided a well understanding about the family of Urticaceae. However, the description about the morphological similarity and the close relationship should be careful because these are probably NOT so. Please see the annoted PDF file.
Additional comments: The manuscript about the new species of Elatostema qinzhouense was well prepared and the result is convincing too, on basis of the morphological and whole plastid genome evidences. But several minor doubts should be cleaned before publication (Pls see the reviewed PDF file).


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: ELATOSTEMA QINZHOUENSE (URTICACEAE), A NEW SPECIES FROM LIMESTONE KARST IN GUANGXI, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper by Longfei Fu et al. "Elatostema qinzhouense (Urticaceae), a new species from
limestone karst in Guangxi, China" contains the description of a new species in the genus Elatostema. Authors have done a thorough work besides the usual morphological description by including cytological and molecular data as well, all suggesting a well defined, different taxon. While the plant material on which the new taxon was described was collected outside protected areas and therefore collecting permits were not necessary,  the authors have fullfilled with the standard requirements in depositing vouchers in known herbaria and copies of the work in digital repositories.
I would like to ask the authors to add as an additional figure a good resolution image of the holotype (IBK00426150). Also, it would be useful to know the number of specimens on which the measurements depicted in Table 4 are based, to evaluate the robustness of the differences.
Experimental design: Morphological, molecular and cytological methods are correct. As expressed before, I would like to know the number of specimens on which the measurements have been done.
Validity of the findings: No comment
Additional comments: This is a very well done work and besides the two minimal observations I would suggest to accept it for publishing in PeerJ. My congratulations to the authors.


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: NEURAL NETWORK ANALYSIS OF CLINICAL VARIABLES PREDICTS ESCALATED CARE IN COVID-19 PATIENTS: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: -The structure of the article is completely inappropriate. The introduction should be written more appropriately.
-Related works is not provided in the introduction and be reviewed
-Descriptions of tables, pictures and diagrams should be given in the text, not in the caption.
-The quality of images and diagrams should be appropriate (at least 200 dpi).
-References should be written in journal format.
Experimental design: -The subject of the article is in the journal scope.
-Research has collected and used appropriate data and features.
-Research in the hospital and laboratory has been done well.
-The need for research in the field of the article is not well explained.
-Research on classification and the use of deep learning networks is very poor.
-Laboratory methods are well described.
-Describing and using deep learning is not appropriate at all.
-No explanation is given about the network used and how the network is configured.
Validity of the findings: -The innovation of the research is only in the use of new diagnostic features that have been well collected.
-Research in the use of deep learning lacks any innovation.
-Due to the lack of description of the deep learning network used, the presented results have no validity in the field of classification and should be reviewed in this regard.
-The results of the deep learning network are not robust.
-The results of laboratory findings are appropriate.
Additional comments: The data collected is very valuable and the research done in the laboratory is appropriate. On the other hand, the results presented in the deep learning classification are invalid due to the lack of explanation of the network configuration. It is necessary to apply the general corrections mentioned below in the article:
-The structure of the article is completely inappropriate. The introduction should be written more appropriately.
-Related works is not provided in the introduction and be reviewed.
-Avoid generalizations and the materials used should be explained realistically and in detail.
-Descriptions of tables, pictures and diagrams should be given in the text, not in the caption.
-The quality of images and diagrams should be appropriate (at least 200 dpi).
-References should be written in journal format.
-Robust deep learning network should be used.
-The deep learning network used should be described in detail and complete metrics provided.


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: NEURAL NETWORK ANALYSIS OF CLINICAL VARIABLES PREDICTS ESCALATED CARE IN COVID-19 PATIENTS: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The structure of the manuscript is messed up and the tables and figures are not well-designed and it is hard for the reader to understand them.
Experimental design: The implemented deep model is extremely week and basic and so the achieved results are not reliable.
Validity of the findings: Not enough metrics for validation have been mentioned. In a valid evaluation, we expect the authors to mention Accuracy; Specificity; Sensitivity, and F1 score.
Additional comments: This manuscript is constructed of few fully connected layers and does not include a novelty that worth publishing in this journal.
 The shared code shows the simplicity of their work. The model architecture clears this fact that the used model is the basic model of deep neural networks and has no innovation. The authors also did not mention enough metrics for evaluating their model like Accuracy; sensitivity or specificity.
For sure implementing a new deep neural network that is more advanced; will result in much higher accuracy than what the authors achieved.


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: NEURAL NETWORK ANALYSIS OF CLINICAL VARIABLES PREDICTS ESCALATED CARE IN COVID-19 PATIENTS: A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The corrections made are appropriate.
Experimental design: The description of the classification method used (neural network) has been improved.
Validity of the findings: With the approval of experts (authors of this article), research findings can be made available to researchers.
Additional comments: Thanks for the corrections. Valuable findings have been collected that can be used in other research by improving classifications and new features.


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: IMPROVING THE GNOMONIC APPROACH WITH THE GNOMONICM R-PACKAGE TO ESTIMATE NATURAL MORTALITY THROUGHOUT DIFFERENT LIFE STAGES
Review round: 1
Reviewer: 1

Output:
Basic reporting: see general comments
Experimental design: see general comments
Validity of the findings: see general comments
Additional comments: In this paper the authors present a package for R to estimate stage-dependent natural mortality (M) using the gnomonic approach developed by John Caddy. They present a simplified approach for estimation and compare the results obtained using the package to those obtained previously using other optimization methods. They also compare their results with stage dependent duration and M values for Pacific chub mackerel.

In general I found the paper to be reasonably well written, although it will require some native English language editing which I do not provide here. The description of the gnomonic approach is not entirely clear and I had to refer to the original articles by Caddy to understand the approach. This approach does not have wide use in fisheries science. While I realize that the present article is largely an application of previously published research, I question some of the validity of that research in my comments that follow as they affect the validity of the proposed R package.

First, while there is a clear benefit to modelling M as age or stage dependent, I question the benefits of trying to model both early life and adult mortality in one approach. Mortality during early life is known to be highly variable particularly for fecund marine taxa, on time scales that are much shorter (annual) than variation in MLF (e.g., Houde 1987). At best the gnomonic approach can provide an approximation of that mortality. That high variation is why the vast majority of stock assessment and ecosystem models model recruitment to a more advanced age (juvenile or later) where mortality is lower and less variable.

Second, the approach is presented as somehow different and perhaps advantageous over other estimators of M which are characterized by the authors as being variable and potentially biased. However, ultimately it uses the same information as many of those approaches, namely longevity. In that sense it differs only a little from estimators proposed based on life-history theory (Charnov) or empirical relationships based directly on longevity (e.g., Hoenig) or indirectly via asymptotic length and growth rate (e.g, Pauly, Ghislason et al., Then et al.).

Third, the authors assume, based on assumptions in a previous paper, that variability in stage-dependent M is driven entirely by variation in fecundity. This is simply not demonstrated. It is well known in demography that changes in mortality will affect longevity unless there is a compensatory response in survival among life stages. Thus to estimate variability in mortality using an estimator that is based in large part on longevity, one needs to consider variability in that parameter. Furthermore, it is also well known that egg and larval stage duration can be quite variable, particularly for many invertebrates with long pelagic stages. Based on the eqn on line 140 is seems that variation in delta1 is also very pertinent.

Fourth, notwithstanding the previous point, nothing shown previously or in this paper demonstrates that the gnomonic approach is a proper estimator of M. Yes, it appears to be able to capture stage/age dependent patterns to some extent, but there has been no extensive evaluation to demonstrate this across multiple taxa and to characterize the bias and variation involved. Caddy’s original work is largely based on theoretical examples, noting that the present author’s ability to reproduce those results only validates the calculation not the validity of the method for estimating M for wild populations. Certainly the data exist for more than just chub mackerel to undertake a proper evaluation of the method. However, even for that species it is clear from the results reported by the authors that the approach does not capture adult, sub-adult and juvenile mortality well (based on the tables biases range from 35-400%). Notably these are the stages for which knowledge and assumptions on M is absolutely critical for stock assessments; early life and juvenile mortality is generally subsumed into ‘recruitment variability’ in these models.

Fifth, the Monte Carlo simulations used by the authors to simulate variability in M are neither theoretically or empirically demonstrated as providing a proper simulation of sampling variability. It is therefore highly misleading to claim that the R package can produce proper confidence intervals on M; ie. that 19 times out of 20 the interval will contain the true M value. Simulated variability is fine to show sensitivity to input assumptions but creating confidence intervals creates an inherent expectation of credibility that is simply not supported.

Other comments:

Abstract – The gnomonic approach is not sufficiently well known to assume that the reader of the abstract will know what it is, nor does the name provide an intuitive idea of what it may represent. The authors should briefly define it.
	-Reader will not know what the proportionality constant and the proportion of overall natural death rate are.
-The acronym MLF is not defined.
-The sentence beginning on line 31 is complex and difficult to comprehend.  Amonst other things, the reference to a constant M isn’t clear and could likely be interpreted as constant in time rather than common across life stages.

L69 – This is a bit of a mischaracterization. Caddy proposes a method for estimating the stage-dependency of M, really as a discretization of a continuous size-dependent process. He does not claim to be estimating M itself.

L140 – I am not certain that I understand the equation, particularly why there is alpha plus one in the brackets. It seems to me that the right side of the equation should be delta1*alpha^(i-1)

L204-206 – This point is much overstated. As described in my comments above, there is no guarantee of applicability and performance. Also I do not see how this package can ‘provide a good understanding of the biological importance of M’; nothing presented here shows this regardless of the method used to estimate M.

L266+  It is not clear how the reader is meant to interpret the supplement.

L276 – what does ‘mainting some fixed parameters’ mean?

L305 – The statement ‘usually when  statistical models are simplified, there is an improvement in their performance’ is unsupported and strictly speaking not true. Parsimony is important, not mere simplicity.

Lines 408-410 – This is not an emergent result, the method is specifically designed to produce the highest values during early stages

Reference

Houde, E. 1987. Fish early life dynamics and recruitment variability. Am Fish Soc Symp 2: 1729


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: IMPROVING THE GNOMONIC APPROACH WITH THE GNOMONICM R-PACKAGE TO ESTIMATE NATURAL MORTALITY THROUGHOUT DIFFERENT LIFE STAGES
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment.
Additional comments: This paper simplifies the use of the gnomonic approach developed in a couple of papers by Caddy to estimate natural mortality (M). I must confess that I was not familiar with this approach to estimate M and therefore cannot comment too profoundly on its theoretical basis and its implicit and explicit assumptions. Nevertheless, I find the approach interesting and the current paper of value, especially for estimating M in short-lived marine organisms. The development of the R package to apply the method certainly adds to the value of the paper. I provide detailed comments below that the authors should address prior to final acceptance of the document. Briefly stated here, my main issues relate to: 1) some of the method’s assumptions; 2) the calculation of G and other computational issues; and 3) the inability of the reader to judge the model validation owing to the lack of simultaneous presentation of results from the current work and published papers.

Detailed comments (line numbers correspond to those in the Word version of the ms):

	Lines 112-114: how reasonable is the assumption that for the first gnomonic interval 〖(∆〗_1) the number of hatching eggs (initial population) is equivalent to the mean lifetime fecundity (MLF)?
	Lines 117-118: What about for life-bearing fish, such as sharks for example that give birth to fully formed pups? What would you consider the initial stage equivalent to “eggs” to be? Age-0s?
	Lines 118-119: MLF is inversely correlated with lifespan.
	Line 124: So the M is proportional to the life stage duration since the G is constant.
	Line 157: Shouldn’t the “n” superscript be “i” since the number of survivors will vary by life stage?
	Lines 160-162: what is the rationale for using 2? 1 male and 1 female?
	Line 163: so the G (constant proportion of M) is a function of the number of life stages and lifetime fecundity only. Unless I’m missing something I get a different value with the first example in the vignette (vignette=1.644; I get 14.459 with MLF=200000 and n=7)?
	Line 170: the n here refers to the number of iterations but it is also used for the number of gnomonic intervals, which is confusing.
	Lines 182-184: Note that the example in the R vignette for high and low fecundity has the same fecundity value. Change the LFM to 135 from 200000 for “model_lf”.
	Lines 231-232: in the very first example in the vignette where the duration of the second and fifth gnomonic intervals was set equal to 4 and 40 days respectively, the output of the model still estimated stage duration (at 2.8 and 37 days). Why?
	Lines 235-237: one can argue that longevity is more directly related to M than fecundity and it is often poorly known. It would be advisable to incorporate uncertainty in lifespan in the stochastic portion of the package.
	Lines 253:256: in the first example given in the vignette, the initial value given to the estimated proportionality constant (alpha) does not seem to affect results at all (I changed it from 2 to 3 and to 0.2 and results did not vary at all). So how important is it to correctly specify an initial value of this parameter, which is the only one estimated in the optimization? Also, how would one go about setting an initial value for this proportionality constant if none exists?
	Lines 264-266: I don’t see a comparison of the results obtained with this package and those from Caddy in the online vignettes referenced here.  According to Table 4 the results were identical except for the M stage 3 value varying in the second decimal.
	Lines 267-273: But Table S1 only shows results obtained with the package so we have to take the authors’ statements at face value. All the tables shown should include a comparison of values from the package and the original studies.
	Lines 286-290: I don’t understand what’s being conveyed here. I only see estimated time durations of the stages, not observed ones.
	Line 326: Most stock assessment models fix M because there is not enough information in the data to estimate it, even for data-rich stocks.
	Lines 347-349: In your examples stage duration is most often estimated. So be explicit in saying that egg state duration is a requirement, but the others are not.
	Lines 357-361: if increasing stage durations is a pre-requisite of the gnomonic approach then its application could be impaired in some cases, like for example  if it were to be applied to long-lived vertebrates such as sea turtles or sharks that may have a subadult stage  shorter than the large juvenile stage.  Discuss this potential limitation of the method.
	Lines 401-402: should be Tables 2 and 5.
	Lines 409-411: but this is dictated by the method itself since M is inversely proportional to the stage duration and the nominator in the equation in line 124 (G) is a constant.
	Line 424: again, it’s not possible to check if these statements are true because a comparison between results of the package and those from the original studies was not provided.
	Lines 429-431: Include the caveat here about long-lived species and the uncertainty in estimates of longevity. Of the species included for “model validation” the longest living one is the grouper with 20 years but the majority are short-lived invertebrates. A caveat should be given about the applicability of the method to long-lived species, especially given that the method assumes the main source of uncertainty in estimating M comes from fecundity, whereas lifespan is very important for many fish species for example, and is also highly uncertain.

Minor comments:

	Line 23: define MLF in abstract.
	Line 46: add “size” as well.
	Lines 55-59: Most of these methods estimate Z, from which F is estimated by subtracting an assumed M from Z.
	Line 245: bootstrapping or Monte Carlo simulation?
	Lines 256-257: I would express “to avoid the stagnation of the statistical optimizer” a bit differently. Something like “to prevent the algorithm to get stuck in local minima”.
	Line 331: independent variables.
	Lines 337 and 394: it’s “sensitivity”, not “sensibility”.
	Lines 337-340: rewrite as the meaning of this sentence is not clear.
	Lines 406-407: most methods shown in Table 6 for adults are based on a catch curve, not on empirical estimators.


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: IMPROVING THE GNOMONIC APPROACH WITH THE GNOMONICM R-PACKAGE TO ESTIMATE NATURAL MORTALITY THROUGHOUT DIFFERENT LIFE STAGES
Review round: 2
Reviewer: 1

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
Additional comments: N/A


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

Input:
Title: THE PHYSIOLOGICAL RESPONSE OF ECTOMYCORRHIZAL FUNGUS LEPISTA SORDIDA TO CD AND CU STRESS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please see my general comments for improvements.
Experimental design: Please see my general comments for improvements.
Validity of the findings: No comment.
Additional comments: I have reviewed this manuscript for its suitability for PeerJ.

The authors aimed to investigate the response of the ectomycorrhizal fungus Lepista sordida to Cd and Cu stress in pure culture.

Studies regarding growth and physiological indexes of L. sordida under Cd and Cu stress were used. However, the article is premature and needs significant additional input from the authors to be published in a journal like PeerJ, especially relative to the lack of experiments carried out to investigate the effects of this fungi (AMF) on the remediation potential in Cd or Cu-polluted soils. Furthermore, the authors should consider adding the quantification of non-enzymatic molecules with antioxidant function (and/or the activity of glutathione-related antioxidant enzymes), besides quantifying reactive oxygen species (such as hydrogen peroxide) to better characterize the antioxidant response and oxidative stress.

For these main reasons, I feel the submitted study now is not of sufficient quality to be published in this journal. Additionally, I provide the following comments for improving the manuscript:

1) In lines 30 to 32, heavy metal contamination was introduced. However, there are other heavy metals besides Cd and Cu. Therefore, I suggest the authors explain why they selected Cd and Cu for the present study. Furthermore, the authors should introduce and explain the importance of studying the toxicity of Cd and Cu stress.

2) Regarding the sentences ´´Mycorrhizal fungi not only can promote plant growth but also protect it against heavy metal stress`` (lines 35 and 36) and ´´Many species of fungi inhabit forest 37 ecosystems, and many can resist heavy metal stress` `(lines 36 and 37), I suggest the authors also provide citations of recent articles.

3)	Regarding ´´Relevant 50 studies have shown that ECMF can promote plant growth and enhance plant resistance to heavy 51 metals so that the host plant can grow better under severe stress`` (lines 49 to 51), I suggest the authors cite recent articles.

4)	In the introduction, the authors should provide more examples of studies focused on Cd and Cu stress (instead of addressing heavy metal in general), citing recent articles.

5)	Instead of writing about heavy metals in general, I suggest the authors rewrite the sentence: ´´ However, little is known about the role of antioxidant enzymes such as ascorbate peroxidase 55 (APX), catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) in reducing heavy 56 metal stress and resist reactive oxygen species (ROS) `` (lines 54 to 56), citing recent studies that evaluated the enzymatic antioxidant response to Cd and Cu stress. Furthermore, in addition to not being included in the list of references, the citations ´´ Grata˜ et al. 2005; Hou et al. 2007; 57 Zhang et al. 2007) `` are too old to write that ´´..little is known about the role of antioxidant enzymes ... ''.

6)	For the introduction, I suggest that the authors explain better on how this study can provide a basis for the bioremediation of heavy metal contaminated soil.

7)	Regarding introduction, the authors should provide the context, explain and better introduce the role of antioxidant enzymes related to this study. Since there are several molecules involved in modulating the Cd and Cu stress response besides antioxidante molecules, I suggest the authors to explain why antioxidant enzymes deserve special attention for the present research.

8)	For the introduction, I suggest the authors introduce oxidative stress induced by heavy metals (especially by Cd and Cu stress) and introduce reactive oxygen species

9)	Regarding introduction and discussion, the authors should explain the difference of the role of the antioxidant enzymes assessed in this study regarding their role in scavenging of reactive oxygen species citing articles.

10)	 I suggest the authors to provide scientific citation for the following sentence (or rewrite it):´´ Osmotic regulatory substances, including soluble sugar, soluble protein, free proline, and
 malondialdehyde (MDA) are membrane lipid peroxidation products, which can develop the  potential of lining cells and osmotic pressure in the cells after exposure to environmental stress`` (lines 58 to 60).

11)	Regarding methods, I suggest the authors provide information on how the activity of the antioxidant enzymes was calculated.

12)	 Regarding the following sentence, I suggest the authors replace the word ´´provoke`` with ´´study`` (or another one to improve the meaning of the sentence): ´´The activities of antioxidant enzymes in L. sordida were analyzed to provoke the response of anti-reactive oxygen capacity to Cd and Cu stress`` (lines 241 and 242).

13)	The discussion is too short. It should include more information including the role of antioxidant enzymes in the cell.

14)	The authors should be careful when it comes to figure captions. In figures 8, 9, 10 and 11, ´´under Cd stress`` was written for both ´´A`` and ´´B``. In Figure 7, the authors should provide information regarding ´´A`` and ´´B``.

15)	The authors should not italicize ´´an ectomycorrhiza`` (line 276) and ´´was observed `` (line 277).


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

Input:
Title: THE PHYSIOLOGICAL RESPONSE OF ECTOMYCORRHIZAL FUNGUS LEPISTA SORDIDA TO CD AND CU STRESS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper showed that the growth and physiological changes of Lepista sordida under different Cd and Cu concentrations in pure culture. By SEM, authors found that the mycelium twisted, broke, sticked together, and even dissolved under Cd and Cu stress. Also, authors indicated the response of Lepista sordida to the different Cd and Cu concentrations by analyzing antioxidant enzyme activities and osmotic adjustment substances. However, the study did not explain whether ECMF has metal tolerance, and why. Finally, the study only described some results without forming a confirm conclusion
Experimental design: Authors need to provide more species to build the more comprehensive evolutionary tree
Validity of the findings: 1. The introduction parts needs more information, such as why chose Zn and Cd as HM stress for this fungus.
2. Add more references to support the explanation of experimental results. The explanation for the inconsistency of the varied pattern of POD under Cd and Cu stress? Cu as a trace element?
Additional comments: The detailed comments are as follows.

1. The English language should be improved to ensure that the international audience can clearly understand your paper.
2. L74-75, ITS primers, wording style.
3. L75-76, Is it L or μL?
4. L115, 60009g? Is the statement correct?


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

Input:
Title: THE PHYSIOLOGICAL RESPONSE OF ECTOMYCORRHIZAL FUNGUS LEPISTA SORDIDA TO CD AND CU STRESS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Some format problems may be due to format conversion please check , for example Fig 3,4,5 and 6 explanatory text
Experimental design: no comment
Validity of the findings: no comment
Additional comments: It is recommended that the error line of the histogram should not be the same color as the column.


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

Input:
Title: THE PHYSIOLOGICAL RESPONSE OF ECTOMYCORRHIZAL FUNGUS LEPISTA SORDIDA TO CD AND CU STRESS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Reviewer’s comments:
The manuscript entitled "The Response of Ectomycorrhizal fungus Lepista sordida to Cd and Cu stress in Pure Culture (#55703)" has been submitted by Yin and Qi. This study aimed to investigate the effects of Cd and Cu exposure on growth and physiological indices of EMF Lepista sordida. However, in my opinion the work lacks novelty, as it merely confirms responses previously observed in many other EMF species. The findings of this manuscript are simple, insufficient and does not bring valuable information.

1.Title of the MS is quite inappropriate. Suggest change the title to “The physiological Response of Ectomycorrhizal fungus Lepista sordida to Cd and Cu stress”.

2.Line 117, It is not clear how to measure the dry weight of mycelia by SEM? please add the related details.

3.It is so easy to measure the levels of Cu and Cd in. Why not to determine metal concentration of mycelia.

4.For different analyses, authors used different time (10 d, 25 d). What was the reason for choosing two harvesting periods?

5.The caption of Figures 3, 4, 6 should be modified as the image, and more concise.

6.The legends of Fig. 8, 9 should be modified as the image

7.Check reference:I noticed few unnecessary abbreviation of author names there (Lines 60-63, 80,82)

8.This article doesn't concern the Proline in the plant tissues, please correct the sentence of Line 157.

9.In discussion section, the authors repeated some results again, but without any further discussion.

10.“when the concentration of Cu increased from 0.1 to 0.5 mmol L-1, the decrease in the colony diameter was not significant (Fig.4)”. However the mycelial dry weight under Cd stress was significantly different from that in the control group in Fig.7B, how to explain this difference?


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: TP53 MUTATION AND MET AMPLIFICATION IN CIRCULATING TUMOR DNA ANALYSIS PREDICT DISEASE PROGRESSION IN PATIENTS WITH ADVANCED GASTRIC CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study aimed to evaluate the mutational profile of circulating tumor DNA in 23 patients with advanced gastric cancer. For this, the authors used the massive sequencing of this material, in addition to evaluating 4 tumors. Furthermore, they used TCGA data to reveal the agreement between findings.
The authors present a concise and scientific writing, but I suggest a refined revision to find typing and punctuation errors, example “pane”, instead of “panel” and final points in the sentences.
In the introduction, I suggest that the authors expand the topic of epidemiology in the first paragraph, since according to the data shown, China accounts for approximately 68% of all cases of gastric tumors in the world. Are there population factors, such as dietary factors that may influence this percentage?
Table 1 - the authors need to provide the most detailed clinical data, such as stage, chemotherapy cycle. What did the authors consider for the tumor margin study? If necessary, provide as a supplement.
Line 146 – “We performed mutation detection on ctDNA in 23 AGC patients and identified the top 20 mutant genes 147 (Figure 2A)” The authors could provide a figure of the sequencing of the four cases analyzed.

Observation: Are the links to the raw data working?
Experimental design: The study is original and extremely relevant to precision medicine, however, some points in the experimental design have weaknesses that can be improved in their description.

Line 83 - “All patients received written informed consent for this study. The 4 paraffin-embedded (FFPE)...clinical characteristics of 27 AGC patients was also collected (Supplemental Material 1, Sheet 1 and 87 Sheet 2).”
The authors' proposed methodology is not clear. Did the authors intend to compare tissue with the corresponding ctDNA? Why for 5 (n = 28) cases, two collections were made and not for the others? Although this will only be revealed in the results, this information needs to be in methods.
Clinical characteristics of 27 cases are collected. It is not clear why a case was excluded. Wouldn't the data be from the 23 cases included in the study? That way, there would be 28 regardless of more collections.

Line 90 - “DNA from blood by QIAamp DNA Blood Mini Kit and DNA from FFPE tissues by GeneRead DNA FFPE Kit 91 (Qiagen, Hilden, Germany) were extracted according to the manufacturer’s instructions”.
Blood DNA? Or plasma DNA?

Line 99 – “The pane l used in paraffin-embedded (FFPE) tumor tissues was the coding sequence encompassing frequently mutated genes in solid tumors. The pane 2 applied in peripheral blood plasma samples from patients, were designed to cover 471 hot-spot mutations of 197 genes…” The choice of two different panels to compare biological specimens that are paired, seems to me a technical error. If the 450 genes are not covered by panel 2 of 471 genes, they are isolated studies, not comparisons. This given choice of experimental design needs to be better clarified.

Line 121 – “Then, we compared the obtained sequencing data with the genetic sequencing data of patients with advanced gastric cancer in TCGA”. Provide the number of TCGA cases analyzed. Place the number in figure 1.
Validity of the findings: The results of the study are well worked out, but need to be further detailed and explained.

Result
Line 141 - NGS sequencing analysis on paraffin-embedded (FFPE) tumor tissues of 4 dead AGC patients and ctDNA sequencing results of 23 AGC patients were included in Supplemental Material 3. The tumor tissues sequencing data of 4 dead AGC patients and the sequencing data of AGC in the TCGA database were compared taken intersection (Table 2).” Authors need to better describe these results. In the supplementary material 3 - sheet 3, the identification of the specimen type is only as tissue, there needs to be identification of which patient it is. Furthermore, the clinical characteristics of these cases need to be better detailed, what is their stage, what is the histological classification?
Table 2 is not clear the authors' proposal. The authors need to better describe these results, or make available what was done with the TCGA data in a supplement. Table 2 illustrates that the mutations found in three cases out of the four in the study, 10 mutations were coincident with those found in the TCGA, but how often?
Line 176 – “It could therefore be seen that MET amplification was specific in advanced gastric cancer” This statement is not correct. If there were two cases with MET amplification, there is no exclusivity. This is confirmed by the authors' own data: Line 180 - "In the analysis of ctDNA for our 23 plasma samples, Kapla-Meier analysis showed that patients with MET amplification also had shorter overall survival than these with MET without amplification (Figure 4C, P ＜ 0.001)". Of the 23 cases analyzed by the authors, how many had amplification and how many did not, for MET?

Discussion
Line 186 – “Liquid biopsy technology represented by ctDNA, not only can avoid these limitations, but also have been integrated into daily clinical practice [29]” Please rephrase the sentence, the liquid biopsy is not just represented by cfDNA.
Line 193 – “To the best of our knowledge, our present report is the first prospective study on the evaluation of ctDNA…” See the article, Int J Clin Exp Pathol. 2020; 13 (2): 203–211.
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: TP53 MUTATION AND MET AMPLIFICATION IN CIRCULATING TUMOR DNA ANALYSIS PREDICT DISEASE PROGRESSION IN PATIENTS WITH ADVANCED GASTRIC CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: The document is mostly clear, although some part of it could be benefited from a rewriting or rephrasing (as quoted in my comments; attached).

More literature in the introduction section is needed to cover basic aspects of the liquid biopsy and cfDNA early research and current research in the cancer reserach field (included in comments attached).

Some extra data should be needed as per my comments in the pdf document (attached).

The results are relevant to the hypotheses.
Experimental design: To my understanding the manuscript falls within the Aims and Scope of the journal.

The methods are not described with sufficient detail and information. This section requires major improvements, as is not well detailed (multiple comments in the pdf attached).
Patients and Samples have to be explained in more detail; data from database have to be explained in more detail; some technical and analytical aspects should be explained in more detail.

The research seems to have high technical standards, however the whole technical section should be better explained (materials and methods requires major improvements).

Research is easy to replicate, and they provide literature which validate their findings.
Validity of the findings: It is an important research, novel enough and with potential impact in its field; however, it has limitations (stated in the manuscript).

More data is required for a better understanding of the research conducted. And a more well detailed methods section is required for a better understanding of the statistical analysis.

Conclusions are related to original research question, but there are limitations (stated in the manuscript)
Additional comments: The introduction section requires a small background about the liquid biopsy and cfDNA/ctDNA application, citing the most important authors.
Materials and Methods section requires major improvements, with extra data and rewriting or rephrasing in some parts.
Please, find in the document attached all my comments.


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

Input:
Title: TP53 MUTATION AND MET AMPLIFICATION IN CIRCULATING TUMOR DNA ANALYSIS PREDICT DISEASE PROGRESSION IN PATIENTS WITH ADVANCED GASTRIC CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors made all corrections regarding grammatical and typographical errors.
They added new references throughout the text, especially in the introduction, making the manuscript more complete.
Suggestions for changes to the figures have been accepted and all are easy to view.
Experimental design: The authors made all corrections regarding my comments and suggestions. They excluded sentences and data that raised doubts about the study's methodology. After the corrections, the data became more technical and easier to interpret.
Validity of the findings: After all corrections and changes in the text, the manuscript is clear and more scientifically robust.
The methodology and statistics used are adequate.
Additional comments: Congratulations on your study and thanks for accepting the suggested changes.


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: TP53 MUTATION AND MET AMPLIFICATION IN CIRCULATING TUMOR DNA ANALYSIS PREDICT DISEASE PROGRESSION IN PATIENTS WITH ADVANCED GASTRIC CANCER
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been widely modified for the previous version, and in general terms is better now.
Introduction is well presented, highlighting the importance and interest of the study being carried, including multitude of literature reference that clearly back their research.
Multiple tables and figures have been introduced, making it easier to intrepret the manuscript and the data presented in it.
Experimental design: The experimental design is clearly stated and explained; however, there are major discrepancies regarding the amount of samples and the test run on some of the samples.
The major issue regarding samples is that it is mentioned in the manuscript that there are 23 patients, but 28 samples in total. For 5 of those 23 patients an extra blood sample was taken.
However, there are no information about those 5 patients, the extra blood sample, the time between the first and the second blood sample, the NGS analysis being carried over the 23 or the 28 total samples, ... Multiples discrepancies not resolved in the results section, and vaguely mentioned in the methods section.
Validity of the findings: Findings are interesting and surely match on the current need of finding new cancer biomarkers and progress into a more personalized medicine.
The amounnt of recent literature provided by the authors clearly showed that multiple efforts by different teams are being directed now to the identification of new and more effective cancer biomarkers in gastric cancer. This research fit within those efforts.
Conclusions and discussion were very clear.
Additional comments: No additional comments