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 EXPRESSION ANALYSIS OF XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) FAMILY IN GRAPEVINE (VITIS VINIFERA L.)
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.) The manuscript needs language improvisation to address issues like the following:
Line 46-47 “Grapevine (Vitis vinifera L.) as one of the most economically fruit crops is globally widespread cultivation (Zhu et al., 2019).”
Line 65-66 "The former hydrolyses β-1, 4 glycosidic bonds of xyloglucan to form the cleavage and connection of xyloglucan chains."
2.) The article provides sufficient background information on the existing problem as to why VvXTH family genes family identification and characterization can be important in stresses ad developmental stages.
3.) Article is properly supplemented with figures and tables.

Here are few additional comments for the abstract and introduction sections, that need to be taken care of:
Abstract:
1.	In order to avoid redundancy, eliminate "gene/genes" after XTH in abstract and text throughout.
Introduction:
1.	Line 46-47 “Grapevine (Vitis vinifera L.) as one of the most economically fruit crops is globally widespread cultivation (Zhu et al., 2019).” This is an awkward line and needs rephrasing.

2.	Line 48-51 “The growth of grapes in natural environment inevitably suffers from a series of abiotic pressures from salinity, drought and extreme temperatures, which changes the morphology of the plant, disrupts the biofilm system and causes oxidative damage, and ultimately affects the quality and yield of the fruit”.

3.	Please include citations for the information presented in the following lines:
Line 48-51“The growth of grapes in natural environment inevitably suffers from a series of abiotic pressures from salinity, drought and extreme temperatures, which changes the morphology of the plant, disrupts the biofilm system and causes oxidative damage, and ultimately affects the quality and yield of the fruit.”

4.	Line 77-81 “Further studies found that each enzyme activity was determined by        several structural characteristics. For example, in the protein structure of TmNXG1, loop2 is the key structure affecting hydrolysis and transglycosylase activity. PttXET16-34 has an important N-glycan structure, which is present in all group I/II members and absent in almost all III-A groups (such as TmNXG1).”

5.	Line 55 “Xyloglucan Endotransglucosylase/Hydrolase (XTH), a cell wall that modifies enzyme” is not clear. Did you mean XTH, a cell wall modifying enzyme?

6.	A statement clearly indicating the novelty of the study should be included in the Introduction section.
Experimental design: In the present manuscript, the authors have explored the genome of Vitis vinifera to identify XTH genes. Detailed bioinformatics analysis was conducted to study the characteristics like their chromosomal location, gene and protein structure, the subcellular location of proteins, phylogenetic classification.  The role of various cis-regulatory elements in the promoters well supports the regulatory roles in abiotic stress and development. Further, the authors have also conducted expression studies of the VvXTH family in drought and salt stresses and developmental stages.
The work has laid down the basic groundwork for future validations of these genes and their utilization in developing resistant/tolerant grapes.
Comments in the experimental design that need to be addressed:
1.	Line 122 “The single peptide (SP) was predicted by SignalP v4.1 server”. Single peptide/signal peptide?

2.	Proper references/citations for software/tools used to carry out various bioinformatics analyses of the XTH gene family are missing from the manuscript.

3.	Define an abbreviation at its first instance; thereafter, use the abbreviated form consistently throughout the text. For instance: in Line 68, At (Arabidopsis thaliana) should be defined.

4.	Line 149: “Gene structures were performed with the Gene Structure Display Server (GSDS:http://gsds.cbi.pku.edu.cn/) software”. The use of correct terminology is important in creating a good influence of the manuscript on the readers. “Performed” should be replaced with either analyzed or a suitable word.

5.	Computational prediction of Cis-regulatory element has very less reliability since most of the motifs are too short (4-6 bases) therefore random occurrence will be very high. I suggest confirmation with at least 2-3 prediction tools to reduce the errors/random occurrences. Or if the authors can prove the regulatory roles of a few selected Cis-elements through wet-lab experiments.

6. I suggest rewriting the Sub-heading "Organ-specific expression analysis of VvXTH gene family". As to how the gene expression was normalized is not clear.

6.	Line 276: “In addition, during the V, MR, and R periods, the VvXTH genes”. What do V, MR, and R periods stand for? Clearly explain?

7.	Why was qRT-PCR verification for VvXTH not carried out in different developmental stages?
Validity of the findings: 1. The authors in the manuscript have mentioned the amino-acid composition of motif 3 i.e “DEIDFEFLG”, which is a conserved motif. But there are certain substitutions across VvXTH protein sequences as shown in Fig: 4e. How can the authors justify this statement?

The authors have discussed most of their findings with relevant references supporting the results.
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: IDENTIFICATION AND EXPRESSION ANALYSIS OF XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) FAMILY IN GRAPEVINE (VITIS VINIFERA L.)
Review round: 1
Reviewer: 3

Output:
Basic reporting: The idea of the article is understandable, but unfortunately not in an easy way. Indee, the article is not simple to read in part because of the English language used in part for the grammatical errors.

The introduction section doesn't inclue the most recent works on the topic (see my comments in the text).

Some ideas of the introduction section seem to lack relevance (like the wide range of applications of the grapevine) or could be further described due to the relevance for the study (the assembly or assemblies used for this study for example) considering that is a genome-wide identification of a not yet characterized gene family in grapevine.

Figures are clear and the importance or use of each one could be boosted.
Experimental design: The workflow for the identification of the genes seems to be appropriate and is similar to others in the literature, but could be further explained without increasing too much the text extension.

The stress induction experiment seems to be properly designed, and covers the expression of the selected genes in a wide range of hours which gives information of a relatively short to mid-term response. Why were these hours selected and not others?

The connection of the two parts of the study (in silico and stress analysis) is quite subtle to me, therefore I suggest to improve this part mainly in the Results section.
Validity of the findings: Although the genome wide identification of XTH has been performed already in other species, is new for grapevine and therefore could be relevant considering the reasons stated in the same article to study the family (the response and effects in drought and salt stress.)
Additional comments: 1. In general the article is “readable” but in general requires a profound revision at the English language level  (Starting from the very first sentence in the Introduction section). I don't go into detail, but the article to me has to be completely revised by a fluent English Speaker.

2. Citations must be consistent with the structure in all the text (lines 100, 101 and 102).

3. References must be checked (how is the order of the Journal? In order of appearance with APA format?)

4. Further important points to have in mind (which I inserted also in the pdf file as comment)

-  Link to CRIBI website is out of use (and is not correctly cited)
-  Indicate version of the genome and annotation used (it's possible to understand that it’s the CRIBI v2 from table 1, but I think has to be mentioned)
- As a general comment: the procedure adopted to identiy and validate the gene/protein models coding for XTH proteins in the garpevien genome has to be better explain and supported. To me teh analysis done is not clear and validated.
- Some XTH sequences were discarded but the reasons are inconsistent and not clear and need to be better explained and supported
- The adopted method for qPCR data analysis is quite obsolete. Indeed the method proposed in the last 10 years of research in based on the method described by Hellemans et al., (Genome Biology 2007, 8:R19) which essentially takes in consideration a selection of the most stable genes for normalization (which has to be identified within the experiment) and the fact that each primer pair has its own efficiency which in the most of the cases doesn't correspond to 2.
-  Names of molecules and bound (b-1,3-glucans, b-1,3(4)-glucans, β-1,4 glycosidic bond) must be consistent between them.
- Is there a correspondence among phylogenetic ,co-expression  in different organs /tissues and cis-elements analysis which could support the idea of a specific co-regulation of specific members having evolved together? if it is the case, add a paragraph about it and discuss this important point.
-  Figures 5 and 7 could have been compared or tried to integrate (in a graphical way) as they refer (both) to gene expression.
-  The selection of genes could have been performed not in a random way, for example using gene co-expression network or similar (AggGCNs, VESPUCCI (Moretto et al., 2016, Frontiers in Plant Science 7: 633 and VTCdb databases (D. C. Wong et al. 2013)), etc), or comparing the behaviour of the orthologs in other species (the ones reported, i.e. tobacco, thale cress, rice, etc) to have a reference for the selection
-The discussion in general should be based on the revised results obtained after the suggestions given, focusing on the evidences base don which some selected members have been selected as putatively involved in abiotic stresses and therefore candidate to further functional characterization.


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 EXPRESSION ANALYSIS OF XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) FAMILY IN GRAPEVINE (VITIS VINIFERA L.)
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have revised and incorporated suggested changes to the manuscript.

I recommend the authors, to make corrections in the following places:
1.) Italicize the gene name.
2.) The word "gene" is to not be added when writing the gene name, for example, XTH and not XTH gene.
Experimental design: 1.) In the experimental section, the authors have not yet properly described as to how was gene normalization carried out.

2.) In the previous review, the authors were questioned, as to why the qPCR validation was not performed for developmental stages. The reason is still not clear.
Validity of the findings: Previously, authors were asked to review the amino-acid composition of a conserved motif, for which they have removed that line from the results section, and added a single line in the introduction supported with previous works.
I recommend that the authors should add a separate line in the manuscript about their own findings regarding the amino acid substitutions in their XTH proteins.
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: IDENTIFICATION AND EXPRESSION ANALYSIS OF XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) FAMILY IN GRAPEVINE (VITIS VINIFERA L.)
Review round: 2
Reviewer: 2

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


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

Input:
Title: EVALUATING A LINKAGE BETWEEN OBESITY AND THE OCCURRENCE OF DENTAL CARIES AMONG SCHOOL GOING CHILDREN IN SAKAKA, AL JOUF, KINGDOM OF SAUDI ARABIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: it was sufficient.
Experimental design: Poor design
Validity of the findings: weak
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: EVALUATING A LINKAGE BETWEEN OBESITY AND THE OCCURRENCE OF DENTAL CARIES AMONG SCHOOL GOING CHILDREN IN SAKAKA, AL JOUF, KINGDOM OF SAUDI ARABIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, I do not have any major comments, however few questions and suggestions i would like to mention.

1. Introduction: line 67-69 -  If obesity remains uncontrolled, it can lead to devastating health conditions such as high blood pressure, diabetes, stroke, and cardiovascular disease.  (Provide references here).

2.	Introduction: line 70-71- Studies have shown that obesity and dental caries have become common childhood diseases that are affecting the overall health and development of children(Wake et al. 2007). (You mentioned studies, therefore provide few more references here).
Experimental design: 3.	Methods: Please write full ethical approval reference number and name of the approval authority.

4.	Method: How do you manage the dmft/DMFT in mixed dentition which contains both deciduous and permanent teeth in different combinations? It seems that this study analyse the dmft and DMFT separately without considering the mixed dentition.

5.	The authors perform regression on DMFT (permanent dentition) alone. How about dmft (deciduous dentition)? The age of the recruited subjects and their number of deciduous/permanent teeth will have impacts on the result and analysis.

6.	The discussion seems elaborate and explaining all concerns related to the current evaluation. However, needed to cite few latest studies.
Validity of the findings: In this manuscript, the author ensures careful study planning, sample size and data analysis.
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: EVALUATING A LINKAGE BETWEEN OBESITY AND THE OCCURRENCE OF DENTAL CARIES AMONG SCHOOL GOING CHILDREN IN SAKAKA, AL JOUF, KINGDOM OF SAUDI ARABIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Accepted
Experimental design: Accepted
Validity of the findings: Accepted
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: EVALUATING A LINKAGE BETWEEN OBESITY AND THE OCCURRENCE OF DENTAL CARIES AMONG SCHOOL GOING CHILDREN IN SAKAKA, AL JOUF, KINGDOM OF SAUDI ARABIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Revised manuscript is now improved. I do not have further comments.
Experimental design: Revised manuscript is now improved. Raised concerns are answered and modifications are made in manuscript.
Validity of the findings: In this manuscript, the author ensures careful study planning, sample size and data analysis.
Additional comments: I congratulate authors for a very well executed study. The manuscript has been revised according to the suggestion and 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: ASSESSMENT OF JOB SATISFACTION, SELF-EFFICACY, AND THE LEVEL OF PROFESSIONAL BURNOUT OF PRIMARY AND SECONDARY SCHOOL TEACHERS IN POLAND DURING THE COVID-19 PANDEMIC
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors conducted a study on the assessment of job satisfaction, self-efficacy, and the level of professional burnout of Polish teachers during the COVID-19 pandemic. Congratulation to the authors to conduct this nice work. The manuscript has good potential and can be accepted after further revision. I have some observations that I think could help the author to improve the manuscript. I have attached my detailed comments in the attached PDF.

The author wrote the manuscript using clear and unambiguous English. I appreciated the author's effort. However, need a minor English language revision, in particular, grammar and punctuation check.

The author nicely wrote the literature review section and provided sufficient references to understand the subject.

The author provided raw data.

High-resolution image must be provided. All tables were good.

The author should give a clear explanation of the hypothesis with justification. I have explicitly commented on the attached PDF.
Experimental design: The article is original and within the scope of the journal.

Research questions were not separately well-defined. I must recommend adding them separately with sufficient justification. See details comment in the attached PDF.

The study designs and methodology are well explained and the different scales used are well exposed. Yet, need a minor revision which I commented on in the attached document.

The ethical standard was ok.
Validity of the findings: In the statistical section, the tests performed, bivariate correlations, as well as the appropriate analysis used, are correctly indicated. The statistical tool used in this study was robust.

The data was robust, statistically sound, and well-controlled.

In the results section, the data presented in the tables are easily understandable and represent the tests performed.

The discussion section was explained well.

The conclusion section needs a minor revision. See attached document.
Additional comments: The manuscript has good potential. However, it can be accepted after further revision.


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

Input:
Title: ASSESSMENT OF JOB SATISFACTION, SELF-EFFICACY, AND THE LEVEL OF PROFESSIONAL BURNOUT OF PRIMARY AND SECONDARY SCHOOL TEACHERS IN POLAND DURING THE COVID-19 PANDEMIC
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic reporting needs improvement (particularly reporting of results in texts and tables, and interpretation of results). Specific comments are provided in the attached manuscript file.
Discussion and conclusion should consider the research design- limitations of the cross-sectional study.
Manuscript also needs careful editing- I noticed typos here and there including in tables!
Experimental design: Clarify sampling and analysis. Comments on methods are provided in the manuscript.
Validity of the findings: Reporting of results needs improvement. Tables needs to be self-explanatory. Current tables are crowded because of unnecessary reporting and poor presentation. Do not write analyses methods in results section. Authors should check published articles in good quality journals to improve their reporting both in texts and tables. Specific comments are attached in the manuscript.
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: ASSESSMENT OF JOB SATISFACTION, SELF-EFFICACY, AND THE LEVEL OF PROFESSIONAL BURNOUT OF PRIMARY AND SECONDARY SCHOOL TEACHERS IN POLAND DURING THE COVID-19 PANDEMIC
Review round: 1
Reviewer: 3

Output:
Basic reporting: In my opinion Authors should  describe how teachers worked, only remotely or also  at school, how many hours a day etc.? If remotely, whether  there were any  problems with a conflict of interest among other family members, including access to a computer. These are factors that could be affecting job satisfaction etc.
Experimental design: I have remarks to the study design. Authors wrote that participants were randomly selected. But we don't know how many schools there are in the region and how many teachers are working in these schools. What percentage of them were randomly selected. Authors didn't explain why data from 412, not 456  teachers (as was indicated in Abstract) were analysed. It is not clear how the survey was performed, it was on-line, internet survey or paper questionnaires? Only in  the line 160, in the descrption of AVEM  Authors  wrote: "A computer program is used for the test" if does it mean that all questionnaires were computer-based? It should be explained in the text
In the lines 131-135 Authors should number questions, because in the line 224 they refer to points that did not occur before in the text: " Group 2 is the group with average satisfaction for questions 1,3,4,5...."
Results displayed in the Table 1 should be shortly disscussed in the text

In the line 198 Authors mentioned about BMI but in further part of manuscript I didn't find information about BMI
Validity of the findings: Findings are interesting and important becasue as far as I know it is a first paper devoted the teachers' well-being during COVID-19 pandemic in Poland and one of the few in the world. However because  the study group covered only one region (which the Authors emphasized in Limitations), they should not use the term Polish teachers in the text, because this term suggests that the results apply to the whole of Poland
Additional comments: Minor remarks
Disscussion
line 304-306 the content is repeated in the lines 306-308

Fig.1 - the meaning of the colors in the bottom line is not explained
Fig 2.  illegible, difficult to understand. Explanation should be placed under the Figure not in Supplement
Table 6 This table is unclear. What it is "Importance" What is the maximum value of Importance, from this table we only know that "Work experience" (23,1) has higher importance than "Sex" (7.5) but we don't know   if it has a big impact or a small one, we have no point of reference


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: ASSESSMENT OF JOB SATISFACTION, SELF-EFFICACY, AND THE LEVEL OF PROFESSIONAL BURNOUT OF PRIMARY AND SECONDARY SCHOOL TEACHERS IN POLAND DURING THE COVID-19 PANDEMIC
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors substantially improved the manuscript that satisfied all the requirements of basic reporting.
Experimental design: The authors substantially improved the manuscript that satisfied all the requirements of experimental design.
Validity of the findings: The authors substantially improved the manuscript where findings were well-validated.
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: ASSESSMENT OF JOB SATISFACTION, SELF-EFFICACY, AND THE LEVEL OF PROFESSIONAL BURNOUT OF PRIMARY AND SECONDARY SCHOOL TEACHERS IN POLAND DURING THE COVID-19 PANDEMIC
Review round: 2
Reviewer: 2

Output:
Basic reporting: This paper is interesting, well done, literature reference are well suited to the topic. The structure of manuscript is professional, according to the journal rules
Experimental design: Study design is correct, however there is  lack of  information on the living conditions of the teacher surveyed. I indicated this shortage of the study in my first review, but Authors didn't answer to this remark:...whether there were any problems with a conflict of interest among other family members, including access to a computer during remote work.
Validity of the findings: Findings are interesting and important because as far as I know it is a first paper devoted the teachers' well-being during COVID-19 pandemic in Poland and one of the few in the world.
Additional comments: Dear Authors thank you for your reply and changes made in the manuscript. Please find some suggestions in the text indicated as Comment or marked in yellow.


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 DNA METHYLATION LANDSCAPE OF FIVE PEDIATRIC-TUMOR TYPES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an interesting study that worth publication. The writing in clear, logical and easy to understand. Research questions were well defined. Methods and data descriptions had sufficient details. Overall, the analyses are technically and statistically sound.
Experimental design: Major concerns:

1) The authors calculated the average methylation for each gene (300 bp around TSS) first, then did the differential analysis. It makes more sense to do differential analysis at probe/CpG level first, then mapped the differential CpGs to genes.
2) During differential analyses (for example, comparing tumor to normal, or comparing different tumors), how the author handles confounding factors such as gender?
Validity of the findings: This is a meta-analysis project. All analyzed data (accession numbers) were provided. Conclusion are well stated.
Additional comments: Other minor problems:

•	Line 9 -10: “Methylation is an epigenetic process of regulating gene expression in which methyl groups are attached to DNA molecules, often in promoter regions”. Such definition of “DNA methylation” is not accurate, and have these problems: 1) in the context of this manuscript, the audience know “Methylation” was referring to “DNA methylation”(5mC), but there are other type of methylations including RNA methylation (m6A) and histone methylation. 2) the methyl groups are attached to the 5th C of the cytosine ring. In somatic cells, 5mC most occurs in the CpG dinucleotides, and CpG CpG dinucleotides form CpG islands (CGIs). Many CGIs are located in promoters, but not all of them.
•	Line 99-100: “We anticipated that many genes (such as tumor suppressor genes) would have consistently low methylation levels because those genes must be consistently expressed to properly regulate cellular division, growth, and other proliferation activities”. This is not always true, TP53 is a well-known tumor suppressor gene, but this gene is inactive or expressed at very low level in normal conditions.
•	Line 238-240: “Because oncogenes are typically expressed at relatively high levels and tumor suppressor genes are typically expressed at relatively low levels, we expected that oncogenes would have higher methylation levels than tumor suppressor genes.” I don’t’ understand the logic here, if you assume oncogenes are “HIGH” expressed, you should expect “LOW” methylation at the promoter.
•	Line 61: gene symbols should be in italics


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 DNA METHYLATION LANDSCAPE OF FIVE PEDIATRIC-TUMOR TYPES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper describes the process of collecting methylation data related to pediatric tumors and a set of normal samples. These samples were then analyzed to attempt to find genes which varied in methylation between the tumor and normal samples. The authors have also deposited all of their source code and the code appears to be well written and annotated. The paper is also well written and clear.

For the data presented in figure one, I’m wondering what the overall distribution of the gene-level methylation value looks like. I think you have two plotting options here, assuming you think this is a good recommendation. Option one would be two histograms showing the average methylation and another showing the CV values. Your other option would be a scatter plot of the average value vs CV (although you will probably have to use geom_hex with ~20000 data points). It would also be helpful to add a few lines to these plots to show where the categorization thresholds are.

Minor:

Typo line 38: “one type of genes” -> “one type of gene”
Typo line 40: “type of genes” -> “type of gene”
Experimental design: I suppose my largest problem with the entire design of this study is I don’t really think the samples you’ve gathered can be compared. Why would methylation data from fetuses through to 18 year olds from diverse tissues be comparable to unmatched tumor samples? I of course realize that there probably isn’t an ironclad great answer to this and you did somewhat address this by indicating that there weren’t dramatic differences in baseline data sets, but I’d like to see this examined more. Are all the genes in the high variance categories in Figure 1 showing significant differences between the normal data sets?

I’m also worried about using batch correction with the study ID as the batch correction factor. As far as I understand, the batch correction makes assumptions about the structure of the data that are only met when you have genuine repeats of an experimental setup, which you expect to show the same result. I think the diversity of these studies breaks that assumption. What does the methylation variance picture look like in the absence of batch correction? Specifically, if you do an analysis that is comparable to Figure 2 between the normal data sets, how many differences are you seeing?

If the other reviewer or editor don’t have a problem with combining these data sets without a deeper dive into differences in the normal data sets, then I’ll defer to their opinions.
Validity of the findings: No additional comments beyond those made in the experimental design 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: THE DNA METHYLATION LANDSCAPE OF FIVE PEDIATRIC-TUMOR TYPES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have responded to all of my concerns and I see no problem with publication. I'll second the cover letter comment that negative results should be a welcome part of the publication record. Sometimes it's more interesting to see that an idea that should work doesn't in the context of a given paper, but can hopefully inspire others to see if it can in new situations.
Experimental design: No comment
Validity of the findings: no comment
Additional comments: No comment


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

Input:
Title: GENOME-WIDE ANALYSIS OF THE STRIGOLACTONE BIOSYNTHETIC AND SIGNALING GENES IN GRAPEVINE AND THEIR RESPONSE TO SALT AND DROUGHT STRESSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The work adds more knowledge to the general understanding of grapevine strigolactone related genes under salt and drought stresses. I estimate that the paper can be recommended for publication in the PeerJ, after consideration of a few suggestions.

The authors need to consider doing a gene duplication events analysis of grapevine SL-related genes with Arabidopsis and rice, which could make the genome-wide analysis more informative.

Line 149-150：The TBtools software does not match the indexed literature (Krzywinski et al., 2009).
Experimental design: It is good designed.
Validity of the findings: The findings are interesting.
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: GENOME-WIDE ANALYSIS OF THE STRIGOLACTONE BIOSYNTHETIC AND SIGNALING GENES IN GRAPEVINE AND THEIR RESPONSE TO SALT AND DROUGHT STRESSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well written and thoroughly covered the literature. This a is a professional article with clear explanation of data.
Experimental design: The experimental design is well perceived.
Validity of the findings: The finding are novel and benefit to scientific community. The data is robust and statistically sound.
Additional comments: I have following comments to improve the quality of the manuscript:

1) Can the authors comment on why vvD27 showed increased expression at high salt concentration even after 12hrs (Fig 7), in contrast to other genes expression profiles (All other genes showed elevated expression until 6hrs and reduced expression after 6 hrs).

2) The authors annotated motifs of protein corresponding to a gene as motif1. motif2, motif3...etc. Instead, if the authors annotate these motifs based on their unique chemical or biological function, it would be more informative.

3) The authors demonstrated through phylogenetic analysis that The results showed that VvD27, VvCCD8 and VvMAX1 share higher homology with corresponding proteins in soybean. To better support the data, the authors should also provide expression profiles of soybean genes and compare with that of grapevine SL biosynthetic proteins (as shown figure 6).

4) It is not clear how the authors generated SL-related protein sequences from the genome data obtained from Grapevine Genome Browser? Also, did the authors perform BLAST analysis on nucleotide sequence or protein sequence?

Minor comments:

1) Line 90 need to be corrected as - "Recent studies have revealed that some SL biosynthetic and signaling genes play critical roles in abiotic stresses response."

2) Although the authors briefly described in line 63-66, it would be beneficial if the authors prepare an image depicting the Carotenoid pathway.

3) Line 63: Instead of using the word "Firstly", it would be better to use "Initially"

4) Line 47-49 is a broad statement, which require numerous citations. Please review the literature thoroughly and cite all relevant citations. For eg: https://www.pnas.org/cgi/doi/10.1073/pnas.1817233116


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: GENOME-WIDE ANALYSIS OF THE STRIGOLACTONE BIOSYNTHETIC AND SIGNALING GENES IN GRAPEVINE AND THEIR RESPONSE TO SALT AND DROUGHT STRESSES
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have responded to all of my concerns in an efficient manner. So, I don't have any further comments.


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

Input:
Title: A EUROPEAN GIANT: A LARGE SPINOSAURID (DINOSAURIA: THEROPODA) FROM THE VECTIS FORMATION (WEALDEN GROUP, EARLY CRETACEOUS), UK
Review round: 1
Reviewer: 1

Output:
Basic reporting: no special comments - see below for general comments
Experimental design: no special comments - see below for general comments
Validity of the findings: no special comments - see below for general comments
Additional comments: I found the paper of interest and a useful addition to our knowledge of European theropods, and have generally few comments. Most of my comments and corrections have been added directly on the annotated manuscript file, which is attached.
A few points of note:

I think the structure of the manuscript would need some improvements. It would be useful to have the descriptions of the material prior to the comments on its theropod and spinosaurid affinitities and the results of the phylogenetic analysis, as knowledge of the morphology is needed to understand these sections. As no new taxon is described, I also don't think that a formal "Systematic Palaeontology" section is needed; however, if you opt to keep it, please place it before the descriptions. Likewise, the comments on the preservation of the remains seems somewhat out of place; I would suggest to move this section to follow the geological setting or the overview of the materials.

Whereas I agree that the anterior dorsal, sacral and caudal vertebrae most probably belong to the same individual, I am skeptical about IWCMS 2018.30.4. This seems much to small to represent the same individual, and what is preserved of the vertebral centrum rather reminds me of ornithopod caudals.

In the phylogenetic analysis, some aspects remain somewhat unclear. First, you state that the analysis had 41 OTUs scored for 1810 characters - are all of these characters parsimony informative for your 41 OTUs? Based on the fact that the shortest trees have only 2451 steps, I think that this is highly unlikely. If you have a high amount of uninformative characters, mentioning of consistency indices does not make much sense, as these will be boostered by uninformative characters. You also mention that these are 1810 binary characters - are there really no multistate characters among such a high number of characters? Although you applied the iterPCR method, it also remains unclear if you computed a reduced conse´nsus tree and what the topology of that is - only an agreement subtree and the identification of problematic taxa is mentioned. Finally, I am somewhat uncertain why you used jackknifing results to state that spinosaurine relationships are not found under this option. As with bootstrapping or Bremer support, jackknifing is simply a method to evaluate robustness of results, but they do not represent an independent test of phylogenetic relationships. Given the extremely fragmentary nature of this specimen (and many other megalosauroids and spinosaurids in general, for that matter), very low robustness of the results is expected.


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

Input:
Title: A EUROPEAN GIANT: A LARGE SPINOSAURID (DINOSAURIA: THEROPODA) FROM THE VECTIS FORMATION (WEALDEN GROUP, EARLY CRETACEOUS), UK
Review round: 1
Reviewer: 2

Output:
Basic reporting: The text is clear, and the work is well-structured.
The figures are relevant, have good quality, are correctly labeled, and well described.
The conclusions are well stated and supported by the results of the performed analysis.
The literature references are adequate, and an update background was provided.
Experimental design: The authors describe an interesting set of osteological remains that increases the fossil record of dinosaurs known in the upper Barremian-lower Apian levels of the Wealden Group. These materials are interpreted as belonging to a giant spinosaurid, which would be the first evidence of this clade in the Vectis Formation and the youngest British record of these theropods.
The methods were described with sufficient detail so the analysis can be replicate.
Validity of the findings: The conclusions are well stated and limited to supporting results. However, there are two questions that, in my opinion, needs more detailed discussion:
(1)	The authors interpreted all the remains as belonging to the same individual, but the materials were found on the foreshore and collected over a period of several months. The authors said that taphonomic and anatomical evidence show that they belong to a single individual, but do not explicit which data, beside possibly the large size and the putative taxonomic affinity, support this interpretation. I think that this question deserves some more detailed discussion in order to demonstrate that all the elements belong to the same individual.
(2)	Please describe a little more detailed the preservation of the sacral centra. From the images it seems that both vertebrae preserve the articular surfaces, and it is curious the fusion of only two vertebrae in the sacrum of such a large-sized individual. How do you interpret this element? Are the vertebrae incomplete and the original articular surfaces are missing?
Additional comments: Beside these questions I would suggest that the authors add a brief description of the studied material in the Material & Methods section.
L. 310. Please eliminate the repetition “ The robust centra are robust…”
L. 492. What are the rib fragments that you mention? IWCMS 2018.30.7 and 8 (Rib fragments). This specimens are both fragments of an ilium, is that 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: POLLINATOR IDENTITY AND BEHAVIOR AFFECT POLLINATION IN KIWIFRUIT (ACTINIDIA CHINENSIS PLANCH.)
Review round: 1
Reviewer: 1

Output:
Basic reporting: I commend the authors for the effort of putting together a collection of experiments on kiwifruit pollinators conducted in New Zealand in the last years. However, the different designs, methodology, sites and cultivars in which the experiments were conducted, and the small sample sizes in some cases make it difficult to obtain robust conclusions from this research.

One interesting point is the visit of non-honeybee pollinators in the 24h study. And I will put it as one of the most important of these studies.

Another one interesting point is the quantity of grey literature used in the discussion, and I encourage the authors to write a review paper on pollination of kiwifruit by insects using all this bibliography.
Experimental design: The exposition of methodology is not clear nor easy to follow, and some effort should be done for clarity. Methods should be re-structured according to the exposition of the objectives.

In some experiments you say the site name, sometimes not.

L149-150. ‘fully netted’. I do not understand well.

L164… Is it necessary to detail that some observations were recorded in a device instead of written on paper?
Validity of the findings: The conclusions are not very robust for the intrinsic limitations commented above.
Additional comments: Title: I cannot see clear the effect on pollination as the pollination service (fruit-set/seed-set, fruit size) was assessed in just one experiment (with honeybees).

I will re-structure introduction from general to particular points, starting with a) importance of pollination, b) importance of pollinator diversity, c) kiwifruit as dependent of insect pollination, d) what is known about diversity of pollinators and pollination service in kiwifruit (knowledge gaps), e) hypothesis/objectives. A weakness of the introduction is that there is not a hypothesis or a clearly-stated objective, and the necessity of this research is not strongly justified.

L94-98. You have not explained nothing about cultivars yet, so they should not appear as part of the objectives.

Some tables and figures are repetitive (showing the same results), e.g. Tab1& Fig2, Tab2&Fig7. One of them could be deleted.

Fig 6 could be also deleted as it does not show relevant information.

Fig 11 and 12 could be pooled in just one

Tables 1-3. Not all readers will know those insects by the scientific names. It would be useful to add Order and maybe Family.

L280. I could not find statistical results for handling time.

L283. Why despite? I would expect: more handling time, more pollen deposition

Discussion. Can you really talk about efficiency of pollinators without measures of pollination service? Could pollen deposition be seen as a measure of such service? More justification is needed

L385-387 (and Tab1). Maybe there are no significant differences (given to the Bonferroni adjustment??), but do you really think that Lasioglossum (mean: 1955) deposit the same number of pollen grains than B. hortorum (mean: 26381)?


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: POLLINATOR IDENTITY AND BEHAVIOR AFFECT POLLINATION IN KIWIFRUIT (ACTINIDIA CHINENSIS PLANCH.)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language used throughout the paper is clear, and unambiguous. The introduction and background showed the context well. Obviously, the literature cited in this paper were arranged well and are relevant to the central topic. The paper is structured well, and figures are relevant.
Experimental design: Research questions were well defined and listed. The investigation performed by the authors, were rigorous. The methods are standard. Methods in this paper was described with sufficient detail and information, except the ‘data analysis’ section was missing.
Validity of the findings: The conclusions in this paper are well stated, linked to original research question and limited to supporting results.
Additional comments: General comments
	In this paper entitled ‘Pollinator identity and behavior affect pollination in kiwifruit (Actinidia chinensis Planch.)’, the authors investigated pollinator efficacy of multiple insect faunas in a score of kiwifruit orchards. The background of this study was interesting and meaningful because kiwifruit is an insect-pollinated crop which is functionally dioecious, so finding out the real efficient pollinator would contribute to the production of this crop. Another significance of this study, is that this paper provided a direct and rigid evidence that kiwifruit is pollinated by insects rather than wind, as anecdotally reported previously. The major finding of this paper is clear and simple, that the authors found many insects other than honeybees performed similar efficacy (in the paper showed as single visit pollen deposition, SVD). This result is meaningful, though not surprising. If the authors could evaluate single visit pollen removal (SVR) in the future, they may find that bees would remove so much pollen from the flower but deposit so little pollen on stigmas, thus bees might not be as efficient as other observed insect pollinators if consider the ratio of deposition/removal. There is also a point that the authors may consider in future studies: the authors recommended to boost populations of Bombus species due to the SVD results showed in this paper, however, despite the ability of depositing similar number of pollen grains with honeybees, bumblebees are also very efficient in collecting pollen grains from flowers, thus reduce possible pollen dispersal of plants, resulting in a waste of male gametes of plants.
	Generally, the experiment has cost a lot of labor. The results and conclusions of this paper is clear and convincible. A big flaw is that the authors did not provide any information about their data analysis. Anyway, it’s proper for this paper to be published on this journal.
        While there are a few minor comments which may help to improve the quality of the manuscript if adopted:
L106 does this sentence mean there exist some ‘impossible’ situation? Is pollination studied in bad weather conditions in some cases?
L198 How were data analyzed? It’s not mentioned in the materials and methods section.
L344 The detail of data analysis is missing, so the occurrence of ‘GAMM’ is abrupt.


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: GENETIC DIVERSITY AND DEMOGRAPHY OF BUFO JAPONICUS AND B. TORRENTICOLA (AMPHIBIA: ANURA: BUFONIDAE) INFLUENCED BY THE QUATERNARY CLIMATE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The ms based on comprehensive samplings on two toads in Japan explored how the climate changes in the region in the past impacted the phylogeographic patterns of the toads. The english is clear. It included sufficinet background. Raw data are shared. And, they proved the hypotheses on diversification.
Experimental design: Eecept only using only one mtDNA marker, the research is meaningful, highlighting the influences by the miocene to pleistocene climate changes on phylogeogrphic profiles of toads in Japan. I have only one question: why you used HKY model for BSP, also with a constant rate?
Validity of the findings: Although they used only one mtDNA marker, the work attempted to supply robust evidences for their conclusions. of course, we are still doutful on the status of B. torrenticola and its closely related clades. Perhaps, in my opinion, in Clade B, there are three species, i.e., clades B1 and B2 represent different species, because they occupied different niche, enough genetic divergence and even no-found morphological differences or behavious divergence. For proving incomplete lineage sorting or gene flow, i think that it is important to using genomic data to detect the possible evens.
Additional comments: Please furhter improve english.


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: GENETIC DIVERSITY AND DEMOGRAPHY OF BUFO JAPONICUS AND B. TORRENTICOLA (AMPHIBIA: ANURA: BUFONIDAE) INFLUENCED BY THE QUATERNARY CLIMATE
Review round: 1
Reviewer: 2

Output:
Basic reporting: the manuscript is carefully prepared, with a clear and professional English. The literature cited is rich, both concerning the taxa treated and the methodology used. The structure of the manuscript is clear and useful. The choice of supplementary material well done and helpful.
The conclusions follow the given results.
Experimental design: The manuscrpt presents original research based on a well defined questions. It concerns the distribution in space of time of a group of toads that have specific adaptations and distribution patterns. The exploration of these patterns should give inside in  the present diversity.
Validity of the findings: The main issue of the manuscript is clearly supported by the data and well argumented.

My main concern goes to the taxonomic treatment of the two species involved.When reading the result section, the discrepancy between the phylogeny presented and the taxonomic interpretation of the Bufo taxa involved in the study seems evident. Then in the discussion section, the problem of the specific status of Bufo torrenticola  and a paraphylectic Bufo japonicus are accepted (but see Igawa et al. 2006). I understand that the morphological divergence is more important between Bufo torrenticola and the Bufo japonicus-lineages and that B. torrenticola has adapted to a new niche. Nevertheless, all published phylogenetic analyses show that B. torrenticola is within B. japonicus. This should be set in the discussion section.
Additional comments: As the results and conclusions of this manuscript are based on a rich material, well representing the treated taxa, and on the pertinent statistical analyses, I am in favor to accept this article. The authors might consider the taxonomic aspect I mentioned.


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: GENETIC DIVERSITY AND DEMOGRAPHY OF BUFO JAPONICUS AND B. TORRENTICOLA (AMPHIBIA: ANURA: BUFONIDAE) INFLUENCED BY THE QUATERNARY CLIMATE
Review round: 1
Reviewer: 3

Output:
Basic reporting: Fukutani et al. reconstructed the phylogeny, estimated the molecular dating, and analysed the demographic of Japanese Bufo from mitochondrial cytb to infer the Quaternary climate-change impact on the focal species. Additionally, the Ecological Niche Modelling data have been used to support the conclusions made from molecular phylogeography analyses. This finding, despite only be inferred from mitochondrial and spatial data, the conclusions can benefit the phylogeography studies of East Asian anurans in general, and the enriched and under-exposed anurans distributed on Japanese archipelago in particular. While the N taxa used for the molecular analyses are robust, and the analyses conducted in this study are adequate to support their conclusions. Despite so, I found the writing in the subtopic related to phylogeny, molecular dating and demographic analysis are not executed well. The scientific terms use such as are not clear, complicated and can be confusing.  The problem with clarity is the result of the writing quality itself rather than the data and figures representations. For instance, the phrasing of “identified old but monophyletic radiation” (L 233) is unclear. What does it means by old here, because monophyletic is referring to clade itself, and radiation attributes to the diversity of the clades across time. Another example, “We specified the possible phylogenetic boundaries” (L 236) is confusing and can be simplified to “We resolved the phylogeny of clades”.
Hence, I suggest a correction on clarity of words, and the use of common wordings may help the message to be conveyed to readers.
Another point, the descriptive results/numbers are almost absented in the demographic analysis. Besides that, I also found a problem with consistency from the content structure, from the abstract to results. For instance, the northernmost clades have been emphasised in the abstract. But the northernmost clades of Bufo was missing in the subtopic related to phylogeny in material and methods and it has been missing in the demographic analysis result. Please ensure the essential contents highlighted in abstract are emphasised again in material and methods and results.

Additionally, some rightful citations clearly were missing in the main text, both for taxonomy literatures to support some claims in introduction, and the figure citations in result section.

Please see my all suggestions for improvement relate to these matters in the annotated pdf.
Experimental design: The N taxa to reconstruct the datasets are robust, although the conclusions are heavily relying on cytb fragment, but I found the molecular analyses and ENM conducted in this study are adequate to support their conclusions about the Quaternary climate-change effects on Japanese Bufo phylogeography. No necessity to re-run any analysis or adding any new analysis. Rather, some missing information which are essential to readers such as the preparation of PCR reactions was missing from the main text.
Validity of the findings: The conclusions are heavily relying on cytb fragment, hence it can be the most weakness found in this paper. But I found the molecular analyses and ENM conducted in this study are adequate to support their conclusions about the Quaternary climate-change effects on Japanese Bufo phylogeography. No overclaim in findings, so the authors must clarify in the conclusion section that better approach and better type of data are really needed for future studies.
Additional comments: The general pattern of result is missing in each figure's description. An improvement in description is needed (especially on Fig. 3). Additional proofreading in general can elevate the quality of 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: GENETIC DIVERSITY AND DEMOGRAPHY OF BUFO JAPONICUS AND B. TORRENTICOLA (AMPHIBIA: ANURA: BUFONIDAE) INFLUENCED BY THE QUATERNARY CLIMATE
Review round: 2
Reviewer: 1

Output:
Basic reporting: Fukutani et al. have addressed most of the critical points required from the first round of revision. I noticed the tremendous improvements made by the authors at improving the clarity of contents, and adding the descriptive results when explaining the molecular divergence and past population dynamics results, as well as improving the general structure of the manuscript. The scentific rebuttal provided by the authors also were acceptable. To increase the clarity in scientific explanations, and for the last round of revision, I suggest the authors to revise the text in the manuscript based on the specific comments I pointed through the annotated pdf.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Improvement in the abstract and revision on the description of Figure 3 are needed for scientific clarity and also as a selling point for the manuscript.


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

Input:
Title: GROSS MOTOR COORDINATION AND THEIR RELATIONSHIP WITH BODY MASS AND PHYSICAL ACTIVITY LEVEL DURING GROWTH IN CHILDREN AGED 8–11 YEARS OLD: A LONGITUDINAL AND ALLOMETRIC APPROACH
Review round: 1
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: In the introduction, the importance of the study in terms of literature should be explained.
In the introduction, the hypotheses of the study should be emphasized.
In method section, Which sampling method was used in the creation of the sample group in the study. Please explain this.
“The age of the children from the birth date was calculated and subsequently rounded down values” please base it on scientific reference.
“Physical Activity Questionnaire”; Has the reliability of the scale been calculated for this study? It must be calculated. Detailed information should be given about the sub-dimensions and scoring of the scale.
Information about the research design should be given. It should be based on a scientific reference.
Detailed information on data collection should be given. When, where and by whom was the data collected? The reason for choosing the morning hours for the collection of measurements should be stated.
An explanation should be given about the time periods in which the measurements are made each year (October 2017 attended third, fourth, fifth, and sixth grade???). If necessary, the times of the measurements should be schematized in the study.
The sub-dimensions of the KTK battery should be explained in detail.
The discussion section is sufficient, but the use of more recent studies is important for the quality of the article. At the same time, the practical application section should be added.


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: GROSS MOTOR COORDINATION AND THEIR RELATIONSHIP WITH BODY MASS AND PHYSICAL ACTIVITY LEVEL DURING GROWTH IN CHILDREN AGED 8–11 YEARS OLD: A LONGITUDINAL AND ALLOMETRIC APPROACH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article presents clear professional English and the contents are unequivocally exposed. However, it requires some one-off fixes. For example:
lines 59 to 62 - "Barnett et al. (2016) suggesting that variables such as age, sex and weight status affect GMC while Queiroz et al. (2020) found a positive modulation and improvements (in addition to the Body mass index (BMI) in young belonging to a family with a high socio-economic-status family that allows greater possibilities to access in environmental contexts, sports facilities or sports clubs." Review the sentence, as there seems to be a word missing, as the idea is not understood.
line 67 - Do the authors want to refer to sex change?
line 70 - "timing and tempo structured". Didn't they mean structured time?
line 73 - "that, ipso facto,...", please review in English.
line 194 - "IBMI" is the first time these abbreviations appear, please write in full.
References are current and relevant to the topics presented. The structure of the article complies with the journal's instructions, as well as the structure of tables and figures. Data supporting the study has been shared.
Experimental design: The Study is relevant, original, and adequate to the objectives of the journal.
However, the objective of the research, as well as the problem, require further refinement and I even suggest reformulation. It is important to define the problem, in the sense of exposing what literature has not yet demonstrated. Subsequently, build the objective, to respond to this gap. The aim of the study was: "the aim of this study was focused on a longitudinal investigation (three consecutive years) of the GMC levels within the relationships between height and body mass using the allometric scaling analyzes in samples of children aged from 8 to 13 years ." To support this objective, we suggest the inclusion and/or develop some topics in the introduction: importance of body mass for the development of gross coordination; characterization of growth and motor development of these age groups. Additionally, it is suggested that physical activity be included in the objective, as it was a result that was evidenced.
Regarding the title, it was "Gross motor coordination during growth in children: a longitudinal and allometric approach". I suggest that it be reformulated and that it represents the main theme of the study, the relationship between body mass and physical activity in gross motor coordination in a certain period of time…

The investigation was rigorous, not least because the statistical method is considered one of the strengths of the article. Ethical procedures were applied as required.

The methods have been described in detail; however some explanations and suggestions are suggested:
- In the methodology, the dates range from 2017 to 2019. But the results go up to 2020 and do not present data from 2019! A brief explanation of this difference is suggested.
- If boys started the research, for example in the 6th year, after 3 years they are 15 years old… from the point of view of growth and maturation it becomes complicated, as they are already in the puberty phase. Please clarify this aspect.
- There is no reason for choosing this sample: children between 8 and 13 years old. And why not, in children between 3 and 7, who are at a fundamental stage in terms of motor development? Please, substantiate this question.
- In the characterization methodology, the BMI, which is a very subjective measure to be one of the main variables of the study and that characterizes growth, according to the title. However, in the results, in the discussion and in the conclusion, they always refer to body mass, namely fat mass and lean mass. I would like to point out that these measurements were not evaluated, but only height and body mass. Therefore, this topic has to characterize only the variables that were taken into account in the statistical analysis. Please review this part and reformulate the results and discussion accordingly.
Validity of the findings: The impact and novelty of the study were mentioned, however, they require some reformulation, according to what was exposed in the previous points.
All underlying data has been provided; they are robust, statistically sound, and controlled. However, the results indicate that this model defines the factors that best define body size/shape... but they did not measure these variables, such as perimeters, folds... for example to calculate morphology, as was done in the study by Dos Santos, 2018… keep this limitation in mind and do not make the result subjective
Regarding the discussion, it should be reformulated, considering the new reformulation of the title and objective of this study. It is also suggested that they only base the results according to the variables evaluated and not talk about fat mass and lean mass, as it was not applied. Review the entire topic, please.
Still in the discussion, the following explanation/suggestions are suggested:
- about the KTK instrument: could the data not be influenced by the “ceiling effect” of the KTK test? Something that has been demonstrated in the literature. I suggest introducing this topic into the discussion.
- line 237 to 239: This part does not have a link to the text. They are substantiating the children's PA has a positive influence with the GMC, but I suggest that you present the main result before discussing. In addition, Faigenbaum, 2020 is linking physical exercise, specifically a strength training program, and so far only physical activity has been talked about and related.
- lines 250 to 255: They are discussing and substantiating the KTK-3, but it is not the purpose of the study.
- lines 256 to 260: The influence of PA is little explored in the discussion. And it is an important result to be explored and discussed.
- lines 267 to 268: They suggest these ages, because they were the only ones that entered the study… But the previous ages? especially the ages included in the fundamental phase of the movement, according to Gallahue, 2013? Where do children learn FMS and work on motor competence? It would be more pertinent to mention that in this study it was at the lowest ages where motor coordination work is considered and not just between 8 and 10. They are suggesting a window of opportunity, but they did not study the previous ages!

Conclusions should be reformulated in accordance with the changes suggested above. Mainly the question of suggesting a window of opportunity to stimulate gross motor skills.
Additional comments: General comments
The purpose of this study was focused on a longitudinal investigation (three consecutive years) of the GMC levels within the relationships between height and body mass using the allometric scaling analyses in samples of children aged from 8 to 13 years. It is a very important study, adds important evidences for the literature and well-structured, so authors should be commended. However it is suggested to go deeper into the introduction, methodology and discussion, and to reformulate the title, objective and conclusion.


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

Input:
Title: GROSS MOTOR COORDINATION AND THEIR RELATIONSHIP WITH BODY MASS AND PHYSICAL ACTIVITY LEVEL DURING GROWTH IN CHILDREN AGED 8–11 YEARS OLD: A LONGITUDINAL AND ALLOMETRIC APPROACH
Review round: 1
Reviewer: 3

Output:
Basic reporting: Well structured article well structured.
Use of current references.
Experimental design: No comment.
Validity of the findings: No comment
Additional comments: The introduction should be restructured, especially the penultimate paragraph that presents information that should not be included in the introduction.
Procedures can be more detailed.
They could mention the limitations of the study.


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

Input:
Title: GROSS MOTOR COORDINATION AND THEIR RELATIONSHIP WITH BODY MASS AND PHYSICAL ACTIVITY LEVEL DURING GROWTH IN CHILDREN AGED 8–11 YEARS OLD: A LONGITUDINAL AND ALLOMETRIC APPROACH
Review round: 2
Reviewer: 1

Output:
Basic reporting: To me, I examined the revised file and rebuttal letter carefully.. Congratulations to the authours. They made big changes in the article.. Also, they made all corrections which I gave.. I think that the article is ready for publication..
Experimental design: To me, I examined the revised file and rebuttal letter carefully.. Congratulations to the authours. They made big changes in the article.. My revisions were related to improving the methods section.. Also, they made all corrections which I gave.. I think that the article is ready for publication..
Validity of the findings: To me, I examined the revised file and rebuttal letter carefully.. Congratulations to the authours. They made big changes in the article.. Also, they made all corrections which I gave.. I think that the article is ready for publication..
Additional comments: To me, I examined the revised file and rebuttal letter carefully.. Congratulations to the authours. They made big changes in the article.. Also, they made all corrections which I gave.. I think that the article is ready 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: GROSS MOTOR COORDINATION AND THEIR RELATIONSHIP WITH BODY MASS AND PHYSICAL ACTIVITY LEVEL DURING GROWTH IN CHILDREN AGED 8–11 YEARS OLD: A LONGITUDINAL AND ALLOMETRIC APPROACH
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The purpose of this study was aimed to explore the developmental changes in GMC during childhood, having controlled for the differences in children's body size and shape using a longitudinal, allometric scaling methodology. It is a very interesting study, adds important evidence well-structured and works well for its clearness, so authors should be commended. The main problems were resolved with manuscript reformulation, and I agree with all changes made to the article.


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

Input:
Title: A SEMI-AUTOMATIC THREE-DIMENSIONAL TECHNIQUE USING A REGIONALIZED FACIAL TEMPLATE ENABLES FACIAL GROWTH ASSESSMENT IN HEALTHY CHILDREN FROM 1.5 TO 5.0 YEARS OF AGE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The current work deals with a topic of interest for all clinicians working with aging young subjects. The manuscript is well written and provides original data concerning the growth of very young children which are not so studied due to many difficulties of the methodology used.
Experimental design: The methodology used is accurate, updated and reliable.
I would only suggest some changes to improve the paper as follows:
Introduction
•	Please complete the panoramic of the methodology available for anthropometric measurements of the face by citing direct 3D computerized digitizers.
•	At line 105 add a reference about the normative data already present in the literature.
Materials and methods
•	In data acquisition some additional info concerning the preparation of the child such as positioning, use of a hair tie, explanations, etc.. could be useful for eventual reproduction of the recording and/or for discussion of the limitation and further comparisons.
Results
•	Please specify which topological mesh errors were found, causing some images’ exclusion.
Discussion:
•	Please add a reference when discussing in landmark location and artifacts, see line 250. topological mesh errors were found, causing some images’ exclusion.
Validity of the findings: The system and the analyses here seem to be reliable and generate sound results that need further confirmation by means of future investigations in larger samples. Therefore, I think that the current manuscript could be considered for publication.
Additional comments: No additional comments


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

Input:
Title: A SEMI-AUTOMATIC THREE-DIMENSIONAL TECHNIQUE USING A REGIONALIZED FACIAL TEMPLATE ENABLES FACIAL GROWTH ASSESSMENT IN HEALTHY CHILDREN FROM 1.5 TO 5.0 YEARS OF AGE
Review round: 1
Reviewer: 2

Output:
Basic reporting: very interesting article, well written and excellently planned.
I suggest the following points:
1) better specify the definition of the analysis areas defined by the template and why defined in this way
2) propose reasons for the curious result of lower variability in the inter-operator repeatability test compared to intra-operator
3) propose solutions to automate even the first manual alignment. In previous studies, landmark alignment was used or less average distance of selected areas. ears?
J Prosthodont. 2014 Jul; 23 (5): 347-52.
Int Int J Oral Maxillofac Surg. 2012 Nov; 41 (11): 1344-9
4) correct citations in the text that are not always correctly formatted
5) I suggest the addition and discussion of the following recent publication, with a different purpose but with an overlapping methodology Children 2022, 9 (2), 187
Experimental design: no structural suggestions
Validity of the findings: ok
Additional comments: well done


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: GENOMIC INSIGHTS INTO LACTOBACILLUS GASSERI AND LACTOBACILLUS PARAGASSERI
Review round: 1
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: Most of the findings in this paper have already been described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633531/, in which it is shown that publicly available genomes of L. gasseri are divided into 2 distinct groups by ANI, and the strains belonging to one of the groups (later denoted as L. paragasseri in 2018) specifically have genes related to gassericin T production.


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: GENOMIC INSIGHTS INTO LACTOBACILLUS GASSERI AND LACTOBACILLUS PARAGASSERI
Review round: 1
Reviewer: 2

Output:
Basic reporting: In their manuscript, Ene and colleagues report on a comparative genomics study including 79 publicly available genomes for Lactobacillus gasseri and Lactobacillus paragasseri. The latter has been described only recently, and the current study proves that several L. gasseri strains described and sequenced before, need to be reclassified as L. paragasseri. This study is of interest for researchers in the fields were these species are relevant. In a wider view, this study shows the strength of genome sequencing, and most likely studies as this one will follow on other genera and species.
The manuscript is well written, though too compact for some aspects.
Experimental design: It is unclear whether the 79 genomes considered were reannotated in this study, using anvi’o, or that the authors have used the gene prediction and annotation as available in the public databases. The latter is not favorable, as one would rely on predictions and annotations most likely performed within a long period of time, thus relying on different information from public databases. Also, when using genome annotation information for a comparative genomics study, one need to be sure about the quality of the genome annotations, so one should take additional, expert steps beyond the automatic pipelines, to assure that the comparative genomics study starts from a high-quality data set. So the authors are asked to detail what they have done regarding genome annotation.

The authors have searched for secondary metabolites, and found multiple strains with gene clusters involved in the production of gassericin T and gassericin S. More detailed information might be useful to mention in the manuscript, for example the percentages identity and similarity at amino acid level, so not having it as supplemental information.
Validity of the findings: In line 240, the authors state that they did not find a candidate gene marker to distinguish between the two species. However, this seems in conflict with the results reported in line 142,  two gene are mentioned to be in present in L. paragasseri and not present in L. gasseri, namely one encoding a phosphatidylserine decarboxylase and one encoding a beta-galactosidase. Please comment on this apparent contradiction.
Additional comments: Minor/textual comments
line 147: paragasseri is not written in italic.


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: EXPLAINING DETECTION HETEROGENEITY WITH FINITE MIXTURE AND NON-EUCLIDEAN MOVEMENT IN SPATIALLY EXPLICIT CAPTURE-RECAPTURE MODELS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The paper “Explaining detection heterogeneity with finite mixture and non-Euclidean movement models” by Marrotte et al. is an analysis of finite mixture, non-mixture, and non-Euclidean distance (non-ED) models to address individual heterogeneity in detection rates of black bears in Ontario.  The paper is well written and clear and the analysis methods seem sound.   Below are my line-by-line comments followed by a summary.

L1.  Perhaps include something in the title to indicate that you are talking about spatially explicit CMR.
L18.  What do you mean by “recently”?  Do you mean that others have recently done this or that you have recently done this?  Please be more specific.
L28.  Wide CIs are not necessarily a bad thing if warranted.  Excessive individual heterogeneity or estimation issues could make the results unreliable but you would want to know that wouldn’t you?  The worst possible scenario is to have an erroneous estimate with narrow CIs.
L32.  The fact that there was no rhyme or reason for why certain resolutions were supported in one study and not in another is a possible red flag.  Sparse data could cause this.  After all, if you test enough covariates, something is going to be significant by chance alone (about 1 in 20 if alpha=0.05).
L33.  Yes, the finite mixture models are a black box and finicky.  However, the wide CIs (and I assume the high point estimates had wide CIs too) is not a good measure of model validity (unless of course they are ridiculously wide).  Wide CIs can be a warning that the point estimate should be approached with caution.
L53.  Prior exposure to sampling devices constitutes a behavioral effect (trap happy/shy) and is modeled differently from individual capture heterogeneity.  I would take that one out of the list.
L101.  Or that the features are similar for every animal.
L216.  The lake sentence seems out of place.
L227.  The sentence seems to refer to only 2 models not 3.  Please clarify.
L245.  Please provide a little more information in the text.  Readers should not have to read another paper to understand what you did.  Were these α2 parameters set by you or estimated from the data?
L263.  What do you mean by “let”?  Was this an option in the algorithm?
L289.  Do you mean water?
L313.  Finite mixtures account for more than just spatial variation.  Are all these covariates on g0 or on σ as well?
L320.  Did you scale the variables to facilitate convergence?  The distance variables can be troublesome if not scaled in some way.
L322.  Did you consider combining some of your study areas with similar habitat?  You could still analyze them as separate sessions in secr but you might allow for some parameter sharing across areas.  Home range sizes and capture probabilities likely do not vary much among your study areas with similar habitat.  The extra data and the sharing of parameters across study areas could really help refine your estimates.
L337.  Maybe this model is telling you not to rely too much on the estimate…
L374.  Troubling that an effect due to roads was not predictable.  Pooling across study areas could help.
L393.  Whereas the finite mixtures operate on other variables besides movement.  A good thing…
L394.  In total one of the largest ever, but the individual study areas were fairly small and that is the level that these estimates were derived.
L403.  Explain what you mean here by comparability.
L407.  Agreed; non-ED models seem very inconsistent.
L412.  Yes, but low precision can be a good thing if estimates really are imprecise.  Estimates that are deemed to be more precise than they really are can be more insidious.  Also, what about plots of various levels of pmix to identify multimodality (https://www.otago.ac.nz/density/pdfs/secr-finitemixtures.pdf)?
L413.  I do not understand this sentence.
L428.  Good point.
L445.  Do you mean run them all simultaneously with each study area a session?
L460.  What about random effect (intercept) approaches as have been developed for non-spatial data?  See White, G.C. and Cooch, E.G., 2017. Population abundance estimation with heterogeneous encounter probabilities using numerical integration. The Journal of Wildlife Management, 81(2), pp.322-336.
Table 2.  The table title does not seem to go with the table.
Table 3.  The difference in log likelihood does not seem very high for any of them.  This looks like a lot of trouble for little benefit compared with finite mixtures.
Figure 2.  Are the non-mixture models the null models or the non-ED models?

This is an important topic and this paper is a good start.  As you know, the spatially explicit estimators already absorb a lot of individual capture variation in CMR models due to the animal’s location on the trapping grid.  The non-ED models just refine the distance part of the detection function.  I always felt like the mixture models in a spatially explicit context were capturing something else.  With bears, there are always individuals that approach a hair trap but never go in.  This may have nothing to do with movement but, instead, relate to the innate behavior of individual bears.  Consequently, it makes sense to me that mixture models had higher N because non-ED models address only capture heterogeneity due to the location of the animal on the trapping grid.  I think that this (heterogeneity not related to movement) effect is probably heightened in bears because of their high intelligence (and individualism).  I like your suggestion to include movement data based on telemetry, but I think that you have overlooked opportunities for pooling data across individual study areas, at least some of them.  Perhaps you could combine data from some of your more similar study areas to help reduce the noise in your study because of estimation problems.  Then you might find more consistent relationships between non-ED variables and scale resolution.  I would want to see clear relationships between the 3 model types, scale resolution, and variables describing costs of travelling.  As it stands now, your study does not present much of a way forward.


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: EXPLAINING DETECTION HETEROGENEITY WITH FINITE MIXTURE AND NON-EUCLIDEAN MOVEMENT IN SPATIALLY EXPLICIT CAPTURE-RECAPTURE MODELS
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are several places where more description is necessary, outlined below in approximate order of importance.
L65 and L74: For the paragraphs starting on these lines, can you provide examples (rather than just citations) of studies that came to these conclusions and support your statements? The first of these 2 paragraphs could also be fleshed out more, or these two could be combined.
L93: Do you mean within SCR frameworks, or independent of whether it is SCR/CR?. These two sentences about finite mixture is awkward within this SCR paragraph.
L137: Check grammar: “models fit was”
L145: Can you briefly describe that the expected sources of individual heterogeneity where?
L200: What was the range in spatial extent across your 51 study areas?
L322: How many samples were discarded due to too many mismatches or missing genotypes?
L342: Why did you expect that performance of non-Euclidean models would increase at finer resolutions? This wasn’t been explained.
L445: Define or provide examples of ‘multistrata’. This term has not been previously used.
Table 2 legend needs more detail to stand alone.
Table 3 legend: Summary statistics are “for” or “of”, not between
Figure 1 caption does not say directly that densities are shown, and does not define RSE. Is this all 51 locations? Why is there “deciduous” in the bottom right corner of the figure if there aren’t any bear densities shown south of that last dotted line?
Experimental design: L384: Study sites for non-Euclidean models need to be located relative to the hypothesized resistance covariate such that the pattern of detections are actually informative. Were there pairs of sites between which the resistance was high, and then also pairs of sites where the resistance was low?
L250: What is the range of observed movement covariates across studies and landscapes? Also, see comment above.
L217: The description of your model set is hard to follow. For example, you describe that you had 5 models all with sex as a covariate on detection and sigma and behavior on detection.  Then you go on to talk about 3 other models, but I do not know what differentiated those first 5 models. A table would be helpful.
L204: What does “two mixed loci” mean? More than three alleles at a locus?
L208: It is unclear when and which samples were discarded. Which sample of the mismatch pair did you discard, and was it the 6-11 mismatches threshold that was used to determine when a sample was ultimately kept or not?
L312: Provide the calculation for RSE.
L270, 281: How did you force/constrain an estimated parameter? I think you are referring to your log() transformation, in which case that line (L247) is better placed here.
L213: The term “integration mesh” is not common usage. Do you mean habitat mask or state-space? If you decide to continue using ‘integration mesh’, quickly define.
Validity of the findings: A landscape may not have extreme covariate values, but another reason for the lack of support for a movement covariate is sub-optimal trap placement. The methods did not describe this aspect of the sampling and therefore how powerful or appropriate the design was for non-Euclidean models, so it is difficult to assess these results. However, I do agree these more complex models require more recaptures and larger sample sizes.

Can you offer any explicit implications or repercussions for inference if a non-Euclidean model is used when it shouldn’t have been? Unrealistically large density estimates, impacts on RSE?
Additional comments: In this manuscript, the authors investigate the ability of non-Euclidean and finite mixture SCR models to improve on the basic SCR model by better accounting for heterogeneities induced by individuals and the landscape. They use a large dataset of over 50 black bear studies in Ontario. The concepts were generally well explained, and I have mainly only minor comments throughout the manuscripts about where clarification or more detail is needed. However, I do have two larger issues. The first is that they describe the non-Euclidean model as a way to account for detection heterogeneity, as evident in their title, but a more rigorous description is that it primarily serves to describe the pattern of movement and habitat use, which more accurately and precisely place activity centers on the landscape, and which also impacts the detection model. The authors never quite directly frame the problem as such and focus their discussion largely on detection. Secondly, the authors do not describe whether their study designs were appropriate for non-Euclidean models, and this was not addressed in the Discussion. The authors conclude that the more complex models are not always appropriate or possible to apply due to small sample sizes or weak landscape patterns (which I agree with), but failed to consider their sampling design. This lies at the crux of their conclusions. I believe that changes to the manuscript that address these and the other smaller points would improve the manuscript for publication in PeerJ.