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: METHODOLOGICAL RECOMMENDATIONS FOR ASSESSING SCLERACTINIAN AND OCTOCORAL RECRUITMENT TO SETTLEMENT TILES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript is well-written and I do not have much comment to add. I now agree that the revised manuscript is ready for acceptance.

Here are some minor problems and comments authors need to fix and consider.

Fig. 1; A scale bar is useful to understand spatial scale.

Fig. 3; Year should be displayed on bottom of each diagram.

Table 1 and 2 can be moved to supplementary.

I cannot see a good reason why R2 values need to be included in those analyses of deviance test tables. My understanding of R2 value is to show a degree of correlation between two factors of interest or to show a degree of estimation for a multivariable regression based on the best combination of factors of interest. In this study’s case, R2 seems to be calculated for the latter purpose, but why we need to know R2 value to show what?
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: NOVEL VISUAL ANALYTICS APPROACH FOR CHROMOSOME TERRITORY ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Generally the English is satisfactory, but there are several errors:
1) The abbreviation "CT" should be defined in the abstract.
2) Figure 3 is not referenced in the main text.
Experimental design: The coordinates in table 1 are either incorrect, or they need better explanation.
Validity of the findings: The manuscript describes a technical advance for visually interpreting the position of objects in 3D space, by dividing the space into 12 cones of sight.  The method is an incremental improvement over a previous method, and therefore is only somewhat novel.  Impact is limited, because the utilization of the method to generate results more easily than other methods has not been reported.  Although, application to chromosome territory analysis is significant, it is very likely that the method is too simple to deal with the complex shape of chromosomes.  Chromosome "painting" shows using 3D fluorescence microscopy that each chromosome is "blob like" and they are in full contact with each other.  However, at a high spatial resolution, the 3D picture is more complex with chromosomes more intertwined with each other.  It is unlikely that the proposed method can deal with such complex interactions.
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: NOVEL VISUAL ANALYTICS APPROACH FOR CHROMOSOME TERRITORY ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: The example chosen (3D Mouse Set), although cute, is inappropriate to appreciate the potentiality of the method. The authors should provide a more realistic example, if possible real data (as  example the ones of their previous paper:  https://doi.org/10.1371/journal.pone.0160303)
Validity of the findings: With the actual 'model dataset' is really difficult to test the validity of the findings and the potentiality of the method. I strongly suggest the authors to provide a more realistic model dataset and if possible to test their method on real data.
Additional comments: Line85: "The cone, as a solid block known from stereometry (solid geometry), cannot be described with the equation." Can the authors clarify this point? Why classical mathematical definition of three-dimensional conics is not appropriate? Maybe, here you refer to to CoS not cone?
Can the author discuss dependency of volume coverage to R? 12 is optimal independently of R?


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: NOVEL VISUAL ANALYTICS APPROACH FOR CHROMOSOME TERRITORY ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The explanation of figure 4 is unclear.  The set of lines, n1, n2, n3 etc are not labeled in the image, These lines (dashed) lines, which are tangential to the sphere cross at the origin.  They do not cross at P0.

Figure 10: a, b and c are not marked in the figure.

Do not use questions in the text.
Experimental design: The manuscript is much clearer than the original submission and it is now clear that the method, DPC12 provides more quantitative, more complete and in some cases avoids errors that would have occurred in standard 3D visualization.
Validity of the findings: The findings have been carefully validated and explained using a simulation of a mouse's head and ears, and using actual 3D image data about chromosome territories (CT) in rice nuclei.

The manuscript describes a novel method to extract quantitative information from 3D images.  This is the main value of the study.  The application to CT is a good choice and I am not too concerned that the authors have not applied their method to determine new biological results about CTs.
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: NOVEL VISUAL ANALYTICS APPROACH FOR CHROMOSOME TERRITORY ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: All fine.
Experimental design: All fine.
Validity of the findings: All fine.
Additional comments: The authors well reply to my points and improved the manuscript as required.


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: QUANTIFYING THE ASSOCIATION OF NATAL HOUSEHOLD WEALTH WITH WOMEN’S EARLY MARRIAGE IN NEPAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: In the introduction (line 87), the term “natal” or “natal household” should be defined first and if possible clarified by providing more general term with similar meaning to ease readers in understanding the whole meaning of the sentences the author wrote.
Experimental design: In the Statistical Method section (line 327), it would be better to present the equation of logistic regression model with random effect stated in line 340 and explain the main difference between this model with the ordinary one.
Validity of the findings: No comment
Additional comments: I hope I can read this paper in PeerJ soon.


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: QUANTIFYING THE ASSOCIATION OF NATAL HOUSEHOLD WEALTH WITH WOMEN’S EARLY MARRIAGE IN NEPAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: I have read the paper with great interest and found it interesting. Early marriage in this part of the world needs to be explored more and the authors did an excellent job overall. However, the paper requires some language editing. The authors should get the manuscript revised by someone who excels in English language for this purpose.
Experimental design: The quantitative experimental design is well organized and hypotheses were tested properly.
Validity of the findings: The findings ensure valid results, but the discussion section needs to be revised. It lacks sound references to compare and contrast implications for the findings.
Additional comments: Overall, it is a good attempt, but the authors need to ensure the language edits and a revision for the discussion section.


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: QUANTIFYING THE ASSOCIATION OF NATAL HOUSEHOLD WEALTH WITH WOMEN’S EARLY MARRIAGE IN NEPAL
Review round: 1
Reviewer: 3

Output:
Basic reporting: This article is well written and structured. The tables are sufficient and the authors note availability of raw data as a supplement. There are a few minor issues that need to be clarified as the meaning is not clear:

On line 109 the authors state:  “Attributing wealth to the correct household is crucial in this context, because it reflects not only the family’s socio-economic status but also its spatial niche”

I do not understand what the authors mean here by spatial niche.

I am surprised that there was little mention of dowry in the background considering how considerable dowry can be and presumably is connected to natal family wealth.  Perhaps the authors can comment on why dowry is not given much attention in the background.
Experimental design: My main issue with this paper is the sampling of married women who are pregnant. What do we miss with married women who are not pregnant? Might there be a relationship between pregnancy and education and thus only including pregnant women distorts the relationship between early marriage and education—women who are not pregnant might have continued education or delayed childbearing to achieve education or livelihood goals?  It would be helpful if the authors could add more justification for why this sample is appropriate to answer their main question(s) and consider how their results might change if their sample was married women (including those not pregnant).

Authors correctly point out that wealth typically measured in marital household but they do not mention that this may because it is difficult to measure natal wealth when girls are married and move to marital homes and this is where they are ‘found’ in child marriage studies.  The authors note on line 380 they excluded “17,335 women who were interviewed in their marital home”  --this represents the majority of women recruited into the study.  They also note “Questionnaires were administered orally to 25,090 married pregnant 239 women aged 10-49 years in the home that they were residing in during pregnancy (Saville et al., 240 2016).”   The supplemental table provided shows that these groups differ on a number of indicators that may be associated with the outcomes of interest.  How else may girls/women (or their natal families) differ when those girls/women are able and supported to return to their natal homes during pregnancy?

The authors acknowledge this issue on line 405: “Whilst these results show that women who went to their natal homes during pregnancy were different than those who stayed in their marital homes, they still represent an important sub group of women with rare data on the socio-economic characteristics of their natal homes.”
I think the authors need to justify this more as their results are not generalizable to women who remain in their marital homes during pregnancy, which likely represents the majority of women married as children globally.

The methods are adequately described and the research appears to be well conducted.

Ethics appear to be well thought through and adhered to.
Validity of the findings: The authors need to be careful not to use language that implies causality when their results only support an association. For example, in the conclusion the authors state:  “When assets are measured in the natal household in this population, there is no support for the conventional hypothesis that household poverty drives families to marry off their daughters early, but it does determine whether they go to school.”  -- this statement implies some causality but this study cannot measure causality.

Similarly, line 541: “Our results show that if we measure assets in the natal household, then we do not support the conventional hypothesis that household poverty directly drives families to marry off their daughters early.”
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: ZOLEDRONIC ACID PROMOTES OSTEOCLASTS FERROPTOSIS BY INHIBITING FBXO9-MEDIATED P53 UBIQUITINATION AND DEGRADATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: Qu et al. described in their manuscript that zoledronic acid facilitates osteoclast ferroptosis.  They concluded that this promoted osteoclast ferroptosis is caused by downregulation of FBXO9 expression in osteoclasts, so that FBXO9-mediated degradation of p53 is blocked. They claimed, “for the first time, we showed that ZA promotes the ferroptosis of osteoclast by increasing the protein stability of p53” (line 84-85). However, I am not convinced by the conclusion drawn by the authors because of following issues:
Major comments:
1.	This manuscript is not written in sound English.
2.	The authors need to make their writing precisely and clearly: the authors must provide precise information of materials (such as catalog number for the bone marrow cells from ATCC); the authors must replace “we found that ZA treatment suppressed (the) cell viability of osteoclasts” (in Abstract, and line 30-31, line 276-277) with “we confirmed…” as this is not their original finding; the authors should use science terms such as “osteoclasts” but not “osteoclasts cells”, etc.; the authors should provide the full name for any abbreviations used, such as the full name for FDA (fluorescein diacetate);
3.	The authors should avoid false information, such as “osteoclasts proliferation” in line 63. Osteoclast does not proliferate.
4.	The authors must provide evidence (e.g., osteoclast-specific marker staining) that osteoclast-like cells were successfully generated by them from both RAW264.7 cell line and the primary cells in vitro. Although cells used in this study were RANKL-treated, or RANKL plus M-CSF treated, I am not convinced that osteoclastogenesis was successfully induced. In other words, there is no evidence in this manuscript showing multinucleated cell formation. (Such as cells shown in Figure 4D).
5.	Even osteoclastogenesis was succussed, cells studied in this manuscript were a mixture of osteoclasts and mononucleated cells (pre-fusion osteoclasts), not osteoclasts as the authors described. There is no cell separation (separate multinucleated cells from mononucleated cells) performed in the study.
Minor comments:
1.	Names for all authors were marked with “1”. This mark should be removed because they are affiliated to a same institute.
2.	Instead of Hotmail and 163, better use academic email address (institutional address) as the corresponding author’s contact address.
3.	I assume that the authors used RANKL alone, and RANKL plus M-CSF (line 97-98) to turn RAW264.7 cells and BMDMs to osteoclasts in vitro, respectively. The authors should clarify this.
4.	Better combine those two paragraphs in line 91-101, because the two paragraphs all talked about in vitro osteoclastogenesis.
5.	Two approaches were used to determine cell viability. The two paragraphs in line 102-115 for this objective can be combined. “The cell viability” in the entire paper should be replaced with “cell viability”.
6.	The authors better describe their methods briefly, instead of simply saying “as the manufacturer’s instructions” (line 119, etc.)
7.	Move line 73-88 to Discussion.
8.	It is unclear at what differentiation stage that the cells were transfected by the pcDNA-FBXO9 or si-FBXO9 RNA.
9.	The RT-qPCR primer sequences for 18s should be provided.
10.	It should be described as cell number per well, not simply cell number (such as line 123: 5x100,000 should be 5x100,000/well; line 149: 1x100,000 should be 1x100,000/well).
11.	Line 150-151, “the concentration was quantified” should be “total protein concentration was quantified”.
12.	Exact amount of total cell lysates (reagents) should be used for the Western blot analysis (and other assays). “Approximately” in line 152 is improper.
13.	Buffer formulation for NP40 buffer (line 160) should be provided.
14.	Line 279-286 in the Discussion section sounds like Introduction.
15.	Figures are not fully discussed.
Experimental design: See in "Basic reporting".
Validity of the findings: See in "Basic reporting".
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: ZOLEDRONIC ACID PROMOTES OSTEOCLASTS FERROPTOSIS BY INHIBITING FBXO9-MEDIATED P53 UBIQUITINATION AND DEGRADATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: 1.It's better to test this mechanisms in in vivo or animal models to make this hypothesis more convincing.
2.in addition, authors should explain more specified about why ZA induced osteoclasts ferroptosis instead of apotosis or autophagy mechanisms.
3.Is FBXO9-related pathway lead to ferroptosis?
Validity of the findings: this study uncovered the important role of ferroptosis in ZA induced osteoclasts apotosis. these results will help to elucidate the mechanism of BRONJ. this study could be considered to be published.
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: ZOLEDRONIC ACID PROMOTES OSTEOCLASTS FERROPTOSIS BY INHIBITING FBXO9-MEDIATED P53 UBIQUITINATION AND DEGRADATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: In this study, the authors showed that ZOL induced osteoclast death through ferroptosis. For the stimulation of the ferroptosis, ZOL inhibited FBXO9 expressions, which facilitate the ubiquitination of p53.
In general, the manuscript writing is clear with proficient English. However, a few spelling and spacing should be thoroughly checked.
-	Introduction and references are proper.
-	Figures are relevant to the content.
Experimental design: The experiments were well-designed and conducted in order to prove the objective. A few points are needed to be revised before accepting.
Materials and methods
1.	Line 134 check the sentence ending
2.	Line 149 and 160 add more detail on what cell type used for the induction of osteoclasts
3.	Line 152 “Approximately 20 μg of l protein were separated….” Spelling check on protein
4.	Line 154 “the membranes were incubated with an-FBXO9…” the author change an-FBXO9 to anti-FBXO9
Validity of the findings: The article will add to the existing knowledge pool and could be applied for the future use.

I would suggest using SD instead of SEM for the statistical analysis.

Discussion
1.	The authors should add the clinical implication of this study in terms of treatment or management of BRONJ.
2.	What should be the future study?

Conclusion is too short.
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: SEROPREVALENCE AND LETHALITY BY SARS-COV-2 IN INDIGENOUS POPULATIONS OF LATIN AMERICA AND THE CARIBBEAN: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Comments:
In a manuscript titled  “Seroprevalence and lethality by SARS-CoV-2 in indigenous populations of Latin America and the Caribbean: A systematic review (#63932)”; since that COVID-19 is currently a global health threat and an international public health emergency, knowledge about seroprevalence and mortality of current emerging disease in indigenous and populous communities is important . Thus, topic is interesting. There are some points that I mentioned for author(s);
Abstract :
1-	In background section explained just about aim of study. Recommended that change the title of this section to objectives( if it is accordance with instruction of manuscript preparation of journal) or to complete using an additional line about background of your subject.

Method :

1-	What was your strategy for facing with grey literatures, such as government reports and non-peer reviewed manuscript? Did you include non-peer reviewed studies in your review? Please explain in your manuscript.

2-	What was your inclusion or exclusion criteria for selecting the under study population of articles? In other words, you reviewed the articles that just conducted on adolescents?  Or  general population (children and adolescents)? , please explain in your manuscript.
3-	Please define “ lethality”. Lethality means in-hospital mortality due to COVID-19?  Or cause- specific mortality due to COVID-19 in community?  Please define under study outcomes such as lethality and seroprevalence in your method .
4-	In “ search strategies and screening” section, how many researchers have participated in search process? is the search process done independently? Please explain in your manuscript.
5-	In “quality assessment” section, as mentioned “Two reviewers independently evaluated the quality of the studies “, if there was disagreement between reviewers about quality of an article, how did you resolve this disagreement? Please explain in your manuscript.
Results:
1-	In “study characteristics” section that is mentioned “The sample sizes of the indigenous populations varied from 15 to 41,855”. I think this sentence is about sample of COVID-19 patients for reporting the lethality. Therefore, It is better to mention that this population is referred to COVID-19 cases.
2-	Presentation of table 1 is ambiguous , it is recommended to;
•	Present the information of seroprevalence and lethality in two separate tables.
•	Present  information of age and sex in separate columns.
•	Please assign a number to each row (study).
•	About seroprvalence and lethality rate, please add columns to separate numerator and denominator of population that studied. For example , total number of patients with positivity of serology test (numerator) present in a column, total number of patients that studied (denominator)present  in another column and ratio of these values present in a 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: SEROPREVALENCE AND LETHALITY BY SARS-COV-2 IN INDIGENOUS POPULATIONS OF LATIN AMERICA AND THE CARIBBEAN: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: The aim of the systematic review is to estimate the seroprevalence and lethality attributed to COVID-19 in indigenous populations of LAC. The chosen theme is current and relevant. The content presented is good, but it needs some repairs. Comments and suggestions below:
Introduction:
1.	The text must be ordered, the information needs to be more interconnected. Example .
1st. Paragraph: write about SARS-COV2 infection, risk factors for its acquisition and progression to sever disease, explaining the social determinants that could increase exposure and more serious evolution. .
2nd. Paragraph: in addition to the cases described in LAC, tell about the social conditions that would facilitate the exposure and more serious evolution of this infection.
After this digression on the virus and LAC, describe the situation of indigenous people who should present high/greater exposure and worst evolution, justifying the objective of the review.
 I believe that a reordering of the text will be enough.
2.	English proofreading is required.
Experimental design: Aims
3.	 It is very clear and delimited. However, the estimation of prevalence and lethality was not made. They have been evaluated.

Methods
4.	The research protocol was registered at Prospero.
Study eligibility criteria were well defined.
The search strategies in the various databases were adequately described.
The process of data collection and risk of bias assessment in the studies were satisfactorily described.
The authors planned to describe the data collected, without more complex analyses.
Validity of the findings: Results
5.	Authors should add a flowchart of study selection, including the total for each database, number of articles excluded after reading titles and abstracts, etc... as recommended by Prisma (Moher et al. 2009). Please make two flowcharts if you feel it is necessary: for prevalence and lethality.
6.	Authors must state the reason for exclusion from the analysis of those articles that were selected for full-text reading
7.	Line 202: "Of the surveyed individuals, 66 and 36 were found to have SARS-CoV-2 antibodies after testing 203 with the WONDFO SARS-CoV-2 Antibody Test (21,25)." This excerpt can be deleted, as the next sentence speaks better (gives the %) of the same information

Discussion
8.	Line 240-42 "Only a few non-241 representative studies were available that measured outcomes of COVID-19 in the indigenous people of LAC countries." I did not understand this sentence. Why non-representative?
9.	L. 252 – 269. The authors discuss seroprevalence as if in your review the rate found was high and still citing studies carried out in LAC, but which were not included in the review, as an argument to affirm the vulnerability sounds indigenous in in relation to the general population. It would be better to discuss the possibility that the seroprevalence found in the review is underestimated.
10.	L.271. Develop the discussion on COVID-19 lethality better, with special emphasis on the sample size of the studies and the lethality rate of hospitals in the region.
11.	After paragraph line 306-320 in which you cite what other authors suggested in order to decrease morbidity/mortality of the indigenous people, it would be interesting to tell which measures that in your opinion should be taken, for the same purpose, such as a contribution to public health.
12.	L.332-28. Elaborate better, as systematic review would not be possible without databases. Include in the limitations: 1. Few studies 2. Studies from few countries 3. Heterogeneous studies in relation to: - sample size in some studies, few included - diagnostic tests - form of recruitment and etc...
13.	Conclusions L. 337-346 In this item of the manuscript you should only include the data of your review. The discussion and recommendations must be included in the Discussion item.
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: SEROPREVALENCE AND LETHALITY BY SARS-COV-2 IN INDIGENOUS POPULATIONS OF LATIN AMERICA AND THE CARIBBEAN: A SYSTEMATIC REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Dear editor,
The authors declined to make many of the suggested changes.
These suggestions were intended to include minimal scientific content, particularly in the background and discussion, as well as trying to correct some misconceptions.


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: SELF-STIGMA AND COGNITIVE FUSION IN PARENTS OF CHILDREN WITH AUTISM SPECTRUM DISORDER. THE MODERATING ROLE OF SELF-COMPASSION
Review round: 1
Reviewer: 1

Output:
Basic reporting: •	The article is written in English and use clear, unambiguous, technically correct text and it’s conformed to professional standards of courtesy and expression.

Please, check Line 151: include bracket before Carvalho

•	Literature references provide sufficient field background/context.

Many DOI are not indicated: are you sure they are not available?

•	The article includes good and comprehensive introduction and background to demonstrate how the work fits into the broader field of knowledge. Relevant prior literature is appropriately referenced.
•	The structure, figures, tables fit the characteristics of a professional article and the figures are relevant to the content of the article, of good resolution, and appropriately described and labeled.
•	Raw data are shared in accordance with our Data Sharing policy.
•	The structure of the article conforms to an acceptable format of ‘standard sections.

•	The submission is ‘self-contained’ and represents an appropriate ‘unit of publication’, The results are relevant to the hypothesis and they are not inappropriately subdivided merely to increase publication count.
Experimental design: •	The submission clearly defines the research question, which is relevant and meaningful from an experimental and clinical point of view. The knowledge gap being investigated is identified (the relationship between self-stigma and cognitive fusion among parents of children with ASD), and statements are made as to how the study contributes to filling that gap.
•	The investigation has been conducted rigorously and to a sufficient technical standard.
•	The research has been conducted in conformity with the prevailing ethical standards in the field.
•	Methods is described with sufficient information, but more information could improve the presentation of the tools in order to be reproducible by another investigator.
1)	The Authors provide information material relating to the questionnaire authors' permission to perform the translation. It would be important to know if a back to back translation method has been followed or, if it has not been followed, to explain why it was not considered necessary.
2)	Furthermore, since the questionnaire was proposed to a clinical population, it would be useful to specify whether a preliminary pilot testing was carried out with a Polish normative sample. Also in this case, if a preliminary pilot testing has not been done, it would be useful to specify why it was not considered necessary at the moment.
3)	These suggestions are related to the hypothesis that the constructs explored (self stigma, fusion and self compassion) are undergoing cultural influences.
Validity of the findings: •	The article is a replication study and – at the same time – a novelty both because it values the influence of self compassion and not mindfulness and because it applies psychological knowledge in the field of ASD research. Authors explain the rationale for the replication and describe clearly how it adds value to the literature.
•	The data on which the conclusions are based, are provided in an acceptable discipline-specific repository. The data are robust, statistically sound, and controlled, but one limit could be considered during the presentation of the results and into the discussion:
 Authors always speak of parents, but, actually, the sample is made up of 218 mothers out of 233 subjects. The validity of the study, therefore, concerns the mothers and not the parents. It could at least be useful include into the discussion the hypothesis that fathers may function better or worse than mothers and therefore may represent a moderating factor or a risk factor that accumulates to others. So, future research could values this hypothesis.

Please check the Line 229 - “while controlling for gender” -: it might be useful to specify whether this control makes sense given the extreme disparity in the number of females compared to males and I didn’t find this analysis in the results
Additional comments: I appreciated the study because it can provide support for psycho-educational interventions related to cognitive psychology to help mothers and fathers coping with the problem behaviors of children diagnosed with ASD. Work to implement self compassion instead of attention to symptoms of depression and anxiety can avoid the clinical designation of parents


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: SELF-STIGMA AND COGNITIVE FUSION IN PARENTS OF CHILDREN WITH AUTISM SPECTRUM DISORDER. THE MODERATING ROLE OF SELF-COMPASSION
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, the paper is well-written and the flow is logical and clear. There are a few minor grammatical errors. I have mentioned several of these in the review. But, the authors should run a grammar check after all the edits to ensure that the rest of the text is checked and edited prior to the submission of the revision. This paper addresses an important area and has interesting findings, It is recommended for publication after minor revision.
Experimental design: Research design and methods are clear.
Validity of the findings: The findings are valid and clear.
Additional comments: INTRODUCTION:

The introduction is well-written and describes the key concepts clearly for the reader. There are only a few minor points to address:

Line 134:
Please add ‘a’ between ‘with’ and ‘different’

Line 136:
Please and in ‘one’s’ and change ‘toward’ to ‘towards’. The edited version is as follows:
‘… to relate kindly to one’s own experiences and to be caring towards oneself’

Line 160:
The term ‘autism disorder’ is used here. It would be better to use the standardised term ‘autism spectrum disorder (ASD)’ at the beginning of the manuscript and subsequently just use ‘ASD’ throughout the text, for uniformity.

METHODS

Line 207:
Please add ‘the’ (‘… items adapted from the Self-compassion Scale …’)

Lines 201-202:
Please recheck the wording. It may be best to rephrase as “Most people blame parents for their children’s ASD” instead of: “Most people do blame parents for the ASD of their children”.

Lines 240-241:
For clarity, I suggest that the authors add the word ‘levels’ as follows: ‘various levels of ASD-related intellectual disability’. The original phrase implies that there are different types but not levels of intellectual disability.

DISCUSSION:

Line 319:
Please change ‘decrease’ to ‘decreasing’.

Line 361:
Please rephrase as follows: ‘… as well as be less likely to suppress …’.

Line 372:
Please replace ‘strong’ with ‘apparent’.

Line 381:
Rephrase as such: ‘… were less likely to experience negative …’.

Lines 382-383:
‘…low self-compassionate attitude towards oneself.’ can be rewritten as just ‘… low self-compassion.’

TABLE 1:
Please replace ‘jobless’ with unemployed. Were homemakers (housewives/househusbands) considered under the full-time occupation group?

 FIGURES:
All the figures are clear and well-presented.


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: AMMONIA-OXIDIZING BACTERIAL COMMUNITIES ARE AFFECTED BY NITROGEN FERTILIZATION AND GRASS SPECIES IN NATIVE C4 GRASSLAND SOILS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript by Hu et al. focused on the effects of N fertilization on AOB under C4 perennial grasses in nutrient-poor grasslands. The results showed that N fertilization rate had a stronger influence on AOB community composition than C4 grass species. Additionally, elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N2O) emission and soil acidity. Most importantly, soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability of AOB communities. The topics is quite interesting, data are massive, and the manuscript is well organized. Thus, I recommended the manuscript to be published after a major revision.
Experimental design: None
Validity of the findings: 1.	Line 25, “ammonia oxidizers” not only include ammonia oxidizing bacteria, while the object of this study is ammonia oxidizing bacteria, so it should be replaced with “ammonia oxidizing bacteria”.
2.	Line 37, Please be more specific about "Soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability of AOB communities" Have you conducted the statistical analysis? If so, please add the p-value after "significantly". Additionally, the “variability of AOB communities” is too vague. Dose it mean the abundance or diversity?
3.	Line 108, the author clarified that the experimental soil is sandy loam, however, the physical and chemical properties of soil should be added here.
4.	Lines 169-171, please check and correct the initial references for AOB primers used in the experiment.
5.	Lines 242-246, “at G and H2, no effect of N fertilization rate and grass species on N2O-N was observed” But, the author concluded that “elevated N fertilizer application increased N2O emission” in lines 434-436, which were contradictory. Additionally, according to the table S5, the relationship between “N fertilizer application” and “N2O emission” was weak. I suggest that the author clarify this problem.
6.	Lines 432-433, “Nitrogen fertilization rate had a stronger influence on AOB community composition than C4 grass species” In this study, the amount of N fertilizer applied in experiment was artificially controlled, as well as the type of grass. How to compare the importance weights of the two kinds of independent variables? This conclusion is not universal and meaningless.
7.	What do the letters "A, B, C" above and below the column in figure 2 refer to? Please clarify.
8.	The author perform the structural equation modeling analysis and showed the results in figure 6. The “AOB community” and “grass species” are non-quantitative variables, how to conduct correlation and variance analysis? Please clarify.
Additional comments: None


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

Input:
Title: AMMONIA-OXIDIZING BACTERIAL COMMUNITIES ARE AFFECTED BY NITROGEN FERTILIZATION AND GRASS SPECIES IN NATIVE C4 GRASSLAND SOILS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article was well written with sufficient literature cited to support the background and discussion as well as the methodology.

The structure of the article was well done in the expected style and format. Figures and tables were well designed and presented the key findings in a clear manner, with one exception. Figure 6 was not immediately clear to this reviewer when first examining it. My confusion came from the color scheme chosen--specifically the use of the color red to portray positive interactions. To me, red is normally associated with negative interactions, but after I realized what the color scheme was, the figure came into focus.

Sequence data was properly noted within the authors' declaration and within the paper. However, this reviewer was unable to find the files on NCBI and assumes that the authors have it embargoed until publication.
Experimental design: The experimental design was appropriate for the study.

No further comment.
Validity of the findings: No comment.
Additional comments: No additional comments


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

Input:
Title: AMMONIA-OXIDIZING BACTERIAL COMMUNITIES ARE AFFECTED BY NITROGEN FERTILIZATION AND GRASS SPECIES IN NATIVE C4 GRASSLAND SOILS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Hu et. al. examined the effects of nitrogen fertilization and grass species on ammonia-oxidizing bacteria in grassland soils, and revealed strongest impact of N fertilizer application rate on Nitrosospira-dominated AOB abundance and biodiversity. The manuscript is generally well written and provided some new perspectives on the potential influence of change in grass species on AOB composition and activity.
My biggest concern is about the introduction. The authors provide many misleading information and the references are often random and not the best. I show some examples below, but the authors should check this part thoroughly.
1)	Line 42-44. Since the author mentioned AOA and AOB, the reference of Frijlink et al., 1992 cannot be enough for both (since first AOA was discovered after year 2000). A more recently review paper should be used to replace or complement this one.
2)	Line 42-44. There is no mentioning comammox.
3)	Line 49. Please read Prosser et. al. 2020 (Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies) and other related papers for ecology of nitrous oxide emissions by ammonia oxidizers, especially by AOB, and provide some more specific information in the introduction, since AOB-driven N2O emission is an important result of this study.
4)	Line 54-55. AOA do not contain HAO.
5)	Line 62-64. I don’t think that is true. Maybe in some cases AOB are more abundant than AOA in agricultural topsoil, but that is not a leading trend. Also “AOB are more strongly correlated to nitrification rates than AOA” in agroecosystems mostly because they are “more responsive to N fertilization”, as the authors already described in previous sentence. Therefore, this statement should be deleted.
6)	Line 65-67. Wrong information. There are tons of papers describing Nitrosospira as the primary AOB in soils, which is also the result of this study. Nitrosomonas is actually not commonly dominate AOB population in soil based on my experience, but more often observed in wastewater treatment plant. Please revise.
7)	Line 84-85. Seems to repeat previous description (Line 58-60).
8)	Line 95-96 How is hypothesis 2 generated. I suppose it has something to do with description in Line 73-82, but please provide additional explanation for a more direct link to this hypothesis.
9)	Line 100. Community composition is also technically an index of diversity (beta-diversity). It might be best to just use richness and evenness to describe “diversity” here and in other part of this manuscript.
Experimental design: 10)	Line 133. To test soil nitrification rate or potential, it is most common to monitor nitrite plus nitrate concentration, because soil also contains nitrite oxidizers which convert nitrite to nitrate. Only measuring nitrite can lead to underestimation of nitrification potential. Please explain the method here.
Validity of the findings: no comment
Additional comments: 11)	Line 123. Add “was” before “used”.
12)	Line 170. Please use the original papers as references for these primers, or don’t cite at all since you also cite your previous paper.
13)	Line 198. Please use the original reference of QIIME. I don’t think the cited papers in 2014 used QIIME2. Please check all other programs and methodologies in the Materials & Methods for their proper references.
14)	Line 257. Show switchgrass qPCR data in correspondence with big bluestem here.
15)	Line 345-350. Have you confirmed that the other related Nitrosospira species in these soils do NOT contain urease and arginine decarboxylases?
16)	Line 384-385. I think it is due to nitrifier denitrification of AOB under low oxygen content. But your soils should be “aerobic” enough.
17)	Line 420-421. But the condition of your soils should not stimulate denitrification (see ref. Hink et al. 2017. Archaea produce lower yields of N2O than bacteria during aerobic ammonia oxidation in soil). Did you measure water-filled pore space in your soil to compare?


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: AMMONIA-OXIDIZING BACTERIAL COMMUNITIES ARE AFFECTED BY NITROGEN FERTILIZATION AND GRASS SPECIES IN NATIVE C4 GRASSLAND SOILS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The revised manuscript has been well revised, clear presentation, sufficient references supporting. Published in its present version.


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: AMMONIA-OXIDIZING BACTERIAL COMMUNITIES ARE AFFECTED BY NITROGEN FERTILIZATION AND GRASS SPECIES IN NATIVE C4 GRASSLAND SOILS
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am happy with the revisions and support the publication of this manuscript.
Experimental design: NA
Validity of the findings: NA
Additional comments: NA


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

Input:
Title: IDENTIFICATION OF EVOLUTIONARY RELATIONSHIPS AND DNA MARKERS IN THE MEDICINALLY IMPORTANT GENUS FRITILLARIA BASED ON CHLOROPLAST GENOMICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a well-written manuscript that uses clear, professional English throughout. The literature references were appropriate and adhered to the format of the journal.

Major comments

The manuscript is laden with redundant information. This makes it quite difficult to follow the main narrative and sieve out the important information. The length of the manuscript can be substantially reduced. Suggested improvements include:
1. Remove redundant background information from the Introduction (see annotated PDF).
2. Move at least half of the table/figure to the Appendix (see annotated PDF).
3. Provide succinct summary of the Results in the main text and avoid repeating information (especially numbers) that are already included in tables/figures (see annotated PDF).

Related to the point above, the study includes several analyses that did not directly address the research questions posed in the Introduction. The connection between these analyses and the research questions should be made clearer. They include:
1. RSCU and codon usage bias analysis
2. InDel identification
3. Divergence hotspot identification

Also, one specific section on the "Specie-specific test for F. taipaiensis, F. unibracteata and F. cirrhosa" appeared abruptly in the Results section, without background information or explanation of its relevance in the Introduction and description of the analysis in the Methods. This section should be better incorporated with the rest of the manuscript. In the Discussion, this section appeared out of place and the findings were too preliminary to justify its reporting in the manuscript. Perhaps it should be tested against all other Fritillaria species?

Finally, the authors should make a clearer case on why the additional cpgenomes of F. unibracteata, F. przewalskii, F. delavayi and F. sinica are necessary for this study. These four species were included in the largest clade in Fritillaria and may not be crucial for examining the general phylogeny of Fritillaria and Liliaceae.
Experimental design: The knowledge gaps and research questions are well defined and have broad relevance to plant science. The methods are clearly described and the experimental design is appropriate and rigorous.
Validity of the findings: No comment.
Additional comments: No additional comments


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

Input:
Title: IDENTIFICATION OF EVOLUTIONARY RELATIONSHIPS AND DNA MARKERS IN THE MEDICINALLY IMPORTANT GENUS FRITILLARIA BASED ON CHLOROPLAST GENOMICS
Review round: 1
Reviewer: 2

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

No. Numerous spelling, formatting and grammar issues are apparent throughout the text. Also, occasional use of non-professional or subjective language is present. Technical terms (specie-specific, subgenera when singular, conservative instead of conservation etc) need to be thoroughly checked throughout the manuscript. The use of a professional language service or a native English speaker is required to thoroughly check the text. Duplicated spacing, punctuation and tabs occur throughout the text and need to be removed.

Intro & background to show context. Literature well referenced & relevant.

Authors provide decent level of background information but also introduce non-scientific information which is presented as scientific literature (e.g. ‘medical’ terms, symptoms) and TCM related items which are not known/used outside China. Non-relevant information is particularly present in the introduction and needs to be removed to bring forward to reason and goals of the study more clearly. Key literature is missing form the introduction, especially of authors having done very similar studies recently (see below).

Morphological traits mentioned are not characters which are known as particularly diagnostic, and hence provide a very shaky foundation to base a classification on. The term ‘ecological stress factors’ is unclear – natural ecological variation is more likely to be appropriate here but the authors do not provide enough information to be sure.

Structure conforms to PeerJ standards, discipline norm, or improved for clarity.

Yes.

Figures are relevant, high quality, well labelled & described.

Yes, but some figures appear to be duplicated in the supplementary materials. I feel many of the Figures could actually be better placed in the Supplementary figures.

Raw data supplied (see PeerJ policy).

Yes.
Experimental design: Original primary research within Scope of the journal.

Yes, somewhat. Part of the work presented has also been done previously by other authors, not all of whom have been cited by the authors.

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

Yes.

Rigorous investigation performed to a high technical & ethical standard.

High technical: No.
Ethical: yes.

Methods described with sufficient detail & information to replicate.

Yes.
Validity of the findings: Impact and novelty not assessed. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.

Setting aside any assessment of impact and novelty, I feel the study is not well written out and the results are presented in a way that inflates the actual value. The setup is not thought through well, giving cause to unfounded speculation in the discussion.

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

Yes. No, No, No. (see comments above and below)

Speculation is welcome, but should be identified as such.

The discussion is far too elaborate, and inflating text is used to expand results beyond its actual value. Many off shoots are described, distracting from the actual results. The authors should refocus the Discussion by sticking to the data generated here and its immediate impact/promise. In particular the phylogenetic results need to be re-assessed, using the scale provided above. A substantial part of the branching is not or weakly supported. Overall, I feel the authors do not have a solid grasp of how to evaluate phylogenetic results and their implication on taxonomy, ecology and a classification in general.

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

No.
Additional comments: Line 54-58: remove subjective language and unnecessary text.

Line 68: remove the word ‘clinical’

Line 69-71: use scientific language for ailments

Line 90: ‘since the bulbs of some Fritillaria species showed great economic value in Asian countries’ – this needs a reference and a value, it is not listed elsewhere, except for China

Line 96: ‘ Identifying the closest relatives could point to additional species that might be analyzed for their potential medicinal value, which might in turn reduce pressure on those species that were currently faced with survival risk.’
Will this not lead to overharvesting there? This is not a sustainable research approach as suggested in the abstract.

Line 98: ‘genuine medicinal plants’ – what is meant by this? This seems highly subjective and contentious as many ‘medicinal’ uses have not been clinically proven.

Line 112: There is no such thing as a ‘partial phylogenetic signal’. It is either present or not, and then it can be weak or strong. Rephrase throughout.

Line 150: you can not assess the utility of molecular markers for population genetics in a study employing only 1 or a few individuals for each species. Remove.

Line 180, 182, 183, 190, 191, 303, : reference missing

Line 201: indels. Correct unnecessary capitalization throughout.

Line 219: Table 1 not relevant, can be summarized in the text or moved to the Supplementary Materials.

Line 257: where is the statistical proof for this statement of significance? If performed, show here, or do a statistical test and show the evidence, or change the statement.

Line 319: unclear, what is the difference between these groups.

Line 325: Vague statement – quantify, and confusing reasoning.

Line 325-346 Strong support >90, Moderate support 80-90, Weak support 65-80, No support <65. Be critical of the results! Many of the discussed nodes have no support whatsoever.

Line 368, 445-467: reassess statements with above valuation of support.

Line 375-385: I have considerable difficulties with this method of assessing species-specific differences, based on only one or several individuals in the study. This is not scientifically verifiable at all, unless more individuals for each species are added. The differences at times are so minute (a 6 bp deletion is reported), that this begs the question how prevalent this is in the wider population of this particular species. Without multiple individuals, the claim that this ‘species-specififc’ is impossible to evaluate, especially in a group where species distinction using morphological characters is difficult and the position of cryptic species complicates identification.

Line 390-393: confusing and not relevant to the manuscript. This is a cp paper and sequencing a whole nuclear genome is out of the original scope and aims, requiring a substantially different approach not employed here.

Line 396, 421: provide correct taxonomic names.

Line 422-424: confusing. Rephrase.

Line 441: What is ‘Internal Gene Space’?

Line 568, 571: Removing subjective text.

Line 388-617: the Discussion is much too long and introduces far too many aspects which are beyond the scope of this study. It needs to be fully rewritten and extensively cleansed of topics not relevant to the experiments performed by the authors.

Line 620: reassess as stated above.

Line 623-626: For this to be valid, this needs to be looked at in much greater detail. At current, there is no correlation provided between geography, traits and phylogeny. At best, one could say that the tree appears to reflect a geographic distribution pattern.

Line 629-631: doubtful and hard to substantiate, without the addition of more individuals for each species.


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

Input:
Title: IDENTIFICATION OF EVOLUTIONARY RELATIONSHIPS AND DNA MARKERS IN THE MEDICINALLY IMPORTANT GENUS FRITILLARIA BASED ON CHLOROPLAST GENOMICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: English
----------
Upon closer reading, it was apparent that substantial improvement on the writing is necessary. There are many grammatical/spelling errors and incorrect terminology; some examples are provided below.

Line 66-67. "Nowadays, DNA-based classification occurred has been applied in angiosperm phylogeny group because of their reliability and readable data" should be "Molecular systematics has been widely applied to clarify angiosperm phylogeny".

Line 67-68. "Basically, accurate identification (eg. using DNA markers) was necessary to discriminate among the original specie and its adulterants" Do you mean "cryptic species"? "Adulterants" usually refer to substance/chemical that is used to alter properties of food product.

Line 70-71. "...the wild Fritillaria populations decreased sharply due to long-term excessive harvesting" should be "...the wild Fritillaria populations experienced sharp decline due to long-term overharvesting".

It is important that the manuscript goes through English editing before it can be ready for publication.

Literature, background and article structure
---------------------------------------------------------
The manuscript adhered to professional article structure and covered sufficient literature and background.

Relevant results to hypotheses
-----------------------------------------
Yes, the results are relevant to the research question.
Experimental design: Knowledge gaps and research questions
-------------------------------------------------------
I appreciate the authors' careful response to my previous comments. The current version of the manuscript is more succinct than before, especially with the removal of redundant information.

However, I am unconvinced that there is a need to perform de novo assembly for the cpgenome of F. unibracteata, F. przewalskii, and F. sinica again, given that this had been done in Chen et al. (2019). Why wasn't the previous cpgenomes used in the study here? What is the value of assembling the cpgenome, de novo, again?

Also, since one of the main objectives was to obtain candidate DNA markers that could potentially be used in species identification of medicinal Fritillaria, the study seemed incomplete with just indel markers that can identify three out of 11 medicinal species. I strongly suggest removing this component. Alternatively, the authors should explore/report markers that can be useful in identifying all 11 medicinal species. How about the DNA barcoding regions? Or ycf that is highly divergent? What would the authors suggest future studies explore in order to find markers for quick and easy species identification?

These would have to be addressed to clarify how the study address existing knowledge gaps.
Validity of the findings: All good. No comment.
Additional comments: No additional comments


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

Input:
Title: IDENTIFICATION OF EVOLUTIONARY RELATIONSHIPS AND DNA MARKERS IN THE MEDICINALLY IMPORTANT GENUS FRITILLARIA BASED ON CHLOROPLAST GENOMICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Following the initial round of reviews and comments provided, I can see that the authors have performed an extensive round of revision and addressed most of the issues highlighted before.

The use of English and correct spelling/grammar has been very much improved. Background research and citations have been improved. The article overall reads much better as a large proportion of redundant text has been removed.
Experimental design: The used methodology is better explained.
Validity of the findings: Interpretation and description of results has been very much improved.
Additional comments: As a minor formatting comment, I would suggest to the authors to read through the manuscript one more time in detail, paying particular attention to the proper use of singular and plurals (and correct formulation of sentences as such), and the unnecessary use of capital letters. Also, I still find four more usages of the word 'specie'. The manuscript has been very much improved from the initial submission overall.


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

Input:
Title: IDENTIFICATION OF EVOLUTIONARY RELATIONSHIPS AND DNA MARKERS IN THE MEDICINALLY IMPORTANT GENUS FRITILLARIA BASED ON CHLOROPLAST GENOMICS
Review round: 3
Reviewer: 1

Output:
Basic reporting: I thank the authors for engaging a native speaker to edit the language of the revised manuscript. The content of the manuscript is almost ready, but I do think that it still needs a final, professional English editing (perhaps from the journal?) to be publishable. Case in point, the first sentence of the abstract is missing an article "the".

Other examples of improvements needed on language editing include:

Line 243-245: As a consequence, ycf1 gene as well as other highly divergent regions would provide useful information for species-specific identification in the future.
Suggestion: For these two species, other highly divergent regions may provide better information for species-specific identification."

Line 403-404: The CP genomes of four Fritillaria species provided support for taxonomic clarification, phylogenetic relationship and development of DNA markers.
Suggestion: The CP genomes of the four Fritillaria species were useful resources for taxonomic clarification, phylogenetic relationship and development of DNA markers.
Experimental design: It is greatly appreciated that the author provided further background on why the cpgenomes of F. unibracteata, F. przewalskii, and F. sinica were assembled, de novo, in this study. Genomic resources are being rapidly produced, so it is completely understandable that other groups concurrently developed these cpgenomes. This is valuable information to the reader and I am glad that author added the explanation.

The exclusion of the preliminary ITS tests and in its place, the inclusion of a more comprehensive and applicable marker development (involving ycf1 and other regions) is highly welcomed. It provides an important resource for species identification, which has wide applications in TCM and species conservation. The new tests are thorough and reliable.

With these two major edits, the study design is now more concise and clearer.
Validity of the findings: No comment.
Additional comments: No additional comments


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

Input:
Title: PLOIDY LEVEL ENHANCES THE PHOTOSYNTHETIC CAPACITY OF A TETRAPLOID VARIETY OF ACER BUERGERIANUM MIQ.
Review round: 1
Reviewer: 1

Output:
Basic reporting: It would be convenient to review the English. For example Lines 52 to 54: description is redundant and not precise. Line 56: ‘Superior’ is ambiguous.
Please provide citations for every statement in the introduction and discussion. For example Lines 58 to 84 require citations on ‘require more energy and carbohydrates’, ‘changes in the photochemical characteristics of the nucleus’, ‘the photosynthetic rate of plant cells is related to the DNA content of the cells’ and so on after every statement.
64
Regarding the structure: the introduction is not complete as it does not offer full information and citations to understand the background and purpose of the research. Methods are not descriptive enough to repeat the research (details below).
Results are not precise and subjective judgements are included: Examples. Line 188. ‘show that the trends of X and S are consistent’, line 190 ‘The peak transpiration rate of X was greater than that of S’, line 195 ‘an obvious "photosynthetic nap" phenomenon is observed’. Line 197 ‘The daily changes of the net photosynthetic rate (A) of X and S leaves from May to September are the same (Fig. 4).’ and so on.
Also, Differences identified on the chloroplast structure should be described by data. On the discussion, basic information is included that should be on methods section instead, like the one in lines 300, 303, 315.
The connection between the differences identified on the chloroplast and the photosynthetic measurements should be supported by the literature.
Figures: Fig. 3 to 6 do not have statistic information, are differences significant?  Fig 1. Please add the 5'->3’ sense of the sequences. There are no figure captions, so figures could not be read for the review. Raw data on photosynthetic study only includes the average values used to build the graphs. There is no raw data then.

Lines 78 to 84: rewrite to clearly state what is the purpose of the study. ‘To reveal the biological characteristics of tetraploid formation’ is a too wide statement; yield is not measured on this study; ‘natural conditions’ are not defined; ‘high light efficiency breeding’ is not defined.
Conclusion is not sustained on data presented: line 415 ‘stronger photosynthesis ability’ needs data to be statistically validated.
Experimental design: The research question here needs to be defined regarding what is the genetic difference between clones ‘S’ and ‘X’ (only chromosome number or also genetic content). Also, the photosynthetic study needs to be justified more in detail.
Description of methods needs to be thoroughly improved.
Raw data and statistical analysis of photosynthetic measurements needs to be provided. A quantitative analysis of differences in chloroplast structure needs to be performed.

- Describe the origin of the plants on methods. How was the polyploid obtained and what is the origin? Is it an autotetraploid or an allotetraploid? This is fundamental as you are comparing a diploid and a tetraploid that, excepting their chromosome number, may have identical or (slightly to very) different genetic content.

- Identify the plants so that the study can be repeatable (Are they part of a botanical collection and have an id name or number?
- Explain the propagation method and how many individuals were used to perform the measurements.
- Photosynthesis parameters have been estimated through punctual measurements. Differences found are punctual and need to be statistically analyzed to verify that they are significant.
- The transpiration rate is not a photosynthetic parameter, please explain why do you include this measurement and what is it relevant for.
- Information provided on methods does not allow to repeat the study (number of plants measured, dimensions of the plants, conditions (field, greenhouse), soil and container, irrigation, temperature humidity and light intensity.
- Define photosynthetic nap and explain why is it relevant for this study.
Validity of the findings: The introduction and discussion should state what is the relevance of the study and findings.
There needs to be a clearer connection between the purpose stated at the end of the introduction, the statements made at the results section, the explanations and analysis provided as a discussion and the study conclusions. Each parameter measured needs to be justified and inter-related with the rest to get to a conclusion.
Additional comments: The topic is relevant for the field and it would be interesting to have this research published. However, the purpose, methods and results of this study need to be worked out to reach a meaningful scientific contribution. I would advise the authors to thoroughly review the manuscript and their research data before further submission of this manucript.


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: PLOIDY LEVEL ENHANCES THE PHOTOSYNTHETIC CAPACITY OF A TETRAPLOID VARIETY OF ACER BUERGERIANUM MIQ.
Review round: 1
Reviewer: 2

Output:
Basic reporting: The basic structure of the publication follows the traditions style and has a good flow.
The usage of the English language is adequate.

The manuscript would benefit from having a bot more background to the system. The authors compare a diploid and a tetraploid genotype of Acer buergerianum. What is the natural stage? Was the tetraploid artificially obtained or both occur in nature? Are there any ecological/arquitectural/niche differences?

Figure captions need to be more detailed.
Experimental design: The experimental design needs detail in all sections.
1. Polyploidy identification -
this preparation described does not result in single cells for flow cytometry. How were the cells separated? How many cells were tested?
The dye utilised is not suitable for chromosome counting, but for bacterial and cell wall staining. It is not possible to count the number of chromosomes, and therefore to infer policy level. How many cells were counted? From how many different plants? A lot more detail is required and better images with accurate counts.

2. Diurnal changes in photosynthesis - how many plants were tested? Were they tested during one one day each month? Or do the graphs show an average of all days of the month?

3. Electron microscope sample preparation of leaf chloroplast
The method described is not for electron microscopy. I did a web search and did not see any Pentaflex electron microscope (https://www.microscopes.eu/en/Brand/Pentaflex/). I wonder if the authors meant light microscopy?

4. Transcriptome sequencing
What genotypes were sequenced? How many samples, how many replicates? What was the objective?
Validity of the findings: As the methodology is very vague, so are the results.
1. chromosome number needs to be accurate (or as accurate as possible, using the correct method)
2. flow cytometry - DNA content needs to be expressed as numbers, not as "about twice".
3. photosynthetic analysis - there is a long description, but no analysis was done. There is no conclusion for this experiment
4. microscopy - what is the length of the cells/organeles? How many were measured? Without this information, there is no reasonable way to decide if the findings are typical. Statistical analysis is needed.
5. Transcriptome analyses - this is the part that was least clear. What was being compared? What are the candidate genes and how are they validated? What is the purpose of this experiment? How does it tie with the rest of the study?
Additional comments: The work on tetraploidization is of great interest to the scientific community. Having a system to work on gives you the opportunity to find interesting information that can contribute to the general knowledge. The efforts of the authors are appreciated. However, the work needs to be clearly explained. What was the goal? What is the background of the work?
The manuscript lacks numbers, proper description of method, analyses and description and interpretation fo the findings. I would encourage the authors to revise it carefully.


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: PLOIDY LEVEL ENHANCES THE PHOTOSYNTHETIC CAPACITY OF A TETRAPLOID VARIETY OF ACER BUERGERIANUM MIQ.
Review round: 2
Reviewer: 1

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

The writing should be reviewed carefully as there are confusing sentences and imprecise use of words.

•	Literature references, sufficient field background/context provided.

No, the authors should try to shape the introduction so that the research can be understood. Many citations are missing.

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

The article structure is not consistent, as there is not correspondence between contents described in introduction (not enough information provided to understand and justify the research), methods (poor descriptions, some parts omitted), results (not properly described, information not well distributed between text and figures/tables), discussion/conclusion (every single content presented on results should be discussed and highlighted on the conclusions.

•	Self-contained with relevant results to hypotheses.

It is not clear whether all the contents presented are relevant to reach the conclusions. Authors should try to order contents and justify them.
Experimental design: •	Original primary research within Aims and Scope of the journal.

Yes

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

The question is not well defined as there is misuse of terms, however it is relevant and will shed light into the field.

•	Rigorous investigation performed to a high technical & ethical standard.

The statistic analysis and some basic information for repeatability are missing. Authors should be more rigorous on how they present their data and also on how they use that data to reach conclusions

•	Methods described with sufficient detail & information to replicate.

No, information is missing
Validity of the findings: •	Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.

Statistic analysis of the gas exchange data needs to be performed to know if the results presented are conclusive about the differences in gass exchange parameters between ploidies in this specie. It would be great if data on growth, chlorophyll content and leaf fluorescence under mild stress could be added to verify that physiology and gene expression are somewhat connected.
Data on morphological measurements should be presented in tables and analyzed statistically. Otherwise the histology should be described in results as qualitative but not quantitative.

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

No, as commented before

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

No. Rewrite the conclusions to be more specific and include all the highlights from different sections describe in the result’s section

•	Speculation is welcome, but should be identified as such.

In this sense, authors need to be more careful and specific when they state their results on the discussion section and avoid long paragraphs presenting basic information without a point.
Additional comments: This study intends to investigate the differences between diploid and tetraploid Acer buergerianum in terms of photosynthetic capacity. For that purpose, physiology (different gas exchange parameters), anatomy (chloroplast hystology) and gene expression (differences observed on a massive study validated by PCR methods) are evaluated.

However, results need to be statistically analyzed to reach conclusions, as the graphs and tables show punctual differences in gas exchange parameters and anatomical evidences that could be related to observed differences on gene expression. I would suggest to apply an ANOVA test to results regarding physiology and present hystology results in a quantitative way.

Unfortunately, without the propper statistic analysis, the research manuscript would not be valid for publication.

I hope the comments here and on the pdf file are useful for your team to improve 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: PLOIDY LEVEL ENHANCES THE PHOTOSYNTHETIC CAPACITY OF A TETRAPLOID VARIETY OF ACER BUERGERIANUM MIQ.
Review round: 3
Reviewer: 1

Output:
Basic reporting: In this manuscript, the authors compared the gas exchange parameters, chloroplast structure, chlorophyll contents, and chlorophyll fluorescence parameters between the tetraploid Acer buergerianum 'Xingwang' and the diploid 'S4', tehn compared the transcriptomes of the  autotetraploid 'Xingwang' and the diploid 'S4' of A. buergerianum. They aimed to find out the effect of ploidy level on the photosynthetic capacity and the possible mechanisms underlying the differences. However, major revisions are needed for the current manuscript before acceptance.
Experimental design: Please add some necessary references for some methods.
Line 170-171, Pn, should be Pn, and so did Gs, Ci all through the manuscript. And did you measure transpiration rate? It should always be with the other parameters.
Validity of the findings: Lin 288, should “identification” more suitable for “detection”?
Lin 290-292. It would be better to move the sentence to introduction section or plant materials subsection.
Line 358, line 372. These two subsections should be simplified and most of the details could be presented in supplementary materials instead of figures and tables in main text. For example, Table 5 should be moved to supplementary materials.

Line 399-407, it would be better to do pathway enrichment analysis of different set of genes related with photosynthesis by suing MapMan (Thimm et al., 2004; Lu et al., 2020). And also the the weighted gene coexpression network analysis (WGCNA) to relate photosynthetic indices with trasncriptomic data.

Table 3 and 4 changed to Figure. Fv, should be Fv, and so did the other indices.

Table 6. The table should be in three lines style.
Figure 10 the quality and readable of the figure is low. Can the authors improve the figures. I think there are other sketch of the biosynthesis pathway of chlorophyll.
Figure 11. The quality of the figure is also low. Can the authors draw a figure instead of add the information in a existing picture. There are some other method to present the photosynthesis pathway.
Did hemB presented in results section？
Additional comments: Title:
The title can not cover the content of the main text.

Introduction.
The first and the second paragraph should be reorganized into two part: the first is the effect of ploidy level on photosynthetic ability, and the second should be the possible mechanisms, including chlorophyll content, the structure of chloroplast, the related genes expression, etc. The authors should conclude into several points instead of list the previous studies.
Lin 94:　add “with Chinese name of” before “Gong Tong”.

Discussion and conclusions:
It would be better for the authors to present a sketch map for the possible mechanisms.


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: PLOIDY LEVEL ENHANCES THE PHOTOSYNTHETIC CAPACITY OF A TETRAPLOID VARIETY OF ACER BUERGERIANUM MIQ.
Review round: 4
Reviewer: 1

Output:
Basic reporting: The manuscript has been revised according to the comments except one point.
1.	For abbreviation Pn, P should in italic, n should be in subscript. Please see literature Gao et al., 2017 for the model. So did so did Gs, Ci, Tr and Fv.
Gao S, Yan Q, Chen L, Song Y, Li J, Fu C, Dong M. 2017. Effects of ploidy level and haplotype on variation of photosynthetic traits: novel evidence from two Fragaria species. PLoS One 12: e0179899. DOI: 10.1371/journal.pone.0179899

2.	The number of tables and figures are too many for a paper. Please merge small pictures into large ones, or move some to the supplementary materials or simplify them. For example, Figure 10 and Figure 11 can be merged into one figure with a and b. So did Figure 7 and Figure 8. Table 1 and Figure 12 can be moved to supplementary materials.
Experimental design: good.
Validity of the findings: good.
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: LONG-TERM FOLLOW-UP OF MANDIBULAR DENTAL ARCH CHANGES IN PATIENTS WITH COMPLETE NON-SYNDROMIC UNILATERAL CLEFT LIP, ALVEOLUS, AND PALATE
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. Plaster models of 75 consecutive patients directly after (T0), 2 years after (T2), and five years after treatment (T5) were available.
T0 - age?
T2 - age?
T5 - age?
The total should be 225. Why 197?
2. complete non-syndromic unilateral cleft lip, alveolus, and palate - any problems in mandible?
3. Line 111 - 130 = Details related to the maxilla. Anything with mandible?
4. GOSLON and MhB measured specially designed to check the condition of the maxilla. What about mandible?
5. 20 Models re-measured 1 wk interval. I think it is too early. Should be 2 weeks or 3 weeks.
6. Changes values are shown. Mean values followed by changes data are easy to follow.
7. Figure 1 - is it from the computer/software generated?
8. Figure 3 - adapted from?
Experimental design: 1. Line 111 - 130 = Details related to the maxilla. Anything with mandible?
2. GOSLON and MhB measured specially designed to check the condition of the maxilla. What about mandible?
Validity of the findings: # 20 Models re-measured 1 wk interval. I think it is too early. Should be 2 weeks or 3 weeks.
Additional comments: None


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

Input:
Title: LONG-TERM FOLLOW-UP OF MANDIBULAR DENTAL ARCH CHANGES IN PATIENTS WITH COMPLETE NON-SYNDROMIC UNILATERAL CLEFT LIP, ALVEOLUS, AND PALATE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear and unambiguous, professional English used throughout. There are a few comments to improve

Page 8, line 70 - CLP is not defined as a short form. The authors have defined terms as cleft lip alveolus and palate but not cleft lip and palate. CLP should be defined as cleft lip and palate when used for the first time. I would also recommend to use one consistent terminology, if possible, throughout the manuscript.

Line 103 - “The aim of this study was to determine long term changes in transversal mandibular … to determine interarch transverse relationship in patients with ..post-treatment.” Please use the word transverse consistently rather than using transverse and transversal interchangeably.

Line 106 “We also studied risk factors that could…” Please use third person rather than first person language such as In this study, or the risk factors that could ….were studied”

Line 117 “ Exclusion criteria were: additional craniofacial….in(complete) or submucous cleft lip at the …” I think the authors meant to convey incomplete cleft as exclusion - the brackets before and after the word complete should be removed.

Line 154 - MHB index - the full form should be written for the first time when it appears in the main text.

The terms T0, T2, and T5 are confusing. They imply that there were 5 time-points. Rather the terms T0, T1, and T2 would be more appropriate with T1 defined as 2 years and T2 defined as 5 years after treatment.

Line 297”In contrast to the lack of data on mandibular arch dimensions in patients with clefts there are a few studies that”. Please use a consistent terminology CLP rather than ‘clefts’

Line 326 - the word bigger is inappropriate rather an adjective such as higher or larger may be more appropriate.
Experimental design: The study is well conducted. The strength of the study is the long followup of patient for 5 years. There are a few comments as mentioned below:

“Line 307 “It means that the mandibular arch did not adapt completely to the maxillary arch because if it did the MHB scores would not det...” I would suggest to rephrase this sentence. Rather than the mandibular arch not adapting the maxillary arch - the MHB scores are affected due to changes in maxillary arch as mandibular arches changes were minimal. Therefore, it can be reworded as maxillary arch changes in the long term may be responsible for the increased MHB scores.

Line 328. Please consider replacing the terms upper dental arch with maxillary arch and lower dental arch with mandibular arch throughout the manuscript. Similarly, changes can be done upper to maxillary when referring to any teeth as well.
Validity of the findings: Intra and inter observer reliability have been stated. Results are adequately explained.
Additional comments: Line 346 - please add a couple lines on the clinical implications and how can use the results of this study be useful for clinical practice.


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: LONG-TERM FOLLOW-UP OF MANDIBULAR DENTAL ARCH CHANGES IN PATIENTS WITH COMPLETE NON-SYNDROMIC UNILATERAL CLEFT LIP, ALVEOLUS, AND PALATE
Review round: 1
Reviewer: 3

Output:
Basic reporting: It was a pleasure to review this well-crafted manuscript. The English language is clear, and the literature is almost enough. I suggested some papers to add and collaborate with this relevant scientific study.
Experimental design: It is original primary research. The null hypothesis is not defined, but it does not belittle the study. There are some flawns to understand the methods, and I suggested adding to collaborate with the investigation.
Validity of the findings: It is a subject relevant and still not evaluated. The literature is well established, despite there are few studies about the theme. This investigation will contribute to knowledge.
All statistical analyses are robust, and the conclusions are well stated, supported by results.
Additional comments: Thanks for PeerJ for the indication of my name to review the paper entitled:

Long-term Follow-up of Mandibular Dental Arch Changes in Patients with Complete Non-syndromic Unilateral Cleft Lip Alveolus and Palate

I only have minor suggestions to recommend before publication to enhance the readers' comprehension of the study findings.

Abstract
Line: 39
It is relevant to consider that 75 patients, three different moments result in 225 mandibular dental casts. What happened with 28 models? Or remove the dental casts number.

Keywords
Lines 60, 61
Mandibular arch is not a MESH term.
Long term outcome is not a MESH term.
Complete unilateral cleft lip is not a MESH term.
Cleft lip is a MESH term.
Cleft palate is a MESH term.
Modified Huddart-Bodenham Index is not a MESH term.

Introduction
Lines 85, 86
I suggest read the paper:
Pucciarelli MGR, Toyoshima GH, Cardoso JF, de Oliveira TM, Neppelenbroek KH, Soares S. Arch Asymmetry in Patients With Cleft Lip and Palate After Rehabilitation Treatment Using Stereophotogrammetry. J Craniofac Surg. 2021 Jul-Aug 01;32(5):e501-e504. doi: 10.1097/SCS.0000000000007460. PMID: 33481468.

Line 105
I suggest including the null hypothesis.

Materials & Methods
Lines 120-131
Were these patients separated in raw data? For patients who needed superiorly based pharyngeal flap at 4-5 years, maxillary protraction and expansion at 5-6 years for 12-18 months followed by minor lip/ala nose correction and finally severe dysgnathia, combined orthodontic-surgical treatment followed by lip/nose correction was performed. How did the authors deal with these patients?

Line 141
Please, clarify the moment of the beginning of the study. After treatment? Which treatment? Orthodontic treatment? Orthognathic surgery?

Line 169
Which one is correct here, the signal – or AND?

Line 173
The first time that DME appears. Please, what does it mean? Inform the meaning in brackets.
DME: duplicate measurement error

Results
Lines 193-195
One patient is absent here, maybe the patient is in the group of the maxillary expansion before bone grafting, or the group of the lateral incisor space closed orthodontically.

Line 212
It is too much figure. Think to be reasonable.

Discussion
Lines 295-297
Is there any scientific evidence to support this statement?

Lines 308-309
If the mandibular arch did not adapt completely to the maxillary arch, how can the authors affirm that changes in the interpremolar distances might be explained as an adaptation to changes in the maxillary dental arch in CUCLAP which is subject to the ongoing constrictive effect of palatal scar tissue?

Lines 322-324
Maybe one of the most relevant pieces of information about the study.

Lines 330-331
Pease read these papers:
1.Pucciarelli MGR, Toyoshima GH, Cardoso JF, de Oliveira TM, Neppelenbroek KH, Soares S. Arch Asymmetry in Patients With Cleft Lip and Palate After Rehabilitation Treatment Using Stereophotogrammetry. J Craniofac Surg. 2021 Jul-Aug 01;32(5):e501-e504. doi: 10.1097/SCS.0000000000007460. PMID: 33481468.
2. Rezende Pucciarelli MG, de Lima Toyoshima GH, Marchini Oliveira T, Marques Honório H, Sforza C, Soares S. Assessment of dental arch stability after orthodontic treatment and oral rehabilitation in complete unilateral cleft lip and palate and non-clefts patients using 3D stereophotogrammetry. BMC Oral Health. 2020 May 27;20(1):154. doi: 10.1186/s12903-020-01143-1. PMID: 32460814; PMCID: PMC7254638.
3. Soares S, Rezende Pucciarelli MG, Hideki de Lima Toyoshima G, Marchini Oliveira T. Stereophotogrammetry to evaluate young adults with and without cleft lip and palate after orthodontic and restorative treatment. J Prosthet Dent. 2021 Feb 12:S0022-3913(20)30733-2. doi: 10.1016/j.prosdent.2020.10.025. Epub ahead of print. PMID: 33589235.

Line 352
Please read this paper:
Caballero JT, Pucciarelli MGR, Pazmiño VFC, Curvêllo VP, Menezes M, Sforza C, Soares S. 3D comparison of dental arch stability in patients with and without cleft lip and palate after orthodontic/rehabilitative treatment. J Appl Oral Sci. 2019 Jun 13;27:e20180434. doi: 10.1590/1678-7757-2018-0434. PMID: 31215598; PMCID: PMC6559757.


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: LONG-TERM FOLLOW-UP OF MANDIBULAR DENTAL ARCH CHANGES IN PATIENTS WITH COMPLETE NON-SYNDROMIC UNILATERAL CLEFT LIP, ALVEOLUS, AND PALATE
Review round: 2
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: The authors have done appropriate modifications


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: LONG-TERM FOLLOW-UP OF MANDIBULAR DENTAL ARCH CHANGES IN PATIENTS WITH COMPLETE NON-SYNDROMIC UNILATERAL CLEFT LIP, ALVEOLUS, AND PALATE
Review round: 2
Reviewer: 2

Output:
Basic reporting: See attached PDF for corrections.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Please, correct the reference: Pucciarelli MGR, Toyoshima GH, Cardoso JF, de Oliveira TM, Neppelenbroek KH, Soares S. Arch Asymmetry in Patients With Cleft Lip and Palate After Rehabilitation Treatment Using Stereophotogrammetry. J Craniofac Surg. 2021 Jul-Aug 01;32(5):e501-e504. doi: 10.1097/SCS.0000000000007460. PMID: 33481468.


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: PUTATIVE FOSSIL BLOOD CELLS REINTERPRETED AS DIAGENETIC STRUCTURES
Review round: 1
Reviewer: 1

Output:
Basic reporting: No weaknesses noted. The manuscript is clearly written in professional unambiguous language. The manuscript cites all the relevant literature and provides sufficient background behind the problem being addressed.
Experimental design: The only weakness noted in the Materials and Methods section is minor descriptions/discussion with respect to the Raman spectroscopy section. These are listed here below:

1) Why was the laser spot size 8 micrometers? Was the laser defocussed to avoid laser induced heating on the sample? To this end, what magnitude objective was used?

2) Is the 785 nm laser used in this work a diode laser?

3) What algorithm was used for baseline correction in the acquired Raman spectra?

4) What is the spectral resolution?
Validity of the findings: The only weakness noted in this manuscript is the interpretation of the Raman spectra, with respect to the assignment of the bands in the region of ca. 1000 to 2000 cm-1. The manuscript assigns these bands to carbonaceous compounds and potentially amides. However, the authors have confused Raman bands with photoluminescence (PL) bands. Fossilized bones and shales, in particular, usually contain notable quantities of REEs. And these types of samples when excited by a NIR laser such as a 785nm excitation wavelength (presumbly a diode laser) typically contain REEs with 4f electronic configuration in which illumination excites the sample's valence electrons, and consequently, PL emissions are then generated through the release of energy in (radiative) electronic transitions. This results in PL bands that are similar in FWHM than those of Raman bands arising from organic compounds, which these PL bands occur between 1000 to 2000 cm-1 in the spectrum when excited by NIR lasers. In sum, these REE-related emissions may easily be mistaken as Raman bands.
Additional comments: Apart from some of the methodology missing and the incorrect interpretation of the Raman spectra, this manuscript is almost ready for publication. I would recommend minor revision.