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

Input:
Title: GENOME-WIDE ANALYSIS OF GROWTH-REGULATING FACTORS (GRFS) IN TRITICUM AESTIVUM
Review round: 2
Reviewer: 1

Output:
Basic reporting: this revised MS addressed most of my concerns.
Experimental design: this revised MS addressed most of my concerns.
Validity of the findings: this revised MS addressed most of my concerns.
Additional comments: this revised MS addressed most of my concerns.


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

Input:
Title: GENOME-WIDE ANALYSIS OF GROWTH-REGULATING FACTORS (GRFS) IN TRITICUM AESTIVUM
Review round: 2
Reviewer: 2

Output:
Basic reporting: The author has solved all the comments except the marking format and document format of the literature. With minor modifications, the paper can be accepted.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Although the author has revised it according to the requirements, There are many mistakes in the quotation and description format of the literature.
1. Line 39, ...‘.in regulating gibberellic acid (GA)-induced stem elongation (Knaap, Kim & Kende, 2000).Line 43, in the N-terminal region of the GRF protein (Kim, Choi & Kende, 2003)......’should be  ...‘.in regulating gibberellic acid (GA)-induced stem elongation (Knaap et al., 2000).Line 43, in the N-terminal region of the GRF protein (Kim et al., 2003)......’ etc. Line 49, 'he C-terminal region has trans-activation activity (Kim & Kende, 2004; Choi, Kim & Kende, 2004; Liu et al., 2014).' should be  ...‘.the C-terminal region has trans-activation activity (Choi et al., 2004; Kim et al. 2004; Liu et al., 2014). ....’ etc.
2. The full name or abbreviation of journals involved in literature should be unified.


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: IMPACT OF MYCOPLASMA OVIPNEUMONIAE ON JUVENILE BIGHORN SHEEP (OVIS CANADENSIS) SURVIVAL IN THE NORTHERN BASIN AND RANGE ECOSYSTEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is generally well written, but could use additional careful copy editing to correct occasional typographical errors and unclear sentences as specified in the general comments to the author below. The introduction and background clearly demonstrate how the work fits into the broader field of knowledge. The article shows professional structure and appropriate figures and table and raw data. The submission is self-contained and is clearly an appropriate unit of publication.
Experimental design: Original primary research within the journal scope. Clearly defined research question. Rigorous investigation to a high technical standard, in conformity with appropriate ethical standards. Clearly defined methods.
Validity of the findings: Underlying data provided, robust sound and controlled. Conclusions well stated, linked to original research questions, and limited to supporting results.
Additional comments: General comments: The manuscript is well written and complete. The study addresses important issues, including the generalizability of the hypothesis of the central role of M. ovipneumoniae in epizootic pneumoniae in bighorn lambs to a new host management subtype and a new ecoregion, and the role of the frequently hypothesized co-factors host genetics and nutrition. The results support the generally very limited genetic diversity in ‘California’ bighorn sheep in both the M. ovipneumoniae exposed and non-exposed study populations, without clear impact on juvenile survival. Similarly, the NVDI analyses failed to identify a major role for nutrition among the study populations. This study presents clear hypotheses (tested with rigor despite what must have been very trying field observation conditions over a sustained period), with appropriate analyses and well-justified conclusions.
Specific comments:
L37 needs clarification which populations ‘those’ refers to.
L41 consider ‘presence’ or ‘exposure to’ instead of ‘persistence’? It’s not the persistence of the bacterium alone; it’s that transmission of the bacterium to the lambs caused fatal pneumonia?
L74 suggest ‘non-immune’. Per Cassirer 2017, previously exposed and infected bighorn sheep remain susceptible to disease triggered by transmission of a new strain.
L78 suggest ‘previously unexposed’
L80 Seems like Parr et al, 2018 studied a population that was not infected with M. ovipneumoniae, so I’m not sure it is relevant to this sentence. Seems to me that there are several reports in the proceedings of the NWSGC symposia that support this point. I’m not sure how many in the broader literature.
L81 The citation presents this hypothesis based on one outbreak, so perhaps ‘thought to be’ would be better than ‘tends’.
L110 same comment as for L80
L140 ‘than’ Oregon (?)
L195 Can the authors confirm the accuracy of the Bowden Hills polygons in Figure 1 (with one of the two seemingly overlapping the Rattlesnake population?
L266 No doubt the deeper sites reflect infection, but nasal carriage may be just (inactive) colonization. Suggest ‘Presence of M. ovipneumoniae was detected…’
L268 I believe the WADDL PCR test was modified subsequently. For the time period cited, the method was published in Manlove et al. Prev Vet Med 2019.
L270 ‘Washington Animal Disease Diagnostic Laboratory’
L319 ‘and’ ?
L356-7 I think I know what this sentence means, but please clarify if possible.
L366-71 It would be helpful if the authors reported their best estimates of the proportion of the adult ewes in each population that were sampled for PCR detection of M. ovipneumoniae.
L396-8 incomplete sentence?
L421 ‘and one in RSP’?
L422-4 Basically, an ‘Indeterminate’ result is a very weak signal which may or may not be due to the target organism. It does not mean that the target was detected, as stated here.
L437-9 Any point in a ‘sensitivity analysis’ to determine if not using these two loci changes anything?
L444 ‘…and post-parturition NVDI varied…?
L487-9 What does it mean that time as a multiplicative effect had more support than time as an additive effect?
L501-507 It would be helpful if the text indicated these were semi-monthly (not cumulative) figures.
L539-41 I would appreciate more discussion about the choice of ‘detection of M. ovipneumoniae infected juveniles’ as the marker for exposure. It could be seen as circular reasoning to conclude that juveniles dying with M. ovipneumoniae associated pneumonia is associated with decreased juvenile bighorn survival. It would be helpful if the authors could comment on this and some related questions: What percent of bighorns were sampled for nasal carriage, by population (to help assess the likelihood that carriers were present but not detected)? Is it known how much bighorn movement exists among the bighorn populations east of Hwy 95 (to help understand the presence of seropositive animals despite the lack of detected carriers in most of those populations)? How are the results in the EMP (with at least one M. ovipneumoniae infected ewe but no detected infected juveniles) reconciled with the point made regarding the potentially pivotal role of chronic carriers in L545-6. Any ideas about how the situation in EMP and also in the other east of Hwy 95 populations with evidence of exposure to M. ovipneumoniae could be replicated (to improve lamb survival in the face of one or more ch
L598-9 Also unpublished data? Or was this reported in Kamath et al. 2019? Was this same strain carried by the detected carrier in EMP?
Figure 1 Consider adding color or hatching coding to indicate populations with cELISA evidence of exposure to M. ovipneumoniae, and to indicate populations with PCR evidence of M. ovipneumoniae carrier presence separately from populations with evidence of M. ovipneumoniae infected juveniles.
In several of the legends associated with the figures and table seem to have formatting issues. Maybe artefacts of pdf generation?
Table S4 There seems to be a typo in the tallies for the RSP PCR population, totalling 0.05.
Table S10 There are three asterisks in the table, but only one is defined. Are the column headers correct? For example, does ‘# adult females at start of year’ refer to population totals (as it seems to read) or to just collared individuals.


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: IMPACT OF MYCOPLASMA OVIPNEUMONIAE ON JUVENILE BIGHORN SHEEP (OVIS CANADENSIS) SURVIVAL IN THE NORTHERN BASIN AND RANGE ECOSYSTEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper describes a clear and original study carried out on different populations of bighorn sheep ranging in different areas of Oregon and Nevada, investigating the impact of Mycoplasma ovipneumoniae and other possible factors (genetic variation, nutrition, population density etc) interacting with survival or mortality of the new generation of weaning Bighorn sheep.

Statistical analysis of results has given a very strong proof of the importance of the exposition to this pathogen as responsible for lamb mortality in all groups screened. Moreover only the DNA evidence on two adults out of n° 13 populations is very difficult to link to clinical pneumonia or outbreaks.

Nevertheless the paper concerns a large collection of ecological and veterinary information for the American “Northern Basin and Range ecosystem” and could be considered an additional contribution to this field, adding scientific data on “at risk” species very important for future  conservation strategies.

Some notes to be considered:

Introduction- overlong with some repetition eg L 58-70 and 83-92

Difficult to follow because of huge compound nouns eg L24-25 Five word noun; L35-36 Four words; L36-37 6 word noun. Sounds like "jargon".

L26 Few readers would understand: California” lineage populations

L30  Really dificult to understand this sentence- please break it down so it is easier to  comprehend

L33 not sure how accurate diagnosis of M ovipneumoniae by behaviour can be

L35-36 We detected M. ovipneumoniae infected juvenile mortalities- do the authors mean they found some young dead sheep positive to M ovipneumoniae?

L36-37	Very difficult to understand: seems to mean that young sheep survived better when there were no infected sheep in the flock

L41-43	Just seems to suggest that the presence of M ovipneumoniae in sheep populations can lead to death which is not surprising but once again “translocated “California” bighorn populations”  won’t mean much to many readers

L44-46	I’m not sure you can conclude much from the loss of one female

L52		some explanation of “k” and “r” is necessary

L64	delete comma after “...2006)”

L74	Please explain “an all-age die-off” readers may not know this jargon. Also L84

Generally discussion could be shortened as some overlap
Experimental design: It’s very difficult to plan such a wide investigation on living, protected animals which is difficult to handle respecting ethical standards, however the study was well performed and described taking into account not only the presence of the pathogen but also some significant genetic and environmental parameters and delivering important information on Mycoplasma diseases risks and genetic variability on  this re-established species in those areas.
Validity of the findings: There are very efficient approaches for analysis of survival data such as weibull or cox model that we don’t see in this work however all data have been always supported by robust statistical approach.
Additional comments: No comments


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

Input:
Title: PATIENTS WITH CORONARY HEART DISEASE, DILATED CARDIOMYOPATHY AND IDIOPATHIC VENTRICULAR TACHYCARDIA SHARE OVERLAPPING PATTERNS OF PATHOGENIC VARIATION IN CARDIAC RISK GENES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper presents genetic informations with low impact for clinical cardiologists due to excessive technical details with not clear clinical utility. It is fundamental that the authors furnish more clinical information and modify some parts of genetic analysis (opinion of genetic section of my hospital). See below
Experimental design: see below
Validity of the findings: see below
Additional comments: Comments for genetic analysis:

1. Authors investigated the cohort of patients by using a NGS panel of 96 genes. The libraries were quality checked by using a BioAnalyzer. However, the diagnostic sensitivity and specificity of this 96 genes panel was not tested. Therefore, for at least a subgroup of variants identified by the NGS panel, their presence should be confirmed by Sanger sequencing.

2 - The potential pathogenicity of the identified variants was investigated by using two distinct classifications. The first consists of a combined score as a result of 10 predictor tools (lines 221-234). By using this, authors classify variants in four classes (from Class I "highest pathogenetic potential" to Class IV "benign"). The second classification is quite common and widely used, the ACMG/AMP classification (lines 234-251). These two classifications gave different results. In fact, as authors state "ACMG pathogenic and likely pathogenic variants were observed in class III, IV and contrary benign and likely benign variants were observed in class I and class II variants". Looking at Figure 3, it appears that 38 variants classified as benign by the ACMG/AMP classification, are present in Class I (highest pathogenetic potential) and in Class II (intermediate pathogenetic potential). It would be better to use the ACMG/AMP classification only.

3 - How authors evaluate the frequency of the distinct classes of mutations in the healthy individuals (KCG group) is confusing. In fact, from the 2150 variants found in KCG group, authors subtract those in common wth the patient group (475). Why they do this? By doing this it is very likeli that authors reduced in the control group the frequency of Class I and II mutations. Therefore, the average frequency of Class I variant in the KCG group is probably higher than the 3.3% claimed by authors.

Clinical observations:

1. A risk stratification assembling VT due to structural heart disease and idiopathic VT is not so clear. The pathogenesis of the different VT forms is totally different and the authors should differentiate more clearly the  different diagnostic  role of genetic analysis  in the various etiologies of VT.

2 Moreover, no information are reported for the different types of idio VT: they include totally different forms (RVOT VT, fascicular VT, aortic VT, etc). More details are fundamental for this aspect


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: PATIENTS WITH CORONARY HEART DISEASE, DILATED CARDIOMYOPATHY AND IDIOPATHIC VENTRICULAR TACHYCARDIA SHARE OVERLAPPING PATTERNS OF PATHOGENIC VARIATION IN CARDIAC RISK GENES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The introduction needs to be expanded to include VT, which is mentioned in the title, the abstract, the discussion and is even one of the keywords, yet is not addressed in the introduction while much space is given to DCM and CHD.

Unfortunately, the WHO reference (number 1) does not seem to be valid anymore and hence cannot be easily accessed. There is a big typo in line 102 with a WHO link that could relate to this. It would be important to find a reference that is readily accessible.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The research question is relevant in the context of human genetics due to an underrepresentation of the population studied in this work (Central asian) in many genetic studies (GWAS and otherwise). While most databases have expanded to incorporate cohorts from a defined geographical origin, coverage of other genetically distinct and/or highly heterogeneous populations has lagged behind. In the context of the genetics of heart disease, the data presented here suggest a common genetic origin to different presentations of VT.

While the percentage of predicted pathological variants is relatively low (less than 6%), the panel was based on known cardiac risk genes hence sampling a relatively small yet clinically relevant group of genes. In addition, most patients (~70%) carried at least one variant from the HGMD with predicted high or intermediate pathogenic potential.

The raw data is available in the NCBI SRA (ID: PRJNA382749), and the analysed data is available in the supplementary material (e.g. Table S2). There is one piece of raw data that it’s not clear if it is available, the sequence data from the 60 Kazakh unrelated individuals (the KCG). The text mentions it as "unpublished sequencing data...".

In the section Distribution of the functional effects of detected mutations, line 327, it says "Based on their molecular function and/or subcellular associations, we assigned the genes into seven groups...". Where was the information obtained from? If a database, which? Was Gene Ontology used? This information would be useful for readers.

The figures highlight the presented data in a clear, understandable manner.

There are a number of typos throughout the text that should be corrected before publication, examples in lines 161 ("...characteristic..."), 241 ("...databases..."), 244 ("...search engine namely Varsome"), 328 ("...we assigned the genes into seven groups...").

Also, formatting errors in lines 91, 92 and 102.


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: PATIENTS WITH CORONARY HEART DISEASE, DILATED CARDIOMYOPATHY AND IDIOPATHIC VENTRICULAR TACHYCARDIA SHARE OVERLAPPING PATTERNS OF PATHOGENIC VARIATION IN CARDIAC RISK GENES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I appreciate the effort the authors have put into addressing the comments from the reviewers (particularly considering the ongoing health situation), and I think the manuscript now closely aligns with PeerJ's publishing standards.
Experimental design: Nothing to add to the previous comments.
Validity of the findings: The authors have not modified the findings in a substantial way to warrant a modification of my positive opinion on the validity of the findings.
Additional comments: There is still a significant number of typos throughout the manuscript:

Line 50 "...were included into study with aim to..."
Line 71 "...subgroups studied which is confirm high impact of this genes in complex pathogenesis of  ..."
Line 96 "...deaths are occur in..."
Etc

The manuscript should be proofread in detail before publication.


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

Input:
Title: THE LONGITUDINAL ASSOCIATIONS BETWEEN BONE MINERAL DENSITY AND APPENDICULAR SKELETAL MUSCLE MASS IN CHINESE COMMUNITY-DWELLING MIDDLE AGED AND ELDERLY MEN
Review round: 1
Reviewer: 1

Output:
Basic reporting: The  manuscript “Skull negatively associated with appendicular skeletal muscle mass in Chinese community-dwelling middle aged and elderly men: a longitudinal study ”  by Xuejuan Xu et al   aimed to investigate longitudinal associations between bone mineral densities (BMDs) and appendicular skeletal muscle (ASM) mass in diﬀerent regions of the body, in Chinese elderly men. The conclusion was that skull BMD was negatively associated with ASM mass, while BMDs throughout the rest of the body were positively correlated with ASM.
The topic may be interesting but the study suffers from several flaws that limit the significance of the conclusions
The article is well written in English.
The structure ofthe article seems to be adequate
Experimental design: Comments.
1). The lack of any information on vitamin D status may represent a limitation.
2).The statement “.osteoblasts of the craniofacial bones, which are  different from other bone tissues of the body,.... and are regulated by different mechanism” does not seem to be supported by adequate references (In fact the study by  Vatsa A was carried out in a murine model and the study by Wu V evaluated  only the morphology of the osteocytes of the jaw).
3). Did the Authors evaluate the coefficients of variation for skull BMD? The precision of Head BMD should be evaluated.
4). Statistical Analysis: i)The Authors should report whether the study variables were normally distributed; if not the statistical analysis should be changed accordingly. ii)The fact that some independent variables are probably  higly correlated may lead to the occurrence of misleading findings; therefore, the multicollinearity of predictor variables should be assessed
5). “Results” section: The values of Head BMD must be reported in both Table S2 and Table S3.
6). “Results” section: The values of Head BMD at each time point (Baseline, 1,2 and 3 year) should be reported in a separate Table.
Validity of the findings: The conclusion was that skull BMD was negatively associated with ASM mass, while BMDs throughout the rest of the body were positively correlated with ASM.
1)  The fact that RIB BMD was inversely associated with muscle mass ( see Tables S6 and S7 should be taken into consideration and discussed.
2). The statement “Compared to ASMI and ASM/SMI, SMI was more sensitive to screen for the low lean mass” (“Discussion” Section; Line 4) should be supported by the results of the present study and discussed.
3). The clinical significance of the negative association between  Skull BMD and appendicular skeletal muscle mass should be better discussed.

Therefore,  the manuscript  in the present form does not seem to be  suitable for publication in PeerJ.
Additional comments: No additional comments


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

Input:
Title: THE LONGITUDINAL ASSOCIATIONS BETWEEN BONE MINERAL DENSITY AND APPENDICULAR SKELETAL MUSCLE MASS IN CHINESE COMMUNITY-DWELLING MIDDLE AGED AND ELDERLY MEN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The present study aimed to investigate longitudinal associations between bone mineral
densities (BMDs) and appendicular skeletal muscle (ASM) mass in different regions of the body, in Chinese community-dwelling middle-aged and elderly men. The authors concluded that  the interrelationship of skull and ASM may be different from that of the bone tissues
throughout the rest of the body and ASM.

Major comments
1. Despite Skull BMD negatively associated with appendicular skeletal muscle mass in Chinese community-dwelling middle aged and elderly men: a longitudinal study, the title of this paper does not mention the relationship between skeletal muscle mass and skull BMD in the introduction. The title reminds us of the biological relevance of the relationship between skeletal muscle and skull.
2. The clinical significance and hypothesis in the manuscript is unclear. The results of this study need to describe what social contributions can be expected.
3. There is no discussion about the relation between sarcopenia or skeletal muscle mass and skull BMD.
4. I want you to specify results that are only important results. Skull BMD does not focus in the results.
Experimental design: I think no problem.
Validity of the findings: The clinical significance and hypothesis in the manuscript is unclear.
Additional comments: Need to structure papers focused on skulls.


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

Input:
Title: THE LONGITUDINAL ASSOCIATIONS BETWEEN BONE MINERAL DENSITY AND APPENDICULAR SKELETAL MUSCLE MASS IN CHINESE COMMUNITY-DWELLING MIDDLE AGED AND ELDERLY MEN
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Overall the manuscript is well structured, and it will add to the current evidence on appendicular muscle mass and bone mineral density in adults. However, I have several concerns over the study and my comments are outlined below,
•	Abstract – Results: “The incidence of low lean mass was 8.2% defined by ASMI, 16.3% defined by SMI, and 8.3% defined by ASM/SMI.”  Is the 8.3% referring to “ASM/BMI” instead of “ASM/SMI”?  “ASM/SMI” is not one of the three indicators to define ASM mass or lean mass in the Methods section.
•	Abstract – Results: Please include the unit for ASMI, SMI, and ASM/BMI (as appropriate).
•	Abstract – Conclusions: “Compared to ASMI and ASM/SMI, SMI was more sensitive to screen for the low lean mass.” Should this read “ASM/BMI”, instead of “ASM/SMI”? Please kindly use the same term throughout the manuscript.
•	Lines 88-104: It will be great if the authors can include the explanations for the contradictory findings.
•	Lines 157-158: Was this trial registered in any clinical trials registry, e.g. Clinicaltrials.gov, Australian New Zealand Clinical Trials Registry, etc.? If so, please kindly include the information in Methods section.
•	Lines 167-177: Is there any reason these biochemical indices were selected?
•	Lines 171-172: “Postprandial blood glucose” – what was the test food (e.g. 75 g glucose) and at which time point the blood glucose was measured (e.g. 1-hour, 2-hour, etc.)?
•	Line 169-177: Please elaborate on “etc.” and it would be helpful to categorize the biochemical indices, e.g. blood lipid profile, full blood count, etc.?
•	Line 180: Please switch the order of “BMD (g/cm2)” and body composition so it’s in line with the heading in Line 179.
•	Lines 184-189: Were these intra- or inter-assay CV?
•	Lines 192-194: “We used three indicators to diagnose low lean mass respectively: (1) an ASMI < 7.0 kg/m2. This approach for defining low lean mass was based on the new Asian consensus definition of the AWGS (Chen et al., 2016).” The previous statements in the Methods (Lines 127-130) stated that “The AWGS proposed a cut-off value for the definition of low lean mass using the ASMI in Asian populations. Using dual-energy X-ray absorptiometry (DXA), the threshold was 7.0 kg/m2 for men and 5.4 kg/m2 for women (Chen et al., 2014).” Please include gender-specific cut off in the Results section, e.g. 7.0 kg/m2 for men and 5.4 kg/m2 for women, instead of using 7.0 kg/m2 for all study participants. Thank you.
•	Line 222: Please define “GGT” and include this in the “Blood sample measurements” section.
•	Line 225: Is there any reason HbA1c was adjusted for, and why gender was not included in the model?
•	Line 233-235: Please include the reason why these variables (i.e. age, weight, HbA1c, HDL-C, Cr, ALT, FT4, diastolic blood pressure, smoking, drinking, and exercise) were included in the model. Thank you.
•	Lines 248-250: “… stratified into two groups based on the ASMI. ASMI <7.0 was used to define low-lean-mass group, and the control group was defined ASMI >=7.0.”  Please use gender specific cut-off to define low lean mass group.
•	Lines 262-263: Please define epidemiological survey data.
•	Line 304: Please change “indcluding” to “including”.
•	Lines 362-363: “We found that using SMI was more easily to find the patients with low lean mass than ASMI and ASM/BMI.” Is this statement referring to the higher prevalence of low lean mass using SMI, compared to ASMI and ASM/BMI?
•	Table 1: Please use gender-specific cut-off to diagnose low ASMI, instead of “ASMI <7.0” for both genders.
•	Table 1: Please kindly include what Q value means either in this table or the Methods section.
•	Figure 3: Please include the unit for ASMI, ASM, and ASM/BMI in the y-axis of Figure 3 (a), (b) and (c).

Thank you!


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: BACTERIAL CONTAMINATION OF NIGERIAN CURRENCY NOTES: A COMPARATIVE ANALYSIS OF DIFFERENT DENOMINATIONS RECOVERED FROM LOCAL FOOD VENDORS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The work presented in this manuscript is interesting, and relevant. The authors have determined the bacterial load on the Nigerian currency notes ₦1000, ₦500, ₦200, ₦100, ₦50, ₦20, ₦10, and ₦5 recovered from local fruit, vegetable, meat, fish, and grain sellers in Nigeria.

2. Please check the manuscript for grammatical errors.
Experimental design: 1.The authors have mentioned that the samples were inoculated on nutrient agar plates and incubated at 37°C for 24 hours. Were these samples also inoculated on other media such as Brain Heart Infusion Agar, Tryptic Soy Agar, Blood Agar, or Mac Conkey’s Agar? Additionally, were the nutrient agar plates incubated at different temperatures and for different time-periods? Using two to four different media and different incubation conditions will increase the accuracy and reduce the bias as compared to using a single medium and incubation conditions.
2.The samples were prepared by immersing the notes in 100 mL Ringer’s solution, the beaker was shaken, the notes removed, and the solution was used as the sample for inoculation. Were these notes inoculated on the agar plates or observed microscopically after sample preparation? It would be interesting to know if the method used efficiently detaches all the bacteria from the surface of the notes or if additional steps are required for successful bacterial detachment.
3.The authors only mention using microbiological techniques for the identification of bacterial isolates. Was 16S rRNA sequencing or MALDI or a similar technique performed for the same? Using one of these molecular techniques in addition to the microbiological techniques is recommended for accurate identification of the bacterial isolates.
Validity of the findings: No comment.
Additional comments: 1. Please check the mean values in Tables 2, 3, and 5.
2. It would be interesting if the authors add a short section comparing the results of the presented study with other similar studies.
3. Figures 2 and 3 contain an additional light orange legend, please clarify what it indicates.


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: BACTERIAL CONTAMINATION OF NIGERIAN CURRENCY NOTES: A COMPARATIVE ANALYSIS OF DIFFERENT DENOMINATIONS RECOVERED FROM LOCAL FOOD VENDORS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Ofoedu et al, report about the degree of bacterial contamination and its dependency on the food vendor type and currency denomination(s). For this purpose, the authors have performed microbiology experiments. Similar information related to Nigerian currency and bacterial contamination has been published earlier, but the authors provided additional information about its relation to the food vendors. This information is useful, however, there are important questions that need to be addressed.
Experimental design: There are several aspects that require revision and/or clarification.
1.	The authors have described, (line 163-164) 100 ml sterile ringer solution was used to immerse each Naira. It would be better if the composition of the ringer’s solution used in this study is also provided. Or details, if it was purchased?
2.	When the authors provided duplicate values, are these values of the same samples (replicates), it’s not easy to understand from the method description.
3.	The author should describe why only nutrient agar was used for the experiment?
4.	I would like to appreciate the amount of work the authors did, characterize >250 samples for each fruit seller/each currency denomination. It’s a lot of work just to characterize the viable colony-forming unit by gram staining and growth media cultivation experiments.
Validity of the findings: 1.	The author mentioned the use of Mannitol salt and Eosin methylene blue media to characterize the isolates, however, there is no information presented in data, how many were pathogenic and non-pathogenic strains of staphylococcus.
2.	Line-203: The TVC for the fruit seller is mentioned wrong, it should be 3X103-2.2X105, (according to the supplementary data provided).
3.	I would like the authors to explain, if the TVC of ₦10 (2nd seller) is 1X103 then, how it is possible to have higher CFU/ml (1.1 for E.coli)?
Additional comments: 1.	The English language should be improved to ensure easy understanding for the international audience.
2.	For eg. Line 160- The wire loops were sterilized by flaming, need to be removed and rewritten. The whole paragraph of preparation of materials /samples should be modified.
3.	Some details are unnecessary, for eg. Line 174- “in an invert position”.
4.	The authors need to cross-check all the values from all the tables, the data described in the table is confusing.
5.	The time duration matters for bacterial transmission via currency note. Hence, the author should describe the time difference/duration between the sample collection and sample processing.
6.	In the case of Meat, fish sellers, the sampling should have been done on blood agar. To provide rich nutrients for pathogenic strains that might be present.


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: BACTERIAL CONTAMINATION OF NIGERIAN CURRENCY NOTES: A COMPARATIVE ANALYSIS OF DIFFERENT DENOMINATIONS RECOVERED FROM LOCAL FOOD VENDORS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The manuscript has definitely improved upon revision. The revised manuscript reads well with a clear methodology, discussion of obtained results, and conclusion.


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

Input:
Title: BACTERIAL CONTAMINATION OF NIGERIAN CURRENCY NOTES: A COMPARATIVE ANALYSIS OF DIFFERENT DENOMINATIONS RECOVERED FROM LOCAL FOOD VENDORS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Changes made.
Experimental design: Changes made.
Validity of the findings: Changes made.
Additional comments: The authors made all the suggested changes and significantly improved the manuscript. I approve the manuscript for publication.


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

Input:
Title: ASSOCIATION BETWEEN FOOT THERMAL RESPONSES AND SHEAR FORCES DURING TURNING GAIT IN YOUNG ADULTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The aim of this work was to examine the shear-temperature relationship using turning gait with varying radii to manipulate magnitudes of shear onto the foot. The study is a very interesting and clearly written. The experiments are appropriated to analyze the research question. However, some aspects need to be addressed before to be considered to publication.
Experimental design: The research question was well defined and relevant. The investigation was adequate to assess this research question. More information is necessary for the methods;

Methodology, participants: Did the participants receive instructions related to nutrition, exercise the previous days, creams, alcohol, tobacco, etc., aiming to reduce the effect of confounding factors and ensure correct skin temperature measurements?

Methodology, line 153: Please, indicate the model of the infrared camera.

Methodology: More information about the infrared thermography protocol is necessary. I suggest to the authors to review this checklist (https://doi.org/10.1016/j.jtherbio.2017.07.006) to check which aspects are necessary to be provided in the manuscript.
Validity of the findings: No comment
Additional comments: In my opinion, the introduction was well written and perfectly explain the rationale of the study. However, I think that it is also important to mention the sweat and vasoconstriction/vasodilation mechanisms of the foot to better understand the foot skin temperature responses during walking.

Introduction, lines 40-42, applicable also for the second paragraph: I think that the authors need to specify better the sentence, describing distances, intensities, or characteristics of walking. This comment is because I have observed reductions in foot skin temperature after walking. A previous study stated this idea after barefoot walking 100 m at a comfortable speed (https://doi.org/10.1080/21681163.2018.1542349). Maybe authors also could show this contrast on the results between studies, which could support also the necessity of their study.

Methodology: It was used tympanic thermometer; however I am not sure if this data was used in the analysis. I suggest removing if this data was not used in the statistical analysis. Moreover, tympanic thermometer has important limitations in the measurement of core skin temperature (http://dx.doi.org/10.1016/j.jtherbio.2014.10.006).

Methodology, lines 154-156: It is interesting the methodology used to ensure consistent baseline temperatures. Do you have references of previous studies that used this methodology? I acknowledgment to the authors to have found a possible solution to the problem of performing several conditions in the same session on the effect of the order on baseline skin temperature. However, I have concerns about if the difficulty to do always in the same way this methodology could be a factor that explains the unexpected results of lower baseline skin temperature at the lower radius, which I think needs to be discussed.

Methodology, figure 2: I suggest to the authors to use the rainbow palette for the figure. This palette is more appropriate for human skin temperature. In addition, I suggest to the authors to modify the figure to represent the ROIs analyzed.

Methodology, line 197; Please, modify subjects by participants.

Methodology, secondary analyses, lines 224-246: It is unexpected that after statistical analysis appears more information regards the definition of more variables. Readers only could understand why authors include this information after reading all the results section. To clarify, I think that it could be better to include explanations of the variables before the statistical analysis section, and the extra analysis within the statistical analysis section without any subtitle.

Results, Figure 3 and 4: I would suggest to authors to reduce the extension of the figure captions and to write in a more systematic way. It is not necessary all these explanations that appear in other sections of the manuscript (e.g. statistical method used) or describing the results (e.g. Figure 2.B demonstrates…..). However, I would suggest the use of symbols in the figures to describes significant differences.

Discussion: Please, check the explanations about the decrease in skin temperature during walking mentioned in this reference (https://doi.org/10.1080/21681163.2018.1542349)

Discussion: In relation to the effect of gender on skin temperature, I would suggest authors check this recent publication (https://www.sciencedirect.com/science/article/pii/S0306456520300681)

Discussion: Please, discuss the practical applications of your results.


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

Input:
Title: ASSOCIATION BETWEEN FOOT THERMAL RESPONSES AND SHEAR FORCES DURING TURNING GAIT IN YOUNG ADULTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This article met the 5 “Basic Reporting” elements identified by PeerJ.  Structure- and format-wise, the manuscript was laid out in a way that was easy to navigate.  It was very clear the authors had spent time thinking about how to present and organize the data, and that the paper was very purposefully assembled.
Experimental design: I have mixed feelings with regards to the 5 “Experimental Design” elements identified by PeerJ.  Divorced from the data, it all looks good.  The authors explored and reported on many variables (both primary and secondary to the research goal), and I appreciated the thoroughness with which data was laid out.  I understand/agree/empathize with the authors’ opinion (implied in lines 84-93) that, methodologically, standard force plates are tricky to use when trying to study lone shear forces.  With all that said, when I consider the “Experimental Design” elements in light of the actual data, much of the data in unexplainable or unexpected, which suggests that something methods-wise wasn’t accounted for or some confounding factors interfered (explained in the following section).
Validity of the findings: My larger questions/concerns with the manuscript are with the data and its interpretation.  I’m not a biomechanics expert and am focusing my review on the foot temperature components.  What follows is a “thought map” to how I perceived the paper.  Bullet-points are used here for communication purposes, but the four concepts are of course intertwined with each other, and some mental wrestling was needed to make this condensed list.
1.	Foot temperature decreased from pre- to post-exercise (lines 288-299 and Figure 4), or rather, it decreased across males and stayed essentially the same across females (lines 349-354).  Based on the majority of previous foot temperature studies, from multiple labs, one would expect foot temperature to increase during walking, regardless of sex, as the text discloses in lines 375-377.
2.	The fact that baseline temperatures varied (lines 275-279, Figure S1) is also unexpected.  The text says these results cannot be explained (lines 388-402).  Since there are differences in baseline temperatures, but no differences in post-exercise temperatures (lines 284-286), this raises questions about the influence of the baseline temperature variation on the post-exercise temperature results.
3.	Experimental procedures included artificially manipulating the subjects’ foot temperature, both through cooling (lines 154-156) and warming (lines 234-246).  I understood that cooling happened once for each trial, but I couldn’t understand if the warming was done once or multiple times, or when it was performed relative to the other procedures.  The text indicates the cooling procedure was to homogenize baseline temperatures (line 154), but that seems at odds with Thought #2 above.  Regardless, this is a lot of artificial manipulation for an experiment that relies on “natural” foot temperature measurements, and may partially account for the results from Thoughts #1 and #2 above.
4.	The floor was notably colder than subjects’ feet (lines 382-383 compared with lines 349-351 and 352-354).  Although the paper initially states that statistics indicated no effect of floor temperature on changes in foot temperature (lines 384-386), the paper then hedges on that in lines 386-388 and again in 440-442.  With regards to line 430, the paper states that males’ broader feet may have resulted in their experiencing lower shear forces; given the floor temperature, males’ broader feet also means increased surface area contact, and in turn greater ability to dissipate heat through the cooler floor, but this concept is not included in the text.  The most parsimonious explanation appears to be that the cooler floor DID have an effect.  I understand the chosen statistics suggest otherwise, but from a bird’s-eye-view of the data that doesn’t make sense.

Other minor concerns included: the sample size (line 125 says 24 subjects would supply 80% power, and this study included data from 18), especially in light of the sex effect; the use of tympanic temperatures as a measurement of core temperature (as these can be misleading); and the suggestion that the method can be used to identify people with conditions like diabetes or “neuropathic” conditions (as suggested in line 30).
Additional comments: Given all of these “moving parts”, I’m uncomfortable with the data, the conclusions, and possible generalizations (especially across sexes or to people with medical conditions).  The wording of the paper may have played a role.  The abstract only talks about increases in foot temperature (lines 14, 22, and 24), and doesn’t mention that post-exercise temperatures were lower than pre-exercise temperatures.  Similarly, the portion of the Introduction related to foot temperature (lines 44-61 and line 71) also only talk about increases in foot temperature.  When the reader gets to Figure 4, the results are quite different from what one would intuitively expect and what the paper has prepared the reader for.  Phrases like “delta-T increased” (lines 288 and 292) are problematical.  The abstract says a positive association between shear forces and temperature increase was found (lines 23-24), and the results indicate that smaller radii were associated with greater shear forces (254-255)…so, it’s less that “delta-T increased”, and more that smaller radii were associated with a smaller change in delta-T from pre- to post-exercise (radius 2 m has larger bars than radius 1 m because the temperature decrease was more blunted in the radius 1 condition than the radius 2 condition due to shear force thermal effects).


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: ASSOCIATION BETWEEN FOOT THERMAL RESPONSES AND SHEAR FORCES DURING TURNING GAIT IN YOUNG ADULTS
Review round: 1
Reviewer: 3

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

General
The writing is crisp, clear and informed by a solid understanding of the topic and previous literature.  It is a joy to read.

Title
The general guideline here is Population, Intervention, Outcome.  If you can squeeze in information about the participants it would be excellent.  Maybe include the phrase “young adults”?

Abstract
Succinct and comprehensive.  I appreciate the inclusion of some actual data here.

Introduction
The argument developed is cogent and well structured.  The logical flow of the literature support for the experiment is clear and convincing.  This is so well written I have nothing to add, and this is an extremely rare event.

Methods
The methods, though complex and highly detailed, are well thought out and seem technically sound.  The writing is again clear and complete, and each decision seems well rationalized.  The experimental design would seem to induce dizziness, but other work on a 1m radius circle did not result in a deleterious or dangerous balance issue for participants.  I believe the methods are sound, with one exception I do not fully understand…

Lines 234-246.  The description of the shear stress calculation is somewhat confusing to me.  I would like to know what the technical difficulties were, and if the MATLAB code has any reliability or validity data?  How accurate was this method to determine sheer stress?  Was this just a method to estimate area?  It’s not clear.

Results
The results are clearly presented and very well polished.  The progression through the variables of interest is appropriate and well ordered.  It’s easy to follow. The integration of the graphical elements into the text is performed flawlessly.  I think the addition of the df and F are generally unnecessary, but in this case I think it is best to include them.  It makes the statistical results more comprehensive.

Graphs
The graphical elements are expertly crafted and illuminating.  I appreciate the clean layout, and the appropriate ink density for the most important aspects.

Tables
--
Discussion
I think this treats the data quite well, and all reasonable confounding factors that may be attributed to the heating of foot tissue are discussed.

I think the venous return should be considered too, and not just arterial supply.  It is more likely that an inability to remove excessive heat from the plantar surface of the foot contributes to foot temperature more than the arterial blood is warming the plantar tissue.  After all, the sheer stress is supposed to be heating the foot from the mechanical friction.  I think a little speculation here about venous return is warranted.

I was also hoping for some comment on the clinical utility or possible pathothermodynamics of the forefoot that might put a diabetic at greater risk of ulceration with elevated plantar tissue.  Just how dangerous is the temperature increase you observed?

References
This seems comprehensive and includes the most salient literature.


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: ASSOCIATION BETWEEN FOOT THERMAL RESPONSES AND SHEAR FORCES DURING TURNING GAIT IN YOUNG ADULTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The only minor comment I should make is that figure 2 indicates "represent the areas to gather the entire foot (white)", and I think it is not white, but green.
Experimental design: The authors provided more details to the experimental design. The only doubt for authors and possibly for future readers is that basal temperatures were not the same, but authors have provided this as a limitation of the results of the study.
Validity of the findings: The presentation of the results was improved.
Additional comments: The authors have addressed all my comments satisfactory. Congratulations to the authors.


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

Input:
Title: GENOME-WIDE IDENTIFICATION, EVOLUTION, EXPRESSION, AND ALTERNATIVE SPLICING PROFILES OF PEROXIREDOXIN GENES IN COTTON
Review round: 1
Reviewer: 1

Output:
Basic reporting: Peroxiredoxins (PRXs) are ubiquitous thioredoxin-dependent peroxidases that have been relatively well characterized in plants over the past 25 years. They display some diversity regarding redox-active Cys and catalytic mechanisms, leading to a recognized classification in the plant kingdom (see reviews by Dietz 2011, ARS, and by Liebthal et al., 2018, ARS). They fulfil key roles in the maintenance of redox homeostasis via the scavenging of hydrogen peroxide, but also in the direct transmission of redox signals to protein partners as shown by the key findings published in the last years.

The manuscript by Feng et al. aims to characterize in a thorough way the PRX families in 4 cotton species, in which these proteins have hardly been studied. Thus, the submitted work is original and contains a huge amount of data related to sequence analysis, expression patterns and subcellular localization. Some, such as those related to alternative splicing, are novel and interesting. Therefore, this work could be a valuable contribution to the field. However, the present version of the manuscript is quite hard to read, even for scientists familiar with the field of plant PRXs. This is notably due to: i) the writing style, ii) an inappropriate classification of PRXs and iii) too little consideration in the bibliographical context. In other respects, the expression data and their interpretation are highly questionable.
Experimental design: The research plan is globally well designed.
Validity of the findings: - 1) The proposed classification of PRX genes in Figure 1 is not appropriate and very confusing for people working on plant PRXs. Further, it does not even correspond to the one used for animal PRXs (Perkins et al. 2015, TIBS). The authors have to take into consideration the extensive work performed by Prof. Dietz’s group and published in several reviews and articles (Dietz, 2011, ARS; Liebthal et al., 2018, ARS). TPX, PRX2, PRX5, PRX1 and PRX6 are in fact PRXIIB, PRXIIE, PRXIIF, 2-CysPRX and 1-CysPRX. This classification is commonly used in the plant field.

- 2) Similarly, the classification proposed by the authors in Fig. 3 (PTC2 and PTC4, lines 241-265) should be reconsidered in the context of what is already known on plant PRXs.

- 3) The expression data (presented in Figures 7 and 8, the quality of which is poor) are highly questionable. The authors have to take care in their interpretation. How do they explain the highly increased expression of several PRX genes 12 h in control conditions? This is very surprising and calls into question the validity of their findings since the control levels should be the same throughout the experience. This is not the case for many genes.
Numerous interpretations are incorrect, for instance, the authors claim lines 373-374 that salt induces the expression in leaves of PRX11D and PRX15D, but when looking at Fig. 8, the increases are very weak.
Additional comments: - 1) The cited bibliography regarding plant PRXs is too limited and not up to date. Indeed, in the Introduction, the authors put relatively more emphasis on animal PRXs than on plant PRXs. Further, important findings regarding plant 2-CysPRX functions, notably in signaling pathways,  that have been obtained in the last years are not cited (Awad et al, 2015, Plant Phys; Cerveau et al., 2016, Plant Sci; Yoshida et al., 2018, PNAS; Vaseghi et al., 2018, eLife; Cerveau et al., JExpBot, 2019…). The references cited are not always accurate. For instance, Cerveau et al., line 468 is not the right one for photosynthesis deactivation. Banmeyer et al, (2005) (line 472) is not present in the reference list. Conversely, Cerveau et al., (2016) is present in the list (line 617) but not cited in the text.

- 2) The manuscript is rather hard to read due to the poor writing style and too many awkward sentences (for instance, “…all PRX genes increased…” lines 546-547).Thus, I recommend the authors to have their manuscript edited by a native English speaker. In addition, the high number of genes cited makes the style very confused (see paragraph from line 291 to line 317) or vey repetitive in some parts (see lines 411-419, where five consecutive sentences are constructed in the same way). The authors should highlight the main results in a more synthetic way.

- 3) The Discussion has to be thoroughly improved. The present version does not take sufficient account of bibliographical data (see first comment). The paragraph from line 500 to line 519 again comments on the results

Minor comments:
- 4) What does mean “PRX protease” lines 46-47?
- 5) Line 331: Suppress the last sentence.
- 6) Lines 463-464: Suppress the title of the reference.


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

Input:
Title: GENOME-WIDE IDENTIFICATION, EVOLUTION, EXPRESSION, AND ALTERNATIVE SPLICING PROFILES OF PEROXIREDOXIN GENES IN COTTON
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper by Feng et al. identified a total of 47PRX genes in the cotton genome. The authors showed that the PRX gene family is divided into six subfamilies according to the phylogenetical analysis of the conserved active site. Furthermore, they also confirmed that cis acting elements could effectively regulate the expression of PRX genes. Based on the results presented in this paper, most PRX members were situated in chloroplasts, and a few members were found in the cell membrane and nucleus.

The language of the paper could be improved a bit if reviewed by a native speaker. The introduction provides a good, generalized background of the topic that quickly gives the reader an appreciation of the wide range of applications for this experiment. The title and abstract are appropriate for the content of the text. Furthermore, the article is well constructed, the experiments were well conducted, and analysis was well performed. Almost in all cases I could find that the references are relevant. The literature cited is relevant to the study, but there are several instances, which have been noted in the text, in which the author makes assertions without substantiating them with references.
Experimental design: The experimental apparatus is quite standard, and is appropriate for the study. I don’t think any additional experiments are necessary to validate the results presented here, However, I believe the authors should add some more information to the materials and method section as some information are missing in the current format. The authors need to improve the clarity of the methodology section by bringing more information on how they did the experimental parts. For example, when comes to phylogenetical analysis, the authors are not precise on how they did the phylogeny, what was the bootstrap value they used, what was the model they used for their phylogeny, and so on. In another example, when the author talks on RT-PCR analysis it’s not clear which statistical analysis used by authors? Please also see my comments on the text.
Validity of the findings: All data to support the idea behind this work have been provided. However, the authors should bring more information on the statistical analysis of their RT-PCR  data as suggested earlier. The conclusion part needs to be written better than the current format. You should develop the conclusion by briefly restating the rationale for your experiment and the purpose of the article, then discussing the conclusions you have drawn. You should also discuss the implications of your experimental findings and where you think research in this field should go from here.
Additional comments: The paper by Feng et al. identified a total of 47PRX genes in the cotton genome. The authors showed that the PRX gene family is divided into six subfamilies according to the phylogenetical analysis of the conserved active site. Furthermore, they also confirmed that cis acting elements could effectively regulate the expression of PRX genes. Based on the results presented in this paper, most PRX members were situated in chloroplasts, and a few members were found in the cell membrane and nucleus.
This is an interesting study and the authors have collected a unique data-set using genomics and molecular genetics approaches. The paper is generally well written and structured. However, in my opinion the paper has some shortcomings in regards to some data analyses and text, and I feel this unique data-set has not been utilized to its full extent. In the text I have provided some remarks on the text. In several instances I also suggested to cite more relevant literature. Furthermore I made additional suggestions for more in-depth explanation of the analyses of the data. Given these shortcomings the manuscript requires minor revisions.


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

Input:
Title: GENOME-WIDE IDENTIFICATION, EVOLUTION, EXPRESSION, AND ALTERNATIVE SPLICING PROFILES OF PEROXIREDOXIN GENES IN COTTON
Review round: 1
Reviewer: 3

Output:
Basic reporting: This paper entitled "Genome-wide identification, evolution, regulation, and alternative shearing profile of peroxiredoxin genes in cotton" focused on the survey and characterization of PRX gene family in cotton species. This is an investigation study important to be performed in different cotton species, due to the low number of studies of the PRX family in plants. The manuscript is generally well written and provides new interesting information to cotton genome annotation. However, I have some suggestions for improvement:
(1) Section Material and Methods, at the final of the 'Plant material treatments and expression analysis' subsection I miss the description of experimental design. How was performed the experiment, completely randomized design or other? Please make this issue clear in the body of the text.
(2) Section Results, subsection 'Genome-wide identification and conserved motif analysis of the PRX gene family in cotton', line 223, change 'The MW and pI' to 'The Molecular Weight (MW) and Isoelectric point (pI)'
(3) Section Results, subsection 'Analysis of cis-acting elements in the promoter region', line 331, you speculate that PRX genes are sensitive to drought stress. However, there are many papers related to this issue. Please, rewrite the phrase or remove it.
(4) In the same section, what are the biological processes that PRX genes participate in?
(5) Supplementary files, please make available the figure S1 in better quality.
Experimental design: Please, see the general reporting
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: GENOME-WIDE IDENTIFICATION, EVOLUTION, EXPRESSION, AND ALTERNATIVE SPLICING PROFILES OF PEROXIREDOXIN GENES IN COTTON
Review round: 2
Reviewer: 1

Output:
Basic reporting: Compared to the initial version, Feng and collaborators have substantially improved the manuscript, notably regarding bibliography, writing style and classification of PRX genes. In the present version, they take in consideration the previous knowledge on these thiol-peroxidases. This is an important point since this modification emphasizes their original findings regarding the various isoforms in relation with Cys number and alternative splicing. Thus, their work provides valuable information about this class of peroxidases that fulfil key roles in maintenance of redox homeostasis in plants as well as in other organisms.
Experimental design: OK
Validity of the findings: Needs some improvement (see below)
Additional comments: Nonetheless, I have a few relatively important concerns that need to be addressed:

1) The writing style of the Abstract is still poor, since it has not been modified compared to the first version. It has to be revised in relation with the changes made in the manuscript.
- The first sentence is too simplistic. The authors should delete “in the body”.
- PRXs are now recognized not only to scavenge peroxides, but also to interact directly with other proteins and modify their redox status.
- Line 4: correct “families” to “family”
- The writing of the sentence “And differential...” needs to be improved.

2) Line 285-305: In this section, the authors already address subcellular localization, which is the topic of the last section in Results. They should move this part from the first section to the last one.

3) Regarding classification, the authors made substantial work to put it in relation with that performed by Prof. Dietz’s group. But there is still a rather surprising point. Several main PRXII types have been characterized in plants by many groups (PRXII-B, PRXII-E and PRXII-F). In cotton, the authors report about PRXII-B and PRXII-E isoforms, but nothing concerning PRXII-F, which is a well known mitochondrial isoform identified and characterized in various plant species (Arabidopsis, pea, tobacco, Acer..). Thus, it’s is very unlikely that there is no PRXII-F in cotton. Is this isoform classified within PRXII-B or PRX-IIE? Or is there another explanation? The authors have to answer and discuss this point. I checked myself sequences and found that some isoforms in the PRXII-E class (previously PRX5 type in the first manuscript) correspond to the PRXII-F type.

4) Regarding expression data, interpretation is not always convincing and the authors have to carefully check the whole part. For instance, the authors claim line 436 that expression of GhPRX14-D in root increases rapidly in response to salt (Fig. 7 N). This is not true, and nothing like the expression patterns of GhPRXs 11-D and 15-D, for which strong increases are indeed observed.

5) There are many errors in References and this is very confusing for the reader. For some, there are only initials (lines 52, 546, 574, 645, 775, 822). For others, first names and last names are reversed: Keisuke et al is in fact Yoshida et al (line 67), Mohamad-Javad et al  corresponds to Vaseghi et al. (line 69), Pablo et al corresponds to Pulido et al (line 79), etc... The authors have to rigorously check all the references both in the text and in the list.

Other points:
-	Line 57, Arabidopsis has not to be in Italics
-	Lines 97-98: delete dots after Gossypium
-	Lines 379, 380, 422 and throughout the manuscript: “”cis” in Italics.
-	Line 277: replace “conservative” by “conserved”
-	Line 389; replace drought-induced” by “drought-related”. Cis elements are not induced.
-	Line 406: insert “one” after “only”
-	-Line 416: what is the relationship between zein metabolism and cotton?
-	Line 546: why “nitrate”?


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

Input:
Title: GENOME-WIDE IDENTIFICATION, EVOLUTION, EXPRESSION, AND ALTERNATIVE SPLICING PROFILES OF PEROXIREDOXIN GENES IN COTTON
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper entitled "Genome-wide identification, evolution, regulation, and alternative shearing profile of peroxiredoxin genes in cotton" focused on the survey and characterization of PRX gene family in cotton species, received a lot of improvement since from the last submission. I considered this paper ready for publication after some minor changes.
1. Please, remove the dots in the final of the genders in the lines 97 and 98.
2. In figure 7-8 is hard to see the different times due to small letters.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This study will be very helpful for a better annotation of cotton genomes and will help future studies on the PRX family.


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

Input:
Title: GENOME-WIDE IDENTIFICATION, EVOLUTION, EXPRESSION, AND ALTERNATIVE SPLICING PROFILES OF PEROXIREDOXIN GENES IN COTTON
Review round: 3
Reviewer: 1

Output:
Basic reporting: In the title, I would suggest to replace "regulation" by "expression". This better reflects the content of the paper.
In Figure 2, correct at the top of the circle "PRXIIE" to "PRXIIF"
Abstract, lines 33-34. There is twice the same idea in the sentence that has to be revised Here is a suggestion for revision: Add "also" before "involved" and suppress ", but also interact directly... redox status".
Line 62: Replace "4 targeted chloroplasts" by "four were found to be targeted to chloroplasts".
Line 68: replace "Keisuke et al" by "Yoshida et al. (2018)".
Line 71: suppress "(Yoshida et al. 2018)"
Line 266: suppress "of the cotton PRX protein sequences".
Line 277: suppress "of the protein active sites".
Lines 284-285: revise by "The two catalytic Cys residues in PRXQ are separated..."
Line 290: replace "to" by "in".
Line 291: replace "which has..." by "and share the conserved sequence..."
Line 293: replace "which have...." by "and display a conserved motif (FG..)"
Line 332: corect to "Li"
Line 385: add "in terms of presence" after "second"
Line 403: correct to "MYB"
Line 460: what is the meaning of FPKM?
Line 464: suppress "only a"
Line 465: replace "...can cause...function," by " ... can modify protein sequence and function".
Line 504: suppress "Most".
Line 506: replace " and as a plastidial thiol-peroxidases" by "and are presumed to act as plastidial thiol oxidases".
Line 511: replace "PRXQ exists on" by "is localized on".
Line 564: replace "may be sensitive" by "respond".
Line 566: suppress "and MYB protein regulation".  This is not comparable to stress or hormone treatments.
Line 569: replace "would like" by "aimed".
Line 573: suppress "Therefore"
Line 577: replace "the induction of" by "treatment with".
Lines 578-280: misspoken sentence. SA is not known to directly scavenge ROS, but to activate the expression of genes involved in this process. Please rephrase.
Lines 581-582: Awkward sentence. Do the authors mean that the genes belong to those having repressed expression?
Line 586: add "the expression of" before "10".
Line 591: replace "and drought will increase" by "which increases".
Line 597: replace "After" by "Since". delete "adversity".
Line 599: replace "identify the element" by "interact with these elements".
Line 606: replace "lowest" by "less".
Line 613: replace "as is the" by "such as".
Line 626: replace "cycle in" by "of".
Line 627: replace "signal transduction" by ", and transducing signal".
Line 627: suppress "and so on".
Line 637: add at the end of the sentence "and localization".
Lines 644-648; Repetition in the end of conclusions. Suppress: ". It aims to study... process of biological evolution".
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Feng and collaborators have further improved the manuscript. The present version is globally satisfying. Nonetheless, the writing style and English language need to be carefully checked and some errors corrected.


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

Input:
Title: GENOME-WIDE IDENTIFICATION, EVOLUTION, EXPRESSION, AND ALTERNATIVE SPLICING PROFILES OF PEROXIREDOXIN GENES IN COTTON
Review round: 3
Reviewer: 2

Output:
Basic reporting: Dear Editor:
Title: Genome-wide identification, evolution, regulation, and alternative splicing profile of peroxiredoxin genes in cotton (#44008)

The manuscript by Feng et al, provides some very interesting results on the successful identification of PRX family genes in cotton. These results could be used to shed light on the functions of the genes of this family in this important plant. I can see that the authors have put a lot of effort to revise the manuscript. In general, I’m happy with the changes that the authors made to the paper and am suggesting that the paper is now acceptable for the publication.
Experimental design: The experimental apparatus is quite standard, and is appropriate for the study. There is no need to any do additional experiments to validate the results presented here as the results are very clear in the current format. I can also see that the authors also addressed my previous concerns on this section.
Validity of the findings: Again, I can see that the authors made changes to the discussion part as was suggested before and now I'm very happy with the validity of their results. The authors also discussed the implications of their experimental findings and answered my question on where they think research in this field should go from here.
Additional comments: The authors addressed all my concerns and implemented all suggestions in the current version of the manuscript. So, In general, I'm very satisfied now with the changes that the authors made to this manuscript and I highly recommend this paper for publication in Peer J Journal.


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

Input:
Title: CODING POTENTIAL OF CIRCRNAS: NEW DISCOVERIES AND CHALLENGES
Review round: 1
Reviewer: 1

Output:
Basic reporting: I read this review with interest. It is focused on subject undergoing intense (and controversial) study, such as the biology of circRNAs and their roles as non-coding but also protein coding RNAs. I found that the the review is of broad and cross-disciplinary interest and within the scope of the journal. Moreover, to my knowledge there are not any similar reviews in this particular subject. However, I found the introduction a little bit scarce, specially for a review paper.
Experimental design: To my view, I found unnecessary the inclusion of this "survey methodology" in a review paper. Moreover, the authors simply describe a series of keywords (such as "noncoding RNAs, circRNAs or protein, among others) and the classical bibliographic databases used to prepare the manuscript. Does it mean that the authors read and analysed ALL the manuscripts retrieved from the searches described in the survey methodology? Because the answer is most likely negative, I suggest a less broad description of the methodology (if totally required by PeerJ). Sources are adequately cited. As mentioned before, I found the introduction a bit scarce, specially regarding the renaissance of circRNAs and the different labs involved in their rediscovery (ie. Salzman Lab, Kjems Lab...). In general, the review is logically organized.
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: CODING POTENTIAL OF CIRCRNAS: NEW DISCOVERIES AND CHALLENGES
Review round: 1
Reviewer: 2

Output:
Basic reporting: There is an important work regarding the number of literature references they managed. However, several major issues in the bibliography which require rectification were found. In line 77, the authors mentioned circHIPK3. However, it is not referenced as Zheng Q et al; Nature communications 2016. In line 140, the authors mentioned that the IRES were originally identified in virus and to illustrate this they used the reference 40. However, this referenced is not appropriate to illustrate this point and the reference Pelletier J, Sonenberg N. Nature 1988 is more convenient. In line 205, the authors referenced Dawood et al as reference 58. However, this reference is Dudekula BD et al. RNA Biol 2016. In line 215, the authors used Legnini et al. as reference 57 but it is the reference 63. In line 236, the reference is wrong, Zhang et al is reference 64, and it is the properly reference when the authors want to illustrate the SHPRH-146aa as they have done in line 306. Line 247, the authors indicate the reference 65 like Yun et al. However, the reference 65 corresponds to Yang Y et al. The authors mentioned reference 74 (line 286) to illustrate about of the siRNAbased therapeutic agents such as Macugen and bevacizumab (lines 286-287). However, this reference shown that Macugene is a VEGF antagonist aptamer and Bevacizumab is a humanized primary antibody which inhibits VEGF-A. Probably was a typing or editing mistake but the review refers to Bevasiranib as a siRNA-based anti-angiogenic agent proposed for the treatment of wet age-related Macular degeneration (AMD). The reference listed as 63 (line 445) is not on the text. When the authors show the evidence for endogenous circRNA direct translation they did a nice job illustrating with very well referenced examples (circZNF609, circMB1, circSHPRH, and circ FBXW7). However, considering that there are few examples of circRNAs with encode capacity, the examples of circLINC-PINT, which encodes for a PINT87aa peptide controlling of cell proliferation and tumorigenesis (Zhang M et al. Nature Communications, 2018. doi:10.1038/s41467-018-06862-2), and circβ-Catenin which promotes liver cancer cell grown (W.-C. Liang et al. Genome Biology, 2019. doi:10.1186/s13059-019-1685-4) should be properly mentioned and referenced.
The structure of the article conforms to an acceptable format of “standards sections”. Figures and the table are relevant to the content of the article. However, the table 1 should be improved including the circLINC-PINT and the circβ-Catenin RNAs examples. The kind of circRNA in virus, artificial circRNAs or endogenous circRNAs showed in the table 1 should be clearly delimit using a color code or enclose them in boxes. There is a minor type issue, in the column; functions, it is typed FALG reporter instead FLAG reporter.
There is a new review about how the circRNAs are translated by non-canonical initiation mechanisms; L.H. Diallo et al; Biochimie 2019. https://doi.org/10.1016/j.biochi.2019.06.015. However, the computational prediction as a tool to predict future circRNAs with potential to encode peptides was not one of the subjects of this review. Additionally, due to the publication dates so close between the reviews, it is possible that the authors were not aware. Nonetheless, it is strongly recommended to include the reference in the new version of the review
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: VISION OF CONSPECIFICS DECREASES THE EFFECTIVENESS OF ETHANOL ON ZEBRAFISH BEHAVIOUR
Review round: 1
Reviewer: 1

Output:
Basic reporting: The introduction is lacking background and references on social isolation/social environment on zebrafish anxiety response

The known anxiolytic effect of ethanol on zebrafish is not mention in the introduction and not until part way through the methods on line 137. It should be mentioned earlier in the manuscript

L.84-85: You start the sentence by saying : "recent evidence..." but failed to cite any references. Please add references at the end of the sentence

L.87-96: in this paragraph you mixing 2 concepts: That visual and olfactory conspecific cues play a role in reducing stress/fear in zebrafish AND that exposing and testing fish in the same environment play a role in reducing stress/fear response. Maybe try to make the distinction clearer by having 2 separates paragraphs

Not sure Table 1 is needed since the authors don't analyze or discuss the data in details. The authors could either discuss the table in more details or (my preferred option) get rid of the table and just have a sentence saying half of the studies looking at the effect of ethanol om...published the last ... years had conspecifics in view….. Also the table is very small and hard to read

Fig 3 needs a legend that explains the colour coding

In your reference list, make sure the species Latin names are italicized.
Experimental design: The methods are well described but could be clearer in some places:
- lines 122 :fish were never housed in isolation. For that to be relevant, we need more background on the effect of social isolation on fish (see earlier comment about the introduction)
- lines 161-162: why not testing the fish in the same arena that it has received ethanol?
- it is not clear why you are using another group of fish to look at distance moved and side preference (it is briefly mentioned in the discussion on l 278-280, this should appear here, in the methods). Presumably, you could have measured those variables using Ethovision while also measuring time in thigmotaxis. time in inner zones...Ethovosion allows you to have multiple zones on top of each other. Testing another group adds more variables that hard to control for (group, time effect...)

Line 214: 3 trials out of how many? Please specify

Line 223: I would recommend using a parametric test with a non-gaussian assumption (e.g.: glm) and instead of running 3 different ANOVA, having all the variables in the same model.

Also, since you used a mix of males and females. have you look at the effect of sex on boldness behaviour? You should add the variable sex in your analyses. See Roy and Bhat (2018) or Dahlbom et al 2011 for sex difference in boldness behavior in zebrafish
Validity of the findings: Statistics: You must provide F values and df when presenting ANOVA results.
Have you check for multicollinearity? Presumably variables such as thigmotaxis, transition and inner zones will be highly correlated variables. It may pay to have only 2 out of those 3 variables in the model rather than having the 3 as it may cause the SD to be inflated. Or alternatively, you could present only 1 of the 3 variables you looked at since presenting the 3 is redundant (i.e.: if a fish spend 70% of its time on the outer zone, it won’t spend more than 30% in the other 2, and knowing only the time spent in the outer zone OR inner zone might be enough)

Conclusion: you results show that the presence of conspecifics decreased boldness OR increased anxiety OR 'canceled' the anxiolytic effect of ethanol. From your results it is not possible to tell which conclusion best fits your results. Something you failed to discussed was the side preference. You always put the conspecifics on the right side of the tank when you tested. It would have been better to randomly placed them on the right or left side to control for that preference. Also, since the focal fish seemed to be attracted by the conspecifics, they would have likely spent more time in the thigmotaxis zone, close to the other fish, influencing greatly the way you measured boldness

Also, something that should be mention is zebrafish visual acuity. How far can zebrafish see? You could look at the literature on the topic and give recommendations regarding the minimum distance fish tanks should be spaced apart when testing fish, to avoid social buffering
Additional comments: Dear authors
Your research question is original and very relevant to pharmacological and toxicological studies involving zebrafish
However, the statistics were not adequate, the methods lacked clarity in places and the discussion is missing some important points (see comments above)


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

Input:
Title: VISION OF CONSPECIFICS DECREASES THE EFFECTIVENESS OF ETHANOL ON ZEBRAFISH BEHAVIOUR
Review round: 1
Reviewer: 2

Output:
Basic reporting: The writing is clear and unambiguous, with appropriate use of references and article structure.
Experimental design: The experiments are designed appropriately and appear to have been carried out in a rigorous manner.
Validity of the findings: The conclusions are clearly stated and well justified by the data presented.
Additional comments: This manuscript details a set of straightforward and seemingly well-executed experiments. The text is clear and easy to follow. As such, I have only a few very minor suggested changes, after which I recommend publication in PeerJ:

Title: I would consider expanding the title to be more easily interpretable / usable by potential readers. I understand that short titles can also help to attract readers but I feel that the current title is too broad. It could potentially be good to mention something about social environment during exposure? Also, instead of “effectiveness of ethanol”, maybe you could be more specific and mention that you investigated the anxiolytic effects of ethanol? My rough attempt at a title like this: “Social context during exposure mediates the anxiolytic effects of ethanol in zebrafish”. This is a rough attempt only so I am happy for the authors to take or leave my suggestions, although I do recommend a more detailed title generally.

Line 63: Perhaps “Belonging to a group can facilitate …”? Not all points mentioned in the list of advantages of social living are true for all social-living species.

Line 70: There should be a comma before “and recently,”

Line 80: Perhaps “can be administered to zebrafish”?

I also have a few more general comments that might be useful / relevant to the authors’ upcoming studies:

1)	I recommend that, for future studies, the authors consider using multiple exposure concentrations so that a dose-response curve can be generated. Furthermore, it would be very interesting to see if changes in the number of conspecifics in view throughout the exposure period might influence this finding (i.e. maybe the group size of the conspecifics that were in view is important).
2)	The sample sizes (15 fish per treatment) are quite low for a behavioural study of this nature, given that behaviour is inherently variable and individuals are likely to be differentially affected by both ethanol exposure and conspecific presence / absence. Was statistical power analysis carried out prior to this study to ensure that significant effects (if any) would be detected with sufficient sensitivity? I suggest that the authors explore power analysis for future similar studies and that 20 individuals (ideally more than 25) be used in treatments such as these—although this should be decided on a case-by-case basis and will, of course, also depend on ethical considerations to do with the number of animals being used.


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: VISION OF CONSPECIFICS DECREASES THE EFFECTIVENESS OF ETHANOL ON ZEBRAFISH BEHAVIOUR
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors did a good job at revising their manuscript. Whereas the introduction and discussion read a lot better, the methods are still confusing and I'm not convinced by the statistical results.
Table 1, even though it has been moved in the appendix is still too small to be readable.
Experimental design: The methods should be streamlined, for example
1-subject and housing
2- dosing (ie.: explanation of the treatments, not filmed, no data collected)
3- anxiety test (explanation of the test and data collected)
4- activity test (explanation of the test and data collected)
At the moment, there a lot of repetitions which makes your methods unclear. Also separating the ethanol/water and in view/isolated treatments in 2 paragraphs is not helping, it should all be combined in 1 paragraph
Also, I'm not convinced with your explanation as to why you did not film fish activity during the dosing. Your experimental design in both Fig 1B and 2B look similar. you should have been able to film both
L. 221-223 unclear, not sure what you mean. please rephrase
L. 241-242: so you did randomize the side the tank was placed but only 3 out of 15 trials. Why? why not do half on one side and half on the other
L.245: p value is repeated twice. Please report U and p value
Validity of the findings: I cannot see statistics reporting interactions in your manuscript. I'm not sure what the W reported l. 290-306 is referring to. Looks like you are doing 2x2 comparisons, which would be alright to present if you had significant interaction in the first place.
Regarding correlations, some variables are definitively correlated. Therefore I still recommend using PCA analyses for your data and used that scored to look at the effect of your treatments on anxiety. See for example: Magnhagen, Carin, and Jost Borcherding. "Risk-taking behaviour in foraging perch: does predation pressure influence age-specific boldness?." Animal Behaviour 75.2 (2008): 509-517.
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: EFFECTIVENESS OF MODIFICATIONS TO PREADJUSTED APPLIANCE PRESCRIPTIONS BASED ON RACIAL DENTAL CHARACTERISTICS ASSESSED BY THE ABO CAST-RADIOGRAPH EVALUATION: A PROPENSITY SCORE MATCHING STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper was well written and well organized. Sufficient literature was provided.
Experimental design: The Authors used the CVM method by Baccetti et al 2002. That method consisted of 5 stages and used Roman numerals. The authors reported 6 stages. Please clarify.
Was bracket placement standardized. Was a direct or indirect bonding technique used? Please report the wire sequence.
Validity of the findings: The methodology of the study was correct. please report the 95% confidence interval in Tables III and IV.
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: EFFECTIVENESS OF MODIFICATIONS TO PREADJUSTED APPLIANCE PRESCRIPTIONS BASED ON RACIAL DENTAL CHARACTERISTICS ASSESSED BY THE ABO CAST-RADIOGRAPH EVALUATION: A PROPENSITY SCORE MATCHING STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: English language need a complete revision, because it is not conform to the professional standards of expression and the overall style is not good.
The language is not very fluent and often appears as a literal translation.
Corrections must be made in all the  parts of the paper.

Litterature references is sufficient and appropiately referenced.

Introduction section introduces the problems covered by the study in a fairly clear and detailed way

As far as the background is concerned, it should be better explained the development of chinese prescription preadjusted appliance

Article is structured correctly and follows author guidelines

Figures have sufficient resolution but the pictures of mandibular occlusal view, both in roth and chinese prescription patients, have been acquired incorrectly and do not allow a good view of the arch

Tables are well organized, but the footnotes must better describe the data reported
Experimental design: The paper is a research article which evaluates a rather specific aspect in the field of orthodontics. It can fall within the aims and scope of PeerJ, even if, considering its high specificity, it could be of interest to a minority part of the readers

The purpouse of the study is interesting,and the paper provides an interesting figure that contributes, even if not to a significant extent,to filling a knowledge gap in the field of orthodontics

Investigation procedures shown some important limits:
1- Indirect brackets bonding procedure was to be preferred as a more rigorous positioning of the bracket was required
2- A standard bolton index is not considered in the inclusion criteria, in order to exclude any dental mass anomalies in patients sample
Validity of the findings: In the results section must be indicated the single values of intraclass correlation coefficient (ICC) and not generally report that were all greater than 0,90.
The findings of the study are sufficiently interesting , well discussed and adequately supported by litterature references
Additional comments: The paper is a research article which evaluates a rather specific aspect in the field of orthodontics. providing an interesting figure that contributes, even if not to a significant extent,to filling a knowledge gap.
Some methodological bias must be corrected and an extensive english language revision is necessary before the paper can be considered for pubblication


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: EFFECTIVENESS OF MODIFICATIONS TO PREADJUSTED APPLIANCE PRESCRIPTIONS BASED ON RACIAL DENTAL CHARACTERISTICS ASSESSED BY THE ABO CAST-RADIOGRAPH EVALUATION: A PROPENSITY SCORE MATCHING STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article has covered all sections in the background with satisfactory literature references. However, the grammatical errors makes it difficult to understand.

Hypothesis is not stated.

Data from tables are readable and sufficient.

Result section does not address the aims of the study entirely.
Experimental design: Research question vague.

Methodology sound but bias still exists inherent to the study design.

Lack of sample size calculation a serious concern.
Validity of the findings: Data provided robust, statostically sound. Propensity score match increases the valididty of the findings. However, lack of sample size calculation and superficial reliability assessment undermine the overall finidngs.
Additional comments: Thank you for asking me to review the manuscript titled ‘Effectiveness of modifications to pre-adjusted appliance prescriptions based on racial dental characteristics assessed by ABO cast-radiograph evaluation - A propensity score matching study’. The study compares the Chinese bracket prescription with Roth prescription. The authors have attempted to eliminate the confounders by carrying out a propensity score match between the groups. Although the authors have carried out a PSM for reducing the effect of confounders, inherent problems with study design still exists.

Major concerns:

The main concern I have in this study is the lack of sample size calculation. Additionally, there is discrepancy in the reporting of overall sample. The method section has no clear information on the number of participants included. The abstract reports 91 participants and Table 2 reports 60 participants.

The study is reported as a Cohort design but the write up feels retrospective. If the study is prospectively carried out, did the authors register the protocol in any public database?

One clinician treated all the included participants. Although this increases the internal validity, the external validity is lost.

The authors failed to evaluate the torque at the end of treatment. The objective of the study is ‘effect of prescription’ and it feels incomplete without torque assessment.

The authors finished treatment on 19x25 SS. The full expression of tip and torque does not happen on this archwire, as the play is high. Perhaps the lack of difference is because of the failure to use a full size archwire?

Following variables during treatment would make an impact on the final score; further information is required on the use of elastics, number and type of breakages, oral hygiene, space closure mechanics used, etc.

When were impressions taken post debond, on the same day? Were bonded retainers fitted on the same day as debond?

Information on bracket slot dimension including company name, archwire sequence and overall duration of treatment should be provided.

Reliability test was carried out using ICC. Bland and Altman test is required in addition to ICC to test both random and systemic errors.

The authors need to check the manuscript carefully for grammatical errors.


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: EFFECTIVENESS OF MODIFICATIONS TO PREADJUSTED APPLIANCE PRESCRIPTIONS BASED ON RACIAL DENTAL CHARACTERISTICS ASSESSED BY THE ABO CAST-RADIOGRAPH EVALUATION: A PROPENSITY SCORE MATCHING STUDY
Review round: 1
Reviewer: 4

Output:
Basic reporting: The manuscript is clearly written and the hypotheses is coherent with the introduction.
Experimental design: The research deals with a topic of limited interest. The research question is well defined but not very relevant. It is difficult to identify which knowledge gap is filled.

The methods are well described, even if the retrospective design of the study should be better underlined.
Validity of the findings: Validity of findings is limited for the possible selection bias due to the retrospective design and the exclusion of all the patients with poor compliance.

Conclusions are well stated and linked to original research question, but they overestimate the finding.
Additional comments: The article deals with a topic that is not very interesting since customization of brackets according to single patient need is possible. The importance of brackets prescription on the outcome of an orthodontic treatment is limited since information might not be fully expressed and in complex cases teeth position is more influenced by side effects of treatment mechanics than bracket prescription. Furthermore, the retrospective design reduces the validity of the study.


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

Input:
Title: EFFECTIVENESS OF MODIFICATIONS TO PREADJUSTED APPLIANCE PRESCRIPTIONS BASED ON RACIAL DENTAL CHARACTERISTICS ASSESSED BY THE ABO CAST-RADIOGRAPH EVALUATION: A PROPENSITY SCORE MATCHING STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The Authors replied appropriately to the issues raised.
Experimental design: The Authors replied appropriately to the issues raised.
Validity of the findings: The Authors replied appropriately to the issues raised.
Additional comments: The Authors replied appropriately to the issues raised.