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: CLINICOPATHOLOGICAL CHARACTERISTICS AND PROGNOSIS OF PULMONARY LARGE CELL NEUROENDOCRINE CARCINOMA AGED ≥65 YEARS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Manuscript is overall well written and meets professional standards in terms of language, context of study,article structure, data . Minor comments are mentioned in note to author below which require correction/revision.
Experimental design: Yes this manuscript has a very good data resource for LCNEC patients which is very valuable to the scientific community. Sufficient background is provided and research aim is outlined clearly. Sufficient statistical parameters have been applied (see below in author comments for additional suggestions). Methods have been clearly explained and raw data has been provided.
Validity of the findings: Since this is the first time such a large dataset has been used for LCNEC patients it is very useful. While it is known that age correlates with prognosis in LCNEC patients, the fact that it is validated in the larger dataset is useful. Further the observation that older patients handle surgery of therapy better (whenever administered) requires further investigation but is still an important advance in the field.
Cohort size is good and standard statistical procedures appear to have been applied
Conclusions are well stated and summarize the study appropriately.
Additional comments: Abstract :
•	Clear, concise and comprehensive.
Introduction :
•	Overall Good description of lung cancers. Importance of study stated but can be improved (see below)
Rephrase of line 65-66 required  : “However, research of older patients with pulmonary LCNEC has, to the best of knowledge, never been undertaken.” This statement is a bit contradictory since median age of LCNEC in several cohorts is 60+!! This paper adds value because it is explicitly comparing patients in two age groups.
•	Connection between LCNEC and NSCLC not explained.
•	No full form for “NSCLC” in line 58
Materials and Methods :
•	Ethics statement is present
•	Inclusion/ Exclusion is clearly stated
•	Raw data is present in supplemental folder
•	Covariates clearly explained. LCNEC strongly correlates with smoking habit. This should be included in paper if data is available.
•	Citation for “AJCC TNM staging system 6th edition”
•	Statistical analysis details were clearly mentioned.
•	It would be interesting to see results of the correlations between the different survival rates and factors being assessed using other tests (besides Cox) such as parametric models (eg. as in PMID: 29582630)

Results :
•	Study has a very good sample size of patients in both age groups specially since this is not a very common cancer subtype
•	All figures/figure legends, tables/table legends look fine
•	Older patients had bigger or smaller tumors? From the table it seems that older patients had higher percentage of smaller tumors (<5%) compared to younger patients?  However statement in Results says  “In the older group, more patients were white (P=0.004), married (P<0.001), stage I (P=0.022), had a larger tumor size ˂5 cm (P=0.013); and the proportion of surgery (P<0.001), radiotherapy (P<0.001), chemotherapy (P<0.001) was significantly lower.”
•	Do older patients have lower surgery rates because of the smaller tumor sizes?
•	It would be very valuable to see what chemotherapy treatment regimen was administered to patients and if different regimens would have different effects based on age (considering chemotherapy regimens could be so different for LCNEC patients)
•	It would be interesting to see how metastasis and location of metastasis correlate with age and prognosis in LCNEC patients
•	It would be intriguing to test how genomic LCNEC subtypes (as classified in the field for eg PMID: 29066508 etc) correlate with age and survival in this study if tissue is available for such analysis
•	Status of expression of neuro endocrine markers such as CD56,CGA,SYN etc (PMID:25596870) or immune checkpoint molecules in tumors across age could be interesting given current developments and trials.

Discussion :
Well written. Results highlighted clearly and good inferences. Strengths and limitations of study acknowledged well.

Minor typos/ Grammatical errors in following lines :
•	Tumor size was a continuous variable was transformed into a categorical variable on the basis of recognized cut-off values.
•	The 5-year OS rate for LCNEC after resection has been reported to be between 13and 57%
•	However, there are only 23 patients (5.7%) large cell neuroendocrine carcinoma, and the sample size is too small.
•	Only a multidisciplinary medical assessment of the patient should be able to evaluate the risks and benefits of a treatment


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: CLINICOPATHOLOGICAL CHARACTERISTICS AND PROGNOSIS OF PULMONARY LARGE CELL NEUROENDOCRINE CARCINOMA AGED ≥65 YEARS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper from Ling Cao and colleagues retrospectively evaluates public data on LCNEC patients from a public registry in order to find differences in clinicopathological features and prognostic factors according to age.

Even if the results are novel and interesting, the authors need to make consistent changes to paper to introduce the problem and adequately support their data.

-Introduction "Therefore, elderly patients often go without proper representation during clinical trials". Please rephrase this sentence

-What is the link between "LCNEC is thought to be an aggressive malignancy with a worse prognosis and more risks of reoccurrence in comparison with other types of NSCLC" and the need to evaluate LCNEC in elderly people?

- References are quite recent, but in insufficient number

Figures:
- update the legends with the number of subjects in each curve/group and how the p-value was determined (cox regression)
- label "follow time" on the x axis is not appropriate
Experimental design: - The authors should be more clear on the aim of their study, besides the lack of previous literature.

- The study is well designed, however the authors should present proper comparison of potential prognostic factors between the two groups and not only between general population (Table 2) and elderly patients (Table 4)

- Methods section is sufficiently detailed and provided supplementary material allows the replication of the analysis.
Validity of the findings: - The author should comment on the differences they found in the CSS/OS rates between stages I/IV and II/III

In my opinion, discussion needs thorough and significant improvements. In detail:

- The author should include and discuss more literature, also on similar studies on other subtypes of NSCLC

- Remove p-values from discussion

- "However, it was discovered by Kujtan and colleagues, that patients over the age of 70, who were comorbid white patients that had sublobar resection of tumors over 20 mm had the worst survival outcomes" This sentence should be rephrased.

- English need some improvements, e.g. avoid the term "discovered"

- "Our findings could be used by clinical workers to better understand..." This sentence should be moved in the conclusions.

- When describing the study limitations, the authors should better clarify what they mean with selection bias. Moreover, they should explain why they think their results are still strong despite these limitations.

- "In conclusion, older age (>65years) IS an independent prognostic factor for..." -> survival in LCNEC patients.

- The authors state that their results "showed that the elderly can obviously benefit significantly from these treatments" (i.e. surgery, chemo- and radiotherapy). The author should discuss the different findings for chemoterapy in terms of CSS/OS between entire population (n.s.) and older subjects (p<0.0001)

- Please include some comment on the limited use of surgery, chemotherapy, radioterapy in the older group.

- The concept that the treatment of pulmonary LCNEC is still based on age alone (see conclusions) has been not satisfactorily explained.

- Conclusions are somehow hasty and does not fit to the real aim of the study
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: CLINICOPATHOLOGICAL CHARACTERISTICS AND PROGNOSIS OF PULMONARY LARGE CELL NEUROENDOCRINE CARCINOMA AGED ≥65 YEARS
Review round: 2
Reviewer: 1

Output:
Basic reporting: please see minor comments below
Experimental design: meets standards of publishing
Validity of the findings: meets standards of publishing
Additional comments: Please rephrase sentences below to improve clarity and avoid grammatical errors:
•	The aim of this study was better characterize the clinicopathological features and prognosis of pulmonary LCNEC in patients aged ≥ 65 years.
•	In the following 1999 and 2004, the World Health Organization (WHO) admitted that LCNEC was a variant of large cell carcinoma, belonging to neuroendocrine tumors and one of the non-small cell lung cancer (NSCLC).
•	Meanwhile, the older group in nearly all the subgroups had the significantly lower OS, except the patients with primary site at main bronchus, bilateral tumor, AJCC stage II , stage III and patients received segmentectomy, pneumonectomy and radiotherapy (Figures 4).
•	What is more, tumor size, AJCC stage, surgery, chemotherapy, radiotherapy were independent risk factors for prognosis in older patients.
•	But now the mainstream view was that primary surgery still should be the first option in operable patients
•	But we still did not know how to choose chemotherapy and chemotherapeutic regimen
•	This study is the largest retrospective analysis on the prognosis effect of age in pulmonary LCNEC. The current research was based on a large population, but there were remain certain limitations that should be noted.
•	However, any retrospective study could not include all possible factors, and our results are still of great clinical value


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: CLINICOPATHOLOGICAL CHARACTERISTICS AND PROGNOSIS OF PULMONARY LARGE CELL NEUROENDOCRINE CARCINOMA AGED ≥65 YEARS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Manuscript have been improved in this revision.
Experimental design: All the methodological issues have been addressed.
Validity of the findings: The discussion is now clearer.
Additional comments: The manuscript have been improved in this revision. However, the manuscript still needs some language improvements, in particular in the new parts of the discussion section. Please, consider revision of the whole manuscript by a native English speaker.


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: LATERALIZATION (HANDEDNESS) IN MAGELLANIC PENGUINS
Review round: 1
Reviewer: 1

Output:
Basic reporting: See below
Experimental design: See below
Validity of the findings: See below
Additional comments: I believe this is a good paper, that extends in a significant way our knowledge on lateralization in vertebrates in a species that so far has been little investigated. The observations appeared to be well-conducted and the data properly analyzed.
I noticed, however, that the authors do not properly managed all the literature (particularly the most updated one), and I make several suggestions on this below.
As to the lack of footedness for stepping and its presence in thermoregulation, I am wondering what type of challenge the thermoregulatory posture would pose to the animals. Apparently little because they were prone. Nonetheless I am wondering whether the extension of one leg makes the other leg forced to play an important role in the control of posture. I am asking this because in other birds species it has been argued that lateralization in foot use maybe a consequence of the foot that is actually used to control posture (see e.g. Tommasi, L., Vallortigara, G. (1999). Footedness in binocular and monocular chicks. Laterality, 4: 89-95; Versace, E., Vallortigara, G. (2015). Forelimb preferences in human beings and other species: multiple models for testing hypotheses on lateralization. Frontiers in Psychology, 6: 233. doi: 10.3389/fpsyg.2015.00233).
I found the interpretation for fight behaviour quite convincing.

Line 45: Please add here also more updated reviews:

https://www.cambridge.org/core/books/divided-brains/442F89DBA8F4BA76CD2F896E960A1E36

https://www.scientificamerican.com/article/evolutionary-origins-of-your-right-and-left-brain/

https://onlinelibrary.wiley.com/doi/abs/10.1002/wcs.100

http://psycnet.apa.org/record/2017-00569-027

https://www.sciencedirect.com/science/article/pii/S0093934X00923034

For evidence in invertebrates see e.g.

https://r.unitn.it/filesresearch/images/cimec-abc/Publications/2012/frasnelli_neuro-biobe.pdf

https://www.nature.com/articles/srep29411

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002340

http://rspb.royalsocietypublishing.org/content/282/1803/20142571

https://www.sciencedirect.com/science/article/pii/S0960982218309187?dgcid=rss_sd_all

Line 47:
https://www.cambridge.org/core/journals/behavioral-and-brain-sciences/article/survival-with-an-asymmetrical-brain-advantages-and-disadvantages-of-cerebral-lateralization/2E4A2B275EED0B6C037FCC84C62F6F7D

https://www.cambridge.org/core/journals/behavioral-and-brain-sciences/article/forming-an-asymmetrical-brain-genes-environment-and-evolutionarily-stable-strategies/0617C9F89F054C0B4CE2537ABCF7303E

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691668/

http://rstb.royalsocietypublishing.org/content/364/1519/861.article-info

https://onlinelibrary.wiley.com/doi/abs/10.1002/dev.20166

Line 56: here a more general view of the functions of the left and right hemispheres should be provided (including e.g. space, emotions, motivation etc). Please refer to the general reviews I suggested above.

Line 66: see however evidence above (suggestions for line 47) concerning the role of social interaction in the alignment of lateralization (see also

Line 79: This statement is obscure to me. Perhaps the authors refer to frequency-dependent selection for asymmetries see above e.g. https://onlinelibrary.wiley.com/doi/abs/10.1002/dev.20166

Line 346 see also

https://www.researchgate.net/publication/8443269_Paw_preference_in_dogs_Relations_between_lateralised_behaviour_and_immunity

https://www.sciencedirect.com/science/article/pii/S0304394010004532

https://www.ncbi.nlm.nih.gov/pubmed/17884191


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: LATERALIZATION (HANDEDNESS) IN MAGELLANIC PENGUINS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Literature survey: this part could be improved while increasing the focus of the paper. For instance: is this paper about functional or morphological asymmetries? Individual or population asymmetries? Social or individual behaviours?

In particular, there is no distinction between individual and population-level asymmetries, although this is a crucial distinction for this paper. Moreover, the authors often shift between morphological and functional asymmetries in different traits. Sometimes there are cases overgeneralisation/oversimplifications; some examples: "Brain lateralization is considered adaptive"...this is a bit vague. "Brain lateralization is thought to be adaptive, especially in social or group behaviors"... what about lateralisaton in individual behaviours such as gap crossing in locusts?; "Brain lateralization appears to enhance cognitive ability by allowing both brain hemispheres to specialize and function simultaneously (Rogers 2017) and is often linked to behavioral lateralization, or to hand, foot, or paw preferences (Rogers 2009)." ... there are different explanations for the advantages of different types of lateralisation. The cited references are valuable but it would be better to refer also to the primary literature;  "The strength of lateralization may be more important than the direction within an individual" ...it is not clear in which sense "more important"?. ; "The left hemisphere (hence, the right side of the body) dominates in vocalization": I am not sure in which sense the right side of the body dominates in vocalisation;  "The optimal dominant flipper may depend on the prey species." ... this is not clear. "A dominant side may be
advantageous when it is rare, leading to an equal ratio of dominant sides in the population)"... this is not clear.

Data should be presented in figures, e.g. bars that present frequency of different outcomes
Experimental design: Lateralisation is a huge topic, and focus and research questions are not defined.
There are some distinctions that should be stated more clearly about the focus of the paper: 1) individual vs population level lateralisation  2) functional vs morphological asymmetry   3) individual vs social behaviours  4) why this species is interesting to address the specific questions.
In this manuscript, the authors mainly look at population level lateralisation but for flipper asymmetries, they look at individual-level asymmetries; sometimes they look at behavioural asymmetries and sometimes at morphological asymmetries but the two measures are not related to the same trait.
Overall, the focus of the paper is less than clear: did Authors select specific traits for any theoretical reason? It should be stated whether the study is a preliminary descriptive observation or whether the traits investigated are theoretically connected. The impression from reading the paper is that this is a general survey of lateralisation in which the investigates traits are not theoretically connected to one another.
If besides the focus of the paper authors have also included other measures, these can be reported in a separate section.
Validity of the findings: Did Authors measure the inter-rater reliability between observations?
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: LATERALIZATION (HANDEDNESS) IN MAGELLANIC PENGUINS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I believe the authors have addressed satisfactorily my comments.
Experimental design: No comments
Validity of the findings: No further comments.
Additional comments: I believe the authors have addressed satisfactorily my comments.


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

Input:
Title: LATERALIZATION (HANDEDNESS) IN MAGELLANIC PENGUINS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Mostly clear but some paragraphs should be moved to different sections (see below)

FIgures: to help comparisons between conditions with diffrent subjects it would be better ti plot proportions (adding counts in tables)

No strong conclusions on the role of temperature can be done since this variable was not directly analysed.
Experimental design: see below
Validity of the findings: No strong conclusions on the role of temperature can be done since this variable was not directly analysed. Speculation on the role of temperature should be identified as such.
Additional comments: Abstract and introduction

24. “regardless of the species” : This sounds to me an oversimplification that implies that all the species exhibit the same pattern.
27 “side preferences”: side preferences might be different from lateralisation and be transitory.
29 and following: usually the abstract doed not contain p values and exact numbers

“Lateralization depended on the behaviour tested and, in thermoregulation, on the temperature”: actually the role of the temperature was not directly tested.

 “solitary behaviour”: here and in other cases: since penguins were usually in groups, would it be more appropriate to use the term “individual behaviour/s”?

56-57: “is thought to be adaptive”: I would rephrase in a similar way as: "Several scholars hypothesise that… ( refs)".

163: it would be important to cite also the original papers about the role of social behaviour/aggression in individual vs social behaviour.

167-169: so that is a case of morphological, not of functional asymmetry.

Materials and methods
Throughout the materials and methods, there are parts that are more appropriate for the introduction: e.g. 215-218, 230-234, 247-250, 300-303 and in the dominant flipper part. A possibility to help the readers to find the information in the sections where it is usually located would be to dedicate paragraphs in the introduction to explain the relevance and details of each variable investigated.

208-211: the heading is about "Study site and species" but this part is about data analyses.

I understand that a binomial test with p=0.5 is a sign test, but for clarity I would use consistently the term sign test of binomial test throughout the manuscript instead of shifting between terms.

223-224: it is possible to automatically adjust the length of steps during walking, without stopping, so I don’t fully understand the rationale of considering only penguins that did stop.

** 237 and below: the Authors explain the inconsistency in feet preference between different year as an effect of temperature. Although this is a possible explanation, other variables not controlled by the experiments might have differed between different years of observations. The fact that the temperature was not analysed to observe whether it made a difference (especially within a year of observation), prevents to draw strong conclusions.  So I would recommend modifying the abstract and discussion/conclusions accordingly.

247-252 I find a bit confusing that the paragraph about gonads (247-252) is included in the section  "Dominant foot" (similarly in the Results section).

303-304: can the circulation asymmetry explain also the asymmetry in eye use?

In the Results (371), the Authors mention videos about the fights but there is no mention of these videos in the methods. It would improve clarity a description of when the videos where recorder and how (unless I have overlooked this detail)

Results

* For not significant results the authors use for instanc “p > 0.2” or “p> 0.5”. It would be more precise to specify the exact p level.

The Results section in research reports typically does not provide interpretation. I would suggest to revise the results section accordingly (see for instance 369-377).

Discussion

406-407: the Authors might want to clarify whether here they are referring to their own results

410 and following: it is important to clarify the limitations of this interpretation (or to provide direct evidence of the association between temperature and lateralisation)

464-469: It is not entirely clear to me the connection between the paragraph 464-469 and the rest of the discussion. Is this rather some information for the introduction? Or can the Authors make more clear the connection with their results?

480: it would be interesting to refer also to the original theoretical accounts.

483: “usually”: can the Authors specify in which contexts?

491-493: this would be more clear using a line plot to illustrate

503-505: it would be important not to make strong claims about the role of temperature is that has not been explicitly investigated (see my comments above)

Figures and captions:
- exact p levels are more informative also in the case of non-significant results

** Figure 8: it is extremely hard to compare counts when the overall number of subjects considered is different (especially in Figure 8B, with 54 mals and 104 females). The AUthors should consider plotting proportions or at least put side by side the bars that can be directly compared: (all data from males) and (all data from females)

** Figure 9: same considerations as above about the counts/frequencies. Plotting proportion and using a line plot would make much clearer how the proportion of use of one side changes with the increase of blood.


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: COMPREHENSIVE TRANSCRIPTIONAL PROFILING OF AGING PORCINE LIVER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript entitled “comprehensive transcriptional profiling of porcine live aging” describes the basis analysis of RNA-seq data obtained from the porcine liver. More in-depth analysis would be appreciated. In addition, the grammar and interpretation need more work to make it an easier read. For example, it is hard to make sense of line 251-254.
Experimental design: qRT-PCR validation should be described within subsection of the type of RNA analyzed, not as a separated subsection and bundled together. Also should be presented as main figures, not supplemental data.
Validity of the findings: 1.	While the authors emphasize on the “understand the transcriptional regulatory mechanism of the liver aging”, work presented is really just basic analysis of RNA-seq data. Therefore, some sentences in the Introduction and Discussion need to be toned down.
2.	Should it be differential expressed, not co-expressed (line 251)?
Additional comments: The font of figure label need to be increased,


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: COMPREHENSIVE TRANSCRIPTIONAL PROFILING OF AGING PORCINE LIVER
Review round: 1
Reviewer: 2

Output:
Basic reporting: (1) There are some problems with sentence structure, verb tense, and clause construction. There are several typographical and grammatical mistakes in the paper, which needs to be proof read carefully and checked. The English of your manuscript must be improved before re-submission. For example, the font of phrase “piglets weaning was performed” at line 79 is not the same as other characters; “OL” should be revised with “OYL” at line 224 and 226; “compared to” should be revised with “between” at line 255; the title of figure legends should be revised to avoid the grammatical mistakes; “NR1H2” should be used the Italic font at line 276 and 180-186 etc. It is strongly suggested that the authors obtain assistance from a colleague who is well-versed in English or whose native language is English.

(2) Literature references should be added up several latest reports in parts of Introduction and Discussion. What are the specific representations of senescence associated liver pathological changes and dysfunctions? How are the above changes related to the results of the transcriptional profiling you reported? Please add up the above literature references and discussion in the part of Discussion. It is advised that the phrase “Compared to the young group” should be added up into the line 176.

(3) The paragraphs from line 212 to 239 could be an individual part and named “The cross-talk between mRNA and non-coding RNA during liver aging”. Statistical analysis should be showed in the part of Materials & Methods as an individual paragraph. SD or SEM and P-values were not showed in the results of qPCR in Figure S2.
Experimental design: It is advised that liver senescence and associated pathological changes and dysfunctions would be detected and analyzed using histology, immunity and metabolism testing to consist with the results of transcriptional profiling. Moreover, please offer the Permit Number on the ethics of animal experiments by the local ethics committee.
Validity of the findings: Statistical analysis should be showed in the part of Materials & Methods as an individual paragraph. Please added up the detail of statistical analysis in each figure legend and showed the SD or SEM and P-values in the figures.
Additional comments: The authors have provided evidences to support the transcriptional profiling of porcine liver aging. Some senescence associated genes of porcine liver were found by RNA sequencing and analyzed by GO annotation. Non-coding RNA were also reported and assessed the cross-talk with the above related target genes. The experiment design and data are sound, but the manuscript is far from qualified to publish in Peer J now. There are some suggestions above that the authors should address to help improve the quality of the manuscript.


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

Input:
Title: COMPREHENSIVE TRANSCRIPTIONAL PROFILING OF AGING PORCINE LIVER
Review round: 1
Reviewer: 3

Output:
Basic reporting: The language should be improved in parts to more clearly convey the author's intended meaning. Some phrasing and sentence structures make comprehension difficult, for example, lines 45-48, 50-52, 62-67 etc. Shorter and clearer sentences will help.

The figures and tables are neat and contain the requisite explanations.
Experimental design: Methods:
- please provide reference for the feed used for the young pigs. Is this the standard feeding regimen?

- The history/conditions of the old pigs was not discussed at all

- Why were 180 days and 8 years selected as the two time points? Please explain the rationale with respect to the normal lifespan of a pig.

- Were any tests performed to determine the health status of the older pigs? This is relevant information considering the results discuss the up-regulation of viral associated immune genes.

- Please mention the version of pig reference genome used in methods section (it is noted only in results)

- Please mention what samples were used for the qPCR? Were they the same ones used for the transcriptome analysis?
Validity of the findings: Results and Discussion:

- The sample size would ideally be 3 samples each for young and old livers but the study only has two which weakens the statistics. Also, it is mentioned that expression of mRNA is counted even if only one of the samples contains expression. This further weakens the significance of the statistics and can potentially skew the PCA plots. Since there are only two samples for each condition, the authors might restrict inclusion of expressed mRNAs only to those present in both samples and re-test the heatmap and PCAs.

- Please explain why mRNA and lncRNA expression was grouped to generate Fig 2A

- The results have been reported well but some of the inferences may be a little weak just with the observed results alone. For example, down-regulation of some metabolism related genes may not necessarily mean it is proof of compromised metabolic activity at an organ level. Authors should acknowledge that further extensive functional validations are required to claim with certainty.

- Validation by qPCR should be performed on multiple independent samples to confirm the expression pattern as seen by transcriptome analysis. This becomes more important since the initial number of samples is only two.
Additional comments: The study seeks to answer an interesting question which is not covered in the literature. The data sets presented can be useful to other researchers. In order to increase utility, you can provide ranked lists of DEGs derived from your raw data in the form of tables.

Overall the manuscript needs work on some sentence structure and phrasing. Simpler sentences will help adding clarity to the reader.


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

Input:
Title: MODERATING FACTORS INFLUENCE THE RELATIVE AGE EFFECT IN AUSTRALIAN CRICKET
Review round: 1
Reviewer: 1

Output:
Basic reporting: See attached comments.
Experimental design: See attached comments.
Validity of the findings: See attached comments.
Additional comments: Please see attached 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: MODERATING FACTORS INFLUENCE THE RELATIVE AGE EFFECT IN AUSTRALIAN CRICKET
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is generally well written, with the introduction and background providing good context for the undertaking of the research.
Literature referenced is relevant. Figures and tables are well constructed and easy to read.

The following needs to be addressed:
a) check consistency of research citations for APA format
b) check for consistency in use of terminology through out the article, that is, correctly introduce relative age effect followed by acronym in brackets then use this throughout article and not interchanging
c) check for consistent use of hyphens throughout the article when using right-hand, left-hand etc
Experimental design: No comment
Validity of the findings: Data is robust, statistically sound and controlled.
Findings are of benefit to improving literature however would have liked to have seen more discussion of findings in relation to applications for talent identification, suggestions on how these findings could influence training design for improving acquisition of skill generally and in the right- hand vs left-hand mismatch scenario
Additional comments: Well researched and well structured paper. Discussion could have been broadened to include practical applications of findings to pathway managers, high performance coaches, talent identification personnel and managers


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: MODERATING FACTORS INFLUENCE THE RELATIVE AGE EFFECT IN AUSTRALIAN CRICKET
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am happy with the revised version of the paper.
Experimental design: I am happy with the revised version of the paper.
Validity of the findings: I am happy with the revised version of the paper.
Additional comments: Thank you for revising the paper.


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

Input:
Title: MODERATING FACTORS INFLUENCE THE RELATIVE AGE EFFECT IN AUSTRALIAN CRICKET
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper with suggested track changes is well written, just a few minor edits added in reviewer track changes
Experimental design: No comment
Validity of the findings: Data is robust and sound. Well presented.
Additional comments: Happy with additions to discussion as per reviewer requests.

Changes to paper have added quality to research reporting and suggestions for applied use, well done.

See attached manuscript with very minor track changes included.


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: CMAH DEFICIENCY MAY LEAD TO AGE-RELATED HEARING LOSS BY INFLUENCING MIRNA-PPAR MEDIATED SIGNALING PATHWAY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is clear with the usage of professional English.

sufficient literature has been cited.

The article has professional structure, figures, and tables.

the manuscript is heavy on hypothetical explanations.
Experimental design: Primary research is based on older data.

The research question is not very well defined, seems like the author wants to cover too many topics in one manuscript.

Rigorous investigations are not performed, most of the data os hypothetical with not experimental investigations.

The methods are described in sufficient detail.
Validity of the findings: The investigation brings a lot of hypothesis with no experimental data.

The data needs more work and investigation.

The conclusions are very speculative.
Additional comments: 1.	Figures 1. Shows 3 datasets for Cmah. Null and WT experiments. Are these 3 datasets are biological replicates? Please mention this in the figure legend. What is the main difference between the 3 datasets?
2.	Line 65, the data cited is old, it dates back to 2015, is there an updated figure? If so, please cite that data.
3.	What is TF? Is its transcription factor, if so please mention the details in the manuscript?
4.	The manuscript is very speculative with a lot of hand waving. It would be advisable if some solid experimental data can be provided to confirm at least some of the proposed hypotheses.


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: CMAH DEFICIENCY MAY LEAD TO AGE-RELATED HEARING LOSS BY INFLUENCING MIRNA-PPAR MEDIATED SIGNALING PATHWAY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language used in this manuscript need to be improved and polished. This reviewer found there are many long sentences with convolved grammar structure, which makes it challenging to read. For example:
1. In line 101-105, this sentence is very long and contains at least two messages: a) the authors aimed to screen more crucial gene and pathways using the published microarray data; b) the authors constructed network maps in order to find potential treatments for AHL. It will be much clearer if the authors can separate this long sentence into two and convey a concise message in each one.
2. In line 285-288, the authors adopted another super long sentence "It has been reported that..., but..., but..., which...". It is very unclear and reads uncomfortable when using two "but" to connect a sentence. Please conform to professional standards of English expression.

Moreover, in the Abstract session, the authors utilized several abbreviations without spelling out at the first use, such as KEGG, ECM, PPAR. Please spell out the full names without bothering readers to look it up.

In the second paragraph of discussion, the authors spent a whole page to describe ECM is essential for structural and functional integrity of organs. This reviewer found it's too distracting and unnecessary. The discussion part should be focus on the reflection on the findings and how to interpret the result.

Another small suggestion: according to PeerJ standard format, headings in structured abstracts should be bold and followed by a period. Each heading should begin a new paragraph. For example:
"Background. The background section text goes here. Next line for new section."
Please review PeerJ template for standard formatting (https://peerj.com/about/author-instructions/#standard-sections).

One small typo, in line 224, it should be AHL but not ALH.
Experimental design: The research questions is well defined: to explore the mechanism of Age-related Hearing Loss (AHL) by using microarray analysis in the Cmah deficiency animal model.

The methods were described with sufficient detail and reference.
Validity of the findings: The microarray data were collected from the Gene Expression Omnibus database, not from the authors' own experiment.

The data analysis and conclusions are well stated and linked to the original research question.
Additional comments: Generally speaking, the data analysis and conclusions are clear. However, the english language can be much more concise and crisp to convey straightforward ideas.


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: CMAH DEFICIENCY MAY LEAD TO AGE-RELATED HEARING LOSS BY INFLUENCING MIRNA-PPAR MEDIATED SIGNALING PATHWAY
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1. This manuscript was written in professional and technically correct English with some minor phrasing problems in the Introduction. To ensure a better understanding of your article by a broader audience the English language in the introduction can be improved and some examples include line 81-82, 89-92.

2. This article investigated CMP-Neu5Ac hydroxylase (Cmah) deficiency induced aging-related hearing loss, hence in the introduction (line 93-94), the authors could provide more background information on Cmah and its disruption in biological processes.

3. I thank the authors for providing all the required raw data and relevant figures in this manuscript. To ensure a better understanding of the study, authors could consider improving the figure legend of Figure 1 by adding an explanation of features in the figure and a brief statement of the results that can be gleaned from this figure.
Experimental design: In this work, the authors aimed to advance the understanding of the mechanism of age-related hearing loss and benefit the therapeutic interventions using the Camh deficiency mouse model. Based on the work published by Deug-Nam et al. the investigators identified additional differentially expressed genes and pathways by constructing protein-protein interaction (PPI) network and miRNA regulatory network. The finding of this work has its value to the field and may potentially fill the gap in understanding of AHL.

Experiments were well designed with proper control. Differentially expressed genes (DEG) were subjected to an intensive investigation to identify their biological functions.
Validity of the findings: The Data presented in this work is statistically sound and properly controlled. The authors should consider the following comments for revision before publication.

1. This study is based on the work published by Deug‐Nam Kwon in 2015. Deug‐Nam Kwon identified 631 up-regulated genes, 729 down-regulated genes in Cmah-null mice derived cochlear tissues compared to control mice. In this work, a total of 700 DEGs were identified with 449 up-regulated and 350 down-regulated from the same set of microarray data. Please specify the reasons for this difference.

2. In figure 6, it has been predicted that PPARG can be regulated by mmu-miR-221-3p, mmu-miR-130b-3p, mmu-miR-27a-3p, mmu-miR-27b-3p and mmu-miR-721. There is no further evidence in this article showing that miRNA-27a-3p is the only or major miRNA regulating PPARG in AHL disease mouse model, I suggest that you improve the description at lines 285- 288 to provide more justification for your conclusion or consider modifying the paper title and the conclusion in line 303-304 accordingly.

3. Line 220-221, the authors concluded small molecules like adiphenine, DL-PPMP, decitabine, and topiramate could potentially reverse the expression of PPARG in AHL. To help broader readers to understand this study, please provide more detail on the data collected from the Connectivity Map. Examples include 1. The genome-wide transcriptional expression data in Connectivity Map was collected from wild-type human cell lines or mutated cell lines? 2. Table 5 listed 69 small molecules found from the CAMP search. Since all DEGs in PPI network were uploaded into CMAP it would be helpful to group these small molecules according to their features such as targeted genes or inhibitors/activators.
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: CMAH DEFICIENCY MAY LEAD TO AGE-RELATED HEARING LOSS BY INFLUENCING MIRNA-PPAR MEDIATED SIGNALING PATHWAY
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments.
Experimental design: No comments.
Validity of the findings: No Comments.
Additional comments: Considering the changes made in the present version of the manuscript, as suggested by the reviewers, I can now recommend this 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: CMAH DEFICIENCY MAY LEAD TO AGE-RELATED HEARING LOSS BY INFLUENCING MIRNA-PPAR MEDIATED SIGNALING PATHWAY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript after revision has addressed all my concerns. This is ready to publish.
Experimental design: The manuscript after revision has addressed all my concerns. This is ready to publish.
Validity of the findings: The manuscript after revision has addressed all my concerns. This is ready to publish.
Additional comments: The manuscript after revision has addressed all my concerns. This is ready to publish.


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

Input:
Title: GENOTYPIC ANALYSES AND VIRULENCE CHARACTERIZATION OF GLAESSERELLA PARASUIS ISOLATES FROM TAIWAN
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is clear, figures are relevant and well described and it includes sufficient introdution.

The only thing that from line 153 to 166 the results section is not very clear, and it would have to be explained better.
Experimental design: Methods described with sufficient detail and it seems a rigorous investigation.
Validity of the findings: The work is interresting. The results provide very good information to be able to differentiate pathogenic isolates from those that are not.
Additional comments: From my point of view it is a good job that provides a lot of information about the characterization of isolates. Something that I would clarify better for the publication of the article in a magazine:

In the introduction, in line 53, you talk about microflora when the correct term would be microbiota.

In material and methods, line 87, do not specify how that selection of farms or at least how they were distributed was made. This information seems to me intersante, being able to even attach a map.

In line 88 it would be interesting to know if lesions were observed in the animals' encephalon.

In the discussion a lot of emphasis is made, even repeatedly that the same strain appears at the same time in different places and its relationship with the mothers and it is true that it is interesting. But I miss a deeper discussion about the possession of group 1 VtaA, for example, have really looked for these autotransporters in healthy animals to make a comparison. Because what is deduced from this study is that almost all isolates are pathogenic when G. parasuis is undesired as a diner as well.

The isolates studied would be by the techniques described in the well-characterized article but a more complete profile on these isolates with other virulence factors or even antibiotic resistance would complete 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: GENOTYPIC ANALYSES AND VIRULENCE CHARACTERIZATION OF GLAESSERELLA PARASUIS ISOLATES FROM TAIWAN
Review round: 1
Reviewer: 2

Output:
Basic reporting: Genotypic analysis and virulence characterization of Glaesserella parasuis isolates from Taiwan.

This is a nice study, however, it should be written as a short communication, as it is only the dendrogram that is discussed.  The discussion is very long and goes over well-established knowledge.  Some of the figures are not helpful in the discussion of the results and a couple of tables would be much better.
Abstract
Line 36 it should say within many clusters

Introduction

Line 52  Watt et all are talking about a new species which is in the process of being named.  They have nothing to do with renaming Haemophilus parasuis.  This was done by Thomas Inzana at a conference in Prato.  Thomas is in the process of publishing this work in the taxonomic journal.
So the sentence should read that H. parasuis has recently been renamed as Glaesserella parasuis
The reference is Inzana, T.J., Dickerman, A.W. and Bandara, A.B. (2016)  Taxonomic reclassification of “Haemophilus parasuis” to Glaesserella parasuis gen. nov., comb. nov.  The Prato Conference on the Pathogenesis of Bacterial Infections of Animals 2016, Prato, Italy.
Line 55 Two references for this statement would be more than enough.
Turni and Blackall 2010 Serovar profiling of Haemophilus parasuis on Australian farms by sampling live pigs. Australian veterinary Journal 88, 255 – 259.
talk of up to 8 serovars on farm.  Then you need one of the references that talks about more than one serovar per pig.

Materials and Methods
Line 94 says that bacterial isolates were identified as G. parasuis by the timeric autotransporter group.  This is not a species specific PCR and the conditions are not geared at specificity.  Some authors have argued that even the VtaA group 1 has problems and the conditions of the PCR to detect the gene were vital to specificity.  The fact that you are using a tiny amount of water (normally 100 to 200 ul are used for one loopful to obtain about 100 ng of DNA) to extract DNA is a worry.  The study suggested that previously positive results for non-pathogenic strains were related to the conditions of the PCR not being exactly followed, as some non-pathogenic strains have a very large trimeric autotransporter whose translocator sequence is characteristic of group 1 vtaA.  (Galofre-Mila N, Correa-Fiz F, Lacouture S et al. A robust PCR for the differentiation of potential virulent strains of Haemophilus parasuis. BMC Vet Res 2017;13:124.)

You are doing the serovar PCR that has a species specific band.  Why did you not go by these results to determine if it is G. parasuis?  It should state somewhere what the species specific outcome of the serotyping PCR was.  As the vtaA group 3 is not a convincing result for species.

Line 101 remove the coma before the and.
Line 103 as in a previous study
Line 140  which city and country does this software come from?

Results
Figure 1 What are all these symbols in the farm column?
Can you take out the S from the serovars, as it is very hard to read?  The case number is of no value to the paper, I would take this out.  The date should only be the year.

Why would you apply a 35% similarity cut-off.  I find your 80% similarity cut off too liberal.  Most authors use a 90% and higher cut off. (Characterization of the diversity of Haemophilus parasuis field isolates by use of serotyping and genotyping. Oliveira S, Blackall PJ, Pijoan C Am J Vet Res. 2003 Apr; 64(4):435-42.) (Short Communication: ERIC-PCR genotyping of Haemophilus parasuis isolates from Brazilian pigs.  Nubia ResendeMacedo,Simone RodriguesOliveira Andrey PereiraLage José LúcioSantoscMarina RiosAraújo Roberto Maurício CarvalhoGuedes The Veterinary Journal Volume 188, Issue 3, June 2011, Pages 362-364
Line 148  I do not understand why we need to show a 35% similarity cut – off . I would remove this section.

I would re-evaluate the whole dendogram with a cut off of 90%.  This would make your results comparable to the rest of the studies published already.

I would have started the results with the serovars observed.  There seems to be only very few serovars that have been found.  The diversity is much more interesting in the light of the few serovars found.  Your vtaA comes up positive for all serovars even serovar 7 and 9, both of which are in general non-pathogenic with one exception for a serovar 5.
Line 154 Are you refereeing to the major serovar being 5.  Can you please spell out the serovar, as you have not explained the serovars before.  But why is subtype 4 and 5 not included for example?

Line 155 you state subtype 5 as having isolates from the same lesion pattern, but that first mentioned patterns has lesion pattern R and GR in it.  So it is mainly the same pattern, but not the same pattern.  13 and 14 are missing in that list.

There need to be some paragraphs when we change topic.  Such as a different paragraph at line 150 and  at 155 when isolates were discussed and 160

The results are extremely difficult to follow as the writing in you dendogram is way to small.

A table such as below for lines 160
Farm	subtype	serovar
F5
F75

Give us some examples of isolates from the same period from endemic herds and the different genotypes and of the different isolates by both subtype and serovar.

Figure 2 is not helpful as you are not showing us in the table this pattern you referring to.  A table would have been much more helpful.  Figure 3 is not needed.  Figure 2 is not readable and a table would be much better to express all the data.

Discussion
Line 197  You have to be careful you only had very few serovars and correlation between small groups is easy then, but might not be real.
Line 204  This might be due to dissemination and could be due to coming from the same breeding stock originally.  Not sure if it has to do with the evolution of G. parasuis.
Line 230 on the same farms
Line 231 and existence of virulence genes.
Line 236 It is well established that various isolates can be isolated……
Experimental design: There is nothing wrong with the design.  However, the species needs to be identified with a species specific PCR.  The cut off for the Dendrogram needs to be 90% or higher.
Validity of the findings: Data needs to be reevaluated with the different cut off
Additional comments: Please see comments in the first area


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: GENOTYPIC ANALYSES AND VIRULENCE CHARACTERIZATION OF GLAESSERELLA PARASUIS ISOLATES FROM TAIWAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: The work exposes interresting results and throws new ways of investigation with this bacterium. It is a professional article structure, figures and tables.
Experimental design: The investigation must have been conduced rigorously and to a high technical standard.

Methods described with sufficient detail and information to replicate
Validity of the findings: The results are significantly rigorous, with their replicas and their statistical treatments. The conclusions are the right ones.
Additional comments: After the first review, the article is read better and the main ideas are clear. From my point of view the development of the work is well explained and the conclusions obtained are optimal to consider this work as valid for publication in this 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: GENOTYPIC ANALYSES AND VIRULENCE CHARACTERIZATION OF GLAESSERELLA PARASUIS ISOLATES FROM TAIWAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: This is a nice report and has now addressed some of the major flaws
Experimental design: Well designed
Validity of the findings: Findings are valid
Additional comments: Thank you for addressing the points.  I have pointed out some minor things still which in my opinion need to be addressed.  I have also addressed some of the points argued in the letter of response.

Looking at the figure 1 and 2 and at the cut-off point it becomes clear that the cut off point is 90%.  At 90% your isolates have the same genotype and a clonal.  When looking at your genotypes then it becomes clear that the 90% gives you that answer.  Looking at the figure 2 and 3 you can see that isolate 135 is very similar to 139 and 140 and could belong in the same cluster.  When you are extending this to the 80% cutoff then you get 133 being the same as 134.  These are definitely not the same on the contrary they are quite different.  So contrary what you wrote before there are definitely not only 37 subtypes.  However seeing that you now changed that into clusters then I am not objecting to your analysis of 80%.  A subtype is a different strain and not a cluster.  So you have 37 clusters.
Seeing that you identified the field isolates beforehand at 95% similarity assures that you had representatives of all the isolates.
At line 155 we talk of 36 clusters yet 37 are in the table.
In line 169  to 173 you are talking about genotypes and calling the cluster a genotype.  The genotype is the subtype/strain.  So there are more subtypes in the cluster as already discussed.  So you can only discuss the clusters here and your table was labelled correctly, but your text is incorrect.

I beg to differ with you argument in the corresponding letter, as we have seen that Glaesserella parasuis is a very diverse pathogen and when Australian strains were added to the MLST database they were all different to existing strains from Spain and the US in the data base.  ERIC is representing this variation.  The discriminatory power of 80% is definitely not representative of the variation and the profile is quite different when you look at the similarity by eye.  ERIC for H. parasuis is very consistent and you will get the same pattern when run on different occasions with some serovars having distinct bands.  You again mixing up clusters with subtypes.
The cut off is meant to give you the same strain (subtype) when above the cut off.  Below you get different strains.  The same farm can have different strains with the same serovar.  A study by Turni et a. (2010) revealed that on some farms, more than one genotype was present for one serovar.
What you are looking at is clusters of related strains and for that you can have the 80% cut-off

An isolate is a non-defined isolate and the differentiation between field isolate and isolate is strange.  The figure just shows which isolates are the same and therefore one strain.
It would have been good to discuss the fact that all bar two isolates had the vta gene, as other studies have not shown that.
The ERIC PCR can not necessarily detect different serovars.  There are cases where the ERIC PCR is the same but the serovar is different.  That might have to do with the change in serovar might not be due to huge changes in the DNA and therefore might not be noticeable in the distance of the repetitive sequences and the banding pattern might stay the same.  This is particularly relevant for serovar 12 and 5, which even the new multiplex PCR can not hold apart.


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: SPATIAL VARIATIONS OF MICROBIAL COMMUNITIES IN ABYSSAL AND HADAL SEDIMENTS ACROSS THE CHALLENGER DEEP
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript presents some interesting, relevant and very timely data. However, the manuscript tends to be very descriptive and - in my opinion – it lacks a clear well defined research aim. What is the hypothesis that is going to be tested, evaluated and discussed? Without a clear focus, the presentation and discussion becomes very descriptive and also speculative – and in my opinion the “conclusions” are rather weak and not substantiated by the presented data.
The wording is often impressive and the authors should streamline the text being more explicit and precise when they discuss and evaluate their data.
In conclusion I recommend acceptance after major revision – most importantly the revised manuscript should provide a clear research focus with a well formulated aim (hypothesis) which could provide the manuscript some direction.
Below please find a list of concrete suggestions.
Abstract
Line 39 “dramatic” is in my opinion an exaggeration – I suggest eliminating “Dramatic” from the sentence.

Line 46; What do you mean by “novel” – please be specific. As written, I am not sure that this claim is substantiated  by the presented data. Also I find the terminology “potential endemic unidentified Clades” very speculative. Please tone down these claims – and simply just write what you have found  with using word like “potential endemic”. Such statements would require additional physiological, biochemical and biogeochemical measurements.

Inroduction
Line 67-68, Improve wording, the grammar is incorrect and the wording unfortunate. Also the statement “with the effect of water current…” is very unspecific - what do you mean?

Line 71-75…; wrong tense – this makes it confusing. Begin with “Previous studies have shown that…. “. Also the structure is un-logic. The section begin with pelagic microbiology, then cold seeps, then landslides, then back to microbiology at the Northern slope and out of nowhere enhanced salinity at 9000m. Try to streamline and be explicit about what you really want to say when leading up to your study.

Line 87; Please define “ecotype”

Line 88; A recent work… does not really complies with referencing a 10 year old study.

Line 93-97…; reads very inconsistent- In fact the whole paragraph reads like a list of information without really synthesizing consensus or identifying the actual challenges to be tackled by this study and our community in general. What is the hypothesis or the aim of this study?

Line 109-116..; this reads like a conclusion, - though very indirect and unspecific- e.g. How should a funneling effect facilitate distinct microbial communities at depth???? This is unclear. Be specific when you explain. The last sentence is very unclear – in what way does this study promote……???? This paragraph should rather present the specific aim of your investigation.

Materials and Methods
Line 124-125; the core sectioning procedure is not very please include the actual sediment horizons for the specific samples in Figure 2. That would help the reader to directly relate observations to the sediment sampling depth.

Results
Line 172-173; how many more “species” (relative speaking) are you missing?

Line 180; Suppose you mean “specific taxa” – not sure this is very dramatic given that different diagenetic pathways operates in the different sediment layers. If you use a word like “dramatic” you must relate it to something … compared to abyssal reference sites or???

Line 189-191; So why would a facultative anaerob be facilitated by “a oxygen flux that was minimized to the best for…”. This is unclear please be specific on what you mean.

Line 198; what do you mean? This seams opposite to the high O2 consumption – please explain and be specific. It becomes very difficult to begin comparing sediments from different sampling sites without any indications on the ongoing diagenetic activity. So does the variations simply reflect that different processes are ongoing in the respective sediment layers across the depth transects given different carbon courses – and remain unrelated to depth (pressure) as such. What is the aim of this study?

Line 204; do you mean “Nutrition” rather than “nutrients”? Otherwise it is unclear to me.

Line 209; How does the data reflect “its uniqueness”? I can accept it is “separate” or “different”, but how do you now it is “unique”.

Line 229-230; What do you mean by”…potential novel species in this phylum except for W…”?

Line 239…249; So do you consider all the phototropic bacteria to be an artefact of recovery-contamination ? Or are they simply buried relicts from depositional material. This is unclear to me? What do you mean please be explicit and clear in your wording.

Line 262-263; Be careful using words like “Unique” or “endemic” – you do not know that!

Line 262-264 How do you know? Could the extracted DNA be E-DNA ?

Line261-283; In this paragraph you argue for that benthic trench communities are “survivors from the surface” to “endemic communities”.. it is not really clear for me what you mean and what are the specific arguments for the respective “conclusions” – please be more specific.  You have absolutely no clue if these play a geochemical important role?

Line 329; So do you argues for methanogenic activity in the deep trench? Or is this just a result of deposition from above (which is a more likely explanation)? Please be clear?

A conclusive section is not needed – this is a very short paper – and punch lines should be clear in the Discussion.
Experimental design: see above
Validity of the findings: see above
Additional comments: see 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: SPATIAL VARIATIONS OF MICROBIAL COMMUNITIES IN ABYSSAL AND HADAL SEDIMENTS ACROSS THE CHALLENGER DEEP
Review round: 1
Reviewer: 2

Output:
Basic reporting: L44-46: What do “clades” mean? In my interpretation of clades mostly higher taxonomic clades I did not find any “endemic clades” thorough the manuscript.

L67-68: Please provide appropriate references for the sentence. If not, it should be deleted or the content should be moved to discussion section.

L75-78: Please provide appropriate references for the sentences. If not, they are likely based on speculation of the authors and are not appropriate for the introduction section.

L84: Recently more papers have been published, e.g. Jing et al. 2018; Guo et al. 2018; Xu et al. 2018; Zhang et al. 2018.

L85: Nishizawa et al. 2013 is not appropriate.

L88-91: The information is not consistent with the reference “Lauro and Bartlett”. The sentence is likely incomplete.

L101: What does preliminary mean? This manuscript lacks both geochemistry and quantitative microbiology data sets and is likely preliminary parts of huge project although the authors analyzed numbers of samples.

L113: Appropriate references should be provided for “due to the rapid accumulation of POC under funneling effect.” If not, the sentence is not appropriate in this section.

L119-: I think all the samples were retrieved from the EEZ of Micronesia. Permission of the sampling should be stated here or acknowledgement section.

L131: Appropriate references should be provided for the primer set used in this study.

L174: For the candidatus phyla, they should be presented as “Ca. XXX” through the manuscript. In addition, previous division names are helpful for readers.

L178: Halomonas should be presented by italic.

L190: “suggesting” instead of “indicating”. The manuscript lacks geochemical data set. Thus, “indicating” is not appropriate.

L203-207: Appropriate references should be provided because due to the absence of geochemical data set, the environmental data are probably not enough to conduct complete statistics.

L222-224: The number of OTUs given in Fig 4 is not sufficient to discuss about the connectivity among the trench phylotypes.

L224-226: The result is interesting, but the information is not sufficient. How about the similarity between the OTU to Methanomassiliicoccus? Only the low-esolution phylogenetic tree in Fig 4 is not enough.

L238-244: Appropriate references should be provided.

L247: Identification of 16S rRNA genes from chloroplast has been identified in subseafloor sediments and discussed (e.g. Kirkpatrick et al. 2016). It is not so surprising. Considering the difference in biomass between the surface water and sediments, the abundance of such sequences is probably too high to speculate as contaminants although the authors did not present quantitative data set.

L251: Appropriate references should be provided because the grouping has not been authorized.

L254-255: Appropriate references should be provided.
L263-266: Appropriate references should be provided.

L268-272: Luo et al. 2018 should also been cited. In addition, there are also reports without in situ oxygen concentration measurements that obtain similar trend.

L286: Please explain why did the data indicate elevated “primary” production.

L294: Appropriate references should be provided.

L304-306: Appropriate references should be provided.

L310: Appropriate references should be provided. Spore deposition or dormant cells in the trench bottom has also been suggested by the isolation of thermophilic Thermaerobacter and Geobacillus (e.g. Takai et al. 1999; Takami et al. 2004). On the other hand, Bacillus is also recognized as a typical contaminants in lab analyses.

L317: Nunoura et al. 2016 is not appropriate reference. The authors should cite oceanography papers.

L326: Because the manuscript completely lack geochemical data set, appropriate references are necessary in discussion between microbial components and geochemical parameters.
Experimental design: The manuscript lacks geochemical data set as the authors mentioned while the authors analyzed numbers of 16S rRNA gene diversity. In addition, quantitative microbiology data such as cell abundance and quantitative PCR for 16S rRNA gene. These are usually requested for complete environmental microbiology papers. In the previous papers enumerating microbial activity between trench bottom and adjacent abyssal plain sediments, microbial biomass was reported while microbial diversity analyses were absent. To compare the results in this paper and previous works, I hope to add quantitative data set in this paper.
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: SPATIAL VARIATIONS OF MICROBIAL COMMUNITIES IN ABYSSAL AND HADAL SEDIMENTS ACROSS THE CHALLENGER DEEP
Review round: 2
Reviewer: 1

Output:
Basic reporting: Through the manuscript: Candidatus phylum can be presented as “Ca. XXX” through the manuscript.

L71: “In contrast” instead of “However”.

L93: Pathom-Lee et al. 2006 is not likely appropriate reference here.

L95: What does “known phyla” mean?

L218: There is no evidence that TIB08 MGII phylotype is derived from thermophile in the reference. Sometimes non-thermphilic microbes are detected from samples taken from high temperature environments. Kimura et al. 2013 in Env. Microb. Rep. and other reports are helpful to estimate the growth temperature from 16S rRNA gene sequence.

L270-: It is not appropriate about the impacts of hydrate on geochemical analyses for samples for the ambient deep-sea sediment samples. The sentences should be deleted.

L293: “under” instead of “in”

L293: The occurrence of the anammox can be a signature of the absence or very low concentrations of oxygen. However, there are many reports that the presence of thaumarchaeal 16S rRNA gene sequence from the depths that oxygen concentrations are not detectable in marine sediments. It is not clear whether they are relics or active, it cannot be a signature of oxygen concentration.

L299: Very old paper presenting higher abundance of Bacillus is not reliable, and probably a signature of lab contaminants.

L309: The finding of “Ca. Woesearchaeota” (DHVE6) in deeper layers in deep-sea sediments has been reported before even in the Mariana Trench sediments. Appropriate paper should be cited.

L315: “thermophilic archaea of MGII” see above.

L320: What are the novel groups found in this study?

L460: The authors list is not appropriate.

Table S4: Please provide analytical method.
Experimental design: I understand the difficulty to provide pore-water geochemistry, but I cannot understand microbial cell counts are not presented in this study while the authors have obtained the data set. Only cell count (or qPCR) would contribute to connect this study and previous and future studies for trench benthic microbial ecosystems except for the geological setting. The data set is essential.
Validity of the findings: no comment
Additional comments: The manuscript has been extensively updated,  while issues listed above still remain.


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: ADSORPTION OF THALLIUM(I) ON RUTILE NANO-TITANIUM DIOXIDE AND ENVIRONMENTAL IMPLICATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a well-written manuscript. The article structure, figs, tables were shared in a professional way. Literature and references were also provided.
Experimental design: NO Comment.
Validity of the findings: The topic is interesting. It would be better if the author could point out the significant contributions and the potential of this work on expanding upon the novel ideas. Also, it would be better if the author could discuss the applications of those finding.
Additional comments: This manuscript titled “Adsorption of thallium on rutile nano-titanium dioxide and environmental implications” by Dr. Liu et al is very interesting. It is mostly well written. However, some specific issues should be stated clearly. That would be better for the readers to understand the experiment design and results. Take the following into consideration.

1. Line 18. Suggest sentence reconstruction.
2. Line 55. To evaluate the adsorption behavior of TI on RNTD, various parameters were chosen to conduct the study. Why the study chose these parameters instead of others as tested? Do these parameters have any special characteristics associated with adsorption behavior or any other reasons?
3. Line 66. Why you chose 25 C for the shake flask study?
4. Line 77. Please change " For evaluating" to " To evaluate".
5. Line 115. Please add the citations. In addition, it would be better if the author could compare your results with other published data, which is related to ionic strength.
6. Line 147. Please list the reasons why you chose the pseudo-first-order model?


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: ADSORPTION OF THALLIUM(I) ON RUTILE NANO-TITANIUM DIOXIDE AND ENVIRONMENTAL IMPLICATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The structure of material & methods and results report is straight forward and clear.
Reference was included properly.
Experimental design: Experimental design is solid.
however, the scientific discussion on the data interpretation needs improvement.
Validity of the findings: Significant results discussion needed in this manuscript
Additional comments: Line 65: more detail samples prep, the number of treatment and treatment procedures etc. needed.
Line 76: after 300 min?
Line 102: figure 1 shows a decrease in adsorption amount with increased dosage. Also, 0.5-2.5 is not matching the figure either.
Line 113: Please double check the data, since the constant adsorption rate did not mean saturated. its still absorbing Ti without decreased rate.
Line 168: explain more about 297K, 303K, 313K etc.
Line 216: what sample was it?
Line 217: where is the figure 10?


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: ADSORPTION OF THALLIUM(I) ON RUTILE NANO-TITANIUM DIOXIDE AND ENVIRONMENTAL IMPLICATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have adequately addressed my concerns in this revision.
Experimental design: The authors have adequately addressed my concerns in this revision.
Validity of the findings: The authors have adequately addressed my concerns in this revision.
Additional comments: The authors have adequately addressed my concerns in this revision. I recommend this paper 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: ADSORPTION OF THALLIUM(I) ON RUTILE NANO-TITANIUM DIOXIDE AND ENVIRONMENTAL IMPLICATIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article meets the standards and has improved from the last edit.
Experimental design: The article meets the standards and has improved from the last edit.
Validity of the findings: The article meets the standards and has improved from the last edit.
Additional comments: Dear Authors,

I reviewed the comments. You provided a relevant explanation as well as additional information requested by reviewers.

The content of the manuscript is ready to publish. However, the font of the reference is different. I would suggest you go through the format and grammar check one more round before publish.

Thanks,
Jiayi


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: TOWARDS A DISTRIBUTED CONNECTIONIST ACCOUNT OF COGNATES AND INTERLINGUAL HOMOGRAPHS: EVIDENCE FROM SEMANTIC RELATEDNESS TASKS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a well designed, well conducted and well written study, examining task dependent modulations in cross-lingual effects among proficient adult bilinguals. It further tests for long term cross lingual priming in the same population. The introduction is overall well written, and provides the reader with adequate theoretical and empirical basis to understand the motivation for the current study

When reviewing the literature, the authors mention a single study that utilized the semantic relatedness task. There are at least two other studies that have used this paradigm in the bilingual research (Prior, Degani, Awawdy, Yassin, & Korem, N., 2017, Cognition; Degani, Prior, & Hajajra, 2018, BLC) and both have observed reliable cross-lingual effects (although Interlingual homophones were utilized in these studies). Further, Bowers, Mimouni, and Arguin, 2000, Memory & Cognition) examined long-term priming of cognates. These studies should be incorporated into the text.

Lines 70-74: the transition should be improved. It is not clear why the word type differences imply differential (or special) representations rather than differences in activation patterns (or even response based differences), and this does not seem to be a critical point here. Further, the transition “another important question…” is rather weak.

Paragraph between lines 202-216 – it is interesting to note here that Prior et al. (2017) utilized a cross modal priming, where the cognate/IH was auditorially presented in one language and their non-target language meaning was nonetheless activated and primed the target word. Thus, the use of a Hebrew accent did not preclude the activation of the Arabic meaning of the interlingual homophone.
Experimental design: The two experiments are described in full, with details regarding the participants, the stimuli, and the analysis readily accessible. All relevant materials are available through the OSF website. The interpretation of the findings is grounded, and adheres to the pattern observed in the analysis.
Validity of the findings: The discussion is well organized. The results and their interpretation are highly relevant, and can provide the basis for substantial advancement in modeling of bilingual research.

The motivation for the direct comparisons between cognates and Interlingual homographs is not entirely clear (the 2*2 analyses comparing these two types of words). As the authors note, these comparisons tell us little about the nature of the difference (cognate facilitation vs. IH interference), and the pattern is more clearly captured by the other 2*2 comparisons (cognates vs. control and IH vs. control). Consider removing these comparisons.

In Experiment 2 pairwise comparisons are reported in which the word type effect is examined within the unprimed trials. It is not clear why similar analyses are not reported in addition for the primed trials (unless I have missed this somehow).

Line 623 – Reassuringly… - not clear why this is reassuring?

Line 1399 -  the authors interpret their findings as providing a broad replication for the cross lingual long term priming observed in previous research. Given the non significant priming effect in all comparisons, this statement is not entirely clear.
Additional comments: Below I outline a few issues which if addressed I think will improve the paper.

Most critically, although the authors do a remarkable job of leading the reader through the complexities of their experiments, the manuscript is still very long and includes several theoretical issues. I would suggest the authors to consider splitting the manuscript into two, with each focusing on either Experiment 1 or Experiment 2. Although the two experiments used the same materials and criteria, the theoretical questions addressed by each experiment are different. I believe the reader would benefit from a more focused paper, dealing either with task dependency modulations of the effects or with the long-term priming of the words. If the authors decide to keep both together, be sure to clearly mark in the figures which Experiment is being depicted.

Second, although the role of phonology is beyond the scope of the current study, it may nonetheless be valuable to mention it in the discussion section – as overlap in phonology is likely to modulate and contribute to the dynamics of activation of cognates and interlingual homographs.

In general, I think this is a highly interesting paper, bridging the gap between monolingual ambiguity research and bilingual cross-language ambiguity research, and is likely to make substantial theoretical contribution. I look forward to seeing this work published soon.

Tamar Degani


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: TOWARDS A DISTRIBUTED CONNECTIONIST ACCOUNT OF COGNATES AND INTERLINGUAL HOMOGRAPHS: EVIDENCE FROM SEMANTIC RELATEDNESS TASKS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, it was not difficult to follow the story. The manuscript is written in clear and professional English. It is also well structured, with the theoretical story laid out very well. It is respectable that the authors have provided the background with appropriate references including the most recent model of bilingual processing.
Experimental design: The authors conducted relatively rare experiments in bilingual processing research. This is important, as the authors stated, for converging evidence; the bilingual-specific language effects we want to understand should not be task-dependent. It is respectable that the authors have introduced an impressive amount of methodological rigor and that they have also preregistered the study. Overall, because the experiment was designed and described meticulously, replication must be possible with the information provided in the manuscript.
Validity of the findings: The analyses were performed with an up-to-date statistical technique. I can confirm that the data and the corresponding analytical scripts (R codes) are available at the public data repository. It is also clear that the authors applied a decent amount of experimental control and conducted the experiment professionally from the participant recruitment stage till the end.
Additional comments: Summary
This study reports two semantic relatedness experiments with two different focuses: (1) a bilingual vs. monolingual comparison in a semantic relatedness experiment and (2) a long-term priming effect on semantic relatedness performance. In both experiments, inhibitory interlingual homograph effects were observed while the well-known cognate facilitation effects were not observed. The authors conclude that the present results are not in line with predictions of the current localist connectionist models for bilingual processing. Instead, they interpret the results with a distributed connectionist model, motivated by insight from monolingual research: interlingual homographs and cognates are processed in a semantic task just like homonyms and polysemous words respectively.

Evaluation
The unique pattern of results involving both cognates and interlingual homographs will certainly be a valuable addition to our knowledge of bilingual processing. Although I initially felt that the manuscript was slightly long, I soon noticed that it is partially due to the meticulous methodological descriptions, and this is great. Overall, I enjoyed reading this carefully written piece of work, and my impression towards this study is highly positive. I believe that this manuscript will be publishable in PeerJ with only minor revisions. I will be happy if the authors can consider the following minor issues (which are more like my requests) and line-by-line comments.

Minor issues

1. "Trial Number" in the models
Distinguishing lexicon-based processes and task-based processes is a key topic in this study. The authors are perfectly aware that "the semantic relatedness task, like any task, involves decision processes. Consequently, the effects [...] could have been due to response competition" (line 1265-1266). Given this, I am wondering whether the authors have ever included the trial count ("Trial Number" in the data frame?) in the regression models. If not, I am curious how this variable will behave. The motivation is that less automatic task-based effects at the response level must be susceptible to the trial number (e.g., It takes some time for participants to suspect that Dutch knowledge is relevant in the experiment). I believe that more insight can be obtained if the following interactions are tested:

Item type * Trial Number — if the item type effects are lexicon-based, they should be observable from the beginning of the experiment

L1 frequency * Trial Number — If participants consciously start suspecting the involvement of Dutch words, the L1 frequency effect should become larger later in the experiment.

2. Visualization

The violin plots are interesting and certainly informative in that readers can inspect the data distribution and the individual differences across different item types. However, perhaps many readers would like to see the partial effects from the mixed-effects models plotted with confidence intervals. I would like the authors to consider this option in case other reviewers, too, submit the same concern (then the violin plots can be kept in the appendix).

Line-by-line comments

line 136: "The problems with .."
-> I found the word "problems" slightly too strong here. Past lexical decision studies were certainly valuable to the filed; they just had "limitations."

line 142: "a disadvantage for interlingual homographs"
-> I understand what you mean here, but "processing cost" or "prolonged processing" might be less subjective and more appropriate than "disadvantage."

line 340-342: "Experiment 1 was ... relevant to the task."
-> Apparently, the authors are safeguarding against potential effects of the language mode or something similar. It might be better to state the motivation and cite the relevant paper(s) here. For example,

Grosjean, F. (1998). Studying bilinguals: Methodological and conceptual issues. Bilingualism:
Language and Cognition, 1, 131–149

Soares, C., & Grosjean, F. (1984). Bilinguals in a monolingual and a bilingual speech mode:
The effect on lexical access. Memory and Cognition, 12, 380–386.

line 448: "random word generator websites"
-> May I ask what those random word generator websites are?

line 535: "separately"
-> Please remove this repeated word.

Koji Miwa


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: FACIAL FLATNESS INDICES: APPLICATION IN ORTHODONTICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is clearly written and follows professional reporting standards. All necessary IRB approvals are presented, and raw data is provided and shared according to data sharing policies. The results demonstrate significant findings for orthodontics and studies of human variation, and present novel steps in future studies correlating the two fields of study for future scientific endeavors. The literature cited, background, and discussion are all adequate to support the authors' arguments.

Minor reporting concerns exist, however, which should be addressed:

1) The authors uses the terms 'gender', a socially-based category and identity in lieu of 'sex', a biological distinction between male and female. The binary distinction of sex is used in the present statistical tests, so reporting 'sex' in this manuscript is suggested.The term 'race', while certainly common in the cited anthropological literature, is here used in the discussion (pg 11 ln274) to reflect the relative homogeneity of the present sample population; I would suggest altering the description of the sample population to exclude the historical weight of the term race (e.g. ancestry). See Tishkoff and Kidd (2004) Implications of biogeography and human populations for ‘race’ and medicine. Nature Genetics 36, 11; S21-S27.

2) Minor typos exist throughout (p6 ln80, p11 ln255, p11 ln275 for example).

3) Tables are not consistently formatted: capitalization, cell format, and font vary in some tables.

4) Define terms (e.g., Class I, Class II, Class II) and acronyms (ANB, ENN) for non-orthodontic audience.
Experimental design: The research design is original and significant; the application of long-held anthropological and cephalometric methodologies to contemporary CBCT images provides a framework for testable hypothesis across numerous fields. Statistical methods are valid and pertinent to the present study, and described adequately in the results section. The methods are replicable, with one minor addition:

1) Which landmark had the lower (0.82) ICC (p8 ln160)? Knowing this will help future researchers evaluate Type I and Type II landmarks are most useful for facial flatness indices.
Validity of the findings: The sample size is robust and statistically sounds, and exclusion criteria are valid. No speculation present in the results or discussion, and conclusions are supported by the statistical results.
Additional comments: This is a well-written and impactful manuscript. Minor edits are recommended, many of which pertain to language usage and its relevance/meaning across varying fields, but they do not detract from the conclusions drawn in 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: FACIAL FLATNESS INDICES: APPLICATION IN ORTHODONTICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The conclusions stated in the abstract do not naturally flow from the stated results. The abstract also lacks statistical evidence of stated results.

I suggest further proofreading of the article. Some phrases are very awkward, e.g., line 66 “modern to old human beings”. This sentence is technically incorrect – “old” human beings would imply individuals who have achieved an advanced age, not fossil hominins.

The summary of the anthropological literature is dated and inaccurate. Facial flatness indices are now rarely used in anthropology. Particularly problematic is the discussion of “mitochondrial Eve” (which was never assumed to be 1 woman, but rather, a small related population). Also, the reason that facial flatness was of interest in paleoanthropology is not clearly articulated. It boils down to the fact that earlier hominins have a greater amount of facial prognathism, and arguments about regional continuity of populations (which were based upon a whole suite of features, facial prognathism being just one). It would be good to clarify the fact that genetic data has essentially resolved the “Out of Africa/Multiregionalism” debate.

The authors alternate between referring to the point of greatest incurvature between ANS and prosthion as “Point A” and “Subspinale”. I recommend choosing 1 term and being consistent. If you choose to use the term “Point A”, please note that most anatomists/anthropologists will not be familiar with this term so it might be useful to initially indicate that this is also known as subspinale.

Please define your technical terms. This paper has been submitted to a journal with a broad scope. A non-orthodontist reader will not know what “ANB” is, for example. Please also define “Class I/II/III” for the reader in more basic (non-measurement-based) terms.
Experimental design: The experimental design appears sound.
Validity of the findings: I am mostly confused about the applicability of the findings, particularly in Class II patients. The authors demonstrate a relationship between the zygomaxillary facial flatness index and skeletal malocclusion, but do not provide any evidence that including this measurement would lead to better/more efficient treatment. Since most practitioners still do not take CBCT scans, what is the added value of taking a scan and collecting this measurement? I think this is especially important given that taking a CBCT scan (may) expose the patient to a greater amount of radiation than a lateral ceph. The authors cite a set of examples in the literature about the transverse relationship of Class II subjects, but it is still unclear how this information would improve treatment. Please clarify.

In the Discussion (lines 273-276) the authors assert that a lack of variation between growing and non-growing patients might be “due to the fact that all individuals of the study sample were ascended from the same race (specie) which confirms their use for the phylogenetic discrimination among populations”. This sentence is problematic. 1) While I assume the authors mean the human race, this is not clear from their wording. (Also, "species" is both the singular and plural form of the word. “Specie” is not correct). 2) The results do not “confirm” the use of these measurements “for the phylogenetic discrimination among populations”. Firstly, what is meant by populations? Different hominin species? Secondly, the authors present no results that indicate that these measurements will discriminate across hominin species (though there is of course other published data on this topic). Please reword this section.
Additional comments: Perhaps a longitudinal study could be accomplished using 3DMD facial images? [This is not a suggestion for the paper, but a more general thought]

Overall, an interesting study applying a new method to (hopefully) improve diagnostic techniques. The applicability of the method to Class II patients should be clarified. Also, the benefits over current methods should be highlighted to address the fact that taking these measurements requires a CBCT scan (still not standard practice for most orthodontists, due to the slightly increased radiation levels compared to a lateral ceph).


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: FACIAL FLATNESS INDICES: APPLICATION IN ORTHODONTICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The suggested edits and recommendations were adequately addressed.
Experimental design: No problems identified- all suggested edits addressed.
Validity of the findings: All edits/rebuttals are sufficient.
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: FACIAL FLATNESS INDICES: APPLICATION IN ORTHODONTICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have done a nice job of responding to both reviewers’ feedback.
I have noted a few very minor edits:
-Line 274: “ascended from the same ancestry” should be “descended from the same ancestry” (thank you for removing the problematic term “race”)
-Line 150 “Tukey” is misspelled
-Line 284: “Class II malocclusions have” or “Class II malocclusion has”
Experimental design: No issues.
Validity of the findings: No issues.
Additional comments: Thank you for your thorough response to the suggested edits, I believe this has improved the clarity of the article. The definition of key terms in Table 1 should particularly help, given the paper’s goal of integrating anthropological and orthodontic research.