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

Input:
Title: THE POSTCRANIAL SKELETON OF CERREJONISUCHUS IMPROCERUS (CROCODYLIFORMES: DYROSAURIDAE) AND THE UNUSUAL ANATOMY OF DYROSAURIDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The topic is ambitious, but it is “self contained” and the results are relevant to the hypothesis. A thorough analysis of postcranial characters is relatively rare and, to me, welcome, especially where it can shed light on locomotor mode and ecology. However, there are significant problems with the reporting that need to be addressed. I will break these into text and figures/tables.
Text:
1. Interpretation of literature. Unfortunately, in several cases the literature is misinterpreted or misused:
Line 1206: “In crocodylians, the height of neural spine is positively correlated to stiffness in lateral direction… (Molnar et al. 2014)” This was a NEGATIVE correlation. The mistake is perpetuated in the rest of the paragraph and also in line 1293.
1356: “the interlocked osteodermal shield of dyrosaurids likely prevented them from performing the gallop” – this statement is not supported by the literature. Several references state that interlocking osteoderms would not have prevented galloping:
Salisbury, S. W, and E.F. Frey. “A Biomechanical Transformation Model for the Evolution of Semi-Spheroidal Articulations between Adjoining Vertebral Bodies in Crocodilians.” In Crocodilian Biology and Evolution, 85–134. Chipping Norton, Australia: Surry Beatty & Sons, 2001.
Frey, E. “The Carrying System of Crocodilians: A Biomechanical and Phylogenetic Analysis.” Stuttg Beitr Naturk A 426 (1988): 1–60.
2. Context of study. The introduction is extremely short and does not give enough context for the study, making it harder to understand the rationale (especially for readers who are not experts in fossil crocs). For example, what types of animal are Congosaurus and Hyposaurus, and why is their anatomy important for a paper about Cerrejonisuchus? Is there any particular importance of Cerrejonisuchus among dyrosaurids in terms of phylogeny or ecology, other than it being an early member of the group? More detail about the existing ecological hypotheses for dyrosaurids would also be helpful. Finally, and perhaps most importantly, no groundwork is laid for the assessment of whether crocodylians overlap with dyrosaurids in morphospace and/or whether they are functionally analogous. Who proposed this and what was its basis?
3. Clarity. The English is generally good, but there are some places in which the wording is confusing and the meaning is unclear. For example, what is it that “shows that basal dyrosaurids [Young et al., 2016] had already developed a massive tail.”? (line 712) Also (line 1006) What is meant by “higher on its legs”? Also (line 1258) “mediolateral rigidity reaches its maximum throughout the trunk” – maximum is the single highest point – how can it be throughout an entire body region?
4. Spelling and grammar. There are a few spelling and grammatical errors also, such as “strait” instead of straight and “convexe” instead of convex (746), “parpophysis” instead of parapophysis (line 256), “aren’t” instead of is not (725). There is an extra “colonized” in line 44. Line 1306: I believe you mean integration, not “irrigation”
5. Formatting of manuscript. In some places, paragraphs are preceded by bullet points for no apparent reason (196, 205, 420-432).
6. Choice of references. The article is generally well referenced (although more references are needed in the introduction – see point 2). I suggest an additional reference for vertebral function and morphology in crocodylomorphs, section 9.1:
Hua, Stephane. “Locomotion in Marine Mesosuchians (Crocodylia): The Contribution of the ‘Locomotion Profiles.’” N. Jb. Geol. Palaont. Abh., no. 227 (2003): 139–52.
Figures and tables:
The structure of the manuscript is clear and straightforward, and the figures are excellent. However, I find it hard to follow because the figures and tables are not well integrated with the text and because the tables themselves are hard to read. In addition, the logic for including some tables and figures but not others is unclear.
1. Relevance of tables and figures. The tables and figures should be carefully chosen to convey the main points of the manuscript. Although the limb proportions are discussed at some length, there is only one table on limbs (table 16), and that table only shows a few obscure ratios that are only referenced once. There should be a table showing basic limb proportions and perhaps comparisons, and it should be referenced in the paragraphs that discuss these topics (e.g., the first 3 paragraphs of section 5.1). Some tables are too short to allow comparison; for example, tables 1-3, 4-7, 8-10 could be combined to allow comparison of vertebral measurements (don’t forget units!) and figures 2-4 could be combined (as is done, very effectively, in SI), allowing the reader to compare similar measurements between regions and taxa. Finally, it would be very nice to have a figure showing a reconstruction of the entire skeleton. Likewise for the comparative vertebral morphometrics and regionalization: their discussion covers several pages, but the only supporting data is in SI.
2. Formatting of tables: While I understand that the identities of the preserved vertebrae are not known with certainty, I think it would be better to use your hypotheses of their identities on the tables and graphs instead of just numbering them in order (which is very confusing!). In addition, the labels used in the tables are not intuitive. For example, in table 1 the column for centrum height is labeled “Aa” instead of “CH” or “Centrum ht,” and row 1 is labeled “UF/IGM 31 C1” instead of simply “C1.” This is a problem throughout.
3. Integration of figures and text. The text does not refer to the figures of bones very often or very specifically. For example (lines 901-902): “The anterior and posterior protuberances, which make the top two rounded tips of the heart in ventral view, also show a dorsal depression between them that can be observed easily in proximal view.” This should refer to figure 12, and the dorsal depression should be labeled on that figure. This is just one example, but each anatomical description should refer to the relevant figure. In addition, each figure part should have a unique letter that is used to refer to it in the text (Figure 12 has two 12 a’s, etc.) Also, I would use “change” instead of evolution to describe patterns along the spine (e.g., fig. 3 caption).
4. Raw data. Morphometric data are supplied in SI in graphical format, but a table of raw numbers would be more appropriate and useful. In addition, part of the labels are cut off on the right side and some of the colors are too similar to be easily distinguished (e.g., Fig. SI 3).
5. Fig. 13f. The area of PIFI attachment is not visible – the yellow color is too light.
Experimental design: The work is original, the research question is well defined, and the manuscript will contribute meaningfully to the literature. The investigation is technically rigorous and well described. I think that the analyses are appropriate (but see point 1 below).
1. Rationale for choice of methods. Why not use a Phylogenetic Principal Components Analysis? Line 1162 says, “In this case, phylogenetic and ecological signals are indistinguishable,” suggesting that pPCA might be better. And why use dimensionless ratios as inputs rather than allowing the first component to represent size? Again, I’m not saying that the analyses are inappropriate in any way, just that alternatives should be considered.
Validity of the findings: The data seem to support the conclusions, and the underlying data are provided (except for the raw morphometric measurements, as stated above). Conclusions are well stated. However, there are some problems, most importantly with the use of supporting references but also with clarity.
1. Use of references to support conclusions. In several places, references are missing or inappropriately used. Line 955: please provide reference or rationale for claim that semicircular femoral condyles are a terrestrial feature. Also, there is confusion in lines 1148-1149 “When Pierce et al. [2009] studied thalattosuchian skull disparity using geometric morphometrics, their results showed the opposite trend.” To be clear, it is not a trend; Pierce et al. found that metriorhynchids were more distinct from other thalattosuchians than pelagosaurs. However, they used a different sample of specimens and species, which could yield different results. Also (lines 1262-1263) “This dorsoventral stiffness probably enabled greater step length [Molnar et al., 2014] in dyrosaurids compared to crocodylians.” Molnar et al. only looked at Nile crocodile vertebrae, and I don’t believe they discussed step length – more references/explanation needed. Also (lines 1366-1367) “elongated zeugopodia … making Cerrejonisuchus one of the most terrestrial dyrosaurids while likely retaining a sprawling posture [Molnar et al., 2015] – This reference deals with vertebrae and did not include dyrosaurids, so it’s unclear how it supports this statement. Please carefully check all references and make sure you are accurately representing their findings!
2. Link between conclusions and results. Going back to point 1 under figures and tables, there is no reference to figures or tables in the conclusions. This makes more difficult than necessary for readers to assess whether the conclusions are well founded. In addition, it would be very helpful to summarize the evidence for each conclusion.
3. Epicondyles vs. condyles. I’m confused about the discussion in lines 818-836 regarding “epicondyles” of the humerus. The discussion of asymmetry, especially regarding effect on ROM (832) usually relate to condyles, but “epicondyles” is used in the text and that’s what is labeled on the figures. If epicondyles is meant, please explain the functional relevance.
4. Link to original research question. “Multivariate analysis of our extensive morphological dataset describing the anatomy of exemplar dyrosaurids, thalattosuchians, and crocodylians reveals that dyrosaurids possess a distinctive postcranial anatomy among crocodyliformes, indicating that the latter cannot be used as a functional surrogate for the former.” (lines 1445-1448) I think you mean crocodylians instead of “the latter” (crocodyliformes). Also, going back to point 2 about the text, it is not possible to evaluate the implications of morphological differences between crocodylians and dyrosaurids without any context.
5. Explanation of findings. When comparative anatomy of several taxa is described I find myself getting lost – I don’t know why particular comparisons are being made or what they mean. For example, lines 955-971 compares the distal femoral condyles (“capitula”) of 8 taxa, but it is not clear how they are related or what these comparisons are meant to show.
Additional comments: No additional comments


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

Input:
Title: THE POSTCRANIAL SKELETON OF CERREJONISUCHUS IMPROCERUS (CROCODYLIFORMES: DYROSAURIDAE) AND THE UNUSUAL ANATOMY OF DYROSAURIDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript includes important new data on the postcranial skeleton of dyrosaurids. These data have implications for phylogeny, function, and locomotion. Introducing some of these implications (that currently are toward the end of the Discussion) in the Introduction would help set up your study and your hypotheses better. In some places the writing needs to be more clear; this is particularly true in the vertebral section where there are a lot of measurement data that become slightly confusing. The figures are helpful in showing the specimens being discussed, but because the preservation of the material doesn't appear to be great line drawings could be helpful.
Experimental design: The authors include a lot of measurement data for these specimens and list many packages used for their analyses. It would be good to be clearer about what hypotheses are being addressed with this work prior to going into a list of packages. Perhaps those would be better listed in a table. Because one of the goals appears to be identifying taxonomically distinguishing features of the postcrania, a comparative figure or two would be very helpful to illustrate your points.
Validity of the findings: The discussion and conclusion sections of the paper are well written. I had a much better idea of the importance of this work once I got to the end of the Discussion section. The research question and hypothesis need to be more obvious earlier.
Additional comments: This paper provides a lot of very useful data on the postcrania of these dyrosaurid taxa. It's clear that the authors put a lot of time into collecting all the measurements and anatomical data for the vertebrae; those details will be very helpful to other researchers. There are some issues with the grammar and word choice that I tried to address in the marked up pdf. The Introduction can be expanded a bit to incorporate your hypotheses, and the Materials and Methods is the section of the paper that will need the most attention to increase readability. There are a lot of figures, which is good, but they could be a bit more in focus and perhaps need accompanying line drawings because the specimens appear flat. Overall, a lot of good information once the authors clean up some things.


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

Input:
Title: THE POSTCRANIAL SKELETON OF CERREJONISUCHUS IMPROCERUS (CROCODYLIFORMES: DYROSAURIDAE) AND THE UNUSUAL ANATOMY OF DYROSAURIDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The text and figures are much improved. I especially appreciate the new reconstruction (Fig. 9).
1) The interpretations of literature have been corrected and sufficient context is provided. A little bit of additional detail about references showing "importance" of postcrania would be helpful (line 94)
2) The introduction has been expanded and provides context and motivation for the study.
3) Clarity, spelling, and grammar are much better, though some minor wording issues remain (see attached pdf). Please avoid imprecise/casual expressions such as "anyhow"  and "let's now describe ..." In addition, section 4.1 could still be better organized. Again, to avoid confusion I recommend reserving the word "evolve" for change over time.
6) Supplemental information is accessible and useful.
Experimental design: The experiment is well designed, and I accept the rationale for using PCA instead of PPCA.
Validity of the findings: Clarity and supporting references are much improved.
1) The organization and wording are much clearer, making the link between results and conclusions more obvious. However, the discussion sections are quite long and it is easy lose track of the main points. I suggest adding a short paragraph at the beginning of each section summarizing the findings and outlining the points that will be covered.
2) The rationale for comparisons with crocodiles has been explained, and comparisons with other extinct taxa are more concise and clearly reasoned.
3) I don't understand the rationale for relating neural canal dimensions to blood flow to the head (lines 1533-1544).
4) The term "bracing system" in the referenced literature refers to a combination of bones, muscles, and ligaments. Here you are only describing ribs and vertebrae, so I might replace it with a different term such as "thoracic skeleton" (Figure 8 caption, lines 886 )
5) The discussion of the influence of the tail in terrestrial locomotion is interesting and would benefit from a more precise explanation of its influence on croc locomotion (lines 1596-1597). I suggest the following reference:
Willey, J. S, A. R Biknevicius, S. M Reilly, and K. D Earls. “The Tale of the Tail: Limb Function and Locomotor Mechanics in Alligator Mississippiensis.” Journal of Experimental Biology 207, no. 3 (2004): 553–563.
Additional comments: I appreciate the careful revision. The authors have addressed all of my concerns, and the resulting manuscript is clear and convincing. I think it will make a valuable addition to the archosaur literature.
Please note: I have added minor comments to the "tracked changes" version of the manuscript (attached), and line numbers in the review refer to this version.


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

Input:
Title: THE POSTCRANIAL SKELETON OF CERREJONISUCHUS IMPROCERUS (CROCODYLIFORMES: DYROSAURIDAE) AND THE UNUSUAL ANATOMY OF DYROSAURIDS
Review round: 2
Reviewer: 2

Output:
Basic reporting: This updated version of the manuscript has much improved flow and clear English throughout. I appreciate the added sections to the Introduction- they greatly clarify the intentions of the manuscript and set the reader up to follow along through the description much more easily.
Experimental design: The hypothesis is much clearer now, and the methods have more detail.
Validity of the findings: No new comments- the authors appear to have addressed all reviewer comments associated with the validity of the findings.
Additional comments: Great job! I think you have made substantial improvements to the presentation of your work. I only have extremely minor changes that are in the attached marked up pdf. I think with those updates the manuscript is ready for acceptance. I look forward to seeing this in print and utilizing your work!


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: NOSTOLEPIS SCALE REMAINS (STEM CHONDRICHTHYES) FROM THE LOWER DEVONIAN OF QUJING, YUNNAN, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, this is a welcome addition to the world of Palaeozoic microvertebrate studies. The biogeographic and biostratigraphical value of such remains has been proven for circum-Arctic regions by many studies over the last half-century, but the distribution of 'acanthodian' scale-based taxa outside Europe and Russia is relatively poorly known. Descriptions of Chinese assemblages help fill in the gaps in our knowledge.

Some of the English needs improvement, I have made suggestions on the annotated pdf.

Sufficient details of context and background have been provided. Literature references are comprehensive and relevant, although some could possibly be trimmed. I have made a few corrections to the reference list, and suggested where some references could be removed.

The article is professionally structured. Perhaps more figures of scale histology for the new species could be added. Figure 7 should be corrected as per my comments annotated to the figure pdf.
Experimental design: Zoobank ID details need to be added to the Materials and Methods section as per PeerJ instructions.
Validity of the findings: I am not convinced by the identification of one of the species, Nostolepis decora. As remarked in the annotated pdf, I wonder if the scales assigned to this species should rather be assigned to Hanilepis wangi. I realize that the type material for that species is older than the assemblage from the Xitun Fm described here, but to me the purported N decora scales are more similar morphologically and histologically to those of H wangi. If the authors agree about this assessment, they would need to amend the title and abstract - or rename Hanilepis wangi as Nostolepis wangi??
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: NOSTOLEPIS SCALE REMAINS (STEM CHONDRICHTHYES) FROM THE LOWER DEVONIAN OF QUJING, YUNNAN, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment in general

As far as I can see, the article is written in clear, unambiguous, and technically correct English. I’ve attached a .pdf file, in which a couple of places are highlighted, where some changes might be done. However I am not a native English speaker, so I guess they are most probrbly unnecessary. The article provides sufficient coverage of Nostolepis taxonomic diversity, morphology, histology and paleogeography, and gives enough contextual information for the presented new data. All figures are of good quality, relevant to the topic, and references to them are given in the text. The article is ‘self-contained’.
Experimental design: No comment

The research theme is clearly defined.
The article describes six Nostolepis species from the Lochkovian of Qujing, eastern Yunnan, including 2 new species. It contributes to closing the gap in knowledge about paleogeographic distribution of Nostolepis and acanthodian diversity in the Early Devonian of South China.
It seems to me that taxonomic descriptions are rigorous enough: both morphology and histology of the scales are described in details and comparisons with the most similar known Nostolepis species are provided.
Maybe more data could be given about the samples, from which the scales were extracted and counts of the scales, but its not obligatory, I think. Methods of the study are described well enough.
Validity of the findings: No comment in general

The described findings are novel and could be of interest not only for paleoichyologists, but also for anyone interested in the large-scale Devonian stratigraphic correlation. For example, it has implications for correlation between South China and Baltica blocks.  The commonly needed data for such type of studies are provided. The photographs of morphological features of the scales in different perspectives as well as the photographs of thin sections illustrating the scales’ histology are given for each of the described species.
Additional comments: Overall I find that the article provides important new knowledge on acanthodian diversity and must be published.
It could be of interest to see a map with localities, were the samples, from which the scales were obtained were collected and stratigraphic columns, but it seems to me that it is not obligatory.
I’ve attached a .pdf file, in which a couple of places are highlighted, where some changes might be done language-wise. However I am not a native English speaker, so I guess they are most  probrbly not necessary.


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: DNA METHYLOME AND TRANSCRIPTOME ANALYSIS ESTABLISHED A MODEL OF FOUR DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AS A DIAGNOSTIC MARKER IN ESOPHAGEAL ADENOCARCINOMA EARLY DETECTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well-written and well-organized.
Experimental design: The authors investigated DNA methylation status of the esophageal adenocarcinoma using public databases. Then they developed a robust diagnostic model of this cancer.
Validity of the findings: The developed model was validated by the other public dataset.
Additional comments: The authors should include the name of 4 genes identified here in the abstract.

If possible, the authors should analyze or comment about the differences of methylation patterns between EAC and ESCC. Is this model able to distinguish from EAC from other cancer types?


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: DNA METHYLOME AND TRANSCRIPTOME ANALYSIS ESTABLISHED A MODEL OF FOUR DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AS A DIAGNOSTIC MARKER IN ESOPHAGEAL ADENOCARCINOMA EARLY DETECTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The work presented by Peng et al. is clear. The manuscript is well-organised and clearly written. The authors made an important effort explaining their results. Moreover, these new findings may serve as a fertile ground for future research in the area of early diagnosis of esophageal adenocarcinoma, based on epigenetic markers.
Experimental design: The experimental methodology is clear to follow.
Validity of the findings: No comment
Additional comments: I have read with interest this research paper. This topic is timely relevant.
Publication is recommended after adressing the following suggestions:
1- Introduction line 66-67: the definition of DNA methylation (.. methylation, a physiological states, involves in methylation of the CpG islands..) could be improved: It is the transfer of a methyl group onto the C5 position of the cytosine..
2- introductuon line 67-68: Although gene silencing by the hypermethylation seems to be the most likely mode of action, there is growing evidence of a more complex view on the effect of DNA methylation in diverse contexts. In particular, for the genes that become hypermethylated, the associated expression level can be unaffected, or even upregulated in some cases (reference: Wan J, Oliver VF, Wang G, Zhu H, Zack DJ, Merbs SL, Qian J. Characterization of
tissue-specific differential DNA methylation suggests distinct modes of positive
and negative gene expression regulation. BMC Genomics. 2015;16:49). The authors could add "in general" after (negatively regulate gene expression), or explain the diversity of epigenetic regulation in this case.
3- methods line 130: stage II/II or I/II ?
4- results line 218: the sentence could be reformulated.


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: DNA METHYLOME AND TRANSCRIPTOME ANALYSIS ESTABLISHED A MODEL OF FOUR DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AS A DIAGNOSTIC MARKER IN ESOPHAGEAL ADENOCARCINOMA EARLY DETECTION
Review round: 1
Reviewer: 3

Output:
Basic reporting: Peng et al report a novel DNA methylome diagnostic signature in patients with Esophageal adenocarcinoma. The authors use a comprehensive tool of plethora of bioinformatic resources to reach some solid conclusions. The writing and the question is clear, with sufficient use of the existing literature. The preparation of the figure is adequate and clear.
I find the topic and the data very interesting and I would support the publication if the authors address some minor, but yet important, comments.
Experimental design: The experimental approach is accurate, with extensive information on the materials and methods section. The scientific question is well-defined and significantly covered throughout the report with high standard analyses.
Validity of the findings: The authors provide their raw data and the statistical model that they have used is efficient and correct. Although their conclusions are well-stated, I would like to suggest some additional analysis in order to straighten their report.

1. In figure 2, the authors should include Gene Ontology analysis of their targets in order to identify potential cancer-related pathways that are affected.

2. Also, the authors should also include Kaplan Meier curves for their proposed 4 gene-signature marker model in patients with Esophageal adenocarcinoma.

3. The authors should investigate and discuss any potential correlation with known mediators of the CpG methylation such as components of the PRC complex.
Additional comments: Peng et al report a novel methylome signature as a diagnostic marker in patients with EA. I believe that this report contributes to our knowledge for the pathophysiology of esophageal adenocarcinoma, and with minor edits this interesting concept should be published. I would be happy to review this work again after their revisions.


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

Input:
Title: DNA METHYLOME AND TRANSCRIPTOME ANALYSIS ESTABLISHED A MODEL OF FOUR DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AS A DIAGNOSTIC MARKER IN ESOPHAGEAL ADENOCARCINOMA EARLY DETECTION
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors properly revised the manuscript based on our 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: DNA METHYLOME AND TRANSCRIPTOME ANALYSIS ESTABLISHED A MODEL OF FOUR DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AS A DIAGNOSTIC MARKER IN ESOPHAGEAL ADENOCARCINOMA EARLY DETECTION
Review round: 2
Reviewer: 2

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


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

Input:
Title: DNA METHYLOME AND TRANSCRIPTOME ANALYSIS ESTABLISHED A MODEL OF FOUR DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AS A DIAGNOSTIC MARKER IN ESOPHAGEAL ADENOCARCINOMA EARLY DETECTION
Review round: 2
Reviewer: 3

Output:
Basic reporting: This is a revised version of Peng et al.
The authors addressed all the comments and suggestions.
I understand that the data of the survival of these markers are not so clinically impactful.
Nevertheless, this concept is worthy publication.
Experimental design: The new data are well controlled and designed.
Validity of the findings: Although the clinical significance of the proposed markers is not strong, it is important that they are discussed and included.
Additional comments: The authors have submitted a significantly improved version of their manuscript.
I support the publication of this interesting concept.


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: TRANSGENERATIONAL EFFECTS ON DEVELOPMENT FOLLOWING MICROPLASTIC EXPOSURE IN DROSOPHILA MELANOGASTER
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: Whilst the research questions is well defined, relevant and meaningful, there are some gaps in the methods described that would make the work difficult to replicate.
These are listed below:
Line 88 - please state whether the two types of nurdles had similar mechanical properties in grinding, i.e. were they equally blunt or sharp, long etc. Where is the proof that the flies actually ate the plastic?
90-93 - can the flies avoid eating the plastic in the media? Did they eat less media altogether because they didnt like the plastic? There is evidence that animals are reluctant to eat plastic and studies on Daphnia have shown that the impact of plastic ingestion is not so much the plastic itself but the reduced ingestion of food.
94 - I am not a Drosophila breeder and did not understand where the embryos came from. Do the authors mean eggs? It is not stated how much water was added to the embryos, therefore removing a set volume is meaningless. Overall I was unsure of numbers of embryos and whether the numbers varied considerably between tubes.
Validity of the findings: This is an interesting study and gives detail of negative results as well as effects of plastics. The data are controlled, robust and sound.
Conclusions are well stated and linked to the original research question. However I remain unconvinced that the authors have ruled out reduced feeding as the source of smaller body sizes. This should be addressed and discussed.
Additional comments: Have you considered whether the fragments are mechanically damaging the gut if they are sharp?
For me the lack of information on the plastic raises some questions about what the flies were ingesting. Do you have any data that proves that they ingested the plastic?


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: TRANSGENERATIONAL EFFECTS ON DEVELOPMENT FOLLOWING MICROPLASTIC EXPOSURE IN DROSOPHILA MELANOGASTER
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: Methods described with sufficient detail & information to replicate.
Methods should be described with sufficient information to be reproducible by another investigator.
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: TRANSGENERATIONAL EFFECTS ON DEVELOPMENT FOLLOWING MICROPLASTIC EXPOSURE IN DROSOPHILA MELANOGASTER
Review round: 1
Reviewer: 3

Output:
Basic reporting: -	The language is appropriate, with a few minor grammar issues (e.g. L20, L144, L201, L206 L270, L313) which should be resolved but do not prohibit understanding of the text in general.
-	The introduction is well structured and covers the relevant literature, but the paragraph on immune responses to microplastics (L60-71) would benefit from summarizing the studies a little, e.g. by types and sizes of plastics that were used, types of responses found, directly contradictory results (same species and plastic type tested in different studies with different outcomes) versus differences between species and plastic types etc. Identifying such patterns would be much more informative for the reader than just a list of studies. Of course this article is not a literature review, however a little guidance for the reader in the introduction section would be useful.
-	The article adheres to the standard section instructions by PeerJ and the information is appropriately allocated to the different sections.
-	The Figures are well presented and the legends contain all necessary information to understand them.
-	The raw data is supplied in an excel file, but it does not contain explanatory metadata. While the variables used are mostly self-explanatory, the data structure as such could be explained to ensure data could be reused appropriately ( e.g. explaining what empty cells versus 0 versus n/a signify, whether rows are individuals/days/…)
Experimental design: -	This article clearly falls within the scope of PeerJ as it presents primary research in the biological sciences.
-	The research questions are well defined and the knowledge gap of how microplastics affect infection outcomes is clearly presented and addressed by the data. To avoid confusing readers however, I recommend revising the text to avoid suggesting that immune responses to microplastics were tested since they were not explicitly looked at in this study (e.g. L163, L220). While I agree that any effects on infection outcomes would likely be mediated by immune response differences, there are other possibilities, such as altered resource availability and a reduced resource availability for both host and parasite. In return, the finding that infection outcomes are not altered by microplastic exposure does not prove that there are no effects on immune responses, they may just be inconsequential for this particular infection.
-	The experimental design is rigorous and conforms to a high technical standard. The methods describe the experiments well and are sufficient except for a couple of details that should be clarified:
L89 The minimum and maximum sizes of the particles are useful, however a distribution of sizes ( at least mean +- std error) would potentially be even more useful to compare the outcomes to other studies and size ranges used therein. As the authors point out in the discussion themselves, microplastic particle size can strongly influence the effects on organisms.
L129 Does this viral injection treatment result in successful infection 100% of the time? If not, it may be more appropriate to talk about virus exposed rather than infected flies in the results. Either way, it might be useful to tell readers that do not work with this virus a few more details about the infection and its effects on the host.
Validity of the findings: -	All underlying data and statistical code have been provided.
-	Speculation is generally clearly marked, except for the assumption that immune responses were tested (see earlier comment in experimental design section)
-	The conclusions are well founded on the research questions, results and discussion. However, they could be easier to grasp for readers if they were summarised more in the categories “within exposed generation” and “transgenerational effects in non-exposed offspring of exposed flies”. Furthermore, given the prominent reference to the result in the 4%PVC treatment, it would be good to remind the reader that this treatment was not tested in the F1 so it is at least not clear whether this is only a transgenerational effect.
Additional comments: L27-28 This sentence can be misunderstood to say that the F2 were descendants of the survivors of the infection experiment, please revise to clarify that the F2 assays were carried out in an unbiased way.
L79 The direction of the fecundity effect is not clear from the text.
L183 Presumably should say “no significant differences between treatments”


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: TRANSGENERATIONAL EFFECTS ON DEVELOPMENT FOLLOWING MICROPLASTIC EXPOSURE IN DROSOPHILA MELANOGASTER
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have substantially revised and improved their manuscript. I am satisfied with those changes and only want to point out a few small mistakes in the newly added text:

L71 The Aljaibachi et al 2020 study did not look at immune responses – did you mean to add a different citation here?
L80 It still says here that the immune response was tested –  this needs changing as in the rest of the text to say resistance to disease was tested.
L213 In the F2, where…
L287 greater
Experimental design: satisfied with the revision
Validity of the findings: satisfied with the revision
Additional comments: No additional comments


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

Input:
Title: THE IMPACT OF COVID-19 PANDEMIC ON NITROGEN DIOXIDE LEVELS IN NIGERIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: • The manuscript is well written but there are areas of improvement (grammatical errors and sentence re-structuring). Kindly review the complete manuscript for improving its quality to ensure that an international audience can clearly understand. Some of the examples are given below:

Line 46: edit (after it originated)
Line 48: edit (measure that was termed)
Line 53: edit ((December 2019/April 2020/results show a significant)
Line 54: edit (during the lockdown/during the pre-lockdown)
Line 71: edit (and is declared)
Lines 102-103: edit (humans as it poses)
Line 113: edit (advent of coronavirus)
Line 129: edit (he Nigerias' air quality)
Lines 144-145: reference needed (In addition, these cities are among the top major inhabited cities in Nigeria and among the most polluted)
Line 147: reference for spatial resolution (spatial resolution of 5.5 km)

2) Although the resolution of figures meets the basic requirements for submission but it is not good for readers and details are hidden due to poor quality.

3) Figure-2: What is disease outbreak status here (number of positive cases or cases per million population or else)

4) Figures-5,6,7,8: there is no legend to interpret whether red is high or blue is high in concentration.

5) Main data for NO2 concentration is missing (can be provided as a table too as zonal statistics for each state that was studied).
Experimental design: 1) I feel that intermittently the paper loses its focus between impact of COVID-19 on NO2 concentration vs its impact on general population.

2)Although the authors have utilized satellite imagery to do a comparative analysis but they haven't justified the use of satellite image versus the actual ground monitoring stations data. Authors need to cite papers that correlate these two sources of NO2 pollution assessment.

3) Comparing NO2 concentrations for December 2019 and April 2020 may not be the best way to proceed as many air pollutants show a trend i.e. they vary between winter, summer, rainy seasons due to several factors and atmospheric phenomenon. It is best to compare apples to apples i.e. baseline data should have been April 2019 and not December 2019.
Validity of the findings: 1)The manuscript in its current form needs major re-structuring including re-running some analysis, improving figures, providing data, refining the introduction and discussion section to emphasize mainly on NO2 pollution rather than COVID-19 cases in general.

2) Authors have just mentioned that there is a significant improvement in NO2 pollution which is based on just two months (unaccounting for seasonality). There is no mention about how much percent improvement was achieved for this period.
Additional comments: Its a good topic and good start but it needs some improvement before others can make use of this information. Best wishes!


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

Input:
Title: THE IMPACT OF COVID-19 PANDEMIC ON NITROGEN DIOXIDE LEVELS IN NIGERIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper poses an interesting and timely question. The writing, however, needs work. Ample suggestions, and most of my review, are shown in the attached review.
Experimental design: The manuscript states that the study "...compares the levels of NO2 density before the advents of the first reported case of COVID-19 in Nigeria and its levels during the lockdown in selected cities to assess its impact on the air quality of Nigeria." Unfortunately the authors simply provide satellite images that represent NO2 concentration over four cities/regions in December 2019 and again in April 2020. The authors did not suggest, nor did they offer any analyses of these images (which, don't even have a legend to suggest what the concentration levels were); their study simply provided a brief visual assessment of the before and after images.
Validity of the findings: The authors repeatedly suggest a "significant decrease", "significant drop" or more troubling, "NO2 pollution has disappeared" - they have offered no technical or statistical assessment to justify their findings.
Additional comments: The title of the paper suggests an analysis of changes in NO2 concentrations over Nigeria before and after the COVID-19 lockdown, but there was little information provided on this question. Most of the discussion provided in the Results was in fact background information on the cities where the authors looked at satellite images. The background information should have been presented in the introduction, but that would have magnified how little NO2 analyses were provided in the Results.

The study does represent an interesting and useful question, but this manuscript really only provides brief discussions on the visual changes observed between the before and after images, which does not provide much scientific information.

To make this study meaningful to the PeerJ community, the authors need to perform enough technical analyses (e.g. statistical analyses of the NO2 data before and after the lockdown) to justify any statements about changes in NO2 concentrations. All information about infection/death rates or economic impacts in each region studied need to be moved out of "Results" and into "Introduction", and the "Results" section should only focus on NO2 data.


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

Input:
Title: THE IMPACT OF COVID-19 PANDEMIC ON NITROGEN DIOXIDE LEVELS IN NIGERIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: There is an overall improvement in the manuscript language, structure and figures.
Experimental design: I believe the authors have done a good job in improving the manuscript for international readers.

The only minor thing that I will suggest adding to the manuscript before publishing it is a better justification of comparing NO2 concentrations for December 2019 and April 2020. No doubt that COVID-19 lockdown has reduced pollution but the seasonality factor needs to be accounted for as well at least when we are not comparing the same time periods. This can be done by simply citing recent articles or comparing a trend during the same period for the previous year. Google Earth engine apps can be helpful as well.
Validity of the findings: The topic is good, results are valid and it is good to be published with very minor edits as mentioned in the previous section.
Additional comments: Good work in improving the script. One last improvement to add and it is all set - best wishes!


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: EFFECTS OF EDUCATION METHODS ON SELF-EFFICACY OF SMOKING CESSATION COUNSELING AMONG MEDICAL STUDENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Generally, the paper is clearly structured and well-written. Concerning literature references, it would be good to aim to incorporate more up-to-date literature, as quite some sources are 10+ years old already; also check small inconsistencies and mistakes in reporting references in-text. Further, the textual description of the results seems to be very complete but perhaps too elaborate, as this hampers its readability. Also, table 1 does not add information on top of what is mentioned in-text.
Experimental design: Several improvements should be made to the methods section of the paper, in order to make replicability of the study more likely.
- the informed consent procedure should be elaborated on;
- it would be important to elaborate on potential bias of asking coordinators to comment on their own education;
- the questions in the questionnaire require more explanation, e.g. answer scales/options, to understand what data was exactly collected;
- although a sample size estimation is given, this requires more elaboration.
Validity of the findings: Several improvements could be made to improve the validity of the study's findings, as described in the following suggestions.
- be mindful not to introduce (new) results (e.g. lines 282-287) in the discussion, but rather focus on an interpretation of results;
- the authors should be careful with making claims about causality (e.g. with lines 327-328 the authors hint at a potential causal relationship, which cannot be supported with the current findings);
- several limitations of the study are mentioned, but no supporting literature is provided to counter-argue these limitations;
- generally, more elaboration is warranted as to what the present study adds for the scientific community, e.g. describing its implications for research and practice.
Additional comments: Thanks for the opportunity to review this interesting paper. In addition to the feedback and suggestions already provided, I would advice the authors to also look at the following comments on the abstract and introduction of the paper.
Abstract:
- clear and concise abstract, though more information on data collection (e.g. paper-based vs digital) can be provided;
- information on data analysis is still lacking and should be added.

Introduction:
- important topics are described from broad to specific, though the authors could elaborate on the ‘new educational methods’ introduced in line 93.


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: EFFECTS OF EDUCATION METHODS ON SELF-EFFICACY OF SMOKING CESSATION COUNSELING AMONG MEDICAL STUDENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is good in language and professional design
Experimental design: Only 22.1% of the students completed the questinnaire and 19.8 % were smokers. This may not represent the real percentage of smokers. Because smokers are usually reluctant to repond voluntarily to such questionnaires. This should be included in the discussion.
Validity of the findings: Only 3.2 % of females in the study group were smokers which is very low.What is the percentage of female students in South Korean Medical Schools? Is  this 34.5 %  females close to the average percentge in medical schools?
Those with smoking experiences tended to be more confident in smoking cessation counseling which is contrary to previous findings in the literature (İcliet al1992,Brutons et al 2005).This may be related to inclusion of former smokers in the smoker group. They are usually more enthusiastic in smokinng  cessation programs.
Additional comments: Congradulations for studying such an important public health problem


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: EFFECTS OF EDUCATION METHODS ON SELF-EFFICACY OF SMOKING CESSATION COUNSELING AMONG MEDICAL STUDENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thanks for giving me the opportunity to re-review this paper. The authors have adequately improved the paper based on the reviewers' feedback. Hence, I do not have any further comments. I wish the authors good luck in finalizing 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: EFFECTS OF EDUCATION METHODS ON SELF-EFFICACY OF SMOKING CESSATION COUNSELING AMONG MEDICAL STUDENTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: well done
Experimental design: No problem
Validity of the findings: Satisfactory  additions  were done related to my  previous  review
Additional comments: Congratulations for dealing with a very important subject of public health


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: COMPETING ENDOGENOUS RNA NETWORK IDENTIFIES MRNA BIOMARKERS FOR OVERALL SURVIVAL OF LUNG ADENOCARCINOMA: TWO NOVEL ON-LINE PRECISION MEDICINE PREDICTIVE TOOLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is well-written and the overall presentation is acceptable. Literature references are appropriate as well.
Experimental design: The authors explored potential post-transcriptional biological regulatory mechanism and prognostic biomarkers for overall survival of LUAD patients. Standard analysis tools were used and the study lacks methodological novelty.

The dataset was downloaded from The Cancer Genome Atlas (TCGA) database, UCSC Xena database, cBioPortal database, and the Gene Expression Omnibus (GEO) database.
This is a comprehensive dataset and adds to the strength of the paper.

The method used to identify biomarker/prognostic RNAs did not use more recent methodologies. Check the following paper for patient specific expression profiles:
Menche, J., Guney, E., Sharma, A. et al. Integrating personalized gene expression profiles into predictive disease-associated gene pools. npj Syst Biol Appl 3, 10 (2017). https://doi.org/10.1038/s41540-017-0009-0
I would recommend the authors to use this methodology for identifying the RNA sets of interest.
Validity of the findings: The authors mentioned:
According to the median of the original gene expression value, the original expression values were converted into “0” for lower expression and “1” for higher expression.
-- Did you use log fold change? Was any distribution used for this step or simply a median threshold was used? There are better methods in place already for this step and the rigor is not clear.

Authors mentioned:
Finally, twenty-two lncRNAs, twenty-nine miRNAs, and seventy-three mRNAs were used to build the ceRNA network for overall survival of LUAD patients.
-- Are these the only differentially expressed RNAs? The regulatory network was created based on the interaction mining from the three databases mentioned. But these are not based on only validated interactions. The authors need to correlate the regulatory network with the expression values seen in their dataset using reverse engineering algorithms.

There were several prognostic models built for predicting the prognosis for lung cancer patients (Xie & Xie 2019; Yan et al. 2018; Zuo et al. 2019).
-- How are the individual biomarkers compare with the group level results form these prior works? For validation, the authors show the relevance of the identified genes in different cancer scenarios; however, this discussion should be better focused for LUAD only.

Since the genetic detection platforms were different, some adjustments are needed to make these predictions more realistic.
Additional comments: Please see the comments mentioned 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: COMPETING ENDOGENOUS RNA NETWORK IDENTIFIES MRNA BIOMARKERS FOR OVERALL SURVIVAL OF LUNG ADENOCARCINOMA: TWO NOVEL ON-LINE PRECISION MEDICINE PREDICTIVE TOOLS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this present study, authors developed prognostic models for overall survival of lung adenocarcinoma patients (LUAD).  The major issue with this study is that authors used gastric cancer data (Table 1) and used this as LUAD patient data for all downstream analysis. Authors need to explicitly explain this discrepancy.
Other comments:
1)	It is not clear how authors computed differential expression analysis. Please elaborate in the method section. The described cut off is 1.5 between tumor vs normal tissues. This is a very low bar and authors should include stringent cut off as well as include FDRs.
2)	The figure legends need improvement. All legends should have enough description for a reader to understand the figure without having to refer back to the main text of the manuscript.
3)	Please improve the resolution of figures.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: COMPETING ENDOGENOUS RNA NETWORK IDENTIFIES MRNA BIOMARKERS FOR OVERALL SURVIVAL OF LUNG ADENOCARCINOMA: TWO NOVEL ON-LINE PRECISION MEDICINE PREDICTIVE TOOLS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The study explored potential post-transcriptional biological regulatory mechanism and prognostic biomarkers for overall survival of LUAD patients . The article is written well and unambiguous, technically correctly throughout. It includes sufficient introduction and background to demonstrate how the work fits into the broader field of knowledge. The structure of the article conform to an acceptable format of standard sections.
Experimental design: The experimental design within aims and scope of the journal. Research question well defined, relevant and meaningful. Methods described within sufficient detail and information to replicate.
Validity of the findings: Conclusions are well stated, linked to original research question and limited supporting results.
Additional comments: In this manuscript, the authors identified some novel differentially expressed RNAs and miRNAs between LUAD tumor tissues and noncancerous tissues, and they established a ceRNA network based on the differentially expressed genes. Two biomarkers candidates were identified from the ceRNA network. The topic is important, it may helpful in studying the pathomechanism of LUAD. English language and style are minor spell check required.


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

Input:
Title: COMPETING ENDOGENOUS RNA NETWORK IDENTIFIES MRNA BIOMARKERS FOR OVERALL SURVIVAL OF LUNG ADENOCARCINOMA: TWO NOVEL ON-LINE PRECISION MEDICINE PREDICTIVE TOOLS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is fine.
Experimental design: The authors have properly addressed all my comments.
Validity of the findings: This is fine too.
Additional comments: A professional English check is needed before final 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: CRANIAL ANATOMY OF BESANOSAURUS LEPTORHYNCHUS DAL SASSO & PINNA, 1996 (REPTILIA: ICHTHYOSAURIA) FROM THE MIDDLE TRIASSIC BESANO FORMATION OF MONTE SAN GIORGIO, ITALY/SWITZERLAND: TAXONOMIC AND PALAEOBIOLOGICAL IMPLICATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a very well conducted, informative and important contribution to the field. .
The manuscript is principially well written but contains few spelling and gramma mistakes, missing or additional blanks.
Some paragraphs are flush left , some are justified.
sometime there is a blank after PIMUZ T 43.. sometimes not. PIMUZ T43...
Experimental design: well conducted and appropriate illustrated

Authors justify why they use the Motani matrix and stated why not using the Moon matrix
I am fine with this.
However, they should be aware that if the Motani et al. 2017 matrix is based on Ji et al. 2016 (which is likley) that this matrix contains some typos and other errors, when not corrected...
but maybe neglegible for this study which mainly wants to analyse the relationships of Besano.
Validity of the findings: This is a detailed, well conducted and important revision of skull anatomy of Besanosaurus.
The conclusion that Mikadocephalus is a junior synonym of Besanosaurus is well supported and was long overdue.
Additional comments: here are some  specific comments
line
42: body size
75 (large-sized)
106 their ? which
175, indicating deep water ?
179, maybe replace features by preservation
you mention that the specimens can be ordered by size in line 192, so I am wondering which order you follow in your description from line 196 to 240
226, delete more
230, please check
what is the rec./estimated body size of GPIT 1793/1 and BES SC 1016
303, maybe replace bad by poor
319 ?and are almost complete
498-499 please rephrase
502, the contact of elements (instead of bone)
675 delete one .
1288- 1290 repetition to line 192
1291 unclear: every author measured every specimen ???
1333 please add taxon name for IVVP specimen
1409 this must be Fröbisch et al. 2006
1458 ?in other
1523-1524 repetition but maybe ok here/add blank
Fig. 10 please add to the Fig. legend whay you choose to show these slices/what is important here
Fig 11 please mark the naris with an arrow(s)
Fig. 12 please add to Fig Legend what exactly you want to show/point out here
maybe undlay the parts of the mx in the outline sketches with a light grey to further illustrate the shape
Fig. 13 ditto please shortly explain what you want to point out/visualize with the UV light
Fig. 15 please label or line pterygoids
Fig. 17 maybe mirrow B
Fig. 19 Fig Legend: Selected plots showing several cranial ratios across studied specimens supporting that the specimens represent an ontogenetic series
Fig. 20 I would move this nice reconstruction after the figs of single skulls (Fig. 10?) correct ichthyosauromorpha
Fig. 21 maybe move also cladogram forward


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

Input:
Title: CRANIAL ANATOMY OF BESANOSAURUS LEPTORHYNCHUS DAL SASSO & PINNA, 1996 (REPTILIA: ICHTHYOSAURIA) FROM THE MIDDLE TRIASSIC BESANO FORMATION OF MONTE SAN GIORGIO, ITALY/SWITZERLAND: TAXONOMIC AND PALAEOBIOLOGICAL IMPLICATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Generally a very strong paper and an important contribution.

There are some minor issues in communication detailed below.

The 3D photogrammetry models were not accessible to me in the Google Drive without prior permission, but this is not a deal breaker.
Experimental design: No critical comments on this front. I appreciate the new descriptive data, figures and analysis of important specimens that have been in collections for many years but not been featured in prior technical publications.
Validity of the findings: The overall description of specimens is detailed seems solid. The phylogenetic analysis builds on previous analyses. Some of the macroecological/macroevolutionary speculation at the end is debatable, but is plausible and well-founded overall. Some suggestions are offered below to clarify this section in a few places.
Additional comments: Abstract.

Line 42 - ‘Clade’ is redundant with ‘monophyletic,’ can be omitted.

Line 42 - ‘Size’ is a bit ambiguous, consider ‘body length’ instead if appropriate.

Line 44 - Minor quibble but ‘never before seen’ seems like an odd characterization for a taxon known since 1996 … ‘never before reported’

Introduction

Line 49 - Consider replacing ‘first’ or ‘earliest’ for ‘oldest’ which can have ambiguous meaning.

The authors avoid discussing the large ichthyosaur remains of Svalbard (e.g.  ‘Pessopteryx’)  which extend downward to the Olenekian. At times some of these have been suggested to have affinities with shastasaurs, including Besanosaurus (e.g. McGowan and Motani, 2003), although this has been questioned and there is a complicated history and taxonomy. (See Maxwell and Kear 2015). I can understand avoiding this as there are contradictory interpretations in the literature, but it might warrant a brief mention?

Line 83 - I think ‘had’ should be ‘having’ to make grammatical sense.

Materials & Methods

Line 209 - Slight ambiguity here: “last preserved caudal vertebra (the distalmost caudals are missing or spaced apart).” Do the authors mean that they measured to the last caudal vertebrae preserved in articulation and ignored the ‘missing or spaced apart’ distal most caudals?

LIne 226 - omit the first, extraneous ‘more’

Line 230 - “Is Preserved’ should probably be “It is preserved” (note missing word & capitalization.

Line 230 - Suggest replacing “position, it” with “position. It” (new sentence).

Results

Line 490 - replace ‘results’ with ‘is’

Line 533 - Again, non-standard use of ‘results’ here to me and the sentence overall is a bit vague. Can you clarify re resemblance to Guizhouichthyosaurus, is the similarity in size or in shape (or both)? NB: Now I notice the colon so I guess the similarity is about the contribution of the frontal? Regardless this sentence needs to be rewritten for clarity.

Line 548 - Again, ‘results’ should probably be ‘is’

Line 610 - replace ‘result’ with ‘be’

Line 742 - replace ‘results’ with ‘is’

Line 791 - ‘e. g.’ Is inconsistently formatted throughout the paper, sometimes with a space (as here), with or without a comma. I think it should be “e.g.,” (no space and with a comma).

Line 1260 - ‘appear’ instead of result?

Line 1281 - Again, I think ‘ result’ should be ‘are’ — Also a bit unclear if you are comparing just the roots as ‘much shorter and broader’ or the overall tooth morphology here

Line 1299 - omit ‘shows to’

Lines 1298/1302 - Figure 19: Not placing the origin of these plots at zero will provide a distorted perception of the slope. Also, allometric relationships are MUCH easier assessed when the data is plotted on a log-log axis, ideally with a reference line for isometry (exponent =1)

Lines 1305 - replace “few” with “little”

Line 1329 - replace ‘resulted’ with ‘turned out’ or just ‘The juggle was one of the most difficult…”

Lines 1327 - 1376 - This information was all already given in methods above so can probably be omitted here.

Line 1419 - I’m not quite sure what ‘relevant’ means here?

Line 1445 - ‘associated with’ instead of ‘associated to’

Line 1446 - Note ‘Peyenson’ is misspelled here, should be ‘Pyenson’ Also I’d probably replace the colon with a period and start a new sentence with, “A longirostrine skull,” also I would say something like ‘facilitates’ or ‘enables’ rather than ‘ensures’ high velocity.

Line 1462 - I would reconsider the use of the term ‘Rammer-like’ here. “Ram-feeding”  was coined initially by Liem 1980 to describe a feeding mode in teleost fish where prey are engulfed via coordinated acceleration of the body and mouth. It has later been applied to describe a variety of feeding modes in other aquatic vertebrates (not always consistently).

I think the authors are implying that Cymbospondylus would have used slower feeding cycle by higher bight forces to subdue larger but less evasive prey. This could involve a degree of ‘ram feeding’ but honestly the raptorial ‘snap-feeding’ suggested for Besanosaurus would also involve a form of ‘ram feeding’ sensu Liem 1980.

Perhaps rephrase as ’Cymbospondylus may have used a more forceful feeding strategy’ or something along those lines? I think that expresses the same idea without invoking a term that has some baggage.

Line 1474 - I don’t follow the reasoning entirely here, as anoxic conditions would be expected to generally favor soft-tissue preservation? In general though, soft-bodied coleoids do not have a fantastic fossil record so maybe the relative paucity isn’t so surprising?

Lines 1475 - 1481 - Nothosaurus giganteus might have filled this role in this ecosystem? Large macropredatory sauropterygians are scarce in the Anisian of North America apart from some fragmentary remains from British Columbia described by one of the co-authors.

Lines 1484-1509 - At first I was a bit skeptical of this scenario but I think the authors do a good job of articulating this, although it needs further investigation. Interestingly both Tomistoma and Gavialis attain very large sizes, among the largest extant crocodilians, which could support this scenario. Also, giant penguins (e.g. Icadyptes) are also extremely longirostrine so the authors might be on to something here.

Nevertheless, It seems to me that this is not the only ecologic pathway to gigantism in marine vertebrates. Deep diving & macropredatory ecologies are also associated with increased body sizes in many marine clades (pinnipeds, sharks & cetaceans).

Likewise there are numerous examples of longirostrine taxa that remain relatively small, among fish and aquatic/marine reptiles & amphibians. For example Mixosaurus cornelianus, which lived alongside Besanosaurus was rather longirostrine but much smaller. So the correlation between longirostry, low trophic level feeding & gigantism is a loose, and Besanosaurus likely represents one of many pathways toward gigantism/longirostry rather than the dominant mode.

Figure 3:

I find the uneven lighting/contrast across these panels to make it a bit difficult to get as much out of this figure as I would like. I know from experience how difficult it is to light and photograph large specimens particularly when they are on a slab and the contrast between bone and matrix is limited. I wonder if there might not be room for improvement, with some post-processing of brightness and lighting?
Alternatively some interpretive line drawings could be useful but I realize that is a lot of extra work.

Figure 19

See comments above.

Figure 21

It might be just the review PDF but the image quality here is a little low, although it does not hamper reading of the figure. The shading should probably be explained in the figure caption, or perhaps even better, labelling of key nodes.

Figure 23

I’m not sure this figure is adding much, it could probably be moved to a supplement. It might be most useful to see Besanosaurus & Cymbospondylus side by side as that comparison is emphasized more in the manuscript text. Why the gray shading on Grippia?


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: FUNCTION, STRUCTURE AND QUALITY OF STRIATED MUSCLES IN THE LOWER EXTREMITIES IN PATIENTS WITH LATE ONSET POMPE DISEASE—AN MRI STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The language is clear and adequate
The literature references are comprehensive
The article is well structures and also the figures are informative
The results although well presented are not very striking
Experimental design: The study design is already proposed in different paper and do not add any novelty
Validity of the findings: The study is not quite original because several previous papers have address this issue and with a number of patients more relevant.
Additional comments: The paper is of some interest but not quite original because this issue have been raised but other studies although not all of them were univocal.
To increase the meaning I would suggest to do a review of all the studies so far reported focusing on similarities, limitations and include these data


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: FUNCTION, STRUCTURE AND QUALITY OF STRIATED MUSCLES IN THE LOWER EXTREMITIES IN PATIENTS WITH LATE ONSET POMPE DISEASE—AN MRI STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comments
Validity of the findings: No comments
Additional comments: Very interesting article giving important information on utility of MRI in muscular involvement in Pompe disease.
A very important information is that CSA correlate well with muscular strength and could be a practical tool in order to follow therapeutics effectiveness.
I just regret that the follow up period and the time frame for enzymotherapy treatment is a little short.
I could be realy relevant to have more date over a longer period.


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: CONCURRENT ANEMIA AND STUNTING AMONG SCHOOLCHILDREN IN WONAGO DISTRICT IN SOUTHERN ETHIOPIA: A CROSS-SECTIONAL MULTILEVEL ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Introduction
Good; but in text reference of the document is not appropriate. Which reference methods do you used?
For example  line 24, line 28&29… “stunting among children aged under-5 years (Mohammed, Larijani & Esmaillzadeh, 2019),   … and access  to hand-washing facilities) level (Assefa, Mossie & Hamza, 2014; Getaneh et al., 2017; Gutema et al., 2014; Mesfin, Berhane & Worku, 2015)”. I think your reference style is Harvard method and in Harvard reference method, If the authors greater than or equal to three, in text reference written as Getaneh et al.,2017.  So you have to correct accordingly the whole in text reference

Methodology
In study area, design, and participants
You wrote “ … and 4 urban kebeles... 6 health centers …. , 2 private clinics, and 2 drug stores, … 3 urban and 22 rural primary schools.”  All number below 10 have to be written in letters like, four urban kebeles … six health centers…..
In sample size estimation
-Were the sample sizes proportionate or disproportionate from each class? And your calculated sample size was 845 schoolchildren but you recruited 864 schoolchildren why? If so, why it is important to calculate sample size? I mean why you are not recruited the sample proportionally?
- You said “We replaced participants who dropped out of school after the selection process with participants of the same class, sex, and age.” Please rewrite this statement including how you had replaced. I mean through which sampling method?
- …… sampling (Ali, Yifru & Woldeamanuel, 2009; Haftu, Deyessa & Agedew, 2014; Komba & Mgonda, 2010; Mekonnen, Tadesse & Kisi, 2013; Mesfin, Berhane & Worku, 2015). In text reference should be improved.

 In data collection tools and procedures
Ten trained enumerators conducted the interviews using a pretested, structured questionnaire that was adapted and developed in English …. From where adapted these questionnaire?  And you have to provide the references that you have adapted.
In statistical method
You wrote; “Independent variables with P < 0.05 in the final model were considered significant”. Write as  … with P ≤ 0.05 …
In ethics statement
You stated that, “Participant privacy and confidentiality were maintained”.
How participants’ privacy and confidentiality were maintained? Please state in what means that you maintain the privacy and confidentiality of participants.
In results and discussion
Well written, but similar to introduction and sample size estimation the in text reference needs improvement like:-
… for Ethiopia (Mohammed, Larijani & Esmaillzadeh, 2019)
… as described previously in Ethiopia (Alelign, Degarege & Erko, 2015 …
… nutritional demands (Soliman, De Sanctis & Elalaily, 2014).
 … findings (de Gier et al., 2016; Shang et al., 2010; Stephenson, Holland & Cooper, 2000).
Revision of the above listed comments of the manuscript is needed. The topic of this manuscript falls within the scope of journal of PeerJ .
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Check the whole manuscript and ensure the proper use of words, grammar ,capital and small letters
For example - in abstract method parts you wrote …  helminth infections … to say … helminthic infections
-	in introduction line 23 you wrote “anaema” in terms  of anemia
-	in Study area, design, and participants line 5   you wrote … “health centres” ….. to say health centers and line 10  you wrote … “parents or guardian were contacted”… to say parents or guardians were
 	The document needs eligible criteria and I never seen it in the document. I mean the manuscript states measurement of height and age for assessing stunting but we cannot assess stunting in the disabled children like anatomical deformed ones, because the stature does not show the nutritional problems.
 	Does this journal not require showing details on Disclosure about funds, Conflicts of Interest to the publication of this manuscript and Authors’ Contributions? However, my opinion suffices to just show in the main documents.


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: CONCURRENT ANEMIA AND STUNTING AMONG SCHOOLCHILDREN IN WONAGO DISTRICT IN SOUTHERN ETHIOPIA: A CROSS-SECTIONAL MULTILEVEL ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The text in English is easy to read. No major issue.
A little more could be added about the justification of undertaking the study in the targeted region.
At some places, some newer references are needed to be added regarding stunting and anemia in Africa.
The structure is fine. The methods are well described.
The results are relevant and bringing a new knowledge.

A few minor comments:

Abstract
Line 28-29: Could be good to indicate what was the sampling strategy. Random selection of 4/22 schools in the district and 24 classes from those 4 schools. May be good to indicate precisely that it was a 3-stage sampling.

Line 44: Is it a positive association for all listed factors?

Introduction
Line 58: Would be good to have a newer reference that this old one. New references about stunting and/or anemia in some countries in Africa can be found on PubMed.

Line 68-69: Same observation. Would be better to add some newer references.

Line 82: Why this region? What is its vulnerability or special status in Ethiopia regarding the health problems targeted by the larger study and by the outcomes covered by this paper?

Methods
Line 104-105: May be good to indicate from which reference is precisely coming each of these percentages. In the Introduction or the Study area, some already mentions of the situation in the area would make easier the choice of the percentage for the sample size calculation.

Discussion
Line 357: What criteria justifies a qualification of "moderate", "high" or else and what are the references?
Experimental design: Well done.
Methods described with sufficient details.
Good statistical analyses performed.
Validity of the findings: Results are strong and increasing the knowledge on a very complex dual burden.
Additional comments: An interesting paper exploring a complex public health issue.
The Abstract could better highlight the 3-stage sampling strategy.
And a number of additional newer studies on anemia and/or on stunting in Africa could be easily found with a literature on Pubmed or other well known public health journals.


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: CONCURRENT ANEMIA AND STUNTING AMONG SCHOOLCHILDREN IN WONAGO DISTRICT IN SOUTHERN ETHIOPIA: A CROSS-SECTIONAL MULTILEVEL ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been improved significantly; however there are some minor issues should be solved before final publication

1. The study conducted in Wonago district only, so adding the phrase Wonago district  to the title will make it more specific and improve the manuscript title.
2. In some area of your document there is un clear statement, like;
 In line169; Independent variables included at school level were participation in a school meal programme. “Were” is not correct in this context, do you mean where? Please rewrite the statement
3. There is inconsistency in writing  words; example , sometimes written as anaemia, sometimes as anemia and in other areas of your document as anema. Please write them in a consistent way and correctly.
4. As I commented before, still there are so many spilling and grammar errors in your document please take it in to consideration and correct the whole documents.
Exampls;
Line 45... southern Ethiopia and vary across classes and schools.  “Vary” change in to varies
Line 59… anaemic or stunted… “anaemic” change in to anemic
Line 61… school access and enrolment has improved,…” has “  change in to have
Line 68 …. few recent global report….. “ report” change in to reports
Line 74 …. with a prevalence rates… “a prevalence rates” change in to prevalence rates/ a prevalence rate
Line 85…co-morbidity of anema and stunting… “anema” change in to anemia
Line 97…. problems that includes… “includes” change in to include
Line 108…”kilometre”…. Change in to kilometer
Line 252 &253…  “missing values addressed before analysis”. Change in to  missing values were addressed…
Line 275 …”indictor” … change in to indicator
Line 295… ‘in each models’ … change in to each model
Line 361…”in all school”… change in to ... in all schools
Line 398 … common shared … changed in to commonly shared
Line 414 The rates of CAS was… change in to the rate of CAS was…
Line 463 …only cereals was served…. “Was” change in to were
Line 470 … two standard technique…” technique” change in to techniques
Line 501  “Acknowledgements”  change in to Acknowledgments
Experimental design: The study is done using appropriate and very correct and impeccably used methodologies. Good statistical analyses was performed.
Validity of the findings: Results are strong and increasing the knowledge on a very complex dual burden.
The conclusions are relevant and important, supported by the generated data.
Even though it was made in Ethiopia, in a particular district setting, the research question and methodologies can, and should, be used in other contexts.
Additional comments: A good  paper to  Visiting  a multifaceted  public health problems.
I consider that, it is  a very important paper and recommend it for publication after corrected this minor comments
The topic of this manuscript falls within the scope of Journal of  PeerJ


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: FIRST COMPLETE MITOGENOMES OF DIAMESINAE, ORTHOCLADIINAE, PRODIAMESINAE, TANYPODINAE (DIPTERA: CHIRONOMIDAE) AND THEIR IMPLICATION IN PHYLOGENETICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I commend the authors for their extensive and detailed work. But there is a weakness, it is in the section "Taxon sampling" which should be improved upon before Acceptance.
There is no information about the places of collection of specimens for genetic analysis, dates, collectors and stage of development, the stored place of vouchers.


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: FIRST COMPLETE MITOGENOMES OF DIAMESINAE, ORTHOCLADIINAE, PRODIAMESINAE, TANYPODINAE (DIPTERA: CHIRONOMIDAE) AND THEIR IMPLICATION IN PHYLOGENETICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Written expression isn't up to publishable quality, although the basic layout of the study and their ideas are sufficient to edit it into shape.  References could be used more extensively, but more or less OK.  Figures are good.

I've attached a marked up copy of the text with editorial suggestions.
Experimental design: Pretty basic experimental design for sequencing.  Comparative and phylogenetic analysis is better designed.  Methods are acceptable and fairly well documented.
Validity of the findings: Comparative genomics findings are well enough done, even if they basically find nothing particularly novel across the 'subfamilies within a family' scope of the study.  The phylogenetic results seem pretty robust on the face of it but are pretty thoughtlessly dismissed as erroneous as they don't confirm previous studies.  I think that the authors need to drill more on this and explore those previous findings before they can make the conclusion that they arrive at.
Additional comments: Zheng et al. present a useful expansion of our knowledge of chironomid mitochondrial genomes.  The sequencing and comparative genomics portions of the paper are well done, even if not particularly novel - it is still useful to know that the genome is fairly conservative across these taxonomic ranges.  The phylogenetic analysis is similarly well done but the write up and discussion of it is poor and needs more work before the final conclusions of the paper can be accepted.  The writing overall needs considerable improvement and a marked up copy of the manuscript is attached with editorial suggestions for improving the text.

1) Citations.  The paper could probably do with more citations (e.g. for the published mt genomes used) and I've marked some places in the text.  But more generally think about if you are giving enough credit to those who contributed to the thoughts expressed in the paper.

2) Phylogeny.  The description in the results is really poorly done, sorry to say.  It is imprecise about relationships and jumps between levels in the tree which make is hard to convey meaning.  You also seemingly report only the outcome of the two inference approaches for one dataset (2 support values) despite doing 5 datasets in the paper (10 support values).  You don't even mention how the datasets differ in their topologies (4 support one, 1 support another topology) or whether any of them is more or less likely to be true.

In the discussion, then you more or less completely dismiss your phylogenetic result because it doesn't match that of previous papers (principally the Cranston 2012 paper).  You need to rigorously examine the findings in both your own and the prior studies before coming to a conclusion as to which is right.  You have pretty good nodal support for relationships between subfamilies (except for made the node Chironominae + (Pod+Tany+Prod+Diam)) - how well supported are subfamily nodes in Cranston 2012?  Do either of the Saether papers include discussion of morphological features which would be consistent with any of your nodes.  It is common for morphology phylogenetic papers to present both a preferred topology and a discussion of contrary evidence - that contrary evidence might support your relationships.

Rather than just give up, decide that mitogenomes can't do subfamily relationships and call it all long branch attraction evaluate how good those previous studies really were in light of these data.
By the by, data sensitivity analysis such as you've done is usually taken as a test for long branch attraction, so that the trees are pretty insensitive to it suggests long-branch effects are not that big an issue here.  A more in depth consideration of the phylogenetic results is needed prior to 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: FIRST COMPLETE MITOGENOMES OF DIAMESINAE, ORTHOCLADIINAE, PRODIAMESINAE, TANYPODINAE (DIPTERA: CHIRONOMIDAE) AND THEIR IMPLICATION IN PHYLOGENETICS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English writing should be improved before submission. Please pay particular attention to English grammar and sentence structure.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Below are some corrections and comments that I believe could help improve the manuscript:

Lines 196-197: The three last numbers (803, 805, 801) do not agree with  the sizes of the D-loop of the respective species presented in Appendix S2. Please correct.
Line 197: The A+T content of the analyzed sequences  is comparable to the A+T content of the D-loop of most insects. Perhaps  the authors could consider modifying the "remarkably" expression.
Line 205: Please correct "families" to "sub-families".
Lines 207-211: Phylogenetic trees in Figure 5 do not all present the exact same topology. Perhaps the authors could consider describing the topologies in more detail.
Lines 215-216: I believe that the difference of about 1200bp among mitogenomes is considerable. I would suggest modifying the "slightly" expression. The fact that this difference is due to the size variation of the control region is rather interesting. Maybe the authors could comment on that (is there any sequence similarity of D-loop among species? Could size differences be attributed to  repeats in the D-loops of larger sizes?)
Table 1: The table does not contain references. The authors should either add this information in the table or modify  the Table title accordingly.


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: FIRST COMPLETE MITOGENOMES OF DIAMESINAE, ORTHOCLADIINAE, PRODIAMESINAE, TANYPODINAE (DIPTERA: CHIRONOMIDAE) AND THEIR IMPLICATION IN PHYLOGENETICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I'm asking you to correct "Prof. Andrey Krasheninnikov" to "Dr. Andrey Krasheninnikov" or to remove the phrase altogether


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: FIRST COMPLETE MITOGENOMES OF DIAMESINAE, ORTHOCLADIINAE, PRODIAMESINAE, TANYPODINAE (DIPTERA: CHIRONOMIDAE) AND THEIR IMPLICATION IN PHYLOGENETICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Suggestions from prior review have been well incorporated in this revision.


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

Input:
Title: FIRST COMPLETE MITOGENOMES OF DIAMESINAE, ORTHOCLADIINAE, PRODIAMESINAE, TANYPODINAE (DIPTERA: CHIRONOMIDAE) AND THEIR IMPLICATION IN PHYLOGENETICS
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In the revised manuscript the authors address all of my comments.

The English language has been seriously improved but a few additional corrections are proposed:
line 39: replace "molecular " with "molecule"
line 64: "...by in a recent..." delete "in"
line 67:  replace "Allowing " with "Along"
lines 158-159: "...while positive AT-skew (0.01–0.05) in the remaining four species." The verb is missing from this sentence.
line 164: Please replace "ND1 was TTG" with "ND1 started with TTG"
line 232: "...from in other..."  delete "in"
line 265: "we sequenced the four..." delete "the"
line 266: Replace "...technologies. And did..." with "...technologies and did..."


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: SEAGRASS STRUCTURAL AND ELEMENTAL INDICATORS REVEAL HIGH NUTRIENT AVAILABILITY WITHIN A TROPICAL LAGOON IN PANAMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Language is clear, intelligible and professional. But there are some typing and grammatical errors which should be corrected.
Introduction is sufficient and gives clear background to understanding of the problem.
Structure of the article is conformed to the acceptable format. Figures have sufficient resolution. However, some minor corrections are necessary in Figs and Tables. Citing literature should be checked.
Experimental design: The research question and knowledge gap is clearly defined. In general Methods described with sufficient detail to replicate. Geographic coordinates of sampling sites provided in Supplemental materials are very useful for further monitoring of the lagoon ecosystem.
Validity of the findings: The findings provide new comprehensive knowledge about seagrass distribution, coverage and biomass within one of the impacted lagoons of the Panama. Also data on the elemental and stable isotopic composition of the seagrass and their spatial variability were obtained. Such data are required to understand the current state of the lagoon ecosystem, health of the seagrass community and to provide baseline data for monitoring programs.
Additional comments: The main goal of the revised study was to provide expaned data on the distribution and coverage of Thalassia testudinum as well as the elemental and stable isotopic composition in its leaves in Bahia Almirante, a lagoon exposed to anthropogenic press, to estimate the current health state of the lagoon ecosystem and provide a baseline dataset for the monitoring programs. To achieve this aim, a comprehensive bay-wide sampling in single survey was done, at each site the coverage, biomass and seagrass bio-indicators such as leaf morphology, tissue carbon, nitrogen and phosphorus content and stable isotopic signatures were obtained. The obtained results are clear and support conclusions. The manuscript is clearly written in professional, unambiguous language. If there is a weakness, then this is some negligence in the design of figures, tables and literature (as I have noted below). The article can be published after revision.

Basic reporting

Language is clear, intelligible and professional. But there are some typing and grammatical errors which should be corrected.
Introduction is sufficient and gives clear background to understanding of the problem.
Structure of the article is conformed to the acceptable format. Figures have sufficient resolution. However, some minor corrections are necessary in Figs and Tables. Citing literature should be checked.

Experimental design

The research question and knowledge gap is clearly defined. In general Methods described with sufficient detail to replicate. Geographic coordinates of sampling sites provided in Supplemental materials are very useful for further monitoring of the lagoon ecosystem.

Validity of the Findings

The findings provide new comprehensive knowledge about seagrass distribution, coverage and biomass within one of the impacted lagoons of the Panama. Also data on elemental and stable isotopic composition of the seagrass and their spatial variability were obtained. Such data are required to understand the current state of the lagoon ecosystem, the health of the seagrass community and to provide baseline data for monitoring programs.

Specific comments
All references cited in the text should be provided in the References list and vice versa. Those are CARICOMP (there are not it in the references list, I believe you mind UNESCO (1998)), Fourqurean & Rutten, 2003 (absent in the references list), Ralph et al. 2007 (does not cited in the text). At lines 180 and 379 Atkinson, Smith (1982) should be 1983. I am not sure but in my feeling the references cited only in Table S5 are not needed in the main References list. Please consult the editor on this matter. Also for references marked with a, b and ets. it is better to give letters as the Reference appears in the text. Sometimes "a" follows "b". This rule is right for the Figs numbers (for example Fig7 a,b,c,d,e at lines 263-279). What are Reference you mean at lines 177 (Fourqurean et al., 1992) and 363 (Carruthers et al., 2005), a or b? At line 430 O’Leary et al. 2017 not O’leary.

Abstract
The statement “The high nutrient availability and depth-restricted distribution of seagrasses suggest that many of these meadows may be approaching or have already surpassed a ‘tipping point’, in which seagrasses retreat to shallower depth” is not fully supported by the results. I suggest that you provide data on depth limit of Thalassia testudinum in intact areas in the other regions or early data on it vertical distribution in the studied area, to provide more justification for this statement.
Figures
The signature of Y axis at Figs. 2b, 4b, 7a and 7b should be changed as g dry mass m-2 or g dry weight m-2. Similarly it should be done in Table S4 (last column) and Table 1 (last column).
Fig. 1. Because you claiming that “Bahja Almirante receives moderate to high freshwater input and nutrient loading from the inflowing rivers” it would be helpful to map the rivers or river mouth in the Fig. This can help audience in understanding of the impact of land runoff on lagoon's ecosystem.

Minor changes over the text
Lines 160-161 check the punctuation.
Lines 164 and 168. The abbreviation DI is not needed after distillated water.
Line 300 The benthic community at all sites was dominated
Lines 327 and 328. While two sampling sites are in reserve areas (Site 4 is in Matumbal Bay Special Use Zone and Site 8 is in Isla Bastimentos National Marine Park)
Line 389. site, we found a significant…
Line 421 - 422. "these meadows may be characterized as relatively eutrophic". Eutrophy is a characteristic of a water area, not of a community.