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

Input:
Title: A TURIASAURIAN SAUROPOD DINOSAUR FROM THE EARLY CRETACEOUS WEALDEN SUPERGROUP OF THE UNITED KINGDOM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The work is clear, well expressed and uses a scientific language. The article is written in English and uses a clear, unambiguous and technically correct text. The article conforms to professional standards of courtesy and expression.The article includes an adequate structure, with an introduction and sufficient background to demonstrate how the work fits the field of sauropod dinosaurs as well as an adequate paleontological systematic, description, discussion and conclusions. The literature is approved by adequate and sufficient references. The figures have quality and are relevant to show the results of the work, however a figure with more information would be convenient to help show the comparison and discussion between similar dorsal vertebrae in different groups of sauropods.
Experimental design: The research will be conducted rigorously and is based on previous works of high scientific quality about the investigated group of dinosaur sauropods. And the research keeps the ethical standards in force in its field. The methods that they expose allow it to be adequately followed by another researcher in order to reproduce it adequately in future works.
	The work describes the presence of a clade of sauropod dinosaurs in UK that is producing novelties in recent years. In this sense, it is an isolated remain of a neural arch and a vertebral center assigned to a sauropod of the Turiasuria clade. This postcraneal remain would be the first time that it is cited in the United Kingdom, specifically a dorsal vertebra; but it is not the first time that this group is mentioned in the United Kingdom, which would not be a novelty, but it would provide new data and confirm the previous published data. Other authors have already mentioned the posible presence of this clade in the United Kingdom with teeth in the Middle, Upper and Lower Cretaceous of the United Kingdom (Royo-Torres & Upchurch, 2012; Mocho et al., 2016)  (i.e. NHMUK R1610 from Wealden Group, Barremian-lower Aptian) and with some cladistic analyses for Haestasaurus (Mannion et al., in press). Also turiasaurs have been cited in the Lower Cretaceous of Europe, i,e, in base to heart-shaped teeth of Angeac (France) where the team of Ronan Allain have been found heart-shaped teeth (Neraudeau et al., 2012; Mocho et al., 2016) included in turiasaurs (Allain et al., 2016) from Berriasian sediments (Benoit et al., 2017).
If we take into account all the antecedents and they are accepted, the data presented here although with doubts in the age, would come to add new information about the presence of the turiasaurs in the Lower Cretaceous of Europe in a coherent way.

Allain, R. et al., 2016. Dinosaures, les géants du vignoble, Ediola editions, 248 p.
Benoit, R-A., Néraudeau, D., Martín-Closas, C. 2017. A review of the Late JurassiceEarly Cretaceous charophytes from the northern Aquitaine Basin in south-west France. Cretaceous Research, 79, 199-213.
Neraudeau et al. 2012. The Hauterivian-Barremian lignitic bone bed of Angeac (Charente, south-west France): stratigraphical, palaeobioloogical and paleogeographical implications. Cretaceous Research 37, 1-14
Mannion, P.D., Upchurch, P., Schwarz, D., Wings, O. In press. Taxonomic affinities of the putative titanosaurs from the Late Jurassic Tendaguru Formation of Tanzania: phylogenetic and biogeographic implications for eusauropod dinosaur evolution. Zoological Journal pf the Linnean Society.
Mocho, P., Royo-Torres, R. Ortega, F. Malafaia, E., Escaso, F. & Silva, B. 2016. Turiasauria-like teeth from the Upper Jurassic of the Lusitanian Basin, Portugal. Historical Biology, 28 (7), 861-880.
- Royo-Torres, R. & Upchurch, P. 2012. The cranial anatomy of the sauropod Turiasaurus riodevensis and implications for its phylogenetic relationships. Journal of Systematic Palaeontology. 10, 553-583.
- Upchurch, P., Mannion, P.D., Taylor, M.P. 2015. The anatomy and Phylogenetic Relationships of “pelorosaurus” becklesii (Neosauropoda, Macronaria) from the Early Cretaceous of England. Plos ONE 10(6): e0125819
Validity of the findings: The work is valued in a positive way, as it provides new data that can help confirm the presence of a clade of sauropod dinosaurs, the turiasaurs, in the Lower Cretaceous of Europe. However that age can not be accepted as safe. The uncertainty of not knowing the origin of the material and that comes from private collections without scientific information should put us in caution to draw conclusions in this regard. Geological information should be displayed with field data, stratigraphic columns and/or geological maps that support the geological age. However, this is seem impossible. Then, the material could be of older facies and belong to the sediments of the Purbeck of the United Kingdom and the material could be even from the Upper Jurassic. Can the author justify with more data the age he presents in his work?

	The material is isolated and the comparison is with two taxa of the clade Turiasauria: Tendaguria and Moabosaurus. The first is also based on material isolated from the Tendaguru Formation, specifically 2 dorsal vertebrae. In both cases the results, although they may be considered valid, should be checked with more and new material in the future. The second taxon, with which it is compared, is Moabosaurus. It has enough cranial and postcranial remains to be assigned to Turiasauria with security and to be able to compare it with the anterior dorsal vertebrae of this work. But the author, it does not compare NHMUK 1871 directly with other dorsal vertebrae of the rest of turiasaurs such as Mierasaurus, Turiasaurus and Losillasaurus. At least it should be compared with the anterior dorsal vertebra of Mierasaurus to give more robustness to the work. In this sense to see the differences and similarities more clearly would be convenient and would help to make the work more interesting if a figure was added with the next information: illustrations of anterior dorsal vertebrae (first or second) for different groups of sauropods. In this way the author can discuss with reference to the figure why NHMUK 1871 is included in a specific group and excluded from others.
Additional comments: The work is very interesting, it provides new information about the group of turiasaurs. I think it should be published and make known to the scientific community the presence of this material as well as the comparison it makes with Tendaguria and Moabosaurus. This will undoubtedly help to know how the anterior dorsal vertebrae are in the Turiasauria clade and its comparison with other taxa. There is only a great doubt in the geological age of NHMUK 1871. This is due to the uncertainty of not being a material excavated by the author. In its history when proceeding from an old purchase by the NHMUK (in 1891) it lacks scientific methodology and the ignorance of its origin should make us doubt also about its age. I think this "uncertainty" should be highlighted in the title, abstract and conclusions to be taken into account in future 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: A TURIASAURIAN SAUROPOD DINOSAUR FROM THE EARLY CRETACEOUS WEALDEN SUPERGROUP OF THE UNITED KINGDOM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript presents a dorsal vertebra which morphology indicates affinities with the turiasaurian sauropod, extending the geographic and stratigraphic range of this lineage. It is a clear and well writen manuscript and I do not have any extra modification or suggestion for it
Experimental design: The designs are in agree with the material and the field
Validity of the findings: The arguments of the affinities are well demonstrated based on recent complete phylogenetic analysis
Additional comments: No additional comments


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

Input:
Title: TRANSCRIPTOME PROFILING REVEALS THE ROLE OF ZBTB38 KNOCK-DOWN IN HUMAN NEUROBLASTOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Authors found that ZBTB38 gene is downregulated in different tumors and its low expression is associated with good prognosis in LGG (Brain lower grade glioma). They studied the ZBTB38 downregulation effects on SH-SY5Y cells: ZBTB38 SiRNA led to a decrease of cell proliferation and viability. Furthermore, the RNA-sequencing has deepened the analysis of ZBTB38 silencing effects, offering possible molecular mechanisms that could be implicated in the signaling cascade.
This story would be of interest, however, there are some points that need clarification and additional experiments to strengthen the claims.
Authors should better described the proposed experiments:
e.g., They have “a total of 2,036 (83.5%) down-regulated DEGs and 402 (16.5%) up-regulated DEGs were selected”. GO analysis is confusing; it is not clear on which group they have done the analysis so it is difficult to understand the data.
Experimental design: Major issues:
- ZBTB38 is remarkable downregulated in UCEC and CESC tumor, but authors write “low expression of ZBTB38 was associated with improved the prognosis of the LGG (Brain lower grade glioma) patients (Fig. 2), suggesting that these changes are closely related to neuronal tumors.” What about UCEC and CESC? How do authors explain this point?
- Taking into account the results, at present data do not support the working model in Figure 8: p53 pathway is proposed to be a key signaling, but it has not been identified by GO enrichment and KEGG pathway enrichment analysis, why?
- How autophagy is related to ZBTB38? Authors should check for autophagic flux by WB or ICC to verify that autophagy is impaired upon ZBTB38 downregulation. In S3 Table. (Top 20 differentially expressed genes associated with autophagy), there are genes that can have opposite effects on autophagy: for example, RB1CC1 (FIP200), ATG2 and ATM positively regulate autophagy induction whereas PIK3CA and PIK3C2A mediate the activation of AKT-mTORC1 cascade that inhibits autophagy through ULK1 (Laplante et al., 2012). Moreover, lose of PTEN, a phosphates that inhibits growth and proliferation signals of phosphoinositide 3‑kinase (PI3K) by dephosphorylating phosphatidylinositol 3,4,5‑trisphosphate (Crino, 2016), should promote the AKT-MTORC1 activation. Thus, this point is unclear and needs further investigations to be clarified; I suggest checking AKT-mTORC1 activation state by WB.
- They should provide results for ROS increase and apoptosis activation upon ZBTB38 silencing.
- Figure legends are not complete or are not clear enough to read.
Minor points:
There are some typing errors.

1 	Laplante M, Sabatini DM. mTOR signaling in growth control and disease. Cell 2012; 149: 274–93.
2 	Crino PB. The mTOR signalling cascade: Paving new roads to cure neurological disease. Nat Rev Neurol 2016; 12: 379–392.
Validity of the findings: At this point, the results are not enough robust to support the conclusions.
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: TRANSCRIPTOME PROFILING REVEALS THE ROLE OF ZBTB38 KNOCK-DOWN IN HUMAN NEUROBLASTOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well prepared, and data presentation is pretty clear.
Experimental design: The study is well organized, and experiment design is reasonable.
Validity of the findings: Data is robust, statistically sound, & controlled.
Additional comments: In this paper the authors aim to demonstrate the possible role of a zinc finger protein ZBTB38 in neuroblastoma (NB). Based on the human neuroblastoma cell line SH-SY5Y model, high throughput RNA sequencing was performed to compare the differential gene expression between the control and ZBTB38 knockdown cell lines. The data revealed a major transcriptional activation role of ZBTB38, with 83.5% down-regulated out of the 2,438 identified differentially expressed genes. Functional annotation revealed the involvement of the neurotrophin TRK receptor related signaling pathway, including PI3K/Akt and MAPK signaling pathway, several other well-known genes like PTEN and p53, and autophagy-related genes PIK3C2A and RB1CC1, providing a pilot investigation about the function role of ZBTB38 in neuroblastoma development and clue for targeted therapy. The study is well organized, data presentation is pretty clear, and results are very interesting.
1. The NGS sequencing data should be submitted and deposited to public data base for easy accessibility;
2. For Figure 1B-E, a P value should be calculated and provided to support their claim of differential expression;
3. For functional annotation of the differentially expressed gene, the author may want to try GSEA analysis module, which will generate a more informative enrichment plot with enrich score and p value, and a heatmap for the enriched gene list, compared to the relative simple bar graph of the genes in each pathway presented here.


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: TRANSCRIPTOME PROFILING REVEALS THE ROLE OF ZBTB38 KNOCK-DOWN IN HUMAN NEUROBLASTOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript is greatly improved and meets the standard to be published in this journal. The very informative data is valuable to the neuroblastoma field.


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

Input:
Title: GENOME-WIDE CHARACTERIZATION AND EXPRESSION ANALYSES OF THE MYB SUPERFAMILY GENES DURING DEVELOPMENTAL STAGES IN CHINESE JUJUBE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Where we can find the raw data for RNA sequencing?
Experimental design: no comment
Validity of the findings: In line 394, You can’t get this conclusion only according to the correlation analysis. I don’t think there are so many MYB genes related to the biosynthesis of flavor.   In fact, as a large TF family, the MYB family regulates a variety of physiological processes in plants, not only the flavor biosynthesis. I suggest  authors refer to the functions of MYB genes in other species that have already been identified.
Additional comments: 1.	Line 55 “in” should be added before “many plants”
2.	Line 120 check the reference
3.	Line 196-197, Line 371-378, these sentences should be moved to the discussion part or deleted.
4.	Line 418-424 these sentences should be deleted, they have already been described in the introduction part.


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

Input:
Title: GENOME-WIDE CHARACTERIZATION AND EXPRESSION ANALYSES OF THE MYB SUPERFAMILY GENES DURING DEVELOPMENTAL STAGES IN CHINESE JUJUBE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Transcription factors  are essential on the regulation of gene expression that found in all living organisms. MYB are one of the largest TF gene family present all eukarytes. They have variable function in biological processes inculding development and environment response. Still, many MYBs function are not clear. The authors reports that genome-based identificaton of MYB genes in jujube and showed structure characteristics with RNA-seq data. It could be useful to further effort to understand their function in plants.
 However, mostly, the paper to Genome-wide analysis of specific gene family showed that a complete overview of those genes is presented including phylogeny, gene structures, protein motifs/domains, chromosome location and their expression pattern to predict a kind of possible roles in biological processes. these can provide other researchers to understand evolutionary relationships (duplication events, specific subgroups by expanded or contracted) and to further analysis for remained functionally characterizations of genes). But the manuscript in genome-wide study of ZiMYB gene family missed several analysis that I have noted above and showed compelling points. In addition, Too many figure with unclear styles could be ambiguous for audiences to find and understand authors' intent or points. Thorough whole manuscripts, many references were used improperly and unclearly.
Experimental design: Some are a little bit ambigous without details
Validity of the findings: 'no comment'
Additional comments: I addressed the major comments like below

Abstract
line 40, expression changes of ZiMYB during tissue and fruit development, that could mean possibility related with those biological processes not clear having function. So. Authors need to tone down.

Introduction
The section of introduction could needs more details, I suggest that the authors explain the history of MYB gene family. The MYB genes  are not plant-specific but founded in all eukaryotes.

line 58, addition to Lipsick, 1996,  more references need in description for MYB domain
line 66, Katiyar et al., 2012 showed MYB expression pattern under drought stress in Arabidopsis and rice not various biotic and abiotic stresses. Authors should check all citations carefully again.

M&M
Authors need more detail descriptions of fruit periods for samples to do RNA-seq.
e.g. white mature stage’s samples were harvested to how long days after pollination or anthesis etc. or indicate proper references if there are.
Line 120, In reference list, There are two papers represented as Zhang et al 2018. Authors distinguish these on author’s instrument about how to depict references.

The authors performed newly RNA-seq anlaysis for fruit development. But they does not describe detail statistics of RNA-seq data including read depth, read length and quality assessment and so on.
I recommend that authors also need open raw data in public database to be useful future reader.

Result
Line 205, GRAVY, need to describe full name at first
I feel that some figures showed redundancy. e.g. to understand phylogenetic relationship of MYB genes, separated figures 1, 2, 3 and 6 could be combined with simplification and clean up or represented supplementary info. Even though Fig. 4, 5 and 7 showed repeat motifs in different subfamily, I’m not sure that separated figure should be need.

thorough whole manuscripts, many references were used improperly and unclearly.

On Fig. 9, in analysis of gene expression, authors’ insist are based on expression dynamics of MYB genes. But to support these, validation experiments such as qRT-PCR for representative MYB genes not all should be need.
Fig 11, the current figure about the correlation analysis of total flavonoid content with ZjMYB genes of jujube fruit are confused to understand. Plz it need reorganization of figure format by clean up and more concise style

I recommend the position of all ZiMYB gene in pseudomolecules chromosomes could suggest distribution and density of MYB genes and added the results of comparison with peach and Arabidopsis. Additionally, authors need to indicate orthologues within table S1 as shown in Zhang et al, 2018

Syntenny analysis in Fig 12. showed somehow complicated and not clear for audiences to understand their meaning.


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

Input:
Title: GENOME-WIDE CHARACTERIZATION AND EXPRESSION ANALYSES OF THE MYB SUPERFAMILY GENES DURING DEVELOPMENTAL STAGES IN CHINESE JUJUBE
Review round: 1
Reviewer: 3

Output:
Basic reporting: A comprehensive analysis of the MYB superfamily members in jujube was done in this study. The authors did a lot of work, including downloading large number of sequences, analysis, making figures and tables.

The authors used clear and unambiguous, professional English throughout the manuscript except for few chinglish.
The authors provided enough Literature references, sufficient field background/context .
The authors shared professional article structure, figs, tables, Raw data.
It is self-contained well with relevant results to hypotheses.
Experimental design: This manuscript is an Original primary research within Aims and Scope of the journal.
Research question is well defined, relevant & meaningful. It is stated well how research fills an identified knowledge gap.
Rigorous investigation was performed, and it reached a high technical & ethical standard.
Methods of this manuscript described well with sufficient detail & information to replicate.
Validity of the findings: Data of this manuscript is robust, statistically sound, and controlled.
Conclusions of this manuscript are well stated, linked to original research question.
Additional comments: Please incline the letters of gene name for the whole manuscript.
please let an english native speaker to revise the manuscirpt before next submission and do not use chinglish.


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

Input:
Title: GENOME-WIDE CHARACTERIZATION AND EXPRESSION ANALYSES OF THE MYB SUPERFAMILY GENES DURING DEVELOPMENTAL STAGES IN CHINESE JUJUBE
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thank you for addressing my comment. I have no further modifications/suggestions to make.


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: EXPLORING WEARABLE SENSORS AS AN ALTERNATIVE TO MARKER-BASED MOTION CAPTURE IN THE PITCHING DELIVERY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Basic Reporting:

	Thank you for inviting me to review this paper. I commend your taking this study on, as I believe the validation of these commercially available sensors is crucial. Much stock is placed in their produced data, and it's imperative that it is interpretable and valid in comparison to research-grade data. With an ever-expanding market of wearable devices, as well as the spectrum of their users, this is necessary. That an influential and notable training facility recognizes this and puts their own capital and labor into supplying the data is refreshing. I am glad to see this study come to review.
The authors present data supporting the reliability of wearable, Inertial Measurement Unit (IMU) sensors for the collection and analysis of biomechanical pitching data. They have spent the time needed to find suitable analogues between the two measurement systems (the wearable IMUs and the "gold standard" motion capture system) and are to be commended for finding a common framework in which to validate these sensors, which many practitioners use, but which aren't commonly validated in peer-reviewed literature.
	Overall the paper is logical and well-written. The approach to validating the IMU sensors is well-constructed and I overwhelmingly agree with the way it's been undertaken. The need for this study is mostly well demonstrated in the prose. The collection of data is valid on its face. The statistical approach taken seems correct and (more importantly) is the proper one. Some of the terminology surrounding reliability and validity needs to be tightened, but overall this is a good paper. My review will be to offer suggestions for revision.

	The approach I will take to this review will be to:

1.	Comment on each facet of the review criteria in these sections (Basic Reporting, Experimental Design, Validity of the Findings, and General Comments for the Author(s)).
2.	Make specific wording suggestions in the PDF itself via annotations.

Again, thank you for the invitation. I hope my comments are helpful and instrumental (pun not entirely unintended) to helping you produce the best possible study for publication. If I can clarify any comments, do not hesitate to contact me: travis.ficklin@dixie.edu.

Clear and unambiguous, professional English used throughout.

Yes, though there are multiple places throughout the manuscript where language could be tightened or clarified. I have made those comments in the annotated PDF directly. There are some spots where the word "valid" or a variant is used when reliability or consistency is meant, or is more accurate. Additionally, there are small grammatical things. None of the notations reflect fatal problems, so no more to mention here.

I will offer this suggestion, though: consider getting rid of any references to yourselves ("we", "us", "our", etc.) and replace them with generic, even passive language if you can. This is a personal preference on my part, and in the end, the editors style guide should rule.

Literature references, sufficient field background/context provided.

For the most part, I agree that it is. However, in demonstrating the need for this study (a "hole" in the existing literature), there are some studies missing. One in particular is very similar to yours, and so it needs to be included, with a rationale for why yours is still important. Here are some references to consider:

1.	Augmented inertial measurements for analysis of javelin throwing mechanics - Sarkka, et. al., 2016, J. Sports Engineering. (This one seems to only make use of the sensor to monitor output kinematics and energetic of the javelin itself, so there is a big difference between it and yours - in fact, maybe this one isn't needed. I cannot insist you include it, but it is worth noting if you do.)
2.	Validation of Inertial Measurement Units for Upper Body Kinematics - Morrow, et. al., 2017, J. App. Biomech. (Upper body kinematics, but applied to performing surgery - whoa - rather than to throwing. Again, huge difference between you and them, but this is a validation study, so it needs to be mentioned.)
3.	A Distributed Wearable, Wireless Sensor System for Evaluating Professional Baseball Pitchers and Batters. - Lapinski, et. al., 2009, International Symp on Wearable Computers (IEEE). (This one is crucial to include - very similar to yours. Key differences: the motusBASEBALL system is already consumer-available and in widespread use - I am not sure their "SportSemble" is, and so there is a need for your validation right there. Also, their relationships are established only qualitatively, while their statistical analysis is a comparison (I think t-testing, but hard to tell from their text) to demonstrate that their sensor values are statistically equivalent to the MoCap values for *average* velocities.)

Professional article structure, figs, tables. Raw data shared.

Yes, and thank you for the raw data to peruse. The tables have some tightening that could be done, and I have annotated those in the PDF. That said, raw scatterplots of the values, with or without a line of slope=1 to visualize the correlations would be good to include. They tell a story in themselves.

Self-contained with relevant results to hypotheses.

Self-contained, yes. As to hypothesis:

1.	Go ahead and include it in the introduction after your purpose statement (it's already in the abstract, so it's odd not to acknowledge it again).
2.	You did hypothesize that the joint angle metrics would be accurate and reliable but not arm speed and stress metrics. You need to follow that up in your discussion. In the end, the IMUs are shown to be reliable, but not valid (consistent, but not accurate in comparison to "gold standard" values.)
Experimental design: Experimental Design:

Original primary research within Aims and Scope of the journal.

Yes. No further comment.

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

This is addressed in my previous comment about the supporting literature. Your case is strong - just have to make it in light of the Lapinski study.

Rigorous investigation performed to a high technical & ethical standard.

Yes. I will add this: you're to be commended for getting the information from Motus to translate from their metrics to the MoCap metrics. They are to be commended for sharing information. Many companies will not, and they hide their algorithms as proprietary. Good on them and you for communicating and then disseminating.

Methods described with sufficient detail & information to replicate.

Mostly. I do think that the information is sufficient to replicate the study. The details of this can be tightened up some. Rather than address those points here, I will do so in the annotated text.
Validity of the findings: Validity of the Findings:

Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.

The strength of your study is the lack of an attempt to dismiss the information rendered by the Motus system (being that it isn't the same as what MoCap renders), but rather to put it into context of the information researchers are used to obtaining with their MoCap systems. You have shown nicely why the information available to consumers/practitioners is worthwhile, yet what grains of salt must be added. This is my awkward way of saying that your non-result result is useful when explained to practitioners. Please see my PDF comments for specifics on this line of thinking.

Data is robust, statistically sound, & controlled.

Yes. Except to say that data is a plural word, so data are robust, statistically sound, & controlled. I make this suggestion in you PDF too. If the Editor disagrees, go with his/her ruling!

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

I'll just state again that the paper will be strengthened by tying your conclusions/discussion directly back to your hypothesis. Additionally, please note any limitations your study has. For example, some of the reliability noted in your conclusion is limited to either all pitches en masse, or off-speed ones only - the stress metrics for fastballs were not strongly correlated enough to generalize the results to them. Also - note your sample pool. Are these collegiate athletes? High school? Pros? That has bearing on the generalizability of results. One last to mention: future work should be done on the day-to-day reliability of the typical use of the Motus sensor (sleeve). You state that it is consistent, but you either need to state that you have pilot data to support that, or that work should be done to establish it.

Speculation is welcome, but should be identified as such.

You really didn't make any speculations that seemed outlandish. The consistency of the sleeved use of the IMU needs to be addressed. See the paper for my note on that. In the end, the IMU is useful. The major caveat to that is that the values aren't really comparable to the MoCap ones. Rather, the usefulness is in monitoring changes in metrics (as training occurs, or as pitches are altered) - hence, reliable, but not valid. You do state this, but I would club the reader over the head with it.
Additional comments: General Comments to the Authors:

Again, good paper. I have made annotations to the PDF for you to use or not use. The purpose of my extended comments above is to document my rationale for voting for a "major revision". I think the paper should be published after the literature updates are added, and the tightening of the language is done. I realize that is right on the cusp between "minor" and "major", but I lean toward the latter because it will prompt one last systematic review before approval, and I feel that is important for any substantive revisions.

I wish you the best, and I hope to see a revised version soon to review again. I believe the changes will make it ready for publication.


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

Input:
Title: EXPLORING WEARABLE SENSORS AS AN ALTERNATIVE TO MARKER-BASED MOTION CAPTURE IN THE PITCHING DELIVERY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic Reporting
1.	Language and Writing: In general, the writing is very succinct and to the point. However, it therefore lacks depth and context for the study. The authors should consider the paragraph structure throughout. There are many very short paragraphs (and in some cases 1 sentence paragraphs in the discussion) that need refining.
2.	The introduction and background are somewhat brief and lack depth in relation to wearables. The focus seems to be on just the baseball application. The authors would be well advised to provide more of a background on wearables (i.e. Chambers et al Sports Medicine July 2015, Volume 45, Issue 7, pp 1065–1081) and why they are necessary. This would ideally be placed before the baseball specific information. Generally, the paragraph structure in this section needs work. E.g. paragraphs 2 and 3 can be merged together.
Line 72 - There is literature out there that have looked at throwing and wearables that have not been included in this background presumably as its not baseball related. However, the study I believe is purely one of part validation of the system and thus other papers that have looked at throwing and wearables needs including. i.e. Wixted et al, Journal Sports Technology Volume 4, 2011 - Issue 3-4: Australian Sports Technology; Spratford et al, 2015 Journal of Sports Sciences Volume 33, 2015 - Issue 7;
I would also suggest in the intro and background that a section on the importance of product validation / comparison to gold standards is needed, as that in essence is what you are doing.
Line 84 needs a full stop at the end.

Figures:

Figure 1 – Geometric details of the sensor placement is needed – i.e. 5cm distal from the medial epicondyle etc etc – to ensure consistency in placement.
Figure 2 – is very dark (in black and white) and thus camera position can’t readily be seen.
Table 1 – Suggest centring the values in the table
Table 2- suggest centring the values in the column and in the row. As the speed measures are all compared to the same value – possibly merge the 3 rows on the Motus BASEBALL column with the same value to highlight that its just one value. Also, column spacing needs re-aligning.
Table 3 – this is unclear – more detail on what correlation is being assessed is needed. Difficult to interpret based on the table. Title of the table needs more detail.
Experimental design: Experimental Design
You state in the abstract a hypothesis yet in the background the contest of the main document this isn’t justified.
Furthermore, in the main document you do not state a hypothesis you only state a purpose. Please check Peer J requirements on this and ensure consistency.
Subjects: Can you provide some details on the years’ experience and the level of the pitchers? This would help contextualize the study further
As per the previous section I believe more context is required in justifying the research area.
Method Section Specifics
The details on the motion capture are well documented.
Line 116 - More detail on the Motus Baseball sensor is needed. Details relating to the sensor type etc will help the reader contextualize the results.
Important point: As the sensor was removed from the sleeve do you believe that would affect the results if it were in a sleeve? I understand why it has been removed.
Important Point: Your study design looks to compare the sleeve sensor to the capture system. Was though given to looking at the repeatability of the measures? Your subjects threw 5-7 fastballs – what was the within subject reliability of these measures? This would enhance the validity of the product. If you find that the sleeve underestimates (which looking ahead it did) then if it consistently underestimates compared to the gold standard measure, then we are able to comment on that when users wear the product. The key aim of a wearable should be to record data but then detect improvements or decrements in performance in its continued use. It is reliable this would assist in that narrative.
Line 144 – The Fleisig paper you reference doesn’t detail the methods used (its further references other papers). I would suggest including some detail on the methods here to allow replication by readers.
Line 181 – More detail is needed on what constitutes the stress measure from Motus.
Line 184-191 – suggest merging these paragraphs
Line 187-191 – You need to report what statistical package you used to calculate your statistics. I also think this study would benefit from some more robust statistics. Whilst correlations are valid, and should continue to be included, Bland Altman plots would really add some great value to this study. (more on the results in the next section).
Here you mention hypothesis again, but you haven’t stated a hypothesis outside of the abstract.
Line 200 – ‘while’ should be ‘whilst’
Line 202 – you have called them groups which implies they were separate subjects – you have used the same subjects for both throws thus I do not think groups is the right word. Suggest ‘condition’.
Table 4 – based on the power levels being below 0.8 for all but arm-slot how do you interpret these? I would also suggest this part of the analysis is associated with processing and statistical interpretation and thus should be included in the methods.
Validity of the findings: Validity of the Findings

1.	Off speed arm extension metrics are greater that the fastball yet the correlation to ball speed, of which fastball was ~ 102 mph quicker were high? Can this be explained to help the reader understand this?
2.	Table 3 – I found this difficult to interpret so I couldn’t comment in much detail. This needs refining and detail added.
3.	You have found that the speed base metrics are grossly underestimated by the sleeve compared to the Opti track. Based on prior comments assessing if this underestimation is consistent may provide some useful information – i.e. if it consistently underestimates then a correction factor could be used to provide similar absolute values, but outside of that if it can detect changes that people could use it from performance improvements 9or decrements.)
Results specifics
Line 202 – you state that the FB group had ‘more’ significant p values – that is not how p-values work – its ether significant or not – it’s not necessarily a scale.

Discussion Specifics
Generally, this needs a lot of work. The authors have started by restating the main findings well (although again paragraph structure needs refining). However, there is minimal explanation of the results.
The discussion would benefit from assessing other papers that have looked at comparing measurement tools (i.e. O Donnell et al Measurement in Physical Education and Exercise Science
Volume 22, 2018 - Issue 1). There are many other sources out there comparing devices to accelerometers etc.
Line 255 – you state that the benefit of wearables is that they can be used in game – whilst this is undeniable, the validity of the method needs stating prior to that occurring. Thus, if the only measure that can be taken with some level of confidence is the arm slot – is it advisable to support its use by coaches? I would suggest further assessment is needed for this statement. The stress metric is unclear from the paper how it is calculated or what it is measuring
Conclusion – You mention variance within here and thus following on from previous comments it would be wise to assess this more formally.
Additional comments: The study is of interest as the world of wearables becomes increasingly popular in the sport and exercise fields to provide more information to relevant people on enhancing performance and potentially reducing injury. With that in mind one of the main flaws of wearables is there reliability and validity compared to gold standard methods, and thus if in fact the wearable is providing a useable measure. This study aims to do this and in part it has achieved this of which the authors should be congratulated. However there are a few flaws that I think need to be addressed that make the study for objective. Further statistical analysis and more interaction with the literature around validity and reliability of measurement systems is advised.


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: EXPLORING WEARABLE SENSORS AS AN ALTERNATIVE TO MARKER-BASED MOTION CAPTURE IN THE PITCHING DELIVERY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The most important areas for the authors to consider in this manuscript in order of importance are the following:
1.	Ensure the purpose statement is clear and sets the foundation for the methods that were chosen and the statistics that were performed. Currently the purpose is written different ways through the manuscript and the statistics only seem to partially address the intended purpose of the article.
2.	The language of the manuscript should be re-visited extensively to ensure it is grammatically and scientifically less ambiguous.
3.	Providing justification or potential speculation regarding the metrics that did not correlate should make up the majority of the discussion.
4.	Visualisation of the correlation data should be performed to allow for analysis of the spread of the data as the r value can be deceptive.
5.	Greater description related to the methods used for the optical motion capture (e.g. was it an existing validated model) and specific information regarding the elbow and shoulder, for example was it the same as the ISB recommendations: https://www.ncbi.nlm.nih.gov/pubmed/11934426) would ensure repeatability of the research.
6.	Greater use of previous literature to support methods, justification of the discussion along with better use in the introduction (of prior validation studies of IMUs in comparison to “gold standard” could better set up the current manuscript and provide the authors examples of potential “best statistical practice” when seeking or performing a validation study.
Abstract
1.	A notation of the language as an example:  it is the data processing along with improvements in the hardware of IMUs that has led to their increased use and expanded measures that are purported to be possible with respect to kinematics and kinetics not simply “technological advancements in IMUs”. Re-visit language and choose to use descriptive biomechanical language (e.g. kinematics and kinetics) and specifics about the advancements (e.g. mixture of processing or programming with improved hardware) to ensure it is not presented as vague or ambiguous.
2.	In hypothesis, “this device” – e.g. which device?
3.	To state “…will be accurate and reliable” is better stated with acceptable reliability and accuracy as there is no definitive line of accurate and reliable as it is a continuous scale that is normally described qualitatively based on thresholds.
4.	Ensure that the tense is appropriate, for example, in methods of abstract to state “will be” should be past tense as it is what they did. Further, methods statement in abstract could be combined to state more specifically. …breaking pitches with simultaneous assessment using motion capture and while wearing a MotusBASEBALL IMU. This would eliminate the need for the second sentence and be more accurate than stating “in the motion capture lab”
5.	Results in abstract, first sentence is difficult to follow. Please re-visit. The term “test population” should be “sample”. The use of “very close” is not scientifically supported, ensure that is followed by the statistical output that supports it being “very close”.
6.	Language of conclusion in abstract needs to be re-visited and ensure it is not a re-statement of that already stated in results.
Introduction:
1.	Ensure the purpose statement at the end matches that used in the abstract and is specific enough to understand what the subsequent methods will require (particularly statistics). For example, to state “compare” typically infers that a group comparison will occur versus your purpose more surrounding validation and accuracy seems to be that what is intended.
2.	Remove reference to the unpublished case study.
3.	Remove the focus on your specific motion capture as the purpose is not about the type of motion capture it is the comparison of the single IMU (MotusBaseball; xxxx; xxx) which is how you should refer to instead of as the unit name, in comparison to the “gold standard”, optical motion capture (which is how you should refer to your system then just provide the (Unit Type, Manufacturer, Location).
Methods
1.	Instead of “selected” state “volunteered
2.	Merge this into a a single first paragraph, correct statement of what is in table 1 in line with below comment about “weight versus body mass”.
3.	Was the model used previously validated or used in prior research?
4.	With the IMU typically fixed with a compression garment, was any analysis performed to determine if this affected the measures (e.g. not having a compression over top?)
5.	Offspeed  = off-speed and state all the different types of off-speed pitches used.
6.	What order butterworth filter?
7.	As the position variables were taken at ball release, can it please be described if this is the same point at which the IMU measures are reported?
8.	Name the app that is used to collect the IMU data specifically and move the equivalent descriptors of the variables provided by Motus up and would likely be advantageous to make a table that provides the descriptors of Motus versus optical motion capture descriptors for ease of comparison.
9.	Need to re-visit the language used surrounding the purpose and subsequent statistics discussed.
10.	State what was significance set at for statistical test, include confidence intervals. Consider addition of Bland Altman but this depends on better or more clear description of the purpose.
Results
1.	Re-visit first lines 199-201 for clarity.
2.	Avoid stating “more significant p-values” as a comparison of p values size unless this is intended to discuss number of significant variables but even then should be clarified.
3.	Power analysis (post-hoc) is not as advantageous as providing the confidence intervals which should be added to the analysis (e.g. 95% CI for r values).
4.	Alpha value should not be in results, should be in methods.
5.	Avoid re-stating in-text the same things that are presented in the tables.
6.	219-223 – this information is not clear and can likely be totally removed.
Discussion
1.	To improve the discussion as a whole it is critical that the authors re-visit and ensure that the expand not just re-state what was reported in the results. Further, one should re-visit the purpose/hypothesis if one states one as done in the abstract. Further, there should be more reference to prior research.
2.	Greater justification and speculation would be useful with respect to the reason for such a difference between optical and IMU systems for the speed measures.
Tables
1.	Table 1 could simply be entitled “Participant descriptive and performance characteristics” to reduce repeated listing of variables and state the subject number in here as (n = 10) remove from first line of table and appropriately name this Age (years). Further, these variables should be provided in metric but considering the sport it would then be advantageous to list the imperial commonly used in the sport. However, scientifically, the metric values should be reported. Further, the reported variables is body mass, not weight as the weight would be a force measured in Newtons. Further, to use the term off-speed here varies from in the abstract where the term used is “breaking” pitch.
2.	Table 2 – ensure all abbreviations are also noted either in the title or below the table (preferable). For example, IR: Internal Rotation. Remember that figures and tables should be made in such a way they can stand alone from the manuscript. Further, clarify the varus stress location (e.g. elbow).
3.	Table 3 – Please correctly label this as correlation coefficient (as an r) or explained variance which is r2. Further, in the table footnote, clarify what significance was set at (e.g. p < 0.05) and the variable names should be labelled identical to that in Table 2 to allow for easy comparison as it is currently listed, it is ambiguous as a standalone of what arm speed or what stress the results represent. Additionally, this table has plenty of room to provide confidence intervals (e.g. 95% for the r values) which will provide better information than post hoc power analysis listed in Table 4.
Experimental design: 1.	Ensure the study purpose and hypothesis statement clearly matches the methods and statistical analysis. For example, it first states “validate” but the hypothesis refers to accuracy and reliability and then the results return back to “valid” for casual use.
2.	The experimental design is set up for a concurrent validation, but an extension of the statistical methods would allow for better support of statements. Including but not limited to: inclusion of confidence intervals, dependent samples t-test and/or bland-altman (which is a measure of agreement which would statistically match to the intention of “validation”). The reliability assessment used does allow for assessment of relative measure but to differentiate absolute versus relative reliability and further as stated to differentiate from agreement will allow you to better conclude the use (e.g. interchangeable or simply linearly correlated which means not interchangeable).
Validity of the findings: The results are valid but require more statistical analysis and greater reporting as suggested previously. The raw data seems appropriate. There is some justification for the authors to consider evaluating individual trials in addition to mean analysis as per suggestions from Mullineaux, D. R., Bartlett, R. M., & Bennett, S. (2001). Research design and statistics in biomechanics and motor control. Journal of Sports Sciences, 19(10), 739-760. doi:10.1080/026404101317015410 to determine if all trials should be used instead of the mean, especially considering the sampel only being n = 10.

Please see other comments regarding a clean link between purpose, methods, statistics, and conclusion.
Additional comments: 1.	The authors should be commended for seeking to perform validation on some of the commonly used IMU devices in the sport technology world. Such an effort should be applauded and is much needed. However, greater attention to statistical detail could further provide useful information for this validation attempt.
2.	Please re-visit the manuscript for errors in capitalisation, use of parenthesis, method of statistical reporting and overall grammar (e.g. tense, ambiguity, passive voice) is re-visited.
3.	Ensure that full development of paragraphs occur within the introduction, though the flow is logical, more depth surrounding the measures to be evaluated should be considered (e.g. the measures of arm slot, arm speeds and varus elbow stress and shoulder IR stress should be introduced).
4.	Label the data more consistently prior to publication for open source


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: EXPLORING WEARABLE SENSORS AS AN ALTERNATIVE TO MARKER-BASED MOTION CAPTURE IN THE PITCHING DELIVERY
Review round: 2
Reviewer: 1

Output:
Basic reporting: This revision of the paper is much improved, and the vast majority of my previous comments and/or concerns have been address satisfactorily. I recommend some minor revisions before acceptance. The updates to the manuscript to clarify statistical procedures and place the findings in the context of other published research make the study stronger. Many of the comments I include here are carried from my first review of the paper. The minor revisions I recommend are noted in comments on the PDF I am uploading. If they do not appear or are unclear, please let me know.

The authors present data supporting the reliability of wearable, Inertial Measurement Unit (IMU) sensors for the collection and analysis of biomechanical pitching data. There is better explanation of the sensors and the metrics included by the manufacture in their software in this revision. Additionally, better discussion is made as to differences between the systems and the limitations imposed by using IMUs.

The paper remains overall logical and is now better-written. There are changes, additions, and clarifications made in the manuscript made in response to reviewers. Once or twice, the changes include explanatory notes which are not necessary to the final reader. I have noted those in the PDF as well. All that said, I commend the authors for their thoughtful responses to review, and look forward to the publication of the paper after minor edits.

Please find in my review:

1. Comments on the review criteria (Basic Reporting, Experimental Design, Validity of the Findings, and General Comments for the Author(s)). These comments center on your changes made in response to my first review. They are brief.
2. A PDF file with recommended edits as annotations/comments. These have much more detail as to wording, etc. If these comments are not appearing, please alert me – I will find another way to make them.

Clear and unambiguous, professional English used throughout.

The writing is much tighter this time – nice work. I made some comments in the PDF for your consideration – or that of the editor. The paper reads more professionally this time. First person references are removed, and passive, scientific voice is now prevalent.
Literature references, sufficient field background/context provided.

The authors have now provided a more complete background for the study. The included references and their salient points in now present and leads logically to the need for their study. I have no further concerns about this part.
Professional article structure, figs, tables. Raw data shared.

The figures and charts are much better. The data plots add much better visualization. Thank you for adding them.

Self-contained with relevant results to hypotheses.

The hypothesis now appears in conjunction with the purpose statement in the introduction, which is much better. The discussion about the reliability of the Motus IMU vs. its validity (or where its validity is lacking compared to “gold standard” motion capture) is much better. I find it to be clear and reflective of the data that are presented.
Experimental design: Experimental Design:

Original primary research within Aims and Scope of the journal.

Yes. No further comment.

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

This is now satisfied. Particularly, the explanation of important differences between the Lapinski study and yours are crucial to bolstering the case for publishing your findings.

Rigorous investigation performed to a high technical & ethical standard.

Yes – no concerns.

Methods described with sufficient detail & information to replicate.

The authors have used reviewer comments to clarify and strengthen their methods. Filtering techniques, instrumentation techniques and placements, and statistical procedures are all clearer. I believe researcher could follow and replicate the study’s procedures.
Validity of the findings: Validity of the Findings:

Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.

No concerns.

Data are robust, statistically sound, & controlled.

No major concerns.

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

Added discussion of limitations is good. Explanation of generalizability of results is improved, and the tying of results to research question and hypothesis is clear. No further concerns.

Speculation is welcome, but should be identified as such.

N/A
Additional comments: General Comments to the Authors:

This is a vastly improved paper. You are to be commended for your attention to detail in responding to my comments and those of the other reviewers. I have made some last comments/annotations on the uploaded PDF that have to do with voice and/or grammar. My major concerns are addressed, and I recommend the paper be published once those minor changes are made. I commend the authors for their professional approach to this review process and look forward to further manuscripts from their 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: EXPLORING WEARABLE SENSORS AS AN ALTERNATIVE TO MARKER-BASED MOTION CAPTURE IN THE PITCHING DELIVERY
Review round: 3
Reviewer: 1

Output:
Basic reporting: No concerns at this point.
Experimental design: No concerns at this point.
Validity of the findings: No concerns at this point.
Additional comments: The article is cleaned up and ready to publish, in my opinion. Congratulations on a good study, and I look forward to more.

-TKF


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: TEMPORAL WHOLE FIELD SAWTOOTH FLICKER WITHOUT A SPATIAL COMPONENT ELICITS A MYOPIC SHIFT FOLLOWING OPTICAL DEFOCUS IRRESPECTIVE OF WAVEFORM DIRECTION IN CHICKS
Review round: 1
Reviewer: 1

Output:
Basic reporting: General
The senior authors published a paper in 2002 showing that saw-tooth shaped spatial/temporal luminance profiles, projected on the retina of chicks, have differential effects on the developmental compensation of the eyes of imposed positive or negative defocus. They attributed this selective stimulation of either the ON or OFF pathways in the retina. They found that predominant stimulation of ON channels had an inhibitory effect on eye growth while stimulation of OFF channels tended to increase it.  A year later they published that pharmacological inactivation of ON or OFF channels had the opposite effects than what one might have expected from initial experiments: inactivation of the OFF channel increased eye growth while loss of ON input decreased eye growth. Obviously, light stimulation elicited not simply the reversed effects of pharmacological inactivation. While there was no simple explanation for this discrepancy, the authors later (2006) showed that low frequency (1-4 Hz) luminance modulation, with no specificity for ON or OFF, triggered increased eye growth in chicks, but only when they wore lenses.
In the current study, the authors refined their low frequency stimuli to more selectively stimulate ON or OFF channels. They find that, at 1 Hz, (1) both ON and OFF stimuli inhibited the compensation of positive lenses, (2) OFF stimulation increased myopia with negative lenses, (3) the effects were largely gone at 4 Hz. Apparently, full field On or OFF stimulation is different from local ON or OFF stimulation, as done in 2002. With full field stimulation, the major effect was relative myopia. While this is an interesting finding, I missed a discussion as to what the differences might for the retina between full field temporal ON or OFF stimulation, and the spatially distinct local ON or OFF stimulations. Also - would it be possible to explain why the 4 Hz stimulation had generally less effect than the 1 Hz stimulation, and how this might relate to the temporal frequency pattern on the retina in the study in 2002?
The authors refer to their “retina ion-drive efflux (RIDE)” model but it remained unclear to me how this might explain the different effects of full field ON-OFF versus mixed spatial-temporal ON-OFF stimulation. A paper by Riddell et al (on which they were senior authors) is cited but I believe that a short description why this paper can help to explain the findings would be helpful.
What surprises me is high variability in the data. They used 166 animals that were raised in 5 different light conditions which would be about 33 chicks per group (hope this correct, otherwise ignore). The SEMs on the axial length data were are in the range between 0.05 and 0.1 mm which would be a standard deviation of 0.05 to 0.1 *6 or 0.3 to 0.6 mm. This may be more than the total average change in axial length with lenses under normal lighting. It suggests that a some chicks have shown no effect and others the doubled effect. Basically, it look as if the different light stimulation paradigms may explain only a (small) part of the variance.

Specific
line 115. The illuminances were generally low, compared to regular office illuminances which should be in 500 lux. This may be a limitation of the LEDs? Or to better match the 2006 study? It is certainly possible that the effects of ON and OFF stimulation would be different under different illuminances. The authors point out that this should be studied in the future (line 301).
line 259ff. That extended sawtooth-shaped light exposure can damage the photoreceptors (even at 97 or 387 lux which is not very bright) is a unexpected assumption. Don’t photoreceptors see temporal modulation all the time?
line 120-125. The details about the voltages that are required for the LEDs seem unnecessary to me and could be omitted.
Figure 1. Could it be that Figure 1B shows the wrong profiles? They don’t look like “fast ON” or “fast OFF” but rather more like sine waves. If the profiles were like that it is not surprising at all that there were no differences between the effects of ON and OFF stimulation at 4 Hz.
Experimental design: The experiments with 1 Hz look alright to me but I was wondering why they considered the 4 Hz stimulus as selective for On or OFF
Validity of the findings: Low frequency low illuminance flicker causes myopia in chicks, with smaller impact of the exact wave form.  May be a "chicken problem". Direct applicability to human myopia is not expected.

Sample sizes are larger than in most other experiments in chicks and the large variability of the effects is surprising

Stats is ok, and references complete

Discussion could also focus on a question listed in the comments to the authors.
Additional comments: see above


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

Input:
Title: TEMPORAL WHOLE FIELD SAWTOOTH FLICKER WITHOUT A SPATIAL COMPONENT ELICITS A MYOPIC SHIFT FOLLOWING OPTICAL DEFOCUS IRRESPECTIVE OF WAVEFORM DIRECTION IN CHICKS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Intro and background are relatively clear. However, they can be bettered. Comments and questions about details are added to the original manuscript, figures, and figure legends.

The “Results” section is really hard to follow. I suggest that the authors only mention the more significant and relevant findings, and leave the details to figure legends, where readers can see the details while looking at the figure at the same time. Consider adding arrows pointing to the specific bars so readers can locate the more striking effect(s) immediately.

The “Discussion” is unenlightening. The authors did not identify the mechanisms by which whole-field, temporally intensity-modulated stimuli used here cause the observed results. Instead, they offered vague statements about “changes in ion and fluid flow”, “polarity effects in the outer retina, or “outer retinal asymmetries” – words and ideas that might explain anything … or nothing.

If there is indeed a proper basis of retinal circuit mechanisms and rational arguments, elaborate on them. Otherwise, focus on clearly documenting and describing the observed effects, while noting that it would be practically impossible to dissect retinal circuit functions in this way.

Regarding conclusions, it will be helpful if the authors tighten up the summary of relevant evidence, tighten the argument and the writing, and try to make one or two well-supported and reasonable conclusions.
Experimental design: As shown in Figure 1b, ON- and OFF sawtooth at 4Hz look similar, nor are they distinguishable from sine-wave waveform. How would this affect the results? This problem needs to be addressed.
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: TEMPORAL WHOLE FIELD SAWTOOTH FLICKER WITHOUT A SPATIAL COMPONENT ELICITS A MYOPIC SHIFT FOLLOWING OPTICAL DEFOCUS IRRESPECTIVE OF WAVEFORM DIRECTION IN CHICKS
Review round: 2
Reviewer: 1

Output:
Basic reporting: General
The authors have raised chickens with -10 or +10D lenses under five different Ganzfeld illumination conditions, fast OFF at 1 and 4 Hz, no flicker, and fast ON at 1 and 4 Hz. Both fast OFF and fast ON generated a general shift into the myopic direction in all animals with lenses, but not in control chicks without lenses. They conclude that full field temporal modulation does not trigger directional effects on refraction and eye growth and that sign of defocus-specific effects require spatiotemporal components in the stimuli.
Most of my previous comments were appropirately addressed. However, I still have a number of more minor comments that would further improve the manuscript, as I believe.
Specific
line 48 - “small hyperopic eyes” in all species does not seem to reflect reality. Chick starts with 7 mm axial length which tree shrews reach much later, and see mice vs horse ...
line 53 - is Wallman 1978 a good reference for complex gene-environment interactions?
lines 63-65 - many of the cited papers here were not dealing with positive lenses but are nevertheless used as a reference for induction of hyperopia
line 83, typo “Schwahn”
line 106, just a comment: while I understand that the authors propose that temporal ON and OFF stimulation may have its effect on refractive error development “aimed at the outer retina”, one should not ignore that at least the ganglion cell receptive fields have also an antagonist spatial receptive field structure. If the authors propose “spatial-temporal” activity of the ON/OFF pathways to inhibit refractive errors, this should also involve the inner retina
line 122ff, it is good that the temporal brightness profiles of the LEDs were measured but It would be good to know why the slow rising or decaying phases have the small steps - is this a issue of the measurement device, or does the light sources really emit at these steps?
line 132ff regarding the experiments in 2002 - could the assymmetrical OKN in left and right eyes and also the head optomotor responses have an effect on the temporal luminance profiles that end up on the retina? It is possible that non-stationary  stimuli (like in the drum in 2002) may stimulate retinal detectors differently from stationary stimuli with defined temporal luminance profiles.
line 164. It is not very common to refract chicks under anesthesia. What drug was used and is it possible that it changed refractive states/accommodation tonus?
line 194ff. The description is not very straightforward. Perhaps better: “As can be seen in Figure 2, all chicks wearing -10D lenses developed myopia under all light regimens. Treatment with +10D lenses resulted in hyperopia in all chicks, except for the 1 Hz OFF stimuli.”
line 250. Britton et al 2013, 2014 are ARVO abstracts - should this be mentioned? In line 334, it is said that some of the the current study was presented at ARVO in 2010 but a reference is not provided.
line 267. The illuminance topic is important and it would be interesting to compare the illuminances (or luminances when it was a screen for stimulation) in related studies.
line 308 ff. It would be better to limit speculations. Why is the refractory period in the range of 250 msec (4Hz) - was this measured?
line 318 perhaps better “the present study demonstrated that both whole field low temporal frequency fast ON and fast OFF flicker ...” and, perhaps  better: “... but does not affect refractive development in chicks not wearing any lenses”
line 323ff - it would be better to mention the animal model in each case for these references
references. Crewther et al 2005 is cited twice
Experimental design: some minor questions were left - see my comments above
Validity of the findings: data seem properly collected and the statistical noise is realistic
Additional comments: General
The authors have raised chickens with -10 or +10D lenses under five different Ganzfeld illumination conditions, fast OFF at 1 and 4 Hz, no flicker, and fast ON at 1 and 4 Hz. Both fast OFF and fast ON generated a general shift into the myopic direction in all animals with lenses, but not in control chicks without lenses. They conclude that full field temporal modulation does not trigger directional effects on refraction and eye growth and that sign of defocus-specific effects require spatiotemporal components in the stimuli.
Most of my previous comments were appropirately addressed. However, I still have a number of more minor comments that would further improve the manuscript, as I believe.
Specific
line 48 - “small hyperopic eyes” in all species does not seem to reflect reality. Chick starts with 7 mm axial length which tree shrews reach much later, and see mice vs horse ...
line 53 - is Wallman 1978 a good reference for complex gene-environment interactions?
lines 63-65 - many of the cited papers here were not dealing with positive lenses but are nevertheless used as a reference for induction of hyperopia
line 83, typo “Schwahn”
line 106, just a comment: while I understand that the authors propose that temporal ON and OFF stimulation may have its effect on refractive error development “aimed at the outer retina”, one should not ignore that at least the ganglion cell receptive fields have also an antagonist spatial receptive field structure. If the authors propose “spatial-temporal” activity of the ON/OFF pathways to inhibit refractive errors, this should also involve the inner retina
line 122ff, it is good that the temporal brightness profiles of the LEDs were measured but It would be good to know why the slow rising or decaying phases have the small steps - is this a issue of the measurement device, or does the light sources really emit at these steps?
line 132ff regarding the experiments in 2002 - could the assymmetrical OKN in left and right eyes and also the head optomotor responses have an effect on the temporal luminance profiles that end up on the retina? It is possible that non-stationary  stimuli (like in the drum in 2002) may stimulate retinal detectors differently from stationary stimuli with defined temporal luminance profiles.
line 164. It is not very common to refract chicks under anesthesia. What drug was used and is it possible that it changed refractive states/accommodation tonus?
line 194ff. The description is not very straightforward. Perhaps better: “As can be seen in Figure 2, all chicks wearing -10D lenses developed myopia under all light regimens. Treatment with +10D lenses resulted in hyperopia in all chicks, except for the 1 Hz OFF stimuli.”
line 250. Britton et al 2013, 2014 are ARVO abstracts - should this be mentioned? In line 334, it is said that some of the the current study was presented at ARVO in 2010 but a reference is not provided.
line 267. The illuminance topic is important and it would be interesting to compare the illuminances (or luminances when it was a screen for stimulation) in related studies.
line 308 ff. It would be better to limit speculations. Why is the refractory period in the range of 250 msec (4Hz) - was this measured?
line 318 perhaps better “the present study demonstrated that both whole field low temporal frequency fast ON and fast OFF flicker ...” and, perhaps  better: “... but does not affect refractive development in chicks not wearing any lenses”
line 323ff - it would be better to mention the animal model in each case for these references
references. Crewther et al 2005 is cited twice


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: TEMPORAL WHOLE FIELD SAWTOOTH FLICKER WITHOUT A SPATIAL COMPONENT ELICITS A MYOPIC SHIFT FOLLOWING OPTICAL DEFOCUS IRRESPECTIVE OF WAVEFORM DIRECTION IN CHICKS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is clear and well written
Experimental design: Design is correct, with a small question: the non-flicker and flickering conditions were carried out with two differences mean luminances (183 vs 97 lux), with the max luminance of the flicker conditions matching the mean luminance of the non-flicker. Why was the maximum matched and not the mean value? The discussion of the article cites potential effects of different mean luminances.
Validity of the findings: Data analysis is sound. Conclussions are clear and well-supported.
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: P-CURVE ACCURATELY REJECTS EVIDENCE FOR HOMEOPATHIC ULTRAMOLECULAR DILUTIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please see attachment.
Experimental design: Please see attachment.
Validity of the findings: Please see attachment.
Additional comments: Please see attachment.


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: P-CURVE ACCURATELY REJECTS EVIDENCE FOR HOMEOPATHIC ULTRAMOLECULAR DILUTIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Summary,: the paper applies p-curve analysis to the first 20 homeopathy randomized-trials papers found in a search, concluding they lack evidential value.

I am not familiar with homeopathic research thus I will focus on the p-curve analysis aspect of the paper. Overall the paper seems sound, I have relatively minor comments only. My main comment, the only one involving more than minimal work, is #3 below: I strongly recommend the authors analyze the data also using more traditional, pre p-curve, meta-analytical tools.

Comments.
1) The selection of studies is pretty clear up to the point of selecting the first 20 reported by the output of the search, this unfortunately makes the study selection difficult to reproduce. If tomorrow the Homepathy research institute changes their search algorithm, or even adds new studies, the study selection is not reproducible. It's difficult to fix at this point, but as a remedy perhaps the authors can conduct the search again and save the entirety of the output as a text file/spreadsheet, and they indicate which studies they selected. This would allow a skeptic, say, to second guess their study selection decisions relatively easily.

2) Clarify the contribution
The article reads "P-curve remains untested. The sensitivity and specificity of p-curve have been estimated by simulation (Simonsohn, Nelson & Simmons, 2014b) but has not been tested using published research"

P-curve analysis has been applied to multiople published literatures. For example, the paper introducing it runs it on 20 published studies in the Journal of Personality and Social Psychology, selected as likely to be p-hacked vs not. Our follow-up paper applies it to the choice overload literature. In another paper we apply to the power-posing literature.

I am not asking those other papers be cited, but the novelty of this paper be more clearly indicated.
I do think this is the first time a literature which scientists believe for theoretical reasons must be examining a null finding concludes that indeed lacks evidential value using p-curve. It is in a sense a stronger test than that in our JPSP demonstration for the papers are not being selected for seeming suspicious based on the methods used, but rather, based on the hypothesis tested. That's valuable, and different, and worth clarifying.

3) Compare p-curve to other methods
I would strongly urge the authors to conduct a traditional meta-analysis of this literature, and rely on traditional tools for correcting for publication bias: Trim-and-fill and possibly PET-PEESE and maybe Fail-Safe method. This would provide valuable information regarding not only the absolute but also the relative advantage of relying on p-curve to assess evidential value.  I assume these other methods will not correct well at all (they will conclude homopathy is super true) but I am interested in seeing those results published regardless (of course). This is actually not a lot of work, with the Z values ready, you are just 2 lines of codes from having the trim-and-fill results. I am thinking of the paper either stating "Only p-curve correctly identifies homepathy lacks evidential value" or "Also p-curve correctly identifies homeopathy lacks evidential value"

 4) Clarify p-value extraction vs test
Looking at the p-curve disclosure table I see that at least sometimes the authors selected a p-value from a paper, rather than a test-statistic, and then submitted the Z-value that is associated with it to the p-curve analysis. That's generally OK, but it should be noted, and also make notes when there is ambiguity surrounding that p-value. Specifically, I opened the first paper in the p-curve disclosure table, Chakraborty et al. (2013),  and see that they claim to conduct a Bonferroni correction, but it is not clear exactly what they do (how many hypothesis they correct for) and whether the p-values reported have been corrected already or not. Looking at their Table 2 it seems the reported p-values are not corrected (as they are all accompanied by the note that the p-value is not significant using the Bonferroni correction), but that's a baseline comparison, in Table 3 it is ambiguous whether the p-values have been corrected. A footnote discussing this and other such ambiguities, or perhaps a supplement/appendix may be useful; it should be clear to readers which issue existed and how they were dealt with.

Note that a right-skewed distribution of p-values will remain right-skewed after a Bonferroni correction, as it divides (all) p-value by a constant.

5) the p-curve figures are high resolution on the app, but appear blurry here. Maybe the authors did a print-screen, instead they can save as to keep it high-resolution.

6) the app reports a cumulative p-curve as it excludes more and more p-value, since the authors exclude one extreme value they may be interested in it, but maybe not.

7) In the p-curve disclosure table i would crate a column with test results ready to be copy-pasted to the online app, so just the Z=xx.x, wirhtout the p-value before it and the z in ()


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: P-CURVE ACCURATELY REJECTS EVIDENCE FOR HOMEOPATHIC ULTRAMOLECULAR DILUTIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: 2nd round, n/a
Experimental design: 2nd round, n/a
Validity of the findings: 2nd round, n/a
Additional comments: I am satisfied with the 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: COMPARISON OF AUTOMATIC AIRWAY ANALYSIS FUNCTION OF INVIVO5 AND ROMEXIS SOFTWARE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written
The references are current but could be more explored (there are a lot of studies exploring this issue)
The structure of the article is ok
The keywords should represent the general aim of the study and not specify the software used.
It's important to comment on the introduction the differences between the studies that have gold standard and the studies that don’t have.
Experimental design: Did the authors calculate the sample size? Why did they use 11 CBCT scans?
How the authors define the boundaries of the upper airway space? This is essential information that is not clear in the text.
About the examiner. Its important cite the experience with this software….
Validity of the findings: Its important compare software but I think that specific points that could be decisive were not discussed as the CBCT protocols, the boundaries of the upper airway, the soft tissues during the acquisition.These issues can influence the airway measurements. Maybe compare software should be a minor finding.

I think that this manuscript doesn’t add any new and important information; it's natural to believe that if you have an automatic segmentation and you repeat the measurements you will have replicated sizes as well. Maybe they have similar results but don’t have a gold standard, so the measures are actual? At least this should be discussed.

Bland Altmann is currently used to compare a standard method and a new one, and it's a good way to visualize if exist differences between the two techniques.
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: COMPARISON OF AUTOMATIC AIRWAY ANALYSIS FUNCTION OF INVIVO5 AND ROMEXIS SOFTWARE
Review round: 1
Reviewer: 2

Output:
Basic reporting: A. The English language used has many grammatical mistakes and is often unclear. The authors use a mix of the present and the past tense while it is custom to report finding in the past tense. The article needs major professional English language editing before it could be suitable for publication. A few examples where the English language could be improved/corrected are lines 24, 31, 41, 51-53, 70, 137, 144.

B. The references are NOT formatted according to the journal's style and contain many mistakes. The journal style has the volume only while they have stated the volume and the issue in many references. Authors names should be last name then first name initials, many references have first name and then last and therefore are not properly alphabetically ordered.  Eg the first reference line 187 “ Oral Radiology, 0(0), 0.” The volume is definitely not zero, it is vol 33 and the pages are not stated.

C. The word “reference” is present a couple of times in the text prior to the in text citation ( lines 136, 162)

D. Naming of the minimum cross-sectional area (MCA) is not consistent in the study, they start by MCA and then they just use minimum area in the rest of the text. Please standardize how you refer to this measurement throughout the text.

E. In the results section the authors report in details numbers/figures that are already shown in table 2 so there is no need to repeat them in the text.
Experimental design: A. I would like to ask the authors to specify how they defined/standardized the upper and lower boundaries of the airway? Whether they included the nasal airway in their measurements or not?  This information is important to ensure the repeatability/ Reproducibility of the measurement especially when drawing the “cube”  in the Romexis software.

B. The Methods described are lacking the machine settings (scanning parameters) used when acquiring the CBCT scans. The authors are using software programs that depend on a set grey value to automatically segment the airways.  Since the gray value of a pixel depends not only on the tissue contrast but also on many other factors, such as the type of CBCT machine used and the scanning parameters. I would like to ask the authors to report the scanning parameters used such as FOV, voxel size, etc. to ensure sufficient details and information to replicate the study.

C. In line 83-84 the authors state “ After the line is drawn, the software will automatically detect the airway within the soft tissue based on the Hounsfield Unit.”  Since the images used in the study are CBCT images, then the software would be detecting the soft tissue based on the Grey Values not on HU. Please correct this in the text.
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: COMPARISON OF AUTOMATIC AIRWAY ANALYSIS FUNCTION OF INVIVO5 AND ROMEXIS SOFTWARE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have added the needed information about their research methodology, corrected their references as requested but from the English language point of view the article, in it's present state, is NOT suitable for publication. Many sentences start in the present and end in the past, many don't even have a verb and are difficult to understand. To name a few examples " line 179 : " this gives a slightly measurement for both software", line 155: There are currently more than fifteen third party DICOM  viewers .... was available commercially." The authors are again advised to have their article edited by a professional academic editing service
Experimental design: The authors described in their materials and methods section how they defined the airway boundries in the Invivo5 software. However, they did not describe how they reproduced the same boundries when using the Romexis software.
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: THE SENSITIVITY AND SPECIFICITY OF METHYLENE BLUE SPRAY TO IDENTIFY THE PARATHYROID GLAND DURING THYROIDECTOMY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a well-written study with clear professional English. It is well-structured with a reasonable rationale. Literature has been reviewed. Figures have high quality.
Experimental design: Research methodology is adequate with sufficient detail. Research question is interesting. Knowledge gap has been identified.
Validity of the findings: Data is valid. Clinical benefit is meaningful and has been stated.
Additional comments: The authors sprayed methylene blue onto the thyroid bed of 47 patients receiving thyroid lobectomy. The area with faded color was suspected to be parathyroid glands. Histopathology was a reference. Sensitivity, specificity, PPV and NPV were analyzed. I reckon the findings from this study are clinical meaningful and very useful in practice.
1.	Methylene blue was sprayed after the recurrent laryngeal nerve and upper and lower parathyroid glands were identified and the thyroid gland was pulled back (Line 78-80). While I believe the high sensitivity of methylene blue will be very useful, this study has shown us that methylene blue may not be necessary if surgeons have high surgical skill and good knowledge on surgical anatomy. Please discuss.
2.	The biopsies were conducted at the area that was suspected to be the parathyroid gland based on surgical anatomy, which had regained its yellow color (Line 83-84). Please report if there was any case and any area which was suspected by surgical anatomy but having blue-stained color. I assume that there were none. Please confirm.


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 SENSITIVITY AND SPECIFICITY OF METHYLENE BLUE SPRAY TO IDENTIFY THE PARATHYROID GLAND DURING THYROIDECTOMY
Review round: 1
Reviewer: 2

Output:
Basic reporting: It was study that was clearly written and could be easily understood. There was a clear rational. The objective of the study was clear. The study report was easily to understand and there were also high-quality figure.
Experimental design: Research methodology could prove the research question of the study very well. It was a study with low risk bias with good quality.
Validity of the findings: Data were valid and could really be used in the clinical practice.
Additional comments: This is a prospective diagnostic study which the authors sprayed methylene blue onto the thyroid bed of 47 patients receiving thyroid lobectomy. After five minutes, Biopsies were conducted for histopathology at both the stained area and the area in which the color had faded. The area with faded color was suspected to be parathyroid glands. Histopathology was a reference. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated.
1.	If after spraying methylene blue, the difference of the area  that can quickly absorb the color and other area could not be observed. Where to make the biopsy or to find parathyroid according to surgical anatomy knowledge. Please discuss.
2.	Using of methylene blue spray is a test with high level of sensitivity but the specificity is not very good so it is suitable to be a screening tool. Therefore, other tests with good specificity should be used along. The conclusion should be toned down.


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 SENSITIVITY AND SPECIFICITY OF METHYLENE BLUE SPRAY TO IDENTIFY THE PARATHYROID GLAND DURING THYROIDECTOMY
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is a well-written study with clear professional English. It is well-structured with a reasonable rationale. Literature has been reviewed. Figures have high quality.
Experimental design: Research methodology is adequate with sufficient detail. Research question is interesting. Knowledge gap has been identified.
Validity of the findings: Data is valid. Clinical benefit is meaningful and has been stated.
Additional comments: The authors have made adequate revisions. Thank you.


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

Input:
Title: THE SENSITIVITY AND SPECIFICITY OF METHYLENE BLUE SPRAY TO IDENTIFY THE PARATHYROID GLAND DURING THYROIDECTOMY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Thank you for your revisions and thoughtful work.  I have no further comments.
Experimental design: Thank you for your revisions and thoughtful work.  I have no further comments.
Validity of the findings: Thank you for your revisions and thoughtful work.  I have no further comments.
Additional comments: Thank you for your revisions and thoughtful work.  I have no further comments.


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

Input:
Title: GENOME-WIDE ANALYSIS OF CIRCULAR RNAS IN GOAT SKIN FIBROBLAST CELLS IN RESPONSE TO ORF VIRUS INFECTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written and organized.
Experimental design: So far as I can tell, the appropriate experimental design was used.
Validity of the findings: The miRNA results and network analyses are suspect. Please see general comments.
Additional comments: The manuscript by Pang and colleagues reports on the analysis of RNAs that are differentially expressed in cell cultures infected with Orf virus. They find numerous novel circRNAs in their dataset, show that the majority are derived from exons and go on to propose miRNA-mRNA-circRNA pathways using differentially expressed RNAs revealed in their study. circRNAs are an exciting new class of ncRNAs who’s functions are an active area of research and information that adds to this field is of value/interest. The manuscript is well written and easy to follow, but there are some serious concerns that the authors need to address before publication. The work that focused on identifying circRNAs was, to my knowledge, done appropriately, and the validation of several circRNAs experimentally makes this part compelling. The remaining work on miRNAs and the network analysis is, however, very concerning. The majority of differentially expressed miRNAs are not from the species under analysis! The downstream networks, making use of miRNAs that come from humans, mice, etc., are likely not real. I think separating the circRNA work and presenting it alone would be one route for salvaging this manuscript. To keep the miRNA analysis and network analysis, they’d have to go back to the beginning and do extensive experimental validations to propose any networks.

Comments:

Although the focus of this study was on the effects of Orf infection on host cell RNAs, it would be interesting to also analyze the transcripts coming from the Orf virus. Indeed, when they performed their initial alignment, it would have been a good idea to align to the Orf virus genome simultaneously to the goat reference genome. Without redoing the whole alignment, it would be interesting to remap reads that did not align to goat to the Orf virus genome and use their pipeline to deduce any potential viral circRNAs. This would definitely strengthen this current manuscript.

Lines 182-3, I have my doubts that the novel miRNAs reported here are real. Looking at Table 4, it is concerning that of the 26 differentially expressed miRNAs, only 7 are from goat; the others are from a variety of other species (e.g. humans, mice), as well as these putative novel miRNAs. This suggests that these might be sequencing artifacts. If they could be validated via stem-loop PCR and if there was evidence for their conservation in other species (e.g. their precursor hairpins), this could raise confidence in their existence.

Could the authors explain why the minority of their miRNAs were not from goat? This is very concerning and it raises questions about all subsequent analyses. The authors should consider reanalyzing the miRNA-Seq data using a different pipeline. Additionally, validating the seven goat miRNAs using stem-loop RT-qPCR would help raise confidence in their putative expression change.

Most of the miRNA nodes are for miRNAs from other species, or for the putative novel miRNAs. The presented circRNA-mRNA-miRNA networks are likely spurious. Are the networks involving goat miRNAs even plausible? I looked at the circRNA184 to chi-miR-92a-5p network and they seem to make sense: circRNA down, miRNA up, genes down…but how do the other nodes look?

Lines 208-16 are confusing. The Figure caption indicates that Fig. 4 is for all diff. expressed RNAs, but this section is included in the integrated analysis section. Were the GO and KEGG analyses performed on only the genes involved in the network shown in Fig. 3?