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: STATE OF BIODIVERSITY DOCUMENTATION IN THE PHILIPPINES: METADATA GAPS, TAXONOMIC BIASES, AND SPATIAL BIASES IN THE DNA BARCODE DATA OF ANIMAL AND PLANT TAXA IN THE CONTEXT OF SPECIES OCCURRENCE DATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The current submission exhibited significant improvements. Language can be improved during copy editing.
Experimental design: Methods/protocols are clear.
Validity of the findings: The reported findings, although not that novel, presented a call to action not just for Philippine workers but for all who are working with biodiversity/DNA-based data.
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: COMPUTATIONAL BIOACOUSTICS WITH DEEP LEARNING: A REVIEW AND ROADMAP
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript, the author attempts to review the field of computational bioacoustics. To my best knowledge, this is the first comprehensive overview of the field, and I very much appreciate the efforts that went into this report. It is well-written and structured, following the PeerJ guidelines. It is comprehensive and extensive in every aspect and would be a great resource for beginners in the field when published. The scope of the review appears to focus on breadth rather than depth, which I feel was a good choice. The manuscript is well organized and covers all important aspects of computational bioacoustics, sometimes even providing hints and insights into related fields (e.g., deep learning best practices) which is a nice addition. Overall, I feel that this report deserves to be published and would be a great resource for students, competition participants (e.g., LifeCLEF), and computer scientists entering the field.
Experimental design: The search query could have included terms specific to the field like “soundscape”, “recording” or general terms like “identification” or “detection”. Yet, after investigating the reference section, I feel that all major publications in this field have been included and so this might not be a shortcoming after all.

I appreciate the fact that the author limited this review to papers published after 2016 as this year saw in fact significant breakthroughs in the field.
Validity of the findings: The review (by design) is biased towards deep learning, but to be fair, it is the most common way of analyzing large amounts of audio data today and has seen tremendous attention in the past. Therefore, I think this bias is justified.

The author sometimes uses self-references as justification or general reference. Typically, this would not be ideal, but given the author’s previous work and engagement in the field of bioacoustics, it is justified in this context.

I very much like the “Roadmap” section, which is an excellent addition and covers all important areas of future research that I can think of.
Additional comments: The “LifeCLEF2016” reference appears to have a duplicate (2016a and b are the same paper)


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

Input:
Title: COMPUTATIONAL BIOACOUSTICS WITH DEEP LEARNING: A REVIEW AND ROADMAP
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, it is a good paper to read reviewing the applications of deep learning on bioacoustic automatic detection, classification, and other works. In general, I wish the paper was better proof-read before its submission. Many acronyms happen for the first time without being spelled out completely. Most of them come out without any short explanations. In addition, there are many small mistakes in the reference, such as in consistent upper or lower cases on months and no year information.

Line 64: We all know NN stands for Neural network. However, people with biology background might not know it immediately. It appears for the first time in the paper here. A full name should be given.

Line 276: On transformer. Facebook presented in 2021 Wav2vec 2.0 for human speech, which was trained self-supervised on sound only and then fine-tuned to other downstream works. Maybe bioacoustics can repeat the success due to the small size of manual labels? I suggest to add one line or two on Wav2vec 2.0 to bring the latest information to the bioacoustics community.

Line 373  occupancy => presence  / absence

Line 640: NVIDIA Jetson Nano and Google Coral: should add NVIDIA to be side by side with Google, or remove Google. Either “Jetson Nano and Google Cora” or “NVIDIA Jetson Nano and Google Cora”

Line 650: ARM CMSIS. What is CMSIS abbreviated for? CMSIS appears for the first time in the paper here. A full name should be given.

Line 828: To verify a method’s performance on recognizing individuals needs a data set consisting of labels of individual IDs. So far, there’re not many data sets available since it does need tremendous work of human experts’s effort. However, the role DL plays is not to accomplish the accuracy increase on a dataset but rather, to make prediction on out-of-sample data while keeping the generalization.

Line 847: Detection problem has been well studied in marine mammal / whale community. Many long-term recordings ranging over months to years have few animal calls and need to be detected.

Line 950: What is TDWG?

Line 956: Could you please explain why W3C Provenance Ontology is needed and what benefits it can bring to bioacoustics community?

Line 959: What is “biodiversity crisis” mentioned? Could you please use one sentence to describe what it is?

Line 960: In the term “multi-agent”, does it mean multiple individual animals? I feel confused since this word is usually used in AI literatures for a robot with sensors.

Line 1010: In “It will be continue”, “be” should be removed.
Experimental design: I wish the author can address the small size problem of labelled data. All the problems that deep learning can apply to have been existing for decades and deep learning came as the tool that improves the accuracies on most applications. However, the problem of small data size hinders us from training a model that offers good generalization to new unknown input sounds.
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: IMMEDIATE AND CUMULATIVE EFFECTS OF UPPER-BODY ISOMETRIC EXERCISE ON THE CORNEA AND ANTERIOR SEGMENT OF THE HUMAN EYE
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This is an interesting and robust study aimed at evaluating the corneal and anterior segment of the eye biomechanical adaptations to upper-body isometric efforts. Thank you very much for the opportunity of reviewing this article that greatly adds to the scientific body of knowledge. I congratulate the authors for the work performed. Hereunder, a few minor comments that could help the readers in the understanding of the article and its background are presented:

In the abstract (line 45) the authors point out that the changes are positively associated with the intensity. I believe that with this statement the reader could understand correlations were performed. Consider rewriting it.

A short definition of isometric contraction (e.g., where the muscle-tendon unit remains at a constant length [Oranchuk et al., 2019]) could be inserted in the introduction to help potential readers as this is not a sport-specialized journal.

In the a-priori sample size analysis, was the effect size calculated based on previous studies? on pilot studies? on the smallest effect size of interest?

Please, consider including information on the fitness level of the participants as this measure could influence ocular physiological responses. This information could be objective (e.g., the maximum isometric force produced, kilograms used for the 2-minute isometric effort, one-repetition maximum, relative strength) or subjective (e.g., years training, days per week training) if objective information was not collected.

I think is not clear how the measurements were taken during the isometric efforts. Did the participants stop the isometric effort by dropping the weights to undertake the measurements each 30, 60, 90, and 120 seconds after starting? Did the participants extend their arms at both sides of the body holding the weights? Could a 2-second pause have influenced the maximum effort participants could perform? Consider rewriting this explanation.

I believe it could be interesting for the reader to have reference values for the interpretation of the effect sizes. Discussion on these values can be found in the article of Lakens (2013).

Please, consider including significance (at least with symbols) in Table 1.

Although there is controversy on the effect that the sex of the participants could have on the intraocular pressure, in one study the sex was found to be a significant predictor of the intraocular pressure variations (Gene-Morales et al., 2021). Could these differences appear in the parameters analyzed in the present study? This could be indicated in the future directions section. Also, different muscle adaptations can be obtained with isometric contractions at different joint angles (Oranchuk et al., 2019). It could be interesting to study ocular adaptations to isometric efforts at different joint angles in future works.

Specific comments:
Line 112, the reference [19] is placed after the full stop.

Line 137, a comma is missing between the parenthesis and before as it is a list of three or more words.

Additional references used:
Gene-Morales, J., Gené-Sampedro, A., Martín-Portugués, A., & Bueno-Gimeno, I. (2021). Do age and sex play a role in the intraocular pressure changes after acrobatic gymnastics? Journal of Clinical Medicine, 10(20), 4700. https://doi.org/10.3390/jcm10204700

Lakens D. (2013). Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs. Frontiers in psychology, 4, 863. https://doi.org/10.3389/fpsyg.2013.00863

Oranchuk, DJ, Storey, AG, Nelson, AR, Cronin, JB. Isometric training and long-term adaptations: Effects of muscle length, intensity, and intent: A systematic review. Scand J Med Sci Sports. 2019; 29: 484– 503. https://doi.org/10.1111/sms.13375


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: IMMEDIATE AND CUMULATIVE EFFECTS OF UPPER-BODY ISOMETRIC EXERCISE ON THE CORNEA AND ANTERIOR SEGMENT OF THE HUMAN EYE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript “Immediate and cumulative effects of upper-body isometric exercise on the cornea and anterior segment of the human eye” aimed to analyze the short-term effects of 2-minute upper-body isometric efforts at two different intensities, on corneal and anterior eye morphology. There is undoubtedly a need to examine the effect of isometric exercise on eye function, especially in the context of the importance in prevention and management of ocular diseases (e.g. glaucoma). Thus, I believe your study will be of significant interest to the readers of PeerJ. The manuscript is well written, easy to follow, succinct and adheres to the required format. I would like to congratulate the authors on their exemplary work. In my opinion, it requires only minor revisions, mainly in the discussion section. I hope my comments will be beneficial to the authors.

Comments
1. Is there a possibility that the ages of participants influenced the results? In the discussion section, please consider adding a limitation such as an age range,i.e. in this cross-sectional  study only young healthy people participated (convenience samples) and causality cannot be fully inferred.
2. Please consider adding a description of the physiology mechanism for possible long-term consequences of the isometric efforts on the cornea and anterior chamber morphology alterations.

Typos
e.g.
Wylȩgała – should be Wylęgała
Experimental design: Generally the experimental design is well done, sample size and statistics are appropriate and predictions well formulated, and technical details are well described. Authors have sufficiently explained each component of the study procedure, and overall the analytical approach was justified. However, I have one doubt regarding the upper-body isometric exercise protocol. Did participants start the experimental session always, with holding the heaviest load? If yes, is it possible that exercises with a higher load could affect the results of those with a lower one ? Was there a warm-up for the examination session performed?
Validity of the findings: The validity of the findings was enhanced by the use of standardized methods  and thoughtful research design. The results are reliable, and importantly, they constitute the starting point for undertaking clinical trials.
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: IMMEDIATE AND CUMULATIVE EFFECTS OF UPPER-BODY ISOMETRIC EXERCISE ON THE CORNEA AND ANTERIOR SEGMENT OF THE HUMAN EYE
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: All the comments raised by the reviewer have been properly addressed. 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: IMMEDIATE AND CUMULATIVE EFFECTS OF UPPER-BODY ISOMETRIC EXERCISE ON THE CORNEA AND ANTERIOR SEGMENT OF THE HUMAN EYE
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I accept the answers and 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: RELATIONSHIP BETWEEN CIRCADIAN GENES AND MEMORY IMPAIRMENT CAUSED BY SLEEP DEPRIVATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.  There are numerous grammatical errors throughout the manuscript that should be addressed.

For example, in lines 94-97:  “An innate circadian clock, a kind of 24 h cell-autonomous period in human-driven by transcription-translation feedback loops of circadian clock genes (Ikegami et al., 2019), controls daily activities and maintains the stable rhythm of organ function in many physiological and pathological processes (Patke et al., 2017).”

Additionally in 97-99:  "In recent years, circadian rhythm has been concerned by many neurological disorders, including schizophrenia, bipolar disorder, depression, and  autism (Johansson et al., 2016)."

Errors like these are distracting and should be corrected prior to resubmission.

2.  Additionally, the section in the intro concerning circadian rhythm biology is overly basic and should include more information about the clock genes assessed in the study.
Experimental design: 1.  The experimental design is reasonable in this reviewer's opinion, although again clarity is obscured at times due to grammatical errors and incomplete explanations.

2.  It is unclear what SD protocols were used and how the control mice were treated in the data not collected by this group. Although a reference is provided for these experiments, a short explanation of how these studies were conducted would be useful.
Validity of the findings: 1.  295-296 The authors state, “The important MCODE module in the PPI network, circadian rhythm genes marked in pink, showed seven circadian clock genes (Fig. 3D-E).  None of the genes listed function as part of the circadian clock, although these may be output genes from the central oscillator.  Based on this and the intro section about circadian rhythm biology, it appears as though the authors lack a solid understanding about how the circadian clock functions and it is recommended that they consult a clock expert as part of the revision process.

2.  It is unclear at times which data set the authors are referring to at times.  The experiments should be better introduced in the results section and perhaps a brief explanation as to why they were performed.

3.  318 - 323  “Therefore, we detected the expression of genes in the heart, liver, and lung, observing that some genes alternated in various organs (Fig. 5F). Seven circadian genes significantly and consistently correlated with two representative indicators of memory function, BDNF, and NPAS4. These results indicated that SD leads to memory impairment and changes of seven circadian clock genes, of which the latter were closely related to memory function.”  Here, the authors assert that changes in clock-regulated (presumably) genes are associated with changes in two memory genes.  However, it is unclear how this correlation can be made given that the gene changes did not occur in the brain.

4.  The authors use changes in expression data to detect changes in immune cell infiltration into the hippocampus using the algorithm CIBERSORT.  . Although potentially interesting, this data is highly correlative and should be confirmed empirically.
Additional comments: The authors seek to further establish the relationship between SD, circadian functionality and the immune system. This is a highly relevant field of research in the sleep and circadian community, which makes this article potentially impactful.  However, numerous grammatical errors and a lack of understanding of circadian rhythms, and overstatement of the authors’ findings detract from the paper and should be addressed prior to submission.


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: RELATIONSHIP BETWEEN CIRCADIAN GENES AND MEMORY IMPAIRMENT CAUSED BY SLEEP DEPRIVATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study, the authors aim to investigate the relationship between circadian clock genes and the alteration of memory function after sleep deprivation (SD). The conclusion is mostly supported by the results shown. However, the authors should address the comments below and re-write the conclusion section of the manuscript (details below).

Authors should use clear and unambiguous English language throughout the manuscript. One such example is lines 84-86 in the introduction. What is emotional processing speed? "Numerous studies have shown that SD has deleterious effects on cognitive function through neurological damage and neurodevelopmental disorders (Sabia et al., 2021), including attention, working memory, emotional processing speed, and reaction (Turner et al., 2007)"
Experimental design: Line 141-142 "In addition, validation datasets (the entire datasets of GSE9442 and other related datasets) and animal experiments enhanced the reliability of the analysis results" How the entire dataset helped in enhanced reliability of the results is not at all clear. The authors should explain this statement and provide details in the method section as appropriate.

Paragraph 154-163 is poorly written and how the GSEA analysis was conducted is unclear. Please rewrite and emphasize how the analysis was done using the web-based toolkit (providing appropriate references)
Validity of the findings: Lines 261-269 Authors should describe in detail the results they obtained, rather than just referring to the figures.

I want the authors to comment on this whether we can reverse the course of memory impairment and other effects caused by SD by introducing a healthy sleep regime? Did they perform any experiments in which they tried to induce a healthy sleep regime on rats (previously suffering from memory impairment) and check their cognitive abilities over time? Is memory impairment caused by SD reversible?
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: RELATIONSHIP BETWEEN CIRCADIAN GENES AND MEMORY IMPAIRMENT CAUSED BY SLEEP DEPRIVATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: see comments below
Experimental design: see comments below
Validity of the findings: see comments below4
Additional comments: Although the authors made significant improvements, this article still needs quite a bit of work.  Specifically, numerous grammatical issues remain that make the article difficult to navigate.  I highly recommend this group consults an outside group for help with this.


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: RELATIONSHIP BETWEEN CIRCADIAN GENES AND MEMORY IMPAIRMENT CAUSED BY SLEEP DEPRIVATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have revised the manuscript in regards to the grammatical errors and English language. With they seeking help from language editing services from PeerJ will help improve this manuscript even further.
Experimental design: More details on the methodology are now added.
Validity of the findings: Satisfactory clarifications are provided to the concerns raised in the previous version.
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: TRANSCRIPTOMICS ANALYSIS OF FIELD-DROUGHTED PEAR (PYRUS SPP.) REVEALS POTENTIAL DROUGHT STRESS GENES AND METABOLIC PATHWAYS
Review round: 1
Reviewer: 1

Output:
Basic reporting: It is ok
Experimental design: it is ok
Validity of the findings: it is ok
Additional comments: This work carries out a field-based transcriptomic study,and reveals potential drought stress genes and metabolic pathways.For the writing and results of the manuscript,I have some comments as follow.
1.	This is necessary to improve logic in language expression.The manuscript needs extensive editing.
2.	The flavonoids and monoterpenoid biosynthesis-related secondary metabolites were needed to identify.
3.	The references are in a very confusing format. Authors should check this part very carefully.


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

Input:
Title: TRANSCRIPTOMICS ANALYSIS OF FIELD-DROUGHTED PEAR (PYRUS SPP.) REVEALS POTENTIAL DROUGHT STRESS GENES AND METABOLIC PATHWAYS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript has many minor grammatical errors. These should be checked properly.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: 1. Line 96: Please re-write the sentence.  Don’t write as “we provide a transcriptomic study….”. You may write it as- The major aim of the study was…..
2. Line 101: ‘Plant materials and growth conditions’ sub-headings should be changed. You have indicated location, plant materials, and experimental setup and data recordings of the experiment. So, please improve the sub-headings or concise the writings if you wish to keep the original ones.
3. Line 190 : 2 -ΔΔCT method please add reference.
4. Line 191-192: Pearson’s correlation software package with reference should be included.
5. Add “Conflict of interest” section in the text.
6. Arrange the references according to the Journal’s guideline.
7. Overall, Justify the text and follow the journal’s guideline.
8. Figure 3c, 3d and 4 not clear please increase resolution.
9. Results can be improved
10. Conclusions must be improved.
11. A total of A total of 1318 DEGs, and 4438 TFs were identified in present study, but only 13 genes were validated by qRT-PCR. It is necessary to use more genes for validation.


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: TRANSCRIPTOMICS ANALYSIS OF FIELD-DROUGHTED PEAR (PYRUS SPP.) REVEALS POTENTIAL DROUGHT STRESS GENES AND METABOLIC PATHWAYS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript by Yang et al reports the results of a global transcriptome analysis of the field drought response of pear, Pyrus spp. The document is well written. The Introduction presents the basic aspects of the response of plants to drought and the importance of the pear fruit crop. The research question and the structure of the article is well defined.
Experimental design: The methodology is well described and the results are clear. The authors use five replicates of both treatments, control and drought, mixing RNA from leaves, branches and young fruits. This is a strong point of this study. In general, Figures are relevant, well labelled and described. I have some comments about the content and legends of the Tables, which are indicated below.
Validity of the findings: The results of this transcriptome analysis identify novel pear genes differentially expressed between drought and irrigation field treatment. They can be considered interesting candidates to be followed up in a pear breeding program. I have not been able to find a link for the raw data. I guess it must be in some repository, but is not indicated in the manuscript.
Additional comments: I have some comments and suggestions about the main document, as follows:
L21-23: I suggest including a statement of the wide range of tissues sampled, i.e. leaves, branches and young fruits. This is an important point of this work.
L54: Instead of ‘deficient’ it should be ‘water deficiency’.
L134-135: RNA integrity was not measured with a Nanodrop, is it an Agilent Bioanalyzer?
L151-153: Equal amount of RNA from the different tissues was mixed prior to library construction. Can you differentiate the tissue-type later?
L161: The threshold used, |log2FoldChange>1| is quite liberal. It would be more appropriate to get a higher, stricter threshold, as highly expressed genes are those with (log2FoldChange < -3.5).
L178 and following: Was the same RNA used for RNA-seq and the qRT-PCR validation of gene expression? This should be specified in the document.
L197: CK is used as abbreviation for control treatment. It is correct but misleading as this term suggests cytokinin.
L204: Those numbers, 10 cDNA libraries (5 repeats for drought and irrigation) were sequenced, should appear in M&M.
L247-248: The statement: ”The second largest group (Figure 5b) contained 293 genes whose expression increased under field drought conditions”, does not agree with the Figure shown. Expression is only slightly higher under drought.
L275-276: Which genes of those shown in Figure 7 are downregulated? It is not apparent from the Figure or the legend.
L300: The sentence mentions 11 randomly selected DEGs, whereas 13 DEGs appear in M&M and Figure 4. Please check the numbers.
L358: Typo, delete ‘in’.
L384-385: The previous sentences talk about WRKY transcription factors. The current sentence does not follow from that. It should be conditional tense, WRKY transcription factors may play important roles in regulating drought stress responses.
L393: How many genes were validated by qRT-PCR, 11 or 13?
Figure 5: There are no differences in expression among the genes clustered in the Figure. They have a similar expression in all the treatments, flat.
Figures 7 and 8: What genes are differentially expressed of those shown?
Table 3: The legend mentions “Highly expressed genes identified in drought samples”, however it should specify “Highly expressed genes in control conditions, down-regulated under drought”. Is C control and D drought?
Table 4: The legend mentions “Highly expressed genes identified in control samples”. As before, I think it should be “Highly expressed genes identified under drought”. C control, D drought?
Table 5: The legend mentions “Top 10 GO terms of DEGs in field drought samples compared to CK”. Indeed, those are the top 10 GO terms for each of the three GO categories. It could be clarified.
Table 7: What is the log2FoldChange to declare significant a difference? Most ot the genes that appear in the table have low values, probably not significantly different.


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: TRANSCRIPTOMICS ANALYSIS OF FIELD-DROUGHTED PEAR (PYRUS SPP.) REVEALS POTENTIAL DROUGHT STRESS GENES AND METABOLIC PATHWAYS
Review round: 3
Reviewer: 1

Output:
Basic reporting: No Comment
Experimental design: No Comment
Validity of the findings: No Comment
Additional comments: Dear Authors, Thank you for improving your article, and I am agreed with the changes.


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: TRANSCRIPTOMICS ANALYSIS OF FIELD-DROUGHTED PEAR (PYRUS SPP.) REVEALS POTENTIAL DROUGHT STRESS GENES AND METABOLIC PATHWAYS
Review round: 3
Reviewer: 2

Output:
Basic reporting: I still have some questions and comments to improve the manuscript.
L138: 5 repeats for drought and irrigation ‘each or respectively’.
L139: Diluted to ‘1 ng μL’ for library construction – It should be ng µl-1 or ng/µL
L224: “Genes that were highly expressed in CK samples …” Instead of CK it is better to use ‘irrigated or control’ samples, as has already been changed throughout the document.
L239-241 and 246-247: The same idea is expressed in both sentences, a group of genes with increased expression under drought. Looking at Figure 5, the profile of the average expression values in group 1 (A) and group 2 (B) is similar, why are they different groups?
L314-315: “A total of 1318 DEGs were detected”. Previously, in the Results section (L216), it was mentioned that “In total, 819 DEGs between drought and irrigation were identified”. The numbers do not match.
L392: “A total of 1318 DEGs were detected”. As mentioned in the previous comment, in the Abstract and Results, the number of DEGs is 819. Please check.
Figure 2: The control, irrigated treatment appears as CK.
Figure 4 legend: In the figure RNAseq and qRT-PCR results for the displayed genes are shown. Both of them should appear in the legend.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The current version of the manuscript integrates most of the comments or suggestions of the reviewers. The document has clearly improved and it reads much better now.


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: TRANSCRIPTOMICS ANALYSIS OF FIELD-DROUGHTED PEAR (PYRUS SPP.) REVEALS POTENTIAL DROUGHT STRESS GENES AND METABOLIC PATHWAYS
Review round: 4
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors made the suggested corrections in the document and addressed all my queries. No more 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: COMPLETE CHLOROPLAST GENOME STUDIES OF DIFFERENT APPLE VARIETIES INDICATED THE ORIGIN OF MODERN CULTIVATED APPLES FROM MALUS SIEVERSII AND MALUS SYLVESTRIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript needs professional language editing.
Experimental design: The experimental design is too simple to answer the question raised by the authors.
Validity of the findings: The major conclusion is neither original nor well supported
Additional comments: Li and colleagues assembled the chloroplast genome of 24 cultivated apple accessions and characterized the features and phylogeny of the genomes. In the past decade, numerous studies have been published to dissect the origin and domestication of apple using both morphological and genomic evidence. Presently, one consensus reached by the community is that Malus seiversii and Malus sylvestris are the two major wild progenitors of modern cultivated apples. This conclusion has been supported by a wide array of population-scale studies on both nuclear and chloroplast genomes, including Nikiforova et al Mol Biol Evol 2013, Duan et al Nat Commun 2017, and Sun et al Nat Genet 2020. It should be noted that some early cultivars as well as the specific local cultivars may have been originated from different wild species (Chen et al. Plant Biotechnol J 2021). However, cultivars used in this study are presumably the descendant of sieversii and sylvestris, which is consistent with finding of this work from small scaled chloroplast genome analysis. In summary, the authors have used a small-scaled dataset to explore a big and largely answered question, therefore I don’t think this study provides new information for the apple research community. By the way, figures in this manuscript are not easy for visualization, which should be revised for future publication.

Specific points:
Line 16: change “in this world” to “in this work”
Line 43 formatting error for “__world”
Line 46-49, the statements are incorrect, there are substantial studies addressing the origin and domestication of cultivated apples, e.g. Cornille et al. 2012 & 2014, Duan et al. 2017, Sun et al. 2020.
Line 66-67, according to the recently published studies cited above, there is an agreement on M. sieversii and M. sylvestris being as the major genetic contributors of modern cultivated apples, however, the relative contribution of the two wild progenitors to cultivated apples varies depending on varieties.
Line 72-73, shouldn’t the nuclear genome be more important than the organelle genomes?
Line 98-100, again, much of this has been addressed in previous studies.
Line 111, I don’t understand why the authors sampled multiple individuals of the same cultivar, since apple tree is propagated through grafting, different individuals should be genetically similar.
Line 117 these are not 24 “varieties”, they are 24 “accessions”.
Line 120, there are apple chloroplast genomes published already, why did the authors choose Pyracantha fortuneana as the reference?
Line 172-175, accession numbers should be provided.
Line 270, it is inaccurate to describe it as a “new branch”


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: COMPLETE CHLOROPLAST GENOME STUDIES OF DIFFERENT APPLE VARIETIES INDICATED THE ORIGIN OF MODERN CULTIVATED APPLES FROM MALUS SIEVERSII AND MALUS SYLVESTRIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript "Complete chloroplast genomes studies of different apple varieties indicated modern cultivated apples originate from Malus sieversii and Malus sylvestris" submitted to PeerJ journal. In this study, complete chloroplast genomes of 24 apple varieties by Next-generation sequencing technology were obtained, and compared with the wild species M. sylvestris and M. sieversii. The similarities and differences of chloroplast genomes of Malus and the genetic relationship between cultivated varieties and wild species were revealed. Several mutation hotspot regions were detected, and phylogenetic analysis revealed that M. sylvestris and M. sieversii were the ancestor species of cultivated apple. These results provide effective information for solving specific molecular markers in taxonomic research, also provide a certain reference value for resources protection and new varieties breeding. The manuscript is clear, substantial and well organized. However, I have some concerns, which need to be addressed before considering being accepted for publication.

1.	In the part of Materials & Methods, why this paper used Pyracantha fortuneana (MH890570.1) as reference using the software NOVOPlasty, whereas not use M. sylvestris (MK434924.1) or M.sieversii(MK434920)?
2.	In line 120-121, please describe the annotation software used in detail. In general, Sequin is not an annotation software.
3.	In line 141, Please describe parameters of MISA software.
4.	In line 162-168, to identify single nucleotide polymorphism (SNP) or short insertion/deletions (indels), you used which as a reference genome?
5.	In line188, please replace “160067-160069” with “160067-160069 bp”.
6.	In line192-193, the author said “M.sieversii and M. sylvestris contained 128 genes, including 83 CDS genes, 35 transfer RNA and eight ribosomal RNA genes.”. However, 83 CDS genes +35 transfer RNA +8 ribosomal RNA genes =126 genes. The same error appears on lines 193-194. Please check it.
7.	In line 210, The rpl16 gene should be italicized.
8.	In line 260, “non coding region” should be unified.
9.	Almost all Figures are not clear, except for figure 2 and 7, please change the picture with a higher definition.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: COMPLETE CHLOROPLAST GENOME STUDIES OF DIFFERENT APPLE VARIETIES INDICATED THE ORIGIN OF MODERN CULTIVATED APPLES FROM MALUS SIEVERSII AND MALUS SYLVESTRIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: English/text : The ms is overall difficult to read. Work to streamline the ms is needed to understand the questions asked and in particular data used. The introduction should better reflect the state of the art (at least remove the contradictory ideas developed in different paragraphs, see comments below).

Figures :
-The figures are numerous (7!) and some of them are difficult to read on my computer (e.g. Figure 1 and 5).
-the legend should be self-explanatory (e.g. avoid abbreviations, e.g.,  in Figure 2 “LSC, SSC and IR” or Figure 7, precise which “Bayesian” inference was used)
-sometimes it is complex to know with which data the Figures were generated, to be precised

Tables: Tables should be self-explanatory, e.g.
Table 1: put the meaning of each header below the table (e.g. what does mean “dimension”?)
Table 2: put the meaning of each header below the table or in the legend (e.g. what does mean “LSC”)?
Tables 3 and 5: could be moved in supplementary material.
Experimental design: The research question is meaningful, but the authors explained that there is an identified knowledge gap on the contribution of wild apple species to the cultivated apple genome, which I do not fully agree with, see my comments below. In addition, the samples used in this study are not fitting to test the hypotheses the authors would like to test. Indeed, using one reference sample of each of the two wild contributors is not sufficient to make solid conclusions on the contributions of wild species to crop genomes. Turning the ms/hypothesis towards the comparative genomics of chloroplast genome among wild and cultivated apples should be more appropriate. Eventually, I found the sequencing method and the way in which they “assembled” the genomes (if it is what has been done?) unclear.
Validity of the findings: Because of the comments above I cannot validate or not the findings.
Additional comments: Li, Ding et al compare the genome structures of the chloroplast (cp) of Malus sieversii and M. sylvestris, the two main wild contributors to the cultivated apple genome (Malus domestica), with the cp genomes of four cultivated apple varieties. Albeit I found the question interesting, I couldn’t understand what the authors tried to communicate in several parts of the ms. See below my comments. Some part of the methodology is often unclear and sequencing technology and methods to extract the sequence information (assembly? Or mapping?) used are not described. I therefore cannot agree or not with the conclusions of the authors as I miss information.

*MAJOR COMMENTS

-I couldn’t understand what the authors tried to communicate in several parts of the ms, please see comments below;
-The authors talk about “Next generation sequencing” without explaining clearly the technique used. Along the ms, it is not clear which data they generated, and which data they retrieved, see comments below;
-In the introduction the authors insist on the fact that there are still debates on the contributions of different wild apple species (initial domestication or hybridisation, lines 46-50 and 66-67) to the cultivated apple genome, but I do not fully agree with: there are a lot of consistent evidences that show that M. sieversii is the initial ancestor, and M. sylvestris has contributed through recent wild-to-crop introgressions.
-In addition, the samples used for answering the question are not appropriate, they used four cultivars of M. domestica (and 1 to 2 repeats per cultivar from different locations, Table 1), and only two already available genomes of sieversii and sylvestris. In addition, the authors do not show how the use of data  (M. sieversii and M. sylvestris) that were not generated with the same sequencing techniques as their genomes (I presume?), could impact (or not) their results.

*MINOR COMMENTS

Line 39: correct “Goldie Delicious” by“Golden Delicious”
Lines 46-50 : this sentence sounds surprising, we now have a good idea of the origin of the apple and the role of the different wild species (see Duan et al 2017, Sun et al. 2021, Cornille et al 2012, Migicovsky 2020). This sentence also stands in contrast with the next paragraph. Please rephrase and add citations.
Lines 66-67: this statement sounds in contradiction with the previous sentence explaining what is known about the contribution of different wild apple species to the cultivated apple genomes. Please rephrase.
Line 79: the authors use “cp” from there in the ms, but never explain this term as referred to as “chloroplast”. This should be clearly stated.
Line 98 “So who are the wild ancestors of cultivated apples in the process of the  origin and evolution of cultivated apples? Is the origin of cultivated apple direct domestication or hybrid origin?” The authors cannot answer specifically to this question only using cp genomes, and with only one sample of each wild contributor.  I would remove or rephrase this sentence. In addition, some studies already investigated these questions, so the authors should adapt their questions regarding previous work done.
Line 103 : “In this study, 24 genomic sequences of four different Malus germplasm were deeply sequenced.” Unclear, what do the authors mean by “deeply” sequence?
Line 104 “Through the detection of DNA variation at the genomic level” pleonasm, remove “at the genomic level”
Line 118: Detailed the sequencing techniques, how the libraries were prepared, and DNA extract? What are the differences in the way in which the M. sieversii and M. sylvestris genomes were generated?
Line 120: precise why Pyracantha fortuneana has been used as reference.
Line 125: the authors used a lot “LSC, SSC, IRS” as abbreviations for the three regions, but did not introduce them before. They should be introduced before for non experts of chloroplastic genomes.
Line 155: Variation analyses of what ? Precise
Line 156: a word is missing after “conserved”, precise
Line 170 “this cp genome phylogenetic placement in the Malus genus”, weird wording, please rephrase.
Line 177: precise which “ Bayesian method”, and explain quickly the method for non-expert (and if you used MCMC, precise the burin and number of MCMC steps, and additional basic parameters).
Line 193: “in cultivated apple,”, unclear, in the four cultivars you mean? Precise
Line 102 to 205: this paragraph is very descriptive and redundant with Table 2? To shorten?
Line 268: remove “that the evolutionary tree had”
Line 278: “assembled”: really? I do not see how the assembly was performed? Explanations in the “methods” part are needed.

I did not continue beyond the “results” part, as I need more clarification in Mat&Meth to go further.

*NOTES ABOUT English/grammar typos (they are likely not exhaustives);
Line 50-51 “To have a better comprehends the origin of cultivated apple and its relationship with main wild resources, many”, correct the sentence
Line 55: “howere” correct by “However”
Line 60: “contended that The”, remove capital letter
Line 68-73: this sentence needs to be correct for English + grammar (“genome level traced ancestry”, “it”, to what refers to “it”: unclear, researches without “es”…)
Line 83 “geneme” correct by “genomes”
Line 84 correct “have” by “has”
Line 86: problem in the author’s name “SSvetlana”
Line 88: miss a space between apple and M. “apple(M. sieversii”
Line 89 “the contribution of wild species to domesticated maternal contribution” unclear sentence
Line 92-93: “In addition, due to complete cp genome analysis can provide more genetic information than gene fragments” Pb in the sentence?
Line 98: correct “who” by “which”
Line 135: add a space between repeat and SSRs “s(‘
Line 144: remove the dot to the title, and U in lower case
Line 187: put results in the past tense
Line 192: add a space between M. and sieversii
Line 271: remove “It was obvious”
Line 272: correct “Goldie” by “Golden”.
Along the ms : problem with the references : there is often a space missing between the reference in bracket and the text.


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: COMPLETE CHLOROPLAST GENOME STUDIES OF DIFFERENT APPLE VARIETIES INDICATED THE ORIGIN OF MODERN CULTIVATED APPLES FROM MALUS SIEVERSII AND MALUS SYLVESTRIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript has been much improved on both languish and content. Most of my previous concerns have been addressed and I support the publication of this manuscript on PeerJ as long as the typos are corrected (see below for comments).
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Line 82, change "the genome of" to "the genome and"

Line 137, please correct the typo "genemes"

Line 148, change "A-tail" to "polyA-tail"

Line 149, change "sequencing junction" to "sequencing adapters"

Line 236, correct the typo "consiststed"


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: HIGH-PERFORMANCE PIPELINE FOR MUTMAP AND QTL-SEQ
Review round: 1
Reviewer: 1

Output:
Basic reporting: This MS describes a new pipeline for MutMap and QTL-seq. The contents are concise and clear, and well written in an easy-to-understand manner.
Experimental design: The programs explained are available from GitHub. They are easy to obtain and install.
Validity of the findings: MutMap and other methods developed by the authors are widely used in other studies. It should be beneficial to provide researchers with this type of pipeline.
Additional comments: I have reviewed this MS in another journal. The MS was already revised and I have no further comments. It just deserves 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: HIGH-PERFORMANCE PIPELINE FOR MUTMAP AND QTL-SEQ
Review round: 1
Reviewer: 2

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


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

Input:
Title: HIGH-PERFORMANCE PIPELINE FOR MUTMAP AND QTL-SEQ
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper is brief, succinct and well written but I do have some suggestions for improvement:

1) Line 32 - Please cite the original papers by Giovannoni et al., 1991; Michelmore et al., 1991

2) Line 33 - I recommend changing the language here and in the abstract (ie line 23) to not limit the method to "agronomically important traits". BSA and QTLseq et al is commonly used in many genetic studies across many biological systems. Changing this language to say something like "to identify loci contributing to important phenotypic traits". This will help the paper be more interesting for a broader readership.

3) Line 40- "QTL-seq was adapted from MutMap to identify quantitative trait loci". - but it is also effective and commonly used for mapping single gene traits.

4) Line 43 -
    a) Maybe better to write "algorithm assumed a mostly homozygous genome"
    b) also, briefly describe the issues with heterozygous references in the context of QTLseq
    c) it is unclear from the manuscript if the "modified QTL-seq" is implemented in the new version of the sofware.

5) Line 47-48 - Since the original programs came out and due to the limitations other software has been released to address those limitations suggest adding something like "As such multiple alternative pipelines have been suggested over the years including PyBSASeq, QTLseqr and others well reviewed here: https://doi.org/10.1111/tpj.15646"

Line 64-65 - "In QTL-seq, a ΔSNP-index is calculated by 65 subtracting one SNP-index from the other" might be better as "subtracting the SNP-index of one bulk from the other"

Line 65 - the multiple correction option:  Explain better how this is integrated in to the the software and where it improves the results also on the github page this option is not recommended for first use and is not clear how the species has an impact on multiple correction, please expand the explanation in the paper.
Experimental design: I understand the minimal format for the software note, but there is very limited explanation of the methods used to validate the new software.
A brief methods section could improve the paper for testing the new implementation.

Line 73 is the place to include a description of the the datasets and their location for download - not the figure legend.

Also briefly describe the method for testing exactly what parameters were used and set.
Validity of the findings: Line 75 and 82 - The improvement in speed is essentially due to updates caused by using other more modern software, not due to improvements in the authors method. I would focus on the improved installation experience and user interface rather than speed as a main result. If there are other more novel functions of the software it is worth discussing those in more detail. For example the use of multiple correction and heterozygous genomes? although as a scan the github help it's not clear if that option is actually implemented or not.
Additional comments: Overall a quick piece that will give users of the new pipeline a paper to cite.
The biggest improvement over the previous version of the pipeline is the installation using conda - this will undoubtedly make the software more accessible to users.
I think the methods need to be better described and some other minor suggestions need to be improved and clarified as 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: HIGH-PERFORMANCE PIPELINE FOR MUTMAP AND QTL-SEQ
Review round: 1
Reviewer: 4

Output:
Basic reporting: The manuscript is concise and easy to understand.
Experimental design: The design of the entire study is solid.
Validity of the findings: The authors optimized the MutMap and QTL-seq pipelines they developed previously in the manuscript. Many components of the updated pipelines are able to utilize multiple cores of contemporary CPUs for parallel computing, so their performance increases dramatically. The updated pipelines are more flexible as well and can handle various input files, from raw sequencing data to files generated in the intermediate steps. Additionally, the new pipelines can be installed with a single command; dependence requirements are handled via bioconda so users do not need to fish around the different components of the pipelines. These new pipelines should be useful for the genetic community.
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: HIGH-PERFORMANCE PIPELINE FOR MUTMAP AND QTL-SEQ
Review round: 1
Reviewer: 5

Output:
Basic reporting: Good
Experimental design: Good
Validity of the findings: It is good to see the improved pipelines for MutMap and QTL-seq. The developed pipelines are user-friendly, and their speed is 5-8 times faster than the old-version pipelines. I suggest to accept it.

Minors:
L106: Brassica rapa should be italic.
L107-108: The first letter each word in title should be lower case except the first word.
Figure S1-E, and G: Y-axle should be ΔSNP-index, do not use Delta(SNP-index).
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: SENSITIVITY OF SOIL HYDROGEN UPTAKE TO NATURAL AND MANAGED MOISTURE DYNAMICS IN A SEMIARID URBAN ECOSYSTEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article reports on H2 soil uptake measurements in rain gardens exposed to three water harvesting practices in arid rain gardens. The potential ecological legacy of water harvest practices on the relationship between H2 soil uptake activity and soil moisture was also examined in a laboratory incubation experiment. The experimental design elaborated by the authors was straightforward and elegant, providing tangible results regarding environmental drivers shaping the biological oxidation activity of H2 in soil. This will contribute to the body of knowledge we need to steer soil microbial communities towards the provision of ecosystem services in built and natural environments.

The text is clear and focused and results are aligned with posited hypotheses. The quality of figures, tables and supplementary information is impeccable. The article includes sufficient introduction and background information related to the biological sink of atmospheric H2 and green infrastructure to demonstrate the relevance of the investigation. Citations were carefully selected throughout the manuscript, but two exceptions:

i) Contrary to the information conveyed by the authors in the abstract (L36-38) and the introduction (L140-141), simulation of H2 uptake activity in arid ecosystem caused by soil wetting is not novel. This phenomenon was reported in the pioneering work of Conrad & Seiler in 1985 (J Geophys Res). This should be acknowledged in the text.

ii) Discovery of high-affinity H2 oxidation activity in the dormant life stage of actinobacteria was reported by Constant et al., 2010, Environ. Microbiol. That citation must be included in the text.
Experimental design: In general, methods are described with sufficient detail information to replicate. The renowned expertise of the research group in H2 and trace gases flux measurements is supported by the rigor regarding treatment replication, gas sampling and analyses. I however recommend a few clarifications :

(i) Description of the experimental design is vague in a statistical point of view. I understand that four replicated plots were included in the study, but the text is not explicit regarding their spatial organization. Was a complete random design or a randomized complete block design implemented in the field? What is the distance between the plots? A schematic representation of the field trial would be valuable to address these questions.

(ii) More information is necessary to better distinguish control and passive irrigation treatments. Besides woodchips (passive) and pea gravel (control) substrates on the ground, what are the differences between both treatments?

(iii) More details are necessary to describe the calibration procedure of the reducing compounds photometer gas chromatography system (i.e. standard gas).
Validity of the findings: Besides correlations of H2 soil uptake rate with soil moisture and temperature, this article provides evidence supporting benefits of green infrastructures to alleviate disturbance of soil microbial processes in arid ecosystems. Promotion of H2 soil uptake activity triggered by soil irrigation with grey water is supported by robust experiments and statistical analyzes. Raw data has been provided and they are robust.
Additional comments: I have a few minor comments to conclude my report.

(i) Text commenting correlations between soil temperature (and soil moisture) and H2 fluxes is erroneous – a positive correlation was observed for soil temperature and a negative correlation was observed for soil moisture. Line 283-285 in the results section needs to be modified accordingly.

(ii) Line 308: The citation “Conrad and Seiler, 1985” is not in the reference section.

(iii) L333-335: The authors propose that more frequent soil wetting events in the greywater treatments can lead to shifts in the soil microbiome, nutrient availability, and carbon inputs. Because this statement is supported by unpublished data (V Buzzard, 2021, unpublished data), I expect the authors are well-positioned to propose potential mechanisms explaining benefits of grey water on H2 soil uptake activity before the monsoon precipitations. Are the authors already aware of microbial successions or enrichment of HA-HOB triggered by irrigation treatments?


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

Input:
Title: SENSITIVITY OF SOIL HYDROGEN UPTAKE TO NATURAL AND MANAGED MOISTURE DYNAMICS IN A SEMIARID URBAN ECOSYSTEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study, Buzzard et al. present observations of H2 fluxes in both managed (Green infrastructure) and unmanaged soil in a semi-arid region.
Both the experimental design and the presentation of the results are sound. This study is suitable for publications provided the following comments  are addressed.

line 67
It is estimated that a quarter of H2 emissions are from human activity, disproportionately impacting atmospheric H2 concentrations and the H2 cycle of urban ecosystems.

How did the authors come to their estimate?
This seems a bit low to me. Ehhalt mentions 50% of H2 production is anthropogenic. If we add fossil fuel, anthropogenic activities would contribute >40% to H2 sources.

line 69
I do not understand why understanding the h2 uptake in urban landscape will significantly alter our understanding of the H2 budget. how much land does urban landscape cover?

line 169
could the authors comment on the impact of these different surface layers on H2 uptake.

line 243 - could you indicate which assumptions are not met.

line 250.
I suggest adding a table summarizing the meteorological conditions during the three sampling periods as well as over the last 10 days preceding the sampling. This table should also include information about the soil moisture and soil  temperature.

It would also be useful to show the timeseries for soil moisture and soil temperature for the different treatments in Fig. 1.

line 263  and elsewhere

I recommend rephrasing the presentation of the raw statistical output of ANOVA in the text.
For instance, line 263 could be rewritten as

We find that the effect of the  green infrastructure (GI) treatment and the
increased wetting events observed during the monsoon season are significant at the 0.05 level and large.

The ges threshold for large/medium/small effects should  be indicated in the method section and in Table 1 (similar to the 0.05 threshold used by the authors for the p-value).

line 264 please also report the partial ges values.

line 265 This seems to convey the same results as the previous sentence (same statistics). Please clarify or remove.

line 277

please indicate moisture level for each manipulation.

line 312

the authors imply that the diffusion limited regime for H2 uptake occurs only during soil flooding. This seems at odds with previous studies which indicate that the diffusion limited regime is quite prevalent. Please clarify.

line 322

the decrease of H2 soil flux with temperature is at odds with the reanalysis of previous observations presented in  Ehhalt et al. (2011) DOI: 10.1111/j.1600-0889.2011.00581.x which showed a clear increase of HOB activity with temperature for temperature <30C.
It is my understanding that following these results, recent modeling studies have assumed that HA-HOB activity increases with T.

Thus  it is important that the authors clarify why their results are different from  previously derived T sensitivity of HA-HOB. In addition they need to discuss  the potential implications of their results for our understanding of the distribution of H2 uptake and its response to future environmental changes. In particular, it seems that the increase in h2 uptake with climate change that is discussed in line 344 based on Paulot et al. (2021) is not supported by the authors' results.

Minor

line 56

Suggest rephrasing to clarify the  connection with GI. Here is a suggestion

The more continuous H2 uptake associated with GI may help reduce the impacts of drought on H2 cycling in semiarid urban ecosystems

line 247

affect -> effect of

line 313

"consistent with research showing that H2 uptake is driven by low moisture levels that activate soil microbes"

I would suggest rephrasing to clarify that under very low soil moisture HOB activity is suppressed.

Fig. 1:
please indicate averaging time period

Fig. 2:
Please use the same acronym in the text (ges) and int the caption (eta_g^2) to refer to the generalized eta square.

Fig. 4 indicate sign convention for H2 flux (atmosphere->soil >0) in caption
Experimental design: No issue
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: SENSITIVITY OF SOIL HYDROGEN UPTAKE TO NATURAL AND MANAGED MOISTURE DYNAMICS IN A SEMIARID URBAN ECOSYSTEM
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed most of my comments.
However, as mentioned in my comments to the first draft, the sensitivity to temperature reported in this study differs from the published literature. The authors need to address this difference in the revised manuscript before I can recommend publication.

Major comments:

1) line 52, line 370 and line 492 ; Fig. 4

the R2 between H2 uptake and temperature reported in the abstract has changed from 0.244 to 0.105.   Was this a typo in the original manuscript?

I would suggest reporting the correlation rather than R2. The sign of the correlation is important and seems to be different from previous studies. This also applies to line 370.

As mentioned in my previous comments, the sign of the correlation with temperature is at odds with previous studies, which show an increase in soil H2 uptake over the T range considered here (see Fig. 1 of Ehhalt (2013)). It is important that the authors discuss this important difference.
Ehhalt (2013) provides a functional form for the dependence of H2 uptake to temperature. Could the authors add this to Fig. 4a?

Such comparison would also be useful for soil moisture (see Fig. 5 of Ehhalt (2013) or the functional form presented by Yashiro (2011) or Bertagni (2021))

3) Line 392. I suggest that the authors revise the text to better convey that H2 diffusivity into soil is reduced by soil moisture.  The text reads as if moisture only impedes H2 uptake under flooded question, which is at odds with the published literature (Yashiro, 2011 ; Ehhalt 2013 ; Bertagni 2021)

Minor comments

1) line 39

"Unlike mesic ecosystems, H2 uptake in arid ecosystems rarely experience diffusion limitation due to water saturated soils and has been shown to increase with soil wetting in arid ecosystems"

This sentence is confusing. Suggests rephrasing

2) Line  109

Could the authors provide the criteria used to define arid and semi-arid regions?
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: SENSITIVITY OF SOIL HYDROGEN UPTAKE TO NATURAL AND MANAGED MOISTURE DYNAMICS IN A SEMIARID URBAN ECOSYSTEM
Review round: 3
Reviewer: 1

Output:
Basic reporting: I am happy to recommend publication.
See two minor comments below
line 37. remove "limited"
line 49. Please define notation used for correlation, i.e. I believe 62 refers to the number of measurements.
Experimental design: n/a
Validity of the findings: n/a
Additional comments: n/a


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 COMPARATIVE STUDY OF THE CAPABILITY OF MSCS ISOLATED FROM DIFFERENT HUMAN TISSUE SOURCES TO DIFFERENTIATE INTO NEURONAL STEM CELLS AND DOPAMINERGIC-LIKE CELLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written in the main. The introduction is logical and leads the reader though to the main aims. There are a few points which I think need clarification. For example, giving the use of iPSCs negatively, when they are actually an excellent opportunity to replace or compliment the use of MSCs. Perhaps to strengthen their example, they could mention the use of retroviruses to generate iPSCs.

The description of differentiation techniques used to direct down a neuronal lineage is well written, but may be better in table form, as it reads rather like a list at present. A table will let readers compare the differs methods use and the the different cell types used.
Experimental design: The methods are clear and concise. Can the authors please clarify the number of donors and which tissue samples were used from donors, as presently it is not clear (e.g. lines 107 and 109). Are the authors aware of the donar age, gender and medical history - these often bias results (but it is understandable if this is unknown)?

The differentiation media used was commercial rather than in-house (it is a shame not to see the ingredients used to initiate differentiation).  The differentiation analysis was routine, with correct markers etc, whilst cell proliferation used the MTT assay (which actually measures cell metabolism).
Validity of the findings: The results are mainly well presented with clearly annotated figures and figure legends.

It may have been interesting to collage some images from figure 1 (differentiation staining) to generate a graph so indicate any differences, rather than just rely on a single representative image.

For figure 2, can the authors (i) have the 24 hours on the same scale as the subsequent two time points (currently it is a smaller scale), and (ii) reduce the scale size of the MTT graphs (so they do not appear stretched vertically)?

Figure 4 is nicely presented - but maybe keep the colour scheme for BM, AT & WJ the same throughout the restyle section (rather than changing the colours with each figure)? This makes it a more consistent read. Also, were stats on the image analysis needed in the graphs (n=3 experiments, but they need to qualify how many microscope images were taken to get the graph data).

Figure 5 & 6 - again, nicely presented, but similar to figure 4 points above.
Additional comments: The results are relatively interesting, but quite limited in scope. Neuronal differentiation via dual SMAD inhibitors is fine, but are there other methods which could be compared and the best method optimised?

There is plenty of opportunity to further test the neuronal differentiation, aside from morphology (light microscopy - any chance to quantify the cell extensions etc graphically?) and neuronal cell markers, to define better the various MSC's ability to generate functional cells. Line 282-285 summarises this - that these cells are intermediate, but further differentiation should be studied - why not in this paper, taking it our longer term?

Also, it would be nice to see an explanation of why there is much higher levels of nestin, PAX6, LMX and Sox2 gene expression with WJ, compared, for example, to BM. However when looking at the corresponding immunofluorescence, these is not observed (the levels are the same).

The conclusion that WJ differentiates better into neuronal-like cells is a bit limited, whilst neuronal markers (immunofluorescence) do seem a bit higher, there are no stats of significance attributed to the immune graphs to clarify any difference observed. Also, as this is a key outcome, It is a shame not to see more protein data, such as a Western blot to bearer identify this.


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 COMPARATIVE STUDY OF THE CAPABILITY OF MSCS ISOLATED FROM DIFFERENT HUMAN TISSUE SOURCES TO DIFFERENTIATE INTO NEURONAL STEM CELLS AND DOPAMINERGIC-LIKE CELLS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Resubmission - the paper it well written on the whole. Minor text corrections have been made.
Experimental design: Resubmission - all fine. However please do date state the donor age and gender (in the resubmission comments authors state that they can find this in the records easily).
Validity of the findings: Resubmission - again, this is fine. Suggested extra work has not been carried out (mainly due to funding and covid) - this is unfortunate as it would significantly enhance the paper.
Additional comments: Resubmission - the authors have addressed some items, but missed some extra work. Please add the donor age and gender (as 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: AN ODE MODEL OF YAWS ELIMINATION IN LIHIR ISLAND, PAPUA NEW GUINEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors proposed and analyzed a deterministic model for yaws transmission and control. Yaws was one of the first diseases targeted for eradication in the 1950s. The World Health Organization (WHO) renewed global efforts to eradicate yaws by 2020 in 2012. Despite this, the disease has been one of the most neglected of al the neglected tropical diseases (NTDs). After carefully going through the manuscript I believe the article can be considered for publication if the authors incorporate the following suggestions:

On page 2 (Line 71-75): More detail is required. It is not clear what gap this study is intending to fill. You need to highlight aspects or factors that you incorporated in your framework that makes it unique, reasonably accurate and realistic.  I suggest that some of the information which is appearing in the Discussion section about the uniqueness of the proposed model and those in literature should also be in this paragraph.
Experimental design: The proposed model is fine, however the more analysis which leads to more essential results is required.
Validity of the findings: A) The main outcome from this study was to determine threshold conditions for yaws eradication through using active and passive case detection and prompt treatment. In particular, individuals in compartments $E,$  $Y_1$, $L_1$, $Y_2,$ $ L_2$ and $Y_3,$ where assumed to receive treatment. Considering that this disease affects individuals living in poorest communities with little or no access to health how feasible will be it to detect individuals in $E,$ $L_1,$ and $L_2$ under both strategies TTT and TCT?

B) Based on item  (A), I suggest that more analysis be done on the proposed model in order to determine different threshold values for disease eradication under different circumstances. After that a comprehensive comparison on the outcomes can be made.  For example, one will be left wondering how long it will take to eradicate the disease when only active cases are considered for treatment, since the disease is predominant in poorest communities. By merely comparing the treatment coverage for TCT and TTT one will not be surprised by the outcomes contained in the article.
Additional comments: A) What are the implications of the relapsing individuals on both short and long-term dynamics of the disease?

B) The main results  of the manuscript are based on evaluating $R_0$ and one is left wondering the implications of the initial population levels on both short and long-term dynamics of the disease?


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: AN ODE MODEL OF YAWS ELIMINATION IN LIHIR ISLAND, PAPUA NEW GUINEA
Review round: 1
Reviewer: 2

Output:
Basic reporting: --
Review comments for manuscript ID: "66746-v0", entitled "An ODE model of yaws elimination in Lihir Island, Papua New Guinea" of the journal "PeerJ".

--
General:

Kimball et al. conducted a modeling analysis to investigate the transmission dynamics of yaws in Lihir Island, Papua New Guinea. The authors developed a compartmental ODE model of yaws transmission and treatment for these scenarios. The qualitative stability of the model was analyzed and computed for disease-free and endemic equilibria. They calibrated the model and validated its predictions on the data from Lihir Island in Papua New Guinea. They demonstrated that the total targeted treatment (TTT) strategy is efficient in preventing outbreaks. However, due to the presence of asymptomatic latent cases, TTT will not eliminate yaws within a reasonable time frame. To achieve the 2030 eradication target for yaws elimination, the authors suggested that total community treatment (TCT) should be applied instead.

This is a nice and well-conducted modelling study, which addressed an epidemiological problem of timely and public health importance. I consider their method reasonable and sophisticated, and the results are presented logically and consistently. The analyzing outcomes support the main results. Thus, I would recommend it for publishing after the following concerns are considered.

--
Comments:

I suggest the authors give brief epidemiological background on the yaws transmission in the introduction section, like mention how many people get infected or die due to the disease each year in Guinea and globally.

--The method used for some parameter estimation is not very clear. I suggest the authors should explicitly state how they estimate some parameters of the model? To allow others to adopt a similar technique in other settings.

 --I appreciate the authors have done a very nice discussion, mainly focusing on the technical part. I would be more appreciative if the author could elaborate on the epidemiology and public health sides.

--Limitations of the study should be clearly stated in the discussion section. Also, I wonder what would be a possible epidemiological or clinical implication of the re-infected on the overall transmission scenarios? Could the authors comment on this based on the proposed model?

--The data-fitting result of the latent yaws using the proposed model is not well fitted? Any explanation for that?

--Did the authors attempt to prove the global asymptotic stability of the endemic equilibrium? If not, I suggest the authors should do that.
Experimental design: See my basic reporting comments
Validity of the findings: See my basic reporting comments
Additional comments: See my basic reporting 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: AN ODE MODEL OF YAWS ELIMINATION IN LIHIR ISLAND, PAPUA NEW GUINEA
Review round: 1
Reviewer: 3

Output:
Basic reporting: There is still some room for authors to improve their mathematical language.(for example, "solved the system for DFE and EE", "created the compartmental model")
Experimental design: I have several major concerns in methodology.
First, for the population that progress from Y1 to L1 and from Y1 to Y2, the model used "lambda_1" for both of them. Does it mean that the time that progress from Y1 to L1 is the same as the time that progress from Y1 to Y2? I have similar concern for lambda_2, rho_1 and rho_2. For the use of "rho_2", can I assume that: during the 2nd latent period, on average, it takes the same length of time for them to "relapse into secondary yaws" and "develop into late yaws".

I noticed that values of these parameters were obtained directly from previous studies and authors' assumption except the transmission rate beta. The values of parameter that are estimated by fitting data in reality certainly can improve validity in this study. Unfortunately, this part was not stated clearly in the main part of this manuscript. For example, the type, source, time, location and availability of data should be reported in METHODS. Also, how did you fit the model to data and what is the fitting algorithm applied here should also be reported clearly.

There are some parameters who were assigned values very arbitrarily.  For example, (page 3, line 94) the assumed value of tau_L2 is "0.01" just because it is assumed that TTT strategy does not find too many secondary latent case. In fact, "0.01" here is equivalent to say that, on average, it takes 100 months to treat a L2 individual. Is that something assumed by authors? Will the results of this study keep unchanged if we assign another number to this parameter?
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: AN ODE MODEL OF YAWS ELIMINATION IN LIHIR ISLAND, PAPUA NEW GUINEA
Review round: 2
Reviewer: 1

Output:
Basic reporting: I happy with the changes made by the authors. I believe a number of issues that were not clear  in the original draft are now clear.
Experimental design: More clarity has been provided by the authors regarding  their model formulation.
Validity of the findings: Additional results have been added  as well as additional explanations.
Additional comments: Overall, I am happy with the revised manuscript.


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

Input:
Title: AN ODE MODEL OF YAWS ELIMINATION IN LIHIR ISLAND, PAPUA NEW GUINEA
Review round: 2
Reviewer: 2

Output:
Basic reporting: --
Review comments for manuscript ID: "66746-v1", entitled "An ODE model of yaws elimination in Lihir Island, Papua New Guinea" of the journal "PeerJ".

 ---
Comments:
I appreciate that the authors have carefully addressed all the issues raised by the reviewers that might improve the manuscript from its initial draft. The paper has improved significantly with well-conducted modelling analyses, which addressed yaws epidemiological problems in Lihir Island, Papua New Guinea. The method was reasonable and sound, and the results were presented logically and consistently. The analyzing outcomes support the main results with biologically and clinically appropriate settings.
Thus, after the following comments are considered, I recommend publishing this work in the prestigious journal of "PeerJ".

--I suggest the authors estimate/plot the confidence interval in figure 3, which could give a more reasonable result.

--Regarding the proof of the global asymptotic stability of the endemic equilibrium, the authors claimed that they did not succeed. Though not necessary in the current work, the authors can use a similar approach as employed in the following works:
1) La Salle JP. The stability of dynamical systems. Society for Industrial and Applied Mathematics; 1976.
2) Yang C, Wang X, Gao D, Wang J. Impact of awareness programs on cholera dynamics: two modeling approaches. Bulletin of mathematical biology. 2017;79(9):2109-31.
3) Roop-O P, Chinviriyasit W, Chinviriyasit S. The effect of incidence function in backward bifurcation for malaria model with temporary immunity. Mathematical biosciences. 2015;265:47-64.

--Finally, I also suggest rigorous proofread of the manuscript.
Experimental design: see, basic reporting comments
Validity of the findings: see, basic reporting comments
Additional comments: None


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

Input:
Title: AN ODE MODEL OF YAWS ELIMINATION IN LIHIR ISLAND, PAPUA NEW GUINEA
Review round: 3
Reviewer: 1

Output:
Basic reporting: ---
R2: Review comments for manuscript ID: “peerj-66746”, entitled “An ODE model of yaws elimination in Lihir Island, Papua New Guinea” of the journal “PeerJ”.

---
General:
I appreciate that the authors have carefully addressed all the issues raised by the reviewers that might improve the manuscript from its initial draft. I think the paper is recommended for publication after consideration of some minor comments below, which needs no further revision.

---
Comments:
--Regarding the GAS proof using the LaSalle Invariant Principle, since the authors did not succeed with the proof, I think there is no need in defining the Lyapunov function (in the added paragraph). Numerical simulations would be sufficient. However, the authors can still cite LaSalle and Yang et al.’s works.
Experimental design: See, basic reporting comments.
Validity of the findings: See, basic reporting comments.
Additional comments: See, basic reporting 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: INHIBITION OF CONNEXIN 43 REVERSES OX-LDL-MEDIATED INHIBITION OF AUTOPHAGY IN VSMC BY INHIBITING THE PI3K/AKT/MTOR SIGNALING PATHWAY
Review round: 1
Reviewer: 1

Output:
Basic reporting: In the manuscript entitled “Connexin 43 participates in ox-LDL-induced autophagy in vascular smooth muscle cells through the PI3K/Akt/mTOR signaling pathway”, by Xuqin Qin and colleagues, it is claimed that Ox-LDL-induced autophagy in VSMC is modulated by Cx43, through the PI3K/Akt/mTOR pathway. It is shown that Gap26, a Cx mimetic peptide corresponding to aa sequence in the first extracellular loop, which is used as gap junction blocker, prevents autophagy inhibition and foam cells formation induced by Ox-LDL. Moreover, it is suggested tht Gap26 effect on autophagy relies on theinhibition of PI3K/Akt/mTOR pathway. This study is biologically interesting and clinically relevant since the unveiling of the mechanisms and signals underlying foam cells formation can open new avenues to design innovative therapeutic approaches against atherosclerosis.
However, the manuscript presents some flaws and weaknesses that limit its novelty and conclusions robustness. Indeed, the conclusions of this study are not supported by the results, which makes it very speculative.
The text seems needs a thorough revisions, in terms of both form and content. Indeed, the sentences are often vague, resorting to terms like “autophagy regulation”, with no description if there is an activation or inhibition of autophagy.
Experimental design: . It is unclear the meaning of “Gap junction channels consist of two corresponding connexins”
. Hemichannels also allow the exchange of molecules between the cytoplasm and extracellular medium.
. Many times, the references used are not appropriate to sustain the sentence. For example, Ref#20 is not the best one to refer to other functions of Cx.
. It should be clearly mentioned that Cx43 can be a substrate of autophagy or a regulatory element of this pathway. This is of utmost importance in the context of this work.
. In M&M section, line 100-105, the two sentences seem similar.
. When using cell cultures, the term “administered” should be replaced by “incubated” or “treated”; also the terms “intervened” or “inoculated” do not sound suitable when referring to cell treatment or seeding.
. The concepts “randomly divided” or “evenly spread” are not appropriate for cell cultures
. The LY294002 group is missing
. Information such as “the six-well plate was removed from the incubator, and the culture medium was discarded” is useless in a scientific publication
. In IF analysis, what the authors mean with  “the samples were sealed”?
. the concentration of reagents (PFA, Triton) should be provided in percentage”
. on the other hand, information about TEM analysis is very minimalist; more technical details are needed
. The Oil red O staining protocol description is not helpful; it should be mentioned that was performed according to the manufacturer.
. The results in Fig. 1 and 2 are not new
. To be more accurate, when referring to protein changes, in this context should be used “protein levels” instead of “protein expression.
. Despite the accumulation of mRNA, how can the authors discard the possibility that Cx43 accumulation is not due to autophagy inhibition (Fig.2)? Autophagy flow should be assessed.
. The legend to Fig.2 should include the concentration and time of incubation with OxLDL.
. the IF images are of bad quality, being difficult to discern any change in Cx43 localization. The most important aspect in Cx43 staining should be its localization to the plasma membrane, which is not visible. IF is a technique mainly to assess subcellular distribution and not for protein quantification
. some explanation should be given concerning the characteristics and action of Gap26 and LY294002, as well as the rationale for their use
. The mimetic peptide Gap26 is not a Cx43 blocker; to be more accurate, Gap26 modulates Cx43 channel activity. Are Cx43 levels affected by Gap26?
. the TEM images are of bad quality and not convincing concerning the accumulation of autophagosomes (the use of arrows is not enough); scale bars are missing
. In order to assess the impact/ role of Cx43, the protein should be silenced; when using Gap26 only channel activity is being affected.
. The impact of LY294002 in autophagy has been widely reported
. When referring to protein phosphorylation changes, the term “protein expression” should not be used. The protein expression cannot be affected (protein levels are the same) but the protein undergoes a PTM.
. In line 226, explain the sentence “This finding may be associated with the degradation of internalized Cx43 via activated autophagy”
. In line 226, there is likely a mistake, and “higher” should be replaced by “lower”
Validity of the findings: In general, the results do not 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: INHIBITION OF CONNEXIN 43 REVERSES OX-LDL-MEDIATED INHIBITION OF AUTOPHAGY IN VSMC BY INHIBITING THE PI3K/AKT/MTOR SIGNALING PATHWAY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Title of this article should be absolutely revised because the authors demonstrated that blockage of Connexin 43 reversed the autophagy inhibition by ox-LDL. Therefore, the title talking about "Connexin 43 participates in ox-LDL-induced autophagy in VSMCs..." are mis-leading to the audience. I am so confused when reading the whole article.
Accordingly, the title should be revised as "Inhibition of connexin 43 reverses ox-LDL-mediated inhibition of autophagy in VSMCs.....".

Abstract should be revised as well, especially in the conclusion, because "....by mediating the PI3K/AKT/mTOR signaling pathways" are absolutely wrong, you should say "....by inhibition of  the PI3K/AKT/mTOR signaling pathways.

English writing should be polished further by native speaker, especially in results part.
Experimental design: The overall experimental design is fine, but the antibodies used in Materials and methods got something wrong. What is anti-Desmin-actin? why need to add "actin" after all name of antibodies?
Validity of the findings: In the results part, the first subheading "Ox-LDL increased p62 protein expression and decreased Beclin-1 protein..." mean nothings. I would suggest to simply the subheading as "Ox-LDL inhibits autophagy induction in VSMCs via downregulation of autophagy-related protein".

In line 209, "To investigate the effect of Cx43 on foam transformation...." should be revised as " To investigate the effect of Cx43 inhibition on form transformation....".

In line 211-213, "These findings is suggested that ..." should be rewritten as "These findings suggested that blocking of Cx43 inhibited the ox-LDL-induced lipid droplet accumulation in VSMCs and suppressed VSMCs foam formation".

In line 217, authors should firstly introduce LY294002 as PI3K inhibitor, otherwise the reader don't know why you use this inhibitor for your assay.

In line 225-226, Cx43 expression in the LY294002 inhibitor group was "lower" instead of "higher" than that in the ox-LDL group.

In line 226-227. The last sentence "This finding may be associated with the degradation of internalized Cx43 via activated autophagy" should be revised because you only demonstrated that Cx43 expression is depended on PI3K signaling by using PI3K inhibitor, how did you show the Cx43 is degraded due to autophagy? Any experimental works to show autophagic degradation of Cx43?
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: INHIBITION OF CONNEXIN 43 REVERSES OX-LDL-MEDIATED INHIBITION OF AUTOPHAGY IN VSMC BY INHIBITING THE PI3K/AKT/MTOR SIGNALING PATHWAY
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Please see the attached PDF


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: INHIBITION OF CONNEXIN 43 REVERSES OX-LDL-MEDIATED INHIBITION OF AUTOPHAGY IN VSMC BY INHIBITING THE PI3K/AKT/MTOR SIGNALING PATHWAY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have introduced some changes to the text that helped to improve its quality. However, key experiments that were requested, to support the conclusions were not performed. It is said that these experiments are planned for upcoming studies.
Experimental design: N/A
Validity of the findings: With the lack of additional experiments, namely the silencing of Cx43, some of the conclusions cannot be taken. The use of Gap26 cannot be used as a tool to downregulate Cx43
Additional comments: N/A


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: INHIBITION OF CONNEXIN 43 REVERSES OX-LDL-MEDIATED INHIBITION OF AUTOPHAGY IN VSMC BY INHIBITING THE PI3K/AKT/MTOR SIGNALING PATHWAY
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I am very satisfied with the revisions and recommend this manuscript for publication as is.


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: ONYX DISPARAMPHIS SP. N. (NEMATODA, DESMODORIDA) FROM SOUTH KOREA WITH A TAXONOMIC REVIEW OF THE GENUS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comments here.
Experimental design: No comments here.
Validity of the findings: No comments here.
Additional comments: Line 24: "relatively tail shape" is grammatically incorrect,, something is missing.
Line 30: "posterior bodies" replace with "posterior body sections".
Line 51: "quite few confusions" makes no sense, "few" means "not many" while "quite a few" means "many" so please clarify what is meant here.
Line 52: "growths" replace with "grows"
Line 66: "drawn out" replace with "extracted".
Line 109 and below: Please provide original binomen (basyonym) for all species that were not originally described in Onyx.
Lines 252-255: Description of the female reproductive system is brief and without any details. Please describe every element of female gonads in details. Please also provide detailed close-up drawings of female gonads.
Lines 308-309: Exactly, so please do not follow the same trend and expand the description of a female sexual characters in your descriptions.
Lines 310-317: In my opinion, it makes more sense and it is much easier to use when heads and tails of each species are paired up in the illustrations.
Figure 11: Please give full names for all species in the figure legend.