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 FIELD-BASED INVESTIGATION OF BEHAVIOURAL INTERACTIONS BETWEEN INVASIVE GREEN CRAB (CARCINUS MAENAS), ROCK CRAB (CANCER IRRORATUS), AND AMERICAN LOBSTER (HOMARUS AMERICANUS) IN SOUTHERN NEWFOUNDLAND
Review round: 2
Reviewer: 3

Output:
Basic reporting: I think the study is straightforward, fairly well-written, and provides important information on the potential impact of invasive green crabs on lobsters in a newly invaded region of Newfoundland. My major comment is the lack of information on densities of green crabs in Fortune Bay in the manuscript (the authors suggest it is fairly low, and the data on green crab captures in this manuscript also suggests that it is low), and with low crab abundance, one might suspect that the impact of green crabs may be limited (at this point in the invasion). It would have been interesting to compare Fortune Bay to Placentia Bay where green crab abundances (based on past work by DFO and other published studies) are much higher, and where the expectation for an impact on lobster catches and lobster densities may be greater. In the newly invaded location, lobsters may also be more naive to the green crab, so could the lack of a difference between green crabs and rock crabs be related to that naivety? A comparison with an older invasive population could provide some understanding there too. I think it would be helpful to reflect on this -- is there any evidence that naivety to green crabs could be a factor in community responses to its presence in a system?

Altogether, I think these data should be published, but I do think the study is a lot less impactful within a single bay, versus comparisons to other bays where the green crab is more established and where its potential impacts on native species may be expected to be more pronounced.
Experimental design: Per my comment in the .pdf, I think more up front description of the trap (and it's effectiveness) would have been helpful. Also, information on abundances/densities of green crabs and rock crabs in Fortune Bay would be important to include. Otherwise (aside from my comment above about comparing to a more green crab established bay), I think the experimental design is straightforward.
Validity of the findings: The findings all seem valid based on the current study design.
Additional comments: My other major comments is that I think the discussion is too long and rehashes the results a bit too much at times. I would like to see more synthesis of the results and why they are meaningful. I have other minor comments in the appended .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: THE COMMUNITY COMPOSITION VARIATION OF RUSSULACEAE ASSOCIATED WITH THE QUERCUS MONGOLICA FOREST DURING THE GROWING SEASON AT WUDALIANCHI CITY, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: Original primari research within Aims and Scope of the journal.
Methods described with sufficient detail and information to replicate.
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, & controlled.

Conclusions are well stated, linked to original research question & limited to supporting results.
Additional comments: This study aims at understanding the change in the composition of the Russulaceae fungal community aboveground, in the root and soil during the growing season in a Quercus mongolica forest in Wudalianchi City, China. This study provides an important scientific basis for the further cultivation of the fungi of Russulaceae family.

Here my following minor comments:

Line 41: Replace “ectomycorrhizal” with “mycorrhizal”.
Land plant species can form mutualistic symbiosis with endo- and ectomycorrhizal fungi. Review the whole period (from line 41 to line 45).
Line 51: Author(s) of species name must be provided when the scientific name of any plant or fungal species is first mentioned. Correct through the whole manuscript and Tab. 1. For plant see “The Plant List (http://www.theplantlist.org)”; for fungi see “index fungorum (http://www.indexfungorum.org/names/Names.asp)”.
Lines 96-97: (1) What the…. (2) How abiotic…..(write all lowercase)

Lines 99 and 103: (1) During the… (3) Fungi sporocarp…..(write all lowercase)

Line 109: 48°37′0 W 126°11′0 N, Latitude and longitude are reversed. Correct as follows: Lat 48.616667° Long 126.183333°. 303m??? Is it perhaps 300 m asl?


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

Input:
Title: THE COMMUNITY COMPOSITION VARIATION OF RUSSULACEAE ASSOCIATED WITH THE QUERCUS MONGOLICA FOREST DURING THE GROWING SEASON AT WUDALIANCHI CITY, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language is grammatically fine; however, the clarity of the language is sometimes lacking. An example is line 49 – the current phrasing does not make very much sense.

Title – please define what the growing season is. Is this an assumed fungal growing season or the plants

Line 40- I believe you mean mycorrhizal fungi, not ectomycorrhizal fungi. Only 2% of plants associate with ECM.

Materials and Methods

There is no explicit statement for where the data will be deposited.

Line 113- How far apart were these plots? This is important for interpreting results from Figure 7. Also, what is the plant composition of these forests. Only Quercus?

Line 159- Is there a citation for the “potassium dichromate volumetric method” and other soil biogeochemistry assay approaches?

Line 167- I’m unfamiliar with the term “tags” in amplicon sequence data. Could you explain more?

Line 229- I am surprised that September and October were so sparse. Would we normally expect fruiting at this time (I assume the time period correlates with the fruiting season)?

Line 245- Table is misspelled here.

Line 330- It is still unclear how morphology and sequencing were used to identify sporocarp species. GenBank is an unsuitable reference database for identifying species of Russula in most cases.

Line 336- mycorrhizae or sporocarps or both?

Line 342- Comparisons of phenology between different geographic locations based on month is irrelevant unless it can be demonstrated that the seasonality is similar to your own study site

Line 357- This argument does not make much sense. More likely these species have a very patchy distribution across the root landscape and do not widely explore soil with extramatrical hyphae. See Agerer (2001).

Line 364- How can you say climate impacts the community when you have one study site? Also, the soil does not vary across months…

Taxonomic entities should be italicized in References

Figure 5- Why not have Root and Soil in the legend?
Experimental design: The sampling and statistical approaches are sound. Some of the methodologies should be cited in References for "standard approaches".
Validity of the findings: The study reveals some interesting phenological patterns of above/below-ground diversity of Russulaceae. It seems odd to compare soil characteristics over the span of only 4 months. I’m not convinced that differences recovered within the same forest in soil characteristics are relevant
Additional comments: Xing & Xu et al. present a well-executed study of phenological patterns of Russulaceae in a Quercus dominated forest during the growing season. The study is multifaceted through the use of sporocarp sampling and metagenomic amplicon sequencing to characterize the entire Russulaceae community. Additionally, a suite of biogeochemical analyses and environmental variables were used to compare correlations for community composition. This is an interesting and novel approach.

1.	The largest apparent weakness in this study’s approach is the scope of only looking at a single site over a single fruiting season. Without a multi-year replication of the study or a comparison with another site with different soil characteristics or climate, it is difficult to infer whether these correlations with changing pH or temperature is actually impacting community composition. The study demonstrates the patchiness of Russulaceae distribution, even within the same forest.
2.	I am a little concerned about the transparency of species determination in this study. The authors should explain how in greater detail how morphology and the “Sanger method” was used to identify species. Was there an identity cutoff used for Sanger sequences?


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

Input:
Title: THE COMMUNITY COMPOSITION VARIATION OF RUSSULACEAE ASSOCIATED WITH THE QUERCUS MONGOLICA FOREST DURING THE GROWING SEASON AT WUDALIANCHI CITY, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Professional article structure, figures, tables.
Experimental design: Method described with sufficient detail
Validity of the findings: Conclusions are well stated, linked to original research question & limited to supporting results.
Additional comments: I have no corrections.


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: IN SILICO ANALYSIS OF MAIZE HDACS WITH AN EMPHASIS ON THEIR RESPONSE TO BIOTIC AND ABIOTIC STRESSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	English must be significantly improved throughout the manuscript. There are multiple grammar and spelling errors as well as unclear or complicated sentences that difficult the comprehension of the manuscript as well as the review process. Some examples are in lines 40, 43, 51, 74-77, 126-127, 234-235, 240-241...(but there are more).
2.	The introduction needs more details, specially when describing the existing knowledge about HDACs in maize (lines 67-71). There are also missing works that could enrich this paragraph, including the one by Forestan C et al 2018 as an example.
3.	Authors should also consider to better explain/detailed the existing knowledge to reach a more widespread audience. For example, what is PR1, WRKY38, WKRY62 (line 57) or Pst DC3000 (line 59)? This comment should be considered along the manuscript.
4.	Acronyms should be defined the first time they are used. JA, SA, MeJA, ABA, etc.
5.	Lines 73-75. What do the authors mean with “…characterization of all HDAC genes…”? This sentence could be interpreted as if there is no knowledge about HDACs in maize at all… please revise.
6.	Please revise figure legend of Figure 2.
7.	Line 186: “…hpi after infection…” sounds redundant.
8.	Please revise sentences in lines 213-215.
9.	Line 234: what do the authors mean with “…was almost consistent…”?
10.	Line 235: what do the authors mean with “…gene expression of HDACs were not obvious in maize…”?
11.	Lines 240-241: what do the authors mean with “…can deacetylate the characteristic deacetylation pattern on H4…”?
Experimental design: 12.	An HDAC phylogenetic analysis including several HDAC proteins from A. thaliana, O. sativa and Z. mays has been already performed (Demetriou et al 2009). This work should be discussed. In what the presented manuscript differs from previous work? What do the authors consider that this new analysis brings to light?
13.	It is unclear how authors proceeded for the identification of maize HDACs. Did authors search for each described At and Os HDAC homologs by sequence BLAST? If yes, please provide a table showing the hits obtained in each BLAST search, including the e-values, score, etc, instead of or in addition to Table 1.
Validity of the findings: 14.	Accession numbers of the transcriptomic data used for the different analyses should be provided, as well as their corresponding reference.
15.	In literature, it is mentioned that there is 15 HDACs in maize (examples are Hu Y et al 2011; Demetriou K et al. 2009). Please comment on this. Which are the two new HDACs that authors have found?  Also, it would be useful to indicate the commonly used (and already published) HDAC names on top of the systematic names used along the manuscript (common names of putative orthologs are only mentioned in the discussion for some genes). This would significantly facilitate to relate this work with previous publications.
16.	Lines 216-219: Authors claim that cold treatment causes a decrease in H3K9ac. However, Figure 8 shows no effect. Also, the other effects on histone acetylation are quite mild. How many times was this experiment done? Are these results reproducible?
Additional comments: The manuscript presented by Kang Zhang et al. describes the effect of biotic and abiotic stresses on the expression of histone deacetylases genes in maize. Using existing transcriptomic data and their own generated expression analyses by RT-qPCR, authors describe the changes in the expression of HDAC genes upon different stresses. The generated analyses contribute to our understanding of how HDAC genes are transcriptionally regulated in maize. However, several improvements of the presented manuscript are needed.


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: IN SILICO ANALYSIS OF MAIZE HDACS WITH AN EMPHASIS ON THEIR RESPONSE TO BIOTIC AND ABIOTIC STRESSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The results are interesting but limited. The study is preliminary and descriptive. No underlying mechanism was provided. The conclusions are ambiguous. Based on the present limited findings it shall be difficult to claim such conclusions. The conclusions are not supported by substantial evidences. And the figures are not easily readable. Figure legends are confusing and unclear. Modify the figure legends.
Experimental design: Materials & Methods need to be improved.
Validity of the findings: The study is preliminary and descriptive. The conclusions are not supported by substantial evidences.
Additional comments: Manuscript ID: peerJ-reviewing-38864-v0

The present investigation revealed the significant role of ZmHDACs in plant development and response to biotic and abiotic response to stresses. Analyses of HDAC gene family by using In silico protein and gene expression analysis. HDAC gene family can be divided into 17 genes, which can be further categorized into three subfamilies, including RPD3/HDA1, SIR2, and HD2. Tissue-specific genes were revealed. GRMZM2G046824, GRMZM2G56539, and GRMZM2G008425 were highly expressed in anther and pollen, while GRMZM2G100146 and GRMZM2G159032 were highly expressed in seed and endosperm. Furthermore, MeJA, SA, fungal, and heat treatment has revealed the role of HDACs genes in maize.
The results are interesting but limited. The study is preliminary and descriptive. No underlying mechanism was provided. The study is preliminary and descriptive. The conclusions are not supported by substantial evidences. The present conclusions include following questions:
•	On what basis HDACs were divided into 12 members? How they are categorized? Is it members or categories?
•	How do authors interpret that the genes present in higher levels in the specific tissues are involved in their functionality?
•	How have authors categorized higher expression and lower expression of genes? What value was designated as higher and lower expression levels?
•	Why have results not been verified and discussed in details?
•	How do authors interpret and discuss the Genes in Cluster3 which have shown a lower expression level in all tissues investigated?

English Level: The English used in the article is not readable and not good enough to convey the scientific meaning correctly. There are several spelling and grammatical mistakes incorporated throughout the manuscript. To enhance the quality and clarity of manuscript, it requires a thorough revision from someone with full professional proficiency. Gene terminologies should be italicized.
For example:
Introduction Line 43: Members of the SIR2 family are conservative from prokaryotic to eukaryotic
Modified to: “conservative” should be modified to “conserved”.
Line 46-49: Needs to be modified
Line 231: Needs to be modified
Overall Recommendation: Reconsider after major English language revision.
Title
The title of the manuscript is broad and misleading. The title should be restricted specifically to the limited findings.
Abstract
 Add the principal results and major conclusions clearly. Revise it and add specific data and
 results of the present work.
Introduction
Good introduction is succinct. The importance and usefulness of this research work is not
clear. Add it.
 Add more related and relevant references. Add additional references, such as:
Hou H, Zheng X, Zhang H, Yue M, Hu Y, Zhou H, Wang Q, Xie C, Wang P, Li L. Histone Deacetylase Is Required for GA-Induced Programmed Cell Death in Maize Aleurone Layers. Plant Physiol. 2017;175(3):1484-1496. doi: 10.1104/pp.17.00953.
Hou H, Wang P, Zhang H, Wen H, Gao F, Ma N, Wang Q, Li L Histone acetylation is involved in gibberellin-regulated sodCp gene expression in maize aleurone layers. Plant Cell Physiol; 2015; 56: 2139–2149
 Forestan C.,  Farinati S., Rouster J., Lassagne H,  Lauria M.,  Ferro N., D.,,and Serena Varotto Control of Maize Vegetative and Reproductive Development, Fertility, and rRNAs Silencing by HISTONE DEACETYLASE Genetics; 2018; 108. Apr; 208(4): 1443–1466. doi: 10.1534/genetics.117.300625

Materials & Methods
Which protocol was used for JA and SA treatments in plants? Or is it a new protocol designed by the authors? Explain it.
Why only one concentration of JA (100 μM ) and SA (100 μM ) were used for the treatment of the maize plant? Why no other concentrations were tested?
Which statistical analysis was used to demonstrate the specific data? Add in the Methodology.
Discussion
In-depth discussion is missing. The Discussion should explain the significance of the results and place them into a broader context. It is often helpful to the reader to indicate the directions in which the work might be built on going forward. It should not be redundant with the Results. But in the present manuscript, this section has mainly presented by the results. There are more relevant references presents.
Modify the discussion section thoroughly.
Discussion section seems to be the repetition of results. For example:
Line 260-266: “In our results, GRMZM2G172883, GRMZM2G046824, GRMZM2G056539,
and GRMZM2G456473 were induced in 3 h and 6 h, and the expression levels of these genes
were gradually decreased after 6 h MeJA treatment. In SA treatment, GRMZM2G172883,
GRMZM5G807054, GRMZM2G898314 and GRMZM2G100146 were gradually down-regulated
at 3 h and 6 h, and then up-regulated at 12 h and 24 h. GRMZM2G172883, ortholog of AtHDA19, showed the similar expression pattern in Arabidopsis. These results suggested that these genes might be involved in hormone signaling pathways and plant defense responses.”
It is not clear. Modify it: “The number of ZmHDAC gene family in maize was almost consistent with those in Arabidopsis, rice and tomato, and gene expression of HDACs were not obvious in maize (Fu et al. 2007; Pandey et al. 2002; Zhao et al. 2014b).”
It is not clear. Modify it: Two members of class II family GRMZM2G046824, GRMZM2G56539
and one members of class II family GRMZM2G008425 were higher expressed in anther and
pollen, suggesting that these genes might be involved in flower development.
Conclusion
Why the future perspective was not mentioned? Describe it and add it in the conclusion section.
Figure Legends
The figures are not easily readable. Figure legends are confusing and unclear. Modify the figure legends.


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: IN SILICO ANALYSIS OF MAIZE HDACS WITH AN EMPHASIS ON THEIR RESPONSE TO BIOTIC AND ABIOTIC STRESSES
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is a revised version of the manuscript presented by Kang Zhang et al. Most of my comments have been appropriately addressed. Nevertheless, there are still some points that might require attention.

1. Despite English improvement throughout the manuscript, there is still some typos and grammar errors to be corrected (examples include the use of caps in “Acetylation” (line 50), space between “plant” and “growth” in line 246), “diacetylation” (line 264) and grammar of the sentence in lines 184-186).
2.	Reference to Figure 2 in line 183 seems wrong. The different classes of HDAC are only depicted in Figure 1.
Experimental design: No comment
Validity of the findings: 3.	Even if highly reproducible, the effect of cold stress on acetylation of H3K9 is not convincing, especially because western blot is a quantitative limited technique and the claimed effect is extremely mild. Authors should consider concluding about this result with more caution.
Additional comments: Suggestion: If possible, it would be useful for the readers to represent Figure 3 in such a way that the clusters and subgroups mentioned in lines 191-201 are labeled within the figure.


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: IN SILICO ANALYSIS OF MAIZE HDACS WITH AN EMPHASIS ON THEIR RESPONSE TO BIOTIC AND ABIOTIC STRESSES
Review round: 2
Reviewer: 2

Output:
Basic reporting: Major English revisions are required.
Experimental design: Methodology: What temperature was used for cold shock or for heat treatment stress and for what time period? Authors need to mention it at appropriate sections in the manuscript.
Validity of the findings: Novelty of the present investigation raises question. As previously it has been determined 18 HDACs in Arabidopsis and Rice. These HDACs are divided into three families. In the present study the authors have used in silico methodologies to determine similar 18 HDACs in maize (abstract Line 31, L32) and in the present study also HDACs were divided into three families. In fact, similar results to response of HDACs to JA and SA and abiotic stresses were obtained. The present data is limited.
Additional comments: Manuscript ID: #38864
New Comments are in “red”.
Previous comments are in “black”.
Authors response to previous comments is in “blue”.
Novelty of the present investigation raises question. As previously it has been determined 18 HDACs in Arabidopsis and Rice. These HDACs are divided into three families. In the present study the authors have used in silico methodologies to determine similar 18 HDACs in maize (abstract Line 31, L32) and in the present study also HDACs were divided into three families. In fact, similar results to response of HDACs to JA and SA and abiotic stresses were obtained. The present study is limited.
Methodology: What temperature was used for cold shock or for heat treatment stress and for what time period? Authors need to mention it at appropriate sections in the manuscript.
Italicized the gene terminology. For example, HDAC (L96, L98, L270, L282, L321, L366, L371, L375, L379, L383), ZmHDAC (L94, L225, L254), etc.
Recommendation: Major English revisions need to be done by a Native English Speaker. Mention what was actually modified in point-by-point response to previous and new comments.
For the following responses to previously raised queries, authors need to mention what was actually modified in the revised version of the manuscript and also mention the line numbers and page numbers to indicate those modifications.
Q1. Why have results not been verified and discussed in details?
Answer: Thank you for your question. All results have been verified and discussed in the revised manuscript.
Q2. The title of the manuscript is broad and misleading. The title should be restricted specifically to the limited findings.
Answer: Thank you for your suggestion. The title has been modified.
Q3. Add the principal results and major conclusions clearly. Revise it and add specific data and results of the present work.
Answer: Thank you for your comments. The abstract has been improved in the revised manuscript.
Q4. Which statistical analysis was used to demonstrate the specific data? Add in the Methodology.
Answer: Thank you for your helpful suggestion. Statistical analysis has been added to the method.
Q5. In-depth discussion is missing. The Discussion should explain the significance of the results and place them into a broader context. It is often helpful to the reader to indicate the directions in which the work might be built on going forward. It should not be redundant with the Results. But in the present manuscript, this section has mainly presented by the results. There are more relevant references presents.
Answer: Thank you for your helpful advice. The discussion has been improved in the revised manuscript.
Q6. Modify the discussion section thoroughly.
Discussion section seems to be the repetition of results. For example:
Line 260-266: “In our results, GRMZM2G172883, GRMZM2G046824, GRMZM2G056539, and GRMZM2G456473 were induced in 3 h and 6 h, and the expression levels of these genes were gradually decreased after 6 h MeJA treatment. In SA treatment, GRMZM2G172883, GRMZM5G807054, GRMZM2G898314 and GRMZM2G100146 were gradually down-regulated at 3 h and 6 h, and then up-regulated at 12 h and 24 h. GRMZM2G172883, ortholog of AtHDA19, showed the similar expression pattern in Arabidopsis. These results suggested that these genes might be involved in hormone signaling pathways and plant defense responses.”
Answer: Thank you for your advice. The sentence has been modified.
Q7. It is not clear. Modify it: “The number of ZmHDAC gene family in maize was almost consistent with those in Arabidopsis, rice and tomato, and gene expression of HDACs were not obvious in maize (Fu et al. 2007; Pandey et al. 2002; Zhao et al. 2014b).”
Answer: Thank you for your advice. The sentence has been modified.
What do authors mean by “was not obvious in maize”? Explain it.
 “The number of ZmHDAC gene family in maize
was found to be almost consistent with that in Arabidopsis, rice, and tomato, and gene expansion of HDACs was not obvious in maize (Pandey et al. 2002; Fu et al. 2007; Zhao et al. 2014b).”
Q8. It is not clear. Modify “Two members of class II family GRMZM2G046824, GRMZM2G56539 and one members of class II family GRMZM2G008425 were higher expressed in anther and pollen, suggesting that these genes might be involved in flower development”.
Answer: Thank you for your advice. The sentence has been modified.
Q9. Why the future perspective was not mentioned? Describe it and add it in the conclusion section.
Answer: Thank you for your advice. The future perspective has been added in the conclusion section.
Q10. The figures are not easily readable. Figure legends are confusing and unclear. Modify the figure legends.
Answer: Thank you for your advice. The figure legends have been modified in the revised manuscript.
Not satisfied with the following responses:
Q11. How do authors interpret and discuss the Genes in Cluster3 which have shown a lower expression level in all tissues investigated?
Answer: Thank you for your question. Genes in Cluster 3 showed lower expression level in all tissues. We presume that the tissues covered by the current RNA-Seq datasets are limited. These genes might be expressed in some specific tissues.
Why the authors are not able to explain the lower expression in Cluster 3?
Q12. Why only one concentration of JA (100 μM ) and SA (100 μM ) were used for the treatment of the maize plant? Why no other concentrations were tested?
Answer: Thank you for your comments. The concentrations of JA (100 μM) and SA (100 μM) had also been applied to many other plants, such as Arabidopsis, rice, tomato, wheat, poaceae, soybean, etc. (Chen et al. 2014; Li et al. 2015; Shalmani et al. 2019; Van Hove et al. 2014; Wang et al. 2017; Wang et al. 2015). In literature, HDA19 was induced by JA treatment, and in the present study, HDA101 (GRMZM2G008425, ortholog of HDA19) was induced by JA treatment and repressed by SA treatment. Hence, we presumed that 100 μM JA and100 μM SA were reliable.
New comments to specific sections of the revised manuscript are as follows:
Title
Title needs to be modified. Suggested title: “In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses”
Introduction
L50: Modify “Acetylation” into “acetylation”
L51: Modify “it was one of the first discovered to influence”
L87: What is PRR?
L90: If it is maize HDAC genes then it is obvious that they are found in the specific maize tissues. No need to repeat maize again and again. For example, “maize endosperm” (L91), maize vegetative (L91), maize aleurone layer (L95), etc. Modify it.
L92: Modify “HDA101 influencing”
Result
L195-L196: Modify “which indicated the associated of these genes”
L211-212: How do authors obtained “The expression levels of GRMZM2G457889 and GRMZM2G107309 were higher before 48 hpi, but suddenly decreased at72 hpi.” The result is ambiguous.
L222, L236: What do authors mean by using the term “obviously downregulated”? Explain and modify it.
Discussion
L245-246: Modify the statement and also correct the spelling mistake “HDACs play critical roles in histone acetylation, which is a improtant part of histone modification (Lee & Workman 2007).”
L246-L248: Incomplete sentence “HDACs have multiple functions in plant growth and development, response to environmental stresses by regulating gene activities through histone
deacetylation (Luo et al. 2012a; Liu et al. 2014.” Modify it.
L255-256: How do authors claim that “gene expression of HDACs was not obvious in maize”? Explain it.
L258-L259: Modify “in relation to previous study”.
L280: What do authors mean by the term “sperm cell germination”? Explain it.
Conclusion
L321: What do authors mean by “Partial ZmHDAC genes? Modify it.
L327-328: Modify “vital to plant development, regulating biotic and abiotic stress response”.


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

Input:
Title: COMPREHENSIVE ANALYSIS OF LONG NON-CODING RNAS AND MRNAS IN SKELETAL MUSCLE OF DIABETIC GOTO-KAKIZAKI RATS DURING THE EARLY STAGE OF TYPE 2 DIABETES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors provide interesting data about the changes in expression of long non-coding RNAs in Goto-Kakizaki rats at the age of 3-4 weeks compared with non-diabetic Wistar rats.
English language needs editing. Often, the sentences are not formed correctly, which makes the understanding difficult.
References are cited appropriately, reference list is correct.Manuscript is structured according to PeerJ standards. Abstract corresponds to PeerJ requirements, but language and style editing is needed.
Figures are relevant, high quality. Figures are well labelled & described, however, Fugure 4 A requires more comprehensive designation of the biological processes to my opinion. For example, „response to cytokine”, „response to peptide hormone”, „glutathion metabolic pathway”, „NADP” metabolic process”, „cellular response to hormone stimulus” are too simplistic and general terms -  either more correct terms or explanation in the legend is needed.
Raw data are supplied
Experimental design: Positive: the manuscript corresponds to the Scope of PeerJ, and refers to basic diabetology area. Research question is well defined, relevant & meaningful. It is stated how the research fills an identified knowledge gap. Rigorous investigation performed to high technical.
Weaknesses:
To my opinion, description of methods needs refining. Importantly, it is not clear how the samples of gastrocnemius muscle were obtained – were the rats euthanized or anaesthetized? Was the dissection of the tissue performed under microscope and miocytes were separated or whole tissue including blood vessels and connective tissue was used? The authors should either give the details or provide a reference, if the procedure has been described elsewhere.
Line 41-42 – The paper of Maeda et al refers to mouse transcriptome, therefore it is not correct to put it into context after mentioning human transcriptome (decribed by Djebali et al).
Line 67 – add „tissue” after „adipose”
Line 68 and thoughout the text and abstract – please use „age of 3-4 weeks”, not „stage”.
Line 71 – „the mechanism of hyperglycemia by which skeletal muscle lncRNAs
regulated in the early stage of T2D in GK rat is still indistinct”- these sentence is not clear to me. Wjat is the cause and what is the consequence? Does lncRNAs regulate the mechanism of hyperglycamia? Please rewrite the sentence clearly
line 79-80 – again, I think the age of GKZ rats of 3-4 weeks is not the same as „early stage” diabetes. In general, diabetes has no stage. It is either present (confirmed by hyperglycaemia), or not. The term „glucose intolerance” or „prediabetes” might be used for glucose values higher than normal but below the diabetic range – please referē to animal reference values to define the condition of the animals at the age of 3-4 weeks.

Line 89 – instead of “Four group rats” please write “four groups of rats”
Line 92-93 – „orbital plexus veins”
Line 95 – please write „samples of m.gastrocnemius of each rat” instead of „Ten gastrocnemius samples” „six gastrocnemius samples”
Line 100 – please provide kit number and manufacturer (Invitrogen?)
Line 104 – use „gastrocnemius muscle” instead of „gastrocnemius”
Line 116-118 – please rewrite this sentence in a more comprehensive style
Line 127, 131, 135 – please write the full name of DAVID, STRING, Python, Target Scan, RNAhybrid, Cytoscape analysis tools/programmes
 line 151-153 – Description of statistical analysis is too short and general. If 4 groups of rats were compared, the authors should have used Anova or Kruskal -Wallis test before pair-wise comparisons. Was the normality of data tested? t-test can only be used for normally distributed data. If the data do not correspond to normal distrubution, they should be presented as medians with corresponding interquartile range or in another appropriate way (not means)
Line 162-163 “The plasma glucose concentration of GK rats aged 3 weeks was
163 significantly increased than that of GK rats aged 4 weeks” – maybe “significantly higher than” sounds better
Line 168 – FDR – abbreviation is used for the first time and is not explained
Line 195 – „processes” instead of „process” should be used
201- „Intolerance” instead of „intolerant”
211 I would suggest „in GK rats at the age of 3 and 4 weeks” instead of „and T2D at 3 and 4 weeks”
213-214 reference is needed after „Glycolysis and glycogen synthase were demonstrated to be involved in glucose homeostasis”. This sentence might be more appropriate in Discussion section
242 – please use „RNA sequencing” instead of „RNA-seq”
322 –„ miR-139 has been identified could target Foxo1 directly and inhibit Foxo1 expression 323 in mice hepatocytes (Hasseine et al. 2009)” – the sentence contains unnecessary words.
323- “leads”
327-329 – why past is used in this sentence? I think you should use the present form of the verbs.
335-338 The last sentence should be rewritten in a comprehensive way, it is hard to understand what did the authors want to say.
Validity of the findings: Positive- The authors have demonstrated sufficient data to justify the need for this study. Negative results have been demonstrated and discussed.  All underlying data have been provided.
Negative - The choice of the methods for statistical analysis needs to be explained thoroughly in the methods, or, recalculation of the data using more appropriate methods is recommended.
Conclusions are not well stated (mot probably due to linguistic problems)
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: COMPREHENSIVE ANALYSIS OF LONG NON-CODING RNAS AND MRNAS IN SKELETAL MUSCLE OF DIABETIC GOTO-KAKIZAKI RATS DURING THE EARLY STAGE OF TYPE 2 DIABETES
Review round: 1
Reviewer: 2

Output:
Basic reporting: I commend the authors for the throughout RNA seq data analysis using various methods and providing maximum information from the data. In addition the results are well framed within existing knowledge.
However two main issues can be highlighted from the manuscript.
First the wellbeing of experiment animals which could have significant impact on results and second about the way how measurements are reported. Also information regarding settings in bioinformatical analyses could be provided in more detail. English proofreading by native speaker is advised.

A) English proofreading is advised. For example: line 67: I suppose "tissue" is missing (or "adipocytes"), line 89: "Four groups of...", ect..

B) Figure 3 legend. There is confusing information in legend part 3C " The blue represents signiﬁcantly downregulated mRNAs in GK rats at 3 and 4 weeks of age.": But there are no blue colored nodes in figure 3C.
Also part 3D "The color represents the degree." does not explain HOW figure 3D is represented by color.

C) Figure 4 legend and Figure 5 legend: "Values are means ± SEM, *P < 0.001, **P < 0.001, ***P < 0.001 vs age-matched Wistar". All star levels display same significance, must be corrected.
 For improved description of results bar graphs should show SD instead

D) Table 1. Please provide SD. Are five decimal places in reporting plasma insulin necessary? I suggest reducing to relevant level of precision.
Experimental design: A) Please elaborate on animal housing (lines 91-92) whether the rats were in social contact with each other.
What was the  evidence for the need to house rats in this way? This could have major impact on observed RNA expression.
Various reports state that individual housing induces stress response in rats and changes in various parameters including (but not limited to):
Variations in biochemical (Perez, Canal, Dominguez et al 1997) and immunological (Baldwin, Wilcox and Baylosis 1995) measurements,
Behavioural changes consistent with social deprivation (such as reduced mobility, increased tail chasing and self-grooming) (Hurst, Barnard, Nevison et al 1997)
The development of an abnormal gait in animals housed in social isolation from
weaning (Roberts, Clarke and Greene 2001).
Therefore, the recomendations are: "Rats should not be housed individually unless ... rats should be able to be in visual, auditory and olfactory contact with other rats." (https://www.animalethics.org.au/)

B) Statistical analysis (line 155). Variance of measurements within groups (standard deviation) is required to better frame the results throughout the manuscript.

C) Study power calcultion is missing. It would give another perspective on presented findings.
Validity of the findings: A) lines 131, 184, figure 3. What kind of evidence were used in construction protein-protein interactions?  That should be disclosed in methods. I would suggest disabling "interactions" based on "text mining" evidence.
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: PEOPLE IN EARLY STAGES OF PARKINSON’S DISEASE ARE ABLE TO INTENTIONALLY REWEIGHT THE USE OF VISUAL INFORMATION FOR POSTURAL CONTROL
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This is a clearly-written manuscript adding evidence about the effect of Parkinson's disease (PD) on body sway control. The Authors measured body oscillations while subjects were in an room moving in antero-posterior direction. Twenty-one patients with early PD performed similarly to 21 age-matched controls in all measures apart from oscillation amplitude, higher in PD patients either when trying to inhibit visual influence of the moving room or not. The author discuss that less accurate proprioception in PD patients could justify these results.
The study is sound, I only report some minor issues:
- Table 1: replace "High" with "Height" and replace commas with decimal dots


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: PEOPLE IN EARLY STAGES OF PARKINSON’S DISEASE ARE ABLE TO INTENTIONALLY REWEIGHT THE USE OF VISUAL INFORMATION FOR POSTURAL CONTROL
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English usage is slightly deficient as written. In the 'Minor Comments' of my comments to the authors I include suggestions/corrections that will correct these deficiencies.

By all other criteria for basis reporting, the article is acceptable.
Experimental design: The authors need to provide a reference for the frequency domain analysis described in the Methods section or they need to give a more detailed description (i.e., equations).

There is a possible mistake in the statement about the visual stimulus amplitude used in the experiments.

All other aspects of the experimental design are acceptable.
Validity of the findings: I offer suggestions in my Major Comments to the authors that ask for a more balanced interpretation of their results and some additional explanation.

The underlying processed data values (sway amplitude, gain, coherence) for each subject are provided. But I note that the spreadsheet with these data include an ID for each subject that appears to be subject initials. Typically it is not considered acceptable to include identifiers that can potentially reveal subject identity.
Additional comments: This study demonstrates that standing balance in subjects with early stage Parkinson’s disease (PD) is slightly more affected by visual disturbances caused by a moving room stimulus than age-matched controls, as judged by changes in the ‘mean sway amplitude’ (MSA, standard deviation of anterior-posterior body sway measured at upper torso level), but there was no statistical difference between PD and controls when response gain was used to compare subject groups. When subjects were asked to resist the influence of the visual stimulus, both PD and control subjects were able to reduce sway to a small extent as measured by both mean sway amplitude and gain measures. These results demonstrate that early stage PD subjects maintain the ability to consciously regulate sensory integration strategies that partially limit postural disturbances due to ‘false’ visual motion cues to an extent that is similar to the ability of age-matched controls. This might be considered a negative result, but it is a result worth making since it demonstrates an important functional characteristic of PD that is not affected or only minimally affected by the disease process.

Major Comments:

1.	The authors appear to have interpreted their results correctly in terms of a standard statistical analysis, but what is missing is a more detailed description and representation of the magnitude of the changes observed between the Resist and the No Info conditions. Rather than just showing mean values and SD error bars in figures 3, 4, and 5 it would be more informative to show box plots that better represent the distributions of the data and show any outliers if they are present. Also, a useful addition to the statistical description of the various results related to figures 3 and 5 would be to state the percent reduction in MSA and gain for the two subject groups and to give the percentage of subjects in each group that actually show a reduction in MSA and gain between the No Info and the Resist conditions. Additionally, the abstract should be modified to give some information about the magnitude of changes observed.
2.	The fact that the MSA results showed group differences but the Gain results did not is not an expected result, but there is no discussion about this. The simplest understanding of the results is that the stimulus-evoked sway would add to the spontaneous sway such that if spontaneous sway was the same and gain was the same in the two groups, then the stimulus-evoked MSA also should be the same. This reviewer suspects that this difference could be due to an accumulation of effects. Specifically, the AP MSA is slightly larger, on average, in PDs versus Controls (Fig. 1) and the Gain is slightly larger in PDs versus Controls Fig. 5). The combination of these two tendencies, even though neither effect reached statistical significance, may have combined to give a large enough group effect to reach statistical significance in the MSA results (Fig. 3). See also Minor Comment #17. This reviewer thinks the ‘big picture’ conclusion should emphasize the similarity between the PD and control groups rather than the small differences. Currently the Abstract does not covey this big picture view.
3.	 Line 136. The authors state that the peak-to-peak velocity of the stimulus was 0.6 cm/s. First, this amplitude should be stated in terms of peak displacement (cm) instead of velocity since all other measures in the paper are displacement measures. Second, are the authors certain the 0.6 cm/s is the peak-to-peak velocity and not the peak velocity? For a sinusoidal stimulus, the relation between peak displacement and peak velocity is Amp_disp = Amp_vel / (2 * pi * frequency). If the peak-to-peak velocity was 0.6 cm/s then Amp_vel was 0.3 cm/s and Amp_disp = 0.24 cm. The stimulus traces that are plotted in Figure 2 appear to show peak displacements of about 0.5 cm (not 0.24 cm) which makes me think that the peak stimulus velocity (and not peak-peak velocity) was 0.6 cm/s, which gives a peak amplitude of 0.48 cm. Or maybe the peak displacement amplitude was 0.6 cm as in the Barela et al., 2009 paper.
4.	English usage needs some improvement – see numerous suggestions below.

Minor Comments:

1.	Line 39. Suggest ‘. . . but both groups showed reduced gain in the . . .’
2.	line 42. Suggest ‘. . . body sway as controls.’ In general, I suggest not using ‘peers’ as this is not as clear as saying ‘controls’ or ‘control group’.
3.	Line 54,55. Suggest ending sentence with ‘deterioration’.
4.	Sentence beginning on line 63. Suggest ‘Additionally, postural control in older subjects may be affected more than in younger subjects by attention demands.’
5.	Line 69. Suggest substituting ‘In contrast’ for ‘Differently’.
6.	Line 77. Should be ‘visual-motor’.
7.	Line 78. Should be ‘. . . to resist it was . . .’
8.	Line 79. Suggest ‘Limited results suggest that the same . . .’
9.	Line 140. Should be ‘. . . asked to resist its influence . . .’
10.	Line 141. How was the auditory masking applied? Through head phones?
11.	Lines 150,151. Common understanding is that a ‘first order polynomial’ would be an equation (A + B*t) which is more clearly described as removing a linear trend.
12.	Line 148. The procedures described in the data analysis section should include a reference that provides more details about the methods used. I note that a coherence value calculated for a frequency analysis gives information about the signal-to-noise ratio of the stimulus-response data at the stimulus frequency and not specifically the ‘dependency’ between the stimulus and response. One could have a constant and unchanging dependency of the response on the stimulus, but if there is additional uncorrelated variability in the response signal (e.g. due to internal noise in the system) then the coherence would be reduced. See Pintelon & Schouten textbook on frequency domain approach to system identification (Wiley-IEEE press).
13.	Sentence beginning on line 187. This sentence is not necessary.
14.	Discussion section. In general, when results are described and summarized, the authors should include references to the specific figures were those results are shown.
15.	Line 255. Should be ‘. . . refute this hypothesis.’
16.	Line 256. Should be ‘. . .to resist its influence . . .’
17.	Line 263. Suggest ‘In contrast’ instead of ‘Differently’. But more importantly, regarding the point being made here that there was a group difference with visual stimulation but no difference without visual stimulation, this statement is relying too much on binary classification based on statistical significance while ignoring trends in the results. Also, I think your statistical analysis that determined that there was a group difference with visual stimulation relied on combined results from the No Info and Resist conditions (and both of these trials three repeats), so this analysis had a repeated-measures advantage in detecting a difference that was not available in the non-stimulated condition. Please provide a description that is fairer to your data.
18.	Line 264. Not clear what ‘This observation’ is referring to. The previous sentence was saying that there were no differences between groups while this sentence is saying that PD subject posture is poorer.
19.	Line 269. Should be ‘. . . with PD are exposed  . . . ‘
20.	Line 217. Suggest ‘. . . such as visual motion, . . .’ and also use ‘controls’ rather than ‘peers’.
21.	Line 273. Not clear what you mean by ‘without the person discriminate such manipulation’. Do you mean that the subject is not consciously or perceptually aware that the visual scene was moving? Was your stimulus at this low, below conscious level? This argument about what does and does not require ‘higher centers’ is a bit tricky since an automatic control mode (I think ‘automatic control mode’ would be a better descriptor than ‘intrinsic dynamic mode’ in line 275, and also who’s to say that automatic control does not require ‘higher centers’ – this reviewer thinks it does) can be operative whether the subject is aware or not of the stimulus.
22.	Line 278. Better to say ‘That is a useful mechanism . . .’
23.	Line 284. Should be ‘. . . displaying corresponding body oscillation.’
24.	Lines 285,286. Suggest ‘. . . body sway in people with PD is intact.’. . .
25.	Line 309. Should be ‘. . . explain the increased reliance . . .’
26.	Line 310. Should be ‘. . .  as previously shown . . .’
27.	Lines 312,313. Suggest ‘. . . but induced body sway still occurred in both people with PD and age-matched controls.’
28.	Sentence beginning line 313. This sentence should be moved to the next section (future studies) if you want to keep it.
29.	Line 319. Should be ‘. . . to reduce the visual . . .’
30.	Line 323. Eliminate the word ‘accordingly’
31.	Sentence beginning on line 325. Eliminate this last sentence since it is repeating things already said.
32.	Lines 330-333. The last part of this sentence is not clear. Suggest ‘. . . developing intervention protocols to improve sensory integration strategies.’
33.   Figure legend 2 should refer to '(A and B)' and '(C and D)'.
34.	The raw data provided in the spreadsheet should not use subject initials as identifiers since this can potentially be used to identify the subjects.


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: PEOPLE IN EARLY STAGES OF PARKINSON’S DISEASE ARE ABLE TO INTENTIONALLY REWEIGHT THE USE OF VISUAL INFORMATION FOR POSTURAL CONTROL
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper investigated the inﬂuence of knowledge and intention on the postural control performance and on the coupling between visual information and body sway in people with and without PD standing upright. This is an original paper with interest findings. However, some points need to be improved.

line 200 - Induced what? Higher?

Table 1: Please change comma for point.

Please improve the resolution of figure 2.
Experimental design: Inclusion and exclusion criteria: Please clarify how was verified each criterion.
Validity of the findings: discussion: “Differently, when vision was not manipulated, there was no difference between groups.”
This was no expected and should be discussed.

discussion: “our result suggests that people in the early stages of PD can allocate attentional resources to alter sensory cue influences on postural control tasks.”
Why are they able to allocate attentional resources similar to the control group? This needs to be better explained.
Additional comments: The paper investigated the inﬂuence of knowledge and intention on the postural control performance and on the coupling between visual information and body sway in people with and without PD standing upright. This is an original paper with interest findings. However, some points need to be improved.

1) Abstract and conclusion: “ … suggesting that they have and/or allocate attentional resources to promote such changes”.
It is not possible to conclude about the attentional resource with the findings of the study. I suggest to remove this suggestion or rewrite. Please look to in the study conclusion too.

2) Introduction: “its diagnosis is initially made by three motor signs: bradykinesia, rigidity and/or rest tremor (Postuma et al., 2015).”
This affirmation is not correct. The diagnostic of the disease occurs the different ways. If the authors are considering the differential diagnostic, there are other aspects that are considered beyond these three motor signs/symptoms. Please rewrite this sentence.

3) Introduction: paragraphs 3 and 4 do not interact. Please improve the writing.

4) Introduction: “Although sparse, results indicate that the same cognitive task did not alter body sway magnitude of people with PD standing upright (Fortaleza et al., 2017).”
Please double-check this information. I’m not sure that it is possible to affirm this.

5) hypothesis: It is not clear the justification for this hypothesis. If the people with PD presents the attentional resources compromised, is not expected that knowledge and intention, which increase the attentional demand, impair the postural control performance?

6) Inclusion and exclusion criteria: Please clarify how was verified each criterion.

7) line 200 - Induced what? Higher?

8) discussion: “Differently, when vision was not manipulated, there was no difference between groups.”
This was no expected and should be discussed.

9) discussion: “our result suggests that people in the early stages of PD can allocate attentional resources to alter sensory cue influences on postural control tasks.”
Why are they able to allocate attentional resources similar to the control group? This needs to be better explained.

10) Table 1: Please change comma for point.

11) Please improve the resolution of figure 2.


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: PEOPLE IN EARLY STAGES OF PARKINSON’S DISEASE ARE ABLE TO INTENTIONALLY REWEIGHT THE USE OF VISUAL INFORMATION FOR POSTURAL CONTROL
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I raise 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: PEOPLE IN EARLY STAGES OF PARKINSON’S DISEASE ARE ABLE TO INTENTIONALLY REWEIGHT THE USE OF VISUAL INFORMATION FOR POSTURAL CONTROL
Review round: 2
Reviewer: 2

Output:
Basic reporting: This reviewer is satisfied with the authors’ responses to the reviewers and with the revisions made to the manuscript. I only offer a number of suggestions to improve the English usage. These are listed in the general comments to the authors. None of these changes are substantial enough to require additional review.
Experimental design: All criteria are met.
Validity of the findings: All criteria are met.
Additional comments: Minor comments:

1.	Line 56. Suggest: ‘The postural control system provides the ability to . . .’
2.	Line 75. Suggest: ‘resist a visual manipulation . . .’
3.	Line 82. Add period at end of the sentence.
4.	Line 122. Suggest: ‘This structure was . . .’
5.	Line 132. Suggest: ‘. . . the room was translated (back and forward) . . .’
6.	Lines 152, 153. Suggest: ‘In addition, the relationship between the room position and body sway was examined. Mean sway variability . . .’
7.	Line 156. Suggest: ‘Coherence was used . . .’
8.	Line 159. Suggest: ‘Gain was used . . .’
9.	Lines 160-163. Suggest: ‘In this case gain indicates the relative magnitude influence of room movement on body sway. Gain was calculated as the absolute value of the Fourier transform of body sway divided by the Fourier transform of room position at the stimulus frequency. A gain value of 1 indicated that body displacement at the scapula level was the same as the moving room amplitude, and . . .’
10.	Lines 166,167. Suggest: ‘Custom routines written in Matlab (The MathWorks, Inc.) were employed for all calculations.'
11.	Line 202. Suggest: ‘. . .to resist the visual manipulation, . . .’
12.	Line 203. Suggest: ‘. . .the condition where there was . . .’
13.	Line 210. Suggest: ‘. . .and condition effects, . . .’
14.	Line 219. Suggest: ‘. . . compared to the condition . . .’
15.	Lines 241, 242. Suggest: ‘. . . in the case when vision was not manipulated.’
16.	Line 247. Suggest: ‘. . . because of the many changes . . .’
17.	Line 254. Suggest: ’. . . discriminating the manipulation . . .’
18.	Line 255. Suggest: ‘. . . not perceptually aware of the visual . . .’
19.	Line 260. Suggest: ‘Automatic control is a useful mechanism . . ‘
20.	Line 262. Suggest: ‘. . . that such a mechanism . . .’
21.	Lines 263, 264. Suggest: ‘. . . postural orientation while requiring low . . .’
22.	Line 272. Suggest: ‘. . . on body sway when given . . .’
23.	Line 280: Suggest: ‘. . . would have still the possibility . . .’
24.	Line 282: Suggest: ‘While the influence of visual information on induced body sway was reduced . . .’
25.	Line 285. Suggest: ‘. . . corroborates observations by . . .’
26.	Lines 287, 288. Suggest: ‘. . . cannot totally ignore available sensory cues even in situations where they . . .’
27.	Lines 304, 305. Suggest: ‘Our observations indicate that people with PD can allocate attentional resources to change the automatic control properties by altering the use of sensory cues for postural control.’
28.	Line 310. Suggest: ‘. . . explore the influence of attentional resources on the use of visual cues, . . .’
29.	Figure 1 legend. This figure legend should define the parameters of the boxplots. There is no standard for the representation of box plots. Presumably one of the lines within the box is a median value and the other a mean value. Maybe the box represents the 25 and 75 percentile points, and maybe the whiskers are 5 and 95 percentiles.


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

Input:
Title: THE EFFECT OF HEPATOPANCREAS HOMOGENATE OF THE RED KING CRAB ON HA-BASED FILLER
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In the manuscript (#43188) entitled “The effect of hepatopancreas homogenate of the Red king crab on HA-based filler”, the authors studied the hydrolysis of hyaluronic acid (HA) in cosmetic fillers and the kinetics of HA hydrolysis using the hepatopancreas homogenate of the Red king crab. The authors found that the hepatopancreas homogenate of the Red king crab exhibits comparable enzyme activity to commercially available hyalurionidases. Turbidimetric analysis of HA from fillers shows a bell-shaped dependence of aggregation with acidic albumin on reaction time, which is totally different from the turbidimetric analysis result of HA obtained from rooster comb. The authors then investigated the structural transformations of HA products during the hydrolysis process using AFM and NMR analysis. The study provides industry an opportunity to use the hepatopancreas of the Red King crab as raw materials for the commercial-scale production of hyaluronidases. It not only has medical advantages than the current commercially available hyaluronidases, mainly from bovin, but also has great economical benefit.

Moderate comments:

1. The authors gave a very simple explanation for the distinct turbidimetric analysis result of HA from cosmetic fillers than that from the rooster comb in the Discussion section. Considering that it is the first important finding of this manuscript, the authors should provide more evidence and analysis to prove their argument. Given the size/molecular weight (and morphology?) of HA regulates its binding to albumin and the forming of aggregates. AFM analysis of the rooster comb HA and the hydrolysates could be performed and compared with the AFM results with filler HA, which may give us some clues.

2. The current study still cannot make a conclusive determination of what contributes to the
hyaluronidase activity of the hepatopancreas homogenate. Is it hyaluronidase or other enzymes? If the authors can clarify it using other sophisticated analytical techniques like liquid chromatography and mass spectrometry, it will be a significant contribution to this area.

Minor comments:

Citation numbers are out of order throughout the text, and references are in different formats, should be cleaned up according to the requirement of the journal. Manually change them or use the correct bibliography style.

Line 96. “distilled water and ice were added in a ratio of 1:8:2”. Do you mean “distilled water and ice were added at a weight ratio of 1:8:2, hepatopancreas:water:ice, ” ?

Line 102. What is the protein concentration, in the range of *** ?

Line 111. For the gel electrophoresis analysis (Fig S3), the two commercial hyalurionidases products, Lidase and Liporase, should be run simultaneously. It will help you figure out which band of the hepatopancreas homogenate corresponds to the presumed hyalurionidase. And it is also a positive control for the detection of hyalurionidase in the homogenate.

Line 192. Figure S1 should be referenced before Figure S2 (Line 177). Numbered in order of first appearance in 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: THE EFFECT OF HEPATOPANCREAS HOMOGENATE OF THE RED KING CRAB ON HA-BASED FILLER
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors characterized the hydrolysis of hyaluronic acid (HA)-based cosmetic fillers by the hepatopancreas homogenate of the Red king crab using several biophysical methods and showed that hepatopancreas homogenate of the Red king crab has hyaluronidase activity. The present work established the potential of commercial-scale production of hyaluronidases from the Red king crab hepatopancreas. The manuscript is written with clear English and professional organizations. The background shows proper context with relevant references. The first reference starts with number 15. The reference order needs to be corrected. The raw data were provided with the manuscript. The figures and tables are shown with good quality and support the hypotheses.
Experimental design: Research questions are well defined, relevant and meaningful. The methods are described in the manuscript in detail and are sufficient to follow.
Validity of the findings: The authors successfully characterized the hydrolysis of hyaluronic acid (HA)-based cosmetic fillers by the hepatopancreas homogenate of the Red king crab by turbidimetric analysis, AFM and NMR techniques. Data were interpreted completely and supported the conclusion that homogenate of the Red king crab hepatopancreas has hyaluronidase activity on HA-based cosmetic fillers.

Can you provide 1H-NMR spectra of native HA from rooster comb and its hydrolysis products after treatment by purified HPC homogenate as supplementary material? Please provide the overlay of 1H-NMR spectra of at different time points as shown in the article for Hyaluform HA and its hydrolysis products by purified HPC homogenate.
Additional comments: No additional comments


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

Input:
Title: THE EFFECT OF HEPATOPANCREAS HOMOGENATE OF THE RED KING CRAB ON HA-BASED FILLER
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Minor comment:
The number format in the graphic legend of Fig. 4 and Fig. 5(a), as well as in Figs. S12, S13, is not consistent (e.g., 114.22 h VS 114,22 h). The first format is better.


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

Input:
Title: THE EFFECT OF HEPATOPANCREAS HOMOGENATE OF THE RED KING CRAB ON HA-BASED FILLER
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors satisfactorily addressed all the comments and provided the requested supplementary figures.
Experimental design: No comment
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: IDENTIFICATION OF PROGNOSTIC SPLICING FACTORS AND EXPLORATION OF THEIR POTENTIAL REGULATORY MECHANISMS IN PANCREATIC ADENOCARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is clearly written with professional standards.
References are sufficient to justify the state of the art however the authors need to check the formatting once more.
For instance: Line 48-49, references have missed the year. Minor issue, please check the correct positioning of full stop "." at the end of sentence and citation "(XY et al, 2019)." or ".(XY et al, 2019)"
No other comments on writing style.
Experimental design: Line 68 to 71: it is not clear if they have used TPM or FPKM for their downstream analysis. It is suggested to have one metric used throughout the manuscript in order to avoid normalization conflicts or contradictory interpretations.
Line 100 and 105: I am not sure if there is a need for multiple hypothesis testing or FDR cutoff. Authors should include a fdr cutoff if possible.
Line 123: Is it r or r2 value. Please, clear whether the threshold is just a cutoff for an association or related to both positive (+0.6) and negative correlation (-0.6) indices?
Validity of the findings: Authors have used SpliceSeq software to calculate the PSI values, which later they have implemented in univariate/ COX models to re-investigate the prognostic index. It would be great if they can use another (at least one more) alternative splicing detection tool (if not doing any experimental verification) to authenticate the reproducibility of their best hits (and corresponding risk score) in silico.
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: IDENTIFICATION OF PROGNOSTIC SPLICING FACTORS AND EXPLORATION OF THEIR POTENTIAL REGULATORY MECHANISMS IN PANCREATIC ADENOCARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is well written and the subject is certainly of interest for both clinic and basic researchers in the fields of oncology and cellular biology.
Experimental design: The research question is well defined, relevant and meaningful, however, my major concern is the fact that this manuscript lacks experimental confirmation. The authors indeed mentioned some important links between literature and its data on some of the top twelve SF genes described, which somehow indicate the robustness of the obtained results, but in my opinion some specific experiments would substantially improve the work presented.
Validity of the findings: Comments on specific points that should be considered in order to improve the paper:

It would be interesting to see if the relevant Splicing Factors and Alternative Splicing events found could be functionally linked with each other. For instance, have some AS event already been reported as regulated for some of the SF encountered?

Comparison between the prognostic splicing factors obtained with other genes already used in clinics or known as relevant prognostic factors would render an interesting control
.
Six out of top twelve SF are not in the top twenty SF list presented in Fig 1. Is that correct? Please check the situation of the genes GPATCH3, IGF2BP3, PTBP3, RBM14, SRPK1, XAB2.

Fig 5 was not described in the text.
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: IDENTIFICATION OF PROGNOSTIC SPLICING FACTORS AND EXPLORATION OF THEIR POTENTIAL REGULATORY MECHANISMS IN PANCREATIC ADENOCARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: Confirmatory experiments is still lacking in this version of the text. On the other hand, the authors indeed improved the text based on the reviewer's comments.
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: COMPREHENSIVE TRANSCRIPTOME ANALYSIS OF REFERENCE GENES FOR FRUIT DEVELOPMENT OF EUSCAPHIS KONISHII
Review round: 1
Reviewer: 1

Output:
Basic reporting: Literature references, sufficient field background/context provided。
Experimental design: Methods described with sufficient detail & information to replicate.
Validity of the findings: Speculation is welcome, but should be identified as such.
Additional comments: Based on the RNA-Seq data of different developmental stages, the MS selected eight candidate reference genes, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH), α-tubulin (TUA), cyclophilin (CYP), ubiquitin-conjugating enzyme (UBC), ubiquitin (UBQ), malate dehydrogenase (MDH/mMDH) and actin (ACT). GeNorm, NormFinder, BestKeeper and ReFinder were used to analyse the stability of reference genes.
1, Why did the MS not select more known internal reference genes for screening?
2, Why the MS just analysis the internal reference genes for fruit, not whole plant, when screening for reference genes of specific species?
3, Suggestions for the author's reference that published in Nucleic Acids Research: ICG:a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.
4, I would give the advices that authors select more genes of different pathways for analysis when evaluating the stability of internal reference genes.


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

Input:
Title: COMPREHENSIVE TRANSCRIPTOME ANALYSIS OF REFERENCE GENES FOR FRUIT DEVELOPMENT OF EUSCAPHIS KONISHII
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the manuscript, the expression stability produced by eight traditional candidate reference genes was studied for normalizing qRT-PCR in fruit development. Four softwares –GeNorm, NormFinder, BestKeeper and ReFinder – were used to identify stability of these candidate genes. Finally, EkUBC23, EkCYP38 and EkGAPDH2 were identified as  top three stably expressed genes.The authors are advised to get the manuscript checked for many spelling/text errors.
Experimental design: 1. The authors should add the expression patterns in other organ and tissues except for three developmental stages in fruits of E. konishii.
2. Specific primer sets should be designed to target the UTR of each gene to ensure the specificity of the reference genes.
3.‘Ct’ and ‘Cq’ have the same meaning? In Figure 1, the expression levels of most reference genes were very low (Cq values about 30), and they are not suitable for reference genes.
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: COMPREHENSIVE TRANSCRIPTOME ANALYSIS OF REFERENCE GENES FOR FRUIT DEVELOPMENT OF EUSCAPHIS KONISHII
Review round: 2
Reviewer: 1

Output:
Basic reporting: The introduction does not systematically introduced the research progress in related fields, especially in molecular biology of this species.
Experimental design: 1, The internal reference gene analysis based on transcriptome data, MS should explain these gene cloning and analysis, primer design and so on.
2, The author may screened the internal reference genes for more representative and wider coverage screening of internal reference genes.
3, The MS may cheese more genes as internal reference genes for analysis, such as Actin and so on.
Validity of the findings: Conclusions are well stated, linked to original research question & limited to supporting results
Additional comments: 1, It is not clear whether the authors have cloned these internal reference genes after transcriptome sequencing, and then designed primers for analysis. The result will be inaccurate because of possible errors in sequencing data, if the MS used the sequences directly.
2, The author only screened the internal reference genes for fruit development. The limitation of this study is very great. For a species that has not been screened for internal reference genes, we can do some more representative and wider coverage screening of internal reference genes.
3, In Arabidopsis thaliana, rice and other plants, a lot of internal reference genes had been screened, and many internal reference genes had been analyzed in different plants. Why did the MS choose these eight genes as internal reference genes for analysis? Instead of choosing a wider range of genes, such as Actin and so on.


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

Input:
Title: COMPREHENSIVE TRANSCRIPTOME ANALYSIS OF REFERENCE GENES FOR FRUIT DEVELOPMENT OF EUSCAPHIS KONISHII
Review round: 3
Reviewer: 1

Output:
Basic reporting: 1, The author carried out the three stages of fruit ripening transcriptome sequencing, and made a detailed description in materials and methods, but did not mention in the results. It is suggested that the author supplement the description, especially the differential expression genes involved in different stages of fruit ripening.
2, The author mentioned that previous studies have been carried out in this species （Liang WX et al., 2019）, but did not include the different stages of fruit development. This paper only focused on the different stages of fruit development. What are the differences between these genes and previous studies? Are the results consistent with it?
3, There are still some small mistakes in the article, which should be corrected. Such as: "while thehigh expression reference gene (EkGAPDH2) was beneficial for quantifying high expression genes", thehigh maybe the high.
Experimental design: The MS only aims at the selection of fruit development internal reference genes, and I suggests that the author should expand the scope of use of these internal reference genes , so that the MS has more general application value.
Validity of the findings: The author may increase the comparison and analysis of the research results with Liang WX et al., 2019.
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: COMPREHENSIVE TRANSCRIPTOME ANALYSIS OF REFERENCE GENES FOR FRUIT DEVELOPMENT OF EUSCAPHIS KONISHII
Review round: 4
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1. In the revised manuscript, the manuscript has been extensively edited. However, Many spelling/text errors still should be checked.
For example,
Line 57: change ‘housekeeping gene were selected’ to ‘housekeeping genes were selected’
Line 58: change ‘Dheda K et al., 2004.’ to ‘Dheda K et al., 2004’
Line 143: change ‘at–80°C’ to ‘at -80°C’
Line 284: change ‘EkGSTU1 performed better than EkGAPDH2 in root’ to ‘EkGSTU1 performed better than EkGAPDH2 in root’
……………
2. the authors are advised to screen the stable reference genes in other organ and tissues except for three developmental stages in fruits of E. konishii to satisfy some researchers who study this species.


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 BAYESIAN APPROACH TO CONSTRUCT CONFIDENCE INTERVALS FOR COMPARING THE RAINFALL DISPERSION IN THAILAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: The contents of this paper are very interested and suitable for publishing in this journal. There are some minor mistake for improving as follows:

1.The title is not suitable. It is not cover all details of the paper.

2.The author should show the source code of all algorithm (If possible).

3.In HPD credible interval, there are many prior distribution, i.e. Jeffreys’ prior, Jeffreys’ Rule prior, Normal-gamma prior. How do the researchers select the prior distribution in real situation?   The author should mention in this matter.

4. Which is the program for the simulation?
Experimental design: The experimental design is suitable. Which is the program for the simulation?
Validity of the findings: The findings for the paper are value to academic.
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: A BAYESIAN APPROACH TO CONSTRUCT CONFIDENCE INTERVALS FOR COMPARING THE RAINFALL DISPERSION IN THAILAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: I think the paper is fine. I find it at stages a bit technical and it might be helpful to write in wording what is actually going on.
Experimental design: The data are coming from routinely collected data and this should be fine.
Validity of the findings: The findings make senes to me but it should be clearly said this is based on the simulation work, which can always be only limitied.
Additional comments: I think the paper is fine. At stages, the text is very technical and it might be better to have a lighter wording for the journal of this type.

It should be pointed out how this paper is different from papers in submission with PerrJ already or with Biometrical Journal or other relevant submissions as we do not want to see the same work publsihed twice.

Details:
p2, line 69: "guaranteed" should be "states" or "argue"
p2, line 89: "Methods" should be "methods"
p4, 126: "be p-dimension" should be " be a p-dimensional"
p15, 368: incomplete reference
p16, 407 delete "Biometrische Zeitschrift"
Lower Mekong Basin: use consistetn spelling throughout


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 BAYESIAN APPROACH TO CONSTRUCT CONFIDENCE INTERVALS FOR COMPARING THE RAINFALL DISPERSION IN THAILAND
Review round: 1
Reviewer: 3

Output:
Basic reporting: The English is good with few minor typos (e.g.: line 84 stands should be stand). But the structure of the paper and its flow is somewhat weak. For example, Tables were not called in order in the text. e.g.: Table 3 (in the text) was called before Table 2 and 1, and Table 4 after table 5, which is very confusing.

Contribution of the paper is marginal and conclusions were not backed well by the analysis in the paper (see below). Overall, It is not clear what authors try to show or contribute in broad.
Experimental design: The purpose of this study was to develop CIs for the ratio of delta lognormal variances through Monte Carlo simulations. Building intervals is quite straightforward. I did not see any significant methodological contributions in the paper.
Validity of the findings: Conclusions are not solid.  For example: in the conclusion section, authors noted that "The findings of this study indicate that HPD-NG is undoubtedly the best and most recommended CI  (with varied δ) for both equal and unequal medium sample sizes" but how? and why it is "undoubtedly" the best? just by evaluating an empirical example?
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: A BAYESIAN APPROACH TO CONSTRUCT CONFIDENCE INTERVALS FOR COMPARING THE RAINFALL DISPERSION IN THAILAND
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The contents of this paper are very interested and suitable for publishing in this journal.


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

Input:
Title: A BAYESIAN APPROACH TO CONSTRUCT CONFIDENCE INTERVALS FOR COMPARING THE RAINFALL DISPERSION IN THAILAND
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am very happy with the revision.

It might be useful to also include the response to my 2. issue into the paper:

2. It should be pointed out how this paper is different from papers in submission with PeerJ already or with Biometrical Journal or other relevant submissions as we do not want to see the same work published twice.
Response: In this submission, confidence intervals for the ratio variances of delta-lognormal are proposed, whereas, other submission proposed CIs for the difference between variances of delta-lognormal populations based on Herbert et al. (2011) and Krishnamoorthy et al. (2011). Although, the difference between them is that the former was considered to estimate the ratio of two delta-lognormal variances (ω_1/ω_2) using HPD-based normal gamma prior. The latter was presented HPDs based on other priors for the difference in delta-lognormal variances (ω_1-ω_2) for large variational situations. According to Herbert et al. (2011) and Krishnamoorthy et al. (2011), the assessment of the range of distribution of (ω_1-ω_2) can be estimated using CIs for (ω_1-ω_2) such that it can be implied that there is the distributed range between (ω_1-ω_2) and (ω_1/ω_2).  Finally, both of random variables are used to check significantly difference in the two independent datasets. The next contrast between this submission and other one is the illustrated data that there are different dispersions and locations in each paper.
Remarks:
Herbert, R. D., Hayen, A., Macaskill, P. and Walter, S. D. (2011). Interval estimation for the
      difference of two independent variances. Communications in Statistics - Simulation and
       Computation 40, 744–758.
Krishnamoorthy, K., Lian, X. and Mondal, S. (2011). Tolerance intervals for the distribution of the
      difference between two independent normal random variables. Communications in Statistics –
        Theory and Methods 40, 117–129.
Experimental design: no further comments
Validity of the findings: ok
Additional comments: see aboe


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 BAYESIAN APPROACH TO CONSTRUCT CONFIDENCE INTERVALS FOR COMPARING THE RAINFALL DISPERSION IN THAILAND
Review round: 2
Reviewer: 3

Output:
Basic reporting: I have no other comments.
Experimental design: -
Validity of the findings: -
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: ECOSYSTEM ANTIFRAGILITY: BEYOND INTEGRITY AND RESILIENCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Nice review paper for interdisciplinary scientist thinking about stability and resilience of ecosystem. After presenting many definitions of resilience measure from the literature, it attempts to ask readers to think resilience in terms of anti-fragility, where the fitness function is an increasing function to environmental perturbations. In other words, as the authors put it, anti-fragile system flourishes and evolve in the presence of environmental stress/perturbation like climate change.

I read the paper as if anti-fragility might be more desirable measure than other existing definition of resilience. Thus, one possible improvement would be to also consider cases where anti-fragile system might be less desirable.


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: ECOSYSTEM ANTIFRAGILITY: BEYOND INTEGRITY AND RESILIENCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see general comments to the author for details.

I believe the language of the article needs work, particularly in paragraph and section organization. I also ask the authors to proof-read the work again for missing references and words. I believe more work on the Introduction is needed to better motivate the study.

The results are novel, interesting, and fitting for the journal but need much work to increase clarity.
Experimental design: Please see general comments to the author for specific comments and suggestion on organization and methods.
Validity of the findings: The results of literature review need to be organized and presented more clearly in order for the argument of the paper to be clearly supported and understood. Please see general comments to the author for details.
Additional comments: This paper reviews the insights of information theory approaches to ecosystem resilience and suggests the potential presence of “antifragile” ecosystems that benefit from fluctuations, i.e. ‘good years help more than bad years hurt’. I find the latter insight particularly interesting and valuable if the authors can better elaborate it using a simple example and illustrate its potential (i.e., concave-up relations) based on the current literature. Following this, my three major comments are:

1 - Unclear motivation, methods choice, and results from the literature review. I struggled with this section partly due to my limited knowledge of information theory, but especially due to the unclear question and organization here.

Introduction/motivation
1.1 - Whilst “ecosystem integrity” is clearly defined, it is not clear how/if this aspect is missing from longstanding theoretical work on ecological resilience. Ecological theory typically defines “ecological resilience” as the the magnitude of perturbations that ecosystems can withstand and return to the target state, as opposed to shifting into an alternative stable state. If a shift from one ecosystem steady state to another is different from losing “ecosystem integrity”, please clarify and emphasize this difference. If it is not different, consider focusing on “ecological resilience” rather than (engineering) “resilience” and “integrity” throughout.

1.2 - the overall focus on information theory needs to be motivated in the introduction - what does an information theory-oriented approach provide that conventional metrics of resilience do not? As this question implies, a comparison with conventional resilience metrics in the literature review could be very helpful.

1.3 - After motivating the information theory approach to resilience generally, the Introduction needs to motivate the specific question of the review. Is it to introduce the readers to potential uses of information-based metrics of resilience? Or the findings of resilience studies that use information theory? Both are valuable but a specific focus is critical for the paper to have a clear goal.

Methods
1.4 - I do not understand why the authors limit the meta-analysis of information theory-based resilience analysis only to papers that also mention “ecosystem integrity”. This seems to needlessly and severely constrain sample size (7 papers!) based on an arbitrary metric of whether the “integrity” language was used. To be clear, I think “integrity” is well-defined in this paper, but in my experience it is not a universally used term in the way “resilience” and “information theory” are.
I suggest (a) use a larger sample size in the literature review by omitting “ecosystem integrity” from the query OR (b) omitting the literature review altogether and just focus on the focal papers you chose.

1.5 - what is the point of figures 4-8? These results are not mentioned anywhere in the manuscript. It may be better to omit or move these figures to an appendix; otherwise, they distract the reader from the main message.

Results
1.6 - I struggled to understand the main findings of this section because many paragraphs simply summarize papers without clearly connecting them to the main narratives. It seems the main results are “We found (see Figure 9) three main narratives (a) Ecosystem properties that enable them to be more resilient; (b) Ecosystem response to perturbations; and (c) Complexity. From this and complementary literature consulted we have identiﬁed 11 possible indicators for ecosystem resilience (See Table 5)”. If so, please:

1.6.1: make these 3 narratives the titles of sub-sections. Start each sub-section with a paragraph reviewing the connection between the narrative and ecosystem resilience/integrity or ecological resilience.

1.6.2: as you reference findings from different papers, be careful to convert them to the standard terminology you use in this paper (see major comment #3).

1.6.3: Throughout, rework paragraphs to have clear topic sentences. That is, the first sentence in each paragraph should clearly main point or theme of the paragraph. Clear writing is especially important when communicating unfamiliar (for ecologists) concepts like information theory or frequently misinterpreted concepts such as resilience. For details, please see “Writing Science: How to Write Papers That Get Cited and Proposals That Get Funded” by Joshua Schimel.

1.6.4: In Table 5 (which is a great summary!), please add a column denoting which narrative/feature each metric relates to.

2 - Better clarify the potential for antifragility and its relation to complexity.

2.1 It is unclear how often antifragility might happen in natural systems, especially at the ecosystem scale. The underlying driver of antifragility is a concave-up relation between “environment” and ecosystem condition. However, it is unclear when, if ever, such a relation could arise and have measurable impacts at the scale of entire ecosystems. In population dynamics, for instance, the most common finding is a concave-down relation - that bad years hurt more than good years help. I would like the authors to:

2.1.1 - add a table that includes examples of concave-up ecological relations AND their observed scale - ie, whether the “response” is measured at the individual, population, or ecosystem level. Some ecological examples that might fit here are:
Storage effects (see Chesson, P. (2000). Mechanisms of maintenance of species diversity. Annual review of Ecology and Systematics, 31(1), 343-366.)
Disturbances reducing meta-population or -community synchrony (Fox, J. W., Vasseur, D., Cotroneo, M., Guan, L., & Simon, F. (2017). Population extinctions can increase metapopulation persistence. Nature ecology & evolution, 1(9), 1271.)

2.1.2 - add a Discussion paragraph elaborating how antifragility might be detected in natural systems. Right-skewness in ecosystem state distributions seems to be one indicator, but perhaps you might discuss potential reasons of how processes unrelated to fragility might also affect state skewness, for instance transient dynamics. Alternatively, if there are too many variables confounding skewness, perhaps the answer is that quantifying antifragility requires a validated, mechanistic model of ecological dynamics.

2.2 - Provide a concrete example of “complexity” and how it translates to fragility using a simple ecological model (e.g., of population size). A good model to use may become apparent after assembling the table mentioned above (2.1.1). One simple example might be the relation between physiological performance (e.g., per capita fecundity F) and temperature, which is concave-up at lower temperatures and concave-down at higher temperatures. The population dynamics would then be dn/dt = F(Temperature)*n*(1-n).

3 - Clarify definitions of terms as used in the paper.

3.1 - Please include a table listing all terms found in the paper and their definitions, such as “integrity”, “resilience”, “complexity”, “sustainability”, etc.. In this table you may omit the metrics that you define in Table 5.

3.1 - “resilience” is an oft-confused term in ecology. Throughout, I suggest you use either “engineering resilience” (return time) or “ecological resilience” (see point 1.1). Regardless, please be sure to define both integrity and resilience (or ecological resilience, if you use that instead) from the very beginning (Paragraph 1 of Intro).

Smaller comments:
	* How is Figure 9 made?
	* Line 65-66: here, please clarify that “persistence time” is only a relevant metric if the current ecosystem state is not globally stable - i.e., that another attractor exists. Much of the current confusion over ecological resilience lies in studies implicitly assuming that in a given system another attractor exists without explicitly defining what it is. Also, here please point out the close relation of “persistence” with “ecological resilience”.
	* Lines 63-64 “and assumes that there is only one balance or a stable state”: I do not think “engineering resilience” assumes a single steady state; it just measures the return speed to a given state. So multiple attractors would each have their own engineering resilience.
	* Lines 67-69: Currently many ecologists refer to “resistance” as the magnitude of disturbance that a system can withstand without a change in phase (e.g., intensity of drought that causes tree mortality and decline in abundance). Please either change this accordingly or provide a more recent reference for the definition you use.
	* Line 71 “Robustness relates to the durability of the stability of the environment”: I don’t understand this sentence.
	* Lines 169-171 “to enhance ecosystem’s long-term sustainability, a particularly densely connected network structure is advantageous”: I am not sure what you mean by sustainability in this MS and how it differs from other terms you use. You may need to caveat this statement because in general high connectance (1) can reduce ecosystem stability (“engineering resilience”, see May, R. M. 1972. Will a large complex system be stable? Nature 238:5364) and (2) can allow phase transitions to spread more readily through a system.
	* Line 291 “...or it exhibits changes in the configuration space comparable to the observer’s time scale”: this is unclear - please reword more simply.
	* Throughout, check for word misspelling and missing references.
	* Throughout, please check for mistakes in grammar and word choice. For instance, on lines 290-291 “a system is complex either it presents” I believe should read “a system is complex if either it presents”.