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 NEW JUVENILE YAMACERATOPS (DINOSAURIA, CERATOPSIA) FROM THE JAVKHLANT FORMATION (UPPER CRETACEOUS) OF MONGOLIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is generally a well-written article, and the osteological description is adequately detailed. There are several places in the ms where I find the phrasing somewhat awkward, as indicated in the attached markup. The ms is well-referenced, although I note that some of the references cited in-text are not also given in the Literature Cited section at the end (indicated in the markup). Where key comparisons are drawn to other taxa, emphasizing the uniqueness of the new specimen, I think some additional comparative figures would be useful. I note in the markup that the correspondence between figures 2A and B is not very good, and feel that the latter should probably be re-done. The lines overprint the LAGs in Figure 9, and should instead be indicated by arrows. Figure 11 is not especially aesthetic (especially compared to Figure 10), and should be redone to improve readability, perhaps by collapsing the genera that comprise Ceratopsidae. A table of standard measurements for the skeleton should be provided to facilitate comparison with other specimens. I would also like to see some additional background information provided about the Javkhlant Formation, which would help frame the discussion concerning the taphonomy of the new juvenile (the taphonomy of the specimen should likewise be placed first in the Discussion).
Experimental design: The methods employed here (cladistics, histology, CT scanning) are standard at this point, and not entirely concerning. Although the authors go to the effort of coding their new specimen into the matrix of Knapp et al., by their own admission, this matrix focuses heavily on the in-group relationships of Ceratopsidae. Therefore, it isn't entirely clear why the authors chose to code their specimen into this matrix. I wonder if the article might not be better served by relegating the results of the Knapp et al. analysis to a supplementary file, and limiting the in-text focus to the analysis of the Arbour and Evans matrix. This would both shorten the article and improve the readability. The authors should indicate how they calculated their support values in their cladograms. The changes made to prior codings for Yamaceratops should be summarized in a supplementary table. The authors should use developmental mass extrapolation when estimating the body size of their juvenile specimen because the standard femur circumference-body mass regressions apply to adults only.
Validity of the findings: I have no major issues with the validity of the findings. Given the weak support values on the cladogram(s), the authors should probably couch their conclusions about the placement of Yamaceratops relative to other neoceratopsians in more considered language. Some of the authors' anatomical interpretations appear to be 'off' in places (e.g., the preacetabular process of the ilium is visibly much shorter than the postacetabular process; the histology of the femur is described as both lacking evidence for remodeling and having it). The morphological significance of the parietal should be downplayed, given the authors' early admission that the identification of the bone is only tentative.
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: VALIDATION OF A DUAL-TASK EXERCISE PROGRAM TO IMPROVE BALANCE AND GAIT SPEED IN OLDER PEOPLE (DUALPRO): A DELPHI STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: General comment (originality, scientific accuracy, strengths and/or weaknesses): Thank you for the opportunity to review the present paper. The topic is interesting and the paper is well written however some minor changes are required.
Originality and strengths: the a Delphi study creating and validating a DT exercise program for older adults to improve balance and gait speed has not been studied before.

Major corrections (main criticisms): Figures are very low quality, also could you not include the results from L265-273 into the figures rather than as text as its very hard to follow with so many exercise being spoken about. There is also some inconsistency with reporting in this paragraph with some exercises missing (N = X).
discussion needed to intertwine your study results into this section, needs to be made stronger. Also missing paragraph on balance - you have emphasis on gait speed but missing the importance in discussion here.
Introduction should be improved
Table 1 should be supplementary and figure 1 needs to be clearer in terms of the text provided - hard to read the figure have to zoom in significantly to understand what is going on but I can not make out what the actual % are within the figure/.

Minor corrections (page, paragraph, line where the author must make the corrections):
abstract
L37: either re-write to keep in results section or keep as is and move to methods section.

introduction
L57: error with reference - requires fixing
L65: more detail required at the end of that sentence as you go into detail about motor deficits but no on cognitive alterations
L70: in reference to "them" what do you specifically mean here?
L76: provide more than one reference to strengthen this
L80; you need to pick a term and be consistent throughout, sometimes you say older adult, older person or ageing patient. pick one.
L92: references required for your statement
L102-103: repeats what you have stated above on L92-93/
L113: missing full stop

materials and methods
L117: consistency of term again noted here - pick one and keep it
L123: how long did the process take?
L158: best to avoid starting with K - rewrite sentence
L168-174 captions required with calculation
L181: was it anonymous to research team or just the participants to other participants? clarify
L195:"them" explain and be specific here in what you are referring to
L197: which was when ... what happened to stop the rounds.
L200: state what all 11 exercises are
L205-206: provide more clarification are you just taking about the exercises or the Delphi rounds?
L211: be very clear which response equaled which Likert scale number

statistical analysis
L225: how were rounds analysed?
L226; version of Excel?
L232: you have already used acronym for Q1 and Q3 so can be used here rather than full spelling

results
L246: extra space needs to be removed
L253: did any experts drop out? how many experts did you start with?
L290: replace or with and
L293: space required between paragraphs
L308: emphasis point which should be made in intro as well
L317: how have all these conditions been taken into account?
L326: remove 'prioritization' after fixed
L333: include reference for statement
L339-346; missing the link to cognitive impairment again -this really needs to be linked into the discussion but is missing
L338: space between paragraphs missing
L356: space between paragraphs missing
L356-363: merge paragraphs together
L380-382: different wording to L107-109 - consistency issue again here
Experimental design: please refer to above
Validity of the findings: please refer to above
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: VALIDATION OF A DUAL-TASK EXERCISE PROGRAM TO IMPROVE BALANCE AND GAIT SPEED IN OLDER PEOPLE (DUALPRO): A DELPHI STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: English language should be revised thorughout the manuscript for minor errors (Examples: "work on physical activities" Line 74; "Training activities such as for gait" Line 98).
"physical activity" and "exercise" are used indistinctly thorughout the text, however, they are not synonyms. Authors are advised to check the terms and make the neccessary corrections.

Background and justification of the study: The background and justification of the study need revising for better structuring the information and addressing how cognitive function declines with ageing, the link between cognition and motor disturbances, and the mechanisms by which dual-task training might exceed the benefits of single task training.

Examples that can be found in the attached pdf provided:
Additional information on cognitive decline and the link between cognitive impairment with gait and balance would be helpful to understand the importance of including not only physical but also cognitive training in older adults (Lines 64-65).

The term dual-task needs further explanation and justification, including why it is relevant in this population (Lines 75-88).
Experimental design: The research question is relevant and meaningful for older adult populations. Overall, the methodology seems appropiate, however, further details on the physical and cognitive aspects of the intervention would be advisable.

No information has been given regarding the cognitive functions addressed through DT training thoughout the text and why those specific cognitive tasks were selected. In addition, information regarding whether the difficulty level of cognitive tasks could be adjusted. Authors are encouraged to include this information in the manuscript.

The authors state the following "divided into five levels that progressively increase in difficulty" (Lines 201-202). Does difficulty come from the type of exercises, the type of prioritization, or both? Authors are advised to specify how task difficulty progression has been designed.

The authors state the following: "For progress at each level, the older people must be able to perform the previous level safely and without an increased risk of falling" (Lines 206-207).This is an important aspect of the intervention. Authors are encouraged to include more detailed and as objective as possible criteria for exercise completion to progress to more complex exercises.

Information on the target population should be given, since it would need adapting for individuals with different levels of physical impairment (Line 209).

The authors state the following: "training in a single task condition is insufficient to improve functional walking (Silsupadol et al., 2009)"(Line 213).To date there is not enough evidence to make categorical affirmations regarding single and dual-task training for DT improvement. Therefore, other terms such as "might", or "it has been suggested" are preferable.

The authors state the following: "in both intervention groups" (Line 336). However, the characteristics of the groups have not been described (controls, a certain intervention...).
Validity of the findings: If the effectiveness of the DT intervention was demonstrated to improve gait and balance to a greater extent than with physical training, a protocolized DT intervention could be relevant to improve functionality and reduce the risk of falling in older adult populations.

The conclusions are appropiate.
Additional comments: The manuscript provides with a promising intervention to improve functionality and reduce the risk of falling in older adults. The methodology to validate the program seems adequate. However, the introduction needs revising to improve the rationales of the study by including more information regarding the link between cognitive and motor disturbances and how dual-task training may be more effective than physical training alone, including previous relevant studies.


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: VALIDATION OF A DUAL-TASK EXERCISE PROGRAM TO IMPROVE BALANCE AND GAIT SPEED IN OLDER PEOPLE (DUALPRO): A DELPHI STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is an interesting and straightforward study on the creation and validation of a DT exercise program that looks to improve balance and gait speed in the older adult population. I would like to commend the author(s) for focusing on a sample that is often difficult to do research on. Delphi studies are very important in our quest to improve the balance and gait speed of older adults. However, there are some issues that I think should first be addressed so that they can meaningfully contribute to the body of knowledge on DT exercise programs for older adults.
Experimental design: The main change in the experimental design would be to condense Figures1-5 into a figure and include either a Table or Figure on what exactly entails the DT program to really show your audience how this DT program is different from all the rest and how it shows the impact it has for improving balance and gait speed for the older adult population.

The research question is well addressed and relevant. It is also well defined and meaning full to the older adult population. Well done on examining an area that has been underdeveloped and bringing to fruition an area that will make a significant impact. I look forward to seeing the DT program put into practice. The paper is well laid out, with just some minor comments in the attachment in regards to being concise and clear in certain areas.
Validity of the findings: The paper is well defined with valid findings from the Delphi study documented.
Additional comments: See attached the PDF of the manuscript with further comments and edits.


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: VALIDATION OF A DUAL-TASK EXERCISE PROGRAM TO IMPROVE BALANCE AND GAIT SPEED IN OLDER PEOPLE (DUALPRO): A DELPHI STUDY
Review round: 3
Reviewer: 1

Output:
Basic reporting: Comments have been addressed. I have no further comments for this manuscript.
Experimental design: Comments have been addressed. I have no further comments for this manuscript.
Validity of the findings: Comments have been addressed. I have no further comments for this manuscript.
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: INFLUENCE OF BIOLOGICAL MATURATION STATUS ON SELECTED ANTHROPOMETRIC AND PHYSICAL FITNESS VARIABLES IN ADOLESCENT MALE VOLLEYBALL PLAYERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The research work presented in this manuscript aimed to analyse the differences between predicted biological maturation status (early, average and late maturer groups) in performance of the selected physical fitness tests, and to determine which kinanthropometric variables could predict better performance in physical fitness tests, in adolescent male volleyball players. The participants were recruited from local region (of Spain) with age range 12-15, and n=48.
The authors concluded that significant differences based on the stages of biological maturation were found in the anthropometric and physical condition variables in favour of the players whose maturation process was more advanced, with the variables related to fat and adipose, muscle and bone development conditioning their performance in the physical condition tests.

The study is in an on-going area of research on the relationship between anthropometric characteristics and fitness/sport performance that may have implications in sport talent identification and coaching. The manuscript is well presented in general.

However, several areas in the article may need further clarification, and I would offer the following critiques for authors’ consideration, aiming to improve the clarity and quality of the manuscript.
Experimental design: As the authors have acknowledged, a limitation of the study was to use the equations developed by Mirwald et al. (2002) to estimate the maturation. The equations were established from a different (wider age range) and non-athlete (not specifically on volleyball) population. Such a limitation has been repeatedly highlighted in the literature. As a reader and a researcher, I would like to know why the authors did not actually measure the PHV (or establish the validity of using the equations in the target population), and how confident the authors were in respect of the conclusions. In case some errors may be embedded in the estimated maturation, would the relationship between the anthropometry and performance measurements be quite different or similar if the chronological age groups were used (e.g., 12, 13, 14, 15 years)? A comparison between the outcomes from the two approaches would be make more sense to inform practice. Or, at least some more in-depth discussion on the limitations would be appreciated by the readers.

How were the fitness tests selected in this study? Are these tests volleyball specific? E.g. no test/s on aerobic power was included. I would suggest add “selected” in the title before “kinanthropometric”, with some justification in the manuscript for the selections.
Validity of the findings: In the title of the article “kinanthropometric” was used, but in the text the measurements were basically “anthropometry”. The authors may consider define and use these terms according to the context.

The second aim of the study was “to determine which kinanthropometric variables could predict better performance in physical fitness tests…”. However, the Result section only showed some significant correlation coefficients. No prediction equation was presented in the text or Table 7. It should also be noted that whatever the correlations were, the application might only be limited to the population studied.
Additional comments: In Table 1, the unit for CMJ should be “m” or the values should be corrected as for “cm”.
Line 217: please use “show”.


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: INFLUENCE OF BIOLOGICAL MATURATION STATUS ON SELECTED ANTHROPOMETRIC AND PHYSICAL FITNESS VARIABLES IN ADOLESCENT MALE VOLLEYBALL PLAYERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study examined the interesting topic of "biological maturation status" and the relationship between "kinanthropometric and physical fitness variables". The study is written in a scientific manner and is easy to understand.
Experimental design: The experimental design is explained in the method section. The number of participants used for the study is sufficient. Experimental methods are explained in an explanatory way.
Validity of the findings: The findings are explained with appropriate tables.
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 AND ANALYSIS OF SUCROSE SYNTHASE GENE FAMILY ASSOCIATED WITH POLYSACCHARIDE BIOSYNTHESIS IN DENDROBIUM CATENATUM BY TRANSCRIPTOMIC ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this work, the authors comprehensively investigated sucrose synthase genes in the plant species Dendrobium catenatum. With the implementation of metabolic, transcriptomic, KEGG enrichment, and phylogenetic analyses et al., the authors revealed expression patterns of SUS genes in various tissue types at different developmental stages in relation to relevant polysaccharide accumulation, as well as their evolutionary trajectories. This work helps understand the molecular mechanism of polysaccharides metabolism. I recommend publication of this manuscript after minor revision.
Experimental design: Experiments are overall well designed and clearly described, the authors may want to include the information regarding how the transcriptomes were assembled.
Validity of the findings: Findings and conclusions are generally well supported, I don’t have major comments, certain typos need to be corrected, e.g., line 149, line 213, fig. 6a.
Additional comments: No


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 AND ANALYSIS OF SUCROSE SYNTHASE GENE FAMILY ASSOCIATED WITH POLYSACCHARIDE BIOSYNTHESIS IN DENDROBIUM CATENATUM BY TRANSCRIPTOMIC ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this study, Jian et al. used the four different developmental stem stages of Dendrobium cantenatum to compare the contents of polysaccharides and mannose and analyze their transcriptomes to explore biological mechanism of polysaccharides biosynthesis. This study is different from other previous related studies. Thus, their results could be formally published. However, at present the manuscript has some apparent weak points as showed below:
1)	The authors simply described the sampling method as that the four developmental stages of D. catenatum stems of ‘Hongxin 6#’ plants, were sequentially collected from the plantation (Honghe, Yunnan, China) for paired-end transcriptome sequencing. Generally, the catenatum dendrobums farms get the seedlings from the seeds and different seedlings have diversity genotypes. More important, several catenatum dendrobums individuals are grew together to form a cluster in the farms. Thus, it is possible that different stems from same cluster have various genotypes. Therefore, it is necessary for authors to check their sampling materials in the four developmental stages of D. catenatum stems are the same genotype or different genotypes.
2)	If different stems from the same cluster have different genotypes, the authors need to be careful about their conclusions, such as lines 467-470, “Furthermore, DcSUS10 had higher expression in S3 and S4 than that in S1 (Fig. 6b), similar to their polysaccharides and mannose content (Table 1), suggesting that the sucrose synthesis in different stem development might be closely involved with DcSUS genes”. It is possible that the results of DcSUS10 having higher expression in S3 and S4 than that in S1 (Fig. 6b), similar to their polysaccharides and mannose content are caused by different genotypes rather than the different development stages.
3)	Lines 68-73: The authors stated that “The activities of sucrose invertase and sucrose-phosphate synthase (SPS) are correlated with polysaccharide levels (Wang et al., 2013), and sucrose breakdown is largely catalyzed by SUS and invertase (Huber and Huber, 1996). SPS and SUS genes have been reported to be related to polysaccharide generation (Yan et al., 2015). Hence, it is reasonable to speculate that SUS gene is likely also involved in the polysaccharide biosynthesis in D. catenatum”. In fact, Wang et al. (2013) suggested that the activities of sucrose invertase and sucrose-phosphate synthase (SPS) are correlated with polysaccharide levels in D. catenatum. However, the conclusion that sucrose breakdown is largely catalyzed by SUS and invertase by Huber and Huber (1996) is a general principle rather than especially for D. catenatum. It is not clear that this general principle can be used in D. catenatum or not. Moreover, Yan et al. (2015) only listed the potential genes that related with polysaccharide generation based on their whole genome sequence results. Therefore, it is not clear how the authors have got the speculation that SUS gene is likely also involved in the polysaccharide biosynthesis in D. catenatum.
4)	Lines 430-433: the authors said that “These tandem duplicates generally played vital role in plant adaptation to response rapidly changing environments (Hanada et al., 2008). Therefore, we have reason to speculate the richness of polysaccharides in D. catenatum might be related to the expansion of these genes”. The authors have not given out any information about the D. catenatum has adapted to response rapidly changing environments. How the authors can speculate that the richness of polysaccharides in D. catenatum might be related to the expansion of these genes?
5)	Line 412: The authors used one plant name D. officinale. Actually, both the names of Dendrobium catenatum and D. officinale are the same entity. So, this sentence can be changed as “which had identified involved in biosynthesis of mannan polysaccharides in D. officinale (D. catenatum) (He et al., 2015)”.
Experimental design: Fine
Validity of the findings: Nice
Additional comments: No


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 AND ANALYSIS OF SUCROSE SYNTHASE GENE FAMILY ASSOCIATED WITH POLYSACCHARIDE BIOSYNTHESIS IN DENDROBIUM CATENATUM BY TRANSCRIPTOMIC ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: In the manuscript entitled “Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis”, the authors used bioinformatic methods to analyze the sucrose synthase gene in Dendrobium catenatum. The amount of data analyzed is large and the results obtained are abundant.

I believe that this article can meet the requirements published in Peerj after reversion.

Comments
1.	The organization of paper writing also needs to be further improved.
2.	Overall, major text in the discussion looks fine. However, a better discussion will help improve the manuscript.
3.	Reference needs further examination. Retain the relevant and recent literature/report.
4.	Before being considered for publication, the manuscript will be corrected by a fluent English speaker, alternatively please use one of the commercial English language editing services available.
Experimental design: well
Validity of the findings: well
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 AND ANALYSIS OF SUCROSE SYNTHASE GENE FAMILY ASSOCIATED WITH POLYSACCHARIDE BIOSYNTHESIS IN DENDROBIUM CATENATUM BY TRANSCRIPTOMIC ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have carefully addressed my comments, I suggest accepting in its current form.
Experimental design: Well
Validity of the findings: Well
Additional comments: No


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 AND ANALYSIS OF SUCROSE SYNTHASE GENE FAMILY ASSOCIATED WITH POLYSACCHARIDE BIOSYNTHESIS IN DENDROBIUM CATENATUM BY TRANSCRIPTOMIC ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed all questions raised by reviewers. I have no more questions. However, I think it will be better if the authors can give more infromation about the variety of ‘Hongxin 6#’.
Experimental design: No comment
Validity of the findings: no commment
Additional comments: no


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: VERTICAL DISTRIBUTION OF SOIL SEED BANK AND THE ECOLOGICAL IMPORTANCE OF DEEPLY BURIED SEEDS IN ALKALINE GRASSLANDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I carefully read the ms “Vertical distribution of soil seed bank and the ecological importance of deeply buried seeds”.
The authors analyzed the distribution of germinable seeds along with other seed traits (e.g. morphology, mass, tolerance to salinity…) up to a depth of 80 cm. The ms is interesting, as it addresses the role of seed banks, focusing on deep layers, which provides important insights in the field of biodiversity conservation and restoration.
I have only one issue that is not very clear to me, that is the reference to “seed density” (e.g line 262, and throughout the text, abstract included), which in my opinion generates confusion. Since the authors used the seedling emergence method (line 185), they actually measured the “seedling density”, i.e. the proportion of germinable seeds. This is fine, but I think that it should be specified more clearly, since possible non-germinable (dormant?) seeds may be part of the seed bank, and some seeds, possibly fallen in deep layers, may have died during the experiment. Thus, I suggest to replace “seed density” with something else (“seedling density”? “germinable seed density”?) throughout the text, when necessary.

Tables and figures: please, note that you provided a double legend for  each table and figure

Supplementary file: please, provide a legend for the supplementary file. Explain in the legend the meaning for WB and SB, and add the unit of measurement to seed traits (e.g. “Seed length (mm)”, Seed mass (g? mg?)”
Experimental design: The experimental design and data analyses were well performed
Validity of the findings: No comment
Additional comments: Below I list minor points:
Line 66: did you mean “shaping” instead of “shaping of”?
Lines 85-90: this sentence is not clear: The diversity and density of soil seed bank is generally highest in the most stressed grassland types due to unfavourable environmental conditions? Maybe the sentence needs to be split in two parts.
Lines 127-128: does alkali grasslands correspond to a Natura 2000 habitat? Can you add the habitat code for the environments that you have investigated?
Line 152: did you mean “are classified” rather than “classifies”?
Line 156: delete the repetition (see line 154)
Lines 216-218: How did you calculated the CWM for each layer? Specifically, on which value did you weighted each seed trait? On the number of emerged seedlings? Please explain the procedure that you used
Line 248: replace “seed density” with something else, here and throughout the text (as explained in my comment on the basic reporting)
Lines 248-254: I suggest to represent these data in graphs (e.g. pie charts, or bars)
Line 282: the letters A-F are missing in the figure
Line 342-355: Are forbs more abundant or less abundant than grasses in your study system? Is it possible that seeds from forbs were more abundant than seeds from grasses because forbs have a higher cover percentage than grasses in the grassland? While the relative abundance along the depth gradient of grasses, forbs and other categories assigned to the seedlings that emerged during the experiment can be compared (e.g. “forbs were more abundant in the deepest layer, while grasses were more abundant in the upper layers”), absolute abundance of given categories (e.g. forbs vs grasses, or grassland species vs weeds) should be discussed in relation to the species composition and species cover of the grassland. Please rephrase the paragraph eliminating or addressing comparison of absolute abundances.
Line 369-375: summarize this paragraph avoiding repetitions (see line 133)
Line 398: delete the question mark
Line 425: did you mean “in other” instead of “is other”?


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: VERTICAL DISTRIBUTION OF SOIL SEED BANK AND THE ECOLOGICAL IMPORTANCE OF DEEPLY BURIED SEEDS IN ALKALINE GRASSLANDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors analyze depth distribution of viable seeds in deeper soil layers down to 80 cm depth which has been rarely done so far in soil seed bank studies that are usually confined to the upper 10 cm of the soil profile. Seed soil bank analyses were done at five alkali grassland sites with Solonetz soils that are characterized by a strong shrink-swell potential due to high clay content and the regular occurrence of desiccation cracks during periods of drought that may facilitate the penetration of seeds to deeper soil layers.
The major finding is that viable seeds – albeit in very low densities - may be found down to a depth of 80 cm which has rarely been shown before. The authors argue that this is probably caused by the physical peculiarities of the studied Solonetz soils, in particular due to the regular occurrence of desiccation cracks. In general, the paper is well written, except some cases where phrasing and wording could be improved (see examples Additional comments).
Experimental design: Technically the soil seed bank analysis is well executed with remarkable depth resolution in steps of 5 cm.
Validity of the findings: The major problem I see with this study is the rather limited explanatory power due to the low number of replicates (five) and the confinement to one soil type which is constraining the detection of patterns in the functional characteristics of seeds in deep soil layers and does not a allow a comparison between soil types with and without desiccation cracks to assess their importance the allocation of seeds to deeper soil layers. Therefore, I feel that the results are overall of limited value and validity. Increasing the number of replicates and including another soil type without desiccation cracks could considerably increase the validity of the study. Nevertheless, the finding of viable seeds in such deep soil layers alone is quite remarkable and may probably as such justify publication.
Additional comments: Specific comments

L 48-49: “Forbs, grassland species and short-lived species occurred in large abundance in deep layers, from where graminoids, weeds and perennial species were missing.” I feel the characterization of plant groups here is a bit confusing, due to overlapping characteristics.

L104-106: There should “to” in front of “enter” and “along” in front of “cracks”

L110-111: “As the area of natural habitats is still rapidly declining, it is an important task to maintain their species richness, to which soil seed bank studies may contribute.” There is something wrong with the logic of this sentence.

L113: Skip the first usually in this line.

L 117: “the chances of the effectiveness” sounds a bit weird and redundant.

L 119 skip “usually neglected” (this was said before)

L310-311: You use the verb “found” three times in a relatively short senence.

References: I feel one important reference is missing: Burmeier, S., Eckstein, R.L., Otte, A. & Donath, T.W., 2010: Desiccation cracks act as natural seed traps in flood-meadow systems. - Plant & Soil 333: 351-364.

Fig 1 and 2: Due to the large number of overlapping points (in particular zero values), box plots would probably give a better impression about the distribution of seeds.


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: VERTICAL DISTRIBUTION OF SOIL SEED BANK AND THE ECOLOGICAL IMPORTANCE OF DEEPLY BURIED SEEDS IN ALKALINE GRASSLANDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: ok
Experimental design: ok
Validity of the findings: ok
Additional comments: I received the revised version of the ms. The points risen during the revision process were properly addressed, so I think that the ms is now ready for publication.


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

Input:
Title: COMPARISON OF GUT MICROBIOME IN THE CHINESE MUD SNAIL (CIPANGOPALUDINA CHINENSIS) AND THE INVASIVE GOLDEN APPLE SNAIL (POMACEA CANALICULATA)
Review round: 1
Reviewer: 1

Output:
Basic reporting: I commend all authors for their study conducted. However, I recommend major revision for this article before getting accepted. Following are the suggestions that the authors need to follow prior acceptance of this manuscript.
1.	Abstract needs to be rewritten and structured with subheadings.
2.	Introduction: Do you have any record, of when did the other snail species invasion took occurred. If so, make a mention of the same here in the introduction part.
3.	Materials and Methods: How were the snails collected? Objective of the study needs to be very clear and you need to mention hypothesis.
4.	Results need to be re-organised and clear. It would be nice if you could provide a table of percentage of phyla and so on, for the species percentage composition for the two species.
5.	Discussion needs to be revised. You need to put forward your explanation of how would the invasion mechanisms would be traced through gut microbiome, as this is also one of your objective of study. You can consider the following flow for writing discussion.
6.	Conclusion drawn from the study conducted and the object of the study are not corelated in the manuscript. Conclusions are not well stated.
7.	Journal Format is poorly followed in the reference section.
	The reference section needs to be revised according to the journal format. The references need to be in chronological order.
	Never copy and paste the references.
	The font size should be 12 instead of 10.5 throughout the reference section.
	Genus and species need to be in italics and not normal fonts even in the reference section.
	Provide DOI number for every article cited, if available.
All figure legends are poorly done, which hardly provide information of what was done in which species. Elaborate the figure legends thoroughly.
8.	Throughout the manuscript insert comma after et al.
9.	All figure should have same font styles.
There is no mention of ethical permission in the article which needs to be added.
10.	Either use symbol or words for “alpha” throughout the manuscript that includes text, figures, figure legends and tables.
11.	For the statistical analysis, “t-test” “t” needs to be in italics. Replace “t” with “t” throughout manuscript
Experimental design: The study design is simple and can be replicated, but the method to collect the individuals is missing. There is no mention of ethical permission in the article which needs to be added. Statistical analysis is done adequately and thus the results are well supported for the tests conducted.
Validity of the findings: Results need to be re-organised and clear. It would be nice if you could provide a table of percentage of phyla and so on, for the species percentage composition for the two species. Discussion needs to be revised. You need to put forward your explanation of how would the invasion mechanisms would be traced through gut microbiome, as this is also one of your objective of study. You can consider the following flow for writing discussion. Conclusion drawn from the study conducted and the object of the study are not correlated in the manuscript. Conclusions are not well stated.
Additional comments: Line No 1-4: Kindly modify title of your manuscript as it is not appealing.
Line No 45-80: Rewrite the introduction. Write the objective of study and hypothesis clearly.
Line No 82-89: You need to mention, how were the snails collected.
Line No 90-93: Why did you mix the digestive system of five snails together and grouped them? Was the sample of each snail gut not sufficient for the gut microbiome analysis?
Line No 106-108: PCR conditions-mention details (rewrite).
Line No 173: What are those 8 samples? You need to mention it.
Line No 173-177: Rewrite. Each group should have its own percentage.
Line No 178: Which two groups??
Line No 186-199: Revise. You should be clear, which group of genus has the respective percentage. It would be more clear, if you could represent the same in the form of table.
Line No 209: Replace “Function prediction of gut microbiota” with “Functional prediction of gut microbiota”.
Line No 232: “The composition and diversity of gut microbiota can be affected by a variety of factors.” Which factors? You also need to mention about the invasion of species and then the differences of native and invasive species.
Line No 243-245: “However, the Chao1 and Observed species indices showed marked differences in gut microbiota abundance between the two groups, with significantly higher abundance in the PC group than in the CC group”. What do you mean here?
Line No 342-347: Conclusion is not well stated and needs to be revised.
Line No 489-492: Change from capitals to small letters.
Figure Legends: Revise the figure legends.
	Figure 1: Here you need to mention, which Alpha diversity indexes have been investigated.
	Figure 4: Revise figure legends. You need to mention the significance values here and add additional details.
	Figure 5: Revise figure legends.
	Figure S1: “Rarefaction Curve based on Shannon index”. Add more details, which species and how many replicates were used.
	Figure S2: Revise figure legends.
	Figure S3: “Venn diagram of shared and unique OTUs among different groups”. You need to mention here, which were the different groups examined.
	Figure S4: Revise figure legends.
	Figure S5: Revise figure legends.
	Figure S6: Revise 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: COMPARISON OF GUT MICROBIOME IN THE CHINESE MUD SNAIL (CIPANGOPALUDINA CHINENSIS) AND THE INVASIVE GOLDEN APPLE SNAIL (POMACEA CANALICULATA)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Comments to the Authors
Review of "Comparison and diversity of gut microbiota between invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) (#68660)"

In this study, the authors compared gut microbiota of two sympatric freshwater snails (invasive golden apple snail and native Chinese mud snail). It is an interesting study for helping clarify invasion mechanism of golden apple snail at microbial level, with comparation from local snail species. However, there still are some questions below. I suggest it would be considered acceptation for publication at PeerJ after addressing the following comments.
Experimental design: The experimental design of this study is good, and the experiment was carried out very well.
Validity of the findings: This paper looks at the interesting comparation of  gut microbiota between invasive snail species and local snail species. The results are very interesting, which can clarify invasion mechanism of golden apple snail at microbial level.
Additional comments: Comments to the Authors
Review of "Comparison and diversity of gut microbiota between invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) (#68660)"

In this study, the authors compared gut microbiota of two sympatric freshwater snails (invasive golden apple snail and native Chinese mud snail). It is an interesting study for helping clarify invasion mechanism of golden apple snail at microbial level, with comparation from local snail species. However, there still are some questions below. I suggest it would be considered acceptation for publication at PeerJ after addressing the following comments.

Major and minor comments:
Introduction
1)	Insufficient focus in the introduction. For example, line 53-59: The authors describe the importance of gut microbes to hosts. However, they did not support the statement "Therefore, comparing the diversity and structure of the gut microbiota between sympatric invasive and native freshwater species may help clarify the underlying mechanisms related to invasion. (line 59-61)". Please provide some references for the statement and reworded the paragraph.
Materials and Methods
1)	Line 89-92: The authors used 20 Chinese mud snails and 20 golden apple snails. Why did you mix five snails as a single sample? Please provide more detailed sample collection information.
Results
1)	Line 215-223: There are F value and t value with one p value. Why does a significant difference have both F and T values? Please illustrate and correct.
2)	Figure 4(A and B): CC group has only one dot in NMDS plot (A and B). Are they overlapped? Please illustrate.
3)	Figures are too fuzzy. For example figure 4 and 5. Please provide high quality figure.
Discussion
1)	Line 249: "golden apple snail" inconsistencies in the text
2)	Line 288-291: "In addition, the ratio of these two phyla can have a significant influence on energy absorption in rats." Does high ratio promote energy absorption? Please make it clear to support your result.
3)	Line 284-285: "Bacteroidetes functions in the degradation of high molecular weight organic matter …" It needs editing for grammar and sentence structure for this sentence.


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

Input:
Title: COMPARISON OF GUT MICROBIOME IN THE CHINESE MUD SNAIL (CIPANGOPALUDINA CHINENSIS) AND THE INVASIVE GOLDEN APPLE SNAIL (POMACEA CANALICULATA)
Review round: 2
Reviewer: 1

Output:
Basic reporting: Initially, I commend all authors for their study conducted. However, I recommend “Minor Revision” for this article before getting accepted. Following are the suggestions that the authors need to follow on prior acceptance of this manuscript.
1.	Title “An insight into the role of gut microbiota in successful invasion of golden apple snail (Pomacea canaliculata)” is not clear and needs to be revised. I suggest you to change the title. You can revise it for example (a) “Investigation of snail gut microbiome between the native (Cipangopaludina chinensis) and the invaded (Pomacea canaliculata) species. (b) “Comparison of the gut microbiome in the native (Cipangopaludina chinensis) and the invaded snail species (Pomacea canaliculata) in China” etc.
2.	Abstract: Include the objective of your study.
3.	Introduction: You need to mention, of what is your hypothesis for the present study conducted. Also, the objective of the study conducted is not stated clearly. Kindly make a mention at the end of the introduction.
4.	Discussion needs to be revised as some information overlaps.
5.	Conclusion made from your study conducted, mentions of community and diversity of microbiomes in the two species (native and invaded), but does not state how the gut microbiome helps in understanding the invasion mechanism which needs to be focused.
6.	Corrections followed by Journal format need to be done in the text and reference section.
Line Number 11; Line Number 26; Line Number 56; Line number 59; Line Number 62; Line Number 62; Line Number 67; Line Number 70; Line Number 94; Line Number 104; Line Number 107; Line Number 119; Line Number 127; Line Number 131; Line Number 136-139; Line Number 143; Line Number 160; Line Number 165; Line Number 168; Line Number 189; Line Number 191; Line Number 207; Line Number 232; Line Number 239-240; Line Number 241; Line Number 249-252; Line Number 430; Line Number 460; Line Number 483; Line Number 486; Line Number 490; Line Number 499; Line Number 514; Line Number 547; Line Number 553; Line Number 598; Line number 624; Line Number 628; Line Number 630.
Experimental design: The study conducted is simple and can be replicated. Statistical analysis are conducted appropriately which are in support of the results obtained for the present study.
Validity of the findings: The objective of the study and conclusion are not well stated. How gut microbiome help in understanding the invasion mechanism needs to be focused here.
Additional comments: Line Number 11: “Lijiang RiverBasin Institute” Replace with “Lijiang River Basin Institute”.
Line Number 26: “Methods” this can be a separate section of abstract.
Line Number 56: Delete “-” after high.
Line number 59: Add “to” after adapt.
Line Number 62: Change to italics “Potamopygus antipodarum”.
Line Number 62: Rewrite this “as invades than the native”.
Line Number 67: Add comma after shown that the
Line Number 70: Add reference in text and include the same in reference section “listed as 100 worst invasive alien species”.
Line Number 94: Replace “no damage to the surrounding environment” with “without disturbing the surrounding environment”.
Line Number 104: Replace “PC1, 2, 3, 4 and CC 1, 2, 3, 4” with “PC-1, PC-2. PC-3, PC-4 and CC-1, CC-2, CC-3, CC-4”.
Line Number 107: Change “gut microbiota DNA” to “Gut microbial DNA”
Line Number 119: Delete “and” before 72 C.
Line Number 127: Which version of QIIME2 software was used.
Line Number 131: Which version of QIIME2 software was used.
Line Number 136-139: Rewrite “Alpha diversity indices, including community richness (Chao1 and Observed species), diversity (Shannon and Simpson), diversity of evolution population (Faith’s PD), evenness (Good’s coverage), were calculated using QIIME2”. Also, include which version of QIIME2 was used.
Line Number 143: “To estimate beta diversity or similarity” Replace “or” with “and”.
Line Number 160: Replace the subheading “Diversity and composition of P. canaliculata and C. chinensis gut microbiota” to “Gut microbial diversity and composition in P. canaliculata and C. chinensis”.
Line Number 165: Delete an extra space after species.
Line Number 168: Insert a space after the symbol <0.001%.
Line Number 189: Replace the subheading from “Taxonomic composition of P. canaliculata and C. chinensis gut microbiota” with “Taxonomic composition of gut microbiome in P. canaliculata and C. chinensis”.
Line Number 191: Delete “Tab” before, Comparing.
Line Number 207: Delete “as” after identified.
Line Number 232: Insert space after “species”.
Line Number 239-240: Rewrite the sentence “It was reported that the microbial community structure of invasive fish Oreochromis mossambicus gut microbiota was significantly different from two habitats”.
Line Number 241: Replace “recently” with “recent”.
Line Number 249-252: Do not include the results in discussion, indeed you can write what inferences you draw from your results obtained. Rewrite this section again. In our study, the beta diversity results showed that the intestinal microbial community structure of samples within the same species were highly similar, but there were significant differences in the community structure of samples among different species(P < 0.05)”.
Line Number 430: Change to italics “Frontiers in Veterinary Science”.
Line Number 460: Replace “Peerj” with “PeerJ”.
Line Number 483: Replace “Peerj” with “PeerJ”.
Line Number 486: Replace “Peerj” with “PeerJ”.
Line Number 490: Delete extra “dot” after snails.
Line Number 499: Replace “Bmc” with “BMC”.
Line Number 514: Delete the space before “the World Conservation Union:12 pp”.
Line Number 547: Delete the space after “860”.
Line Number 553: Replace “Peerj” with “PeerJ”.
Line Number 598: Replace “Bmc” with “BMC”.
Line number 624: Add space before and after “<”.
Line Number 628: Add a space before and after “=”.
Line Number 630: Add a space before and after “=”.


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

Input:
Title: COMPARISON OF GUT MICROBIOME IN THE CHINESE MUD SNAIL (CIPANGOPALUDINA CHINENSIS) AND THE INVASIVE GOLDEN APPLE SNAIL (POMACEA CANALICULATA)
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors almost addressed all the comments from reviewers, and it is fine by me to accept this revised version.
Experimental design: The authors almost addressed all the comments from reviewers, and it is fine by me to accept this revised version.
Validity of the findings: The authors almost addressed all the comments from reviewers, and it is fine by me to accept this revised version.
Additional comments: No additional comments, thanks.


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: MONTREAL COGNITIVE ASSESSMENT (MOCA) PERFORMANCE IN HUNTINGTON’S DISEASE PATIENTS CORRELATES WITH CORTICAL AND CAUDATE ATROPHY
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: Introduction
1.	I suggest to the authors to revise and or update the disease stage of the patients included in the study. Please revise this article about diagnostic categories in HD. [Ross CA, Reilmann R, Cardoso F, McCusker EA, Testa CM, Stout JC, Leavitt BR, Pei Z, Landwehrmeyer B, Martinez A, Levey J. Movement disorder society task force viewpoint: Huntington's disease diagnostic categories. Movement disorders clinical practice. 2019 Sep;6(7):541.]

Statistical analysis

2.	Wat was the purpose of using the Shapiro-Wilk test with standardized residuals of a linear regression analysis. Why not using the test with the variables?
3.	After the linear regression, what is the decision rule for one statistical analysis or another? Please clarify as this does not seem to be relevant for the statistical analysis presented by the authors.
4.	What is the purpose of using the effect size? It does not seem to have a purpose in the description of the results and in the discussion section

Results
5.	For p-values, I suggest only 3 numbers after the dot (e.g., line 197). p<0.000 instead of p<0.0008
6.	In the sections reporting the correlations between the MoCA and other variables, I suggest including the correlation coefficient with the p-value (e.g., rs=0.99; p=0.000)
7.	In Table 1A, I suggest including the sample size in the second row of the table. Also, it is not necessary to include t-value, W-value and the effect size
8.	If the significance level is defined at the beginning, it is not necessary to include symbols to indicate whether the result is significant. If the p-value is 0.009, it is clear that this value is lower than 0.05
9.	In Table 1B, please indicate p-values as <0.000 and not as exponential values

Discussion

10.	In the interpretation of the results, please be aware that the strength of the association is given by the correlation coefficient and not by the p-value. For example, the following result (e.g., rs=0.32; p=0.000) means a significant low correlation. The p value means that the correlation coefficient is significantly different from zero. However, the strength of the correlation is weak.

Conclusion
1.	Lines 321 and 322, referring to the MoCA test as an intervention tool may be a mistake as it is a screening or assessment tool


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: MONTREAL COGNITIVE ASSESSMENT (MOCA) PERFORMANCE IN HUNTINGTON’S DISEASE PATIENTS CORRELATES WITH CORTICAL AND CAUDATE ATROPHY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a well-written article presenting novel data. There are some details lacking in the manuscript which would help to clarify the results and conclusions
Experimental design: The study is well designed. The main drawback is the small sample size but this is acknowledged by the authors in their limitations section. Some more details would be helpful:

1.	The cohort could be better characterised. Have all the HD gene carriers been given a clinical diagnosis of HD i.e. according to the Diagnostic Confidence Score? Or are they all classified as early HD just on the basis of TMS and TFC?
2.	It would be useful to include range in the tables in addition to mean and SD. For example, the mean CAG is relatively high at 44. Are there any very high CAG carriers driving this mean as can happen with a small sample? It is possible that they may be atypical in their presentation as there is evidence that CAG length can influence disease trajectory
3.	Which version of Freesurfer was used? Was any quality control performed on the data and if so was Freesurfer rerun on any poor quality segmentations or were there any rejections?
Validity of the findings: Do the authors have any suggestions for why there is a significant difference in intracranial volume between gene carriers and controls? Although evidence has been presented for reduced ICV in juvenile HD to my knowledge this has not been shown in adults. Importantly, software packages including Freesurfer can introduce bias in intracranial volume measurements https://pubmed.ncbi.nlm.nih.gov/23827332/
Additional comments: The authors refer to 'volume loss' but since this is just a cross-sectional study and they can't assess an ongoing atrophic process it would be more appropriate to refer to 'volume differences' between HD and controls

In the limitations section the authors suggest extending the study to more severely affected HD patients. Scanning is rarely practical beyond stage 2 due to movement artifact so I don’t know whether this is a reasonable study design.

The authors state that it was not possible to study the effect of medication on cognitive performance which is completely understandable given the small sample and variable treatments and dosing regimes etc, but many studies at least report medication usage in their cohort even if not used for analysis. This could be added to Supplementary Data, even just under broad classes such as antidepressants, antipsychotics etc. As the authors point out this is likely to have an impact on cognitive performance so it would be useful to understand roughly what proportion of the sample were receiving treatments.


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

Input:
Title: A SPOTLIGHT ON NON-HOST RESISTANCE TO PLANT VIRUSES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: The authors described about the possible mechanisms of nonhost resistance against plant viruses in multiple aspects. Authors suggested suppression of viral replication could be due to host factor – virus incompatibility, RNAi mechanisms in terms of adaptation of virus on host / nonhost machineries. Furthermore, the authors also introduced several researches about interactions between host plant – insect vector - virus which may contribute to host range of viruses.
 The authors enumerated various researches about NHR against plant viruses including the recent cases (2019 ~ 2020). Though the first half of the manuscript is conceptually not much distinguished from the previous review articles (such as Baruah et al., 2020, Panstruga and Moscou, 2020), this manuscript introduce more current researches about NHR against plant viruses.
 For the other half of the manuscript, virus and insect vector interaction part provides intriguing aspects. However, this part should be more organized (to be flowing well) and specific to support the statements.
 This manuscript provides useful information about current state of NHR against plant viruses. However, some parts are not easily understood, so I would like to offer some suggestions to improve them to be published.

Major points
1.	 Some parts are not enough specifically (vaguely) described about references/previous researches to support statements. For example, Line 203 – 205, 262 – 263, 269 – 274, 286 – 288, 288 – 291, 300 – 303, etc (other detailed comments are attached in Minor points).
2.	 Authors defined the ‘true’ and ‘apparent’ NHR, but in this manuscript, only one case of previous research (Line 214 – 217) was designated as apparent NHR.
3.	 I suggest to add table containing the information about which referenced researches are true/apparent NHR, or which specific factors are (+ how) contributed to those NHR according to the author’s classification (RNA silencing, host target incompatibility etc).

Minor points
Line 21, does NHR is another mechanism compared to host defenses?
Line 25 & 64, does NHR is non-specific resistance? Authors described NHR as associated with recognition based or non-specific resistance in line 156 ~159.
Line 67 – 70, cannot easily understand this sentence
Line 125, NHR plants => nonhost plants
Line 147, no references of ‘various studies’
Line 163 – 166, description about arms race between plant RNA silencing and virus suppressor seems not well matched with sub-heading: Active and passive mechanisms.
Line 188 – 190 and 192 – 195, referenced same article, divided paragraph seems not necessary and confusing.
Line 242 – 248, authors never described what’s R gene in manuscript, clarify its definition, and R gene-mediated resistance section should be more described in detail. This section only composed of several examples without clear/distinct definition of concept and conclusive descriptions.
Line 255 – 260, redundantly re-defined NHR and described about its multi-layered nature.
Line 250 – 267, authors only described about cytosolic receptors and NLRs in this section but claim as PTI and ETI may function for recognizing viruses in plants. Maybe Line 269 – 280 (section described about PTI) could be better to be integrated with Line 250 – 267.
Line 307 – 312, no reference
Figure 1. These is no ‘D’ section in the image


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 SPOTLIGHT ON NON-HOST RESISTANCE TO PLANT VIRUSES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have reviewed nonhost resistance mechanism to plant viruses. Different to fungi or bacterial pathogen, plant viruses have a specific feature to infect plants. In this point, introduction needs to be revised to include plant virus infection process such as virus recognition, replication, and how to cause disease. The paragraph to summarize virus infection process could make the readers to understand the manuscript more clearly.
Experimental design: In the section of 'Rationale, intended audience and contribution to the field', the first paragraph(line 80-93) and the second paragraph(line 95-101) are overlapped with the next section 'NHR:the terminology and its usage'. I think that those sections need to be merged into one section.

I think that the section of 'How non-host plants recognize the viruses' needs to be moved next to introduction section.  This section seems to mention host resistance mechanism against plant virus, which suggest the possibility to occur similar mode of action in NHR. Some NLR proteins such as ty-2 and pvr4  are known as resistance genes against virus. As the authors emphasize the improvement of crop resistance to virus, NLR genes against virus needs to be mentioned.
Validity of the findings: No comment
Additional comments: The authors have reviewed nonhost resistance to plant viruses in several aspects including host range, host factors, and insect vectors. The manuscript is well-written and provides insight to durable resistance against viral pathogen. If the manuscript is re-organized, it could be more easy to understand.


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 SPOTLIGHT ON NON-HOST RESISTANCE TO PLANT VIRUSES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors revised manuscript as suggested.

 The main body of manuscript is now divided into four parts

1. How the plants recognize viruses
2. Possible mechanisms of NHR against virus in plants
3. Virus and insect vector interaction in non-host plants
4. Update on NHR-based research in plant virology

 In the first part, authors discuss only about PAMP recognition, but start with a sentence as 'NLR plays in significant role in plant-viral defense', the first sentence seems not matched for this part.

 In the third part, the authors enumerates a bunch of case studies but its hard to draw a conclusion, I hope the authors add conclusive paragraph summary the insight from those case studies at the end of section.
Experimental design: no comments
Validity of the findings: no comments
Additional comments: Line 162 - only this subheading contain (:) at the end of  text
Line 175 - No period (.) at the end of sentence


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 SPOTLIGHT ON NON-HOST RESISTANCE TO PLANT VIRUSES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been revised according to the suggestions and comments of the reviewers. This manuscript could help readers to understand plant nonhost resistance mechanism against viral pathogen. Some minor points could be revised to improve the manuscript.

1. Line 141. The intracellular receptor ~~ : This sentence doesn't fit in the paragraph 'PAMP recognition'. it needs to move to (v) R-gene mediated resistance in NHR.

2. The paragraph of (ii) Active and passive mechanisms (Line 212 - Line 220) : in this paragraph, the author mentioned 'antiviral silencing' briefly and it is not enough to represent active and passive mechanism. The section seems like 'introtduction' of other section.  Also, RNA silencing has been well written in the next section of '(iv) RNA silencing' I think this paragraph could be deleted and merged into other section.

3. Line 246. In revised manuscript, there is no description of  true NHR and apparent NHR. The sentence of 'Accordingly, the terminology of 'true NHR' and apparent NHR' were defined earlier.' does not fit in well with this paragraph. I think that it needs to be explained more for readers.

4. Line 298. A. thaliana : Arabidopsis thaliana (appeared first in the manuscript)
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: DIETARY FATTY ACID PATTERNS AND RISK OF OESOPHAGEAL SQUAMOUS CELL CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: While the English overall is OK there are some bits that are not clear and it is not always clear whether this is a problem with English or something else.
The Abstract methods mention using a Forest plot to show effect modification, but you have not said what effect modifiers are to be studied.
What is ‘hard’ food?  This is not meaningful to an international audience.
The first sentence of the introduction is poorly written. Should be incidence rather that incident and should give a reference to the source of the data as well as mentioning GLOBOCAN 2018.
I did not assess whether any key references were missing but think the following is misquoted. Line 208, ref 27 is specifically about MCFA not SFA and it is for MCFA that in animals attenuate weight gain.
There are no hypotheses provided.
Data is shared.
There is a problem with the reference list as most refs don’t have author names, just initials.
The legend for Fig 2 talks about error bars but there are no error bars on the figures, just shaded areas to represent 95% CI.
Experimental design: The introduction does not well justify why there might be an association between dietary fat intake and ESCC.  If it has not been explored then use evidence from other studies to support why this might be important.
Why is multinomial logistic regression used?  Isn’t the outcome ESCC yes/no?
In Abstract results there are too many significant figures in ORs and 95% CIs.
More information on the control selection is required.  Were there any exclusion criteria applied to controls?
Was a sample size calculation performed?
More information on how FFQ responses were converted to nutrient intakes is required.  How were serve sizes determined?
Why do you use percentage energy from the different fatty acids for the dietary pattern analysis when you have calculated the energy-adjusted fatty acid intakes using the residual method?
Line 144-5, we still don’t know what effect-modifiers are being considered and presented in Forest plots.
Why did you choose to dichotomise age at 54 years as shown in Table 1?
In Table 2 how did you decide which fatty acids defined each factor? It was clearly not just based on the magnitude of the loading alone.
Validity of the findings: The section headed ‘Cross-stratified heterogeneity test between dietary fatty acid score and ESCC incidence’ is very difficult to follow.  Describe in words what all this actually means.
Line 267-268, even if you accept that the associations between dietary fatty acid patterns and ESCC in this case-control study are causal, factor analysis did not reveal the association between dietary FAPs and ESCC risk.  Factor analysis just identified some patterns regarding how fatty acid intakes correlated with one another.
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: DIETARY FATTY ACID PATTERNS AND RISK OF OESOPHAGEAL SQUAMOUS CELL CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a novel topic, and it addresses the relation between the dietary fatty acid pattern and the risk of ESCC.
Experimental design: This manuscript is well organized and has an appropriate sample size.
The statistics for the analysis were clear and well described.
The inclusion criteria for the study were clearly stated in the article as well.
Validity of the findings: The authors made broader and more generalized conclusions based on the data than specified in the methods. The inclusion criteria stated that only the “Chinese Han population resided in Fujian Province” which differed from the conclusion.

Please include a paragraph or several sentences describing the limitation of the inclusion criteria in the discussion section.
Additional comments: Please improve the quality of the English in the manuscript.

1.	Follow the general English writing rules, such as using a space after a punctuation mark.
2.	There are some grammar mistakes, such as on lines 236-237 where the sentence cuts off abruptly.
3.	Please only use English in the manuscript (line 315 need to be deleted).
4.	Please use consistent formatting for references in the article and do not switch in between.
5.	Adjust the font type of the manuscript to stay constant throughout and enlarge the font size of references.


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: DIETARY FATTY ACID PATTERNS AND RISK OF OESOPHAGEAL SQUAMOUS CELL CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have improved the manuscript but still some basic problems with the quality:
SFA is not defined in abstract.
Introduction: Spaces missing between text and brackets.  This is a problem throughout the manuscript.
Line 44 oesophageal carcinoma is 6th leading cause of death globally but line 47 it is 4th most deadly cancer. Does this mean 4th leading cause of death? Is this for Asia rather than globally? Need to be clear.
Line 53, remove word ‘remarkably’ this is not appropriate here.
Please check carefully line 192-3, seems to be some confusion between pickled and fried foods.
The sentence lines 259-60 is not complete.
There are still some problems with the reference list.  For example 329 Hajizadeh B, Jessri M, Akhoondan M, Moasheri S, and Rashidkhani BJDoteojotISfDotE. 2012. Nutrient patterns 330 and risk of esophageal squamous cell carcinoma: a case-control study. 25:442-448. 10.1111/j.1442- 331 2050.2011.01272.x
Check manuscript for typo where ‘fired food’ mixed up with ‘fried food’.
Line 166, what do you mean by the ‘most powerful’ factor?
Experimental design: In general the experimental design is appropriate but the section in the discussion that relates to the effect modification analysis is unconvincing, seems to be looking at additional risk factors for ESCC but not why they might modify effects of FAPs and this part of the analysis is not justified in methods. I would still like to see some justification for the stratification by hard foods and other variables in methods.  Are they ESCC risk factors? Why would they modify the associations between FAPs and ESCC?
Line 133, you mean fatty acid intakes were energy-adjusted by the residual method (Willett ref) before the factor analysis?
Validity of the findings: It is reasonable to assume that the conclusion is valid for the population in your study but a limitation is that the results may not be applicable to other populations with different dietary habits and lifestyles.  Given that China is a country with a high risk of ESCC the findings are unlikely to be relevant to countries with lower rates.
Additional comments: In general the authors have responded appropriately to reviewer's comments but the manuscript is still not at a publishable quality.


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: DIETARY FATTY ACID PATTERNS AND RISK OF OESOPHAGEAL SQUAMOUS CELL CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed all my concerns.
Experimental design: The authors have addressed all my concerns.
Validity of the findings: The authors have addressed all my concerns.
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: CONTINUOUS MUTATION OF SARS-COV-2 DURING MIGRATION VIA THREE ROUTES AT THE BEGINNING OF THE PANDEMIC
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper i well written and easy to read with som clear messages. The number of new publications within the field of COVID-19 is overwhelming and it can be difficult to keep and overview. However, the author gives a good and sufficient introduction to the subject.
Experimental design: The origin and spread of SARS-CoV2 and the emerging of new variants is a very important subject. In this paper the author analysed 8.974 sequences of early samples of SARS-CoV-2, using principal component analysis (PCA) instead of using phylogenetic threes.
The mathematical background for PCA is hard to understand for a clinician, but PCA is a validated and recognized method.
The sequence data were obtained from the DNA Data Bank of Japan and GISAID. It is not stated whether the 8.974 samples represents all sequences in the data-bases or if not, how they were selected.
Validity of the findings: Data shows that bats and pangolins are not the intermediate animal for the origin of SARS-CoV-2. Further it spread and mutated through three routes.
One of the main conclusion is that the rate of mutation for SARS-CoV-2 is comparable to Influenza A H1N1. However, the mutation rate is only mentioned in the discussion and not in results.
The data and conclusions are valid.
Additional comments: This paper add to our knowledge about the origin and spread of SARS-CoV-2. It has som clear and important messages.

Suggest that the first sentence in the introduction is changed form: Years have passed since... to More than a year have passed since...


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: CONTINUOUS MUTATION OF SARS-COV-2 DURING MIGRATION VIA THREE ROUTES AT THE BEGINNING OF THE PANDEMIC
Review round: 1
Reviewer: 2

Output:
Basic reporting: Tomokazu Konishi presented principal component analysis (PCA) of SARS-CoV-2 from DNA data bank of Japan and GISAID. The author collected data up until 1 Sept 2020 and claimed some benefits of PCA over phylogenetic based analysis. However, I have some major concern on authors assumption and analysis
1)	Pangolin CoV: Articles published by Jimmy Lee (Lee, J., Hughes, T., Lee, MH. et al. No Evidence of Coronaviruses or Other Potentially Zoonotic Viruses in Sunda pangolins (Manis javanica) Entering the Wildlife Trade via Malaysia. EcoHealth 17, 406–418 (2020). https://doi.org/10.1007/s10393-020-01503-x) showed that specimens collected from naturally occurring Pangolins were negative for Coronavirus at family level. Thus detection of CoV from Pangolins seems like contamination through the wild animal marketing chain. Thus, this is unlikely that Pangolin played any key role in the origin of SARS-CoV-2. I would suggest the author consider this point and reanalyze the PCA by excluding the sequences reported from pangolins and then make a comparative analysis   (including pangolin CoV and excluding Pangolin CoV).
2)	Tiger CoV: The sequences reported from Tiger were almost identical to human. The most likely explanation is that the tiger received the virus from a human and there is no modification of the virus in the Tiger. Thus, Tiger might be a very poor host for SARS-CoV-2 in terms of viral mutation.
3)	H1N1 influenza virus (author mentioned N1H1 at line 200): The purpose such comparison is not clear to me. Not enough data was presented on the H1N1 virus.
4)	Data is too old: The dynamic if SARS-CoV-2 is changing very rapidly – the analysis using data up until Sept/2020 seems too old now. Most of those viruses is now replaced with delta and other VOC. Please update the data and re-analyze them. Write the discussion relevant with recent VOC including alpha, beta, delta, lambda variants.
5)	Abstract: The abstract is  written poorly, please mention the source of data and duration of data collection in the method of Abstract. Write the raw findings in the results section of the Abstract.
Experimental design: NA
Validity of the findings: See the comments above
Additional comments: NA


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: CONTINUOUS MUTATION OF SARS-COV-2 DURING MIGRATION VIA THREE ROUTES AT THE BEGINNING OF THE PANDEMIC
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author has addressed my comments adequately! This looks a better draft now.
Experimental design: NA
Validity of the findings: With the acknowledgment of Pangolin's CoV and tiger's CoV -- the paper has a clear communication now.
Additional comments: Well done and happy to accpet!


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: RNA SEQUENCING REVEALS THE EMERGING ROLE OF BRONCHOALVEOLAR LAVAGE FLUID EXOSOME LNCRNAS IN ACUTE LUNG INJURY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. Overall, this article was written clearly and professionally, however, some text may be ambiguous or unclear.
ie:
a. The second sentence of background in the abstract (line 31-32) was grammarly incorrect.
b. Some method was not explained clearly. For example, the sex of control mice (line 34), how exosomes were obtained  (line 35), and what does it mean that nothing was given to control group mice (line 117).
c. Some abbreviations were not explained at first use, ie LPS.

2. The article has included an introduction from a wide perspective to explain the background of the work and demonstrate how this work contributed to the field. However, it would be better if the author could explain: why do you select exosomes instead of other types of extracellular vesicles (EV) in the study, what was the significance of exosomes compared with other types of EV, ie MV and apoptosis bodies.

3. This article was structured properly with an acceptable format of 'standard sections'. All appropriate raw data was supplied. Figures and tables were relevant to the content of the article of sufficient resolution.
However, it would be helpful if more descriptive information could be explained in the captions of the figures and tables to allow them to explain themselves independently.
For example,
a. Sample size, sex of mice, etc in each figure/ table.
b. Use of abbreviations, ie FPKM (table 2), log2FC (table 2).
c. This might not be your fault, but the title of table 1 was not in the correct place.

Overall, the current study was represented as an appropriate unit of publication and include necessary results relevant to the hypothesis.
Experimental design: This is original primary research within the aims and scope of the journal.

It has clearly defined the research question relevantly and meaningfully. The knowledge gap has been defined and being investigated, and the results have contributed to filling that gap.

The investigation was at a high technical standard, ie exosomes sizing, miRNA profiling, etc. The research was conducted in conformity with the prevailing ethical standards in the field.

The method of the current study was described with sufficient detail and information to replicate.
Validity of the findings: 1. The current study gave an outcome based on the results, the findings were novel and meaningful.

2.  Most necessary results were supplied. However, it would be better if you could show how the raw data from RNA-sequencing was normalised and validated (prior to table 2).

3. Conclusions were well stated. However, in the discussion, it would be better if you could talk further and deeper in: to what extent do lncRNA were the same/ different between exosomes and other resources, and between humans and mice. Also, in conclusion, you should emphasise that these findings were based on mice study rather than human.
Additional comments: Overall, this research was novel and meaningful, however, minor revisions should be made.


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: RNA SEQUENCING REVEALS THE EMERGING ROLE OF BRONCHOALVEOLAR LAVAGE FLUID EXOSOME LNCRNAS IN ACUTE LUNG INJURY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language should be improved for a better flow of the story. For example, sentence structure errors in lines 31, the lack of a full stop at the end of line 120, choice of words (i.e. bottom) in lines 151 and 152 makes comprehension challenging.

The main figures should not contain sentences or paragraphs since they are already in the figure legends. In my opinion, the order by which Figures 2 and 3 are presented should be reversed for a better flow, i.e. the current Figure 3 (exosome characterization) should be Figure 2 and the current Figure 2 (histological examination of the lung tissue upon exosome injection) should be Figure 3.

For Figure 6, what does the panel legend (N and S) represent? Do the authors mean "control vs ALI group"?

The authors discussed about the top 30 differentially expressed lncRNAs between the ALI and control group but only provided the top 20 lncRNAs in Table 2.

In Table 2 under the column of "log2FC", what does "Inf" represent? The authors should provide clear elaborations for any acronyms used in the manuscript.
Experimental design: The authors mentioned in line 117 that nothing was given to the rats in the control group. In my opinion, the authors should repeat the experiment with PBS solution for the airway injection for the control groups so as to eliminate any possibility that the lung injury could be induced during the injection process, rather than the LPS.

The authors "randomly" selected 5 of the top 30 differentially expressed lncRNAs for qRT_PCR validation. In my opinion, it is more biologically meaningful if the authors could provide a rationale for the selection process, or select the top 5 most dysregulated lncRNAs of a particular important KEGG or GO pathway for qPCR validation, or simply the top 5 most differentially expressed lncRNAs for qPCR validation so as to provide the basis for future studies.
Validity of the findings: The authors concluded that there was an increased neutrophil infiltration (line 230-231) in the lung tissues of the ALI group compared to control, but there is no quantitative measurement to convincingly demonstrate that. The authors should perform via for example, flow cytometry, to quantitatively demonstrate the % neutrophil infiltration and examine any differences between the two groups.
Additional comments: Major comments

1) For the current Figure 2 whereby the authors demonstrated the histological differences between rats injected with PBS or ALI-derived exosomes, more quantitative assays should be performed just as in Figure 1, i.e. Wet-dry ratio, neutrophil infiltration, cytokine secretion.

2) While characterizing the exosomes isolated from the BALF of the rats (Figure 3), the authors should also checked for any differences in the abundance/quantity of exosomes between the ALI and control groups since it has been reported that LPS (infectious stimuli) can lead to an increase in EV secretion.

3) While the authors provided the lncRNA-miRNA regulatory network predictions for the 5 validated lncRNAs, it may be more biologically meaningful to compare any overlaps of the network between the 5 lncRNAs or provide a merged network for some of the differentially expressed lncRNAs of the same GO or KEGG pathway. This would provide a stronger basis for future experimental studies to characterize these lncRNAs and their potential diagnostic and therapeutic roles in ALI.


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: RNA SEQUENCING REVEALS THE EMERGING ROLE OF BRONCHOALVEOLAR LAVAGE FLUID EXOSOME LNCRNAS IN ACUTE LUNG INJURY
Review round: 1
Reviewer: 3

Output:
Basic reporting: BASIC REPORTING
a.	Clear, unambiguous and professional language? See notes
b.	Intro shows context? Relevant background and context is presented but there are key pieces of information missing
c.	Well referenced and relevant literature? Mostly, there is one or two occasions when reference is required but missing
d.	Structure conforms to peerJ standards? As far as I am aware, yes
e.	Figures are relevant and high quality, well labelled and well described? Figures are well-described, some specific comments below.
f.	Raw data supplied? Raw data availability is clearly stated in methods

•	Lines 31-32 in abstract, missing contextualisation for comprehension - currently statement is the subordinate clause of a complex sentence
•	Line 34 Undefined acronyms in abstracts (for example LPS)
•	Lines 69-72
•	Lines 82-83, 127-29 appear disjointed from the flow of information presented around it
•	General disjointed flow of information, often there is too little detail more is needed (for example the explanation of EV see below) and too much information when it is not required (for example lines 104-120 in methods could be made more concise and irrelevant information could be removed).
•	Language used could also be improved to better reflect norms of the English writing, for example:
•	lines 215-216 uses "the" when it could be removed and improve general flow of writing
•	Line 239 the plural were should be used over singular was
•	Line 266 the plural "sponges" or addition of "an" before the noun
•	Subheadings in results section could be improved for better precision and clarity in understanding
•	Results are concise and well-focused in general. The final subheading (lines 266-269) does not describe any results - the language is methodological. The key aspects of the figure could be described.
•	Use of inappropriate adverbs at the beginning of sentences in the discussion decreases the clarity of information
•	Figure 3 B; if scale bar is correct, there is an arrow idiciating an exosome pointing to a structure many magnitudes too large
Experimental design: •	Aim of the study could be presented a more clear and logical manner, no clear hypothesis is stated.
•	More detail or improved language in the description of control animals - were they subjected to anaesthesia even though controls did not receive a control saline injection?
•	Lines 133-134 do not clearly convey method
•	At the moment, the reporting of EV isolation and characterisation does not conform to ISEV minimum reporting standards. The description of EV isolation lacks reporting centrifugal forces, models of centrifuge, volumes of starting material etc. reference to ISEV minimum reporting standards could be included.
•	Authors give no explanation for mapping rat RNA sequencing results to the human genome assembly?
•	Authors state that an ALI standard was used to exclude data without definition or reference to source
•	Authors clearly state the availability of data but do not make comment on the quality of the RNA sequenced
Validity of the findings: •	Both the conclusions and aims, whilst well stated, do not accurately reflect the detail of the experiments presented and are more conceptual. The characteristics of BALF-derived exosomes from ALI and control is described and compared with key differences. Potential functions and interactions with miRNA are explored but not experimentally validated. Therefore the conclusion that BALF-derived exosomes play an important role in the development of ALI is perhaps overreaching the scope of the experimental design.
•	The discussion appears to jump between analysis of the pathways or mechanisms involved in progression of ALI and applicability of findings as biomarkers, this can make some sections of the discussion confusing and disjointed. The consideration of BALF as a clinically accessible and viable source for biomarker detection is good.
•	Both the conclusions and aims, whilst well stated, do not accurately reflect the detail of the experiments presented and are more conceptual. The characteristics of BALF-derived exosomes from ALI and control is described and compared with key differences. Potential functions and interactions with miRNA are explored but not experimentally validated. Therefore the conclusion that BALF-derived exosomes play an important role in the development of ALI is perhaps overreaching the scope of the experimental design.
•	The discussion appears to jump between analysis of the pathways or mechanisms involved in progression of ALI and applicability of findings as biomarkers, this can make some sections of the discussion confusing and disjointed. The consideration of BALF as a clinically accessible and viable source for biomarker detection is good.
Additional comments: •	Exosomes and EVs are poorly defined and differentiated from one another in first presentation. Role of exosomes as messengers between relevant cell types is not clearly defined or explained during early introduction.
•	The mapping of rat-derived genetic information to the human genome is never justified, discussed or explained however the lncRNA id's are listed as rat IDs? Is the methodology reported correctly? miRDB names are reported as human miRNAs.
•	Figure 1, can all the data points be added to the graph as in figure 3c.
•	In Figure 2, please add the wet/ dry data to allow comparison with figure 1b.
•	Figure 3 is only a snap shot of the size, if nanoparticle data tracking is available, this data should be presented as it gives a more representative indication of particle size.
•	What was the result of the RNAseq analysis, as well as the identification of significantly differentially regulated lncRNAs, what other species of RNA were identified and differentially regulated?
•	What is the evidence that the selected lncRNAs act as miRNA sponges, is there any evidence the lncRNAs are they implicated in other functions and disease?
•	Can the authors provide the detailed analysis data to the reviewers, for the qRT-PCR, Ct and delta Ct information. Were the lnc RNA Taqman probes commercially available or custom generated?
•	Can the authors comment on the on the reasons for using the polyA+ set of RNA as opposed to all long RNAs?
•	Is there any evidence that the cytoscape figure is enriched for miRNAs implicated in the pathways highlighted in Figure 5?


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: RNA SEQUENCING REVEALS THE EMERGING ROLE OF BRONCHOALVEOLAR LAVAGE FLUID EXOSOME LNCRNAS IN ACUTE LUNG INJURY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Please ensure that the added text and figures/figure legends are well read through for the English grammar and structure.
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: EXHAUFS: EXHAUSTIVE SEARCH-BASED FEATURE SELECTION FOR CLASSIFICATION AND SURVIVAL REGRESSION
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript, Nersisyan et al. reported a novel method to tackle the long-lasting issue of feature selection in practical application, especially the use in dealing with biological data. This research is of high quality, with a clear illustration of the motivation, method, results, and prospective. It is also well-structured with a professional presentation of the figures and results.
Experimental design: This study aims to improve the feature selection method when dealing with large transcriptomic such as gene expression array, and clinical data, such as survival analysis. This research is within the aims and scope of PeerJ. In short, the authors developed a novel method called ExhauFS, which is a feature selection tool based on exhaustive search. I have a few comments on the design:
1, Is any domain knowledge required for the feature pre-selection step? If so, what would be the steps to select the features at the beginning? I imagine that the initial feature set may bias the results, so any randomization (control) method is suggested to show the pre-selection is appropriate?
2, I also suggest the authors pay some attention to the interpretation of the results. For example, when a set of features were selected, how well can they explain the initial hypothesis? If the data contains bias or noise, what additional methods are required to validate the results?
In general, ExhauFS has been tested on multiple datasets and shows promising output compared with current methods. I suggest a minor revision with the above two issues.
Validity of the findings: The authors have tested ExhauFS using multiple datasets by comparing it with current tools. The results also show its robustness in multiple applications focusing on feature selection, including microarray data, survival analysis. The codes of this work have been deposited in GitHub and Python PyPI with a detailed user manual and instructions. The conclusion is also clear and well stated.
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: EXHAUFS: EXHAUSTIVE SEARCH-BASED FEATURE SELECTION FOR CLASSIFICATION AND SURVIVAL REGRESSION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript reported a useful tool, ExhauFS, for classification and survival regression, and authors further used three examples to show the performance of this tool. In my opinion, I think the studies are well-designed and implemented.
Experimental design: Overall good.
Validity of the findings: no comment.
Additional comments: I would like to suggest that the authors discuss the broader potential application of this tool.