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: SHORT-TERM EFFECTS OF THINNING ON THE DEVELOPMENT AND COMMUNITIES OF UNDERSTORY VEGETATION OF CHINESE FIR PLANTATIONS IN SOUTHEASTERN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The submitted manuscript entitled Short-term effects of thinning on the development and communities of understory vegetation of Chinese fir plantations in Southeastern China (#41940) presents results of experimental study on the effect of different intensity of thinning of young Cunningamia lanceolata trees on understorey vegetation.
The article is understanding and easy for following. Its structure is consistent with the PeerJ journal standards. The introduction illustrates well the importance of the research problem. However, please note that effect of tree density and thinning on understory vegetation were many times studied outside of China and obtained by Authors results are consistent with them. Hence the study topic is not very novel. The Authors mainly refer to publications from China, not referring to many other similar research conducted in other parts of the world i.e. Torras and Saura (2008), Brunet et al. (2010),  and Lindh and Muir (2004) and literature cited therein. Some other studies suggests that soil conditions have higher influence on understorey vegetation that tree stand character i.e. Piwczyński et al. (2016).
Brunet J, Fritz Ö, Richnau G (2010) Biodiversity in European beech forests – a review with recommendations for sustainable forest management. Ecol Bull 53:77–94
Lindh BC, Muir PS (2004) Understory vegetation in young Douglas-fir forests: does thinning help restore old-growth composition? For Ecol Manage 192:285–296. doi: 10.1016/j.foreco.2004.01.018
Piwczyński M, Puchałka R, Ulrich W (2016) Influence of tree plantations on the phylogenetic structure of understory plant communities. For Ecol Manage 376:231–237. doi: doi.org/10.1016/j.foreco.2016.06.011
Torras O, Saura S (2008) Effects of silvicultural treatments on forest biodiversity indicators in the Mediterranean. For Ecol Manage 255:3322–3330. doi: 10.1016/j.foreco.2008.02.013

The tables, figures and its captions and supplementary materials are well prepared and do not raise objections.
Experimental design: The study hypothesis and goals are clearly presented and well discussed with obtained results and other research. The authors analysed in detail species composition and biomass of scrubs and herbs in each treatment and soil chemistry. They also consider the terrain conditions which may have influence on character of understory vegetation. The statistics are well chosen and properly interpreted. The documentary data together with used R script has attached to the manuscript as supplement.
Validity of the findings: Replication experiments is low, but it may be justified by a large amount of field and laboratory work. The research project was correctly designed and conducted with high technical and ethical standards.
The conclusions are appropriately stated, connected to the study aims and hypothesis and supported by the results. The authors should consider whether to extend the introduction and discussion so that the work is less local. In my opinion, the results are universal enough that similar patterns maybe expected in other areas of the world. Some fragments of Discussion should be better supported by literature references.
Additionally, before publishing in PeerJ journal some fragments of manuscript should be corrected.

Specific comments:
Authority on Latin binomial should be provided after each common name the first time referred to in the text.
The tables should be self-explanatory.
L.47. ‘Cunninghamia lanceolate’ -> Cunninghamia lanceolata
L.60, L.133, L.292. Ma et al, 2007 -> in references are listed two papers Ma et al, 2007
L.91. ‘Traditionally speaking’ -> Generally speaking?
L.117-119. The Authors should complete some information about source of climatic data and provide reference to soil classification.
L.148-149. ‘the species were identified according to the information obtained from the Chinese website eFlora (www.eflora.cn).’ -> Unfortunately, I cannot connect with this website address. The browser redirects me to the following website http://www.efloras.org/flora_page.aspx?flora_id=2 with electronic version and pdfs with volumes of Flora of China. If I was redirected correctly, I suggest quoting selected volumes of Flora of China (pdf/printed version) here.
Anyway, this sentence must be changed, i.e. ‘The vascular plants species were identified according (citation)’.
L.153. How vegetation cover was measured. Please specify it.
L.277-278. The abbreviations of treatments should be given.
L.314-316. This fragment should be rewritten, because in current form is difficult to understand.
L.339-348. This fragment should be discussed with literature references.
L.369. Siefert et al., 2012 -> lack in references
L.379. Seibert et al., 2007-> lack in references
L.371. Yang and Da, 2006; Yang and Da, 2005; -> Yang and Da, 2005, 2006;
L.460, L.516, L.528. Chinese text in reference should be converted to English
L.468. (2016b) -> (2016)
L.442, L.458, L.470, L.489. L.490, L.503, L.535, L.575. Lack of colon (:) or/and volume, issue or pages numbers
L.568. Probably invalid reference
Moreover, full journal titles should be given; year of publication should be given without quotes; author’s manes, year of publication and volume number should be bolded; species Latin names should be written with italics.
Additional comments: Reading the manuscript in its current form, I get the impression that it is addressed to a very narrow audience. The authors could present their results as more universal, and not only relating to the plant biodiversity of C. lanceolata plantations in E China. This may be beneficial to the future citation of the article.
Kind regards


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: SHORT-TERM EFFECTS OF THINNING ON THE DEVELOPMENT AND COMMUNITIES OF UNDERSTORY VEGETATION OF CHINESE FIR PLANTATIONS IN SOUTHEASTERN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper presents the effects of thinning of different intensities on understory and soil properties in Cunninghamia lanceolata plantations located in China. The study is interesting and, generally, well designed. Moreover, the results can potentially be important for practical foresters with regard to management of relatively extensive areas overplanted with Cunninghamia lanceolata plantations. In the research interdisciplinary approached was applied, which increases the scientific value of the study.

However, in my opinion, before the possible publication in PeerJ the paper should be amended with regard to the points listed in the section "General comments for the author".
Experimental design: Please see the general comment above.
Validity of the findings: Please see the general comment above.
Additional comments: Major points:
1.	The suggested by the Authors effect of thinning intensity on growth of the overstory species (Cunninghamia lanceolata) should be substantially rethought. In fact, in my opinion the suggested effects (e.g. l. 275-278, 284, 394, 400) are unfounded by the obtained results in this study. In the present article version, the results (Fig. 5) show only that the thinning executed in 2013 was done with regard to smaller trees mainly (in fact, if the highest/thickest trees were cut the results would be opposite). Thus, the presented results do not prove any effects of thinning intensity on growth dynamics of the overstory species. Besides, I suppose that differences of mean DBH values showed in Figure 5 are insignificant between the studied variants, which were not considered by the Authors (why?). Thus, I suggest rethinking and improving this point of the study. Alternatively, the issue could be skipped in this paper in favor of another one (see the next point), which would not probably negatively influence achieving the aims of the study.
2.	Discussion should be partly rethought and rewritten. There are many direct references in this section to results presented in tables in figures, which make sentences alike Results section rather, but not Discussion. Besides, the novelty of the obtained results should be stronger highlighted in this section to a reader. The Authors state several times in Discussion that the obtained results confirm previous studies. After that, a reader could have an impression that the only real novelty of the paper is the found effect of topography on the studied issues (l. 373-376). Thus, I suggest more focusing on this part of the study instead of examining controversial issues related to growth dynamics of the overstory species.

Moderate points:
1. l. 91-97: The logic of this lines should be changed. You refer here to studies conducted with regard to different tree species which clearly varied in ecology (Pinus, Pseudotsuga species etc.), and subsequently also their effects on understory. Thus, it is not surprised that the results of the previous studies are opposite. The sentence in l. 95-96 suggests that you potentially aim at showing “universal and unified” effects of thinning on understory characteristics. However, it is possible only with regard to one species or group of plant taxa, which are of similar ecological characteristics (light requirements, growth dynamics etc.), and subsequently similar effects on undergrowth. Thus, l. 91-97 should be corrected. You could start with showing the effects of thinning practices on understory in global approach, but next you should be more specific, and move exactly to the investigated species.
2. Subtitles of the Result section should be shorter, e.g. “Effects of the different thinning intensities on the soil properties and understory vegetation characteristics” could be changed for “Effects of thinning intensity on the soil and understory characteristics”.
3. With regard to plant nutrition Mg is macronutrient. I do not understand why Mg was treated, together with Mn (e.g. l. 41), as microelement throughout the paper.

Minor points:
l. 26: Following other acronyms used in the paper (LIT etc.) it is strange for a reader that CK, but not CS, is used here and throughout the article for “control section”.
l. 47: Cunninghamia lanceolata – “a” not “e”
l. 104: The end of this sentences which is placed in this line should be corrected.
l .107: change “To” for “to”
l. 110: You probably mean “most important factors”.
l. 119-120: I suggest including Soil Taxonomy in References
l. 123: The use of “respectively” is unclear in this sentence.
l. 124: delete “observed to be”
l. 125: Please say some more about the site index. E.g. were its values calculated for the age of 100 years? Is SI 18 m low or high for Chinese conditions and for the studied species?
l. 133: et al., 2007
l. 133-140: The mean values given in these lines should be followed with ±SD or SE  values, when relevant.
l. 169: I recommend deleting “ground”, because it can mislead a reader. In fact, soil samples were not grounded before sieving, but aggregates were separated for +-single grains.
l. 171: “w/v” is not necessary here
l. 174, 176, 179, 180/81, 215, 216, 217 (and wherever else relevant): replace “content levels” with “contents”
l. 180-182: In the previous paragraph the methodology of collecting of soil samples for this part of the study should be described.
l. 189: Which kind of correlation was applied (Pearson; Spearman…)?
l. 206: replace “as well as detect” with “as well as to detect”
l. 228: Start the sentence just with “It was observed/stated that…”
l. 229: You should state clear what kind of “values” do you mean in this sentence. In fact, you say here (and also in other parts of the paper, e.g. l. 234) about “the strongest relation”. However, if you want to write about “values” of sth, you must specifically define what you mean.
l. 241-242: It should be clearly stated which relations you specifically mean here.
l. 265: delete “in this study”; I recommend replacing “confirmed” with e.g. “revealed”
l. 266: replace “C-N content levels” with “C and N contents” – here, but also in Table 6 and wherever relevant
l. l. 268: delete “had successfully”
l. 268/69: replace: “variations in the species distributions” with “variation in the species distribution” and “the data variations” with “the total variation”.
l. 270” change “plotting” for “plot”
l. 285: “opening (…) microenvironment” ?  What do you mean?
l. 307: replace “affecting” with “affected”
l. 324: You mean input to the soil.
l. 355: C:N
l. 386: “access” – do you mean “assess”?
l. “growth” is too general. Say precisely which parameters you mean here to be correlated to soil nutrient contents.

Figure 3:
I think that the asterix (*) is not necessary in the figure.
I recommend inserting a label into the figure explaining clearly which signs are related to particular thinning variants. At the present version of the figure it could be problematic to distinguish LIT vs. MIT.

Table 1:
In the last column you probably mean canopy closure. If so, the column header should be changed and values changed for %.
The additional column should be inserted showing number of trees which were measured

Table 2:
l. 2: delete “were observed”
To be consequent the acronyms of thinning variants (CK, LIT etc.) should be also described in the table foot.

Table 3:
Replace “Correlation analysis between” with “Correlations between”
l. 1: At the end it should be stated, e.g: “Other descriptions as in table/figure x”  The same statement is probably also necessary with regard to other tables/figures.

Table 5 and l. 260-262.
The results of this analysis are not significant, thus I suggest removing this. Alternatively, the Authors could try to motivate in the paper that the results prove sth new to the study. At the present form they do not.

Table 6:
The table’s title does not strictly reflect the table’s content. Not only soil characteristics are shown in the table.


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: SHORT-TERM EFFECTS OF THINNING ON THE DEVELOPMENT AND COMMUNITIES OF UNDERSTORY VEGETATION OF CHINESE FIR PLANTATIONS IN SOUTHEASTERN CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript entitled Short-term effects of thinning on the development and communities of understory vegetation of Chinese fir plantations in Southeastern China (#41940) presents well planned and well described results of experimental study on the effect of different intensity of thinning of young Cunningamia lanceolata trees on understorey vegetation. The manuscript, figures, tables and supplementary materials does not raise any methodological reservations. I am also fully satisfied with the authors' replies and provided corrections.
Experimental design: Original research with clearly defined their goal. Research issues relevant and on time.The statistics are chosen correctly and well described. Scientific data and calculation script well documented in supplementary materials. The authors introduced all necessary corrections.
Validity of the findings: The article fill a significant gap in knowledge on biodiversity of understorey vegetation in different forest thinning / management. The obtained results may have practical applications for sustainable forestry and nature conservation.
The conclusions are correct and linked with conducted research. All underlying data have been provided; they are robust, statistically sound, & controlled.

The manuscript after some corrections in quoting will be suitable to publishing in PeerJ journal.
The corrections are needed in these fragments:
L.96 (Xiong et al., 1995; Wang et al., 2010; Zhou et al., 2016; Wang et al., 2019).
L.295 (Cheng et al., 2017; Cheng et al., 2014)
L.347 Legare et al. (Legare et al., 2001)

Kind regards
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: SHORT-TERM EFFECTS OF THINNING ON THE DEVELOPMENT AND COMMUNITIES OF UNDERSTORY VEGETATION OF CHINESE FIR PLANTATIONS IN SOUTHEASTERN CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper was substantially amended by the Authors following carefully my suggestions. Consequently, I recommend publishing the paper in PeerJ after minor revision only - after considering by the Authors the two still remaining points:
1.	Following my suggestion, the Authors skipped in the study the issue of the effects of thinning intensity on growth dynamics of the overstory species, which was beneficial for the paper. However, I expected that the effects of topography would be treated with more detail instead. Unfortunately, the Authors inserted only some words on this topic, which, in my opinion was not sufficient. Thus, the results referring to slope aspect still should be clearer described and discussed. In fact, in the present version of the paper a reader is informed only that topography was found to be important for the study, but the nature of this effect was not described in detail.
2.	With regard to the column referring to the canopy density in the Table 1 I suggest inserting the unit (%) only in the column head.
Experimental design: The study was designed properly.
Validity of the findings: The paper is interesting and shows some novel findings, which could be useful also for practical foresters.
Additional comments: The paper was substantially amended. I suggest the Authors considering the two remaining points listed above, and I wish them to successfully publish it in the journal.


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

Input:
Title: SHORT-TERM EFFECTS OF THINNING ON THE DEVELOPMENT AND COMMUNITIES OF UNDERSTORY VEGETATION OF CHINESE FIR PLANTATIONS IN SOUTHEASTERN CHINA
Review round: 3
Reviewer: 1

Output:
Basic reporting: After correcting by the Authors the drawbacks, now I can suggest publishing the paper in PeerJ.
Experimental design: The study was designed properly.
Validity of the findings: The paper is interesting and shows some novel findings, which could be useful also for practical foresters.
Additional comments: After correcting by the Authors the drawbacks, now I can suggest publishing the paper in PeerJ.


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

Input:
Title: REPERTOIRE OF MORPHABLE PROTEINS IN AN ORGANISM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The abstract is not informative about the paper's contribution which is stated at a general level. I´ll try to give more details about this in the Comments to the authors section.
Experimental design: The structure of the experiments needs to be guided by specific objectives or specific questions the authors would like to answer.
Validity of the findings: The current results and analysis are not enough to see the impact it can have on structural biology research. A clearer explanation of how this work differs from the one of Anzai et al. 2018, should be given.

I will suggest to the authors to provide a rationale for working with the protein’s chains separately. I believe this could work for a certain type of structures but for others also C-alpha distances between different chains will be required to characterize the structure. I will expect the authors to contribute to the explanation in what cases their approach will have different outcomes by using a single chain versus all chains.

Please also explain why the approach is not just another way to characterize secondary structures, for instance, you can compute the UMF for alpha helices and beta sheets and see how much they contribute to the total UMF. Like this, there are many aspects that the authors need to analyze to see a clearer picture of their contribution.
Additional comments: Some additional observations are:

ABSTRACT

By reading the abstract it is hard to understand what the actual contribution of the work is. For instance, it is not clear whether or not the main tool of analysis, the UMF, is proposed in this work.

Furthermore, at the end of the abstract it is stated ¨ The data and the method
presented here also conform to FAIR data principles,¨ however, the abstract does not present said method.

The problem statement is vague ¨ Efforts in the field of structural biology have contributed to uncovering the shape and the variability of each component¨

It will help to clearly state what is the open question this research address right from the abstract

Also, statements like ¨The distribution of UMFs obtained for an organism is expected to represent how rigid and flexible components are balanced. ¨

In the paper, you do not show how your approach explains the flexibility or rigidity of a protein.

INTRODUCTION

In the last paragraph of this section the actual contribution of the paper is starting to become clearer.

ARCHIVING

In the supplementary files, there are only 2 .xls all other files mentioned should be also included.

Mapping of UMFs to the proteome set

What is SCAMPI, please provide a reference for it the first time you introduce it.


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: REPERTOIRE OF MORPHABLE PROTEINS IN AN ORGANISM
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are typos and unclear sentences that need to be corrected. See general comments for the author.
Experimental design: The method that the authors are developing is solid and reliable.
Validity of the findings: See general comments for the author.
Additional comments: The authors have applied their own developed methods to the EMS data and compared the X-ray data. Generally, the findings in the manuscript is interesting but, I have already mentioned, there are typos and unclear sentences that need to be corrected. The reviewer suggests that the manuscript should be revised before publication.

1.
The abbreviations, xUMF and eUMF, are used on L.67 but they are defined at L.130-131. They are important key words in the manuscript and the definition of these special words before L.67. The word, xeUMF, is found on L262 and this word is not defined in the manuscript.

2.
L36-45, L126-131
The advantage of the “UME” score comparing to DSA score is not clear from the text.

3.
The captions of Fig2 (B) and (C) are probably exchanged, because Fig2 (B) is a semi-log plot and Fig2 (C) is a log-log plot. In Fig2 (B) (I think this figure is “semi-log plot of ECOLI set”) the cluster of ribosomal (mentioned on L181-183) should be clearly indicated ( for example colored). COP9 in Fig 2D (L184-135) is also indicated.

4
The scale of longitudinal axis: “10, 100, 1000” are used in Fig. 2 and 4, and “10^1, 10^2, 10^3, …” are used in Fig. 5. A same scale representation is better.

5
To make one figure of ECOLI set (Fig. 3A) and human protein (Fig. 3B) is helpful to see the difference. For the scale of longitudinal axis. % is better (In L.237-242, the authors discuss using %).

6
The caption of Fig.4 tells “eUMFs are shown as black squares” but it is difficult to identify these black squares. Make larger or change the color.

7
In L241-242 authors wrote “Four other proteins are also outstanding in the unusual value of eUMFs”. What are other 3 (or 7, see below) proteins?
I see 8 deviated values in Fig 4A and B (near 105 in the longitudinal axis). In L259 authors wrote “… out of the eight proteins with unusually high eUMFs …”. Is the correct number 4 or 8? And which points correspond to which proteins?

9
Minor:
In caption of Fig 3: plotof -> plot of
In caption of Fig 5: obtainedfrom -> obtained from
In caption of Fig 6: plotobtained -> plot obtained


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: REPERTOIRE OF MORPHABLE PROTEINS IN AN ORGANISM
Review round: 1
Reviewer: 3

Output:
Basic reporting: The work entitled “Repertoire of morphable proteins in an organism” by Izumi and collaborators describes the use of an index (DSA) to describe structural variations in the PDB reported for the same protein that belong to the same organism, in this case Escherichia coli and Homo sapiens.

The work is in generally well written, yet there are several important aspects that need to be clarified in order to clarify the relevance of this work. These concerns will be described in the following sentences.

- The authors refer to a UMF in the abstract to refer to “experimentally observable structural variation”; in the text and methods, there is no single reference as to how to calculate such UMF, even though, the authors used this term to present their results in several figures. On the other hand, the authors described the DSA (distance scoring analysis) and described the general formula and advantage of its use. How UMF is related to DSA is not clear from their description. One can assume that figure 1 describes what UMF is, but it is not clear from the figure legend “Scheme of score calculation” or the description of the figure. I’ll assume for the sake of arguments that the all intramolecular Ca-Ca pair distance variations (score = media (distance(Ca-Ca))/stdev) is the UMF.

- Figure 6 and its description do not contribute much to understand protein movement or morphness. For instance, linear dependency could means that proteins did not suffer any rotation or large motions of some of their parts, like it is observed in multidomain proteins. In single-domain proteins, it is less likely that such movements take place, hence the no-linearity may emerge from low resolution at the N and C terminus end of the protein, that may vary from one crystal structure to another. This level of analysis may improve the level of relevance of their score that can capture these properties.
Experimental design: - The methods do not provide sufficient information to understand or reproduce how the authors calculate the UMF. For instance, the procedure to calculate Ca-Ca distance is not described. The reference from Anzai referred to another work of this group by Asano and colleagues, where they state that "The overall pairwise root-mean-squared deviation and correlation coefficient were obtained by Discovery Studio Visualizer 3.1 (Accelrys Inc.) and pca-excel 1.0 (ss-nakano Inc.), respectively". Discover Studio Visualizer is commercial software that although is freely available, does not specify the type of distance that calculates. There are several distances that can be obtained from an euclician space (see for instance: https://en.wikipedia.org/wiki/Distance). The most common one is referred to as euclidian distance, which is a 2-norm distance. In this case, the authors have not specified what type of distance they used for their studies. This is an important aspect since from the description of their work, their interest is to measure the distribution of variations. For that goal, there are different approaches that may be appropriate, such as divergences. If the authors are not using that distance, it would be relevant to justify why to use the Euclidian distance. This is relevant for instance, in terms of computational efficiency, there are important differences on how fast these distances can be computed. If the database growth surpasses the current capacity of their method, this may become an issue later on and perhaps the authors would need to change their distance. It is expected that changing the distance may change their results and consequently their conclusions. Thus, it is fundamental for the authors to make a better description of their procedure to compute distance and make an appropriate justification of their procedure.

- The previous point is relevant for the results presented in figure 3. The plots show a Poisson-like distribution, a form of normal distribution for small sets (see for instance https://en.wikipedia.org/wiki/Poisson_distribution). This distribution is possible to be induced by the way the authors processed their data. That is, the authors used the media of the Ca-Ca distances and divided this by the stdev; both media and stdev, are parameters of normal distributions.  As the authors claim in favor of the DSA “the amount of numeral usage is far more than the pair-wise based analysis”; with more numbers to analyze, it is feasible to analyze the distribution of their values (Ca-Ca distance values) to test whether these follow the observed distribution in Figure 3 or not. If these distances do not follow the distribution of Figure 3, then their treatment of this data is likely inducing a behavior that is not present in the original data. This in turn may have an effect on the author’s results and conclusions. Hence, it is important to show this analysis of distances to test for the lack of induction of their method.

- Furthermore, the Ca-Ca distance distribution would allow for better interpretation of their data. For instance, in the section “Distribution plot”, the authors described how the UMF values vary from a minimum of 15 to a maximum; however, there is no interpretation of these values to the protein itself. For instance, contiguous Ca-Ca distances are usually between 6-12 A apart; hence the limit for UMF=15 is probably the consequence of this range. The authors also mentioned the value close to 0 for unstructured proteins. Yet, considering that UMF=DSA, we can conclude that for unstructured proteins, the DSA would have large average distances and potentially low stdev, hence, that value would tend to be large not close to cero. But looking into their Ca-Ca distance may solve this apparent discrepancy. The interpretation of their results may focus on the protein structure and not so much on the UMF value itself. For instance, since the distance between alpha carbons cannot be extended too much, it seems that the upper limit of the DSA depends on how small the stdev is. Understanding why different structures of the same protein maintain the same orientation of each pair of alpha carbons may depend on the crystallographic conditions used. If the different structures were crystallized with the same procedure and obtained very similar resolutions, this may explain this small variation. The authors do not discuss this.
Validity of the findings: - The term morphable and its score are not clear what they try to capture from the protein structure. Considering the formula and their description, it seems that the authors’ interest is to capture the structural divergence between different experimental conditions used to solve the same protein. If that is the case, I would expect a clear relationship between their UMF score and a similar one derived from the crystallographic B (thermal) factors. However, the authors did not present any data to show this possible relationship. In any case, it is important for authors to show that their values reflect some aspect of the experiments to solve the structure, the nature of the protein or both.  The current work lacks any analysis in this regard. For instance, the authors could extract information that is part of the PDB entries, such as CAVEAT, COMPND, SOURCE, AUTHOR among others, to infer how different the conditions used to solve two or more structures were. If there is a correlation between these experimental differences and the UMF, then this last score would be a valuable resource to resume lots of experimental information. The same applies for structural changes of the protein that reflect the structural flexibility of the protein as noted in the previous point.
Additional comments: Minor concerns
- Figures are presented in the text not in the order in which they are numbered; for instance, figure 7 is refer first than figure 3, which in turn is referred first than figure 2.

- line 102 “are now can be processed” may be clearer to say “can be processed now”.

- lines 117 to 120 in Methods, refer to results, not to methodology. This has to be changed.

- line 129 states “UMF converges as the number of used chains increases”; it is not clear to what converges to the UMF.

- line 141 “and 22.3%” would be better as “or 22.3%”.

-line 151 states that “Since 222 out of 1043 xUMFs are of the possible 6293 membrane proteins,”; it may be clearer to state “Since 222 out of 1043 xUMFs presumably are part of the 6293 transmembrane proteins,”.

- Figure 1; in the text the authors claim to have used the average distance between all pairs of alpha carbons, the image only shows the score for 1 pair, so it does not illustrate what the score is.

- Figure 2. The legends of the figure do not correspond with the plots.

- Figure 7 A and C, the symbols are too small.

- Figure 7. It is not clear what the authors mean by "This value appeared to be possible to converge to a lower one, whereas even the progress plot (Fig. 7A, C) could not be made with just one data point (number of chains = 3). The unused entry contains two regions of chain-break within the almost full-length model.".


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: REPERTOIRE OF MORPHABLE PROTEINS IN AN ORGANISM
Review round: 2
Reviewer: 1

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: The paper has been improved, however, additional improvements are required so that the reader can fully understand your contribution and other researchers can reproduce your results. The main concern is that I still find it difficult to reproduce what was done here, and I will suggest the authors to address all their effort in making every step as clear, detailed and self-contained as possible. Some examples of things that need to be improved are listed below.
1. You need to provide a clear, mathematical definition for UMF, with an example for it and the reference that proposed it for the first time, which I understand is due to Okada, 2018.
2. According to your definition what is considered flexible and what is rigid? Does it mean that if you have 20 experimental structures for the same protein and all of them represent the same conformation then this protein is rigid? Please give a physical explanation of the rigidity (flexibility) that is measured by the xUMF?
3. How do you support the following statement?
“ demonstrating how rigid and flexible components are balanced. ”
Can you provide a more detailed explanation about the composition of rigid and flexible components for the E. Coli proteome? How many proteins are rigid, how many proteins are flexible, what is the threshold in xUMF that separates one from the other?

4. It is not clear if only continuously modeled proteins are included, and if by this you mean proteins whose chains have no missing amino acid between the N-terminus and the C-terminus? The readers do not need to read Anzai´s work to discover this.

5. It seems that there is a contradiction with this sentence in the abstract ¨By collecting a new index “UnMorphness Factor” (UMF), proposed in this study and determined from DSA for each of the proteins,¨ and the following one in the Introduction ¨We previously proposed that “UnMorphness Factor” (UMF), (Okada, 2018) which is defined as a converged average score for a protein, is an alternative to conventional RMSD-based comparison.¨
The abstract says that you proposed UMF in this study while the Introduction suggests that it was proposed in Okada, 2018. Please clarify, and if needed correct.

Minor details,

English still needs to be carefully revised. For instance, in the last paragraph of the Introduction you need to change ¨ The present work is intended to assign an UMF¨ by  ¨The present work is intended to assign a UMF¨
In the first paragraph of the Methods section
¨showing that about 30% of the ECOLI proteins have at least one X-ray entries¨ Vs. ¨showing that about 30% of the ECOLI proteins have at least one X-ray entrY¨


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: REPERTOIRE OF MORPHABLE PROTEINS IN AN ORGANISM
Review round: 3
Reviewer: 1

Output:
Basic reporting: See ¨General Comments for the authors¨
Experimental design: See ¨General Comments for the authors¨
Validity of the findings: See ¨General Comments for the authors¨
Additional comments: The authors have answered and properly addressed all of my 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: LIFE HISTORY STAGE EXPLAINS BEHAVIOR IN A SOCIAL NETWORK BEFORE AND DURING THE EARLY BREEDING SEASON IN A COOPERATIVELY BREEDING BIRD
Review round: 1
Reviewer: 1

Output:
Basic reporting: See review below
Experimental design: See review below
Validity of the findings: See review below
Additional comments: The authors present an interesting study looking at differences in social network position of individuals across different life stages. This is a neat idea, and the study is reasonably well presented. But, I’m afraid that I think there is a potentially major confound that hasn’t been sufficiently accounted for, which may have some impact on the results. In addition, it isn’t clear that the networks are sufficiently robust to conduct these analyses; at least not with the current hypothesis-testing approach.

The potentially major issue with the analysis as it stands is that the majority of the results could be explained by one factor – the number of observations of each individual. The more often an individual is observed, the more opportunity there are to observe connections – thus individuals with more observations typically have a higher degree (# obs also affects other network metrics too). It often takes very many observations to remove this effect. In our great tit networks the threshold was c. 100 observations per individual(!). As the authors included their data with their submission, I had a quick look at the potential for this effect. For 2016, I found that probably all of their patterns are explained by the number of observations. The correlation between #obs with degree was 0.81, with betweenness was 0.56, and with clustering coefficient was -0.67. However – don’t despair! The very simple solution to this is to switch null models to one that explicitly and correctly controls for number of observations (please don’t add #obs into a linear model because the relationship is rarely linear). Doing pre-network permutations would allow the authors to do this – in fact the code to do this is hardly more complicated than the existing approach they use (it’s just one command in the asnipe package). At the same time, the authors could also control for space (by randomising within sampling point). Should the authors have any questions – I always reply promptly to any questions regarding the application of my R packages. There is also useful examples of code in the appendices of the Farine & Whitehead 2015 paper which is cited in this manuscript.

Building a little bit on the previous point, another issue that is present with the current work is whether the networks are robust. The authors cut off their minimum data at 3 observations. In Farine & Strandburg-Peshkin 2015 (RSOS) and Davis et al. 2018 (Animal Behaviour), we first provide guidance on how to estimate robustness, and also suggest that a good rule of thumb is that dyads should have the denominator of the simple ratio index sum up to 20. It could be that this is the case at present, but it’s unclear from the existing text.

Moving away from the methods a bit and to the broader perspective – it wasn’t clear to me what a network really means in a territorial system such as this. I understand that one might study within-group networks, but beyond this I can’t really pin much meaningful biology on it. For example, what does it mean to have a higher degree? Birds in larger ‘family’ units will have a higher degree, and maybe those with more nearby neighbours. But in the broader context, what does a population-level network capture? I don’t have an answer to this, but feel that the authors should provide one. On that note, it also seems a bit internally inconsistent to state that data were collected after conducting playbacks (L141) and then going on to state that this did not create artificial associations (L146).

I also had a question in terms of field data collection, related to the point immediately above. On L154, the authors state that ‘We assumed that all birds detected together at a point were associated’. This seems fine. But, in the next sentence, they state that ‘We also recorded opportunistic observations of aggregations of jays from non-adjacent territories.’ First I don’t understand what this means – but if my interpretation is correct (which is that you distinguished between groups that were from the same territory and those that were from different territories), I worry that a priori information about the social structure of the population is creeping into the field data being collected. This should be avoided at all costs. (Note-I work on a system where birds live in stable groups, and it’s an ongoing battle to stop students from incorporating their knowledge of system into their observations).

From my reading of the manuscript, I’d say that the authors will have no troubles addressing the comments outlined above. However, it may be that their results won’t be so clear. I hope that this won’t prevent them from publishing the manuscript irrespective of whether the current results stand or not—but I do encourage the authors from publishing a manuscript based on the most robust analysis they can achieve.

Damien Farine
(I sign all of my reviews)

Minor comments:
L30: Here and throughout the opening section of the introduction the citations seem very old. The first 7 citations are over 10 years old. I’d argue, for example, that the first citation does not show evidence that networks are a powerful way of quantifying social behaviour. The work done since then does.

L32: In Farine 2015 (Animal Behaviour) I deal with this question of interactions vs. observations more explicitly than the current citations.

L46: In the broader context of social associations, Alberts 2019 JAE should be cited here.

L56: The first sentence here reads really awkwardly.

L60: The sentence here doesn’t make much sense. You could have an accurate representation of the real world that is difficult to predict. For example, we can accurately measure earthquakes, but we cannot predict them.

L63: Why are you evaluating social networks? This ‘aim’ seems to pop up a few times in the introduction and elsewhere but it isn’t well justified or explained.

L82: At the end of the sentence here it feels that there should be a point made, but it isn’t made.

L100: Why is this a hypothesis? Where is the justification for calling it a hypothesis?

Table 1: I suggest adding a column that summarises the support (or not) for each prediction (see Brandl et al. 2019 Proceedings B for an example).

L141: The use of the playbacks brings into question whether what is being measured here area really social networks. They are something – but not really social networks in the context of how the introduction is framed. At least some more biological justification is required here.

L146: How are they not artificial? Would you expect that the associations that you have observed would have happened if you hadn’t performed the playbacks? How would you know this?

L161: Why choose 3? What is the justification behind this choice?

L164: It would be useful to give some more justification for why these three metrics were chosen. What are some biological insights that have been gained from them?

L189: I don’t understand the use of ‘distance to nearest sampling point’. If you sample individuals only at sampling points, how do you estimate this? Is it a property of the territory they are living on?

L195: I totally failed to understand what the difference is between the two sets of models. I re-read this section at least 10 times, and still couldn’t come away with a difference. The results seem to contain only those for one set of models (Table 3). The only difference between these two sets of methods is that the first says ‘each social network variable’ and the second says ‘social network metrics’ – but the first fits sex, etc. suggesting an individual-level analysis (and therefore applying to social network metrics).

L197: Why did you sqrt the degree? Was this done for the previous model as well? Needs a justification.

L199: Node permutations do not control for number of observations or space. (also were the randomised data only swapped within year?)


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: LIFE HISTORY STAGE EXPLAINS BEHAVIOR IN A SOCIAL NETWORK BEFORE AND DURING THE EARLY BREEDING SEASON IN A COOPERATIVELY BREEDING BIRD
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The aim of this study was to determine the extent to which life history stages of Florida scrub-jay, a cooperatively breeding bird, corresponds to position in a social network resulting from life history stage-specific social behaviour. The authors indeed report substantial differences in network connectivity observed, for instance, between helpers and breeders. The authors conclude that their network-derived results are in line with a priori expectations based on previous longitudinal studies on the subject. While the topic of the study is interesting, the described data collection procedures are admirable, I have one major comment. I struggle to understand the main aim of this study or, specifically, the rationale behind the study design except the apparent novelty resulting from the application of the SNA method. As currently written, it is rather unclear whether the application of SNA in this study adds to what have been previously known regarding the interplay between social behaviour and life history stages in cooperatively breeding species. Can the methods used in this ms shed some new light on previous studies (e.g., that used non-SNA methods) regarding the social behaviour of cooperatively breeding species? Which aspects of SNA results, if any, lead to different conclusions compared to what would be expected by applying methods based solely on dyadic interactions? Some of the results presented here provide a hint to such questions. For example, discussing the variation in helper network connectivity in relation to transitioning to breeders I find very interesting indeed (although I have some serious doubts regarding the chosen methods as well as the interpretation of the results-see below in specific comments) and I think that this aspect of the ms should be elaborated. Therefore, I would suggest to re-frame the focus of this ms and put more emphasis on the network position variation within a specific life history stage (e.g., helpers, and how this variation relates to a potential reproductive success) rather than merely making a case for demonstrating that SNA is capable of replicating what other methods do. Such refocus would also allow for making much more specific and biologically relevant hypotheses compared to what is currently presented. I have also several specific comments regarding both the theoretical side of the paper and statistical analysis:
.	Line 30 why is SNA ‘powerful’, how does it relate to social behaviour derived from dyadic observations only? It has to be explained for a general audience as not everyone is a SNA expert
.	Line 56-57 ‘when life history strategies differ among stages’ -unclear, rephrase
.	Line 69 would it be possible, if data allow, to quantify the extent to which this kin factor affects social network position among helpers?
.	Line 85-86 maybe the variation in the network connectivity within the life stages and its possible implications should be discussed to a much greater extent
.	Line 303-305 it would be useful if the authors provide some information how such a drawback would potentially affect network metrics
.	Line 325-330 From how it is phrased here I assume that the authors compared the network connectivity of helpers in 2016 that stayed helpers in 2017 to corresponding network connectivity of helpers in 2016 that transitioned to breeders in 2017. Only such comparisons would warrant a claim stating that ‘an individual’s social behavior as a helper may affect its probability of transitioning to a breeding position’. However, the Fig 3 that the authors refer to (as well as methods described in line 205-209 and reported results 250-255) seem to show completely different and irrelevant to the conclusions made by the authors comparisons. Please clarify.
.	Line 342-346 An interesting point, it would be interesting to incorporate data on such within-life history stage variation in mass and social dominance rank into the current data set

.

.


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: LIFE HISTORY STAGE EXPLAINS BEHAVIOR IN A SOCIAL NETWORK BEFORE AND DURING THE EARLY BREEDING SEASON IN A COOPERATIVELY BREEDING BIRD
Review round: 2
Reviewer: 1

Output:
Basic reporting: See general comments
Experimental design: See general comments
Validity of the findings: See general comments
Additional comments: The authors have done an excellent job with revising their manuscript, and I applaud the efforts they have made to consider (and implement) the reviewers' comments. The manuscript is now much stronger, and clearly more robust. I have only two comments, both of which are relatively minor. These can be dealt with easily, and I do not need to review the manuscript again.

The main point is that the authors should ensure that they are putting in the right network data into the betweenness measure. In igraph, the betweenness measure (for some reason) interprets the weight of the edges as a cost or distance (see this thread on Twitter: https://twitter.com/mattjsilk/status/997029135548669957). Thus, the authors might want to follow the advice given about how to deal with this rather annoying issue. I'm sorry that I didn't pick this up in the first review.

Also in L62, I felt that two citations would make the introduction more complete:
Webber, Q. M., & Vander Wal, E. (2018). An evolutionary framework outlining the integration of individual social and spatial ecology. Journal of Animal Ecology, 87(1), 113-127.
He, P., et al. (2019). The role of habitat configuration in shaping social structure: a gap in studies of animal social complexity. Behavioral ecology and sociobiology, 73(1), 9.

It has been a pleasure to have had the opportunity to review this work.

Damien Farine
(I sign all of my reviews)


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: LIFE HISTORY STAGE EXPLAINS BEHAVIOR IN A SOCIAL NETWORK BEFORE AND DURING THE EARLY BREEDING SEASON IN A COOPERATIVELY BREEDING BIRD
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed all my suggestions and I have no further comments.
Experimental design: The authors have addressed all my suggestions and I have no further comments.
Validity of the findings: The authors have addressed all my suggestions and I have no further comments.
Additional comments: The authors have addressed all my suggestions and I have no further comments.


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

Input:
Title: FLUID RESUSCITATION-RELATED COAGULATION IMPAIRMENT IN A PORCINE HEMORRHAGIC SHOCK MODEL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The aim of the study and the methods used are straightforward, and importantly the authors' conclusions are justified based on the findings.  The manuscript is generally well written and clear; although there are some minor syntax errors; here are a few recommended corrections:

line 69: "Massive blood loss as a hemorrhagic shock trigger requires resolute and efficient action".  The word "trigger" needs to be deleted, or re-phrase the sentence.

line 89: "...less frequently applied colloid that.".  Delete "that"

line 98: "We thought to explore the influence of..".  I would suggest that "We thought" is deleted and this sentence begins with "Our aim was..."

line 99: "...which enables to analyze fibrin polymerization, clot..".  Should read "...which enables to fibrin polymerization analysis, clot..."

line 120: delete "their"

line 268: should be changed to read "..can be explained by.." delete the word "with"

Figure 1: define BLH (I assume this refers to baselines)

Figure 1 & 2 axes,  Table 1 legend: most of the manuscript provides the units as "kg-1" etc. yet here there's a mix in how the units are expressed e.g. "HR: heart rate (min-1); CI: cardiac index [l/min/m2];"  Stick with one way to express things either superscript numbers or /.
Experimental design: The study is well designed, carried out by qualified researchers and in my biased opinion the authors have used an appropriate, human-relevant model to study haemorrhagic shock and resuscitation.  All ex-vivo analysis is well described.

I need some clarification on the anaesthesia protocol.  It's clearly stated that the pre-medication/sedation is via i.m. ketamine and midazolam; but it's not clear which vein the Fentanyl and propofol where injected prior to intubation.  I assume this happened before a central line was inserted.  Please clarify.
Validity of the findings: Conclusions are well stated and do not go beyond what the results and methodology provided.  The statistics are fine. The comparison with human data was very interesting.  As a personal aside, I found the haematocrit data interesting, the low anaemic baseline numbers (when compared to human values)  match those we see in our experimental pigs.
Additional comments: I would encourage the authors to keep using large animal models for their research.


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: FLUID RESUSCITATION-RELATED COAGULATION IMPAIRMENT IN A PORCINE HEMORRHAGIC SHOCK MODEL
Review round: 1
Reviewer: 2

Output:
Basic reporting: See final section
Experimental design: See final section
Validity of the findings: See Final section
Additional comments: I would like to congratulate the authors on a well written and conducted paper.The structure conforms to PeerJ standards. Figures are relevant, of sufficient quality and are well labelled & described. In addition, raw data are supplied.

Although generally very well written, some examples where the language could be improved include lines 220 (not as low), 226 (remained at a higher level), 227 (Regarding clot formation time following GP, only the BES group returned to the baseline level) – the phraseology is sometimes imprecise and so makes the results section a little difficult to follow.

The Introduction & background are well written to show context. However, in recent guidelines, there is an aim to limit early fluid resuscitation and to use crystalloid rather than colloid in the first instance. I have a concern that the premise of this study is based on out-dated practices. While the EMA may have more recently watered down their previous negative risk assessment on use of HES, in practice colloids are not used first line in resuscitation in early haemorrhagic shock. This is due to evidence from human studies. In addition, the coagulopathy noted has been previously well described in humans where experiments using TEG have also been conducted (e.g. Hemostatic changes after crystalloid or colloid fluid administration during major orthopedic surgery: the role of fibrinogen administration. Mittermayr M1, Streif W, Haas T, Fries D, Velik-Salchner C, Klingler A, Oswald E, Bach C, Schnapka-Koepf M, Innerhofer P. Anesth Analg. 2007 Oct;105(4):905-17).

I feel that a much stronger justification for conducting this study needs to be put forward with a more thorough review of the literature that reflects current knowledge and practice. For example, references 13 and 15 do not, in my opinion, support the argument in the text. One is a small study in elective ovarian cancer surgery with goal-directed haemodynamic outcomes. The second showed a worse outcome in ICU patients (increased AKI).

It is stated in the text that “This study represents an independent sub-project and complementary hypothesis of a research project that investigated the cerebral effects of solutions for fluid resuscitation”. It may be reasonable to present these data given that this project is part of a larger project as described. Were it not part of a larger project I would find it difficult to see how ethical approval might be forthcoming given that TEG in haemorrhaging pigs is likely to add little to the already-conducted human studies of TEG in haemorrhaging adults.

The research question is well defined, but, as stated earlier is somewhat less relevant & meaningful than would be expected from primary research in this area. It is stated how the research fills an identified knowledge gap but I am not sure that such a gap has not been explored in human studies. Nonetheless it appears that investigation was performed to a high technical standard. The methods are described with sufficient detail & information to replicate. Conclusions are well stated, linked to original research question & limited to supporting results.


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: PROGNOSTIC ANALYSIS OF VERY EARLY ONSET PANCREATIC CANCER: A POPULATION-BASED ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1, the language of the article still need to be improved.
2, all p value are missed in these tables.
3, was Cumulative incidences of death conducted in R? what is the package you used in this process.
Experimental design: 1,the sample from the TCGA database is too small.
2, there is no exploration of any molecular mechanism
Validity of the findings: the explanation of the results of your research could be better.
Additional comments: I reviewed the manuscript. The work is quite interesting and provides an epigenetic insight into PDAC.
In general, the data presented are of good quality and largely support the conclusions.


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: PROGNOSTIC ANALYSIS OF VERY EARLY ONSET PANCREATIC CANCER: A POPULATION-BASED ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear, unambiguous, professional English 	(NOT satisfactory)
language used throughout.
Intro & background to show context. 		(YES)
Literature well referenced & relevant. 		(YES)
Structure conforms to PeerJ standards,
             discipline norm or improved for clarity.
Figures are relevant, high quality, well
             labelled & described.				(NOT satisfactory)
Raw data supplied (see PeerJ policy).		(YES)
Experimental design: Original primary research within Scope of	       (YES)
             the journal.
Research question well defined, relevant		(YES)
            & meaningful. It is stated how the
            research fills an identified knowledge gap.
Rigorous investigation performed to a		         (YES)
             high technical & ethical standard.
Methods described with sufficient detail &	         (YES)
             information to replicate.
Validity of the findings: Introduction and discussion should be elaborated, and more literature need to be cited.
Additional comments: Dai et al developed a nomogram for predicting the death caused by very early onset
19 pancreatic cancer (VEOPC)

1.	Introduction is short and authors should elaborate and give details of all the factors that play a role in pathogenesis of pancreatic cancer.
2.	Manuscript is badly written and English language is not good. There are many spelling mistakes. It seems authors are in hurry to send the manuscript.  For example, line 46 “Duo”. The first sentence of introduction itself does not make any sense “Pancreatic cancer (PC) patients are estimated with a 5-year survival lower than 10%.
3.	Line 144 r package can be changed to “R” package.
4.	Line 161-165 is poorly written and very confusing. Author should consider it for rephrasing.
5.	Line 180 the whole sentence is confusing
6.	Author should provide list of abbreviations used in manuscript
7.	figure 4 e should be in brackets (e)
8.	Table 3 is not clear
9.	Figure legend should be in detail


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: PROGNOSTIC ANALYSIS OF VERY EARLY ONSET PANCREATIC CANCER: A POPULATION-BASED ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overall:  The authors have presented work similar to what they have done for other cancers (breast).  Using SEER data presents some problems as other factors that might be associated with prognosis including tumor and germline genetic factors and behavioral factors (smoking, alcohol consumption which seem like they would be important in a competing risk model) are not available.  The TCGA data were inadequate for identifying RNA based molecular differences.  A similar paper regarding competing risk analysis and nomogram development has been published for patients with resected pancreatic cancer of the head with clear explanation of the value of competing risk analysis and the justification and utility of competing risk models and nomograms  http://www.jcancer.org/v09p3156.htm.  A more detailed discussion and justification for using competing risks especially in this young age group, is needed.

The varying use of age groupings was confusing.  The analysis is described in the abstract as a comparison of very young to older patients (older is undefined while it is clear that younger is <45 years) and this is how the data are presented in Table 1 (patient characteristics).  Then for the MV and prognostic analyses (Table 2) the older age group is then sub categorized into 4 groups that are compared with the very young.  Finally the nomogram analyses are limited to the very young but in two age groups within this group (Table 3 and Fig 4).  None of these groupings are justified or discussed making it difficult to understand who these patients are and what is the primary message being conveyed.   It would be helpful if Table 1 provided patient characteristics for all age groupings or a supplemental table should be provided.

The grammar and sentence construction needs work.  Someone who speaks English as a first language or is fluent in written English needs to help with the re-write.  Awkward wording e.g. use of “involve” rather than “include” when talking about variables in the MV models, poor grammar and incomplete sentences e.g. “While the other studies found age was not a risk factor for PC patients.”, “And there was no significant prognostic difference between VEOPC and older PC in resectable PDAC.” are scattered throughout the manuscript.  I note some but not all additional awkward grammar below in my critique.

Table headers need to be more descriptive and detailed. A table should be able to stand alone- without the paper.  There is insufficient information in the table titles and table notes for a proper interpretation of the data being presented.  Also, the figures need to be reformatted to address issues with hidden (overlapped with graphical presentation) and missing text ( labels).

Abstract:

Correct incomplete sentences:
“While the other studies found age was not a risk factor for PC patients.”, “And there was no significant prognostic difference between VEOPC and older PC in resectable PDAC.”

Define the older age group in age in years.

Introduction:
Line 43: The first sentence is awkwardly written.

Line 45: Should be “patients is 70 years”.

Line 46:  “which was defined as very early onset PC (VEOPC)3.” Is this for this paper or is this standard terminology?  In the next paragraph it is stated that definition of “young” has varied widely.

Line 49: wrong verb tense

Line 60:  “To our best knowledge” is awkward phrasing.

Line 64: typo in  “United States”

Line 65:  “includes” instead of “involves”- this should be checked and corrected throughout.

Line 66: grammatically awkward and incorrect phrasing “Since pancreatic adenocarcinoma (PDAC) is the main type of PC, which has a worse prognosis than other histology types of PC and is frequently occurred in old patients, we choose the PDAC patients as our target cohort.”

Line 152: Reword subheading “Differentially analyses of miRNA and mRNA between VEOPC and older PC patients”

Line 163:  The race data have not been presented this way in the text or the table.  Be consistent.

Tables (as noted above need to be more detailed)

Table 1.  Define acronyms, round % to 1 digit after the decimal if >1%, indent under main headings to make groupings easier to read/distinguish, add p-value for univariate comparison, add total N at tops of columns.

Correct the total number of unmarried

Table 2: What variables are included in the MV model?  How was the "best" model selected?  Age groups >70 are very similar and could be collapsed based on these results.

Table 3:  Why this age grouping? How many patients are included in each group (as the data have not been presented previously)?

Under LNR- what is the maximum size i.e.  0.4 - ?

Figure 1:  Reposition the legend as it overlaps with the curves.  It is unclear what the red and black curves are- is that what is meant by the "right 1 and 2 represent..."?

Figure 4:

A more detailed description including the relevancy of these curves is needed for the reader to better understand what they are looking at.  Competing risk analyses are not common and use of calibration curves for model prediction is probably not familiar to many readers.
Experimental design: Line 59:  This is opinion and not backed up.  Why is a nomogram needed?  PDAC has few treatment options so it is difficult to see this being translated into clinical care (also this is a complex nomogram).  Is it perceived that this would be useful for risk stratification in clinical trial recruitment, QOL interventions, future basic science or population based studies?  Not clear.

Study variables and endpoints

Line 96:  What are “small categorical variables”?

Line 97: Justify the groupings for marital status –especially as this is carried forward into the analyses within the VEOPC only, is statistically significant and included in the nomogram.  Literature indicates that widowed younger people die earlier and in general are more likely to be single. This suggests that the married /not married grouping might not be the best for analyses within VEOPC.

Line 105- What was the stage distribution in the older PDAC patients?

Statistical Analysis:

Line 129- State whether the p-value is two-sided

Prognostic analysis of age in PDAC patients

Given that age is assessed in multiple groups (unexplained groupings) it seems table 1 would benefit by presenting data with this same grouping for "older" patients or at least provided as a supplemental table.

Line 147: It is not stated what other variables are included in the MV model.

miRNA and mRNA analyses

Given the small sample size and inability to conduct meaningful analyses of miRNA and mRNA this information is unhelpful and does not contribute anything meaningful to the analysis.  The results mention that only 3 differentially expressed miRNAs and 17 differentially expressed mRNAs were found but it does not state the comparison groups.  At least 3 different age group analyses were conducted so this is unclear. It could be mentioned in the discussion that this assessment was of interest but cannot be conducted at this time with data currently available.

Table 3 analyses
Given “Other” race is statistically significant and that most patients in this group are likely to be Asian (and thus driving the association) “Asians” should be broken out into their own category (for all analyses).
Validity of the findings: Abstract:
Reword this sentence “We observed VEOPC had better cancer specific survival (CSS) than older PC in patients with unresectable PDAC.” Does this mean both groups had unresectable PDAC or just the older patients?

Conclusion:  Clarify that the first sentence pertains the VEOPC compared with older patients and that the second sentence pertains only to the VEOPC patients.

Overall
The relevance and importance of the nomogram is needed - other than it has not been done.  A nomogram is a tool and it is not clear where the nomogram would be applied and why.

Statements and conclusions about the overall results of VEOPC vs all older PDAC, VEOPC vs older PDAC groups and within the VEOPC group need to be made extremely clear.  Multiple analyses have been done which causes confusion when statements are not qualified according to the specific group of comparisons.

Weaknesses have been noted but it also should be noted that only factors available in the SEER registry were examined.  The population to whom these results can be generalized needs to be made very clear.

The discussion and conclusion for the miRNA and mRNA analyses do not fit with the results section presentation- specifically there is too much teext devoted to this in the discussion.  The results mention that only 3 differentially expressed miRNAs and 17 differentially expressed mRNAs were found (but not between what groups of patients).  No other findings were statistically significant.  A lot of discussion and speculation is given to these very underwhelming and limited findings- more so than to other aspects of the analysis.  Additionally results are presented in the discussion that are not presented in the results section i.e. the specific miRNA and mRNAs that were identified.  There is no segue that connects the discussion of PAF1 to the RNA analyses nor why PAF1 is relevant to the miRNA and mRNA results from this analysis.
Additional comments: No additional comments


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

Input:
Title: PROGNOSTIC ANALYSIS OF VERY EARLY ONSET PANCREATIC CANCER: A POPULATION-BASED ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: English is clear and understandable. Literature references are sufficient.
Experimental design: Experimental design are under the scope of Journal. Methods section is in detail.
Validity of the findings: Conclusions are well stated.
Additional comments: Thank you authors for revising the manuscript.


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

Input:
Title: EARLY CHANGES IN THE URINE PROTEOME IN A RAT LIVER TUMOUR MODEL
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English language should be improved throughout to ensure that an international audience can follow the rationale for the study, the Methods and the Results.  Several sentences are difficult to follow and untangle.  For example, the opening sentence of the subsection 'Urine collection and sample preparation' (lines 105-106) is ambiguous.

There have been a number of clinical and experimental publications to date in this expanding area of proteomics, It would be helpful to expand the literature review applied to clinical biomarkers of hepatocellular carcinoma (perhaps to include serum too) in the Introduction (lines 62-68). The authors might consider referencing the following papers:
https://www.ncbi.nlm.nih.gov/pubmed/27847095, https://www.ncbi.nlm.nih.gov/pubmed/26675302,
https://www.ncbi.nlm.nih.gov/pubmed/21518826.

It would be helpful for the reader to tabulate which animals were used for which study (histology, urine collection).  It isn't clear why urine samples were collected from only three controls and three experimental animals, given the study started with seven controls and 12 experimental animals.

Given a range of papers have already shown early urinary biomarkers of HCC can be detected using proteomics, the hypothesis would benefit from being more specific.  Whilst there is some value in another documentation study a more hypothesis-driven study would be appropriate.
Experimental design: This paper would benefit from a more specific Research Question.

Various subsections in The Methods are difficult to follow, including Tumor cell line and Culture, Rat models of liver cancer, Histological analysis, Urine collection and sample preparation.

Did the statistical tests allow for multiple comparisons?  Whilst the replicates were used for mean+/-sd values, were the replicates also included in the independent sample t-tests?  From Tables S1 and S2, were the controls measured at days 3,5,7 and 11 or only at baseline?
Validity of the findings: Which of the urinary proteomic findings may be attributed to changes in body weight?

The Results are discussed in detail, but as many of sentences in the Discussion are listing proteins it is difficult to follow.  Early biomarkers should be the main focus of the Discussion, in line with the title of the paper.
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: EARLY CHANGES IN THE URINE PROTEOME IN A RAT LIVER TUMOUR MODEL
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript submitted by Zhang et al. is focused on early changes of urinary proteome in animal model of liver tumor.  The subject is very important and proposal interesting. Although, everyone agrees with sentence at lines 343-344 (“…a panel of urinary differential proteins may be an ideal choice to improve the sensitivity and accuracy of early diagnosis for liver cancer”), however, they don’t allow important results; it is to underline some criticisms concerning both experimental diagram and results.
Experimental design: Experimental design needs to be improved, see specific comments.
Validity of the findings: Work don't report relevant results to hypotheses
Additional comments: The manuscript submitted by Zhang et al. is focused on early changes of urinary proteome in animal model of liver tumor.  The subject is very important and proposal interesting. Although, everyone agrees with sentence at lines 343-344 (“…a panel of urinary differential proteins may be an ideal choice to improve the sensitivity and accuracy of early diagnosis for liver cancer”), however, they don’t allow important results; it is to underline some criticisms concerning both experimental diagram and results.
Authors used 7 controls and 12 tumor-bearing animals; but only 5 animals were used to collect liver and three of them for urine collection at different times.
Authors missed an important time-point; it should be interesting for proteome analysis.
Concerning sample preparation, urine required to be centrifuged after collection and before storage at -80°C to eliminate the urinary debris related to cells and membranes.
To improve validation of biomarkers it is mandatory to compare proteomes obtained from both urine and liver collected at the same time.
Because repeatability was not good within the time, it should be better to analyze a greater number of samples; in fact, authors report to have used 12 animals, but three of them seem to be used.
Concerning comparisons, authors have to perform kinetics (at each time-point including T0) for each animal to reduce variability due to specific animal. Important comparison is also treated versus control animals at the same time (day), because growth may be  important for proteome changes.
Hierarchical clustering is not very good, because animals are not correctly segregated for time-points.
About sentence reported at lines 204-205, it is not possible to be in agreement because Figure 4 indicates that is limiting the organ where tumor cells were injected  (only 19 proteins out of 275, resulted common); in fact, authors report at line 244-246 that “…the same tumor cell grown in different organs may be different.”  It should be interesting to allow the identity of shared 19 proteins.
About discussed proteins, such as LGALS3BP, authors need to evaluate recent works concerning urinary proteome, specifically obtained from urinary exosome (see ExoCarta website and recent articles and reviews).
In the Introduction section authors report the importance of AFT as liver related tumor biomarker, but this protein was not identified in their analyses and no comments were done.
Authors collected  interesting sets of samples, but they need to complete both proteome analysis (including livers and T0 time-points) and comparisons.
Minor Comments
It is not clear because authors made 10kDa filter (line 118).
Reference list is very long, but it is not appropriate.
Also, it is not clear what the treatments according the bioethical roles.
Collected volume of urine is not reported.


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: COUPLED INFLUENCE OF PRECIPITATION REGIMES AND SEEDLING EMERGENCE TIME ON THE REPRODUCTIVE STRATEGY IN CHLORIS VIRGATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.Materials and methods are acceptable. My question is why do you chose this species again? You have done the work about the effects of precipitation regime on reproductive strategy of this species in the former work. Why did you not design the coupled factors in hte former work?
2.Figure 3, the legend (T1, T2 and T3) should appear in Figure 3A not Figure 3B.
3. Line 72 and 91, the blank spaces should be deleted.
4.Line 69 The sentence: “Precipitation is one of the major factors that limits seed productivity in arid and semiarid areas”. Did author research on other factors, for example nitrogen, temperature or extreme weather? And which factor is more important for this species in the research?
5. Line 106: The left spikes from each plant were recorded and kept in individual paper bags. The authors meant that "the number of left spikes from each plant were recorded and the spikes were kept in individual paper bags"?
6. Seed yield in Figure 3B. Why the data is so different with the former study (in 2018)?
7. Please check the format of the journal and revise the references as the journal requirement. In addition, you can delete some older ones if they are not so important.
8. The “Spike number (plant-1)” in Table 3 should be“Spike number (n plant-1)” ?
9. Please check the format of the journal and revised the subtitle in the manuscript as the journal requirement.
10. please check all the figure legends and revise them according to the journal requirement.
Experimental design: The experimental design is rational. Materials and methods are acceptable. The species is so important in arid and semiarid area.
Validity of the findings: There are some works about effects of precipitaion on plant growth and reproduction. While the authors can simulate the precipitation regime and precipitation time, which are  important factors in the North of China. However, there was few work about the effects of two factors on plant's reproductive strategy. Therefore, it is innovative.
The raw data have been provited. The authors discussed the results linked the data. Finally, they sumarrized the findings in manuscript.
Additional comments: Comments to the Author(s)
The authors showed the reproductive strategy in Chloris virgata under coupled factors of different precipitation regimes and seedling emergence time. C. virgata is so important in recovering bare patches of alkaline soil in Songnen plain. Overall, I think the aim of the paper is interesting and worth pursuing. Especially, delayed spring precipitation occured frequently in some area.
    However, there are still some flaws need further work and clarification. I suggest this paper can be published after minor revision.


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

Input:
Title: COUPLED INFLUENCE OF PRECIPITATION REGIMES AND SEEDLING EMERGENCE TIME ON THE REPRODUCTIVE STRATEGY IN CHLORIS VIRGATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: In summary, the language, experimental design, and results of manuscript is fine. However, some section need to carefully revise. Detail informations are seen general comments for author.
Experimental design: This is a water control experiment, but I cannot find that how the author controls soil moisture. Need detail information in materials and methods section. Furthermore, the author should list the value of soils moisture in each treatment using figure or table.
Validity of the findings: no comment
Additional comments: The research collected many data and analyzed impacts of interaction of precipitation regime and seedling emergence on reproductive strategy of Chloris virgate, a vital species in Songnen grassland, China. The research providing some new support for regeneration in this annual species. However, the paper need to do some revision before acceptance.

Firstly, this is a water control experiment, but I cannot find that how the author controls soil moisture. Need detail information in materials and methods section. Furthermore, the author should list the value of soils moisture in each treatment using figure or table.

Secondly, the author using seed size and seed mass per spike in the manuscript, I think, both of them are same thing. Keep one parameter is enough. And, this is a pot experiment, but the author expressed seed yield using g per square meter. Normally, you can calculate seed yield in the field experiment, not for pot experiment. I suggest you change seed yield as seed number per pot. Thus, in the results, the author only keep spike number, seed no. per spike, seed weight per spike, seed no. per pot is enough.

Specific comments
1.	Abstract: do not use T1, T2, T3 in here.
2.	Results: move ANOVA results to the first paragraph at each sub-section.
3.	Line 64-67. Does this species is a tuft grass? How use this species used to restore degraded grassland? Normally, it is the first species in natural succession process, but not an ideal species to plant artificial grassland. Need more explains?
4.	The significance level was set at P=0.05. No need presented here. Delete.
5.	Try to combine table 1, 2, 4 into one new table. Too many tables.


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: COUPLED INFLUENCE OF PRECIPITATION REGIMES AND SEEDLING EMERGENCE TIME ON THE REPRODUCTIVE STRATEGY IN CHLORIS VIRGATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have well revised manuscript according to the comments from reviewers and editors. However, there still needs some minor revision, particular for English expression. In summary, it should to be accept after further minor revision.

Specifically comments
1. Abstract. Line 4-5. It is not a full sentence. Need to revise. Such as: Here, we simulated the changes in the precipitation regime and seedling emergence time to clarify how the tiller and seed production response to...
2. Line 79. Revise it into Experimental design and treatment.
3. Line 105. Data collection enough.
4. Line 116. Should be Data analysis.
5. Line 123. Non-reproductive not correct. Should be Vegetative tiller.
6. Line 144. Change seed traits into Seed production.
I suggest author revise this kind of expression mistake throught the manuscript.
Experimental design: fine.
Validity of the findings: fine.
Additional comments: The authors have well revised manuscript according to the comments from reviewers and editors. However, there still needs some minor revision, particular for English expression. In summary, it should to be accept after further minor revision.

Specifically comments
1. Abstract. Line 4-5. It is not a full sentence. Need to revise. Such as: Here, we simulated the changes in the precipitation regime and seedling emergence time to clarify how the tiller and seed production response to...
2. Line 79. Revise it into Experimental design and treatment.
3. Line 105. Data collection enough.
4. Line 116. Should be Data analysis.
5. Line 123. Non-reproductive not correct. Should be Vegetative tiller.
6. Line 144. Change seed traits into Seed production.
I suggest author revise this kind of expression mistake throught the manuscript.


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

Input:
Title: COMPARISON OF LIPID ACCUMULATION PRODUCT AND BODY MASS INDEX AS INDICATORS OF DIABETES DIAGNOSIS AMONG 215,651 CHINESE ADULTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript needs proofreading. There are editing errors in the text and in the tables.
Experimental design: The BMI cut-off value for obesity used in this study needs to be described because it is the standard cut-off used in China but not necessary other parts of the world.

The multiple logistic regression analyses need to be described in more details.
Validity of the findings: The conclusion, the title, and the aim of the study did not match well.
The title suggested that the study was to compare LAP and BMI as indicators of diabetes risk. However, the purpose of the study appeared to "find the optimal cutoff point for diabetes diagnosis". Furthermore, in the conclusions, the authors stated that "LAP could be a better anthropometric measurement to predict the risk of diabetes". It is not clear whether the authors plan to use LAP simply as a tool for diabetes diagnosis or to predict risk of developing diabetes (which is not possible with a cross-sectional study design).
Additional comments: Title: The target population should be mentioned in the title as “….. diabetes risk in 215,651 Chinese adults”.

The authors need to carefully proofread the manuscript to correct the typographical errors, such as (1) The “N” after Motamed in Line 54 should be deleted; (2) “liquid” should be “lipid” (Line 60); (3) the (mean +/- S) for BMI should be deleted in Table 3; (4) The word “proved” should not be used (Line 62).

Methods: The use of 28 kg/m2 As the cutoff value for obesity needs to be explained that it is the standard point used in China. There are international variations in the cutoff value.

Methods: The variables included in the multiple logistic regression model should be shown along with the LAP and BMI so readers can get a sense of their magnitude and statistical significance. In addition, please mention whether procedures, such as stepwise, was used to eliminate variables that were not significantly associated with diabetes in the multiple logistic regression model.

Discussion: The authors mentioned that “we did not review the course of diabetes for each participant, which may have affected our results” (Line 230). The meaning of this sentence is not clear. And, if the course of diabetes is known, what can be done to increase the validity of the results?

Tables: Conventionally, percentages should be calculated as column percentages rather than row percentages. For example, the percentage of the males with diabetes should be 48.3% rather than 14.2% (Table 1). The same applies to Table 2 and Table 5. This will match with the description in the Results. Please revise the tables, as appropriate.

Table 1: Please round the values to sensible precision in reporting. For example, one decimal place is sufficient for height and weight.

Table 3: There is no need to show the prevalence in the table.

Table 3: The columns for odds ratio and P value should be placed in reverse. That is, the column for P value should be placed on the right side of the odds ratio.

Table 3: The variables included in the multiple logistic regression model should be listed in the footnote.

Table 4: Are there notable differences in predictive accuracy of LAP and BMI between males and females?

Table 5: Are there notable differences in the distribution of LAP between males and females?

References: They are a number of errors in the style of references. For example, title case rather than sentence case should be used for journal titles. Please double check according to the journal style.


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 LIPID ACCUMULATION PRODUCT AND BODY MASS INDEX AS INDICATORS OF DIABETES DIAGNOSIS AMONG 215,651 CHINESE ADULTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a study of the association between diabetes and lipid accumulation product (LAP) taking advantage of a huge study sample. The nature of the study is confirmatory and replicates earlier studies.
The language is mostly clear, but the text needs rewriting as there are typos like for example “liguid” instead of “lipid” several places. Furthermore, since this is a cross sectional study there is only an association between diabetes and LAP, and it is then not appropritae to describe LAP as a marker of diabetes or stating that is exhibits a higher diagnostic accuracy.
The paper lacks a description of the basic study in which 10% of the population in Urumqi was requited to a physical examination. How were they recruited? Have any analysis been performed to compare the participants to non-participants? Are there any bias or confounders to take into consideration.
Could the authors please provide a reference for the BMI definiotions?
Experimental design: The paper lacks a description of the basic study in which 10% of the population in Urumqi was requited to a physical examination. How were they recruited? Have any analysis been performed to compare the participants to non-participants? Are there any bias or confounders to take into consideration.
With regard to statistics, this seems appropriate, but somewhat insufficient with regard to adust met. I lack a description of what the authors adjust for and a justification for the decisions.
Validity of the findings: The resuls are valid, but the papers lack a justification for replication of the known association between diabetes and LAP. The paper needs to be changed to avoid language implying there are more than an ordinary association between LAP and diabetes.
Additional comments: No additional comments


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

Input:
Title: COMPARISON OF LIPID ACCUMULATION PRODUCT AND BODY MASS INDEX AS INDICATORS OF DIABETES DIAGNOSIS AMONG 215,651 CHINESE ADULTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: How to get the cut-off? Please  explain in section of method.
Experimental design: no comment
Validity of the findings: 1、What is the meanings  of calculating the prevalence of
diabetes in LAP and BMI as a quartile? The cut-off value can show the relationship between diabetes and LAP.
  2、Is the difference  of AUC between LAP and  BMI(see tab 4)   statistically significant.?please explain
Additional comments: The sampling size is large, but AUC area is less than 0. 75. It is not suitable to be a screening criteria. Should statistical methods be used properly?


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 LIPID ACCUMULATION PRODUCT AND BODY MASS INDEX AS INDICATORS OF DIABETES DIAGNOSIS AMONG 215,651 CHINESE ADULTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have adequately revised their manuscript.
Experimental design: The authors have adequately revised their manuscript.
Validity of the findings: The authors have adequately revised their manuscript.
Additional comments: The authors have adequately addressed all my comments except there is a typographical error in both Table 3 and 4. The upper range (55.68) of the 3rd quartile of LAP should not be greater than the lower range (≥ 55.67) of the 4th quartile of LAP. Please fix the error.
In addition, the full form for WC in Table 1 should be given in the footnotes.


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 LIPID ACCUMULATION PRODUCT AND BODY MASS INDEX AS INDICATORS OF DIABETES DIAGNOSIS AMONG 215,651 CHINESE ADULTS
Review round: 2
Reviewer: 2

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


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

Input:
Title: COMPARISON OF LIPID ACCUMULATION PRODUCT AND BODY MASS INDEX AS INDICATORS OF DIABETES DIAGNOSIS AMONG 215,651 CHINESE ADULTS
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors have adequately revised their manuscript.
Experimental design: The authors have adequately revised their manuscript.
Validity of the findings: The authors have adequately revised their manuscript.
Additional comments: The authors have adequately addressed my 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: GENE FLOW BETWEEN SUBPOPULATIONS OF GRAY SNAPPER (LUTJANUS GRISEUS) FROM THE CARIBBEAN AND GULF OF MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: It's an interesting manuscript, using standard methods on a different place, with a species without overfishing nor protection status. I suggest considering two methodological observations: 1) a common mistake in population genetic studies is to violate the independence assumption and 2) considering that authors didn't identify genetic subpopulations, analyze the potential presence of barriers through appropriate statistical tests.
Experimental design: No comment
Validity of the findings: Authors must discuss the effect of the lack of deviations to HWE in some microsatellites used in their analysis.
Additional comments: It's an interesting work that will help to explain the connectivity among the Gulf of Mexico and the Caribbean, but need to be reinforced in some areas.