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: TRANSMISSIBILITY OF CORONAVIRUS DISEASE 2019 IN CHINESE CITIES WITH DIFFERENT DYNAMICS OF IMPORTED CASES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Q1: The quality of writing needs improvement, especially for grammar and typo. The following are only examples - the full text needs such review.
a. The authors name of the first page. Change “Hengyan Liu1” to “Hengyan Liu”
b. Line 191-192. Change “…the disease is useful in 1. Determining whether there is sustained community transmission in a population and 2. evaluating whether the…” to …the disease is useful in determining whether there is sustained community transmission in a population and evaluating whether the…”
Experimental design: Q2:Please include a formal case definition for “import case”. It is not clear whether the definitions in Hangzhou and Shenzhen are consistent. Besides, I note that none of the authors listed are from Shenzhen. How do you know the case definition of Shenzhen?
Validity of the findings: Q3: Your introduction needs more detail. I suggest that you improve the description at this part to provide more justification for your study (specifically, you should expand upon the knowledge R).

Q4: A short explanation on the disparity of Rs between the regions in China and other countries would be useful in the Introduction or Discussion section.
Additional comments: The article appears to lack novelty, and most of conclusions also seem hard to draw easily from the results. I suggest that authors could amplify in the Introduction and the Discussion on the added value of this study and how it is novel for this field. Besides, I don’t clearly understand the main objective of this study. However, it is also an interesting experiment to compare Rs in different regions. I suggest that you can change this article type into a Letter and resubmit 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: TRANSMISSIBILITY OF CORONAVIRUS DISEASE 2019 IN CHINESE CITIES WITH DIFFERENT DYNAMICS OF IMPORTED CASES
Review round: 1
Reviewer: 2

Output:
Basic reporting: none
Experimental design: none
Validity of the findings: There was not a sufficient causation inference in the paper.
Additional comments: This article introduces us to an interesting topic. The author tried to test the hypothesis of this phenomenon with mathematical theory. But in general, there was not a sufficient causation inference in the paper. Therefore, I suggest that the author resubmit the article as a short report.
1. Line 124 to 126 .The definition of imported case was very important to the present study. The authors defined this only based on the travel history. The authors should consider the possibility that one patient was infected locally (not imported case) while he had a travel history to other provinces 14 days prior to symptoms onset. Whether the case was local or impoted should be based on the epidemiological investigation.
2. Line 201-203, 250-252. The author speculated that the low transmission intensity of COVID-19 in Shenzhen in early January was likely due to the decrease in number of local susceptibles as residents left the city during Chunyun. Was this phenomenon also occurred in other big cities such as Beijing or Shanghai? The authors should find more studies related to Chunyun to further demostrate its high influence on the transmission of COVID-19.


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: TRANSMISSIBILITY OF CORONAVIRUS DISEASE 2019 IN CHINESE CITIES WITH DIFFERENT DYNAMICS OF IMPORTED CASES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The  writing quality of the revised manuscript has improved.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This revision is much improved after adding more background information and more references on R0. I suggest authors could provide more details (e.g.: numbers of migrant workers, the proportion of number left cities) between Shenzhen and Hangzhou.


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: TRANSMISSIBILITY OF CORONAVIRUS DISEASE 2019 IN CHINESE CITIES WITH DIFFERENT DYNAMICS OF IMPORTED CASES
Review round: 3
Reviewer: 1

Output:
Basic reporting: The quality of writing is clear and unambiguous.
Experimental design: Methods described with sufficient detail and  information to replicate.
Validity of the findings: The impact and the novelty of this study  is not so great, but it is interesting to compare the Rs among different cities.
Additional comments: The quality of writing is clear and unambiguous. The impact and the novelty of this study is not so great, but it is interesting to compare the Rs among different cities. Please add the Rt of Shenzhen city in the Abstract section (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: TRANSMISSIBILITY OF CORONAVIRUS DISEASE 2019 IN CHINESE CITIES WITH DIFFERENT DYNAMICS OF IMPORTED CASES
Review round: 3
Reviewer: 2

Output:
Basic reporting: none
Experimental design: none
Validity of the findings: none
Additional comments: The author made some improvements in this revised manuscript, but did not specifically answer the previous questions.


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: BISCOT: IMPROVING LARGE EUKARYOTIC GENOME ASSEMBLIES WITH OPTICAL MAPS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript from Istace et al. is written clearly, is easy to follow, and addresses an interesting question. The language, scientific terminology, and structure is sufficient for a manuscript of this kind.
Experimental design: The authors chose publicly available datasets for one human and three plant genomes. I think this is a strong start. The method is explained well with sufficient detail.
Validity of the findings: The examples used in the paper are good and report results for a human genome and three plant genomes.

I think that the authors need to test their methods on more genomes. It would also be useful if there were a positive control experiment. I understand the correction for contigs when they share anchors or regions or one being a subset of another.
Additional comments: I liked the work presented by the authors in this manuscript. I have a few comments:

1. A positive control could help confirm the validity of the BiSCoT code. I am not sure if such an experiment exists.

2. I am surprised that the method developed by Bionano Genomics doesn't do it as is. As I understand, most community uses the software made by the community, which makes me further speculate the magnitude of the issue brought to light by the authors. Is this a common issue when using optical maps for scaffolding?

3. Is there a risk in doing this contig correction analysis on unphased assemblies? If an issue, this would escalate further in plant genomes.

I send my best wishes to the authors.


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: BISCOT: IMPROVING LARGE EUKARYOTIC GENOME ASSEMBLIES WITH OPTICAL MAPS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript does not discuss prior work, except regarding the Bionano product. There are ”traditional” scaffolders, working with paired-end and mate-pair reads, that handles overlapping contigs. There are also other scaffolders than Bionano’s, why cannot they be used?

I think you are re-defining the contig concept a bit, which made me confused when reading your results. My understanding of contigs is that they are the result of overlapping and merged reads (short or long) from the assembler. Then a scaffolder is further putting contigs together using auxiliary information (such as linked reads or optical maps, sometimes ever RNA evidence). It does not make sense to me to classify a scaffold as a contig just because identical sequence has been identified by the scaffolder. I can understand your thinking and will not insist on my definition (which may be outdated), but I think you should clarify this reclassification of scaffolds into contigs.

Please consider making BiSCoT available on PyPI (pipy.org) so that all a user needs to do is ”pip install BiSCoT”. It is actually pretty easy to set it up and it makes your tool so much more available.

Text issues:
* Change ”long reads sequencing” to ”long read sequencing” (first occurrence in the abstract).
* The key sentence in the abstract, "We developed BiSCoT (Bionano SCaffolding COrrection Tool), a tool that uses informations produced by a pre-existing assembly based on optical maps as input and improves the contiguity and the quality of the generated assembly.” has several deficiencies in my opinion. (1) An assembly does not produce information. It might for example ”provide” or ”contain” information, but you could also rephrase. (2) It is unclear what the actual input is. (3) The sentence does not quite state what BiSCoT does, only that it improves quality. It would be good to be more explicit and explain that is is ”post-processing of Bionano scaffolds” or something like that. (4) I was confused about what ”pre-existing assembly” would mean. One can read that as ”any assembly from a repository”, but you are actually only working with Bionano-scaffolded assemblies. (5) The phrase ”… of the generated assembly” is unclear since it is not obvious that your tool is generating an assembly. (6) Finally, ”information” should not be used in plural.
* The word ”apparition” is not strange in this context. ”The appearance of short read technologies” is better.
* I don’t know what an ”endonuclease nicking site” is.
* ”several folds higher” is not good English, use ”several times higher”.
* Change ”doesn’t” to ”does not”.
* ”contained into” should probably be ”contained in”.
* In ”Case 1”, what is meant by "First,the right-most shared label identifier l is extracted”?
* Please define variables and functions clearly. Reading ”C_k (P_l(C_k))” is just confusing (see ”Case 1”). I suggest rewriting in the style ”The position P_l for a label identifier l” etc.
* What is really meant by ”The position l … on both contigs … is searched”?
* The columns in Table 1 should be justified so that it is easy to read and compare numbers. The left-most column should be left-justified and the data-columns should be justified on decimal point.
* Bold text for best values in the tables (including Supplemental tables) is not consistent. There are several places where there are several numbers that are equal but only some are in bold.
* Capitalisation in the reference list should be corrected for words like ”Nanopore”, ”Promethion”, ”Solanum”, ”BLAST”.
Experimental design: ## Code ##
I looked at your code. I would strongly recommend to structure the code by defining functions for any kind of logical block of code you have. Limit the length of a function to one screen page. You have one function, ”main”, and it encompasses the program in its entirety. There is not a single block of code that is easy to test. This makes it hard to build upon your code.

I also note that you have code like
try:
    …
except:
    pass

That is a bad practice. If an error occurs, the ”pass” statement simply hides it from the user. There is usually a good reason for an exception to occur, so don’t hide them — handle them.

## Method ##
You start the method section with "Briefly, BiSCoT loads all necessary files into memory”. That is not specific enough for me. I should not need to guess what is considered needed. In the same sentence, you refer to alignments, but at that point it is not clear where the alignments come from.

For Case 2, for contigs that are linked (I presume, it is a bit unclear) but do no share labels, you align contig ends if the estimated distance is at most 1000 nt. Why 1000? Is that a ”safe” distance?

I am deducing that the distance between two contigs is _estimated_ using Equation 1, but I think you should make that clear. How well is that distance estimated?

It is not clear to me that ”Case 3”, merging of contigs sharing labels indicating that one contig _may_ have accidentally been excised from another contig. How can you exclude that the smaller (in your case) contig is not simply a partial duplication? What is the rationale?
Validity of the findings: I find the findings believable, but it is a weakness that there are only four test assemblies.
Additional comments: This manuscript reports a tool to refine scaffolder output from Bionano tools to identify and fix cases of linked contigs having overlap. The method has been tested on four genome assemblies. The code is publicly available and the small scale testing is on public data.


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: BISCOT: IMPROVING LARGE EUKARYOTIC GENOME ASSEMBLIES WITH OPTICAL MAPS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thank you addressing reviewer comments. I do not have any further questions, and send my best wishes to the authors.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: BISCOT: IMPROVING LARGE EUKARYOTIC GENOME ASSEMBLIES WITH OPTICAL MAPS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Basic reporting looks good.
Experimental design: The experiments are still somewhat limited, but given the scale of data and the type of tool we are looking at, the tests are sufficient to make the point the authors are looking for.
Validity of the findings: Good.
Additional comments: I am pleased with the improved 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: DIVERSITY OF THE GUT MICROBIOME IN THREE GRASSHOPPER SPECIES USING 16S RRNA AND DETERMINATION OF CELLULOSE DIGESTIBILITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Grasshoppers are the notorious pests for some agricultural crops. It is of great significance to determine the potential role of gut bacteria in the utilization of plant hosts for insect pests. Although the authors have presented some interesting findings here, this manuscript can not be accepted for publication now because of some visible defects. Firstly, the English language should be improved significantly because there are many grammar mistakes and awkward sentences. Secondly, the results of this manuscript were not well summarized and presented. The data were described too generally, but the major results were not summarized concisely and directly. Therefore, it is very difficult to catch up what the major findings the authors presented here. Thirdly, some important progress has been done on the interactions between insect pests and their gut microbiota. However, the authors did not pay sufficient attention to these achievements on  this topic in 2018-2020. Moreover, many sentences on describing experimental methods can be found in the section of results. It is better to remove them because this section should often focus on what you have found by your experiments. Finally, the authors did not present any direct evidence to support the cellulose digestibility of three grasshoppers was from their gut bacteria. But the authors did only do some correlation analysis and try to support their view. In my opinion, it is not enough to support this finding. It is better if the authors can isolate and identify some cultivable bacterial species from the guts of three grasshopper species.
Experimental design: Some important experimental information missed in this manuscript. For example, the authors said they collected the adults of three grasshopper species in field and fed with wheat seedlings in lab. However, the authors did not introduce which wheat species or variety was used to feed these insects. Furthermore, the authors did not tell how long these collected insects were fed in lab before the following experiments and the conditions that were used to rear these insects in lab. Last, the authors did not tell the statistical method and how they complete the statistical analysis.
Validity of the findings: The major findings of this manuscript were not summarized and presented well. Because of the absence of some novel important publications, the findings of this manuscript were not well explained in the section of discussion. The authors should clearly present what great differences on gut microbiota among these three grasshopper species and what impact of these differences in their gut bacteria on the cellulose digestibility.
Additional comments: Some format questions on reference can be easily found in the text and reference list of this manuscript. Therefore, the authors should correct these questions carefully.


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

Input:
Title: DIVERSITY OF THE GUT MICROBIOME IN THREE GRASSHOPPER SPECIES USING 16S RRNA AND DETERMINATION OF CELLULOSE DIGESTIBILITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This paper describes the gut microbiome of three grasshopper species, and attempts to correlate the differences in microbiota structure with the ability of the host to digest cellulose and hemicellulose. The data is potentially interesting and should be useful for subsequent studies of grasshopper gut bacteria. However, it should be noted that this paper represents only very weak association between change in gut bacteria and the food digestion. Without further data showing the function of gut microbiota in helping digesting cellulose, it is difficult to justify the rational of the current study. Therefore, the authors need to do a better job with any claims that the difference in several bacterial species is actually causing the difference in host’s digestion. For example, the claim that the hemicellulose digestibility of Shirakiacris shirakii was significantly higher than that of the other two species of grasshopper DUE TO the presence of Psudomonas, Stenotrophomonas, Glutamicibacter, Corynebacterium, and Brachybacterium in its intestinal tract, was not supported by the current analysis, and needs to be re-phrased.
Numerous language problems have to be fixed first to make the paper readable, probably by sending to a native English speaker to check. Finally, It is strongly suggested that the authors assembly the figures into multiple-panel figures.


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: DIVERSITY OF THE GUT MICROBIOME IN THREE GRASSHOPPER SPECIES USING 16S RRNA AND DETERMINATION OF CELLULOSE DIGESTIBILITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Grasshoppers are the notorious pests for some agricultural crops.The authors presented some interesting findings on the gut microbiota of three grasshopper species and gut bacteria confer the cellulose digestibility to help the host to achieve nutrients. This manuscript has been improved significantly and it can be accepted for publication now.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This manuscript has been improved significantly and it can be accepted for publication now. However, there are still some small problems on the journal names in the reference list. Please corrected them before publication.


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

Input:
Title: CHARACTERIZING CARBONYL COMPOUNDS AND THEIR SOURCES IN FUZHOU AMBIENT AIR, SOUTHEAST OF CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript measured the 16 carbonyls concentration two sites in Beijing in early summer. The authors tried to indicate the contributions of potential sources with ratios and model. Eventually, the manuscript is well written and provides full technical information. However, there were two critical concerns. The first one is the quantification of acetone with DNPH is highly questionable, even this includes in TO-11A method. The artifacts have been widely reported in the recent literatures. So, the uses of acetone ratios and their associated source apportionment are doubtful. The authors should take account this factor. Second, very honestly, the data expression and use of C1/C2 and C2/C3 ratios are outdated approaches (>20 years). One advantage of this manuscript is shown the use of OBM. However, this section is very unclear and short.  This manuscript must be greatly improved before consideration for publication.
Experimental design: Line 215: Acetone could be potentially coeluted with the derivatives formed between air oxidants and DNPH. Please check the following references. Even ozone could be removed by the ozone scrubber, other oxidants such as NO and NO2 reacted with the DNPH during the sampling.

Ho, S. S. H.; Ho, K. F.; Liu, W. D.; Lee, S. C.; Dai, W. T., Cao, J. J.; Ip, H.S.S. Atmo. Environ. 2011, 45, 261-265.

Schulte-Ladbeck, R.; Lindahl, R.; Levin, J. O.; Karst, U. J. Environ. Monit. 2001, 3, 306-310.

Williams, J.; Li, H.; Ross, A.B.; Hargreaves, S.P. Atmo. Environ. 2019, 218, 117019.
Validity of the findings: Line 213: When did these two peaks appear? Noon and when? The authors should also explain their different origins instead of elaborating the differences only.

Line 288-289: The discussion on the total quantified carbonyls are not critical. Each carbonyl has unique formation pathways and photochemical reactions.

Line 348-386: The uses of C1/C2 and C2/C3 ratios could be used as references but not accurate indices to illustrate the sources, particularly considering the concentrations of acetone could be overestimated.
Additional comments: Specific comments:

The molecular number on a chemical formula should be subscripted.

Please standardize to use O3/ozone, HCHO/formaldehyde in the entire manuscript.

Please aware the scientific figures expressed for all numbers. They are inconsistent


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: CHARACTERIZING CARBONYL COMPOUNDS AND THEIR SOURCES IN FUZHOU AMBIENT AIR, SOUTHEAST OF CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper was very clear, well written and easy to follow.  There are a few sentences where there is some confusion in language for the reader and I tried to point this out for improvement.  In addition, there were a few places to improve the background context and add context for those familiar with basic atmospheric chemistry but not with the specifics of why it is important to study carbonyls.  The raw data and figures were shared and there were a few legends that needed correction or more information, which was pointed out in the detailed comments.  But overall, the paper is to the point and direct, the data well presented, easy to follow, which is appreciated, and does not speculate.
Experimental design: The methods are described in sufficient detail except in a few places where more detail is suggested.  I do think some more context is needed on the why it was important to study this city, and how the overall results here compared to other cities in the region or the country.  What was the knowledge gap and what do we know now after this study?  It seemed there was more that could be concluded from the data and I suggested where in the detailed comments.  The sampling methods and chemistry were well done with sufficient information provided to be able to replicate.  This was a strong point.
Validity of the findings: The data are robust and statistically sound.  My main suggestions were to describe the differences between sites more in the Methods (it was hard to keep track of which was suburban and which wasn't, plus only 8 km apart, I wondered if they could be considered "different"), and to provide more context on what the results mean - should there be more research/sampling sites in the area, were these sites adequate to measure air quality in the future, is the city more or less impacted by carbonyls compared to others in the region or country?  I was very curious as to the impact of traffic as a source, too.

I was also curious to know more about the comparison between the model and measurements.

The authors were very careful not to speculate, but it is OK to put results in context and think of possible sources, and possible recommendations for the future.
Additional comments: The reader appreciated the study's focus on measurement over modeling.  It is critical to still go out into the field and measure to observe.  The authors chose a very reproducible method and real world measurements of carbonyls are often lacking.  I appreciated this work and look forward to see the revised manuscript.


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

Input:
Title: CHARACTERIZING CARBONYL COMPOUNDS AND THEIR SOURCES IN FUZHOU AMBIENT AIR, SOUTHEAST OF CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: This work investigated carbonyl compounds in ambient air in a coastal city (Fuzhou) in southeast China.  Air samples were collected at an urban site (Jinjishan) and a suburban site (Gushan). The average total concentration of 16 carbonyl compounds at the urban site was 15.45 ± 11.18 ppbv, and the average total concentration at the suburban site was 17.57 ± 12.77 ppbv. Formaldehyde, acetaldehyde, and acetone were the main species detected in the samples, and acetone had the highest concentration among the species detected. The suburban site had a higher formaldehyde/acetaldehyde ratio and lower acetaldehyde/propionaldehyde ratio than the urban site, implying that biogenic sources potentially contributed to the carbonyl compound concentrations at the suburban site. The results are interesting in general.  However, there are many errors and language issues that require a major revision.
Experimental design: 1.	Line 125, what was the sampling time?  2 hours?  Please specify sampling time.
2.	Was there any stability measurement for the samples stored for upto month?
Validity of the findings: 3.	Table 2,  acrolein should not be 0.  It might be due to within one month storage and transport.  Please use below detection limit instead of 0.
4.	Line 377 to 386, it states that “the lower the A/P value, the greater the influence of anthropogenic sources. The conclusion that “The A/P value at the JJS site was higher than the A/P value at the GSS site, indicating that the JJS site is was affected more by human activity than the GSS site.”  is contradictory to the statement.
5.	Also in the abstract about A/P value and GSS lower acetaldehyde/propionaldehyde
            ratio than the urban site, implying that biogenic sources potentially contributed to the carbonyl compound concentrations at the suburban site.
6.	Line 198,  Please specify low and high temperature such as in Fig. 1.
Additional comments: 7.	There are many errors and language issues in the manuscript.
             Line 91: 3-5 times that of Hong Kong changes to 3-5 times of that in Hong Kong.
             Line 94, delete high activities in “The high concentrations high activities of carbonyl…”
             Table 1 and 2:  Spelling errors for crotonaldehyde.


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: CHARACTERIZING CARBONYL COMPOUNDS AND THEIR SOURCES IN FUZHOU AMBIENT AIR, SOUTHEAST OF CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: I think the authors have improved the manuscript. Beside some grammatical mistakes and typos still there, it could be considered for publication in PeerJ.
Experimental design: No further comment
Validity of the findings: No further comment
Additional comments: No further 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: ROBUSTNESS ANALYSIS IN AN INTER-CITIES MOBILITY NETWORK: MODELING MUNICIPAL, STATE AND FEDERAL INITIATIVES AS FAILURES AND ATTACKS TOWARD SARS-COV-2 CONTAINMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors present a network analysis of an inter-cities mobility network based on Brazilian data from 2016 in order to describe the government initiatives concerning SARS-CoV-2 strategy measures of containment. The manuscript is clear, well-structured, with relevant results illustrated by Figures. Data comes form IBGE – Instituto Brasileiro de Geografia e Estatística.

In relation to the figures, I have two comments: the visualization of Figure 1 may be improved using blue color for the nodes with smaller degrees and light gray for the links; the captions of Figures 2, 3 and 4 should include that the procedure of removed nodes is based on different strategies as described on “Robustness” sub-section (deleting nodes with a higher degree, vulnerability, betweenness and strength). Moreover it is not clear in the caption how the COVID-19 cases (what means “temporal sequence”?) and “failure” curves are constructed; it is not clear the meaning of giant component and remaining flow for those curves. Finally I did not figure out the reason that there is a value of robustness measure for COVID-19 curve in Figure 4 but not in Figures 2 and 3.

I think that the authors should present in a supplementary material a more complete list of results obtained from their analysis. For instance, in discussion section, the authors refer the two cities (or states) with the higher values of network measures in relation to the 3 selected networks: Brazilian cities (BR), Brazilian states (BS) and São Paulo state (SP). I suggest the authors include a complete list (in supplementary material) that reveal the order of states (BS) in relation to the higher values of the considered network measures; for BR network, the authors may select the capitals of the states, and for SP network, they may select, for example, 30 cities with highest number of cases.
Experimental design: The authors set up a methodological procedure assuming the local initiatives as failures and the federal initiatives as attacks on the networks. I have some questions related to those assumptions as well as some conclusions associated with the obtained results.

First of all, it would be reasonable to provide an explanation to those assumptions; for instance, in conclusions section the authors affirm that the attacks are isolation measures determined by the federal government and applied at a municipality level. As far as I know, there is a legal debate in Brazil about the assignment in relation to isolation of the municipalities. Is there a final decision about it? In case of affirmative answer, I suggest to include a reference about it; in case of negative answer, it would be interesting to justify the assumptions.

In order to highlight the results, it is essential to clarify how the disease information concerning the temporal sequence of COVID-19 cases is related to the procedure of removed nodes that is fundamental for the methodology.
Validity of the findings: The authors perform a comparative analysis of the network measures, pointing out which one is better or worse for each network. In general they conclude that the strength is a more suitable measure to guide the attacks due to the smaller value of R. As far as I understood, the attack is more effective than the failure for BR and SP networks since  the curves fit better for the flow than for the giant component; however, both of them fits well for BS network. Do the authors agree with that summarization? Does that result provide any suggestion about the relevance of the strategies of the state government strategies?

Undoubtedly the findings are relevant since it assigns a robustness analysis based on mobility network of a large country with a significative number of COVID-19 cases. The analysis may be useful for other transmitted diseases in the country. However, since it is a complex system, other factors get influence in the government decision of isolation; for instance it is very hard to isolate some large cities that are essential for the distribution of food and drugs. In this sense, it is not easy to determine which cities should be isolated. How do the authors make compatible their findings with that actual scenario?
Additional comments: I think that the manuscript may be published in PeerJ after clarifying the arisen points that I have classified as minor revision, since I suppose the authors had obtained the results suggested for supplementary material.


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: ROBUSTNESS ANALYSIS IN AN INTER-CITIES MOBILITY NETWORK: MODELING MUNICIPAL, STATE AND FEDERAL INITIATIVES AS FAILURES AND ATTACKS TOWARD SARS-COV-2 CONTAINMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors report a timely study of a Brazilian transport network to identify potential strategies assisted by network analyses to contain the spread of Covid-19. The manuscript is clear, structured and easy to read. However, some notations could be more intuitively defined, for instance, why are the number of nodes in the giant component called P∞( f ), I don’t understand what infinite has to do with it? More importantly, regarding the reproducibility of the results and access to raw data, I did not find any Git repository or an open server where the data and associated scripts to reproduce the results are deposited. I strongly suggest the authors to make their code and data available in an open platform.
Experimental design: Overall, I am convinced with the technicality of the analyses design. However, a main concern I have is using the size of giant component to assess the performance of the targeted attack. May be a complimentary metric such as the actual number of connected components (or clusters) for each node removal might indicate how the network is effectively destabilized, even when the giant component is intact. This might mean certain transportation among major cities are very strongly connected, however, many rural cities could be disconnected. So, in addition to the 2 metrics the authors have used to assess the network performance after node perturbations, I would like to see a metric that captures how many components or clusters remain after each perturbation. This might give a picture of how the cities are actually disconnected after node removals. I can see that fraction of remaining flow within the network could be useful but, still I suspect a few large components in the network might dominate the flow.
Another strategy to choose node(s) for removal could be to employ minimum cut sets? i.e. the idea is to identify a minimal sets of nodes that disrupt the entire (or major) topology of the network? More details about this could be found here: Klamt and Gilles, 2004, Bioinformatics
Validity of the findings: Although I could partly agree with the author’s claim that global (or Federal) actions are more effective compared to local (or municipal) actions to disrupt the transportation network, I am not entirely sure if this can be concluded from the results presented as it is. As I mentioned in the earlier paragraph, I would like to see more complementary metrics to assess the network disruption both locally and globally. And may be an intermediate strategy where both local and global policies must be coordinated could also emerge if more metrics are included in the study.
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: ROBUSTNESS ANALYSIS IN AN INTER-CITIES MOBILITY NETWORK: MODELING MUNICIPAL, STATE AND FEDERAL INITIATIVES AS FAILURES AND ATTACKS TOWARD SARS-COV-2 CONTAINMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors present a revised version of the manuscript with huge changes of the manuscript related to the text structure and, at least some added results  since they extend the period of their analysis until September 2020. In some sense it is a “new” manuscript and due to that, in my point of view, it would be reasonable the authors point out, at least, the number of lines where they have introduced the changes that were required by us in the previous report. Following the tracked-changes version of the manuscript, I tried to catch the required changes. Another relevant point is to highlight in the cover letter the implications of extending the time interval of analysis for the discussion of the results. Summarizing the authors tried to answer the editor's criticisms about the text – that was relevant for improving the quality of the manuscript – but do not take care to make clear in the letter what was done point by point, at least when the changes are related to the content of the manuscript (for isntance, it was not necessary to do it for English revision).

The authors have improved the quality of the figures and its description in figure captions. Now, based on an extended data bank (until September), it is possible to a value of robustness measure for COVID-19 curve in Figures 2 and 3 as in Figure 4.

 As I have suggested, the authors also present in a supplementary material a detailed analysis that is useful for reproduction as well as relevant for comparison with other scenarios.
Experimental design: Again, I am not quite sure whether, how and where (which lines???) the answer for that question (presented in the letter) was introduced in the manuscript.

Reviewer:  In order to highlight the results, it is essential to clarify how the disease information concerning the temporal sequence of COVID-19 cases is related to the procedure of removed nodes that is fundamental for the methodology.

Authors:   We improved the explanation within the manuscript. The reactive strategy consists of the removal of cities/nodes according to the date they documented the first case of COVID-19 (see Comment #1). This ordering may not impact the mobility like attacking the nodes according to their corresponding centrality measures (targeted attacks - starting with the node with higher centrality value towards the nodes with smaller). Three metrics evaluate the impact of the reactive strategy and the targeted attacks in mobility: the number of components, the size of the giant component, and the total remaining flow of people.
Validity of the findings: Concerning the summarization of the results, do the authors summarize it as below (which lines??)

Authors: "Attacks usually cause more impact on the networks than both the reactive strategy and random failures. The only exception is when one evaluates the size of the giant component in the BS network under η0, where all the strategies perform roughly the same. We observed that attacks guided by strength are more effective to diminish the total remaining  flow of people; those guided by degree usually result in smaller giant components and; the ones guided by betweenness generate more isolated components."

In my point of view, it is reasonable to explain to the reviewers whether and which results were changed taking into account a longer time interval besides the value of R in Figure 2 and 3.

Due to the changes in the manuscript, I think that the discussion about federal and municipal actions, at least in the context of Brazil and Brazilian networks analysed in the manuscript was diminished in the discussion section of the revised version but it is still in the abstract and also in the introduction. In my opinion, in the discussion it is important to emphasize how the results reveal what is affirmed in the abstract below – which is not so direct - or reduce the emphasis in the last two sentences of the abstract.

Authors:  "The municipal and state initiatives are here abstracted as nodes' failures since there is no well defined country-level organization, and the federal actions are the targeted attacks. The results reveal that individual municipalities' initiatives do not cause a high impact on mobility restraint since they tend to be disconnected from the country's global interventions. Oppositely, the coordinated isolation of specific cities is crucial to detach entire network areas and thus prevent spreading. Besides, the targeted attacks pose better results than the reactive strategy."

For instance, to introduce in the abstract the idea that the association is a reasonable ssumption"

Reviewer: "Assuming the municipal ….the targeted attacks, the results reveal that individual ….."
Additional comments: I think that the manuscript may be published in PeerJ after clarifying some points in the letter for reviewers since there are many changes in the revised manuscript that in some features lead to, at least, modified emphasis of the manuscript, in my point of view. Please see the comments introduced in the above sections: basic reporting, experimental deseign and validity of the findings.


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: ROBUSTNESS ANALYSIS IN AN INTER-CITIES MOBILITY NETWORK: MODELING MUNICIPAL, STATE AND FEDERAL INITIATIVES AS FAILURES AND ATTACKS TOWARD SARS-COV-2 CONTAINMENT
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed all the points raised. This manuscript can be published in its revised state
Experimental design: The authors have addressed all the points raised. This manuscript can be published in its revised state
Validity of the findings: The authors have addressed all the points raised. This manuscript can be published in its revised state
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: DEEP-LEARNING CONVOLUTIONAL NEURAL NETWORKS WITH TRANSFER LEARNING ACCURATELY CLASSIFY COVID-19 LUNG INFECTION ON PORTABLE CHEST RADIOGRAPHS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: It is unclear whether the labels they used originated from the metadata associated with the publicly available pCXR images. The authors mention that “a chest radiologist evaluated all [] images for quality”. Were any images filtered out or relabeled as a result of this step? Did the radiologist re-classify the images? If that’s the case, how does their input compare with the starting classification? Were there other factors that were used to diagnose each disease type? For example, in reference 19, were symptoms and/or RT-PCR used in conjunction with the examination of pCXR lung images?

The authors mention splitting their data set into training and testing. It would benefit the reader to know how, for example, did the authors use random sampling, stratified sampling, etc. ? In addition, was five-fold cross-validation implemented for the test set separately?
Validity of the findings: no comment
Additional comments: I have read the study entitled “Deep-learning convolutional neural networks with transfer learning 2 accurately classify COVID19 lung infection on portable chest 3 radiographs” by Kikkisetti et al.  In this study, the authors develop a deep learning convolutional neural network able to classify pCXR lung images into 1) COVID-19 infections, 2) other viral infections, 3) bacterial infections, and 4) normal. They report encouraging quality metrics, specifically for the CNN that was trained on segmented lung pCXRs. I especially commend the authors for clearly outlining their methodology as well as the limitations of their study in the discussion section.

With that said, one minor comment I have regards the training data. It is unclear whether the labels they used originated from the metadata associated with the publicly available pCXR images. The authors mention that “a chest radiologist evaluated all [] images for quality”. Were any images filtered out or relabeled as a result of this step? Did the radiologist re-classify the images? If that’s the case, how does their input compare with the starting classification? Were there other factors that were used to diagnose each disease type? For example, in reference 19, were symptoms and/or RT-PCR used in conjunction with the examination of pCXR lung images?

The authors mention splitting their data set into training and testing. It would benefit the reader to know how, for example, did the authors use random sampling, stratified sampling, etc. ? In addition, was five-fold cross-validation implemented for the test set separately?


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: DEEP-LEARNING CONVOLUTIONAL NEURAL NETWORKS WITH TRANSFER LEARNING ACCURATELY CLASSIFY COVID-19 LUNG INFECTION ON PORTABLE CHEST RADIOGRAPHS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: This manuscript by Kikkisetti et al. reported their study on Portable chest x-ray (pCXR) combined with deep-learning convolutional neural networks (CNN) to classify COVID-19 lung infections. Segmented lungs showed better performance compared to the whole pCXR. In general, the manuscript is clearly presented and written, and contains appropriate introductory material, methods, statistics and reasonable. As noted above, the entire study sounds entirely plausible and provides useful information for further COVID19 lung infection classify at this special period. However, there are several minor concerns as described as follows. I would suggest the paper being accepted for publication if the authors can incorporate these comments in their revision.
There are several concerns proposed as follows:

Minor concerns:
1.	The abstract is very good and has clear logical analysis, but the results of the paper are less clearly described. For example, In the abstract, there are many data COVID-19 pneumonia (N=455), normal (N=532), bacterial pneumonia (N=492), and non-COVID viral pneumonia (N=552). But how these data used to analyze and got the results should clearly present in the RESULTS part and also labeled in the table legend. The results part not just describe the figures and tables, it should follow your research logics and provided the information why you did this experiment and how you did it and what result you got.
2.	 On line 205, “but some hot spots were located outside the lungs”, could you explain why this situation appears and how to improve this?
3.	For Figure 2 and Figure 4, you just give some examples, that’s fine. But would you give a semiquantitative analysis to show how many samples are represented by the images in each figure?
4.	You may move Figure 1 to supplemental materials.


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: DEEP-LEARNING CONVOLUTIONAL NEURAL NETWORKS WITH TRANSFER LEARNING ACCURATELY CLASSIFY COVID-19 LUNG INFECTION ON PORTABLE CHEST RADIOGRAPHS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Only minor english language use/punctuation issues e.g. lines 52,110,111,112.

In the few months since the manuscript was written, the number of US COVID-19 related deaths has almost doubled. In the revision this should be updated. Lines 55 and 56.

Lines 60-62 the authors state that PRC has a low sensitivity, high false negative rate and long turn-around time of 4 days.  The authors should double check if this is uniformly still the case or is unique to the USA.
Experimental design: Description of deep learning convolutional neural networks. For readers not familiar with convolutional neural networks there needs to be more detail explaining how it all works. The authors also need to explain what the following jargon means:
VGG16 model
one-hot-encoded
convolutional layers and sublayers
filters
max-pooling
dropout layers
soft max function
etc, etc
Validity of the findings: No comment
Additional comments: This timely paper nicely demonstrates how with relative ease, CNN and be used on portable chest x-rays for assessment and analysis of a new disease when clinical experience is limited. This could change management in sick patients and be life saving.


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

Input:
Title: AN UPDATED EVOLUTIONARY STUDY OF THE NOTCH FAMILY REVEALS A NEW ANCIENT ORIGIN AND NOVEL INVARIABLE MOTIFS AS POTENTIAL PHARMACOLOGICAL TARGETS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: In this manuscript, the authors searched and analyzed Notch protein sequences from organisms of all kingdoms. As a result, a large number of Notch proteins are identified in bacteria, protists, fungi, plants and invertebrates in addition to the previously well characterized Notch1~4 proteins. Based on evolutionary analysis to 603 unique Notch protein sequences, they inferred existence of ancestral Notch sequences in bacteria, protists and plants. Furthermore, they successfully identified characteristic motifs A to E in EGF domain. These motifs have conserved glycine(s) in addition to conserved cysteines, which can be potential pharmacological targets for future studies. The results present in this paper enrich our knowledge on distribution, evolution and structure of Notch proteins in various organisms. I would recommend publication of it in PeerJ after the following minor revisions are made.

Lines 39 to 48: The abstract has too many words as ‘introduction’. Please reduce them and add words to describe results and significance of your work.

Line 109: Please specify the query item. Is it the word “Notch”?

Line 161: The number is 613 here. It is 603 at other places (line 116 etc). Also, line 49 says “603 different organisms”. But, line 116 says “603 unique, non-duplicate protein sequences”. Please check.

Lines 223 to 236: (Figure 5) should be (Figure 6), I guess.

Line 278: (Figure 6) should be (Figure 7), I guess.

Line 452: The reference is a duplicate of line 450.

Table 2: It is better to replace the tick with number of Notch genes found in each phylum/class among the 603 unique sequences. Also in Table 2 (and in the whole manuscript), it is better to replace “Multicellular” with “Invertebrates”, because multicellular organisms include chordates.

Figure 3: Please specify how many sequences are used to generate this graph. Is it the same with Figure 4 (603 Notch sequences)?

Figure 7: It is better to put the color block beneath tree branches but not on them, so that the tree branches can be visualized. Besides, please indicate how many sequences were used for construction of this tree.


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

Input:
Title: AN UPDATED EVOLUTIONARY STUDY OF THE NOTCH FAMILY REVEALS A NEW ANCIENT ORIGIN AND NOVEL INVARIABLE MOTIFS AS POTENTIAL PHARMACOLOGICAL TARGETS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this paper, the authors aims to provide an updated evolutionary history of the Notch family members. This question is very interesting as the last paper dealing with it may be a bit old from now and new genomic data coming from various species may help to better understand and dissect the evolution of this family. However, the paper in this state does not allow to answer this question, due to several flaws in the methodology used (see below). Also the evolutionary considerations are not accurate (ex : l63 "indicating the progressive differentiation of Notch family"; l163 "simpler organisms", l349 "inferior organisms", L335 "the CNS has evolved in early metazoans, referring to ascidians which are far from early metazoans etc etc; ;phylogeny "map" (abstract), separation of the animals into "multicellular vs chordates" in the table 2 etc etc...  . I am also not sure the literature references provided are relevant and accurate, for ex in the introduction the authors cites "Durieux et al 2019" and" Fairclough et al 2013" to describe the length of the notch proteins in bacteria and animals respectively. I did not see any mention of Notch protein in those papers and I do not think that notch proteins do exist in bacteria (maybe a specific domain of the notch protein, but not the protein itself). Finally, the link with pharmacological targets is not clear to me.
Experimental design: The most important issue of the paper is the selection of the proteins to be included in the analyses. The way to select/identify proteins in order to do comparative genomics is to blast a protein query (here probably human) against databases of interest. The key word search is not an alternative way of doing it, as it is biaised (it depends on the way the protein has been submitted to the database) and highly incomplete. 2nd, the authors needs to define what is the minimal domain composition of a protein to be considered as notch. The presence of one or few domains, not specific to a notch proteins is probably not sufficient. Short "notch" sequences from bacteria such as Legionella X, have even no domain detected (search by NCBI CD search tool). How the authors deal with such different sizes of proteins ? how the alignment for the tree was done ? What about the missing data ? Did the author select just specific domains ? what about the variable number of EGF ? The notch protein phylogeny is quite hard due to all this specificities. Surprisingly, the authors used a very old method, not used any more to do their phylogenetic reconstructions (UPGMA), with no or few method of statistical support.
Validity of the findings: Based on the flaws mentioned above, the results provided are not conclusive.
The tree (figure 7) is non resolved. In the figure8, what are the number on the branches ?
Why the authors made a separation between multicellular and chordates ? are chordates unicellular ?
Additional comments: No additional comments


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

Input:
Title: AN UPDATED EVOLUTIONARY STUDY OF THE NOTCH FAMILY REVEALS A NEW ANCIENT ORIGIN AND NOVEL INVARIABLE MOTIFS AS POTENTIAL PHARMACOLOGICAL TARGETS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Authors has made excellent efforts in compiling the MS with detailed, clearly, consistently communicated a rational design followed by their outcomes, interpretation and significance of the work.
Experimental design: No changes required in the compiled version
Validity of the findings: Author has made great effort in contributing the new novelty in the present MS. My detail comments are in the author section.
Additional comments: The topic seems excellent addition in the current literature however, before accepting for the publication, it should advisable to refine further by making necessary minor corrections as suggested in the bottom which should provide more clarity to readers.

Comments on Manuscript
Couple of Comments/suggestion should be incorporate to improve English, Formatting and Uniformity.
1.	Title-Please include the before the Notch family
2.	Affiliation 5, cedex should have ‘C’ in capital letter
3.	Line 50, abstract, please add ‘s’ after human
4.	Line 73, Introduction: replace ‘to’ with ‘in’
5.	Line 76, provide symbol for approximation and replace the word amino acids with ‘aa’ for uniformity
6.	Line 97, insert comma after TAD domain
7.	Line 97, remove the word in before the length
8.	Line 98, remove the before vascular…..
9.	Line 101, add ‘the’ after involved in, so sentence looks like The pathway is involved in the….
10.	Line 102, Insert comma, after learning
11.	Line 113, insert ‘s’ after score; 114, replace which with that; Line 115, symbol will come before 95%
12.	Line 137, insert ‘a’ before threshold
13.	Line 158, insert ‘to’ before as noisy….
14.	Line 136, in the Figure 1, author should provide axis information along with as an insert total number of protein
15.	Line 166, insert amino acids or aa after 4835
16.	Line 185, replace a with the before most conserved site…..
17.	Line 193, insert ‘s’ after alignment…
18.	 Line 196, delete ‘a’ before non-polar
19.	Line 198, add they after since….are repeated….
20.	Line 205, insert ‘the’ before evolutionary history……
21.	Line 206, replace the It’s remarkable that with Remarkably,……
22.	Line 207, insert ‘ly’ after significant
23.	Line 217, Correct the spelling of Caenorabditis……
24.	Line 221, insert ‘s’ after appear
25.	Line 224, delete ‘of’ before containing calcium…..
26.	Line 225 and 226, replace ‘s’ with ‘z’ for the word heterodimeri….
27.	 Line 237, insert ‘the’ before human notch1
28.	Line 243, charge on calcium should be superscript and similar mistakes should be corrected other places
29.	Line 275, add with and delete to comes before the possibility,,,,,
30.	Line 320, rewrite the sentence like be at the beginning of…
31.	Line 343, remove ‘A number of’ and start the statement with Several……., replace has with have
32.	Line 347, insert ‘s’ after year… and replace showed with shown….
33.	Line 374, remove ‘the’ before half of our…..
34.	Line 375, remove are before the bacteria..
35.	Line 450-452; 472-475; 530-533, remove the additional duplicate reference from the MS.


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

Input:
Title: AN UPDATED EVOLUTIONARY STUDY OF THE NOTCH FAMILY REVEALS A NEW ANCIENT ORIGIN AND NOVEL INVARIABLE MOTIFS AS POTENTIAL PHARMACOLOGICAL TARGETS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Fine
Experimental design: Fine
Validity of the findings: Fine
Additional comments: All my concerns on the original manuscript have been properly addressed by the authors. I am comfortable with the revised paper.


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

Input:
Title: AN UPDATED EVOLUTIONARY STUDY OF THE NOTCH FAMILY REVEALS A NEW ANCIENT ORIGIN AND NOVEL INVARIABLE MOTIFS AS POTENTIAL PHARMACOLOGICAL TARGETS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors is advised to proof read again the MS as there are very minor improvement is required in terms of grammar.
Experimental design: Authors has made necessary revisions in the revised MS
Validity of the findings: No Changes
Additional comments: The authors has made suggested changes in the revised MS and I do not have any additional correction in the present form of MS


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: MORTALITY OF NATIVE AND INVASIVE LADYBIRDS CO-INFECTED BY ECTOPARASITIC AND ENTOMOPATHOGENIC FUNGI
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English text was very clear and unambiguous throughout the manuscript. The literature references and background in the field was provided. The structure of the manuscript including figures and tables are professional. The raw data was shared in supplementary files. A hypothesis was presented and tested.
Experimental design: The research question was well-defined and meaningful. The research clearly fills a knowledge gap. The experimentation was suitably rigorous. The materials and methods were described in sufficient detail.
Validity of the findings: All data have been provided and they are adequately robust and appear statistically sound. Conclusions are well stated, linked to the hypothesis statement and supported by the results.
Additional comments: Dear Authors:
This is an interesting article seeking to experimentally manipulate pathogen densities to better understand why the invasive ladybird Harmonia axyridis has a competitive advantage over native ladybirds such as Olla v-nigrum in North America.

A few suggestions to improve the text:
1. Please add a few sentences in the Introduction or Materials and Methods to tell the readers that He. virescens is likely two separate stains in this study. One for Ha. axyridis, and one for O. v-nigrum. I see that you mentioned the two strains in the Discussion section.
2. In Figure 1, please change the x-axis label, maybe to Mean Percentage (+/- SE) of Mortality.
3. In Figure 2, I am hesitant to believe that the authors can honestly compare the infection rates between ladybird species, if He. virescens strains differ between ladybird species. Do the authors have any unpublished data to show that one strain is not more virulent than the other?
4. Line 426: Add italics to the sci. name.
5. Line 461, 469: BioControl


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: MORTALITY OF NATIVE AND INVASIVE LADYBIRDS CO-INFECTED BY ECTOPARASITIC AND ENTOMOPATHOGENIC FUNGI
Review round: 1
Reviewer: 2

Output:
Basic reporting: The theoretical framework must be more in line with the objective of the study. The information on lines 40-50 gives contradictory messages and it is unclear whether this study was designed from a fundamental ecological perspective, that is, to understand the impact of biotic interactions on the structure and dynamics of populations or if it was designed in a more applied perspective to contribute to finding the best solutions to control populations of Ha. axyridis. I wonder, is this period really necessary?

Literature, article structure, figures, tables and raw data are adequate.

Manuscript use a clear, unambiguous and correct text. We found nice profissional standards of courtesy and expression.
Experimental design: My major comments goes to experimental design.

The study adresses a timely topic of research and is of interest to ecologists, both those working in areas of biological invasion as well as those in the field of applied ecology. PeerJ is a suitable venue for its publication.

It is not clear why the procedure described in the lines 136-138 was carried out. Can I assume that this was only done to obtain more Hesperomyces infected ladybirds? Again, it is not clear why this procedure presented in lines 138-139 was carried out. Can I assume that this was done to obtain diferent Hesperomyces infectations levels?

I recomend that authors explain to what extent “14 or more thalli” exert a significant imumitarian response on ladybirds and that this response does not change differently to any value above 14 thalli and thus, does not alter susceptibility of hosts to aditional infections (see lines 151-153). This fact may explain the high variance in the percentages of ladybird mortality.

Authors should explain why they tested 1 mL of 2.5 × 105 conidia/mL suspension and not another concentration? Moreover, despite considering acceptable submerging ladybirds in a suspension with conidia, wouldn't it have been possible to use Potter's tower to spray ladybirds?

Why statistical comparisons of daily mortality between H. axyridis and O. nigr are performed without data of control tratments?
Validity of the findings: The study intends to test the effect effects of infections of multiple natural enemy on Ha. axyridis. Two merits/novelties can be highlighted from this study; i) the setting up of dual infection assays conducted on ladybirds and ii) the first account of differential susceptibility to M. anisopliae between the invasive Ha. axyridis and the native O. v-nigrum. The study is of interest to ecologists, both those working in areas of biological invasion as well as those in the field of applied ecology.
Additional comments: The study intends to test the effect effects of infections of multiple natural enemy on Ha. axyridis. Two merits/novelties can be highlighted from this study; i) the setting up of dual infection assays conducted on ladybirds and ii) the first account of differential susceptibility to M. anisopliae between the invasive Ha. axyridis and the native O. v-nigrum.

The experiments in the current study, contrary to what the authors advocated, does not fully allow to make comparisons of infections, and dual infections, between two host species. I believe that the study only allows the characterization of the effect of their two specific fungal parasite. This is clearly recognized by the authors when they refer to the need for additional experiments to disentangle the interactions. In view of this, it does not make sense to compare the daily mortality rate as shown in figure 2.
Minor comments:

Line 40: I recommend to replace “In nature and in agricultural ecosystems…” by “In nature…”.

Line 130-134: I recommend mentioning here the fact that the adult states have been mixed.


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: MORTALITY OF NATIVE AND INVASIVE LADYBIRDS CO-INFECTED BY ECTOPARASITIC AND ENTOMOPATHOGENIC FUNGI
Review round: 1
Reviewer: 3

Output:
Basic reporting: This manuscript aims to assess how mortality of two ladybird species, one native and one invasive, is mediated by the co-infection by entomopathogenic fungi. The question raised by the authors is very interesting and novel, dealing with the interactions among different parasitic fungi on the survival of two ladybird beetles. And the results are very interesting and meaningful. It is well written, with appropriate literature and good structure.
Nevertheless, I think that the introduction (background/context) should be modified in order to be more clear about 1) the previous information regarding these types of interactions; 2) the interaction between H. virescens and other fungi; 3) the fungi species selected and their origins; and  4) how the origin (of both ladybird beetles and fungi) could mediate the outcomes of these interactions (how co-evolutionary processes may mediate the interactions among these fungi with the ladybird beetle host species). Some of this information is provided very late in the manuscript, in the Discussion.
Very importantly, the hypothesis should include an explanation for why native and invasive ladybird species should respond differently to native or non-native fungi.
Experimental design: In general, the methods and statistical analyses are appropriate, and described with sufficient detail. A few issues that are not completely clear in the text are clarified when looking at the supplementary Tables.

Experiments include the establishment of laboratory–reared colonies of ladybirds, thus controlling for the initial parasitism state (absence of parasitic fungi), and age. It would be necessary to include a better justification of why using native B- bassiana and a commercial B. bassiana strain There´s nothing in the hypothesis dealing with fungi origin (native, exotic, natural or commercial strains). The authors should revise the hypothesis.
Validity of the findings: What it is not so clear to me is the Result section (see specific comments). Specially, I would like to see in the figures the results for the control treatments.

Hesperomyces virescens is a complex of multiple species, which is only reported in the Discussion. Because of this, in the Materials and methods I think it is necessary to be clearer about the origin of the Hesperomyces used in the trials. Did they come from H. axyridis? O. v-nigrum, both?

Specific comments:
L. 138-139: why the change in source/target numbers?
144: number of ladybirds per container? I suppose H. axiridis and O v-nigrum, infected and non-infected with H. virescens were reared in different containers. Yes?
L. 148: individually placed in the tubes?
L. 186-187: the controls are also treatments. How are they included in the analyses (in Table 1, the P-values are between each treatment and the corresponding control? There are no comparisons among all different treatments)?
L. 191-192: trials = assays? Pease, be consistent
L. 210. It is not clear to me how Table 1 confirm this result. It seems to me that it would be more appropriate citing Table 1 at the end of sentence in Line 211 (after “no additional effect detectable among co-infection treatments…”.
L. 330-331. I don´t see this result in Fig. 1 because, again, controls are not shown.
In addition, I would like to see the results of all eight treatments in Figure 1 (as in Table S3). Why it is not reported the Controls without H. virescens for H. axyridis and O. v-nigrum? (i.e., only 7 bars –and not 8- shown for each ladybird species). Is it that all results are the difference of these treatments with the corresponding control? Sorry I am not familiar with the concept “manifold of mortality”. Please, clarify.
Table 1 and 2 should be merged.
Fig. 2: An interesting result is that apparently the survival of O. v-nigrum (in presence of H. virescens) is more affected by the infection of native Bb than GHA Bb. Again, why the controls (survival of H. axyridis and O. v-nigrum without H. virescens) are not shown here?
Additional comments: My general comments are already stated in the previous sections


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: MORTALITY OF NATIVE AND INVASIVE LADYBIRDS CO-INFECTED BY ECTOPARASITIC AND ENTOMOPATHOGENIC FUNGI
Review round: 2
Reviewer: 1

Output:
Basic reporting: Same as before (in my previous review)
Experimental design: Same as before (in my previous review)
Validity of the findings: Same as before (as in my previous review)
Additional comments: In the Intro. or M & M section, please indicate that two strains of the fungus (Hesperomyces virescens) are likely present in the field. Please add a sentence or two to reveal this important information to your readers.

In Figure 2, I believe it is difficult to compare infection rate between lady beetle species, if the fungus (H. virescens) exists as two distinct strains, one on Harmonia axyridis and the other on Olla v-nigrum. The Results should be slightly revised to address this problem.


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: MORTALITY OF NATIVE AND INVASIVE LADYBIRDS CO-INFECTED BY ECTOPARASITIC AND ENTOMOPATHOGENIC FUNGI
Review round: 2
Reviewer: 2

Output:
Basic reporting: Regarding the Introduction, I do not see major changes. Only one final paragraph was added and none of my suggestions or concerns were considered, and their arguments for not doing so are not convincing. I think the authors should modified the introduction (theoretical background/context) as requested before (reviewer 2 also pointed out that theoretical framework must be more in line with the objective of the study; in this case, the comparison between the invasive H. axyridis and the native Olla v-nigrum to co-infection). It is not adequate to mention O. v-nigrum just at the end of the Introduction, without any justification what it is pretended to test with the inclusion of this native species in the analyses.
The origins of the fungi should be mentioned in the Introduction. For H. virescens, Roy et al. (2011; Biocontrol) state that is probably native to North America or at least present there since 1931. See also Orlova-Bienkowskaja et al. (2018) Plos One. Are the other species native to Northamerica? If not, when they were introduced to the country? For how long have they been in contact with H. axyridis and O. v-nigrum in US? This information is very important when comparing the response of native and invasive ladybird species to the infection by pathogens.
I insist the hypothesis has to be revised, including what was expected when comparing native versus an exotic ladybird species because the manuscript, since the beginning (title), put special emphasis in how native versus exotic ladybird species respond to co-infection by ectoparasitic and entomopathogenic fungi.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Most of my suggestions to the original version of the manuscript were considered in this new version. Nevertheless, I think that the Introduction has to be modified according to my comments above.
I insist Tables 1 and 2 should be merged. They both address the same thing, but for the two species of coccinellids.
Figure 2 is incorrect. All three plots are the same (see Fig. 2 in the original). Also, I insist that controls must be included in this figure. This point was also raised by reviewer 2 and the authors' response is not satisfactory. The design includes controls without H. viriscens and these should be included in all analyzes.


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 MODEL OF INVASIVE DUCTAL CARCINOMA OF THE BREAST BASED ON DIFFERENTIALLY EXPRESSED GLYCOLYSIS-RELATED GENES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript by Li et al constructed a model based on the RNA-seq data of glycolysis associated genes in breast cancer. Overall, this study is interesting. It provides a new model to predict the survival of IDC breast cancer. It is well designed and performed. I only have several minor concerns.
Minor points:
1.	They should include the references for all the software and data they used in this this study.
2.	Can they change the color of Fig. 1B to make it look brighter? The background is a little dark right now.
3.	The analysis of STRING showed that there were interactions among 6 genes (P4HA2, P4HA1, PGK1, G6PD, HK3, PMM2) in DGRG. They should have some introduction of these 6 genes, so that readers can understand it better.
4.	In Fig. 10, did they include all the tumor tissue or just the IDC tumor tissue?
5.	They could consider combine Fig. 9 and Fig.10 together.
6.	They found 185 DGRGs between tumors and normal tissues. If they can include a table as supplementary data to show these 185 DGRGs and the p values, it will be better.


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

Input:
Title: PROGNOSTIC MODEL OF INVASIVE DUCTAL CARCINOMA OF THE BREAST BASED ON DIFFERENTIALLY EXPRESSED GLYCOLYSIS-RELATED GENES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an interesting manuscript by Li et al. which investigates the role of expression of glycolysis-related genes (GRGs) in predicting prognosis of breast cancer within the type of IDC. The manuscript is well written and the tables and figures are well organized.
Experimental design: The present study performed a systematic analysis of GRGs in IDC of breast cancer to explore its prognostic significance and uncover its potential function and mechanism using the database of TCGA. The analysis is classic, well described and reasonable, and the results are convinced.
Validity of the findings: Generally, the findings are meaningful and the conclusion is clearly stated based on the results. But there is still some weakness:
Major comments:
1.	GO and KEGG enrichment analysis are good to reveal the underline function of the GRGs. However, the functions and networks the authors found are not directly related to the biology of breast cancer. I suggest the author could perform further KEGG analysis or GSEA analysis to find whether the GRG signature has close relationship with cancer gene sets, like immunity, proliferation, DNA damage and so on.
2.	Analysis of the miRNA is not necessary. I suggest the author could delete this part.

Minor points:
1.	The abbreviation of differentially expressed glycolysis-related genes is DGRGs in the manuscripts. It is better to use (DEGRGs).
2.	It is a bioinformatic analysis, and the potential functional mechanisms were not studied. It is better for the author to address the limitation in the “Discussion” section.
Additional comments: 1. Focusing on the role of GRGs in IDC of breast cancer is a good direction.
2. The anaylsis is quite clear and comprehensive.
3. The weakness is the part which uncover the function and mechnism of GRGs. The authors could make some further analysis, and/or explain more 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: IDENTIFYING MYOCARDIAL INJURIES IN “NORMAL-APPEARING” MYOCARDIUM IN PEDIATRIC PATIENTS WITH CLINICALLY SUSPECTED MYOCARDITIS USING MAPPING TECHNIQUES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an interesting study which focused on "normal-appearing" myocardium in pediatric patients with clinical suspected myocarditis. The authors try to identify myocardial injuries of "normal-appearing" myocardium using T1 mapping and T2mapping techniques. They compared the T2 values, native T1 values and ECV of "normal-appearing" myocardium among acute myocarditis patients, subacute/chronic myocarditis patients and healthy children. The results showed that diffuse myocardial injuries are prone to occur in subacute/chronic myocarditis with prolonged inflammatory response. The study affirmed the value on the diagnosis and monitoring of myocarditis of mapping techniques.

I have the following comments for the authors to embellish:

1. In the “Methodology” (line 36), “among” maybe better than “between”.
“T2 values, native T1 values and extracellular volume (ECV) 36 of “normal-appearing” myocardium between three groups were compared. ”

2. In the “Discussion” (line 279), “characteristic” maybe appropriate than “characterization”.
"However, it is not very sensitive in very mild cases, which might perform diffuse myocardial  tissue characterization changes."

3. The sentence in line 297 maybe unnecessary.
"Diffuse  myocardial  injuries  in  DCM  have  been  reported  by  mapping techniques."
Experimental design: The study design is sound for purpose and the results are well presented.

CMR imaging protocol: How many SA slices were performed during mapping sequences? And how to decide the position, for example “basal, mid and apical ventricular SA planes”.
Validity of the findings: Please provide the p values between AM and CM in table 2.
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: IDENTIFYING MYOCARDIAL INJURIES IN “NORMAL-APPEARING” MYOCARDIUM IN PEDIATRIC PATIENTS WITH CLINICALLY SUSPECTED MYOCARDITIS USING MAPPING TECHNIQUES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript was well-written with clear and unambiguous professional English. Introduction part and references gave adequate background information, and demonstrated the novelty of this study. Tables and figures were well-prepared.
Experimental design: This manuscript addressed an interesting topic of diffused injury in “normal-appearing” myocardium of patients with myocarditis, demonstrating that subacute/chronic myocarditis patients may show higher ECV even in non-LGE non-edema myocardium, and higher ECV may be correlated to impaired LVEF. The authors employed T1/T2 mapping technique, and provided plenty of details of this study in Methods part.
Line 165-166 states that “The papillary muscles and trabeculations were included as part of LV mass”, while reference 26 says “For calculation of global ventricular volumes, mass and function the papillary muscles were included in the ventricular cavity”. I think it might be a typo.
It would be better if the authors gave more information about the criteria of included region (normal-appearing myocardium)/excluded region (focal myocardial edema or necrosis/fibrosis). For example, (line 168-170,177-178) Were focal myocardial edema in T2WI and necrosis/fibrosis in LGE defined by visual assessment?
Validity of the findings: The authors described results of their study comprehensively and provided robust raw dataset of studied CMR parameters, which supported the conclusion of this study.
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: IDENTIFYING MYOCARDIAL INJURIES IN “NORMAL-APPEARING” MYOCARDIUM IN PEDIATRIC PATIENTS WITH CLINICALLY SUSPECTED MYOCARDITIS USING MAPPING TECHNIQUES
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this study, the authors analyzed diffuse myocardial injuries of “normal-appearing” myocardium in pediatric patients with clinical suspected myocarditis using T1 and T2 mapping techniques and evaluated the associations between diffuse myocardial injuries and cardiac function parameters. The authors found that the extracellular volume of “normal-appearing” myocardium significantly increased in subacute/chronic myocarditis compared with controls and it was associated with LVEF.
  The authors need to address the following:
  1. There are too many language questions in this article. I suggest the manuscript be edited by a native speaker, or correct the grammar issues cautiously.
  2. Abstract: Line 33: “Methodology” or “Methods” ?
  3. Line 64-66: Diffuse, as opposed to focal, myocardial injuries in myocarditis may perform as “normal-appearing” myocardium without comparison of normal myocardium. This sentence is confusing.
  4. Line 108: 15control
  5.How were 15 control children included in this study? Please add the corresponding inclusion and exclusion criteria.
  6.The authors focused on the “normal-appearing” myocardium, which was defined as no focal myocardial edema or necrosis/fibrosis in the T2-weighted and LGE images in this study (line 176-178). Did it also assess normal myocardium? How to distinguish between normal myocardium and diffuse myocardial injuries, I think it should be explained in the Materials and methods.
  7. Sample size was small and all the subjects were male (line 216-219), the results were limited and it might not be sufficient to support the conclusion.
  8. Line 275-277: LGE has become the “golden standard” to evaluate focal myocardial necrosis/fibrosis or other forms of irreversible injury infiltration in myocardial diseases. I think this sentence is not accurate. Pathological examination is usually the gold standard to evaluate the degree of myocardial necrosis and injury, but it is difficult to carry out in living people.
  9. The duration of symptoms to CMR timing range is broad in CM group. Does this affect results?
  10. Table 4 shows the associations between ECV and cardiac function in subacute/chronic myocarditis patients. Is there the data that shows the associations between ECV and cardiac function in all groups?


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: IDENTIFYING MYOCARDIAL INJURIES IN “NORMAL-APPEARING” MYOCARDIUM IN PEDIATRIC PATIENTS WITH CLINICALLY SUSPECTED MYOCARDITIS USING MAPPING TECHNIQUES
Review round: 2
Reviewer: 1

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


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

Input:
Title: IDENTIFYING MYOCARDIAL INJURIES IN “NORMAL-APPEARING” MYOCARDIUM IN PEDIATRIC PATIENTS WITH CLINICALLY SUSPECTED MYOCARDITIS USING MAPPING TECHNIQUES
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed my concerns. 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: IDENTIFYING MYOCARDIAL INJURIES IN “NORMAL-APPEARING” MYOCARDIUM IN PEDIATRIC PATIENTS WITH CLINICALLY SUSPECTED MYOCARDITIS USING MAPPING TECHNIQUES
Review round: 2
Reviewer: 3

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: DURATION OF HEMODIALYSIS ASSOCIATED WITH CARDIO-RESPIRATORY DYSFUNCTION AND BREATHLESSNESS: A MULTICENTER STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Writing generally good; needs slight English language polishing which will likely be done in the editing process.

In the abstract, the sentence "These patients are also related to poor respiratory performance due to pulmonary impairment" should be removed, as it is presumptively asserting facts which this study is aiming to prove.
Experimental design: It should be stated explicitly in the abstract and in the methods that this was a prospective study.

There needs to be more detail about what "chronic cardio-respiratory conditions" were exclusion criteria; does this include any restrictive or obstructive respiratory pathology? Obstructive sleep apnoea? Heart failure? How about smoking history?

How was duration of haemodialysis defined for the analysis- in years, or months?

Where continuous data was expressed as mean and standard deviation, were tests of normality performed to check if this data was normally distributed? (If any of the continuous data variables were non-normally distributed, median +/- IQR would be more appropriate)
Validity of the findings: Line 142 to 144 do not make sense: "Patients with CRF who had a long duration of HD had a high prevalence of restrictive pulmonary impairment at 47% (n = 47) compared to individuals with normal pulmonary function (3.00%, n = 3) (X2 = 8.575, p = .003)." This paragraph is concerned with comparisons between long duration of HD and short duration of HD groups, not Chi-Squared comparisons within the same group.

Table 4 is totally missing. Furthermore, even if Table 4 were included, it is unclear what is the purpose of the  logistic regression analysis. Is it univariate or multivariate logistic regression analysis?

It appears that the binary dependent variables being studied in the regression are long duration of HD and short duration of HD. However, these are not outcomes that are influenced or predicted by other independent variables- they are simply a function of the passage of time since the patient started dialysis. Using clinical/respiratory parameters to "predict" whether someone has been on dialysis for a long time has no practical utility. I would remove the logistic regression analysis altogether.

In the discussion, line 196/197 "The present study found that the association between FVC and inspiratory muscle strength was observed in HD (data was not shown)" is inadequate: if this is an interesting point, this data should be shown in the manuscript with the appropriate statistical analysis. Perhaps this data, comparing the assocation between different respiratory variables in this cohort, should be presented instead of the above-mentioned logistic regression.
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: DURATION OF HEMODIALYSIS ASSOCIATED WITH CARDIO-RESPIRATORY DYSFUNCTION AND BREATHLESSNESS: A MULTICENTER STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: - The number of literature references could be more extensive to provide suitable context.

- The article structure is suitable however in this topics below I suggest:
Introduction: Hypotheses should be described in this section. What is the rational for including the comments about GFR and this variable was not described in methods, tables or discussion? I think that GFR is a very important variable.
Experimental design: The research question was well defined and relevant however there are many studies about these questions. Rigorous investigation of technical and ethical aspects.

The methods section was sufficient but I have a question: Why the authors did not use reference formulas to predict distance in TC6 and values of PImax and PEmax? These equations are essential to described and interpreted because comparing values against healthy adults.

Was the sample size estimated?
Why the authors chose the categorized dialysis duration (defined as < 5years and ≥5
110 years)? Was based in previous literature?
Validity of the findings: The results showed a benefit to literature however, the external validity is hard to be concluded. The power of study was not showed without a priori calculate of sample size.

Information about laboratory analysis of renal function would be very important in this population.

Conclusions were linked to original questions.
Additional comments: General comments: Thank you very much for allowing me to review this manuscript.
Overall, this article is very interesting and does provide additive data to the existing published literature.


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: DURATION OF HEMODIALYSIS ASSOCIATED WITH CARDIO-RESPIRATORY DYSFUNCTION AND BREATHLESSNESS: A MULTICENTER STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: No further issues
Experimental design: No further issues
Validity of the findings: No further issues
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: DURATION OF HEMODIALYSIS ASSOCIATED WITH CARDIO-RESPIRATORY DYSFUNCTION AND BREATHLESSNESS: A MULTICENTER STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The changes done were adequate.
Experimental design: The changes done were adequate.
Validity of the findings: The changes done were adequate.
Additional comments: The changes done were adequate.