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

Input:
Title: COMPUTATIONAL PERSPECTIVES REVEALED PROSPECTIVE VACCINE CANDIDATES FROM FIVE STRUCTURAL PROTEINS OF NOVEL SARS CORONA VIRUS 2019 (SARS-COV-2)
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is much improved. The authors have responded positively to the key suggested revisions and comments. The English too is improved, but could be bettered further by a final general proofreading, though I don't think that the remaining shortcomings impact upon the understanding or reproducibility of the work. This is ultimately an editorial decision.

A few of the more obvious instances that can be quickly amended:

Line 363 : recognized - change to identified
Line 530 : Lower case Haddock, upper case everywhere else
Line 572-574 : The sentence doesn't make its point
Line 659 / 669 : Species name should be in italics
Line 769 : yeast
Experimental design: No further comments.
Validity of the findings: No further comments.
Additional comments: This is a good and timely study and a solid foundation for further work.


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

Input:
Title: THE RELATIONSHIP BETWEEN INDIVIDUAL PHENOTYPE AND THE DIVISION OF LABOUR IN NAKED MOLE-RATS: IT’S COMPLICATED
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper tests the hypothesis that in captive colonies of cooperatively breeding, eusocial naked mole rats, an individual’s traits, including age, determine whether or not it will work, and the duration of work undertaken. While the paper does not deliver a clearly significant outcome enlightening our understanding about which individuals work in such colonies, it provides evidence that increasing age rather than weight or behavioral rank determine how often a naked mole rat works, regardless of sex. The authors, however, realize the limitations of their captive study working with relatively small, fixed size colonies, and highlight that their data suggest a potentially malleable involvement in colony work depending on prevailing conditions and colony size. This paper will make a useful addition to the cooperatively breeding animal literature.
Experimental design: p.5, Material and Methods, 1st paragraph. Include here how many colonies studied comprised fewer than 20 members, and how many comprised more. It is not clear from Table 1.

p.5, 1st paragraph. “Where colony samples did not include a breeding female, one was selected (colonies 11A, 11C and FF)”. Please add the details for colony FF to Table 1. And, does this mean if the randomly selected individuals from a colony did not include the queen, she was added to that colony’s observation list anyway? It is not clear.

p.5, 2nd paragraph. “Red vagina” means closed, non-perforated external genitalia? Or can a non-perforate vagina be observed externally in naked mole rats?

p.5, 2nd paragraph. Provide citations previously validating the use of male mating or copulating (is this really just mounting, only?) and nuzzling female (queen?) genitals? If none, justify why these behaviors reliably identify male breeders.

p.5, 3rd paragraph. Maybe change “alarm behaviors” to “increased behavioral activity”? How were observers positioned relative to the colony under observation? In other words, could the colony detect vibrations from laptop key presses?

p.5, 4td paragraph, and p.6, 1st full paragraph. These basic methods should start the methods section at the top of p.5.

p.7, 2nd paragraph. Provide citation showing that naked mole rats with greater body weights are older.

p.8, Results. Replace “lucky enough to work” with “during”.

p.9. Fig. 1A-1C. The visual image of 0 or 1 values contributing to a best-fit line of some sort is not helpful to the reader. For a visual image, in addition to the modeling performed, could the authors substitute the ratio of working to non-working animals by age, weight and rank, e.g., if at 1 year of age 20 animals worked and 3 did not, that value could be represented by a ratio of 20/3 or 20/23? If no exercise like this is helpful, then the authors should only state values in the text or an extended Table 3.
Validity of the findings: p.3, Introduction. The authors need to also introduce some rationale for potential benefits to individuals to cooperate that may include kin selection, and provide some explanation as to why division of labor evolves during natural selection for cooperative breeding. Such added arguments would provide more justification for the study and its design.
Additional comments: All comments are entered above.


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

Input:
Title: THE RELATIONSHIP BETWEEN INDIVIDUAL PHENOTYPE AND THE DIVISION OF LABOUR IN NAKED MOLE-RATS: IT’S COMPLICATED
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper breaks down one established myth about the naked mole-rats and as such is worth publishing. There are, however, some methodical and interpretational problems and the literature is insufficiently covered. While the methodical problems can probably hardly be removed, they should be nevertheless discussed. The authors should also more critically revise (and reword or complement) some points of their interpretations and complement the references. While the authors break down one myth, they uncritically adopt others.

Terminology:
Which evidence is there that a female mates with up to three males, apart from a single study by Jarvis (1981) done on one incomplete family? Please provide references.
The authors introduce a new – in no way supported – category "possible breeders". This is rather absurd. Is there any evidence that whatever sexually mature naked mole-rat would not breed, i.e. would be an "impossible breeder", if given an opportunity?
Note that "colony", though widely used in literature, is not a correct term to designate a social group of naked mole-rats. A group like this, should be called in mammals a "family". A colony is a group of e.g. ground squirrels or seals which aggregate but are principally of solitary habits.
The authors are discussing "red vagina" as a trait characterizing breeding females. This is anatomically not correct. What they observe is "vulva" or, at best, vagina opening. The vagina is the tube between the vulva and the cervix.

Methods and interpretations:
Six times ten minutes observational time per one animal is a rather insufficient sampling. Particularly if sampled randomly, irrespective of any activity pattern. Both measures of activity do not correlate what the authors explain through their different characters (number of bouts versus length of bouts). I agree – note that it is a general characteristics of mammals (including human) that older individuals have fewer bouts of activity and these have longer duration than juveniles.
It would be much better and more informative to express both activity measures in per cent for every animal. I understand that N would not be so impressive (600+). The authors use per cent in their mix models, unfortunately not in figures.
	The studied families differ greatly in their age structure. Two of them involve only young animals. It has been reported in the literature that young (fledgling) families behave differently. The authors should have focus on the largest, and with respect to age mostly differentiated families and observe all individuals in them.
The large figures at the end of the manuscript often show that the curve is pulled in a certain direction only thanks to a few outliers, otherwise there is no apparent trend.
The authors state (lines 230-233): Our analyses of 618 observation periods, encompassing 103 non-breeders from eight colonies, indicated that the probability of being observed working was explained by age - with older individuals working less - but not by sex, weight or rank. I do not fully agree that with this conclusion. Regarding age, this trend is apparent in six from eight families, regarding body weight in five out of eight families! Moreover inspite of diverse growth rate differences, age and body size always somehow correlate: youngsters are always smaller.

Work with literature:
It is strange that the authors cite and discuss studies on ants, wasps, lions, dolphins etc., but ignore papers on sociality in the next relatives of the naked mole-rats, particularly on Fukomys anselli and F. mechowii, published by the Czech and German teams which also address the age-polyethism, starting with the papers by Burda published in 1989 and 1990 and closing with the most recent of those studies: the paper by Skliba et al. (2016) in Scientific reports entitled: "... Ansell’s mole-rat indicates age-based rather than caste polyethism". This paper shows clearly that the main factor for any work (activity) ist the family-context – if there is less food and hard soil, all family members must work.
Moreover, a negative relation between body weight and digging work in mole-rats has been reported in the literature. However, in some families it may be not apparent, due to the context (motivation, requirements of the family). This was found i.a. by Lacey and Sherman (1991), as well as by two relevant papers ignored in the present manuscript: Gaylard et al. (1998), Skliba et al. (2015).
The authors define eusociality as used for arthropods by Crespi and Yanega (1995) (not Yanegra as written by authors) and ignore a highly cited paper by Burda et al. (2000) discussing eusociality in naked mole-rats.

In conclusion:
I believe the conclusions of the authors regarding the best explanation of differences in working frequency being the age-polyethism. Yet, the authors should more discuss also the effect of motivational context, as pointed out in papers by Lacey and Sherman (1991), Gaylard et al. (1998), Mooney et al. (2015), Skliba et al. (2016). The authors should include into the discussion more relevant papers by other authors on Fukomys mole-rats, rather than (or additional to) papers on insects, dolphins, lions etc. The authors should mention and critically discuss some shortcomings in the methods and interpretation. The paper can thus be improved by editorial work without necessity to do further experiments.
Experimental design: no further comment - please note that I reported about this aspect above in context of the whole contribution
Validity of the findings: no further comment - please note that I reported about this aspect above in context of the whole contribution
Additional comments: no further comment - please note that I reported about this aspect above in context of the whole contribution


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

Input:
Title: THE RELATIONSHIP BETWEEN INDIVIDUAL PHENOTYPE AND THE DIVISION OF LABOUR IN NAKED MOLE-RATS: IT’S COMPLICATED
Review round: 2
Reviewer: 1

Output:
Basic reporting: In this revised manuscript, the authors have clearly and thoughtfully responded to previous review concerns. I have no additional concerns.
Experimental design: Clear and rigorous, well described.
Validity of the findings: No comment.
Additional comments: The revised manuscript makes a more convincing case concerning the complexities of understanding which individual naked mole rats contribute to "working", for how long and in what ways. Thus will make a useful addition to the literature demonstrating even in a unique example of highly evolved eusociality in placental mammals, the mechanistic understanding of how eusociality is maintained is highly complex.


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: STUDY OF MARSH WETLAND LANDSCAPE PATTERN EVOLUTION ON THE ZOIGÊ PLATEAU DUE TO NATURAL/HUMAN DUAL-EFFECTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors analyzed marsh wetland landscape pattern evolution on the Zoigê Plateau from 1977-2016 by remote sensing and geographic information system technology. Generally the manuscript is well prepared. The authors provided relativelt sufficient field background.  The conclusion can be supported by their results. And the the findings are important for wetland conservation and management.
Experimental design: This is an original work and the research question is well defined. The methodlogy in this stuy is reasonable and described in detail. .
Validity of the findings: The conclusions are well stated and can be supported by thier results.

You can add the alpine wetland protection policy based on your results to improve your article.
Additional comments: - Try not to use commas in the middle of the title.

- The article structure is suggested to be adjusted. Many data processes in the results parts, which should be moved to the method part. It’s also suggested that discussion and conclusion part should be separated, and it’s better to discuss first and then come to a conclusion.

- It is suggested to compare the results of this study with some similar studies which is done before (e.g., Effects of alpine wetland landscapes on regional climate,Advances in Meterology 2013), which can contribute to analyze the driving fators.

- You can add the alpine wetland protection policy based on your results to improve your article.

- There are some editting errors needed to be corrected before resubmission . For instance,

1) Lines 84-85: Rephrase, suggestion: “…, and a digital topographic map of the research area (with a resolution of 90 m) were used

2) Lines 221-223: Rephrase the sentence, suggestion: “…, which can also be confirmed by the above patch scale results. The correlations between…”

3) Lines 263-265: integrate the sentence, like this “…TA and PLAND declined gradually…”


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: STUDY OF MARSH WETLAND LANDSCAPE PATTERN EVOLUTION ON THE ZOIGÊ PLATEAU DUE TO NATURAL/HUMAN DUAL-EFFECTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript reports a landscape change during the passing decades for the Zoige Plateau.  The authors present a clear background why the study is meaningful, and I agree with them. The English using is fine with grammar and spelling. The organization is also fine. However, the writing style is like a project report but not a scientific paper.  For example, the result section is very redundant and can be reduced by 1/2.  The discussion is fully of speculations, mostly without supporting evidence.
Experimental design: I have two major concerns:
1) There is no detail about how to distinguish the so-called swamp meadow and "mesophyte" meadow? --Moreover, I like using marshy meadow rather than swamp meadow because generally there is no trees or shrubs in the extensive meadow.

2) The authors attribute climate change and human disturbance to the change in landscape.  This is perhaps a fact. However, they don't show evidence and they did not quantitatively determine to what extent these two factors influenced the landscape change.
Validity of the findings: Considering the vague description of the method section, I am not sure about the validity of the conclusion.
Additional comments: As noted above, this manuscript seems much immature to be a 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: STUDY OF MARSH WETLAND LANDSCAPE PATTERN EVOLUTION ON THE ZOIGÊ PLATEAU DUE TO NATURAL/HUMAN DUAL-EFFECTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The thesis takes marsh wetland of Zoige Plateau as the research object, and analyzes the changes in the area and center of mass of marsh and swamp meadow in the past 40 years, as well as the evolution of landscape patterns, which are of great significance for wetland protection.
But the article is still inadequate, and it needs to be revised after being published.
(1) The discussion part needs to be strengthened and the latest research results need to be added;
(2) The legend in Figure 3 is marsh and marsh meadow. According to the description in the article, it should be marsh and swamp meadow, please check and correct it;
(3) The significance of studying the evolution of landscape pattern should be discussed in the introduction, please add it in the subsequent modification;
(4) In addition, there are some minor errors and irregularities in the article that need to be carefully checked, especially the usage of comma and definite article.
(5) I found some minor mistakes. Please check the manuscript carefully.
Line 199, tomographic should be topographic.
Line 227, variation should be various.
Line 347, of the local should be in the local.
Line 418, significances should be significance.


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: STUDY OF MARSH WETLAND LANDSCAPE PATTERN EVOLUTION ON THE ZOIGÊ PLATEAU DUE TO NATURAL/HUMAN DUAL-EFFECTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors analyzed marsh wetland landscape pattern evolution on the Zoigê Plateau from 1977-2016 by remote sensing and geographic information system technology. The language of the revised manuscript is better than previous version. The authors provided a sufficient field background. The conclusion can be supported by their results. And the the findings are important for wetland conservation and management.
Experimental design: The experimental design is reasonable and the methodology was provided in details.
Validity of the findings: The conclusions are well stated and can be supported by their results.
Additional comments: The authors have solved all my concerns. I have no furhter comments on it. I recommend its acceptance for publication in the journal.


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

Input:
Title: STUDY OF MARSH WETLAND LANDSCAPE PATTERN EVOLUTION ON THE ZOIGÊ PLATEAU DUE TO NATURAL/HUMAN DUAL-EFFECTS
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 most of my concerns. However, there still remain some issues that need to be resolved which are listed below.

1. Figure 1: Please improve the quality of the graph by adding DEM data as background. Please adding geographic grid and axes labels of longitude and latitude. I suggest adding a locator submap in Figure 1 to show location of Zoigê Plateau in China and Sichuan province.

2. Figure 3-9: Please save those figures in high resolution as it is pixelated. I suggest 800 dpi or greater.


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

Input:
Title: A GLYCOLYSIS-RELATED GENE PAIRS SIGNATURE PREDICTS PROGNOSIS IN PATIENTS WITH HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study wanted to establish novel GRGPs signatures to better diagnose and predict HCC. The authors used clear English to explan the problem of interest, statistical methods and results. Sufficient background in the HCC prediction field was provided. The figures and tables were also clearly provided.
However, there is one part in the figure that needs modification:
Figure 3B is missing a vertical line (mentioned in the caption but missing in the figire).
Experimental design: The authors clearly stated the gap in establishing GRGPs signatures for patients with HCC. They used statisticcal methods to establish the signatures in one cohort and validated that in another cohort. The selection of gene was also reasonable. The authors compared 26 glycolysis-related DEmRNA between HCC and normal tissues to construct the GRGP signature. However, there are two parts that is not quite clear:
1. Line 162 to 164 in the word document: "Forty-four gene sets were upregulated in HCC, and 20 gene sets were highly enriched, with normalized P < 0.05 among the 50 gene sets (Fig. 1, Table S1)". This part is a little bit confusing. It would be good if more explanation on the table and figure is provided
2. Line 175 to 176 in the word document: "k = 2 seemed to be a more appropriate clustering choice". It would be better if the authors could give one or two sentences explanation on why k=2 is the best choice.
Validity of the findings: The authors clearly showed the data in the figures and tables. They also gave reasonable tests on whether GRGPs signature is independent and whether it has better accuracy than TNM stage.
The authors got the conclusion using TCGA dataset, they also provided vaildation of the GRGPs signature using ICGC cohort, which is self-consistent.
Overall the result is reasonable. But it would be great if more details are provided on the discovery of the seven GPGRs signatures.
Additional comments: No additional comments


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

Input:
Title: A GLYCOLYSIS-RELATED GENE PAIRS SIGNATURE PREDICTS PROGNOSIS IN PATIENTS WITH HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well written, and I have little trouble understanding the writing. The author provides clear literature citation and background where relevant, and frequently link their results with results of past studies.

The figures are the ones that I have trouble reading, because they are too small and have too low a resolution for them to be properly read. Figure 2B and Figure 8A and E are prime examples. The texts there are just not readable. For Figure 5, the texts can be read if more efforts are put in, but enlarging the font or splitting them into two figures may help readability. Figure 3B also has unreadable texts to the left of each line.
Experimental design: The experiment and analysis is well designed and described. The methods described in the materials and methods are in sufficient details for replication.
Validity of the findings: The main question asked by the study is whether a glycolysis-related gene pairs (GRGPs) can be used to predict prognosis of HCC, and the answer is yes. The authors find that seven GRGPs can be used as molecular biomarkers to predict HCC. Authors also find that the low-risk group based on these seven GRGPs have better overall survival (OS). Overall I find that the authors have strong data and analysis to back up their conclusions.

I only have a few comments to improve the manuscript:
1. Line 155: authors say that glycolysis ranked first. It is not immediately apparent in Figure 1 how glycoloysis rank first. It will be appreciated if authors can provide clearer explanation.
2. Figure 5E and 5F: more explanation is needed to explain how to interpret the heat map. There are only two colors, red and green, in the heat map, and they supposedly correspond to high and low levels, whereas there is another color scheme for high and low risk. I am confused by this heat map.
3. Line 290: CTMN1 is not in the seven GRGP and not in Table 1. It suddenly appears in the discussion here.
4. Figure 3: it is said that the vertical dashed line is at the optimal log (lambda) value. There are two vertical lines. Which one?
Additional comments: The writing of the article is excellent. There are just a few corrections that the authors may have missed:
1. Line 127: 'Data about 243 patients...'. Please change to 'Data of about 243 patients...'
2. Line 143: 'considered statistical significance' to 'considered statistically significant'
3. Line 203: 'largest contribution' to 'largest contributor'
4. Line 283: 'poor prognostic' to 'poor prognosis'
5. Line 297: ' which related with...' to 'which is related to...'


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

Input:
Title: A GLYCOLYSIS-RELATED GENE PAIRS SIGNATURE PREDICTS PROGNOSIS IN PATIENTS WITH HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1. The writing has a significant number of grammatical and phrasing errors, wherein sentences are sometimes confusing. The writing needs significant improvement.
2. In some places, the GRGPs is misspelled as GPGRs. I believe this is a typo.
3. Most figures are extremely poor quality currently. Multiple figures such as Figure 2 have text that is too small to read. While, other figures have texts of different sizes, while others such as Figure 1 have words overlaid onto the figure itself, making it hard to see. Many figures seem like they were taken as programmed output and directly put into the final figure, this is unacceptable.
4. Figure legends have to be significantly improved and need to be more clear. Such as in Figure 4A, lower panel it is unclear what the numbers indicate.
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: A GLYCOLYSIS-RELATED GENE PAIRS SIGNATURE PREDICTS PROGNOSIS IN PATIENTS WITH HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author addressed the questions raised in the review comments. And they also made effort to improve the reliability of the model by generally comparing more glycolysis-related mRNAs in this new version of manuscript, rather than just comparing 26 DEmRNAs. And the conclusion makes more sense than the previous version.
However, there are some parts that doesn’t read smooth in gramma:
1.	PDF file, material and methods section, line 95-96: ‘To explore whether the specific gene sets were significant differences between tumor group and normal group’, should be ‘significantly different’
2.	PDF file, Line 129, ‘were used to verify whether the GRGPs signature was significant associated with OS’ should be ‘significantly associated’

Another thing is about the figure, Fig 2C doesn’t have descriptions in the figure caption.
Experimental design: The experiment design was reasonable. As mentioned above, instead of comparing 26 DEmRNAs, more RNAs are considered and more filters are used to indicate the relavent RNAs. This is a better design than the previous version.
Validity of the findings: The TCGA datasets were training sets, and the other datasets were used as validation datasets. From the report, the tests on the validation datasets fits the model well.
Additional comments: No additional comments


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

Input:
Title: A GLYCOLYSIS-RELATED GENE PAIRS SIGNATURE PREDICTS PROGNOSIS IN PATIENTS WITH HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is written relatively clearly. The figure sizes and text readability have significantly improved from the first manuscript. Explanations to each of the figure have also improved, even though I find that there are more explanations needed for some figures.

In general, the manuscript seems to be written for a very specialized audience, assuming that the audience understands the field very well. A lot of explanations for interpreting graph, etc, are missing, so it is hard for people outside the field to understand the manuscript. I suggest that the authors take some time to provide more explanations to certain concepts, e.g. the lasso model, ROC, nomogram, etc.

There is one grammatical correction I hope to suggest:
- Line 47, 57, 224, etc. "have been proved" can be changed to "have been shown"

Here are some of the concepts that can benefit from more explanations:
- Figure 2A and 2B. What is the purpose of showing the graph? What should be our takeaway? The text says that lasso regression model revealed that 17 GRGPs as independent prognostic factors. From Figure 2A, should I focus on the lowest partial likelihood deviance? What is partial likelihood deviance? What is lambda? What are the numbers on top of Figure 2A? What do the two vertical lines represent? These are not explained. For Figure 2B, what does each colored line represent?
- For Figure 2C, there is no explanation of it in the Figure itself.
- Figure 6A and E. How to read a nomogram? Do we just draw a vertical line? My understanding is the line can be at a certain angle, not necessarily vertical. If you can provide an example, say a person with risk score of -1 and at stage III, what will be the 1 year survival? What do 'points' and 'total points' mean, and how are they derived?
- Figure 6D and H, it helps for readers to understand the graph if you explain that higher area under the curve (AUC) means better modeling
- For Figure 6H, the five year survival is almost 0.5. Can you comment on that?
Experimental design: In general, the study is well designed.
Validity of the findings: I find the findings to be valid, and it helps that the authors discusses the limitation of the study, in addition to its potential as biomarkers and targets for patients with HCC.
Additional comments: No additional comments


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

Input:
Title: A GLYCOLYSIS-RELATED GENE PAIRS SIGNATURE PREDICTS PROGNOSIS IN PATIENTS WITH HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 3

Output:
Basic reporting: No Comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I think the authors have sufficiently addressed all the concerns, and this manuscript looks good for publication now.


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

Input:
Title: IDENTIFICATION OF HUB GENES AND SMALL MOLECULE THERAPEUTIC DRUGS RELATED TO BREAST CANCER WITH COMPREHENSIVE BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Hao et al in this manuscript employed already established bioinformatics approaches to detect candidate biomarkers, pathways and candidate drugs of breast cancer. The results are well presented with figures and Tables.
Experimental design: Authors analyzed 5 breast cancer data sets downloaded from the GEO database.
A series of bioinformatics approach was used to evaluate the prognostic biomarkers and candidate drugs. Methods are well explained.
Validity of the findings: no comment'
Additional comments: 1) The novelty of the study is not clear; can you please write how your approach is is different than others and what is the contribution of your work?
2) Please clarify in the introduction how is your work than previous works.
3) The roles of hub genes can be explained more detail in the discussion.
4) In line 343, authors claimed the identified pathways provide more insights into the development of breast cancer. This needs relevant mechanistic discussion, how the findings may improve the pathogenesis.
5) Please consult these two latest papers to clear your biomarkers and drug repositioning part of your manuscript which still needs development; best systems biology papers:
https://doi.org/10.3390/medicina55010020
https://doi.org/10.1089/omi.2018.0048


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

Input:
Title: IDENTIFICATION OF HUB GENES AND SMALL MOLECULE THERAPEUTIC DRUGS RELATED TO BREAST CANCER WITH COMPREHENSIVE BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In general, this study was comprehensive and analysized five breast cancer data sets. Several minor concerns are as followed. First, the GEO data set selected by the author is much larger than the normal samples. How did the author avoid this statistical deviation? Second, GEO has amounts of data on breast cancer, and we recommended the authors select more sets of data for expression and survival analysis validation. Third, HUB genes screened by the author have been reported for many times, and we believe novel genes shall be explored to improve the quality of this study.


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

Input:
Title: IDENTIFICATION OF HUB GENES AND SMALL MOLECULE THERAPEUTIC DRUGS RELATED TO BREAST CANCER WITH COMPREHENSIVE BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Table 2: The borders are not added in the table and it is not clear which drugs are relating to the target gene(s).

The authors will have to work more on their introduction/background section, by adding more relevant content and doing an in-depth literature review. The fact that the abstract to the paper (26 lines) is longer than the introduction (25 lines) is an indication of how short it is!

Line 81: Perhaps the authors can use the term overlapping DEGs to refer to the genes that are differentially expressed across all the 5 datasets (also in other parts of the manuscript).

Figure 2A: There are scales present for 2 datasets, while none for others (or isn't visible clearly). Figure 2F has only 2 components, the third is not represented - were no hub genes found in this feature?

Line 187: Since the 6 hub genes were taken from the list of overlapping genes, they will be sig. dysregulated.

Most figure legends do not explain the key used and provide very little information. The figures also feel cramped, and already 10 images with 5 suppl. images. The authors can choose to move more data to the supplementary and plan their paper with 5-6 main figures.
Experimental design: One of the major (potential) pitfalls of this study is the use of 5 GEO datasets sequenced on the Affymetrix Human Genome U133 Plus 2.0 Array platform. While it is acceptable that this platform has previously been widely used, in today's context of high-throughput, deep NGS sequencing, and with the availability of many datasets from RNA-seq projects, it seems a bit outdated to use Chip data, the most latest of which is 5 years old. Perhaps the authors can throw more light on their choice of platform?

Line 94-96: Was the selection of the verification dataset done at random, or was there any reason behind the choice?

Fig. 1 can be amended to include information about the downloaded MCF-7 dataset.
Validity of the findings: The authors have used data from multiple datasets available publicly, to identify a set of genes, which were further compared against public databases/tools to assess their role as a potential target using available drugs. However, the manuscript has not been written in a concise and clear manner, thereby casting apprehensions over the validity of these results at many junctures. The work would greatly benefit from being re-written with a more simplified approach.
Additional comments: This work by Hao and colleagues titled "Identification of hub genes and screening of small molecule therapeutic drugs for breast cancer based on comprehensive bioinformatics analysis" explores published datasets for genes that can be used as targets for drugs and other sources from traditional Chinese medicine. The manuscript has many errors in different sections and would greatly benefit from being edited by a native speaker or by a professional language editor.


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

Input:
Title: IDENTIFICATION OF HUB GENES AND SMALL MOLECULE THERAPEUTIC DRUGS RELATED TO BREAST CANCER WITH COMPREHENSIVE BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed this reviewers comments and I would recommend to accept 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: CLOSTRIDIOIDES DIFFICILE INFECTION AFTER CARDIAC SURGERY: ASSESSMENT OF PREVALENCE, RISK FACTORS AND CLINICAL OUTCOMES—RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: the paper is written clearly and convey a clear and well-structured message
Experimental design: no comment
Validity of the findings: 204/5000
the paper analyzes an interesting link between a key population such as patients undergoing cardiac surgery
Indeed cardiac diseases such as diabetes are major risk factors for CDI
Additional comments: The paper is remarkable because showed Clostridium infection complication in a peculiar surgical key population as cardiac surgery
The link between seasonal and antibiotic use in CDI was reported by other authors and there re evidence in the geographical area of Poland (Jachowicz, E.; Wałaszek, M.; Sulimka, G.; Maciejczak, A.; Zieńczuk, W.; Kołodziej, D.; Karaś, J.; Pobiega, M.; Wójkowska-Mach, J. Long-Term Antibiotic Prophylaxis in Urology and High Incidence of Clostridioides difficile Infections in Surgical Adult Patients. Microorganisms 2020, 8, 810.)
Please comment these findings take in account the use of third-generation cephalosporins and Fluoroquinolones reported in table 3.
Globally, guidelines and papers confirm that metronidazole has a lower efficacy compared with vancomycin and support the use of vancomycin over metronidazole in C difficile infection. To optimize vancomycin treatment evaluated in recurrent C difficile infection, it might be possible to use a pulsed or tapered regimen of vancomycin.( Guery Benoit, Galperine Tatiana, Barbut Frédéric. Clostridioides difficile: diagnosis and treatments BMJ 2019; 366 :l4609)
Please, comment why the treatment with metronidazole is over vancomycin in the 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: CLOSTRIDIOIDES DIFFICILE INFECTION AFTER CARDIAC SURGERY: ASSESSMENT OF PREVALENCE, RISK FACTORS AND CLINICAL OUTCOMES—RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is clear and unambiguous.
The article include sufficient introduction and background.
The references were appropriately cited
Experimental design: Original primary research within Aims and Scope of the journal.
The submission clearly define the research question.
The investigation has been conducted rigorously and to a high technical standard.
The research must has been conducted in conformity with the prevailing ethical standards in the field.
Methods are described with sufficient information to be reproducible by another investigator.
Validity of the findings: The statistical results should be improved.
The conclusions are appropriately stated,.
Additional comments: The study evaluated the course of CDI in patients after cardiac surgery.

Major concern
In this study additional statistical analyses should be performed to improvement the quality of the paper.

Comments
1)	To facilitate the reading of the Tables with statistical tests, the authors should write in bold the significant p-values and in brackets the type of test used (for example (C) in the case of chi-square test)
2)	Lines 112-113: “There was no correlation between gender and incidence of CDI (P = 0.595)”
The authors describe only some no significant results, but they do not describe all no significant results. Please, check it
3)	Lines 118: the authors claim to consider all tests with p <0.05 as significant, but the history of malignant neoplasms has a p=0.05. Please, check it.
4)	I suggest that authors use additional tests for parameters where a normal range is defined (Table 1, 2, and 4). In particular they should compare the percentages of patients with abnormal values (for example for BMI, Platelets, WBC, etc) . These tests could provide important information that may not emerge from the comparison between medians or means
5)	In Table 2 the authors should also compare the subcategories of Type of surgery.
6)	Line 128: “of cases were found in January (n=2, 3%), (P = 0.038 between March and rest of the months).
Which test is used by the authors? If a multiple-comparison chi-square test was used,   which post hoc test was used to find the most frequent proportion?


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: CORAL REEFS AS A SOURCE OF CLIMATE-ACTIVE AEROSOLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The review sums up what is known about potential links between DMSP production by coral, aerosol production via nss sulfate oxidation, low level clouds, SST, irradiance, and coral response. Although all of these links are highly uncertain, the authors are able to pull information from enough studies together to create different scenarios based on potential responses of coral to stressors. One concern is the likening of the coral reef – aerosol – climate system to the CLAW hypothesis throughout the paper. If the CLAW hypothesis is to be invoked, evidence against it should also be mentioned including the disconnect between a given coral reef and feedbacks on local climate due to long range transport of sulfate and the time it takes from production of DMSP to the production of nss sulfate and formation of CCN. An additional disconnect is hinted at it Figure 1 – emission of DMS to the marine boundary layer but production of new particles in the free troposphere. This is not to say that coral reefs do not have an impact on climate but rather that a local climate bio-feedback regulation mechanism as suggested by CLAW is unlikely.

Lines 134 – 135: Organo-halogens likely only contribute to new particle formation in coastal regions like Mace Head (e.g., McFiggans, Nature, 433, https://doi.org/10.1038/nature03372, 2005).
	Also – please be more specific on “other organic compounds”? What organic compounds other than DMS are of sufficient concentration in the marine atmosphere to be a significant contributor to the particle or CCN number concentration? And does this statement relate to all open ocean regions or only coral reef regions?

Lines 136 – 137: Please explain what is meant by “until recently”. What newly identified sources of MBA have been reported?

Line 229: Should be “…although ocean temperatures NORTHEAST OF Australia…”

It appears that the Jackson et al. 2018a and 2018b papers are the same paper.

Table 1: It is interesting that of the coral reef regions listed, only the GBR stands out with maximum atmospheric DMS concentrations higher than non-coral reef regions. Is this a function of the expanse of GBR?

Future directions: Many of the papers cited are based on modeling studies yet modeling is not discussed in this section. A paragraph on how to best to model this complicated system to predict coral response to stressors would be an important addition.


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: CORAL REEFS AS A SOURCE OF CLIMATE-ACTIVE AEROSOLS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In “Coral reefs as a source of climate-active aerosols” Jackson, Gabric and Cropp review the impact of coral reefs on local climate through stress induced emissions of aerosol forming precursors.
The review discusses a very interesting topic at the interface of coral reefs as threatened ecosystems and the response of biological changes inside this system that might influences climate through secondary aerosols.
I assume this topic will be very interesting both for coral reef ecologist as well as climate and atmospheric scientist. However, there are several points the author might want to address before the review can be published.

Line 31: Sounds odd. Services to whom? Maybe specify.
Line 39: “and” sounds repetitive. Consider rephrasing this sentence.
Line 43: is this information about alternate states necessary?
Line 72: Maybe specific whether these are secondary aerosols.
Line 108: Its great that the authors provide their literature search methods. Where the here described search terms the only search input? Maybe the Search Term “coral AND aerosol” would have been useful as well. To provide the reader an overview of the efficiency of the search terms maybe the authors could provide the number of hits for the different terms.
Line 122: Consider revising the last sentence about enhancement of the cooling effect of aerosols. According to IPCC Fifth Assessment Report (2013), “earlier assessments considered the radiative implications of aerosol-cloud interactions as two complementary processes—albedo and cloud lifetime effects—that together amplify forcing”, as the authors imply from line 122 to 124. “However, compensating adjustments have been identified that make the system less susceptible to perturbation than might have been expected based on the earlier albedo and lifetime effects. Increases in the aerosol can therefore result in either an increase or a decrease in aerosol–cloud-related forcing depending on the particular environmental conditions.”
Line 135: Maybe expand a little on primary aerosols here. How are they generated and how relevant is this in coral reefs?
Line 182: IS there a study supporting the claim of oxidative stress protection?
Line 272-273: marine biogenic aerosol and continental aerosols come from different sources and have different composition and properties. Consider rephrasing.
Line 278: stress may not be the only cause of DMS emissions. Could differences in primary productivity be a more plausible cause for the seasonal shifts?
Line 287: the previous paragraph indicates that the northern GBR sees the highest aerosol concentration in winter. This sentence seems to disagree with that assumption. The authors may want to distinguish between nucleation events with total aerosol emissions as these processes might not be coupled.
Line 365: Are MBA the only contributors to aerosol optical depth? Even if the link between DMS and aerosol production is sustained, corals are not the only source of DMS. The conclusion in line 368 needs more evidence.
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: CORAL REEFS AS A SOURCE OF CLIMATE-ACTIVE AEROSOLS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is written in clear and unambiguous, professional English throughout.
Literature references, sufficient field background/context provided.
The structure of the article is appropriate for a literature review.
Two of the Figures are relevant to the content of the article, and are appropriately described and labeled. The third Figure is not informative but illustrative of the diversity of coral reefs. I would keep it.
There are not raw data to share.

The review is of broad and cross-disciplinary interest and within the scope of the journal.

To my knowledge, the field of coral reef-aerosol-cloud interactions has not been reviewed recently. The review is interesting and timely.

The Introduction is clear and comprehensive, it adequately introduces the subject and makes it clear what the motivation is.
Experimental design: The article content is within the Aims and Scope of the journal.

In my opinion, a rigorous literature search have been performed.

References are relevant and unbiased. Sources are adequately cited.

With a few exceptions (see the general comments to the authors), the review is organized logically into coherent paragraphs and subsections.
Validity of the findings: The observations and arguments reviewed address the major questions posed in the Introduction.

The Conclusions summarize the main points of the manuscript, yet they are a bit disappointing because they essentially consist of a list of unknowns and uncertainties. Honest enough, though. There is a section named Future directions, which is meant to outline where to move towards, although it makes the case for the importance of pursuing this research more than giving concrete directions.
Additional comments: The manuscript reviews current knowledge of the production of aerosol precursors by coral reefs, and their potential to affect the regional radiative budget and alleviate the physiological stress of temperature and solar radiation on corals. The topic is timely because coral reefs are amongst the most diverse ecosystems on Earth, and ones that provide invaluable ecosystem services. There is strong evidence that they are suffering losses and transformations due to global warming, eutrophication and other severe environmental stressors. Understanding how coral reefs cope with stressors is of crucial importance to anticipate their evolution and design conservation policies. The review addresses an atypical and speculative mechanism (I would name it “emergent mechanism” because it involves several environmental compartments with distant connection and unlikely or indirect evolutionary drivers): coral reefs are strong emitters of aerosol-forming substances, mainly DMS, which enhance the formation, lifetime and albedo of low stratiform clouds, hence reducing the solar irradiance on the reef.

The authors mostly focus on the Great Barrier Reefs (GBR) essentially because most relevant data come from these reefs. But, in my opinion, there is another reason: if the proposed mechanism occurs, it is most relevant to the GBR, because it is vast enough for local emissions to see a local effect on clouds. In smaller reefs, any effect on clouds will occur hundreds of km downwind, making very unlikely that these effects will feed back on the emitting ecosystem. As a matter of fact, even the relevance for the GBR must be demonstrated. In my opinion the authors make a strong case that small aerosol numbers, and low-level cloud cover, are enhanced over the GBR. However, some reference is missing on reaction and transport times to support the feedback hypothesis. Lifetime to oxidation of a major aerosol precursor, DMS, in the atmosphere is in the order of 0.5-1 days. What are tyipical transport velocities? Is it feasible that DMS oxidation to sulfuric acid plus nucleation plus growth plus activation as CCN all occur in the air mass still over the GBR?

Specific comments:

I like the introduction, it is succinct but comprehensive enough to set the stage.

L228: Similar tot what? I guess you mean similar to WPWP, but this was two sentences before.

You repeat several times that Acropora spp are the dominant reef-forming corals.

Even though the point is well made that aerosol numbers are enhanced over the GBR with respect to the open ocean, could this also be contributed by increased sea-spray production in the surf zone (I mean, by wave formation and water splashes to the reef)?

L340: exceeds (s missing)

L337-351-368: I think the wording is a bit confusing, and it is not clear under what conditions DMS emissions are maximal. Acclimation to increasing thermal stress favours DMS emission, but severe stress suppresses it. It is better explained further on, but a better organization of the sentences would be appreciated.

You talk about MBA all the time, and sometimes develop them as “DMS and other volatiles”, but you actually focus on DMS. No hint is provided as to what other MBA precursors could be. Is there evidence of any remarkable emission of other MBA?

L390-397: Not clear to me if you buy Green’s arguments. Will the replacement of corals by fleshy algae result in similar/increased/reduced DMS emissions?

L424-426: Rewrite sentence – both what?

Figure 1: how do you connect DMSO to DMS (this way) through photo reactions?
Is DMSP not released by corals? Only through grazing on phytoplankton? Only DMS and DMSO are realeased by corals? It is not totally clear from the photo-diagram who does what. Grazing on phytoplankton is next to the arrow that originates in the coral.

Figure 2: In my opinion, the arrow from nucleated nss-sulfate should connect to marine aerosol, not to CCN. That is: marine aerosol can originate either from (a) condensational growth of pre-existing particles (by pre-existing I mean transported into the reef MBL from elsewhere, or locally emitted as primary aerosol), or (b) nucleation of sulfuric acid and further growth (either in the MBL or by entrainment from the FT). Then, part of the marine aerosol will activate as CCN.


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: CORAL REEFS AS A SOURCE OF CLIMATE-ACTIVE AEROSOLS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have adequately addressed the reviewer 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: CORAL REEFS AS A SOURCE OF CLIMATE-ACTIVE AEROSOLS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors adressed most of my comments, although many of the responses seem a littel spares. Mayeb reconsdier the influience of primary SSA, that are also formed through breaking waves in the surf zone.
Experimental design: NA
Validity of the findings: NA
Additional comments: NA


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

Input:
Title: CORAL REEFS AS A SOURCE OF CLIMATE-ACTIVE AEROSOLS
Review round: 2
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: You have adequately addressed my comments and concerns as well as those from the other reviewers.

However, the figures still contain some flaws:

Fig 1 - DMSO is not converted into DMS by photolysis. To my knowledge, this can occur in aqueous medium in the presence of some photosentitizers, but has not been shown in seawater. Rather, DMSO undergoes microbial reduction to DMS (Griebler & Spezak 2000, https://doi.org/10.1080/03680770.1998.11901690; Asher et al. 2017,  https://doi.org/10.1002/2016JC012465). Therefore, photolysis should be replaced with microbial reduction.

Fig 1 - An arrow should connect free-living algae to DMS, since not all phytoplankton DMS production occurs through dissolved DMSP upon senescence or grazing, but quite a proportion of the DMS is released or leaked by microalgae, most likely under stress.

Fig 2 - Atmospheric reactions as depicted are a bit misleading. I know it would be impossible (or beyond the scope of this paper) to draw a simple diagram with all the pathways and processes. But the drawing seems to imply that H2SO4 is the species transported to the FT, and it is not shown what happens up there. A number of papers suggest that part of the DMS makes it to the FT, where it is oxidised to H2SO4, which, due to the low condesational sink, nucleates to form new particles that can partly entrain into the MBL. Suggestion: you could delete the arrow from H2SO4 to the FT but send a parallel arrow from DMS to the FT (labeled vertical transfer), then simply write "oxidation and nucleation" up there, and connect it to the entrainment. I think this would be fair enough.


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

Input:
Title: THE MECHANISM OF THE PLANT ROOTS’ SOIL-REINFORCEMENT BASED ON GENERALIZED EQUIVALENT CONFINING PRESSURE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors present an experimental investigation of the mechanical effect of a root system on the shear strength of a particular type of soil. They vary root content, root placement (vertical, horizontal, mixed), confining pressure and testing conditions. The paper is overall suitable for publication in PeerJ with significant results. The presentation is globally correct, sometimes a bit rough and difficult to understand. It would have been good to provide at least one image of the samples. The results are given in terms of a Table and several plots, and discussed in full detail later. The concept of generalized effective pressure is used to quantify the effects of roots. I understand this by stating that part of the confining load is transferred to the root system. The "geometrical cohesion" induced by the roots, provides an equivalent description.
Experimental design: The experimental design is based on classical testing. The sample preparation is well-explained.
Validity of the findings: The discussion of the results is well conducted. I believe it would have been more elegant to discuss the results as they are presented. But this is a question of style. I think this work provides new insights about the effect of roots on the shear strength of soils and merits publication.
Additional comments: I have a number of suggestions below, which the authors may use to improve the paper.

lines 18-19 : I do not understand this sentence : …the generalized equivalent confining pressure (GECP), which was equivalent to confining pressure,…

The abstract should provide a clear statement about the content without referring to the definitions of terms like GECP. This term is also used in lines 34-36 to conclude that this is a convenient quantity while the reader has no idea of what it is. Please define it in the abstract.

Lines 58-59 : What is c ? I do not understand this sentence.

Lines 65-67: Please explain what are the numbers 0.34-0.50. The sentence is not clear.

Line 70: « Shallow landslides are highly consistent with rainfall » What does it mean?

Lines 159-160: The sentence is quite unclear.

Line 162: Where does this equation come from? Why square-root of K_p?

Line 171: Equation (5) is simply the same as equation (2) in which a cohesive strength (equal to 2c sqrt(K_p)) has been added to the failure axial stress.

Figure 4: Please give more details in the caption of the figure. What does 50-0.25% means in the figure. The quality of the figures are quite low.

Line 255: Please provide a brief presentation of the Wu-Waldron model.

Line 312: What is meant by « the value phi is trivial »?

Lines 325-326: What is meant by « A decrease in the soil particle gap is more conducive to making plant roots interlock with soil particles »?

Lines 332-334: I do not understand why fewer plant roots enhance the water transport and the lubrication of the soil-root. I would expect exactly the inverse.

Line 346: « evaluate » is repeated two times.


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

Input:
Title: THE MECHANISM OF THE PLANT ROOTS’ SOIL-REINFORCEMENT BASED ON GENERALIZED EQUIVALENT CONFINING PRESSURE
Review round: 2
Reviewer: 2

Output:
Basic reporting: Line 62, missing some background sentences explaining the Wu-Waldron model, is this a standard model in this field?

Line 69, I found the problem statement was not very obvious for this paragraph. So if the Wu-Waldron model is not accurate, what are the missing pieces? how your study will help fill in the gap?

Line 70, "Shallow landslides are highly consistent with rainfall"? I don't understand this sentence. Do you mean shallow landslides are more common in areas receiving great precipitation? And this correlation cannot be the reason of rainfall being the major cause of slope instability. Soil characteristics (e.g., texture) can be another dominant reason.

Line 70-76, I found the importance of this paragraph was not obvious. Delete it?

Line 77, there are lots of variables can influence the soil shear strength other than these three, for example, soil texture. It was not clear that why picking these three.

Line 85, no need to have details of different levels of root contents.

Line 93, "a pH of 6.2".

Figure 1, Complex roots, I thought the ratio of horizontal to vertical was 1/2, however, this diagram was 2/1.

All font size in Figure 3-5 and Table 1-2 should be increased.
Experimental design: Line 127, I suggested authors add sentences/background to explain why choosing these three patterns of root distribution. Normally plants grow vertical roots, but I guess horizontal roots will be more common on the slope. And why the ratio of horizontal to vertical was set to be 1/2 for the Combined form?

The Method missing a section of Data analyses (methods to analyze the data, ANOVA? and in what statistical program).
Validity of the findings: Throughout the Result section, p values need to insert next to each sentence describing the significant differences. There was only one place (line 227) showing the p value, but if this was a correlation test, both p value and r value should be displayed.

Line 182, what is the "Mohr-Coulomb failure criterion"? I feel this term or analysis should be addressed in the Method section, the missing data analyses part.

Line 181, 201, 216, 226, honestly, I don't like the format of starting the first sentence (topic sentence) with Table 1 or Figure 1 showing what variables...I prefer to start a sentence summarizing the main results/effects and put the corresponding tables or figures in the parenthesis next to this sentence. The table or the figure should not be the subject, it is the main result.

Line 194, was this decrease significant? better to apply a statistical test, ANOVA or regression

Line 199, 214, 224, was there a correlation test? or just ANOVA? Because when authors used the word of "relationship" in the subheadings, readers expected to see a correlation. Or just use "GECP varied by drainage condition..", something like that.

Line 239-254, when authors discussed/explained their findings, better to put the corresponding tables/figures in the sentence, so readers know which statement was from this study and which statement was a conclusion from the literature. For example, Line 252, "the root content to soil mass ratio is small in the soil-root composite...", I believed this was a finding from this study, authors can insert (Figure X) next to it.

Line 266, confused sentence: "When root content is relatively low and increases..."?

Line 283, was this very common in the field? because plants can extend their horizontal roots to overlap with the vertical roots of their nearby plants.

Line 330, this topic sentence reads like a Result, please rewrite.

Line 354, this sentence was very similar to the sentence in line 330, please rewrite. And the following sentence is vague "Some assumptions are given to explain this phenomenon, but more research is needed to find the cause". This sentence is saying nothing! Please detail the assumption and limitations. The "Conclusion" section should include some highlights to advance this field, not just saying more research is needed...
Additional comments: This study examined the generalized equivalent conﬁning pressure under different drainage conditions and root distribution and contents for silt loam soils rooted by Indigofera amblyantha. This manuscript missing some background information in the Introduction and data analyses in the Method. The importance of this study to the literature and the key take-home message should be more clear throughout the manuscript. Please see my comments above.


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

Input:
Title: THE MECHANISM OF THE PLANT ROOTS’ SOIL-REINFORCEMENT BASED ON GENERALIZED EQUIVALENT CONFINING PRESSURE
Review round: 3
Reviewer: 1

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: First I would like to thank authors for their efforts in revising this manuscript. The structure and the problem (knowledge gap) setting in the Introduction are improved a lot. I only have one minor opinion regarding the "Data analyses" section in line 204. The current description is too simple, the performed tests (e.g., ANOVA? t-test?) should be detailed in here.


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: LOSS OF INNER KINETOCHORE GENES IS ASSOCIATED WITH THE TRANSITION TO AN UNCONVENTIONAL POINT CENTROMERE IN BUDDING YEAST
Review round: 1
Reviewer: 1

Output:
Basic reporting: The text is clear and unambiguous, but I recommend using the “CENP” nomenclature for proteins as well as the standard yeast names where possible. Text is unnecessarily long in places (see comments).

References are sufficient.

Article structure is OK. Figure quality is rather poor. Fig 2 is badly designed. Fig 3B is difficult to read. There is an error in Fig 1. See comments.

Self-contained. Hypothesis and results.
Experimental design: All items are OK. Need more details about how dyad density was calculated (Fig 4).
Validity of the findings: All OK.
Additional comments: This is an interesting manuscript. Previous work by Kobayashi et al (2015) found that, uniquely among the budding yeasts, two species in the genus Naumovozyma have point centromeres that deviate strongly from the standard point centromere consensus sequence established for Saccharomyces cerevisiae (with CDE I-II-III regions). Kobayashi et al also found that, in Naumovozyma, the locations of the centromeres on the chromsomes have changed. This led them to propose that in Naumovozyma, the new type of point centromeres displaced the old type (as opposed to a model where the old type gradually evolved into the new type). In the current manuscript, Vijay shows that 4 proteins in the inner kinetochore, which are usually quite well conserved, have been completely lost in Naumovozyma species. He speculates that these gene losses were either a cause or a consequence of the displacement of the point centromeres.

The methods used in the analysis are simple. Vijay used the YGOB comparative genomics browser to examine the locations and synteny of 68 kinetochore genes, and looked for species that have no homolog of each gene. He found that 4 inner kinetochore genes, IML3, CHL4, NKP1 and NKP2 are missing in two Naumovozyma species, and that 2 other genes CNN1 and WIP1 are missing in some other yeast species. IML3 and CHL4 interact with the centromeric histone-like protein CSE4 (a.k.a. CENP-A or CenH3) via the N-terminus of Cse4, and Vijay shows that the N-terminus in Naumovozyma is unusually long, indicating that it may have coevolved with the loss of the two proteins. He also shows that the new centromere sites in Naumovozyma have different properties than the previous centromere sites: they are more AT-rich and they have more dyad symmetry.

Overall, this manuscript contributes some useful insight into the change in centromere structure that occurred in Naumovozyma. In general, the conclusions are justified by the data.

Major comments

The Introduction section needs to provide a better introduction to the structure of the kinetochore for non-specialists. At the moment, it gives almost no background information at all. The nomenclature of kinetochore genes is complicated, because there are 70-80 proteins, in different (sub)complexes, and species-specific names are used in many organisms. The “CENP-” nomenclature system is an attempt to use standard names across multiple species (e.g. van Hooff et al 2017) and is widely used, but Vijay does not use it in this manuscript. I had to manually look up the facts that Iml3 is Cenp-L, Chl4 is Cenp-N, Cnn1 is Cenp-T and Wip1 is Cenp-W, so that I could then relate these proteins to the kinetochore structure figure in van Hooff et al (2017). Similarly, the names of complexes differ between species, for example I am not sure if CCAN means the same thing as Ctf19-associated complex.

NKP1 and NKP2 do not appear in van Hooff et al (2017) so the manuscript needs to explain where they fit into the structure of the kinetochore. The current text merely says that they “localize to kinetochores” (line 142). Is there evidence that they interact directly with CENP-A, L and N (which interact with each other)?  If not, what part of the kinetochore do they interact with?

The Abstract should name the genes that are the focus of this paper: NKP1, NKP2, IML3, CHL4.

The text is too long in several places. Lines 194-213 contain a lot of discussion about genes that are in 2 or 1 copy in post-WGD species, but it seems to be inconclusive and only peripherally related to the main point of the manuscript which is gene losses.

Minor comments

Throughout the text, the author uses the word “intron” where he means “intergenic DNA”.

Results lines 135-137: It would be simpler to say that a group of 5 genes (name them) is lost in both pre-WGD and post-WGD species, with additional losses of 2 genes (name them) in pre-WGD species and 3 genes (name them) in post-WGD species.
Results line 139: Please explain why you only discuss 6 of the 8 genes that were lost in post-WGD species.

In Figure 1, I think that “Saccharomycetales” is a typo for “Saccharomyces”. But the topology of the tree is also incorrect. Naumovozyma and  Kazachstania are sister genera, with Saccharomyces outside them.

Figure 2 and Supplementary Table 1 are difficult to read and understand. The author has simply downloaded the data file from the YGOB database, imported it into Excel, and colored some cells. For Figure 2, it must be possible to present the data in a clearer way (it is not necessary to show the gene names for each species). For Supplementary Table 1, most readers won’t know what they are looking at, and I don’t know why BIR1 and FIN1 were included.

Figure 3 highlights the unusual evolution of the N-terminus of Cse4. If it evolved under selection to compensate for the loss of the 4 inner kinetochore proteins, it could show evidence of positive selection on the sequence, which could be detected by using a program such as PAML. Did you investigate this?

In Figure 4, how was “dyad density” calculated, and what exactly does this term mean? I presume that It means inverted repeats, but what is the smallest size of dyad permitted? The Methods section does not say how it was calculated.


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: LOSS OF INNER KINETOCHORE GENES IS ASSOCIATED WITH THE TRANSITION TO AN UNCONVENTIONAL POINT CENTROMERE IN BUDDING YEAST
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall the manuscript is of an acceptable standard. Points that could be improved are listed below:

- the word 'gene' is repeatedly used interchangeably with 'the gene's product', i.e. the encoded protein. For example lines 255-256: "... the genes that recognise and bind to centromeres...", and lines 41-42: "Kinetochore genes that form protein complexes...". This is scientifically incorrect, and should be amended.

- line 133 states that "eight Pre-WGD and twelve Post-WGD yeast species" were used for the analysis and that these are shown in Figure 1. However, the figure only lists a total of 14 species. In addition, the scale bar in Figure 1 labeled '20' is missing a unit, and the author needs to reference the source of the phylogenetic tree, or name the program and settings that were used to generate it.

- Figure 2 is too small to read. In addition, it would greatly benefit from clarifying the illustrated information. For example, the author could transpose the rows and columns, such that each gene of interest is given a column, and each species a row. The species could be grouped into pre- and post-WGD.

- Figure 4: the figure is very small, which could be mediated by making square rather than rectangular (i.e. stretch the y-axis). In addition the colours are to similar to distinguish between the groups (particularly comparing blue and black, or orange and brown). Also, the four CEN that only have (partially) inferred sequences should not be included in the analysis.

- The author might want to consider the order and / or headings for his results section. The paragraphs between lines 190 - 239 are under the heading N-terminal divergence of CSE4, and yet this protein is not mentioned once in these lines. Rather, at least some of these paragraphs would be better placed under the first results heading "patterns of kinetochore gene loss". Alternatively, additional heading(s) could be introduced to more accurately reflect the results that are described.

- lines 226-227: "... we are able to understand some of the variance seen in dyad density across budding yeast species". Based on the information provided, it is not clear how our understanding of the variance has improved. I suggest the author either clarifies this by clearly stating the insights that have been gained, or the author removes this statement.

- the manuscripts lists only a single author, and yet the manuscript consistently states "we". Unless additional authors are listed, I suggest replacing "we" with "I"

- I recommend using the past tense throughout the manuscript. In it's current state, the manuscript frequently uses the present tense, for example line 46 "Another unexpected observation is ...".

- line 41, the author quotes the kinetochore machinery to be a "Ship of Theseus". This is not a frequently used phrase and thus it's meaning unclear. I suggest either removing the phrase, or providing a meaning.

- the author refers to the 'origin' of point centromeres on lines 28, 29, 63, 91, 277, 285, 338 and 483. I would suggest to use the term 'emergence' rather than origin, which usually refers to a starting point.

- lines 177 (2x), 181, 183: the N- or C-terminal region of a protein is called N/C-terminus (i.e. the noun to terminal is terminus).

- line 220: the author refers to 'sensu lato' and 'sensu stricto' yeasts, but does not provide a definition. I suggest adding these labels to Figure 1, so as to clarify their meaning.

- line 143: "... proteins [...] produce viable single gene mutants...". This sentence should be clarified to state that "when deleted" the proteins produce mutants.
Experimental design: The methods section does not provide sufficient information that would allow readers to recreate the analysis.  The author should specify how the checks for ORFs was performed and how the lack of homology was determined (lines 107 - 109). Importantly, the specific settings used for the multiple sequence alignments (listed on line 116) need to be provided.

Further minor suggestions are:

- line 98: include the actual GO term that was included, i.e. 'kinetochore', not just the associated number
- line 102: I suggest removing "Despite our precautions" as it is unclear what the author is referring to.
Validity of the findings: - lines 233 and 236: The author claims that there is a lower GC content in the new CEN in N. castellii. However, this is not apparent in figure 4. Instead the GC content appears comparable. The authors should determine the mean and median (including standard deviations) to support their statements. In addition, it would b greatly beneficial to include the genome-average mean and standard deviations for the GC content.

- The discussion and conclusion focus in particular on gene flow and speciation. However, the introduction is focussed on the CEN and kinetochore - gene flow is not mention, and the term 'speciation' occurs only ones in the introduction. The author could consider to adjust the emphases.

- lines 304 - 310: This discussion paragraph describes an analysis that was performed and as such should be relocated to the results section.
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: NO ONE-SIZE-FITS-ALL SOLUTION TO CLEAN GBIF
Review round: 1
Reviewer: 1

Output:
Basic reporting: L36-37: Suggest add a citation in "Here, we evaluate the effect of 13 recently proposed filters on the inference of species"
Experimental design: L102: Please clarify why you did not choose to add filters when accessing data from GBIF. In particular "hasGeospatialIssue", a subset of basis of record, and a year range would have removed records before downloading impacting the % results. The equal lat/lng and zero tests are carried out in GBIF.org processing.

L106: Please clarify what you mean by "raw". The GBIF downloads include verbatim data as provided by the institutions and interpreted data but it is unclear which were used.

L294-328: All citations are incorrect in lines 294-328 with a typing error (doi.org repeated twice).
Validity of the findings: L192: Recommend add a fourth reason that the data are shared through multiple databases - e.g. BOLD or Plazi may publish the same data as the institution
Additional comments: This is nicely written with clear accessible language.

I would like to see mention of data cleaning performed in GBIF.org before downloading (zero's, lat/lng test) which were seemingly overlooked, allowing you to emphasize the importance of the other aspects, such as country centroids which GBIF doesn't test for today.

You may refer to the country centroid blog (https://data-blog.gbif.org/post/country-centroids) and the gridded data blog (https://data-blog.gbif.org/post/gridded-datasets-update/) noting that GBIF intends to include automated tests to detect those issues.


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: NO ONE-SIZE-FITS-ALL SOLUTION TO CLEAN GBIF
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is quite clean and readable, and I very much enjoyed reading it. There were a couple of English gaffs in it, but really very few, so I have no complaints at all in terms of basic reporting.

"We downloaded only records with geographic coordinates and limited the study area to latitudes smaller than 33◦ N and longitudes smaller than 35◦ W and larger than 120◦ 101 W reflecting the Neotropics" ... this is a little convoluted.

"as this represent the grain size of many macro-ecological analyses" ... should be representS"

The maps have a too-bold and too-black coastal outline, and need country boundaries.

The lit cited is not pretty
Experimental design: I appreciated the explicit reporting of study findings. The methods were clear, based on tools that are in the public domain, and as such the study appears to be robust and repeatable. Indeed, I also very much liked the "community effort" feel of this manuscript, in that it was a combination of taxonomic experts with analytical specialists. Very nice contribution.
Validity of the findings: I am convinced that the findings reported are robust. My only set of concerns with the manuscript is as regards the depth to which the data cleaning approaches were implemented. That is to say, the authors implemented a very basic set of tools, but I did not see a next level of tools, in which one would seek intrinsic and extrinsic consistency in data records. For instance, for each group, are there synonyms represented among the names, and do the names match consistently to one authority list. Or for geographic referencing, do the coordinates reported fall within the administrative boundaries of the higher-level areas reported (e.g., states, countries). These ideas of intrinsic and extrinsic consistency lend considerable additional support to a data record, and can be implemented rather easily in R. This does not necessarily need to be added, but could be mentioned as next possible steps.

My apologies for the self-promotion, but a paper in which I was involved might be relevant to this analysis also ... Peterson, A. T., A. Asase, D. A. L. Canhos, S. de Sousa, and J. Wieczorek. 2018. Data leakage and loss in biodiversity informatics. Biodiversity data journal 6:e26826.
Additional comments: In general, a nice contribution! All the best, Town Peterson


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: NO ONE-SIZE-FITS-ALL SOLUTION TO CLEAN GBIF
Review round: 1
Reviewer: 3

Output:
Basic reporting: This manuscript reports on a workshop where the participants evaluated issues with the quality of data obtained from GBIF, relative to their own taxonomic expertise. The report reads well. I have some minor suggestions.

Great to see the GBIF downloads cited with DOIs. However the URLs are incorrect ("doi.org" is duplicated). It would be helpful if each one was labelled by the corresponding taxon name. I found it frustrating having to try several times before I go specific taxa I was interested in.

Table 1 could be made more visually interesting by inserting images of the taxa at the start (e.g., from http://phylopic.org). Fig. 1 shows nice example of the taxa, but this is disconnected from the data presentation.
Experimental design: See below under comments on "Validity of the findings"
Validity of the findings: My overall sense is that the authors somewhat overstate their conclusions. The headline (line 38) of “29-90% of records are potentially erroneous” gets rolled back in the body of the manuscript. As they note later in the article (line 192) “Duplicated records do not represent errors *per se*”. Indeed, they are standard practise in botanical collections. The “basis of record” test doesn’t handle DNA sequence-based records (e.g., from DNA barcoding) which are typically recorded as “MATERIAL SAMPLE” (e.g., numerous records for the Entomobryidae). Issues with sea versus land (e.g., Diogenidae) seem in part to be due to coarse georeferencing taking a locality as being terrestrial rather than costal. For example, GBIF occurrence https://www.gbif.org/occurrence/699114012 comes from the MCZ (https://mczbase.mcz.harvard.edu/guid/MCZ:IZ:CRU-12772) and is a record from the Thayer Expedition to Brazil (see http://biostor.org/reference/4104) from “Victoria”. I suspect this is actually “Vitória, Espírito Santo”, a city on the coast of Brazil visited by that expedition.

Hence I suggest that what we have is a series of idiosyncratic data handling issues across a range of datasets. It’s not clear to me that these are errors. Indeed, the fact that these issues made little difference to the how well the automated assessments matched those by the IUCN could be taken as evidence that those methods are robust to these “errors”. Perhaps the conclusions are really that each taxon and datasets may be subject to various (sometimes taxon or data specific) issues, but these don’t have a major impact on their utility.
Additional comments: As I note in the section "Validity of the findings" I'm not convinced that many of the issues are, indeed, "errors". There are some taxon-specific practices (e.g., duplicates in botany), some egregious data handling issues (e.g., the date range for the snake specimens), and flagging DNA barcoding records on a "basis of record" term that seems perfectly valid. There's not much evidence that these "errors" actually impact the utility of the data in this case.

Ultimately I think the more interesting topic is where do these data issues come from, and how do we fix them so that future researchers benefit from data where these problems have been removed.


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: NO ONE-SIZE-FITS-ALL SOLUTION TO CLEAN GBIF
Review round: 2
Reviewer: 1

Output:
Basic reporting: Acceptable.
Experimental design: Acceptable.
Validity of the findings: Acceptable.
Additional comments: I liked this manuscript from the outset, and the authors responded appropriately with revisions to meet my requests in my first review. My only remaining concern is in regard to the comment about further data-cleaning efforts that could be implemented and that should be mentioned. The authors responded to the *extrinsic* point (e.g., comparisons of data from GBIF with extrinsic range map summaries. They did not, however, respond to my suggestions of using *intrinsic* consistency as a further filter of data quality. For instance, one can compare the administrative unit in which the geographic coordinates associated with the data record fall with the administrative unit given as the country, state, or county in the data record. This consistency can be a useful corroboration of the geographic referencing... and such consistency assessments can be extremely useful in detecting data problems. So it is not all extrinsic, as the authors interpreted, but there are also intrinsic dimensions in which their assessments of data quality could be expanded. Other than that--i.e., simply mentioning these possibilities among future thoughts and possible avenues--I am quite happy with this manuscript. Town Peterson


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: NO ONE-SIZE-FITS-ALL SOLUTION TO CLEAN GBIF
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I'm happy with the changes made, this is an interesting manuscript.

I have one minor quibble. In Table 1 on p. 7 the caption says "Pictures from www.phylopic.org, in the public domain." This is not the case, or at least, not for the one image I checked. The hermit crab image http://phylopic.org/image/6b0a5129-4184-46ca-a7b8-e38838e12194/ is CC-NC-SA which requires attribution - "You must give credit to Ekaterina Kopeykina (vectorized by T. Michael Keesey)". I suspect that others will have their own licences. Creative Commons is NOT public domain. I can imagine the authors frustration that having recommended phylopic I'm now criticising the way they've used it, and I realise that this may come across as pedantry (it is). Sadly Creative Commons licensing is a bit of a mess for this very reason.

But I suggest that the authors look at each image's conditions of use, and if it requires attribution then the name of the person who created the image is added to Acknowledgements. If this seems excessive (it would be tedious, but the illustrators have asked to be appropriately credited), then at least remove the "public domain" statement as that is false.


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: NO ONE-SIZE-FITS-ALL SOLUTION TO CLEAN GBIF
Review round: 2
Reviewer: 3

Output:
Basic reporting: Clear and understandable language, easy to read, and well-structured.

Some minor comments on detail:

•	116/117 refers to "raw data downloaded from GBIF", while line 104 mentioned downloading GBIF-interpreted data. Assuming that the paragraph still refers to the same download of interpreted data, suggest rephrasing 116 to "(...) first filtered the data as downloaded from GBIF ("raw", hereafter) (...)", to avoid misunderstandings around "raw" (unprocessed, original) data that are also available from GBIF.
•	242/243: the same link is duplicated. Should the second one point at a different URL?
•	266: "(...) that between one to half of the occurrence records (...)": for clarification: is it between one record and half of all records, or is some other word missing?
•	Fig.2: suggest to consider labeling map axes in degrees lat/long or decimal degrees
•	Fig.2, title/legend: suggest to be more explicit in the legend to signify absolute numbers of occurrence records removed/flagged in filtering
•	Fig.3, legend: see Fig 2, above
•	Fig.4: suggest to consider adding the total number of species (n= ) for each of A-D, assuming that the total size of the group matters to number of species removed
Experimental design: An interesting design to compare the impacts of a uniform approach across diverse species groups, highlighting varying importance of different data fields for diverse taxonomic groups. Clear questions outlined at the beginning.

With the added rationale for not making use of the issue flags already available from GBIF data processing (110-114), the study goal now appears somewhat ambiguous between an evaluation of GBIF-mediated data in particular in their suitability for biodiversity analyses and required preparatory work (e.g. 266ff, title) on one hand, and the evaluation of the importance and impact of specific data filters to be applied to any kind of database used in such analyses, with GBIF unfiltered data just chosen as a case study (112-114), on the other. Could this be clarified?
Validity of the findings: The findings are plausible and well-documented. The study provides a welcome perspective on the caveats and value of using data aggregated from a multitude of contributing datasets in environmental research, testing against an established, expert-driven process.
Additional comments: Very minor comments (side notes, feel free to ignore):
•	233: the terms "extinct" and "fossil" are not necessarily always coupled, since a species may be more recently extinct, with specimen (not fossil) vouchers
•	274: "to allow users to provide (...) feedback for particular records": technically, this is already possible. It is rather the visibility and rapid re-integration of feedback that is an issue.
•	Tab.2, Biodiversity institutions: "or because they represent individuals from captivity or horticulture": that would be expected and by design. Following the Darwin Core standard, such records should be identifiable by a basis of record of "living"
•	Tab 2, Individual count: "number of recorded individuals is 0 (record of absence)": some database management systems default to 0 for numerical values; other measures for status (present/absent) or abundance (% coverage) can help to disambiguate


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: ISOLATION AND CHARACTERIZATION OF A MOTILITY-DEFECTIVE MUTANT OF EUGLENA GRACILIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The work of Muramatsu et al. is a straightforward communication where Euglena gracilis cell suspensions were Fe-ion-irradiated and a mutant strain with defects in flagellum formation and locomotion was isolated and characterized. This paper was already subjected to two rounds of review in another journal, it is well written, contains the adequate background, and is well structured.
Experimental design: The research question is straightforward and the experiments made to characterize the obtained mutant are clear-cut.
Validity of the findings: The paper describes the isolation of a immotile Euglena gracilis mutant that may have potential in certain biotechnological applications.
Additional comments: The manuscript may benefit if the authors make some minor corrections:
-line 62: "taxes" should read "taxis"
-line 89: add "industry" after "food"
-line 257 should read: "As judged by both light and electron microscopy, the M -3 ZFeL cells were more rounded than the wild type cells."
-line 380: change "the immotile cells have
merits in observing and manipulating cells in the limited area under the microscope." to "the paralyzed cells can be observed and manipulated in a limited area under the microscope."
-line 398: change "are" to "may be".
-Legend to Figure 1: it reads "(A and B) Photographs of wild type (A) and M -3 ZFeL (B) grown in KH liquid medium...." should read "(A and B) Photographs of wild type (A) and M -3 ZFeL (B) colonies grown in KH liquid medium...."
-I suggest to use the terms "non motile" or "paralyzed" instead of "immotile".


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: ISOLATION AND CHARACTERIZATION OF A MOTILITY-DEFECTIVE MUTANT OF EUGLENA GRACILIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors present the results of the isolation and characterization of a novel low-motility strain of Euglena gracilis. They test several physiological parameters on it, stating that it has potential use for industrial applications. In general terms is a quite interesting study and the authors “created” the strain and show its potential uses and advantages. This research can have a high applicability and should be published.
Experimental design: The experimental design is appropriate for the study. Is recommended to include some statistical analysis that will consolidate the results of the study.
Validity of the findings: Novel findings that show the potential of "creating" ad-hoc algal strains for industrial use.
Additional comments: Really nice work. However, there are minor changes required. There is overlapping between the materials & methods and results sections, with part of the methodology being described in the results, which makes the paper a bit hard to follow. It is recommended to clearly separate both sections, leaving all the methodological work and description of protocols in the material and methods part.