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: CHARACTERISTICS AND OUTCOMES OF HEMODIALYSIS PATIENTS WITH COVID-19: A RETROSPECTIVE SINGLE CENTER STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Further Reviewer Comments to R1
Original Comment-2: Hemodialysis patients were a high-risk group of SARS-coV-2 infections. As shown in PubMed, more than 70 papers concerning COVID-19 in Hemodialysis patients have been published since the outbreak of COVID-19. However, the authors claimed several times that "Currently, the research about hemodialysis patients with COVID-19 is scarce. 143 This study is one of the first to report clinical characteristics and outcomes exhaustively". The authors did not search in Pubmed? Compared with these published papers, the current manuscript added little to this area.
Author Response-2: We appreciate the views of the reviewer. We read through the full text, corrected errors, and re-edited some sentences. For specific modifications, please see the revised manuscript.

Further Reviewer Comments to this reply: The authors should clearly clarify what’s they added to this area.

Comment-4:The diagnostic criteria was from WHO, but the treatment was using Chinese guideline 6th edition?
Response-4: We thank the reviewer for their detailed and professional comments. As mentioned by reviewer, for COVID-19 patients, especially hemodialysis COVID-19 patients, the medication treatment approach may be different from other countries or regions, or it is well outside the standard of care practiced in the United States and other nations. In particular, we introduced traditional Chinese medicine treatment for different patients' conditions (Table S2). Therefore, the treatment is to use the 6th edition of the Chinese Guidelines.
Further Reviewer Comments to this reply: The authors should check and make sure they used WHO diagnostic criteria while not the local criteria of China.
Experimental design: Further Reviewer Comments to R1
Original Comment-2: Hemodialysis patients were a high-risk group of SARS-coV-2 infections. As shown in PubMed, more than 70 papers concerning COVID-19 in Hemodialysis patients have been published since the outbreak of COVID-19. However, the authors claimed several times that "Currently, the research about hemodialysis patients with COVID-19 is scarce. 143 This study is one of the first to report clinical characteristics and outcomes exhaustively". The authors did not search in Pubmed? Compared with these published papers, the current manuscript added little to this area.
Author Response-2: We appreciate the views of the reviewer. We read through the full text, corrected errors, and re-edited some sentences. For specific modifications, please see the revised manuscript.

Further Reviewer Comments to this reply: The authors should clearly clarify what’s they added to this area.

Comment-4:The diagnostic criteria was from WHO, but the treatment was using Chinese guideline 6th edition?
Response-4: We thank the reviewer for their detailed and professional comments. As mentioned by reviewer, for COVID-19 patients, especially hemodialysis COVID-19 patients, the medication treatment approach may be different from other countries or regions, or it is well outside the standard of care practiced in the United States and other nations. In particular, we introduced traditional Chinese medicine treatment for different patients' conditions (Table S2). Therefore, the treatment is to use the 6th edition of the Chinese Guidelines.
Further Reviewer Comments to this reply: The authors should check and make sure they used WHO diagnostic criteria while not the local criteria of China.
Validity of the findings: Further Reviewer Comments to R1
Original Comment-2: Hemodialysis patients were a high-risk group of SARS-coV-2 infections. As shown in PubMed, more than 70 papers concerning COVID-19 in Hemodialysis patients have been published since the outbreak of COVID-19. However, the authors claimed several times that "Currently, the research about hemodialysis patients with COVID-19 is scarce. 143 This study is one of the first to report clinical characteristics and outcomes exhaustively". The authors did not search in Pubmed? Compared with these published papers, the current manuscript added little to this area.
Author Response-2: We appreciate the views of the reviewer. We read through the full text, corrected errors, and re-edited some sentences. For specific modifications, please see the revised manuscript.

Further Reviewer Comments to this reply: The authors should clearly clarify what’s they added to this area.

Comment-4:The diagnostic criteria was from WHO, but the treatment was using Chinese guideline 6th edition?
Response-4: We thank the reviewer for their detailed and professional comments. As mentioned by reviewer, for COVID-19 patients, especially hemodialysis COVID-19 patients, the medication treatment approach may be different from other countries or regions, or it is well outside the standard of care practiced in the United States and other nations. In particular, we introduced traditional Chinese medicine treatment for different patients' conditions (Table S2). Therefore, the treatment is to use the 6th edition of the Chinese Guidelines.
Further Reviewer Comments to this reply: The authors should check and make sure they used WHO diagnostic criteria while not the local criteria of China.
Additional comments: Further Reviewer Comments to R1
Original Comment-2: Hemodialysis patients were a high-risk group of SARS-coV-2 infections. As shown in PubMed, more than 70 papers concerning COVID-19 in Hemodialysis patients have been published since the outbreak of COVID-19. However, the authors claimed several times that "Currently, the research about hemodialysis patients with COVID-19 is scarce. 143 This study is one of the first to report clinical characteristics and outcomes exhaustively". The authors did not search in Pubmed? Compared with these published papers, the current manuscript added little to this area.
Author Response-2: We appreciate the views of the reviewer. We read through the full text, corrected errors, and re-edited some sentences. For specific modifications, please see the revised manuscript.

Further Reviewer Comments to this reply: The authors should clearly clarify what’s they added to this area.

Comment-4:The diagnostic criteria was from WHO, but the treatment was using Chinese guideline 6th edition?
Response-4: We thank the reviewer for their detailed and professional comments. As mentioned by reviewer, for COVID-19 patients, especially hemodialysis COVID-19 patients, the medication treatment approach may be different from other countries or regions, or it is well outside the standard of care practiced in the United States and other nations. In particular, we introduced traditional Chinese medicine treatment for different patients' conditions (Table S2). Therefore, the treatment is to use the 6th edition of the Chinese Guidelines.
Further Reviewer Comments to this reply: The authors should check and make sure they used WHO diagnostic criteria while not the local criteria of China.


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: CHARACTERISTICS AND OUTCOMES OF HEMODIALYSIS PATIENTS WITH COVID-19: A RETROSPECTIVE SINGLE CENTER STUDY
Review round: 3
Reviewer: 1

Output:
Basic reporting: The paper has been improved, but some language problems persist. I advise a new revision by an English-native speaker.
Experimental design: Clear and well-explained.
Validity of the findings: The data are well-presented.
Additional comments: The paper has been improved after revision steps. However, these data are not so original, since larger studies of the same topic have already been published.
Nevertheless, the paper may be of interest to clinical nephrologists.


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 MORPHOLOGICAL AND MOLECULAR STUDY OF HYDRODYNASTES GIGAS (SERPENTES, DIPSADIDAE), A WIDESPREAD SPECIES FROM SOUTH AMERICA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The current study is well addressed and showed important results for the scientific community. However, some points need to be clarify for a better understanding, especially on the discussion section. The discussion needs to better addressed according to the goals of the study. I also suggest the authors to incorporate a strong relationship about the weak and strong points of their results with a better interpretation.

Below I point out some my suggestions to improve the manuscript:

Title:
The title of the paper mentions the different hydrographic basins from South America, however, I do not see along the text any discussion about the different basins. What are these basins? How they differ from each other and how it affects your results? It will be also good to see the different basins with the rivers on a figure 1.

Abstract:
I suggest that you improve the statement at lines 27-29, I do not understand which populations are you mention here if before you were talking about the species.

Text:

For the introduction, I would like to see the problematic of the species group for the reader to be able to follow the context.

Lines 71-72: When you explain about the distribution of Hydrodynastes gigas in Brazil, I suggest you to mention the Brazilian states as you did for H. melanogigas.

Lines 75-77: When you mention about “… the morphological and molecular variations between its populations”, I also suggest you to mention between population and species. Hydrodynastes is a widely distributed genus with different species as you mention before.

Lines 77-78: I suggest you to explain more about the influence of the basins on the speciation of aquatic and semiaquatic fauna. This sentence is out of the context and I did not see any explanation before in your text about speciation process or ecological differences along species and populations.

Lines 79-80: I suggest you to mention the two species name that you are going to evaluate the taxonomic status.

Line 80: Change “Thus, our objectives were” for “Thus, our objectives are”

Lines 80-82: I suggest you to provide a better justification for your goals here. Are you going to test whether Hydrodynastes gigas comprises a complex of cryptic species based on? Also it will be better addressed if you can explain a little more how you are going to verify the taxonomic validity of H. melanogigas.

Lines 87-89: I suggest the authors to provide a justification for the use of 3 species, if at the introduction (Lines 80-82) they only talk about 2 species.

Line 95: A reference is missing “in the Geneious v.9.1.8 program”.

For the methods section I suggest the authors to provide a better explanation about the use of those methods according to their goal and hypotheses.

Line 129: I suggest you to subset the methods for “Hemipenis morphology” as you did for the discussion.

Line 130: Change “Amazon” for “Amazonia”, also on all the text.

Line 181: I suggest the authors to start the discussion with a general statement about their main results and conclusion, then start to discuss about this.

Lines 183-186: I don’t see any link about the influence of rivers on the speciation process along your text. It seems very out of context here. Any time along your introduction and methods you  addressed biogeographic methods or hypotheses, so I don’t think it is well included here. Also the references are only about terrestrial organisms, so you cannot talk about aquatic species here.

Lines 211-213: the reference is missing.

Line 215: it is missing the reference about the “other authors”

Line 304: Change “…besides to elucidating the events of the diversification of aquatic and semi-aquatic species and Squamata.” for “…besides to elucidating the diversification events of aquatic and semi-aquatic Squamata species.”

--

Figure 1: It is really hard to see the different shades of gray in the map (the basins). I suggest you to change it. Also I suggest you to improve the legend of the map. When you say that the map B “specimens analyzed” , what kind of data are you mention? Please explain better here.

Figure 2: During your Results section you talk about the sample of H. melanogigas in the Figure 2. However, it is not clear in the figure which one are these samples. Also you need to provide a better statement about the Figure, for example the samples marked with starts are not clear on the legend.

Table 1: Change “Table 1. Specimens used in the molecular analyses,..” for “Table 1. Specimens used for the molecular analyses,..”.

Table 2: I suggest the authors to improve the legend giving more details about the models.

Table 3: Please include a statement about the bold number on the legend.
Experimental design: I commend the authors for their extensive data set. The methods are good, but if there is a weakness I would say that a strong relationship and a better explanation about the method with the hypothesis that the authors are testing would improve the manuscript. Further, most of the figures’ legends need more details or/and are missing something, I suggest to improve them.
Validity of the findings: I think that the findings of the study are very important for science. As I mention before the date is robust and well analyzed. My suggestions made above will improve the manuscript and also impacted the conclusion, which support the results.
Additional comments: In general the paper is good and shows important results for the scientific community. I am glad to see this work and I hope the changes are going to improve the paper.  Some points need to be clarify for a better understanding, especially on the discussion section.

Finally, I think that is very important for any study to mention the Funding, which are missing in the current project.


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 MORPHOLOGICAL AND MOLECULAR STUDY OF HYDRODYNASTES GIGAS (SERPENTES, DIPSADIDAE), A WIDESPREAD SPECIES FROM SOUTH AMERICA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study by Carvalho and collaborators compile data on genetic, morphological, and coloration patterns of Hydrodynastes species in order to identify the taxonomic status of the species in the genus. The research topic and study are interesting, as I am familiar with the doubt related to the validation of H. melanogigas status as a species. However, there are a few issues that require some attention from the authors. The Introduction needs work, improving the connection of ideas, and highlighting the importance of the study (contextualization). For example, you mention about variation on color patterns, but don’t discuss why it is relevant for the species in question. More context is needed for the relation of hydrographic basins and genetic structure expected, highlighted in the figures and the title, but briefly mentioned in the discussion and not included in the Introduction. This restructuring of the Introduction will need to be followed in the Discussion. The English language needs an overall improvement to ensure a clear understanding of the text. More details are mentioned below to help the authors in revising the manuscript.
Experimental design: If the changes in the Introduction improve the sets up of the arguments of the study, the experimental design will make more sense, as I recognized the question as meaningful. Then, as the genus Hydrodynastes only includes three species and genetic data on H. bicinctus is included, I missed the addition of morphological, coloration patterns, and hemipenis morphology description for the species. It would make an interesting parallel on the conserved morphology founded on H. gigas/melanogigas. I would also suggest authors consider running an additional analysis (PCA or discriminant analysis) on the morphological data for easy visualization of the morphological variation in both species.
Validity of the findings: While I recognized some changes that would improve the quality of the manuscript,
the taxonomic conclusions are supported as they can be, given the lack of genetic and morphological variation. As only one hemipenis of H. melanogigas was analyzed, a comparison to published data would improve the support of the statements made.
Then, while the genetic tree does not support H. melanogigas as a distinct species, it does appear as a separate group, and as a relatively geographically isolated population of H. gigas. However, I am fine to let future studies and the community to decide whether to accept the taxonomic decision.
Additional comments: Abstract – background: please specify what integrative approaches means
Line 24: Hydrodynastes melanogigas in italic
Line 38 to 46: The paragraph is confusing and needs some rewording.
Line 48: “database” is a weird word for this statement
Line 54: please cite more studies
Line 79: I missed more details on the aims of the study. A paragraph explaining why a taxonomic study of the group is important, why you would expect H. gigas to be a complex of cryptic species, the relation with hydrographic basins. You mention briefly on line 75 but more details are needed, and references should be included to support.
Line 78: Please include a reference to your statement
Line 87: remove the word “total”
Line 203-204: more hemipenis morphology data for H. melanogigas, or comparison to other studies would reinforce your statement, as you only have the hemipenis of one individual
Line 302: highly recommended sounds weird
Line 304: broad; please be more specific
References: Please check reference format of the journal e.g. full title of the journal should be in italic
Figure 1: “a” and “b” should be in caps lock; please remove the last zero of the coordinates (e.g. 10 instead of 100); be consistent on the symbol used for the species on the maps a and b
Figure 2: specify what the asterisk means in the legend
Figure 3 to 6: can you please specify which ones were H. melanogigas? Also, avoid acronym on the legend, writing Hydrodynastes instead of just “H. “
Table 1: consistency - et al in italic or not; can you check the localities of the samples with the authors of the papers?
Table 3: appears in the text after table 4 and 5; on the table, please substitute the numbers 1-5 for the name of species, for clarity


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 MORPHOLOGICAL AND MOLECULAR STUDY OF HYDRODYNASTES GIGAS (SERPENTES, DIPSADIDAE), A WIDESPREAD SPECIES FROM SOUTH AMERICA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Below I left some of the improvements that need to be addressed, however the paper needs a minor revision.

Text:

Lines 17-178: The sentence does not show the results. You examined fully melanic specimens and I would like to know what you found here.

Lines 186-189: I didn’t understand this sentence at the results section. It should be at the methods section and I didn’t see below the “variation” that you want to mention. I suggest you to change it.

Line 210: I suggest you to remove the word “however” and put a comma. The way these sentences are structure now don’t mean what you want to say.

Lines 219-221: I would like to see a study example (reference) about this statement.

Figure 1: At the title of the Figure 1A you mention only Hydrodynastes but at the legend you mention the species names. Just be consistent with the names. I also suggest you to combine the maps so we can see the whole distribution of the species.

For most of the figures, be consistent with the letter style, for examples in the text the Figures letters are uppercase (Fig. 4F) and in the figures they are lowercase (4f). I don’t know if is the journal style.

Figure 10: I suggest you to combine the figure 1 with the figure 10 and explain in the legend the different samples used for the analyses and literature (maybe different colors).
Experimental design: I am glad to see the improvement on the manuscript from the last time. The authors made a good job accepting the suggestions. In general, the text has a better flow now and is easier to follow.
Validity of the findings: I am glad to see the improvement on the manuscript from the last time. The authors made a good job accepting the suggestions. In general, the text has a better flow now and is easier to follow.
Additional comments: I am glad to see the improvement on the manuscript from the last time. The authors made a good job accepting the suggestions. In general, the text has a better flow now and is easier to follow. However, some parts are still need improvement for the publication. At the discussion section, the structure needs to follow the rest of the paper, for example if you talk first about molecular, morphological and hemipenis data on the other sections, you need to do the same at the discussion. Also, I suggest you to integrate more the paragraphs for the discussion, try to see the big picture here, combining the all the results that you have instead of discussing them separated. The third paragraph (Line 222) is a good example of integration, but the fist 2 paragraphs are a bit disconnected. I accepted the paper with minor revision.


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

Input:
Title: A MORPHOLOGICAL AND MOLECULAR STUDY OF HYDRODYNASTES GIGAS (SERPENTES, DIPSADIDAE), A WIDESPREAD SPECIES FROM SOUTH AMERICA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I think the revised version is much improved and almost ready for publication- there are still some points needing clarification that I would like to mention. Most of my comments are suggestions, that can or cannot be adopted by the authors unless the editor believes the changes are necessary for publication. The only bit that I believe really needs to be solved is if the authors removed the allometric effect of the body size for the PCA analysis (see more below).

The title and abstract are good, but in my opinion, the first paragraph of the Introduction needs some rewording. The idea is there, but the repetitiveness of the “however, however, on the other hand, thus” seems a bit odd. Here is just an idea to try to help, rewording your words, but of course (please) feel free to edit as you want – “Taxonomic studies on species description are traditionally based on morphological characters to delimit species. However, in many cases, species are difficult to delimit due to the limited number of morphological differences or the absence of them, preventing the recognition of valid cryptic species. Morphology alone might result in more than one name being assigned to individuals belonging to the same evolutionary lineage (i.e. species). This result in many species been described based solely on morphological parameters, which could merely reflect interpopulation variation, instead of evidence of lineage separation”.

On the methods, line 107-108 you mention “using the standard Polymerase Chain
Reaction (PCR) technique”. The ideal is that you mention in the Supplementary Material the time and temperature in each cycle of the PCR, or the paper that shows it, to facilitate replication of your study. For the PCA analysis, have you removed the allometric effect of the body size? If yes, please mention in the text. If not, this is a necessary step, as the size is associated with individual growth, and you are focused on the shape (that must be size-free). Please refer to many studies and different normalization methods.

On the discussion, line 210, please remove “. However,”. For consistency with the way the authors presented the methods e results, I would move the paragraph about hemipenis (line 212-221) to line 245, before the last paragraph (“More studies are needed”).

I would move Figure 10, maybe Table 1, and Table 2 to the Supplementary Material.
Experimental design: No comment
Validity of the findings: No comments
Additional comments: I  hope the suggested changes are going to improve the paper. Great 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: REMOTE SENSING INVERSION AND SPATIAL VARIATION OF LAND SURFACE TEMPERATURE OVER MINING AREAS OF JIXI, HEILONGJIANG, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The introduction has sufficient literature references and reasonable hypothesis.
Experimental design: The experimental design is good.
Validity of the findings: The findings are solid and valid.
Additional comments: This study investigated the  spatial variation of Land Surface Temperature over Mining Areas in Southeastern China using Landsat-8 imagery. The results indicated that the mining activities have led to significant increases in LSTs, linked to vegetation loss and environmental degradation. In general, this manuscript is well written and easy to follow, making significant contributions to the literature.


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

Input:
Title: REMOTE SENSING INVERSION AND SPATIAL VARIATION OF LAND SURFACE TEMPERATURE OVER MINING AREAS OF JIXI, HEILONGJIANG, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The standardization of spatial thematic mapping should be strengthened. The legend should include all the data-layers.
Experimental design: Methods described with sufficient detail & information to replicate.
Validity of the findings: The conclusions can be  further refined, and the tables and charts should be compressed.
Additional comments: Mining area is a kind of complex human activity, its internal type is complex, including mining site and industrial facility site. The mining area with high surface temperature is mainly caused by the operation of factory facilities. The current conclusion generally says that the temperature in the mining area is higher than that in the urban area, and there may be some problems. It is suggested that higher resolution remote sensing images can be used to obtain the data of inner structure or field operation of the mining area, and the reasons of influencing the temperature level should be discussed more pertinently.


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: REMOTE SENSING INVERSION AND SPATIAL VARIATION OF LAND SURFACE TEMPERATURE OVER MINING AREAS OF JIXI, HEILONGJIANG, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The mnuscript is well within the scope of the journal. However, it requires few improvements before being accepted.
Experimental design: The framework and structure of the manuscript is alright.
Validity of the findings: The manuscript presents a good overview over the relationship between LULC and LST.
Additional comments: The present work is very interesting. However, I have observed few basic fundamental issues in the manuscript, which needs to be addressed by the authors before the acceptance of this manuscript. Hence, I recommend major recommendation before being accepted.
Specific Comments to the Authors:
1.	The authors have used maximum likelihood classifier for the image classification. It is not clear why the authors have employed such outdated techniques, when more updated and better methods like random forest etc. are available. It has received wide applicability in producing comparatively better LULC.
2.	In the methodology section, authors have mentioned about confusion matrix for the validation of LULC. Again, in the result section, they showed the values of Kappa coefficient. In this case, the authors have not provided any clear view on the number of samples that are adopted for validation and how the sample size is determined.
3.	In case of vegetation coverage estimation, the authors have mentioned NDVIsoil and NDVIveg. It is not clear how the authors have obtained the NDVI value of pure soil and pure vegetation. There are also no citations against those arguments.


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: REMOTE SENSING INVERSION AND SPATIAL VARIATION OF LAND SURFACE TEMPERATURE OVER MINING AREAS OF JIXI, HEILONGJIANG, CHINA
Review round: 1
Reviewer: 4

Output:
Basic reporting: The paper mainly deals with the assessment of spatial variation of Land Surface Temperature (LST) over a Mining area of China using GIS and RS techniques. Most of the methods used in this study are backdated and these were used widely used in many previous research studies. However, a number of serious issues preclude me from positively recommending the paper for publication.
1.	The introduction is too short to raise the scientific contribution of the study.
2.	The introduction fails to address the novelty of the work. Author should properly address the previous literatures dealing with the assessment LST over the mining cities.
3.	 Language needs to be changed.
4.	Line 40, author states “In the process of resource development in resource-based cities, the land-use patterns  in mining areas are constantly changing, which brings about a series of impacts on the regional 42 ecological environment” without any valid scientific reference.
5.	Table 1 is unnecessary. So it would better to remove the Table 1
6.	In Table 2 and 4, author calculated normalized temperature index but how they have identified the threshold value for each class?
7.	In Table 3 and6, I hope It would be better to add; Standard Deviation’.
8.	Authors analyzed buffer zone but not showed on maps.
Experimental design: 1.	The authors just considered year 2019 for showing the spatial vitiation of LST over the study landscapes. But without temporal analysis, it has no scientific base. If one never analyzes the   temporal pattern of LST then how one can know whether the LST has changed or not even how fat different geophysical parameters have a role on LST or over the study area?
2.	The author should change the discussion part. In discussion part author gave more focus on the result of the study. In discussion part author must deal the rationality of the result of the other studies.
3. Teh reserch questions of the study needs to be addressed properly
5. The methods needs to be more scientific and updated
Validity of the findings: 1.	The heading of the discussion part creates ambiguities. Author should correctly write the subheading in discussion part.
2.	Author must address the major driers of spatial variation of LST of the study area.
3. The findings of the result were not properly adressed.
4. The athors should clearly focus the litertures of the pervious reaserch study and relevent litertures needs to be used.
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: REMOTE SENSING INVERSION AND SPATIAL VARIATION OF LAND SURFACE TEMPERATURE OVER MINING AREAS OF JIXI, HEILONGJIANG, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have used Maximum likelihood classifier for the image classification. It is not clear why the authors have employed such outdated techniques when more updated and better methods like random forest etc. are available. It has received wide applicability in producing comparatively better LULC.
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: REMOTE SENSING INVERSION AND SPATIAL VARIATION OF LAND SURFACE TEMPERATURE OVER MINING AREAS OF JIXI, HEILONGJIANG, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Although author revised the paper as per as suggestions  but still there is a lack of important literatures . Therefore I would suggest  author to use following references for enrichment of the papers
(i)  Das, M., & Das, A. (2020). Assessing the relationship between local climatic zones (LCZs) and land surface temperature (LST)–A case study of Sriniketan-Santiniketan Planning Area (SSPA), West Bengal, India. Urban Climate, 32, 100591. https://doi.org/10.1016/j.uclim.2020.100591
(2) Das, M., Das, A., & Mandal, S. (2020). Outdoor thermal comfort in different settings of a tropical planning region of Eastern India by adopting LCZs approach: A case study on Sriniketan-Santiniketan Planning Area (SSPA). Sustainable Cities and Society, 102433.https://doi.org/10.1016/j.scs.2020.102433
(3) Estoque, R. C., Murayama, Y., & Myint, S. W. (2017). Effects of landscape composition and pattern on land surface temperature: An urban heat island study in the megacities of Southeast Asia. Science of the Total Environment, 577, 349-359.
(4) Pal, S., & Ziaul, S. K. (2017). Detection of land use and land cover change and land surface temperature in English Bazar urban centre. The Egyptian Journal of Remote Sensing and Space Science, 20(1), 125-145.
(6) Wang, R., Hou, H., Murayama, Y., & Derdouri, A. (2020). Spatiotemporal Analysis of Land Use/Cover Patterns and Their Relationship with Land Surface Temperature in Nanjing, China. Remote Sensing, 12(3), 440.
Experimental design: The contents are very suitable  for this journal. But it has few common mistakes. I can't  identity  the research gaps. Please identify and specify
Validity of the findings: I would suggest author to add above mentioned literature to stand the novelty of the paper. Without this, I can't  recommend to accept the paper
Additional comments: Although the authors have made a good attempt to all the responses.  But still i found some mistakes.
(i) In figure 2 red color denotes 'high' but in figure 5 it denotes 'low'. Please use same color scheme. Even use common knowledge in using color scheme.  When you are using red color it never treats as low, It has its own significance.
(ii) In line 161, it should be 'Where' not 'where'. Please check all the mistakes.


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: EVOLUTIONARY ANALYSIS OF CHLOROPLAST TRNA OF GYMNOSPERM REVEALED THE NOVEL STRUCTURAL VARIATION AND EVOLUTIONARY ASPECT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The structure of the manuscript is well organized and easy to follow, but the english language is not of sufficient quality.
Experimental design: The authors used the speceis tree to reconcile the tRNA phylogeny to identify gene loss and gain events. No figure legend was provided for the figure s1. What is the difference between the "D" and "cD" on the nodes of the phylogeny?
Validity of the findings: The authors claimed the phylogenetic tree of tRNAs showed the presence of three major clusters covering 64 groups of all tRNAs. How the three major clusters are recognized? This conclusion could not be obtained basing on the current form of the figure 3. The authors should provide more details about getting this conclusion.

The authors found that "tRNAAla has been found to be absent in R. piresii and T. mairei while tRNAVal has been found with inexistence in T. mairei". It would be interesting to investigate whether the absent of these tRNAs affected the codon usage of the protein coding genes in the chloroplast of these species.
Additional comments: This study aimed: (1) to determine nucleotide diversification of secondary structure of gymnosperm tRNAs; (2) to identify the detailed genomic aspects of chloroplast tRNAs; (3) to assess the evolutionary relationship between different chloroplast tRNAs; (4) to evaluate the duplication or loss on all involved tRNAs. This appeared to be original. There are a few points that need to be further clarified as mentioned 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: EVOLUTIONARY ANALYSIS OF CHLOROPLAST TRNA OF GYMNOSPERM REVEALED THE NOVEL STRUCTURAL VARIATION AND EVOLUTIONARY ASPECT
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basically, it is interesting to study the evolution of tRNAs encoded in the chloroplast genomes of gymnosperms, considering that they are maternally or paternally inherited, with evolution rates about five times slower than that of nuclear genomes. However, the manuscript is immature in its present form.

Major concerns:

a) The English of the manuscript needs to be improved substantially; the sense of many sentences is unclear, cryptic or misleading.

b) The resolution/quality of Figure 1 is too low. I am also not convinced to classify the tRNAs shown in Fig. 1 as “non-cloverleaf-like structures”. They adopt cloverleaf structures, but additionally have more or less rigid variable arms.

c) Table 4: it is not immediately clear which part of the tRNA these consensus sequences represent; for example, in the column “Ψ arm”, the reader is wondering if this is the sequence of the T stem 5’- or 3’-strand? Indicate this more clearly, also give sequence polarity. The authors should include a tRNA secondary structure where the mark the sequence elements specified in Table 4.

d) These endless listings of tRNAs (for example, in lines 265 to 313) makes the manuscript hard to digest. The authors should illustrate their findings in additional summary figures. The clustering of tRNAs is not comprehensible for the reader. The authors should exemplarily delineate the sequence criteria underlying the clustering of the respective tRNA; explain why some tRNAs appear in more than one group. The evolutionary clustering of gymnosperm chloroplast tRNAs, cumulating in the phylogenetic tree of Figure 3, is at the heart of this story and should thus be more intelligible to the reader.

e) The CAU anticodon of tRNA-Ile: it is known from bacteria that the enzyme TilS converts the 5’-C  residue in the CAU anticodon of specific tRNA-Ile molecules to lysidine (2-lysyl cytidine; abbreviated as L  or k2C ) to decode 5’-AUA  (Ile) codons instead of 5’-AUG  (Met) codons (Reference: Soma A, Ikeuchi Y, Kanemasa S, Kobayashi K, Ogasawara N, Ote T, Kato J, Watanabe K, Sekine Y, Suzuki T: An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol Cell 2003, 12(3):689–698). This mechanism may also be operational in chloroplasts. The authors should discuss this issue and should check the literature if there is evidence for the same mechanism in chloroplasts.

f) Figure 2: describe this predicted W. nobilis RNA structure more cautiously as a tRNA-Gly-like structure, as it has a (most likely) non-functional acceptor stem that is not charged with glycine.
Experimental design: Difficult to assess at present.
Validity of the findings: Difficult to assess at present.
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: EVOLUTIONARY ANALYSIS OF CHLOROPLAST TRNA OF GYMNOSPERM REVEALED THE NOVEL STRUCTURAL VARIATION AND EVOLUTIONARY ASPECT
Review round: 1
Reviewer: 3

Output:
Basic reporting: See comments to author.
Experimental design: See comments to author.
Validity of the findings: See comments to author.
Additional comments: Here are the comments which can be useful but not limited in improving the structure and quality of the manuscript.

1. Authors did not talk about the presence of modified bases in tRNA?

2. The English used in the manuscript is very poor and needs to be improved heavily so as to reach an average science audience. It was very hard to understand at multiple places that the reader loses connectivity with the theme of manuscript. Use of few words (e.g. besides) at unnecessary places needs to be avoided. Please avoid long and complex sentences such as line no. 76-80. Also, multiple sentences are repeating in every section. Because of poor English, at many places there arises a doubt on the experiments performed. So the whole manuscript has to be restructured.

3. All the figures need to be submitted online with proper fig captions. Please rename fig 1b as 2 and so on if possible. Fig. 3 for the phylogenetic tree is not at all clear hence I could not validate the results based on it. The manuscript contains most of the data based on that figure. Hence, at this stage the results cannot be validated.

4. It will be useful to include a line or two in the abstract or introduction stating the importance of this study or how these results are promising over the past studies.

5. The experimental protocol needs to be explored in more precise stepwise manner (probably English improvisation could help).

6. Line no. 138 says bacterial parameter in tRNAScan-SE. Why this was used?

7. Protocol described for phylogenetic tree construction from line no. 144 is unclear and its present written form will be difficult to reproduce the results. Also from line no. 161 various methods were used to filter the data. What is the rationale behind such multiple filtering? How each filter can be correlated in case of this gymnosperm tRNA analysis?

8.Please include the results of gene manipulation (line no. 169) in the main document as they are much essential to interpret the results stated in the manuscript.

9. Line no. 265-313 & 424-438 is totally un-interpretable because of poor resolution of fig 3. Also, line no. 349-355 correspond to fig S1 and table S2. Please make them available in the main text.

10. For this line, “Notwithstanding, it is still unclear that how the tRNA captured with CAU anti-codon to distinguish Methionine and Isoleucine and carry them respectively” authors may look into these references; Nucleosides, Nucleotides and Nucleic Acids. 27, 1158-1174, 2008; RSC Advances, 4, 14176- 14188, 2014;

11. Please provide a reference to the statement made in line no. 377.

12. Line no. 397 mentions a novel tRNA structure lacking the acceptor arm. I would like to know how the authors have re-validated its occurrence. Please explain.

12. The conclusions do not completely reflect the findings. Please fortify this section by correlating the key findings from results sections.


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

Input:
Title: EVOLUTIONARY ANALYSIS OF CHLOROPLAST TRNA OF GYMNOSPERM REVEALED THE NOVEL STRUCTURAL VARIATION AND EVOLUTIONARY ASPECT
Review round: 2
Reviewer: 1

Output:
Basic reporting: I satisfied with the revision of the manuscript, and recommended it to be accepted for publication as it stand.
Experimental design: I satisfied with the revision of the manuscript, and recommended it to be accepted for publication as it stand.
Validity of the findings: I satisfied with the revision of the manuscript, and recommended it to be accepted for publication as it stand.
Additional comments: I satisfied with the revision of the manuscript, and recommended it to be accepted for publication as it stand.


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: EVOLUTIONARY ANALYSIS OF CHLOROPLAST TRNA OF GYMNOSPERM REVEALED THE NOVEL STRUCTURAL VARIATION AND EVOLUTIONARY ASPECT
Review round: 2
Reviewer: 2

Output:
Basic reporting: Review on Ms. #43190, 1st revision

1. Basic reporting:
The manuscript has improved to some extent, but there are still some unclear major and minor points. As this is a detailed bioinformatic study, the authors have to convince the reader that the analyses were meticulously carried out, taking into account that the reader cannot examine the correctness of every detail. However, at several positions in the text doubts are created whetherthe study was performed with maximum diligence, as some of the described findings and conclusions are either misleading or not comprehensible. Ín my previous review, I already criticized the endless listings of tRNAs in the text. The authors should illustrate their findings in additional summary figures in the main manuscript. I have made proposals for Fig. 4 and Table 4 (see below). Very helpful would also be a sequence/structure alignment of all analyzed gymnosperm chloroplast tRNAs (e.g. as in the tRNAdb).

Major concerns:

a) At multiple positions in the text, gaps between separate words are lacking.

b) for censensus sequence motifs, use “N” instead of “X” to indicate any of the four bases, or further differentiate (R, Y, S, W, K and so forth).
c) I find the Introduction somewhat too long in the second part describing the basics of tRNA sequence and structural elements and their functions.
d) lines 199/200, “… contain a loop structure that is similar to the anti-codon loop in the variable region of tRNAs.” This is misleading. What you want to say is that there are tRNAs with expanded variable loops, some of which form extended stem-loop structures, some shorter stem-loop structures and others are void of base-pairing within the variable loop. This is also a feature of corresponding bacterial tRNA species. My proposal for rewriting in line 199: “As shown in Fig. 1 and Fig. 2, tRNALeu, tRNASer, and tRNATyr contain expanded variable (stem-)loops.” I does not make sense to say that these variable loops are similar to the anticodon loop.
Also, some of the variable loop structures in Fig. 1 and 2 are incorrect: in Fig. 1F, a loop with a single bp in the stem is unliekley to form; likewise, in Fig. 2F, a stem without apical loop does not form. In Fig. 2B, the variable loop stem can be extended to 4 bp.
e) lines 201/202: tRNASer-GCU of D. spinulosum does not follow the consensus N-U-N-G-A-A-N. In lines 202-206, the authors should better differentiate between variable loop region (the entire sequence), and stem-loop elements in the variable loop region. I propose to rewrite from line 202 on: “The variable loop region is predicted to fold into stem-loop structures with apical loops of 3 to 7 nt in tRNASer and several tRNALeu variants. The stems contain up to 7 bp (Fig. 1 and 2). The expanded variable loop structures may play important functions during the protein translation process in chloroplasts.” At some point, these structural features should be compared with those of bacterial counterparts.
f) line 224, Tables 2 and 3: for C. lanceolata, two tRNATrp isoacceptors are indicated in Table 2, but only 1 in Table 3.
g) lines 230-235 (“A” is present in the first and the last position of the D-loop): this is not true for tRNAGln, Gly, Ile, Leu, Met. /

(In addition, in the final two positions of the Ψ-arm, all of the tRNAs were found to have conserved “G-G” nucleotides, except for tRNAArg): according to Table 4, this is also not the case for tRNACys, Phe and Val.

h) lines 233-235: it is unclear here if you found the consensus U-U-C-X-A-X2 only in a multiple sequence alignment of 20 members of the tRNA gene family or in all tRNAs analyzed here; please clarify.

i) lines 238-251: generally use “bp” when describing the length of stems; line 240: an acceptor stem of 1 or 2 bp is non-existent. In Fig. 3, the acceptor stem of W. nobilis tRNAGly likely forms a labile 7-bp acc. stem with two non-canonical A-C bp. This should also be changed in Table S1, replace “2” by “7” or “(7)” in the column “AC-arm” for W. nobilis tRNAGly. How does the AC-arm for tRNAThr of Sciadopitys_verticillata_94443 (1 bp) look like?. Provide a legend to Table S1 where you define how you counted the base pairs in the AC-arm; how do the AC-arms with 3 or 6 bp look like?

j) line 242, C in the last position of the D-arm: is this true for all tRNAs?

k) Table 4: here, the sequence of both strands of the stems should be shown; I assume that the entire sequences of the loops are listed in this table. Use a presentation such as in the tRNAdb.
Change the title to “Conserved sequence motifs in chloroplast tRNAs from gymnosperms”; what did you mean by “selected gymnosperms? All those anlyzed here?

l) line 307, correct: “… the highest transversion rate of 12.5 was found in tRNAAla and the lowest transversion rate of in tRNAAsp (Table 5). Correspondingly, tRNAAla lacks any any transitions (Table 5).”

m) line 328-330: it is unclear what you mean here; are you alluding to the possibility that these missing tRNAs are encoded in the nuclear genome and are imported into the chloroplast? Might there be tRNA editing in chloroplasts?

n) lines 345-349: please rewrite, not clear what you want to express here beyond what is expressed before.

o) line 371: there is no tRNA with a 2-bp acceptor stem (see above); please rewrite.

p) lines 378/379: the consensus U-U-C-X-A-X2” motif in the Ψ region: isn’t this a general consensus motif of canonical tRNAs? Please discuss this point.

q) line 423: what do you mean by “Transition and transversion analyses of tRNAs indicated that tRNAs are iso-acceptor specific”? Do you mean that transition/transversion patterns were isoacceptor-specific?

r) Fig. 4 is too trivial: here the authors should integrate into the tRNA 2D structure the conservations they found in their gymnosperm chloroplast tRNA set, differentiating between base identities that are e.g. >50%, > 75% and 100% conserved.

s) add legends to supplementary figures and tables with explanations for the reader.

Minor comments:

- line 209, rewrite: “The genomes of the species analyzed were found to code for at least two copies of tRNAMet-CAU/tRNAfMet-CAU. Each of the gymnosperm chloroplast genomes encodes 25 to 31 anticodon-specific tRNAs (Tables 2 and 3), where E. equisetina …”
- line 224, rephrase: “Two tRNATrp isoacceptors are present in E. equisetina chloroplasts, compared with a single one in the other gymnosperm species analyzed in this study.”

- line 228: separate paragraph heading from text.

- Table 4, footnote 2, rephrase: “Note that the consensus sequences are shown from 5’ to 3’.”

- line 270, rewrite: “… tRNAs in cluster III were found to group individually, where these tRNAs …”

- line 333_ “… in the chloroplast of Oryza …”

- line 359 ff., rewrite: “In our study, we identified cloverleaf-like tRNAs with expanded variable loop regions (Fig. 1 and 2). Numerous tRNALeu, tRNASer, and tRNATyr were found to have specific variable loop configurations in terms of length and structure, suggesting significant structural variation among chloroplast tRNAs. Future studies will have to determine the biological importance of these variant tRNAs. Noteworthy, a novel tRNA structure lacking the D arm was found for tRNAGly in W. nobilis (Fig. 3).” (As said before, compare with bacterial tRNAs)

- line 378, rewrite: “The consensus sequence “U-U-C-X-A-X2” was found in the Ψ region (Table 4).”

- line 385: “… appeared several times in the phylogenetic tree, and thus …”

- line 414, rewrite: “A CAU anticodon is encoded in tRNAMet as well as in tRNAIle. A novel tRNA structure lacking the D arm was identified for the chloroplast tRNAGly of W. nobilis. Numerous tRNALeu, tRNASer, and tRNATyr types were found to have expanded variable regions, forming stem-loop structures with up to 7 bp in tRNAsSer.”
Experimental design: Requires improved illustration of results
Validity of the findings: expand comparison of gymnosperm chloroplast tRNA features with those of bacterial tRNAs in the discussion
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: EVOLUTIONARY ANALYSIS OF CHLOROPLAST TRNA OF GYMNOSPERM REVEALED THE NOVEL STRUCTURAL VARIATION AND EVOLUTIONARY ASPECT
Review round: 3
Reviewer: 1

Output:
Basic reporting: See attached PDF
Experimental design: No comment
Validity of the findings: No comment
Additional comments: See attached PDF


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

Input:
Title: EVOLUTIONARY ANALYSIS OF CHLOROPLAST TRNA OF GYMNOSPERM REVEALED THE NOVEL STRUCTURAL VARIATION AND EVOLUTIONARY ASPECT
Review round: 3
Reviewer: 2

Output:
Basic reporting: 1.	In figure 1 and 2; it would be good to label the expanded variable loop of tRNAs by making coloured box just to differentiate with other loop regions.
2.	In fig 3; at the hinge region it looks that there is one extra ‘A’ or its counterpart base is missing. Just check?
6.	In the caption of Fig S1; it should be multiple instead of multiply.
7.	In table 4; There must be some modified bases in the tRNA; especially in the anticodon loop of tRNAs; so it would be good to mention ‘symbols’ of modified bases at 32, 34 and 37 as well as other positions if they are present.
Experimental design: 9.	Overall, the study is good and can be published in Peer J with some minor revisions.
Validity of the findings: No comment
Additional comments: Manuscript title: “Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect”
Manuscript ref Number: #43190-v2
Comments to authors (Manuscript ref Number: #43190-v2)
Dear Editor,
Herewith, I am submitting review report on the manuscript entitled “Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect” (Manuscript ref Number: #43190-v2). This is the revised version of this manuscript which deals with computational analysis of genomic data of chloroplast tRNA from various gymnosperms in order to assess primarily the structural variations, nucleotide variation, consensus sequence analysis and phylogenetic analysis with respect to study base substitution and tRNA gene manipulation.
1.	In figure 1 and 2; it would be good to label the expanded variable loop of tRNAs by making coloured box just to differentiate with other loop regions.
2.	In fig 3; at the hinge region it looks that there is one extra ‘A’ or its counterpart base is missing. Just check?
3.	In the material & method section; line no. 127-128; please mention BLAST properly.
4.	In these lines; 136-138; authors have mentioned default parameters of ARGAON; in which they have mentioned as; taken sequence source as a bacterial? Why?
5.	Authors sat that they have observed a novel tRNAGly in W. nobilis (Fig. 3) lacking DHU loop; it would be good to speculate the probable significance of this tRNA for the general readers.
6.	In the caption of Fig S1; it should be multiple instead of multiply.
7.	In table 4; There must be some modified bases in the tRNA; especially in the anticodon loop of tRNAs; so it would be good to mention ‘symbols’ of modified bases at 32, 34 and 37 as well as other positions if they are present.
8.	In the conclusion section few results are mentioned, so it would be good to remove these results part and keep only conclusion of this study. By doing this authors can also reduce the size of the conclusion which is unnecessarily large and mention.
9.	Overall, the study is good and can be published in Peer J with some minor revisions.


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: EVOLUTIONARY ANALYSIS OF CHLOROPLAST TRNA OF GYMNOSPERM REVEALED THE NOVEL STRUCTURAL VARIATION AND EVOLUTIONARY ASPECT
Review round: 4
Reviewer: 1

Output:
Basic reporting: Three minor points should be changed before publication.

a) line 316: If I understand it correctly the sentence should be changed to: "According to previous studies (Treangen & Rocha, 2011; Mohanta et al., 2019), it is likely that the deficiency of these tRNAs is compensated for by the transfer of corresponding tRNAs from the nucleus or mitochondria."

b) in Table 4, first lines, Alanine tRNA: the 3' or 5' should not be moved to a next line; it should remain attached to the sequence; if this is a space problem, the authors may also consider to indicate only 5'- or 3'-end.

c) Fig. 4: in the legend to the figure, the authors should explain more clearly what "% conservation" means. If you consider the whole set of gymnosperm tRNAs, there cannot be > 95% conservation (green) at all positions in the acceptor stem and T arm; or is this the conservation you find for the individual gymnosperm tRNA isotypes? Please clarify.
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: PARTIAL REVISION OF THE NEUSTONIC GENUS SCAPHOLEBERIS SCHOEDLER, 1858 (CRUSTACEA: CLADOCERA): DECODING OF THE BARCODING RESULTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is a relevant contribution to cladoceran taxonomy. The language is in general acceptable but occasionally should be improved (see general comments, and especially the annotated manuscript). Considering the high number of figures, I suggest removing at least the last one. Occasionally, I miss references for some statements (see annotated MS).
Experimental design: Presentation of the Methods may be improved (see details in the annotated MS).
Validity of the findings: The findings are valid but considering the content of the manuscript, the title should certianly be changed to match it. The present controbution is far from an integrative revision of the genus.
Additional comments: The manuscript of Garibian et al. provides some additional genetic data for the neustonic cladoceran genus Scapholeberis (partially expanding the recently published paper on the same taxonomic group - and with overlapping authors - based on different mitochondrial markers), and detailed taxonomic treatment of one species group with redescription of S. kingii and description of the new species S. smirnovi.
It is far from an integrative revision of the genus (the title should certainly be changed, as it is misleding in the present version!) but it is a valuable contribution to the cladoceran systematics, and worthy publication after modest revisions. The paper would fit nicely to a specialized systematic journal but I understand that after the removal (hopefully temporary) of Zootaxa from the Clarivate's Journal Citation Reports, the authors seek other publication outlets.

As is typical for the Kotov group, the manuscript is strong in the detailed treatment of all aspects of cladoceran morphology (including thoracic limbs), with high-quality drawings. It also provides SEM photos (though of varying quality). However, there are various repeatedly occurring typos and expressions that can be improved, which I have corrected or commented in the annotated manuscript file. The accompanying molecular data are discussed from the systematic perspective, and are important for interpretation of the morphological data and vice versa. I do have various comments on how the methods (and partly results) are presented, mostly provided in the annotated manuscript provided as a separate file.

Introduction is rather brief but to the point. When the results of molecular analyses are discussed in the manuscript, it is not always easy to differentiate between new data and those already presented by Taylor et al., this is something the authors should highlight more thoroughly. The discussion is the section that can be most improved –some of its parts seem like rather haphazardly amassed information, which, although relevant, could be arranged more smoothly. Occasionally, I miss references to statements in the text, or feel some statements are unnecessary (these parts are commented in the annotated MS).

Taxonomic sections:
I have indicated various typos and awkward expressions (that are often repeated across multiple taxa) in the annotated manuscript.
Differential diagnoses are written without comparison with other taxa, sometimes the differences are rather mentioned elsewhere in the descriptions. If the characters described in this section are unique for the given taxon, it should be clearly stated. I would nevertheless suggest that key differences between the focal taxon and the others are specifically stated. Alternatively, a table summarizing the differences in key taxonomically relevant characters among taxa or populations of the S. kingii group in a concise manner could be helpful.

Figures:
I am not convinced the violin plots (fig. 3) are informative – these are based on pairwise divergences, so obviously their shape heavily depends on the number of sequences available for a particular clade. Considering that the sequences were not selected to be representative but summarize all the available data, the patterns are not comparable among species groups. If the authors decide to keep the plots as they are, they should interpret them more thoroughly.
In the descriptions of limbs, the setae in the same figure are often repeatedly labelled with the same numerical values (when on different part of the limb). I fully understand that the vast majority of readers interested in thoracic limb structure will not have any problems with this. Those who want to learn more and want to orient themself in the figure and match it to the text, however, may find this challenging, especially when the different parts of the limb are not labelled themselves. Consider adding extra labels to differentiate limb parts.
In SEM photos, it would help if relevant structures are indicated by arrows or symbols. The photos are of very varying quality and while I understand that is often due to quality of the original material, at least the authors should make sure the readers properly interpret them.
Fig. 18C does not have a scale for parts other than A and B
Fig. 4B seems to depict a distorted specimen. Is there a reason for that?
Scale bar is invisible in fig. 20L
Fig. 21 is in my opinion unnecessary, a little text will deliver the same information, and the paper is long even without 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: PARTIAL REVISION OF THE NEUSTONIC GENUS SCAPHOLEBERIS SCHOEDLER, 1858 (CRUSTACEA: CLADOCERA): DECODING OF THE BARCODING RESULTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper, in my opinion, is an excellent example of combining classical morphology and molecular genetics methods in taxonomical studies, which are frequently biased one way or other. It deals with ecologically important genus of littoral cladocera, and has potential to be well-cited.

Figure 11 is badly composed, drawings (which are very good by themselves) are located too closely to each other, it is hard to distinguish between them. In my opinion, such composition is rather unrespectful for the readers. I strongly suggest it should be rearranged, probably changing size of each drawing. Morphology of postabdominal seta (11 K) is fully illustrated on drawing of postabdomen (11 I), figure 11 K gives no new information and can be ommitted.

I'm not a native speaker, so I'm unable to judge English of the paper.
Experimental design: No comments
Validity of the findings: No comments
Additional comments: In my opinion, the paper can be improved if authors include identification key for the kingi-group of Scapholeberis.


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: PARTIAL REVISION OF THE NEUSTONIC GENUS SCAPHOLEBERIS SCHOEDLER, 1858 (CRUSTACEA: CLADOCERA): DECODING OF THE BARCODING RESULTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This paper is a fine example of an integrative approach, and illustrates nicely how molecular markers can guide taxonomical work. The point that taxonomic labels in Genbank and iBOL are often preliminary or even directly wrong is not new, but underlines the importance of supporting barcode libraries with voucher specimens available for morphological analysis by specialists. An interesting aspect is the observation of evolutionary rate differences between genera, which bears on the utility of molecularly defined taxa (like BINs in the iBOL database).
The paper includes COI results that complement mtRNA results from a previous paper. Although the phylogenetic reconstructions based on these markers are largely congruent, some interesting discrepancies occur. These are briefly discussed. The authors conclude that the phylogeny and taxonomy of the subfamily is now “relatively well-done”, but I suspect that this conclusion is slightly premature. A number of clades need further morphological examination, and expanding the geographic coverage is likely to refine the picture. For example, S. microcephala is not represented by populations from its terra typica. Nuclear markers may also alter the picture. Nonetheless, this work represents a significant step forward.
The sequence data are apparently deposited in Genbank as stated, but they are not released yet so I could not verify them.
I have no major objections to this work, and the following comments pertain to details. I hope they can be of some help. In my opinion only a minor revision is require.
Specific comments
Materials and methods, Genetics: References should be provided for the various software applied, as done for MrBayes. These are mostly well known, but the statement about BOOSTER providing less ‘eroded’ support values particularly needs a reference (presumably Lemione et al. 2018).
L. 102-103	«Selected individuals were placed into the plates…»  What kind of plates is meant?
L. 110-111	Please provide information on primers used for sequencing
The bulk of this paper deals with morphological details, and below follow a series of details from descriptions and figures which should be addressed. I note that in figures of limb III some setae are labelled with a question mark. I recommend that the use of question marks should be explained in the Materials and methods section. There are some inconsistencies in how these setae are referred to in the text and in the figures (see below).
L. 153		OLD should be ODL
L. 194		må sjekkes NCBI
L. 317		Limb III endite 3 seta «5?» in text is probably designated just «?» in Fig. 6C.
L. 320		Seta 1 in text (on distal corner of the gnathobase) seems to be labelled “1?” in Fig. 6C
L. 470		Reference to Fig. 11 D is erroneous, as the figure shows the labrum (not the ventral carapace margin)
L. 476		Delete “in” in last sentence
L. 480		Reference to Fig 12 I-J should be Fig. 11 I-J
L. 482		ditto
L 484		Reference to Fig. 10 L should be Fig. 11 L
L. 498-499	“Two ejector hooks of different length. Two ejector hooks almost similar in size”. According to the figures, only the latter statement seems to be correct.
L. 508		Seta called “5” in text probably corresponds to “?” in Fig. 13G
L. 511		Seta called “1” in text seems to be “1?” in Fig. 13G
L. 569		Reference to Fig. 16E should be Fig. 17E
L. 571		Reference to Fig. 16E must be a mistake
L. 579		Reference to Fig. 16F should probably be Fig 16C (?)
L. 585		Reference to Fig. 17A should probably be Fig 16A (?)
L. 614		Reference to seta a-d covered by short denticles – should probably be setae 1 and 2?
L. 646		“cased a surprise” – maybe “caused a surprise”?
L. 647		Insert “the” before “real distribution”
L. 652		Insert “the” before “distribution”

Figure 1, Legend, final sentence: «…just the only localities are represent» doesn’t make sense, please rephrase
Figure 2, Legend: If colours represent species groups, please add information on the blue-coloured group (S. cf. microcephala group?)
Experimental design: The study includes all material available at the time of submission, and is in that sense comprehensive. The data are adequate for testing the phylogenetic hypotheses addressed. No objections.
Validity of the findings: The conclusions drawn are supported by the data and the analyses presented. No objections.
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: PARTIAL REVISION OF THE NEUSTONIC GENUS SCAPHOLEBERIS SCHOEDLER, 1858 (CRUSTACEA: CLADOCERA): DECODING OF THE BARCODING RESULTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript have improved in most aspects that were commented upon by the referees. While I do believe that some figures may have been removed or improved, I understand the authors' decision to stick to their original ideas.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I have throroughly checked the non-systematic parts of the revised paper (and only briefly went through the tracked changes in the systematic part). I trust the authors they have carefully checked all details in the systematic section.

I do have a few additional minor corrections in the text (typos, inconsistencies, suggested improvements), these are marked in the annotated PDF. Overall, I am happy with the present version, and look forward to seeing it published.


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: ANTIBACTERIAL ACTIVITY OF HUMAN DEFENSINS AGAINST STAPHYLOCOCCUS AUREUS AND ESCHERICHIA COLI
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article was written clearly, including sufficient background, intact structure/tables/data and good results.
Experimental design: Activity of three defensins against clinical S. aureus and E. coli and their combination with antibitocis have been conducted rigorously; the methods in this study were described in detail.
Validity of the findings: The data in this study will provide a good guidance for clinical application of defensins.
Additional comments: Author detected the antimicrobial activity of three human defensins (HNP-1, hBD-1, 274 and hBD-3) against clinical 27 S. aureus and 24 E. coli isolates. The combination of three defensins with rifampicin or amikacin against these clinical isolates was assessed by FICI. It is very interesting work; similar to antibiotics, some AMPs also develop bacterial resistance. So, please consider the resistance of AMPs although AMPs may be one of alternatives to antibiotics in the future. However, some questions need to resolve before publishing:
Please give the resources of 27 S. aureus isolates and 24 E. coli isolates if it is possible.
Table 1: please give the unit of length.
Table 5: please indicate “-”; “since MIC values of …were > 64 mg/L or since MIC of …was > 64 mg/L” in legend.
What about the resistance of three defensins?
Line 116: It is uncompleted sentence “…modified according to…”
Other minors:
Line 120-131: lowercase ml and μl
Table 4, 5: numbers in bold in column 3-5
Line 293-295, 315-316, 320-321: the formats of references.


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

Input:
Title: ANTIBACTERIAL ACTIVITY OF HUMAN DEFENSINS AGAINST STAPHYLOCOCCUS AUREUS AND ESCHERICHIA COLI
Review round: 1
Reviewer: 2

Output:
Basic reporting: The structure of the article adheres to the PeerJ guidelines, however there is an imbalance in the information content of the sections. While the introduction and the results are formulated concisely, the discussion section is rather lengthy and contains discussion about concept that are far beyond the research question that has been addressed by the study. For example, the author discussed the disadvantages of peptide stability during human usage over two paragraphs and provides an example concept on how to solve this (cyclic AMPs), however, peptide stability was neither monitored in this study nor was the study designed in such a way that peptide instability due to human peptidases would have been an issue. I highly recommend to use the results of the study as a fundament for the discussion and thus write the discussion as concise as the rest of the article.

Apart from that, the article is nicely written, well-structured and formulated in a clear English. All arguments presented by the author can be easily followed. However, there are some minor mistakes (e.g. usage of wrong words as in line 121: I assume the author wanted to use the word "diluted" not "dissolved"). I would therefore recommend to proof-read the article by a native speaker before final publication.

The author provided a supplementary file containing the MIC data (that also have been shown in the main result tables) as well as the results from the checkerboard assays and the calculation of the FICI. This data is labeled as “raw data”. While the dataset seems to be complete, it is not real “raw data” but has been processed already. For example, the MIC values have been provided in a consolidated form using a non-disclosed method instead of providing the value for each independent MIC experiment. I would recommend to add the single measurement values for each of the experiments (“raw data”) in addition to the consolidated values (e.g. mean) as they can be helpful for the readers to judge variation of the assay.
Experimental design: The concept of the study and the experimental design the author has chosen is puzzling: In the introduction the author justifies the importance of his work with increasing antibiotic resistance (39ff) and suggest the usage of AMPs together with conventional antibiotics as potential solution to antibiotic resistance (91f). In the discussion the author furthermore connects the data obtained in this study to a potential new strategy for overcoming antibiotic resistance (186ff). The message that is transported with this argumentation is: the use of AMPs together with antibiotics might help to reduce the impact of antibiotic resistance (i.e. makes resistance strains susceptible to the antibiotic again). While this has been postulated and shown by others (e.g. DOI: 10.1128/IAI.71.7.3730-3739.2003) the experimental design cannot support this hypothesis: The author has selected the antibiotics rifampicin for S. aureus and amikacin for E. coli and showed synergistic effects with AMPs, however, none of the strains was resistance against the antibiotic tested. The question if the usage of AMPs together with the antibiotic is really capable of pushing MIC values of resistant strains below the clinical breakpoints (and thus makes the antibiotic useful for the treatment of such strains again) remains therefore unanswered. In case of the selected antibiotics such an observation would be highly relevant as resistance against both molecules is typically based on target modification or compound inactivation. Interestingly enough, the author did include strains with various antibiotic resistant phenotypes in the experiment e.g. the S. aureus strains SA9 to SA27 are amikacin or methicillin resistant. Even though the author did use amikacin in his study, he did only determine FICI values of AMPs and amikacin against E. coli (which are all amikacin sensitive) and not against the resistant S. aureus strains such that a real benefit of co-treatment of AMP and antibiotic against a specifically resistant strain has not been shown. Using this setup, the claim to contribute to a potential solution to the antibiotic resistance crisis cannot be made. I would either urge the author to perform an additional experiment where e.g. the AMN or MRSA phenotype strains are indeed tested together with AMP + amikacin or methicillin (i.e. using an antibiotic where the strain has really acquired resistance to), or avoid making the claim that the cotreatment presented in this study could help to overcome antibiotic resistance.

Minor issue: The author referred to the peptides as recombinantly produced (99f) by an external provider (Cloud-Clone, USA). The author furthermore listed the sequences of the peptides in table 1. When checking the peptides at the catalog of the provider I realized that those are his-tagged. However, the author did not add the his-tag in the sequence table. If a his-tag is indeed present, it would be good to list the tag in the table and mention this in the text clearly as this might have an impact on the activity of the peptide.
Validity of the findings: Antibiotic susceptibility is tested under standardized conditions as defined in CLSI or EUCAST guidelines. This includes the usage of Mueller-Hinton broth (MHB) as medium for cultivation of the strains. While the author used EUCAST guidelines to test antibiotic susceptibility of the clinical isolates against standard antibiotics (108), the protocol was changed fundamentally for testing synergism with AMPs (121ff). Here the author uses 48-fold diluted MHB (2.1%) for testing. Such a dilution changes salt concentration and osmolarity of the medium dramatically, which are know to have a direct effect on the integrity of the cell membrane of bacteria. The AMPs used in this study are membrane-active and the author (and others) postulate that the synergistic effects of AMPs with antibiotics are due to increased permeability of the membrane for antibiotics (i.e. the antibiotic reaches the target more efficiently). Testing synergism under such a highly atypical condition raises serious concerns about the validity of the findings described here. As the synergistic effect is the key finding of this study, I would highly urge the author to repeat the experiment under conditions following EUCAST guidelines or give a clear indication why such conditions have been used for testing and how this would translate to a potential application.
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: ANTIBACTERIAL ACTIVITY OF HUMAN DEFENSINS AGAINST STAPHYLOCOCCUS AUREUS AND ESCHERICHIA COLI
Review round: 2
Reviewer: 1

Output:
Basic reporting: It includes a clear desicription of backgroud and context.
Experimental design: The experiment was designed well and this research is meaningful.
Validity of the findings: Authors have provided all data and the conclusion are well stated.
Additional comments: Authors have resolved my questions.


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

Input:
Title: ANTIBACTERIAL ACTIVITY OF HUMAN DEFENSINS AGAINST STAPHYLOCOCCUS AUREUS AND ESCHERICHIA COLI
Review round: 2
Reviewer: 2

Output:
Basic reporting: The author has taken care of all issues raised by me in this section. Thanks.
Experimental design: By rewriting some parts of the manuscript the scope of the study now becomes clearer and the context now is correct.
Thanks to the author for the explanation regarding the nature of the peptides.
Validity of the findings: Thanks for the clarification. Indeed, from the section written in the materials and methods I, mistakenly, assumed that diluted MHB was used for the experiments.
I would suggest that the concentration of MHB is ether given as amounts of each of the components (2.0 g beef extract, 17.5 g casein hydrolysate, 1.5 g starch), or as total amount of medium powder (21 g/L) instead of %. This will avoid confusion.
Additional comments: All points raised during review have been addressed. Many thanks!


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

Input:
Title: SPATIALLY RESOLVED DENDRITIC INTEGRATION: TOWARDS A FUNCTIONAL CLASSIFICATION OF NEURONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. Line 40: "Filters" should be "filter", just grammatically.

2. Line 39 -1: If by punctual you mean point-neuron models, these have no dendrites at all.  Furthermore, the statement, "dendrites are not passive media that filters electric input" makes it seem
like there is no passive filtering at all, which there is.  More generally, the study clearly focuses on active, nonlinear properties of dendrites, but the article would improve by acknowledging the existence of passive, linear properties, and especially by briefly explaining your reasoning for focusing on dendritic spikes.

3.  Table 1: Please include brain region for each cell - for instance, hippocampal vs cortical pyramidal cells

4.  While I understand that the model has been previously published elsewhere, I believe this study would improve from a slightly more detailed description of it.  Could you elaborate on the justification for the probability of spike propagation between compartments being < 1?  Is there experimental evidence that in the absence of inhibitory inputs, dendritic spikes fail to propagate once initiated?
Experimental design: 1. The list of included cells is heavily biased towards pyramidal cells.  Adding some more diversity to the cell types investigated would greatly increase
quality of the study.

2. Do you perform any quality control on morphologies you're using (i.e. check for irregularities in diameter or other artifacts)?  Some  artifacts are present in morphologies available on NeuroMorpho, and sometimes morphologies from certain labs can be plagued with specific problems.  Some of these probably have little impact on the results, but it would be helpful to know if the cells you chose pass any sort of initial testing.

3. It seems as though the dendritic spikes and backpropagating action potentials are treated equivalently here.  If this is not the case, please clarify.  If it is, however, I do not believe there is sufficient justification.  Since spikes generated in the dendrites are mediated by NMDA or voltage-gated calcium channels, and backpropagating action potentials are mediated by sodium channels, this will impact the spiking dynamics, or in the context of this
model the state transition probabilities.  I would expect this would also distinguish their impact on energy consumption.

4.  What seems to me a shortcoming of the model is that the probability of generating a spike
in one compartment is not influenced by the synaptic activity (subthreshold post synaptic potentials)
in adjacent compartments. Another is the uniformity of dynamics. Different types of spike are generated in different parts of the neuronal arbor.  Furthermore, some review, even if cursory, of what has been seen experimentally regarding dendritic spikes in the cell types studied here.  For instance, are dendritic spike as prevalent in pyramidal cells as in Purkinje cells?
Validity of the findings: 1.  How does categorization of cells based on energy consumption compare to their anatomical and
physiological categories?
Additional comments: This study addresses some important, pressing questions in neuroscience: What is the relationship between morphology and dendritic spiking, and what are the energetic requirements?  The authors employ interesting and novel methods to explore these questions. I have two general comments that if addressed I believe will greatly improve the manuscript. First, while all models make simplifications, I think it would be worth further addressing what this model ignores and why it ignores it.  Second, I think it would be useful to try drawing more of a connection between your results and physiology (e.g. What particular cell types might belong to which energy consumption categories? Or how does the dynamic range of dendrites observed in this study compare to experimentally observed dendritic spike frequencies?)


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: SPATIALLY RESOLVED DENDRITIC INTEGRATION: TOWARDS A FUNCTIONAL CLASSIFICATION OF NEURONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript is well written overall with sufficient background context and references provided. However, the following points might be improved for readers to better comprehend the major findings of this manuscript.

1. At the end of the introduction, the authors stated that the analysis of the topological structure of dendritic trees would help the classification of neurons. Here the authors should clarify what it means to classify neurons, in terms of functionality, or types of excitatory/inhibitory synapses, or anatomical regions, or consumption of energy.

2. In the method section, the authors did a great job describing the SIRS model but the readers will understand more easily and intuitively if the equations are provided explicitly.

3. In the method section, it seems that the authors did not specify which software/HPC was used to run these simulations.
Experimental design: 1. The authors selected 26 digital reconstructions from NeuroMorpho. However, it is unclear why these 26 neurons were picked. It will make the study more impactful if the authors show that the samples in this study are representative of most neuronal topological structures.

2. The use of network metrics such as closeness centrality is very clever in evaluating the neuronal structure. However in this study based on SIRS model, only excitatory input is considered whereas in reality each neuron is embedded with a combination of inhibitory and excitatory inputs. The coexistence of inhibitory and excitatory inputs, theoretically, could make the spiking properties much more complicated. I am wondering if the authors could provide some insight on how the addition of inhibitory input would affect the classification.

3. SIRS model, in terms of computational cost, is relatively low. In this case, is it possible to test one neuron from each of the three categories by imposing a soma-to-soma connection within an Erdos-Renyl network given a fixed connection probability? On a network level, consumption of energy and closeness centrality would be more functionally relevant.
Validity of the findings: Based on the various centrality and consumption of energy properties, the authors proposed a 3-category classification of neurons. However, if possible, a more thorough functional implication is appreciated to show if this classification is any indication with respect to its anatomical region.

Furthermore, to validate the symmetry of the dendritic modeling, the manuscript will be more impactful to include some electrotonic analysis. For example, dendritic structures from NeuroMorpho could be imported in NEURON or other simulators, where the inward/outward impedance could be easily computed. I understand that at this stage adding in dendritic diameters would add considerable complexity, but this type of validation is necessary to make any functional connection between dendritic topology and firing properties.
Additional comments: The authors proposed a very novel and systematic way of analyzing neuronal dendritic topology by adopting concepts such as the consumption of energy and centrality metrics. In conclusion, the authors classified neurons into three categories based on their dynamic range and firing behavior.

However, in the field of computational neuroscience, multiple simulators are on the market for biophysically realistic modeling of complicated dendritic structure, on both cellular and network levels. With the help of HPCs and parallel computing, multi-compartmental models of neuronal networks have been proposed. Under this circumstance, the insight drawn from a simplified model without dendritic spatial structure or diversified synapses is limited. Therefore several aspects could be improved to make this work more impactful and helpful to the modeling society.


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: SPATIALLY RESOLVED DENDRITIC INTEGRATION: TOWARDS A FUNCTIONAL CLASSIFICATION OF NEURONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I'd like to thank the authors for taking my prior comments, as well as those of the other reviewer, seriously and thoroughly addressing each of them.  I think the manuscript has greatly improved over the previous draft and recommend it should be accepted for publication.


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

Input:
Title: SPATIALLY RESOLVED DENDRITIC INTEGRATION: TOWARDS A FUNCTIONAL CLASSIFICATION OF NEURONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: In the revision, the authors have addressed all of my previous concerns.
Experimental design: In the revision, the authors have addressed all of my previous concerns.
Validity of the findings: In the revision, the authors have addressed all of my previous concerns.
Additional comments: Overall, the revision clarified the major findings and limitations of this work extensively and, hereby, addressed all of my previous concerns.


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: DPM1 EXPRESSION AS A POTENTIAL PROGNOSTIC TUMOR MARKER IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment.
Experimental design: no comment.
Validity of the findings: no comment.
Additional comments: Major comments:
1. Because HCC usually develops from chronic injured liver, the cause of
chronic liver disease (CLD), such as viral infection, alcohol, fatty
liver, is of importance. They should analyze the relationship between
the expression of DPM1/2/3 and the etiology for CLD.

2. There is no comparative analysis between DPM1/2/3 and already-existed
markers such as AFP, DCP, and GPC3. To highlight the significance of
DPM1/2/3, additional analyses would be necessary.

3. The authors documented that HCC cases with low DPM1/2/3 expression
showed significantly longer overall survival. From a perspective of its
biological function (various protein glycosilation), please discuss why
the DPM1/2/3 overexpression contributes to favorable prognosis.

4. It is hard to realize Fig.5. There is no information about genetic
mutations. Amplification is one of the genetic alteration, but not
mutation.

5. They conducted functional enrichment analyses. However, they analyzed
50 genes similar to DPM1/2/3, but not DPM1/2/3. Please clarify this
issue.

Minor comments:
1. Please spell out all abbreviations when they were firstly written.
Additionally, names of cancer types in Fig.1 were spelled out in its
legend.

2. Please confirm that there is no problem to use images downloaded from
Human Protein Atlas in your manuscript. The reviewer has never
experienced such a case.

3. Labels in Fig. 3 was too unclear to recognize. These should be
modified using drawing software.


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: DPM1 EXPRESSION AS A POTENTIAL PROGNOSTIC TUMOR MARKER IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper presents the results of gene expression analysis of DPM1, DPM2, and DPM3 as a potential prognostic biomarker of hepatocellular cancer patients. It describes interesting data on expression of these genes in retrospective data sets. This research contains interesting findings with a focus on DPMS, but there are several questions and comments.
1. The authors represent the relationship between the DPMS expression profile and survival based on online database.  UALCAN, GEPIA, and cBioportal are analytical tools based on TCGA database and others. However, cBioportal uses data of gene amplification as well as gene expression.  Although results by each tool were similar, the role of gene amplification could be discussed in cBioportal.
2. Please provide sufficient information in Figure 1. Do the blue and red labels indicate the normal and cancerous samples, respectively?
3. In Figure 1, statistical significance of the difference between normal and cancerous samples should be stated.
4. Please provide sufficient information in Figure 3. What meaning did the colors refer to?
5. Genetic alteration should be replaced to genomic alteration in Figure 5.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I have no anything else.


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: DPM1 EXPRESSION AS A POTENTIAL PROGNOSTIC TUMOR MARKER IN HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The reviewer considered that major comments 1 (analysis between the relationship between the expression of DPM1/2/3 and the etiology for CLD) and 2 (analysis the relationship between DPM1/2/3 and already-existed markers such as AFP, DCP, and GPC3) was extremely important to improve the quality of your paper. Therefore, additional data based on further analyses, but not discussion, was requested. In addition, they could not respond a major comment 4 (improvement of Fig.5). Alteration of DPM1/2/3 genes would be divided into (Amplification, deletion, somatic mutation etc).
Regrettably, the authors have not followed the reviewers' comments, and the revision is quite insufficient.


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: DPM1 EXPRESSION AS A POTENTIAL PROGNOSTIC TUMOR MARKER IN HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript has been revised well, and the authors respond to the comment point by point.


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: DPM1 EXPRESSION AS A POTENTIAL PROGNOSTIC TUMOR MARKER IN HEPATOCELLULAR CARCINOMA
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript was satisfactorily revised compared with the previous version.