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: ENGRAILED-2 PROMOTES A MALIGNANT PHENOTYPE OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA THROUGH UPREGULATING THE EXPRESSION OF PRO-ONCOGENIC GENES
Review round: 1
Reviewer: 1

Output:
Basic reporting: English has to be revised, the authors were recommended to seek language support.

Sufficient literature references.

Data are well presented.
Experimental design: The adopted experimental design is usual for such (basic) investigations. Figures are self-explanatory; methods sufficiently described in the Material&Methods section.
Validity of the findings: The findings represent an incremental benefit to the current knowledge. The authors were suggested to improve the Discussion section, as this is just a mere repetition of the results.
Additional comments: This study involves the investigation of engrailed 2 and its downstream genes during the progression of ESCC. Using lentiviral-mediated transduction to overexpress or CRISPR/Cas9 to delete EN2, the authors describe the role of this gene in proliferation, migration and invasion of ESCC cells. Furthermore, they characterize the role of SPARC as a downstream effector for EN2. The study brings incremental knowledge to the current literature, data is well presented. The authors should seek a native English speaker to correct through the text whenever necessary; some suggestions are offered below.
Major concerns
1.	The authors indicate that they focus in their study on two cancer cell lines i.e. Eca109 and Kyse109, yet they show in Fig. 5, 6 and 7 experiments only with Eca109 cells. For consistency of data, they should show, at least some of these results, whether they could confirm their results in Kyse109 cells.
2.	In Fig.5E one would welcome showing taller blots (more above and below the bands) and not only the bands themselves.
3.	In Fig. 7, the authors show that SPARC abrogation hampers the pro-oncogenic effect of EN2 suggesting SPRC downstream of EN2. To substantiate these, the authors should investigate whether they can restore the migration / invasion phenotype upon ectopic expression of SPARC after knocking down EN2; with other words to restore the phenotype in Figure 4 upon overexpression of SPARC.
4.	The discussion chapter is a mere repetition of the results. The authors should discuss their findings with respect to what is known so far, provide eventually an outlook to the field.

Figure legends
Figure 2D – please rephrase, CCK-8 assay is just a read-out for cell growth; “….as demonstrated by CCK-8 assay”
Lane: 280-281: please provide reference.
English language
Lane 75: 	should read “All patients…”
Lane 215: 	should read “Here we sought to…”
Lane 217-218:please rephrase
Lane: 222:	should read “EN2 is highly expressed in ESCC…”
Lane 226:	two cell lines used….in the text / three cell lines… in Figure legend / four cell lines presented in Fig. 2A
Lane 243:	“migrated faster…” instead of “much more quickly”
Lane 256-257:please rephrase
Lane 258:	do you mean “assessed”?
Lane 284: 	should read “a drastic…”
Lane 286:	rephrase
Lane 287:	“These data demonstrate…”
Lane 296:	do you mean “containing a mutated EN2…”
Lane 297:	should read “two mutant transcripts…”
Lane 298: 	please rephrase, comprehension difficult
Lane 303:	do you mean “assessed”?


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: ENGRAILED-2 PROMOTES A MALIGNANT PHENOTYPE OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA THROUGH UPREGULATING THE EXPRESSION OF PRO-ONCOGENIC GENES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an interesting study reporting the implication of engrailed-2 (EN2) in the tumorigenesis of esophageal squamous cell carcinoma (ESCC). Overall, the experiments are appropriate and the conclusions seem to be supported by the evidence provided. It is unclear, nevertheless, the rationale for focusing this study on EN2. Other homeobox genes were also found associated with malignant transformation in several tumor types. Thus, it should be clarified further why this study was centered around EN2 and not another homeobox gene(s).

The authors published recently a very similar paper in this journal focusing on HOXC6 in ESCC (https://doi.org/10.7717/peerj.6607). However, there is no mention to their previous study in this manuscript. The authors found similar implications of HOXC6 in the promotion of ESCC cell migration, invasion, proliferation, the activation of oncogenic genes, and claimed that “HOXC6 may be a new significant biomarker for diagnosis, therapy, and prognosis”. Therefore, the results observed for EN2 should be compared with the ones for HOXC6 to address if there is a dependency or if they are completely independent biomarkers.

The microarray raw data performed in this study should be deposited in a public repository, such as GEO or ArrayExpress, in compliance of the Data Sharing policy.

The figures of this study were provided as bitmaps instead of vectors and were displayed substantially pixelated. It would be recommended to provide vector images for graphs and figures other than pictures.

Overall, the writing of the manuscript is clear, although it should be double checked to avoid certain typos, such as ‘identity(Idaikkadar’ on line 56, ‘lentivrial’ on line 228, ‘an drastic’ on line 284 and ‘homoedomain’ on line 302.
Experimental design: The experiments performed in this work seem to be adequate. The pictures of the colony formation assay, however, are suboptimal and show a strong variation in terms of perspective and shadows. It is not indicated if colonies were counted manually or using a software like ImageJ. In case of the latter, the variation in perspective and shadows from picture to picture might represent a confounder.

The unpublished data described in lines 211-212 regarding the evaluation of a panel of homeobox genes in ESCC should be incorporated in the Supplementary section.
Validity of the findings: A major concern of this study is that findings were reported in only a few cell lines and 32 ESCC tumor samples. It would be necessary to validate these findings in a larger and independent dataset, such as The Cancer Genome Atlas (TCGA) or the International Cancer Genome Consortium (ICGC).
Additional comments: Table 1 is not essential to follow the narrative and could be moved to the Supplementary section.


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: ENGRAILED-2 PROMOTES A MALIGNANT PHENOTYPE OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA THROUGH UPREGULATING THE EXPRESSION OF PRO-ONCOGENIC GENES
Review round: 2
Reviewer: 1

Output:
Basic reporting: None at this stage.
Experimental design: OK.
Validity of the findings: OK.
Additional comments: None at this stage.


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: ENGRAILED-2 PROMOTES A MALIGNANT PHENOTYPE OF ESOPHAGEAL SQUAMOUS CELL CARCINOMA THROUGH UPREGULATING THE EXPRESSION OF PRO-ONCOGENIC GENES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors fulfilled many of the suggestions requested by this reviewer, such as depositing the microarray data in a public database, showing clearer colony formation assays and improving the English, among others. However, the authors failed to provide a rationale for focusing this study on EN2. An explanation based on a bioinformatics analysis of TCGA data is provided in the rebuttal letter, but not in the manuscript. Thus, the authors should provide this information in the manuscript, including the corresponding figure of the TCGA analysis. In addition, the authors should include the figure of the lack of correlation between EN2 and HOXC6 mRNA expression as supplementary figure and provide further insight about their potential use as biomarkers in esophageal squamous cell carcinoma despite not being correlated.
Experimental design: It is nice that the authors repeated the colony formation assay to show better pictures for the Kyse150 cells in Fig. 2G, although this was not necessary. However, it is concerning that the figure of the quantification for the new colony formation experiments (Fig. 2H) is exactly the same as in the previous experiments.
Validity of the findings: A major concern of this study was that findings were reported in only a few cell lines and 32 ESCC tumor samples. The authors did not show a validation of their findings in a larger and independent dataset, such as The Cancer Genome Atlas (TCGA) as requested, even though they claim to have done some of such bioinformatics analyses from TCGA. Therefore, the authors should provide TCGA analyses to support their findings in the manuscript.
Additional comments: No additional comments


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

Input:
Title: INVASIVE VEGETATION AFFECTS AMPHIBIAN SKIN MICROBIOTA AND BODY CONDITION
Review round: 1
Reviewer: 1

Output:
Basic reporting: Excellent. See attachment for details.
Experimental design: Excellent. See attachment for details.
Validity of the findings: Excellent. See attachment for details.
Additional comments: This is a well-designed, rigorous study and the manuscript is exceptionally well written and transparent. I had a few questions and suggestions for minor revisions. Please see attached document for details, but in a nutshell, my main comments were:
-  I wondered why there were no tests to determine which ASVs differed among treatments.
-  I asked for clarification on whether there were differences in salamander microbial community compositional among treatments
- I had a question/suggestion about how you tested the extent of filtering occurring at the host-environment interface.


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: INVASIVE VEGETATION AFFECTS AMPHIBIAN SKIN MICROBIOTA AND BODY CONDITION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have presented the main objective of the study, the results and conclusions clearly. The article is very well written and easy to understand.

As a minor comment, I suggest that the results from the Bd analysis be presented in the abstract, particularly because the abstract currently mentions that individuals were tested for Bd. This could be done briefly (e.g. in one sentence that mentions that the incidence of Bd in the study was very low: one Bd+ individual).
Experimental design: Overall, the study was well designed to assess how Eucalyptus invasion might influence amphibian skin bacterial communities and body conditions.

As minor comments:

 1- While the introduction clearly explains how the amphibian skin bacterial communities can be a good model system to assess the impact of Eucalyptus invasions on host-associated microbial communities, I believe that the knowledge gap could be better defined here (please see general comments).

2- The statistical analyses conducted in this study are appropriate for assessing the changes across the two type of forests (Eucalyptus vs. Quercus dominated forests) in the skin bacterial communities and body condition of Batrachoseps attenuatus. However, I recommend that the authors include more details about the statistical analyses. For instance, although details are provided in the R-script, it is relevant to mention: 1) that normality tests of response variables were conducted; 2) the error distribution used in the mixed-effect models; and 3) that significance of predictor variables was calculated with likelihood ratio tests. In addition, it would be informative to readers to know which R functions and packages were used for the analyses.

3- In addition, as a suggestion, the presentation of the results from this study could be improved by conducting an analysis showing the differentially abundant ASVs/indicator ASVs across sampling sites, which explain a larger portion of the observed variation in community structure. For visualization purposes, the identified indicator ASVs could be presented either in a heatmap or a stacked-barplot showing the differences in relative abundance of the ASVs (at the phyla level or family level, if possible) across sites or forest types. An indicator species analysis or a linear discriminant analysis Effect Size (LEfSe) might be used.
Validity of the findings: In this study, the authors aimed to determine the potential effects of Eucalyptus dominated forest on the skin-bacterial communities and body conditions of the salamander species Batrachoseps attenuates. This study would be a great contribution to our current understanding on the ecology of amphibian-associated microbial communities, especially since this study focused on a threat to amphibian diversity (i.e. invasive species) that has not yet been explored in the context of skin bacterial communities.
Additional comments: Line 48 – It would be good to be more specific in describing the effect of invasive plants on the ‘patterns’ of native communities. For instance, could it be an effect on the natural diversity pattern of the native communities across a gradient? or a change in the structure of the native communities by changing the relative abundance of dominant species?

Line 68 – Please replace ‘to’ with ‘in’.

Line 72 – Consider replacing ‘Cascading’ with ‘Resulting’.

Lines 86-88 – It seems that this is a good place to highlight the knowledge gap and/or further explain the rationale of the study.

Line 89 – Please clarify the phrase ‘potential for invasive vegetation-induced changes’ to something like ‘…potential changes induced by invasive vegetation on the microbial communities…’.

Line 92 – I would recommend to start this sentence with ‘Specifically,’ since this sentence objectively describes the approach taken to assess the changes induced by the invasive plant on the skin bacterial communities.

Lines 118-120 – It is not totally clear if the same sites from Sax (2002) were used in this study. If so, it would be good to clearly refer to Sax (2002, Table 1) in order to direct the readers to where they can find the elevation, slope, and slope orientation of the study sites.

Line 122 – Please specify the new site in parentheses: (N#).

Line 127 – Were the salamanders caught using gloves? If so, was a new pair of gloves used for each salamander? Please provide such details.

Line 129 – It seems that there might be a discrepancy between the swabbing method described in Hernández-Gómez et al. (2017b) and that used in this study. Hérnandez-Gómez et al. (2017b) mentioned that individuals were swabbed with cotton tip swabs for 30 seconds, whereas it is reported here that individuals were sampled by applying the cotton swab 30 times. Please clarify.

Line 131 – It would be good to mention how the authors controlled for recapturing the same individuals during the field surveys.

Lines 144-146 – Assuming that the original concentration of the master mix is 2X, a 15 ul final volume seems insufficient given the reported concentrations of primers and the volumes of DNA template and sterile water. Thus, I believe that the total reaction volume might not be correct. It seems to me that it should be 25 ul. Please verify.

  Lines 152-153 – Same comment as above.

Line 176 – Please add “ 6:e27295v2 https://doi.org/10.7287/peerj.preprints.27295v2” after the words ‘PeerJ Preprint’ in the Boylen et al. (2018) reference.

Line 202 – Perhaps the categories ‘Eucalyptus/Quercus skin’ could alternatively be call ‘Eucalyptus/Quercus salamander-skin’.

Line 204 – I would suggest a minor change in the subtitle: ‘Effects of Eucalyptus invasion on soil bacterial composition, diversity, and stability:’.

Line 210-211 – Considering that the authors are using beta diversity metrics that take into account community composition (unweighted UniFrac) and also relative abundances (weighted UniFrac and Bray-Curtis), I think that the authors could say that they are assessing not only the changes in ASV composition, but also in community structure.

Line 220 – Same comment as above. Suggested title: ‘Effects of Eucalyptus invasion on B. attenuates bacterial composition, diversity, and stability:’

Lines 224-226 – It is not clear in this analysis whether the calculated proportion of shared ASVs at the individual-level, or a presence-absence matrix of all shared ASVs, was used as response variable. The error structure used in the described GLMM (i.e., binomial) suggests that presence-absence data was used. Please clarify.

Line 232 – Same comment as the one from lines 210-211.

Line 251-266 – I recommend to remove the description of the protocol used to detect and quantify Bd from the ‘Statistical Analysis’ section, and to add a new sub-section just for the Bd protocol – probably right before the ‘Statistical Analysis’ section.

Lines 268-273 – I would recommend to add this information in the ‘Material & Methods’ section. Perhaps the number of salamanders sampled could go within the ‘Field Methodology’ sub-section, and the information associated with the sequence processing, including the SRA number, could go within the ‘Microbiota sequence analysis’ sub-section.

Line 277 – Please report the ‘F values’ of the Adonis tests as ‘pseudo-F’, given the permutational approach of the test.

Line 285-290 – I would recommend to report in this text the number of core ASVs associated with the sample types (i.e., Eucalyptus soil, Quercus soil etc.), as well as the number of these core ASVs per phyla.

Line 287 – Are the values in parenthesis an average of the ‘% of reads per sample’ across all samples? Please verify.

Line 293 – It would be informative to provide an average and a standard deviation of the calculated proportion of shared ASVs between the skin of salamanders and their corresponding soil samples across the two habitat types.

Line 311-318 – same comment as the one from lines 285-290.

Line 325 – The prevalence of infection was calculated using 51 as the total number of sampled individuals, however, based on the number of samples swabbed for the microbial analysis, it seems that the total number of samples should be 50. Please verify.

Line 355 – Please replace ‘seems to’ with ‘might’.

Line 360 – It seems that changes in relative abundances of core taxa might be associated with changes in community structure rather than with alpha diversity directly. Perhaps it would be good to mention a potential mechanism by which changes in relative abundance of core taxa might directly influence alpha diversity (e.g., increased probability of a less abundant bacteria to disappear due to competitive-exclusion). Another option could be to just remove the word ‘consequence’.

Line 368-370 – Considering that the authors determined a lower alpha diversity in the skin bacterial communities of the salamanders from the Euclyptus dominated forests, it would be relevant to expand this argument with a brief discussion about what the implications of the observed reduction in alpha diversity might be in terms of the salamanders’ health/fitness.

Line 416 – This sentence states that body condition was not correlated with skin microbiome characteristics, however, no methods neither results testing this statement can be found throughout the manuscript. Please verify.

Figure 3 – Please add (D, E, F) after ‘… and Batrachoseps attenuates skin microbiota samples’.


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: INVASIVE VEGETATION AFFECTS AMPHIBIAN SKIN MICROBIOTA AND BODY CONDITION
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The comments and suggestions have been adequately addressed.


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

Input:
Title: THE E2F FAMILY AS POTENTIAL BIOMARKERS AND THERAPEUTIC TARGETS IN COLON CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper, authors utilize bioinformatics tools (such as GEPIA and DAVID) investigate the role of E2F family in colon cancer tool, followed by real time PCR validation. First, I don't know why author only investigate the correlation of E2F and colon cancer, rather than other cancer types? In addition, I don't think the method used in the study with enough novelty. The experiment description is not very clear as well. These are also lots of typo errors in their manuscript! Considering the current study provides limited insights, I do not feel that the paper overall presents a clear concept to warrant publication.

Some further comments are given below.

Q1. In the introduction part, why you only interesting in E2F and colon cancer, rather than other cancer types? The E2F genes show specific expression pattern in colon tissue (can check GTEx)? Is it more significant change pattern (fold change) between tumor and normal tissue? The author should explain this!

Q2: Line 70, about the sample number. In fact, there are only several hundred normal samples in the TCGA samples. The author should read the reference carefully~! The 8587 normal samples should come from GTEx database. You should add more clear description about your data used in the study!

Q3. Line 73, boxplot is just a method for visualization. It is not suitable to use detect

Q4. Section 2.3, add more description. How many groups? Where is the group information come from? I can not follow you if without Figure.

Q5. Section 2.4, please cite the reference of HPA.

Q6. Too many typo errors, e.g. line 87 Gene ontology (GO) should be Gene Ontology (GO). Similar to Cellular Component (CC) etc.

Q7. Line 92, about DAVID software, please cite the reference and provide the version! Line 96, similar to ImageGP software.

Q8. Line 99, 32 should be "Thirty-two". Arabic numerals can not be used as initial of one sentence.

Q9. About Section 2.5, please add more description for your method. What about the RNA quality for RT-PCR? RIN value > 7 or 8? How many technical for each gene? What about the sd? What software used? How about the correlation between RT-PCR and TCGA?

Q10. Section 3.1 and 3.2, I am confused, why you treat the expression level and TMD as two parts? Is there any difference? You just focus on relative compare? In addition, about the P value is raw p-value, or after multiple corrections? Please also specific which test you used. Check GEPIA.

Q11. Line 124, why you say strong correlation? Which test? P-value? Is there any statistical analysis?

Q12. Why you did enrichment analysis? There are only 8 genes! I think at least 50 genes are need for gene set enrichment analysis. If they are transcriptional factors, you should focus on their target genes!

Q13. Line 142, which test?

Q14. No conclusion part?

Q15. Figure 6, what's the error line? Standard deviation? I can't see the lower boundary.
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: THE E2F FAMILY AS POTENTIAL BIOMARKERS AND THERAPEUTIC TARGETS IN COLON CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a very interesting paper that investigated the role of E2F family in colon cancer.
In general the manuscript is very good and English language is adequate. Please check throughout the text for grammar and spelling errors; please provide a full explanation for all the acronyms when they are mentioned for the first time in the text (i.e. line 69 GEPIA).
The figures are very clear and useful.
I would suggest to include more statements in the discussion section and updated references in order to emphasize the growing importance of biomarkers for diagnosis and therapy of colorectal cancer    (i.e.  Vacante  M et al, World J Clin Cases. 2018; Barbagallo C et al, Mol Ther Nucleic Acids. 2018).
Experimental design: Please in the statistical analysis paragraph, report the names of the tests used to calculate the statistical significance (i.e. t-test; chi-square).
Validity of the findings: The results look interesting and appealing. I would include a statement in the conclusion paragraph on the possible clinical or surgical implications of the results and future perspectives as regards the prognostic or predictive role of these novel biomarkers.
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: THE E2F FAMILY AS POTENTIAL BIOMARKERS AND THERAPEUTIC TARGETS IN COLON CANCER
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: Please add the references for real time PCR data.
Additional comments: This manuscript investigated the association between E2F family genes and colon cancers through a series of bioinformatics analysis on gene expression data, immunohistochemical data, and real time PCR data. Though the findings seem to be valuable, I am not fully convinced by some technical details in the manuscript. My comments are list as follow.

1.	The main conclusion seems to have some conflicts with another E2F family study in colon cancer published on 2014 tilted as “The relationship between E2F family members and tumor growth in colorectal adenocarcinomas: A comparative immunohistochemical study of 100 cases”. It has already reported E2F1 and E2F2 as biomarker of colon cancer. So the sentence in the conclusion part of this manuscript: “E2F1, E2F2, E3F3, E2F5, E2F7 and E2F8 are novel biomarkers for the diagnosis of colon cancer.” needs to be revised.
2.	A follow-up question of my question 1 is that what are the E2F family’s expression in tumor versus normal from TCGA COAD data only? TCGA COAD has around 40 normal samples which should be enough to reproduce or validate some results. My major concern is that GEPIA combines the normal samples from TCGA and GTEx. Although the batch effect correction is considered in GEPIA, it is still worth investigating the original TCGA tumor versus normal.
3.	The significant p value cut-off is set to 0.05 which usually introduces inflated false discovery rate. It would be better to use p values after multiple testing correction.
4.	In addition to overall survival analysis in figure 4. It is also recommended to use progression free interval (PFI). There are some reports that suggesting PFI in TCGA data has better follow-up comparing to overall survival.
5.	What is the data source of real-time PCR? Please add the corresponding 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: THE E2F FAMILY AS POTENTIAL BIOMARKERS AND THERAPEUTIC TARGETS IN COLON CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: The author have addressed my concern.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The author have addressed my concern.


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

Input:
Title: THE E2F FAMILY AS POTENTIAL BIOMARKERS AND THERAPEUTIC TARGETS IN COLON CANCER
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed all of my comments and concerns in the revised version. I have 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: FACILITATING OPEN-SCIENCE WITH REALISTIC FMRI SIMULATION: VALIDATION AND APPLICATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: I couldn't find anything that could be improved in terms of use of English. Regarding the structure, in the description of the first (validation) experiment, P21 L370, different contributions and considerations regarding the simulated signal are repeated (and already mentioned) on P19 and P20.

You might potentially think to restructure the headings to better fit with the journal guidelines - right now there are 3 main sections: fmrisim, validation and application, with their own subsections of intro/methods/results/discussion. These now read as three separate papers.
Experimental design: I really appreciated the ipython notebooks that can be explored.
Validity of the findings: This tool could really help with planning fMRI experiments by offering a way to simulate outcomes depending on sample size, effect size (for some reason always assumed to be 0.8), timing and type of analysis.

As explained in your discussion(s), nonlinear effects are not (yet) included, but this software goes a long way to have a means that assesses effects of noise on fMRI findings. Do you have plans or a timeline to incorporate the nonlinear effects in this tool?
Additional comments: No further comments; I enjoyed reading this


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: FACILITATING OPEN-SCIENCE WITH REALISTIC FMRI SIMULATION: VALIDATION AND APPLICATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a well-written paper which is sufficiently referenced and provides full sharing of all data and code.
Experimental design: This paper introduces fMRI simulation software building on previously published packages with a new focus on multivariate analysis and matching simulated data with real data. I believe the software is discussed in enough detail and validation of the methods is provided as well as a worked through example of how this software will benefit researchers.
Validity of the findings: The validation studies have been carried out with rigour and demonstrate the usefulness and appropriateness of the package. I appreciate the authors being self-critical on the limits of simulation and being very explicit about the assumptions made during the simulation process.
Additional comments: I believe this paper is a useful addition to the literature and complements previous work on simulating fMRI data. My only remark would be around the usability of software for non-expert researchers. Could you please add a section on which skills fMRI researchers require to adopt your software for planning their experiments? I am personally thinking of what level of programming skills, level of detail of understanding of simulation procedures, etc.


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 HIGH MN(II)-TOLERANCE STRAIN, BACILLUS THURINGIENSIS HM7, ISOLATED FROM MANGANESE ORE AND ITS BIOSORPTION CHARACTERISTICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study conducted for the removal of Mn(II) by microorganisms isolated from Mn(II) contaminated ore soil. The background of the study explained well in introduction part however, required the addition of some point as mentioned in general comments. Figures are relevant but the title should need to detailed information as mentioned in the general comments
Experimental design: Experimental design is explained well which come under the scope of the journal. The experimental results are reported with the instrumental supporting evidences like SEM and FTIR analysis.
Validity of the findings: The results finding is applicable for the removal of Mn(II). Their finding is elaborately discussed with comparison of other study results. Conclusion is well framed and short out the study results.
Additional comments: Introduction: Line 47-49 – Hullo et al. demonstrated……. (Tang et al. 2016). From these references, in what mechanisms used by microorganism for the removal of Mn(II). Explained it.
Line number 63-65 – Reference not given. If the data not published, please provide the methodology of tolerance test.
There is a high fluctuation of environmental condition like pH, temperature (day and night)..etc. in real field condition. The results finding from this study, is that applicable to real field especially Mn(II) contaminated soils?
Elaborate the figure 4 title and What is A and B?.


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 HIGH MN(II)-TOLERANCE STRAIN, BACILLUS THURINGIENSIS HM7, ISOLATED FROM MANGANESE ORE AND ITS BIOSORPTION CHARACTERISTICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.	The authors should think more about the objective of this study and only elucidate relevant information that truly benefits the interested reader. I also noted that relevant information is missing in the introduction.
2.	The results and discussions confirm previous observations and do not extend the available knowledge base of major output from this study. Especially, the section of discussion mostly includes general information and perspectives. Current discussion section is not worthy to interpret major output from this study. I think authors should be improved in discussion section.
3.	Generally, this manuscript was properly written, but there are several spelling errors (first character upper case; singular and plural; tense) in the manuscript. It would be better to use the right spelling throughout the manuscript, and the manuscript needs to be revised by a nativate English speaker.
Experimental design: no comment
Validity of the findings: L29-38: Authors need to focus on the soil environment and bioremediation.
L 76:  Can you give us some examples for the sample characteristics?
L 78-79: Before the samples were stored at −80°C, was there any pretreatment?

L84-90: Provide more detail culturing conditions for your isolation (e.g. which culture media is used in this study?).
L 97: How do you do sequencing of full length of 16S rRNA region using Illumina Hiseq? As far as I known, full length of 16S rRNA regions is impossible using current NGS technology. Please provide your strategy and methodology.
L 103-104: Provide Blast criteria
L288-293: I could not agree with this sentence. It seems to be speculated rather than interpretation from the results.
L 319-320: I could not find any data supporting this sentence. Please provide appropriate results of rephrase this sentence.
L 321: Check English.
L 318-339: I think this paragraph is no meaningful. Careful text editing will improve clarity.
Additional comments: No additional comments


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

Input:
Title: A HIGH MN(II)-TOLERANCE STRAIN, BACILLUS THURINGIENSIS HM7, ISOLATED FROM MANGANESE ORE AND ITS BIOSORPTION CHARACTERISTICS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript entitled “Bacillus thuringiensis HM7 isolated from manganese ore revealed high Mn(II)-tolerance and potential for plant growth promotion” presented the effects of Bcillus thuringiensis for removing manganese at different parameters. However, lots of papers have already announced that Bacillus thuringiensis has the ability to remove heavy metals, as well as the manganese. Thus, I recommend authors should figure out the novelty of this experiment. Please provide some reasonable explanations for the manganese remove mechanisms. Moreover, there are many grammatical errors in your language expression. Hence, this manuscript should be revised very thoroughly. Besides these overall comments, I have some general comments for further improvement in the manuscript.

1.	Was the manganese changed to other compounds or totally absorbed by HM7? Fig. 5b shows that the manganese was fully covered on the surface of microbes, does it mean that the activities of HM7 could be reduce by the accumulation of manganese. On the other words, the manganese was not removed, but absorbed by microbes, right?

2.	The title of manuscript should be changed, because of the plant growth promotion is not the purpose of this experiment.

3.	There are problems with the experimental setup. What is the other parameters when you fixed one parameter (pH, Temp, Conc….)

4.	Analytic procedures was not clearly described. The OD600 is the main analysis method in this experiment, but which is not mentioned in “Materials and Methods” section.

5.	Lots of conjectures were presented in the manuscript without data support. Ex: “Line 186, HM7 might release alkaline substances during growth”. Alkaline is a material which is easily to measure, authors should be better to give practical data when you make an important conclusion.

6.	There is no explanation of Table 3 in the manuscript.


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

Input:
Title: A HIGH MN(II)-TOLERANCE STRAIN, BACILLUS THURINGIENSIS HM7, ISOLATED FROM MANGANESE ORE AND ITS BIOSORPTION CHARACTERISTICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am satisfied the corrections made in the revised manuscript. Therefore, I can accept the manuscript without needing further review.
Experimental design: I am satisfied the corrections made in the revised manuscript. Therefore, I can accept the manuscript without needing further review.
Validity of the findings: I am satisfied the corrections made in the revised manuscript. Therefore, I can accept the manuscript without needing further review.
Additional comments: I am satisfied the corrections made in the revised manuscript. Therefore, I can accept the manuscript without needing further review.


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 HIGH MN(II)-TOLERANCE STRAIN, BACILLUS THURINGIENSIS HM7, ISOLATED FROM MANGANESE ORE AND ITS BIOSORPTION CHARACTERISTICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: There are still lack of data interpretation and analysis, while I believe that current revised manuscript could provide more insights for bioremediation research area.
So, I believe now this is an acceptable version.
Experimental design: no comments
Validity of the findings: no comments
Additional comments: I appreciate that authors addressed the raised comments carefully and reflected those to the revised manuscript.
I believe the manuscript is ready to be published in the journal.


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

Input:
Title: A HIGH MN(II)-TOLERANCE STRAIN, BACILLUS THURINGIENSIS HM7, ISOLATED FROM MANGANESE ORE AND ITS BIOSORPTION CHARACTERISTICS
Review round: 2
Reviewer: 3

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


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

Input:
Title: SCELVIS: EXPLORATORY SINGLE CELL DATA ANALYSIS ON THE DESKTOP AND IN THE CLOUD
Review round: 1
Reviewer: 1

Output:
Basic reporting: Writing:
The article has a clear unambiguous and to my knowledge technically correct English with only minor mistakes that can easily be corrected:

l. 56 “communication need” -> “communication needs”
l. 68 “Further, ,” -> “Further,”
l. 68 “(yet)” -> "yet" or "remove"
l. 73 “… Docker image strongly depend on” -> “… Docker image strongly depends on”
l. 84 “graphic web” -> “graphical web”
l. 129 “in more complex framework” -> “in a more complex framework” / “in more complex frameworks”

References:
The article contains an appropriately amount of references to back up the content and all references matches the content they have been placed in.
A DOI seem to be missing at:
l. 158-160. You might add this: https://doi.org/10.1038/sdata.2016.18

Sections:
Overall I like the different sections. However, the discussion part seems to be very vague and more resembles a summary of the paper rather than a discussion. In that sense it resembles a slightly more detailed version of the conclusion part. If both a discussion and a conclusion are necessary to be included I suggest that the authors in the discussion elaborate a little about for instance the perspectives in the field of single cell analysis/visualization, what the next steps might be (either for the tool or the community in general) to improve these kind of analysis/visualization tools.

Figures:
I generally like the figures in this paper but I have some comments on them:

Figure 1: I think it is a bit of a pity that the figures are so small that you cannot see the details of them so easily. For instance, it is not possible to see the legends on the gene-centric plots. If not making the plots bigger a possible solution could be to make them vectorized so that the reader can zoom in and read. With the figures I received, this is not possible due to the resolution. Also, I would also suggest to briefly describe the two visualization fields “cell-centric view” and “gene-centric view” in the figure caption.

Figure 2: It seems a bit odd that the plots are overlapping, especially when there are only two plots. Again, I think it would be better with higher resolution/vectorized plots. With the current settings it quickly becomes pixilated when zooming in.

Raw code on GitHub:
Generally well-documented code and this I think don't need further improvement to pass. FYI: There are some TODO’s in the code. Also, small inconsistencies are observed in the documentation style in for instance in _version.py. For instance the multiline documentation style for describing the function is a bit different between the Get_keywords & versions_from_parentdir functions. There also seem to be differences in the ways the functions are described. Some functions have formal sentences, while other have first/third person comments e.g. ‘I’/’you’/’we’. I think the documentation could be improved by using a more consistent style instead of mixing the two styles.
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: SCELVIS: EXPLORATORY SINGLE CELL DATA ANALYSIS ON THE DESKTOP AND IN THE CLOUD
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper did  not report the advantage of this tool among other available tools.
Experimental design: The authors in this paper developed a web tool to improve the analysis of single-cell RNA data for non-bioinformatician.
Validity of the findings: I run the tool but gets error after uploading the data
Additional comments: The authors in this paper developed a web tool to improve the analysis of single-cell RNA data for non-bioinformatician. The tool is very beneficial to the field however many limitations should be addressed.
1- I had a difficult time running the tool because of unclear guidance and lack of tutorial. I strongly recommended making a Youtube video for users with all details.
2- Made some examples of Tags such as the below two lines(not everyone understand tags):
docker pull quay.io/biocontainers/scelvis:0.5.0--py_1
 docker run -p 8050:8050 -v data:/data quay.io/biocontainers/scelvis:0.5.0--py_1 scelvis run --data-source /data
docker run quay.io/biocontainers/scelvis:0.5.0--py_1 scelvis --help

3- http://localhost:8050 worked for me not http://0.0.0.0:8050/.
4- When I uploaded the data: hgmm_1k.h5ad, I got nothing.
5- When I  converted the data "dummy_raw.zip", I got the below error:\Internal Server ErrorThe server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application.
6- Scatter, violin and dot plots are not sufficient for the tool.
7- I recommend authors to look at other available tools:https://amp.pharm.mssm.edu/biojupies/
8- Authors should compare existence tools with their tool. What is the advantage?


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: SCELVIS: EXPLORATORY SINGLE CELL DATA ANALYSIS ON THE DESKTOP AND IN THE CLOUD
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper “SCelVis: Powerful explorative single cell data analysis on the desktop and in the cloud” describes the software for visualization of single-cell data with the ability to run both on the desktop and in the cloud. The paper nicely explains the background by the development of this software and shows examples of the software when used.

In general I think the text is nicely written, however, it focuses a lot more on the computational advantages of the method, than on the biological part. If the package is aimed towards biologists with close to no bioinformatics background, I think this should to some extent be reflected in the language of the paper. I do not think the introduction to the computational advantages should be removed from the paper, but some more focus on why it is advantageous to use the software as a biologist would improve the paper considerably.

The language could be improved the following places:
-	Line 40-42: This sentence seems a bit out of place compared to the rest of the paragraph.
-	Line 50-56: I think this explanation is too long and ends up overcomplicating the aim of the package.
-	Line 61-76: The walkthrough of current tools is really informative, but the flow of this paragraph could be improved.
-	Line 90: This sentence is unclear and maybe unnecessary.

The language could be less subjective in the following places:
-	Line 63: “to our knowledge quite rare” is a vague statement.
-	Line 114-115: the sentence seems subjective and unclear.
-	Line 122: The use of “interesting” is subjective.
-	Line 126 + paper title: the use of the word powerful seems subjective and not sufficiently supported by the results in the paper

There are minor mistakes the following places:
-	Line 68: two commas
-	Line 73: depend -> depends
-	Line 91: On the one hand -> On one hand
-	Line 105: 1000 is the exact number of cells in the dataset, the tilde should be removed
-	Line 173: 10x website -> 10x Genomics website

I would suggest the authors to make the paragraph on the different options of data visualization more specific, e.g. instead of “such as cell type” on line 92, it should state exactly the annotations that are possible to view here. If this depends on the annotations provided in the data preprocessing, this should be mentioned. And the phrasing “such as” should be changed.

Figure 1:
-	From the figure now it looks like both an hdf5 file and raw text / cellranger output is needed to run SCelVis. The figure would be better if constructed in a way that makes it clear that only one of these data sources is required. This should also be underlined in the figure text.
-	The axes and letters of the plots are too small. Either the authors should increase the font size so that the numbers and letters are readable, or the plots could be simplified by removing numbers and letters, if the data presented in this figure is not used for further analysis.
-	The plots in general are too small to be clearly understandable, and they could be simplified by e.g. focusing on fewer samples and/or genes.
-	The colors of the boxes are relatively dark on print. Additionally, there’s a lot of colors on the figure, which does not facilitate the understanding. I would suggest the authors to also simplify the plot color-wise.

Figure 2:
-	The overlay of A and B does not work properly, as it hides the majority of the plot in A.
-	The text in the screenshots is too small to be easily read.
Experimental design: I think the paper needs a more detailed research question, and a closer link to the biological research that this package facilitates. I would strongly suggest the authors to improve this through more analysis and demonstration of findings that are possible with this package, for instance by focusing more on the results presented in the figures and commenting on these results in the text. The use of the publicly available dataset from 10x Genomics is fine for this.

I would like a bit more background on what a AnnData object is, why this format was chosen, and especially which data to convert into AnnData – in line 80 it says raw text, but it is unclear whether this is in the form of raw counts or log-normalized data. Additionally, the option to upload raw text is non-existing in the user interface, only the option to upload and convert CellRanger Output is found.

I would suggest the authors to improve the discussion by including more perspective on why to use this package in addition to “visualization and explorative analysis” on line 114. There should be some suggestions to the nature of this explorative analysis. Additionally, I would suggest the authors to do a more direct comparison to some of the methods described in the introduction.

I think a simulated dataset is superfluous here, as it can only be used for illustration purposes, a purpose that the provided dataset from 10x Genomics also fulfills.
Validity of the findings: The example datasets are not provided in the package, as the paper states, only found on the Github.
Additional comments: I think the software presented in this paper could be of value to some researchers working with single-cell RNA-sequencing data. However, to best present the advantages of this software, I think some points in the paper needs revision before publication, especially describing the analyses that are possible to conduct using this software.

Minor comments for improvement:
-	The option to add logarithmic axes on the violin and scatter plots could be beneficial in some analyses.
-	I think other words than “perspective” in line 91 could better reflect the design of the software, for instance “viewpoints”.


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: SCELVIS: EXPLORATORY SINGLE CELL DATA ANALYSIS ON THE DESKTOP AND IN THE CLOUD
Review round: 2
Reviewer: 1

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


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

Input:
Title: SCELVIS: EXPLORATORY SINGLE CELL DATA ANALYSIS ON THE DESKTOP AND IN THE CLOUD
Review round: 2
Reviewer: 2

Output:
Basic reporting: scelvis is cloud tool to analyze single cell RNA. However, there is no clear statement on how scelvis is different from the existing tools.
Experimental design: I encourage the author to compare his tool with other tools such as the below table
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716224/table/Tab1/?report=objectonly
Users need to know what new features scelvis can give them.
Validity of the findings: My major concern about scelvis is the novelty. It only provides violin and scatter plot for the data. The tool is not easy to be run by biologist without bioinformatics background. It also needs long time to upload even small data (I waited 15 min to upload a data with size 50 M and still could not upload the data). There is a limitation of this tool as it only provide violin plot and scatter plot. I encourage authors to improve its GUI, add more features and solve the speed problem.
Additional comments: The tool is not easy to be run by biologist without bioinformatics background. It also needs long time to upload even small data (I waited 15 min to upload a data with size 50 M and still could not upload the data). There is a limitation of this tool as it only provide violin plot and scatter plot. I encourage authors to improve its GUI, add more features and solve the speed problem.


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

Input:
Title: SCELVIS: EXPLORATORY SINGLE CELL DATA ANALYSIS ON THE DESKTOP AND IN THE CLOUD
Review round: 3
Reviewer: 1

Output:
Basic reporting: A lot of improvement have been done.
Experimental design: Authors added table 1 that compared their algorithm with available packages. They also improved the tutorial and the documentation.
Validity of the findings: I recommended if they add a paragraph about the limitations of the tool and what should be done in the future to expand its usage.
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: THE EXPRESSION OF SMALL RNAS IN EXOSOMES OF FOLLICULAR FLUID ALTERED IN HUMAN POLYCYSTIC OVARIAN SYNDROME
Review round: 1
Reviewer: 1

Output:
Basic reporting: see last page.
Experimental design: nothing to add
Validity of the findings: see last page.
Additional comments: First of all , your abstracts needs more detail. I suggest that you improve the description at line 11 ”functionally diverse,including infertility” change to “functionally diverse in lots of diseases, including infertility”. And line 17 ”6.6% and 8.6%” change to “6.6% in PCOS and 8.6% in non-PCOS group ”.

The next most important item is your introduction. I suggest that you improve the description at lines 48”secreted by cells” change to “secreted out of the cells”. Besides,at line 50, the “Necrotic debris (NDs)”, please explain it, I couldn't find it in reference 3. If it's irrelevant, you should delete it. And it'll correspond with the next sentence. What’s more, at line 71, the “high ribonuclease activity”, please point it out, as I couldn't find it in reference 15,16, and I am curious about it.

Most importantly , the English language should be improved to ensure that an international audience can clearly understand your text. Some examples where the language could be improved include lines 59, 61,62, the current phrasing makes comprehension difficult.Especially at line 62,”which have target cell signaling functions by containing various RNAs” is better. Moreover, at line 84, the ”enhanced” word, it should change to “increased”. At first, “enhanced” usually describe qualilty instead of quantity, secend, “increased” correspond with “decreased”.

Last, I assume that “34-8” which at line 126 is just a slip of the pen.

I commend the authors for their extensive data set, compiled over many years of detailed fieldwork. In addition, the manuscript is clearly written in professional, unambiguous language.


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

Input:
Title: THE EXPRESSION OF SMALL RNAS IN EXOSOMES OF FOLLICULAR FLUID ALTERED IN HUMAN POLYCYSTIC OVARIAN SYNDROME
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: 1- data for samples is lost. please data table of a sample characteristic
Validity of the findings: please compare in a biomarker for this research with older literature.
Are there common ncRNAs between the different study groups?
Additional comments: 1- data for samples is lost. please data table of a sample characteristic
2- please compare in a biomarker for this research with older literature. Are there common ncRNAs between the different study groups?


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

Input:
Title: THE EXPRESSION OF SMALL RNAS IN EXOSOMES OF FOLLICULAR FLUID ALTERED IN HUMAN POLYCYSTIC OVARIAN SYNDROME
Review round: 1
Reviewer: 3

Output:
Basic reporting: See general comments section
Experimental design: See general comments section
Validity of the findings: See general comments section
Additional comments: Polycystic ovarian syndrome (PCOS) is one of the most common causes of infertility in women, which is due to failure of ovulation and excessive ovarian androgen production.  The follicular fluid (FF) in the ovary play an important role in the maturation of oocytes.  The follicular somatic cell and oocyte interact with each other in FF through exosomes (EXs) during oocyte maturation.  In this paper, Hu et al. isolated exosomes from FF of PCOS patients and analysed their small RNAs content to find a novel biomarker for PCOS diagnosis.  Although this paper contains valuable scientific data, the presentation of the paper needs to be improved.
1.	The title of the paper is unclear, which should be changed so that it can reflect the outcome of the study. For example, the title could be “The expression of small RNAs in exosomes of follicular fluid altered in human polycystic ovarian syndrome”.
2.	Although it is informative, the abstract is difficult to read. So, the abstract should be re-written in such a way that it is easy to understand
3.	The introduction is relevant to the study carried out in the paper.  However, it is not clear and therefore it should be re-written so that the reader can understand what is known and what is unknown in the field.
4.	Methods are described with sufficient detail and the results section is clear.
5.	The discussion section can be cut down by removing the repetition of results (for example Fig. 3 results in the 2nd paragraph).
6.	There are several typos and grammatical mistakes in the manuscript that require attention.


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

Input:
Title: THE EXPRESSION OF SMALL RNAS IN EXOSOMES OF FOLLICULAR FLUID ALTERED IN HUMAN POLYCYSTIC OVARIAN SYNDROME
Review round: 2
Reviewer: 1

Output:
Basic reporting: See general comments section
Experimental design: See general comments section
Validity of the findings: See general comments section
Additional comments: Many of my comments are addressed in the revised manuscript. However, the abstract is still unclear and there are several typos and grammatical mistakes that require attention.


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: GREENHOUSE GAS EMISSIONS FROM RIPARIAN ZONE CROPLAND IN A TRIBUTARY BAY OF THE THREE GORGES RESERVOIR, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: •	The methods are not sufficient and provide almost no details required to evaluate the results of this paper. The methods must be greatly modified before a proper review of this paper can be performed. Specific concerns and examples are provided below, although this list is not exhaustive.
o	Statistical software programs are specified, but citations are required.
o	Diurnal data are presented and discussed, but there is no mention of such sampling in the methods. In fact, the methods state that GHG sampling was conduced between 9 and 11 am. Moreover, the methods state that this time period was representative of mean daily fluxes, but provide no evidence to back up this statement. Also, calculation of diurnal flux is not presented, and the units are in m-2 hr-1, which do not seem like diurnal emissions which typically would be mass/area/day?
o	Soils data are presented and discussed, but there also is no mention of such sampling (how,when,where).
o	The location, number, and distribution of static chambers is not provided. How many were samples per site, how were they distributed, etc.
o	The methods state environmental parameters, and presumably fluxes, were analyzed and that P<0.05 was ‘considered acceptable.’ There is no mention of what statistical tests were used, or how they were structured. This is unacceptable for a peer-reviewed article. Also, it is not clear what ‘considered acceptable’ means when referred to the p-value. This should read something similar to P values <0.05 were used to infer statistical significance, etc.
o	Similarly, for the RDA, no information is provided as how the RDA was structured or which options were selected in Canoco. Further, it appears that the soils data were used as covariates for the GHG flux data, but it is not clear if this is appropriate due to the lack of methodologies. For example, fluxes were measured ~monthly over 2 years. Were soils collected at similar times and locations, or were they a one-time sample. If so, the soil properties could differ, especially among years, and the may not be appropriate for relating to flux measurements collected at different times. Moreover, were they collected from the same locations, what depths were they collected from, how were they analyzed, etc.?
o	Since opaque chambers were used, CO2 flux could represent both soil and plant respiration if vegetation was present within the chambers. Please clarify in the methods whether there was vegetation present in the chambers, and if so possibly adjust your discussion and conclusions accordingly.
o	A formula is provided that describes the calculation of cumulative flux, but it is not clear what the cumulative flux represents. For example, were the values from the sample dates simply summed, or were the data extrapolated for the number of days between sample events; if so, how was this done?
o	One of the soil variables is ‘humidity.’ It is not clear what this refers to (humidity typically is water vapor in the atmosphere?), and there are no units provided on Table 3. Since it appears that water contents also is presented in Table 3, I assume that this simply isn’t a terminology issue where water content is referred to as humidity. Either way, these variables need to be defined in the methods, and sampling methods, etc. need to be presented.
o	The methods sate that ‘an area from 165-175 m was chosen’ and that sites were classified into different elevations “165-180”; these two do not match.
•	As detailed below, I’m not sure how informative comparisons are of GHG flux between wetland and upland sites, as the abiotic conditions that regulate flux are quite difference among these environments. Moreover, it is not clear which sites were inundated and dry during sampling, and this information would be quite helpful for analyses and interpretation of results.
•	Figures 1, 4, & 6 are not referenced in the text.
•	Number the figures and tables in the order that they are presented. For example, the first reference for Table 2 follows the reference for Table 4.
•	All figure and table legends/captions should be improved to include relevant information (what/where/when) and to make them stand-alone. For example, define abbreviations such as TN from table 1 and include units for all variables. Also, provide relevant information as to when and where data were collected, etc. Information pertaining to statistical differences also should be included and described. For example, it is not clear which year is represented by figures 4 and 5, nor is it clear which ‘treatments’ were significantly different.
•	Table 1: it is not clear where these data are from or when and how they were collected; there is no methodology presented.
•	Why in some cases (e.g., ghg flux from land use types) are only data from 2016 presented?
•	In the results, when discussion trends are relative fluxes between treatments make sure to present the associated data/numbers and reference related figures/tables.
•	In the Discussion, there are several instances where you make statements/speculations on things that you did not test; this should be avoided. If making a general statement that is supported by other literature, make sure to make it clear that you are not referring to results of your study, but general theories/processes supported by other research. Following are a few examples:
o	Soil water content affected the methane consuming capacity of methane-oxidizing bacteria by changing the transmission rate and the soil environmental condition (Koh et al., 2009), resulting in a significant difference in the CH4 fluxes (P<0.05) among the paddy fields uplands and grasslands.
o	Crop harvest combined with continual dry and hot weather in August increased the CO2 emission especially in paddy fields
o	Application of farm manure provided the substrate for soil microbial growth, promoting nitrification and denitrification reaction and leading to an increase in N2O emissions
o	Soil CO2 fluxes peaked in August, indicating that both soil and root respiration increased with the increase in air temperature
o	N2O fluxes in grasslands in this paper were higher than in other wetlands owing to the surface flow from neighboring farms. In addition, N2O fluxes in wetlands were lower than that in croplands because of fertilization.
•	The raw data could be formatted to facilitate examination or importing into statistical software. Also, metadata are required, as well as information pertaining to calculations, etc.
•	Language:
o	The paper is fairly well written, but the English could be improved. I suggest an additional edit with the goal of improving the language and work selection. Following are a couple of examples:
	It is not clear what ‘unsystmatically cultivated’ refers to
	It is not clear what ‘speculative reclamation in the riparian zones’ refers to
	…frequent anthropogenic activities against periodic water-level fluctuation; against doesn’t seem to be appropriate here
	The 3 aims were to compare flux differences; I would say they were to compare fluxes, not differences
o	Once you define an acronym, use it thereafter. For example, after you define GHG, use GHG rather than writing out greenhouse gas.
o	Be sure to check standard formatting such as ‘et al’ should be ‘et al.’, etc. Also, double check for missing/extra spaces, etc.
o	Check all of your unit presentations, for example, kg·ha-2 should be kg·ha-1 (line 139).
o	Consistent use of terminology related to the study sites and land uses would be beneficial to avoid confusion. For example, it appears that croplands and uplands are used interchangeably, which causes confusion. Further, grasslands typically are considered uplands, which once again, adds some confusion. Lastly, riparian zone also is used, but it is not always clear which samples are included. I suggest using clearly-defined terminology for each land use type and then being consistent with the usage.
Experimental design: •	It is well accepted in the GHG discipline that methane fluxes differ greatly between wetlands and uplands; thus, I’m not sure the comparisons between the two areas are relevant or provide any valuable information.
•	The Methods were not to sufficient to appropriately assess the experimental design.
•	Inferences are made in this paper that land-use practices, etc. effected N2O flux, despite the fact that these hypotheses weren’t tested. It has been well established that N2O flux is to a large degree driven by soil moisture, but this wasn’t even examined here. It would seem that in a riparian area characterized by fluctuating water levels, that soil moisture would be a primary variable of interest that likely has great influence on GHG flux, especially N2O. Thus, I suggest exploring these relationships, especially since Table 3 suggests that WC differed by elevation.
Validity of the findings: •	The conclusions state that differences in N2O flux were due to agriculture and fertilization. I would argue that soil moisture or water levels may play and equal or greater role and should be examined more thoroughly.
•	The paper references submergence and submerged time, but there are no data or analyses.
•	The authors state that crop harvest increased CO2 flux, but this statement isn’t strongly supported by data and analyses; I suggest providing greater support for such statements.
•	Data and analyses should be provided for conclusions such as “Farming practices changed humidity, C, N of soil” etc.
•	Since comparing wet and dry sites, differences could be due to hydrology rather than land use. I suggest examining all abiotic covariates among the land-uses and elevations, in addition to fluxes.
Additional comments: •	GHG fluxes from the transitory, riparian zone of reservoirs are lacking; thus, the goals of the paper address a relevant topic.
•	In its current form this paper is not acceptable for publication. After considerable revision, however, the work represented here could result in an acceptable manuscript. To do this, the methods require significant modification, and the focus of the study should be refined. Also be sure to make sure all study goals and conclusions are supported by data, and that alternative explanations for results are acknowledged. Due to the deficiencies with the methods, as well as concerns with the results and conclusions, I point out major aspects to be revised, but do not provide comprehensive comments throughout the paper.


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

Input:
Title: GREENHOUSE GAS EMISSIONS FROM RIPARIAN ZONE CROPLAND IN A TRIBUTARY BAY OF THE THREE GORGES RESERVOIR, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article objectives are well explained.
The site description is detailed.
Experimental design: It is necessary to detail the chromatograph method, as collum, oven temperature, detectors used…
Detail the figures of the merit of the chromatograph method.
Detail the methods used to measure SH, ST, WC, TC, TN, nitrogen compounds…
Validity of the findings: Line 152. Try to use new IPCC reference and updated GWP
Line 159: detail CANOCO
What is the difference between the RDA and PCA (principal components analysis)?
The results are well presented and also discussed.
Additional comments: The article can be published after minor corrections.


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: GREENHOUSE GAS EMISSIONS FROM RIPARIAN ZONE CROPLAND IN A TRIBUTARY BAY OF THE THREE GORGES RESERVOIR, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: •	The English language is adequate, but the grammar, sentence structure, and tense could be improved. Special attention should be payed to singular versus plural tense. A few examples are: LN 114: rice straw was cut/corn straw was left…; LN 133: September represents…; LN 328: did not show…
•	The Introductory and background information and the references provide adequate background and are appropriate.
•	The structure of the paper follows general standards and is acceptable.
•	Table and figure legends must be improved to make them stand-alone and to aid in interpretation by a reader. Include all relevant information as to ‘what/where/when.’ For example, rather than say …collected from study sites in this experiment in 2015, specify where the experiment was conducted, etc. Also, make sure to define all acronyms, etc. (e.g., GHG, TGR). The overall goal should be to include sufficient information so a reader would not have to search the text to identify ACRONYMS, treatments, etc.
•	Figure 1: The caption says water level of riparian zone in Pengxi River while the text (e.g., LN 68) says water level in TGR. I assume the figure is reservoir level, but please clarify.
•	Figure 2: There are multiple panels, with two labeled as A and C; there is no B. Further, the panels are not presented or described in the caption. Each panel, including the image, should be described and referenced (here and elsewhere). Further, there are 2 legends in the figure, and the formatting is not consistent between them. Lastly, the reference to Fig. 2 on LN 102 should be moved to LN 98 where the study area is referenced; the figure does not provide information pertaining to dates of agricultural activities discussed in LN 102.
•	Figure 4: Each panel should be described/referenced in the caption. Also, information in the legend should be specified, including units, (i.e., elevation). For panel A and F, appropriate breaks/scaling should be used so the data can be clearly observed. For example, the bars in panel A are not visible or readily interpretable.
•	Numbers indicating statistical significance (e.g., Table 2 and elsewhere) should be superscript (here and elsewhere)
•	Figure 5: The terminology in the caption (upland/grasslands) does not match the legend (dry lands/grass fields). Also, the panels are not described in the caption. Panel B does not have a label for the Y axis.
•	Table 4. The caption states ‘diurnal variation…’ but the Table also includes TDF; modify the caption for completeness and accuracy. Define TDF, replace upland with dry lands. May and July are not abbreviated so do not require periods
•	Table 5: variables (e.g., VWM, MWC, ST) need to be defined and units provided for all (e.g., VWC). Also, flux units need more specific to differentiate between CH4/CO2/N2O fluxes and CO2-equivalents (GWP).
•	Table 6: similar issues to other tables, plus formatting of references is inconsistent.
•	Figure 7: shows WC while the text uses MWC. There are other instances of this throughout the paper as well. Change WC to MWC throughout.
•	Figure 8: I suggest making the X and Y axes scales even for each panel. The X and Y axes titles are insufficient (define RDA1, RDA2, etc.) and the % within are not explained. What dates were considered spring, summer, and autumn? Are the points individual samples, means by date, etc.??
•	The raw data (supplement) is incomplete and presented in a manner that is difficult to decipher. The supplement only includes GHG data from 2016? The supplement should provide all data collected and analyzed for the study by site, land use, elevation, and date.
•	Some raw data is supplied, but there are no metadata or variable descriptions to help decipher the data. For example, definitions and units should be provided for all variables. Also, with some work a user could figure out the elevation using the column headings, but land-use type isn’t obviously included. In the end, these data could be structured better and more information must be provided for a user to replicate the results. As an example, I suggest including columns that identify date, site, elevation, land use, and concentration of GHG’s for the sample replicates. It also would be useful to present the final flux value calculated from these raw data, as well as the model used to calculate flux for each sample. Or, describe these models and the process in the methods of the paper.
•	While some of the raw GHG data is supplied, the soils and covariate data are not; thus, results of the analyses cannot be replicated.
Experimental design: •	The experimental design seems acceptable, although additional details are required to confirm this (see general comments).
Validity of the findings: •	GHG data, especially CH4, almost always are highly skewed and require a data transformation to meet model assumptions of normality. If the data were transformed prior to running the ANOVA this should be detailed. If not, it may be appropriate to state that data were distributed normally and didn’t require transformation or something like that.
•	The methods (LN 129-131) describe gas samples collected every 10 minutes for 30 minutes. The methods (typically regression) used to determine change in concentration over 30 minutes are not provided. Please describe the methods/models used.
•	LN 144: how was the concentration of GHG in standard atmospheric conditions measured/determined?
•	LN 147: it is not clear what dc/dt is; please define each term. As presented, it also isn’t clear how change in concentration was determined. The methods here seem like there was a time 0 and time 30 sample, but samples were collected at 10, 20, and 30 minutes? Please clarify methods.
•	LN: 153-154; define ‘t’
•	LN 165: should WC be MWC (here and elsewhere)?
•	LNs 177-183: How was the ANOVA parametrized? Were repeated samples over time treated as repeated measures or unique samples? How was CANOCO parametrized for the RDA (i.e., which options were specified in CANOCO)? Were any of the data transformed? Are means presented in the tables arithmetic means or LS means from the ANOVA?
•	Providing an ANOVA results table for all analyses would be helpful (F and P values, DF, etc.)
•	It is a bit unclear, but the methods description makes it appear as if there is no replication among the land uses? Essentially it is written as if there was a single chamber in dry lands and paddy lands for each elevation, and the seasonal means are based off of these. Based on the error bars in Figure 4 I assume that there were multiple sample paddys and dry lands sampled at each elevation? Please clarify this (e.g., describe number of sample sites), and present the sample size for all analyses and field sampling. This raw data also should be supplied in the supplement. Presentation of sample size should be included in the tables/figures/analyses.
•	LN’s 186-188: the ranges for CH4 presented here do not match the data provided in Figure 4, which shows means exceeding 2 for dry lands and 10 for paddy fields. Also, the text references April–August while the figure provides data through September.
•	Ln 199: the N2O flux value does not match the value in Table 2; please re-check all values in text and tables for accuracy.
•	LNs 197-198: I would caution against making such statements since there were no significant differences and the means are associated with very high variability. In essence, there may be visible trends in the overall means but they are very weak owing to the high variation. Comment applies to similar instances elsewhere (e.g., LNs 215-218).
•	LN218: The value (se) presented for dry lands does not match the value from Table 3; please re-check all values in text and tables for accuracy.
•	LNs 220-223: The author’s highlight ‘obvious’ diurnal changes and relate them to ‘similar’ patters in temperature. While there is some variation, the trends are much weaker than indicated. There are some instances where CO2 and N2O show higher daytime values, but there are also many instances where they do not. Also, the relations between trends in GHG and temperature are not ‘similar trajectories,’ rather I would say that some of the higher flux values coincide with peak temperatures but drop off much more rapidly than temperature. In the end, I suggest modifying conclusions so as to not overstate the trends in your data. Further, you could perform formal correlations between temperature and flux if you would like to demonstrate/evaluate these relations.
•	LNs 232-234: the authors state that CO2 flux increased and the amplitude of diurnal variation also was high and peak emissions were above 1000… I would caution against attributing the high value to harvest since there are similar peaks from other ‘non-harvest’ time periods. Are there other factors that could contribute to these observations?
•	LNs 252-255: I suggest including the GWP for each gas in Table 5, along with the cumulative fluxes. This will allow a reader to determine the relative importance of each gas. As it stands only the total GWP is presented along with normal fluxes for each GHG.
•	LN 257: I don’t see the value of this single-sentence paragraph? Moreover, it isn’t correct. First, decreased/increased between which date and August, July? And if so, why single out this time period. Second, ST didn’t decrease in August. Third, there are variable trends in the means (up and down) over time. If the goal here is simply to present these data I wouldn’t discuss trends unless you are going to analyze them formally or explore them further. These data also may be more appropriate as a table, appendix, or supplementary file.
•	LNs 258-269: Why only mean soil temp for 2 of the 3 land uses? I don’t see the point in a statistical comparison for air temperature since it was a localized study area where temperature should be consistent? Results are provided by land use in some instances, elevation in others, and yet by elevation only for single land uses for others; why the inconsistency and what is the purpose of these comparisons? Also, trends are discussed but the data aren’t presented in a table or figure? This entire section is confusing and needs to be modified and supported with tables/figures if it is even retained.
•	LNs 271-274: why only this detailed information for 8a and not the other panels?
•	LN 282: what does P value represent and why 0.1 (methods state 0.05 as cutoff)? Were all axes/relations significant?
•	LNs 270-282: for the RDA a table showing the correlations between axes and variables would be helpful.
Additional comments: This revised manuscript is improved from the original submission, and the authors attempted to address most of the previous review comments. I believe that the story the authors are trying to tell can be supported by this study, but major revisions to the manuscript still are required to meet standards of a peer-reviewed journal. Specifically, the methods require greater detail, presentation of results must be improved, conclusions must be supported by the data, and the formatting must be improved. The data supplement also required additional information and revision. While not exhaustive, this review provides comments, suggestions, and guidance to address weakness of the paper that, if properly addressed, should result in a paper suitable for publication.

•	It may be an artifact of converting to .pdf for review but there are numerous instances throughout the paper where spaces between words is required (e.g.,’ Wuyang Bayin’ from Figure 4 caption and differntseasons from Table 4 caption). If this is not an artifact of conversion please check the paper carefully.
•	LN 63: the acronym NCCC is not needed as it isn’t used elsewhere.
•	TGR, the acronym for Three Gorges Reservoir, should be defined after the first use in LN 68, rather than LN 69 (2nd use).
•	LN 70-71: this sentence is not clear. 632 km2 were submersed is clear, but it is not clear what the ‘14.9% of total affected lands’ refers to?
•	Include sample size (n) for data in Table 1
•	Ln 92: You are not comparing fluxes of different water-level elevations, you are simply comparing different elevations, correct? The riparian zone was not submerged during the study, correct?
•	LN 111-112, what is ‘a-1’ in the fertilizer amount, year-1??
•	Values presented in the text (e.g., LN 205) should match values in the table (Table 3) and not be rounded differently.
•	In LNs 211-212 you say that CO2 increased for all land uses after harvest; this implies a relationship between harvest and flux. Why would grassland CO2 increase since there would presumably be no harvest? Also, what was harvested in August, rice, corn, or both, and was the harvest before or after the mid-August sample event? Could this trend be associated with something other than harvest (temperature/precipitation, soil moisture)?
•	LN 228: reference Table 4 after presenting these values.
•	LN 236 and 238: Specify September of 2016…
•	LNs 238-239: September of 2015 was lower than this value.
•	LNs 243-244: the values from 9-11 may be similar to the daily mean, but it is difficult to tell simply by looking at these graphs because of the variability. If this determination is important, simply calculate hourly and daily means in a table to show whether this is the case or not. Further, this statement doesn’t logically fit here; I suggest moving it elsewhere, such as the first paragraph of this section discussion diurnal variation.
•	LNs 285-286: single-sentence paragraphs aren’t appropriate. Suggest combining this with the following paragraph.
•	LN 287: where is this mean value from? New data that hasn’t been previously presented in the results should not be introduced in the Discussion. It is not even clear how this mean was calculated or what time period it represents, etc.
•	LN 288: what were the values (i.e., ranges) reported for other catchments?
•	LNs 293-294: the P-value cutoff does not need to be presented in the Discussion, and the Table should be referenced for these flux values. Or, simply reference the table rather than the numbers since they have already been presented.
•	Line 301: replace soil humidity with term used previously throughout the paper.
•	LNs 304-305: where is this double peak shown or demonstrated? Figure/Table?
•	LN 308: should the table referenced be Table 5 rather than Table 2? Also, the GWP for individual gases is not provided to support this statement. Only the overall GWP is provided.
•	LN 316: TC was not sig. lower in croplands than grasslands (see Table 3)
•	LNs 319-320: this sentence is confusing. It seems as though you are saying grasslands have similar attributes as croplands. I think you mean that the reasons stated before is why cropland have lower emissions? Grasslands would have higher emissions because they did not have those characteristics.
•	LNs 324-325: what is meant by submerged time and where was this trend examined???
•	LN 334: where are these values from? It is not appropriate to present new data in the Discussion. Also, reference tables/figures in this section when discussion data/trends.
•	LN 346: Figure 7 does not show drought or any climate data. It does show some soil moisture data, but this drought prior to August isn’t evident and August 24 is not shown?
•	LNs 355-359: why compare grasslands to natural wetlands? Wouldn’t differences in N2O be expected? Also, is fertilizer applied to grasslands (358-359)?
•	LN 360-362: what cropland and wetland systems are being compared here?
•	LN 364: what natural wetland/marsh is being referred to here?
•	LN 382: you say that to potentially mitigate GHG…farming practices should be considered. But, this study showed that in terms of GWP, N2O was least important. So is this really important?


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: GREENHOUSE GAS EMISSIONS FROM RIPARIAN ZONE CROPLAND IN A TRIBUTARY BAY OF THE THREE GORGES RESERVOIR, CHINA
Review round: 3
Reviewer: 1

Output:
Basic reporting: a.	I commend the authors for publishing in a second language, and while the writing is improved from previous versions, the language is not quite up to standards for an English language peer reviewed journal. I have provided comments for improvement, and suggest an additional edit by English language expert to improve readability and comprehension.
b.	Overall the background and introduction provide sufficient context for the study and the literature is relevant. I do provide comments, however, where more appropriate citations could be provided in certain instances.
c.	The overall structure of the manuscript conforms to standards.
d.	The figures and tables have improved compared to previous versions, but still require modification in some instances (see specific comments).
e.	The raw data are supplied and appear complete.
Experimental design: a.	The research is within Scope of the journal and can help address the knowledge gap associated with GHG fluxes from riparian areas of large reservoirs. The experimental design and methods appear sound and the description of the methods and procedures is sufficient.
Validity of the findings: a.	Overall the findings and conclusions are reasonable. However, there are a few instances where the language should be modified where statements are not supported by analyses and/or data (see specific comments). Moreover, some of the results and trends should be re-evaluated based on comments provided.
Additional comments: a.	Comments and suggestions are provided here as well as in an annotated version of the .pdf. When making recommendations on language and phrasing, I only provide the comment for the first instance or two with the expectation that the authors will address similar issues throughout the paper. Specifically, most of the editorial suggestions are provided in the introduction section and should be applied throughout the manuscript where appropriate.
b.	Overall the authors made an effort to address all comments from the previous reviews.
c.	There are a few instances where the authors attribute results to a factor or variable without formally testing a hypotheses or statistically examining relations; most of these, however were rectified since the previous version of the manuscript. In these instances, I suggest simply modifying the language so as to not make statements that are not supported by data. Following is an example: Line 28: the authors state that CO2 was the main contributor because of high OC. However, this hypothesis was not tested and there could be other confounding factors. Simply saying ‘…most likely because of…’ would be more appropriate.
d.	LNs 62-65: This sentence is a bit confusing, it says that agricultural emissions = 11% of 820 (~90), but that emissions from rice and agricultural uses were 374. What is the difference between agricultural emissions and rice and agricultural land uses?
e.	LN 123: here and elsewhere I would reword this. GHG emission were not measured, rather gas samples were collected and GHG emissions were calculated.
f.	LN 163: typically when referring to the molecule NO3-/NH4+ are used; when referring to nitrate/ammonia nitrogen the following are commonly used: NO3—N/NH4+–N. I suggest considering these.
g.	Lines 180-186: Here is says that the data were log transformed and analysed using a 1-way ANOVA. It also says that a Kruskal-Wallis H test was used to deal with non-normal distributions. If multiple tests were used, you need to identify which data were not normally distributed and which test was associated with each analyses presented in the results. As currently described it is not clear which test was used with which data?
h.	LN 197-199: Why are only the data from 2015 shown here? The methods state that sampled were collected monthly during 2015-2016?
i.	LN 204: at first use in the text and in all table/figure captions define what the error estimates are (e.g., +/- se, sd)?
j.	LN 211: here and elsewhere, please present the degrees of freedom along with the F and P values.
k.	LN 219: here and elsewhere, I suggest changing the language from “GHG flux differences…” to simply “GHG fluxes from…” Overall, you are not presenting differences, you are presenting fluxes and testing for differences, of which there are none in many instances.
l.	LN 222: Table 3 only is referenced for the CH4 data; I suggest referencing it for the other gases as well.
m.	Line 230: the P value is missing the 3rd digit value. Here and elsewhere make sure all F and P values have all of the required digits/information.
n.	LN 234: The F value is not presented with the P value.
o.	LNs 235-238 and Table 3. The statistical results for N2O among the 3 land uses appears to be wrong. The dry lands and grass fields have nearly identical values, while the paddy field value is much less. However, sig. differences are presented for the dry lands and grass fields but not the dry lands and paddy fields? Based on the high variability and mean values I do not see how this is possible if the sample sizes are somewhat equivalent and the test was run properly. Please check the results and interpretation of this test, and if necessary, provide the sample size information.
p.	LNs 246-248: I do not see the trends identified here. In some cases the daytime values may be higher, but in others they are not. Also, unless you run a formal experiment or test you cannot say that the trajectory was influenced by air temperature; at best you could say that they appear correlated. I suggest rewording this discussion and if you are going to identify trends make sure they are demonstrated and be specific. For example, if 2 dates show a slight trend and 2 do not I’m not sure you can identify the trend. If you do, I would then identify the dates where you observe any trends and the dates where you do not. This would allow for you to address the trends or lack of trends in the Discussion.
q.	Ln 249: Throughout the diurnal section ‘amplitude’ is used, but it is not always clear what it refers to. Are you using amplitude to refer to the difference between the highest and lowest values within a day? Or, does it mean something else? I suggest providing a brief definition of amplitude after the first use to avoid confusion.
r.	Ln 268: What does this mean value represent? Which samples were includes and how was it calculated? Is this presented in a table anywhere? Overall, what is the implication or relevance?
s.	LN 271: when you say higher than in paddy field, is this qualitative or quantitative? Similar comments elsewhere (e.g., LN 275)
t.	LN 271-273: I am not clear what this sentence means or refers to. Please clarify or provide further details, refer to values in a table, etc.?
u.	LN 276: it is unclear what “beneficial to the high flux of CO2” means?
v.	LNs 278-279: This is a bit unclear, do you mean that CO2 emissions represented the greatest proportion of GWP of the 3 gases?
w.	LNs 286-288: the phrase ‘significant variations in soil water content exhibited an increasing trend’ if fairly confusing. Moreover, as best as I can tell the data in table 2 do not show such a trend. Please modify this sentence and identify the data that show this trend?
x.	LNs 295-310: describing the relations between environmental variables and each axis isn’t very informative. Rather, I suggest focusing on the important relations between the significant environmental variables and the GHG fluxes.
y.	Ln 314: you say that the study area is a strong CO2 source. It may be worthwhile to mention that you are only looking at CO2 emissions and not ecosystem uptake (e.g., NPP). Basically, the net flux may be different?
z.	LN 316-317. This comparison to values from the literature is okay. However, the systems referenced here are small, ephemeral mineral soil wetlands. thus, it may be beneficial to also include estimates from more comparable systems (e.g., large reservoirs)??
aa.	LNs 319-322: you did not test the transmission rate…etc. and thus can not say that if resulted in a change. I suggest modifying this and similar language to reflect whether you are speculating or discussing probably relationships or whether you are discussion something that you tested scientifically.
bb.	LN 395: what natural wetland are you referring to? This study did not sample natural wetlands, only croplands, grasslands, and paddy’s??
cc.	LNs 405-405: CH4 also required organic carbon, so I’m not sure this is the primary reason the CO2 emissions were higher. Is it not more likely due to environmental and biotic conditions that influence flux? Or at least some combination?
dd.	All figure and table captions, identify what the data and errors are: e.g., mean GHG fluxes +/- se, etc.
ee.	Figure 4: I suggest using the same format for the x axes of the left and right panels (1 vs. 2-digit months). Make consistent among all figures/tables.
ff.	Table 5: The caption could be modified to better describe the data presented.