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: RISK ASSESSMENT OF FLT3 AND PAX5 VARIANTS IN B-ACUTE LYMPHOBLASTIC LEUKEMIA: A CASE–CONTROL STUDY IN A PAKISTANI COHORT
Review round: 2
Reviewer: 1

Output:
Basic reporting: The comments of the first review have been taken into account. Literature has been updated. Analysis have been improved. However:

1. Despite the comments in the rebuttal letter, the English has not been improved very much. There are still many mistakes in grammar (i.e. there are far too many commas) like in line 185: "According to previous studies, association of First and second-degree..."
This should be: "According to previous studies association of first and second-degree..."
in line 106: "subjects greater than 15 years" should be "subjects older than 15 years"
in line 26: "PAX5 polymorphism rs3780135 risk allele ‘A’ frequency was more in B-ALL subjects than ancestral allele frequency ‘G’". This should be rewritten.
2. There is no consistency about gene names (FLT3 and PAX5 are either normal or italic), while they should be italic through the entire manuscript.
3. There is no consistency about blanks (before and after commas, sometimes blanks are missing at all, sometimes there too many blanks.) This also refers to the tables, in which the numbers should not simply be centered, but the dots of digital numbers should be in line.
4. There is no consistency about the numbers (i.e. Table 3: 0.6(.26-1.35) or 0.497(0.18-1.35). It should be: 0.60 (0.26-1.35) with two digits after the dots.
5. Overall, the readability could be improved by adding some articles (the and a, i.e. in the present study....)
6. The following sentence attached to Table 1 should be rewritten: "Parameters with P<0.05 is significant studied are linked to B-ALL. (*) show significant."

7.  Structure: the entire information about genotyping (lines 121 - 145) should be shown as a table.
8. Remarks about education: You state: "Our result showed that mothers (39.4%) and fathers (16.3%) were educated." As this information is not used in further analysis, I would take this statement out.
Experimental design: Methods:
Overall, one must admit, that the number of cases and controls is rather small, which will limit the conclusion of the manuscript. This also holds for other risk factors such as family history, smoking or parental consanguinity. If the numbers would be ten-fold, these risk factors would be for sure significant like it has been shown in other publications before.

1. The idea to perform a multivariate logistic regression model has been applied. However, the intention was not to check for interactions. This is not relevant for material of this size. The clear intention was to check, whether SNPs would still show significant effects if corrected for environmental effects. Thus, you should leave out the interaction topic.
2. As the authors deal with several SNPs, there should be a correction applied for multiple testing. Please, check the Bonferroni corrected P-values! p*<p/n, where n is the number of tests performed.
Validity of the findings: Overall, one must admit, that the number of cases and controls is rather small, which will limit the conclusion of the manuscript. Thus, the authors should be careful with their conclusions and statements. The data is not robust, even though it is balanced.
Although I know that it might be difficult to collect a sample set, I would suggest to validate these results in a second data set. One could also split the original data into two random sets. However, as the set has already been analysed, the results would be biased.

Authors mentioned

Table 3: Family history: OR and CI are not correct: 0.6(1.7-0.21). As stated above, please check for consistency. (.26 vs. 0.26).
Take out the P (interaction).
Additional comments: The authors have presented a small overview on the risk assessment of FLT3 and PAX5 variants in B-acute lymphoblastic leukemia. Their case - control study has been performed in a Pakistani cohort. Due to the fact, that the material is small, conclusions are limited for both factors - for the genetic factors such as the SNPs as well as for the environmental factors.
One important overall comment: authors should avoid the following statements like: "that FLT3 SNP rs35958982..." SNPs might be close to a gene, SNPs might be even in the identical genomic region, but SNPs are not identical with a gene as such. one suggestion: for locus 3p22.1 (rs9848754, ULK4) P-values reached significance.


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

Input:
Title: RISK ASSESSMENT OF FLT3 AND PAX5 VARIANTS IN B-ACUTE LYMPHOBLASTIC LEUKEMIA: A CASE–CONTROL STUDY IN A PAKISTANI COHORT
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have made satisfactory improvements to the manuscript and the results are more clearly presented and most errors have been taken care of.
Experimental design: Satisfactory
Validity of the findings: satisfactory
Additional comments: Please refer to the annotated pdf


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

Input:
Title: ABUNDANCE OF ARTHROPODS AS FOOD FOR MEADOW BIRD CHICKS IN RESPONSE TO SHORT- AND LONG-TERM SOIL WETTING IN DUTCH DAIRY GRASSLANDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Manuscript entitled “ Above-ground arthropod biomass response to short- and long-term soil wetting in Dutch dairy farmland” provide valuable information and is scientifically correct and well written although there are few grammatical mistakes. Manuscript meets the journal standards.  I recommend to accept it after making changes to the manuscript. I have proofread the manuscript using track changes
Experimental design: experiment design is good and results meet the aim of the manuscript.
Validity of the findings: Manuscript fulfils the AIM of the study. I have not seen much work on this topic.
Additional comments: Following corrections should be made prior to the acceptance of the manuscript.

28 should be “very” insted “a very”
75 should be “intensively” instead of “intensive”
77 should be “areas, where farming takes place in ecologically benign forms,” instead “ areas where farming takes place in ecologically benign forms”
98 should be “were” instead “was”
121 should be “the adjacent canal” instead “adjacent canal”
175 should be “the analysis.” instead of “the analysis,.”
172 should be “into two periods” insted “in two periods”
188 should be “divided into three” insted “divided in three”
222 should be “the late season,” insted “the late season”
228 should be “Also, in” insted “Also in”
286 should be “mean,” insted “a mean”
296 should be “irrigated” insted “irrigate”
334  should be “in control” insted “in the control”
349 should be “in control” insted “in the control”
361 should be “insects are” insted “insects is”


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: ABUNDANCE OF ARTHROPODS AS FOOD FOR MEADOW BIRD CHICKS IN RESPONSE TO SHORT- AND LONG-TERM SOIL WETTING IN DUTCH DAIRY GRASSLANDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Text is awkward in many places.  There are also some spelling and punctuation troubles; proofreading should have caught these errors.  To illustrate, a few of the problems, consider these (there are others):
-In the summary, last line of Methods followed by extra “diet.” and first Results sentence is hard to understand.
-L65: “composed of” is used incorrectly the proper verb and construction would be “diet of chicks entirely comprises arthropods”
-L89 needs to be reworked.
-L118, change “On” to “In”, line 121 needs an “an” before adjacent canal.
-L175, random comma at end of sentence.
-Rework L197

-Results summary from first page: “The land use analysis revealed a very low intensity management in the fields of the surrounding (20 km radius) area which was characterized by (very) high intensity land use.”  This sentence seems like a contradiction.
Experimental design: The main limitation of the work appears to be the experimental design. If the goal was to test the influence of land-use intensity, I question whether this design was appropriate. It seems appropriate to study a range of land-use intensity. The chosen farm had low levels of land use and thus authors appear to have thought it had the highest chance to harbor good insect populations; however, perhaps the farm has a depauperate insect population for some historic, climatic or some other land use prior to 2009—a low population that the short duration of wetting could not overcome. Perhaps nearby farms have applied some other management strategy or tactic that is greatly limiting insect populations in the region. By only having one farm in one year, authors have no idea.  They did not generally test the influence of wetting, they tested the influence of wetting on that farm in that year.  A more appropriate experimental design may find different results. An ideal study design would have many focal farms embedded in many landscapes that varied in the complexity of their land use; this has been the common recent approach for testing the influence of landscapes.  This paper provides an ambitious design to which author might aspire:
Happe, A.K., Alins, G., Blüthgen, N., Boreux, V., Bosch, J., García, D., Hambäck, P.A., Klein, A.M., Martínez-Sastre, R., Miñarro, M. and Müller, A.K., 2019. Predatory arthropods in apple orchards across Europe: Responses to agricultural management, adjacent habitat, landscape composition and country. Agriculture, Ecosystems & Environment, 273, pp.141-150.

Studying only one farm in a landscape context seems problematic. Low replication, or more likely pseudo-replication (two fields within the same farm, subject to the same landscape), do not appear to have provide a robust design. Even if one does not agree that two plots of each kind within one farm is pseudo-replication, then having just two replicates for one year, is problematic. The design is not robust.

The near-water field should be considered a control, as opposed to a treatment. This field is described as a treatment throughout the manuscript (lines 23, 32, 91), yet no treatment is applied to this field. It is more like a positive control.
Validity of the findings: The most robust result is that adding water made soil moist, cooler, and softer. This is not very notable.

The effect of the irrigation treatment on arthropod abundance was small (L336); this would be expected after just one season of irrigation. Some insect larvae spend multiple years in the soil, and even univoltine populations would likely take more than a year to respond to lower soil temperatures and higher soil moisture. This study would require more field sites (in multiple landscapes with varying management intensities) and multiple study years (as briefly noted in L391) to confidently conclude that landscape effects overshadow in-field irrigation. The research conclusion (L405-406) is a bold statement to make from an experiment conducted at only one location, in a single year, with only two replicates per treatment. A more suitable conclusion would be based on short-term difference (or lack of differences) caused by irrigation.

Invoking a landscape explanation for the lack of an influence of wetting on arthropod abundance seems hard to defend because only one farm in one landscape was studied. Would authors have obtained the same results in a different landscape, say one that was surrounded by forest?
Additional comments: Overall, I appreciate their research goal is solution-focused, as opposed to just pointing out a problem.

Specific comments:
Were ibuttons buried, or on the soil surface? Clarify this in L140.

Line 254-259 discusses the differences in plant composition across sites, yet in line 354-356 this is contradicted. There may be value in performing NMDS with plant species composition.

Also it may be valuable to run NMDS with arthropod communities, especially since there does appear to be a community shift between the near-water site and the irrigated field (dipterans and hemipterans).

Would be valuable to include more discussion of the effects of soil temperature on insect survival and emergence rate (expand upon L327)


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: ABUNDANCE OF ARTHROPODS AS FOOD FOR MEADOW BIRD CHICKS IN RESPONSE TO SHORT- AND LONG-TERM SOIL WETTING IN DUTCH DAIRY GRASSLANDS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Line 22, “no water added”

Line 43, this first sentence is too general. Because the first paragraph is describing loss of arthropods and the second paragraph is about bird species. I would suggest to make this first sentence more specific like “Biodiversity in insects…”

Line 56, vague, positive effects on what aspect for arthropods and birds? Mortality? Population?

Line 58, “which represents…”;and this sentence needs to be more detailed. Abundance of species being good indicators or other factors about bird population?

Line 61, similar pattern? The same declining rate? Better change to “Same declines in….” or listed the range of decline rate for those species.

Line 66-69, add “…improving food availability for bird”

Line 69, “the rapid rate of declines in bird population…”

Line 70, use “immediately” instead of “short-term”? and how authors define the short-term vs. long-term? within a year (seasonal) vs. more than 10 years?

Line 72, this first sentence is not a good topic sentence for this paragraph. “we hypothesized that..” usually follows the sentences of objectives. This paragraph should be a short summary of published papers concluding wetter soils have larger arthropods biomass.

Line 82-88, this paragraph should be put in the Method section, not here

Line 89-92, authors should have a better paragraph describing the objectives and hypothesis. Again, put hypothesis next to the objectives.

Figure 1B, increase the symbol sizes to be readable.

Table 4. two digits for p value should be enough
Experimental design: Line 95-102, should this paragraph come next to the paragraph of “study site”? and authors should provide the background of why they need this analysis in the Introduction. How this result helps interpret this study? It is very sudden to see this paragraph at the Method section.

In the paragraph of “study site”, it is better to describe the climate (annual temperature, precipitation) because soil moisture is related to climate.

Line 143-146, what was the measurement interval for soil moisture? Every hour?

Line 167, was there an equation built for each species?

Line 188-189, why these three classes are not continuous? So there will be no arthropods at the length of 3.5 mm or 1.5 mm or less than 1 mm?
Validity of the findings: Overall, in the Result section, I don't think authors need to show all ANOVA, F value, R2, only provided the p value should be satisfying.

Line 244, missing the magnitude in the near-water treatment?

Line 247, omit this sentence, put p value next to the last sentence

Line 249, “…was observed in the control...”

Line 251-253, this correlation test was not mentioned in the "data analysis" in the Method section

Line 279,285, p values here?

Line 321-326 and line 373-383, those two paragraphs should be merged together because they both discussed the landscape analysis

Line 356-358, this is an interesting point, is there any published paper supporting this point?

Line 391, this discussion point can be merged with line 367? as this site might not be ideal for studying arthropods because the majority of them were in small sizes and were not suitable for energy intake for birds. Thus, repeating the experiment in a new site with bigger sized arthropods would be ideal.

Line 397-399 is the same sentence as line 72-74, Please use different sentences.

Line 404, change to "...was negligible, probably because the arthropods..."?
Additional comments: This paper reports the effects of irrigation and near-water treatment on arthropods species and biomass, soil temperature, moisture and resistance at a farm in the Netherlands from May to June. This paper found an improvement in soil conditions under occasional irrigation but not in arthropods abundance probably because of their small sizes. This paper adds some value to the society and should be considered accepted with the above questions 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: ABUNDANCE OF ARTHROPODS AS FOOD FOR MEADOW BIRD CHICKS IN RESPONSE TO SHORT- AND LONG-TERM SOIL WETTING IN DUTCH DAIRY GRASSLANDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am satisfied with the changes made by the author. I recommend accepting the manuscript.
Experimental design: ok
Validity of the findings: ok
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: ABUNDANCE OF ARTHROPODS AS FOOD FOR MEADOW BIRD CHICKS IN RESPONSE TO SHORT- AND LONG-TERM SOIL WETTING IN DUTCH DAIRY GRASSLANDS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The basic reporting of the manuscript is fine.  Previous concerns about details of the writing appear to have been addressed.
Experimental design: I continue to believe that the experimental design is inadequate; authors have not convinced me otherwise.   I appreciate the limitations that authors address at the beginning of the Discussion, but this hedge wording does not make up for a poorly replicated design or sampling arthropod for just a few months after wetting.  Insect life cycles in northern Europe are often univoltine, so sampling ignored large portions of he community.  Moreover, citing a published study that also has an inadequate design does not justify also using an inadequate design.
Validity of the findings: Results continue to be questionable given the poor design.
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: ABUNDANCE OF ARTHROPODS AS FOOD FOR MEADOW BIRD CHICKS IN RESPONSE TO SHORT- AND LONG-TERM SOIL WETTING IN DUTCH DAIRY GRASSLANDS
Review round: 2
Reviewer: 3

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: This paper has been well revised based on reviewers' comments. I really appreciated authors' hardworking. I don't have any further comments in regards of this revised version.


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: ABUNDANCE OF ARTHROPODS AS FOOD FOR MEADOW BIRD CHICKS IN RESPONSE TO SHORT- AND LONG-TERM SOIL WETTING IN DUTCH DAIRY GRASSLANDS
Review round: 3
Reviewer: 1

Output:
Basic reporting: The abstract is too long it should be concise.
Although the info in the discussion section is sufficient and it convinces the aim of the study, but the presentation is not in a proper flow, especially the starting of the discussion section.
In conclusion section at line, no 434 author starts a sentence with the phrase "We hypothesized that ....." How come the author is hypothesized in spite of concluding in the conclusion. My suggestion to the author is to read the conclusion of a few published literature and modify the conclusion section.
English also needs brushing.
Experimental design: Experiment is well designed
Validity of the findings: 'no comment'
Additional comments: The abstract is too long it should be concise.
Although the info in the discussion section is sufficient and it convinces the aim of the study, but the presentation is not in a proper flow, especially the starting of the discussion section.
In conclusion section at line, no 434 author starts a sentence with the phrase "We hypothesized that ....." How come the author is hypothesized in spite of concluding in the conclusion. My suggestion to the author is to read the conclusion of a few published literature and modify the conclusion section.
English also needs brushing.


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: ABUNDANCE OF ARTHROPODS AS FOOD FOR MEADOW BIRD CHICKS IN RESPONSE TO SHORT- AND LONG-TERM SOIL WETTING IN DUTCH DAIRY GRASSLANDS
Review round: 3
Reviewer: 2

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: None


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: LNCRNA TMEM51-AS1 AND RUSC1-AS1 FUNCTION AS CERNAS FOR INDUCTION OF LARYNGEAL SQUAMOUS CELL CARCINOMA AND PREDICTION OF PROGNOSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The results are based on bioinformatics analysis and they require to be validated.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1. The authors have provided a series of bioinformatics analyses among the relationship among expression (mRNA, miRNA, lncRNA), methylation (lncRNA) and clinical outcomes. And it is challenging to evaluate the correctness of their work in a short time. The authors should provide at least a workflow to present their major procedures, especially for the data cleaning steps.

2. Figures 1 and 2 need detailed annotations to present the meanings of them. Figures 4 and 5 might be rearranged according to their findings of ceRNA axes. Figure 6 could be combined with figures 4 and 5 to reinforce the story.

3. Table 3, please state whether the p values were corrected or not.

4. Page 13, line 183-4, what is the test to check whether the expression trend is the same?

5. There are several typos in the manuscript.
p21, line 339, an unexpected "," exists between rare and reports.
p13, the link "(http://127.0.0.1:26738/library/stats/html/wilcox.test.html)" is not correct.


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: LNCRNA TMEM51-AS1 AND RUSC1-AS1 FUNCTION AS CERNAS FOR INDUCTION OF LARYNGEAL SQUAMOUS CELL CARCINOMA AND PREDICTION OF PROGNOSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: In this study Hui and co-workers described re-analysis of the published laryngeal squamous cell carcinoma (LSCC) gene expression data set and methylation profile analyzed by microarray. Here, the authors focus on the interaction relationships between miRNAs and lncRNA/mRNA pairs and their correlation with DNA methylation. They identify a subset of lncRNA-miRNA-mRNA and established them in a ceRNA network. They evaluated the prognostic value of some of the identified biomarkers and also linked them to other clinical features. The author concludes that the lncRNAs may be used for therapeutic and prognostic application in LSCC. This is a nice work, however, sample size seems very low for accurate statistical output. The limitations of the study were also discussed. I have few comments and suggestions to improve this manuscript before the publication is warranted.
1. Abstract: The author did not provide any evidence on therapeutic applications of the lncRNAs in the ceRNA network. Therefore, any conclusion on this issue should be avoided.
2. Materials and methods: How did the author determine the cut-off for differentially expressed lncRNAs and miRNAs? For example |logFC(fold change)| > 0.263 which interprets the real fold change as 1.19, seems not to be a very sensitive threshold to identify robust differentially expressed biomarkers.
3. Materials and methods: Does the P-value reported for the statistical analysis are FDR corrected to avoid the occurrence of false positive?
4. Materials and methods: Please correct the spelling of miRecode to miRcode at line 193.
5. Figure 2: It is not clear what does “contra-regulated” means? I think the figure needs
more explanation to become useful to the readers.
6. Figure 3: The text, nodes, and edges in this figure represents interactions pairs in the
ceRNA network, which I find difficult to visualize. I strongly suggest authors to reproduce a high quality figure and highlight the interaction relationships.
7. Results: To confirm the importance of the OS and RFS DELs, DEMs and DEGs the author investigated the association with other clinical features. Could author also show whether the expression level of the biomarkers is not confounded by other clinical features? In other words, I suggest author to check the prognostic independence of biomarkers against clinical features by multivariate Cox regression?
8. Discussion: needs to be shortened.


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: LNCRNA TMEM51-AS1 AND RUSC1-AS1 FUNCTION AS CERNAS FOR INDUCTION OF LARYNGEAL SQUAMOUS CELL CARCINOMA AND PREDICTION OF PROGNOSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: I went through the revised manuscript. The author substantially improved the conceptual background of the manuscript. I am satisfied with their provided point by point response on my comments. However, I still have few comments/suggestions to improve the manuscript.

1. Figure 1. Please correct Set III to Set IV for the methylation profile.

2. Discussion needs to be shortened.

3. In general, written English of the manuscript is poor. I strongly recommend proofreading of the manuscript by a native speaker.


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: OCEANOGRAPHIC HABITAT AND THE CORAL MICROBIOMES OF URBAN-IMPACTED REEFS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is generally well written with clean, professional figures.

The data used are publicly available from the NCBI Short Read Archive, but it would be nice to mention to readers where to find the accession numbers for the samples or runs as well (i.e. SRR3632944, SRR3632945, etc) if they were looking to reproduce the analyses.

There also seems to be extra data (32 extra samples) other than that used in the study provided, at least in the provided ASV feature table where I looked. I'm not sure why this is present, perhaps the authors could clarify or perhaps I missed something. The ASV feature table also reports the minimum feature count as 434 rather than the 403 reported (Line 154), and the number of ASVs as 26918 rather than 27692 reported (Line 334). I'm not sure where these discrepancies come from.

I do find the combined presentation of the Shannon diversity metric with taxonomic composition in Figure 4 to be a bit unusual and confusing at first glance. I would prefer that the taxonomic composition be presented separately such that all the bars are scaled to 1.0  or 100% to so that readers can compare the relative abundance of individual taxa across sites and months more easily.

Figure 5 is busy—I find the interpretation of % coral cover (mapped to symbol size) especially difficult because of the different symbols used.

Figure 6a would be better if it showed the month of sampling and/or identity of the site for each sample.

Figure 7 has overlapping points, reducing the opacity of points would improve the ability to discern separate points.
Experimental design: The article is well within the scope and aims of PeerJ.
The authors present a MiSeq 300-bp dataset consisting of 55 samples. Assuming that a standard Illumina v2 300-bp reagent kit, approximately 15 million reads or read pairs are produced. The data were rarefied down to 403 counts per sample for a total of (403 * 55) = 22,163 sequence variants. Thus, roughly 99% of the data from the Illumina run was not utilized. Additionally, 403 reads seems like a small number—it's possible that study could be better off with the smaller libraries thrown out.

There are better alternatives to throwing away nearly all of the data through rarefaction (see McMurdie & Holmes, 2014). The authors may also find Amy Willis' discussion on rarefaction and alpha diversity in microbial ecology useful: https://www.biorxiv.org/content/10.1101/231878v1 . The small library size of the smallest samples and the rarefaction likely mean that alpha diversity analysis is prone to bias, or at the very least an underestimation of the true alpha diversity.

The authors might also be interested in Gloor et al., 2017, which suggests additional methods for dealing with compositional microbiome data, but implementing the methods suggested by Gloor et al., 2017 (e.g. CLR, ILR, ALR, Aitchison) is not necessary for the acceptance of manuscripts in journals at this time.

The general reproducibility of the paper could be improved with the inclusion of the QIIME2 & DADA2 scripts. Further information on this part of the analysis would also be appreciated to check. I am interested in checking that the primer regions of the reads were appropriately fully removed before processing with DADA2. I am also interested to know the rationale for the trimming that was done in general, since it doesn't make sense to me right off the bat. DADA2 is able to handle low quality bases, so trimming off of the ends of reads isn't strictly required as in other amplicon workflows, but does provide a boost to the speed of processing the reads. In my opinion, the reproducibility of this work & usefulness for future work would also be improved by providing the sequence variants found—this is one of the greatest benefits to an ASV-based pipeline: the exact variants can be reported and compared across studies. Including two files, the taxonomy file containing the taxonomic lineage information for each sequence variant and a FASTA file containing the sequence of each ASV would likely make this study more amenable for future use by others. Including the Newick tree file also would make the code in the Jupyter notebook reproducible, but currently it is not easily reproducible.

I would like to see how the authors arrived at the statement of > 95% of the variance being explained by host species in Line 418. If this is from adding up the first two axes of their PCoA, I don't think this interpretation of PCoA axes (more specifically the complete attribution of the % variance of each PCoA axis to host species) is correct. A PERMANOVA might be more appropriate for determining how much of the variance is explained by host species.

Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. 2017. Microbiome datasets are compositional: And this is not optional. Frontiers in Microbiology 8:1–6. DOI: 10.3389/fmicb.2017.02224.
McMurdie PJ, Holmes S. 2014. Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. PLoS Computational Biology 10. DOI: 10.1371/journal.pcbi.1003531.
Validity of the findings: It may be that the findings still hold after re-analysis of the data or the authors may even find additional patterns, but I would like to see the dataset re-analyzed to address the comments I made in the "Experimental Design" section, primarily with the use of a method of accounting for library size differences without the use of rarefaction.
Additional comments: Overall, the manuscript appears to be in pretty good shape, and I would most likely expect it to be acceptable after the suggested changes.


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: OCEANOGRAPHIC HABITAT AND THE CORAL MICROBIOMES OF URBAN-IMPACTED REEFS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Authors used clear English throughout the manuscript.
Authors clearly stated their objectives and hypothesis.
The manuscript is clearly written, with proper citations, and provides sufficient background.
It is especially noted, and appreciated, that authors provide helpful context, references, and explanations for physical data/phenomena that may not be familiar to biologists or non-experts.
The article is well-structured, reads logically, and flows well.
Tables and figures are helpful and formatted well.
Raw data is archived in publicly available databases.
Experimental design: The research is original – studies regarding the impacts of physical parameters on microbiomes is limited and the data presented here help to fill that knowledge gap.
Researchers appear to have included sufficient replication in their experimental design by collecting replicate tissue samples from multiple sites (n=3) within multiple reefs (n=4). However, the number of colonies sampled per site should be clearly stated in the methods section.
I understand these samples and data were collected as part of a previously published study; however, it is unclear why more fine scale depth data were not collected by divers. Also, it seems reef water samples, and specifically turbidity data for reef water, were collected in the previously published study by Staley et al. 2017. Is it possible to ground truth the satellite derived turbidity data with these data, or if I am not mistaken in the details of the collection, use the reef water turbidity data in the current analysis?
Validity of the findings: Thorough statistical analysis was employed with the data. However, being that the data is mainly observational and not experimental data, it is difficult to control for multiple environmental variables. That being said, the authors did a good job in honestly assessing the limitations of their data and discussing their findings within the appropriate context.
One topic that was absent in the discussion but that should be further explored is the likelihood that a combination of physical and chemical properties are shaping microbiomes. Again, it seems some seawater chemical nutrient data were collected for the original study and, if appropriate/relevant, this manuscript might benefit from including those data.
Conclusions were clearly linked back to their original research question.
Authors did not over-speculate when interpreting and discussing their findings.
Additional comments: Overall, this was a very well-written manuscript. It read logically and flowed easily. It is clear that the authors paid close attention to detail in all aspects of the manuscript. There were also very few spelling/grammatical/etc. errors. The following are suggested edits/comments for the authors:

Introduction:
Line 74: Do the authors mean to reference opportunistic bacterial pathogens here?
Line 75: Replace “effected” with “affected”
Line 79: Please provide a citation

Methods:
Lines 122-123: Please detail how diver-collected temperature data were recorded. I did not locate this information in the publication or supplemental materials in Staley et al. 2017 (Later I see “dive-watch sea temperature” is mentioned in lines 258-259. Please also include this in the methods section)
Lines 125-128: Please list how many colonies were sampled from each site (or at least refer the reader to Table 1 for that info). Also, detail whether or not two polyps per coral head were combined to equal one sample or analyzed separately (based on the numbers in Table 1 I’m assuming they were combined, but this should be clear to the reader and explained in the methods).
Line 133: How was the skeleton sampled with a syringe? In Staley et al. 2017 the methods detailed in the supplemental information state “Coral tissue was collected by syringe biopsy, where the syringe was held firmly against the coral skeleton and the plunger pulled back, causing a suction that draws the entire coral polyp into the syringe (while causing no damage to the coral skeleton)…” Also, Were polyps macerated/homogenized prior to filtration?
Lines 143-148: Further detail is needed regarding the bioinformatic analysis. For example, how many sequences were obtained per sample? What was the minimum merge length? What type of quality filtering was used? Average sequence length? What type of clustering was used to determine ASVs? How were chimeras and singletons addressed?
Lines 188-191: Unclear as to why specific depth data wasn’t collected by divers when individual colonies were sampled. Please explain the rationale for deriving seafloor depths from NOAA’s data.

Results:
Lines 254-258: Recommend moving this information to the methods sections
Figure 6B: Two of the vector labels are overlapping and difficult to read.


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: OCEANOGRAPHIC HABITAT AND THE CORAL MICROBIOMES OF URBAN-IMPACTED REEFS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I greatly appreciate the effort that authors made in implementing the suggestions made.

If the authors used ggplot to produce figure 6A, the 'ggrepel' library could be used to quickly improve the readability of the text labels.

Minor typos:
Line 127: "scrapping" should presumably be scraping?
Line 171: "asses"
Experimental design: I also greatly appreciate the authors addressing my concerns about rarefaction in their study by clarifying the language used and testing the sensitivity of their data to rarefaction by running the analysis with the samples with the lowest numbers of reads dropped.

While I still hold concerns that, in general, rarefaction is not ideal for alpha-diversity estimation, in light of the the robustness of the findings to rarefaction at a higher number, I do believe that the patterns described are true and find the evidence sufficient for publication.
Validity of the findings: The findings were robust to re-analysis of the data without the two samples w/ very low read counts.
Additional comments: WIth the changes made, I find this manuscript suitable for acceptance. It is evident that a lot of work went into this study.

I did make some minor suggestions in Section 1: Basic Reporting, which could be easily fixed before the final version, but I don't find that these changes would merit a recommendation of 'minor revisions,' so I am recommending that the article be accepted at this stage. The authors may choose to make those changes if they see fit.


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: OCEANOGRAPHIC HABITAT AND THE CORAL MICROBIOMES OF URBAN-IMPACTED REEFS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors used clear English throughout the manuscript.
Authors clearly stated their objectives and hypothesis.
The manuscript is clearly written, with proper citations, and provides sufficient background.
It is especially noted, and appreciated, that authors provide helpful context, references, and explanations for physical data/phenomena that may not be familiar to biologists or non-experts.
The article is well-structured, reads logically, and flows well.
Tables and figures are helpful and formatted well.
Raw data is archived in publicly available databases

NOTE: Upon reviewing the figshare files, I did not see that the QIIME2 code was uploaded as indicated. Please upload this information as soon as possible.
Experimental design: The research is original – studies regarding the impacts of physical parameters on microbiomes is limited and the data presented here help to fill that knowledge gap.
Researchers appear to have included sufficient replication in their experimental design by collecting replicate tissue samples from multiple sites (n=3) within multiple reefs (n=4). However, the number of colonies sampled per site should be clearly stated in the methods section.
SATISFACTORILY ADDRESSED BY AUTHORS

I understand these samples and data were collected as part of a previously published study; however, it is unclear why more fine scale depth data were not collected by divers. Also, it seems reef water samples, and specifically turbidity data for reef water, were collected in the previously published study by Staley et al. 2017. Is it possible to ground truth the satellite derived turbidity data with these data, or if I am not mistaken in the details of the collection, use the reef water turbidity data in the current analysis?
SATISFACTORILY ADDRESSED BY AUTHORS
Validity of the findings: Thorough statistical analysis was employed with the data. However, being that the data is mainly observational and not experimental data, it is difficult to control for multiple environmental variables. That being said, the authors did a good job in honestly assessing the limitations of their data and discussing their findings within the appropriate context.
One topic that was absent in the discussion but that should be further explored is the likelihood that a combination of physical and chemical properties are shaping microbiomes. Again, it seems some seawater chemical nutrient data were collected for the original study and, if appropriate/relevant, this manuscript might benefit from including those data.
AUTHORS ADDRESS THIS CONCERN BY PROVIDING A REFERENCE ON THE ROLE OF PHYSIO-CHEMICAL PROPERTIES ON SHAPING MICROBIOMES, BUT I THINK A SENTENCE OR TWO TO EXPAND ON THIS, OR PROVIDE AN EXAMPLE, IS NEEDED.
Additional comments: ALL OTHER COMMENTS SATISFACTORILY ADDRESSED BY AUTHORS


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

Input:
Title: ALLERGIC RHINITIS, RATHER THAN ASTHMA, MIGHT BE ASSOCIATED WITH DENTAL CARIES, PERIODONTITIS, AND OTHER ORAL DISEASES IN ADULTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Some of the text needs rewriting to correct errors (e.g. Lines 39, 40, etc.) and other parts of the manuscript could, I think, be expressed more simply and clearly (e.g. Lines 43–44, 47–49, 52, etc.). I suggest careful proofreading throughout.

It is unclear what a “co-confounder” (Lines 40, 74–75, and elsewhere) is—Google provides only 18 hits for this term and most of these appear to be spurious matches.

The term “rate” is usually reserved for cases where the denominator is non-trivial (e.g. per year). The use on Line 45 and elsewhere is the trivial case of per person and normally this would be described as prevalence or incidence as appropriate instead.

When stating that adjustment was made for “confounding factors” (e.g. Line 50), it is important that the reader has a list of these variables in mind so they can judge whether this is likely to be adequate or inadequate for the purpose.

The study is not longitudinal (Lines 82 and 237–239) in any meaningful sense—while the data were collected over time, the analyses as described here are strictly cross-sectional in nature.

A traditional Table 1 for patient information is needed to present their demographic characteristics.

Tables 1–2: Note that tildes are usually used to indicate “approximately” rather than a range of values.

Tables 3–4: 95% CIs should also be provided here along with effects

Tables 1–4: Results should be presented for both sets of models, not just p-values.

All tables should indicate the exact statistical models used to produce the results presented there. There were some parts of the statistical methods that did not seem to clearly match what was in the tables.

While the raw data is supplied, it needs a data dictionary. For example, it is unclear simply by looking at the data whether sex=1 or sex=2 represents males (I appreciate that this question can be answered by comparing the frequencies in the data with those in the manuscript, but I think that this should be apparent from the data alone). A data dictionary for all 40 columns needs to be available. I suggest using a second worksheet in the workbook for this purpose. It might be a consequence of the lack of a data dictionary, but I couldn’t see a variable for the presence/absence of aphthae/stomatitis.
Experimental design: While the manuscript frequently mentions adjustment for confounders, there is no discussion of an underlying causal model that has informed the design of the study. Without careful consideration of this, perhaps through a directed acyclic graph, it is difficult to know what the actual research question being investigated is. While the section named “Determining confounding factors” (Line 129) discussed what variables were included, there is only one reference in this section and that is for how urban/rural levels were created. All confounders and other variables included need to be justified, and references should be provided as part of this whenever possible. This process will include identifying potential confounders that are not available, which will lead into the limitations later on (Lines 248–250). Note also that at least some of the variables as described here will clearly leave residual confounding (SES was dichotomised, for example, and obesity appears to be based on a diagnosis rather than BMI) if they are indeed confounders. Can the authors explain why they collapsed these variables to fewer levels? It is unclear to me why pregnancy is grouped with sex and obesity in this text (Lines 138–139). Sex and obesity could, potentially and depending on the causal model, be confounders whereas pregnancy does not seem likely to me to be a confounder. Finally, could you please explain in the manuscript how AS is a confounder for the AR->oral disease association, and how AR is a confounder for the AS->oral disease association?

Loosely related to this, “multivariate” (Lines 146, 150, 151, and possibly elsewhere) should be “multivariable” (the former refers to multiple outcomes, the latter to multiple predictor variables).

If logistic regression models are going to be used for multivariable models, why use Chi-squared tests for the univariable models (Lines 145–146)? The mathematical assumptions are slightly different, but the p-values will be similar either way and by starting with univariable logistic regression, there is a smoother transition through the analyses. Even better, though, in my opinion, would be to use modified Poisson regression (https://doi.org/10.1093/aje/kwh090), or some other approach, to model relative risks rather than to estimate odds ratios which will inevitably be confused by some readers as being RRs (which they will not approximate well given the common outcomes investigated here). For the comparisons of frequencies (Lines 149–150), t-tests will be inappropriate due to the inevitable skew in these outcomes and their discrete nature. Poisson, or negative binomial, regression might be appropriate here depending on the data.

What model diagnostics were performed for the statistical models? The reader should be informed about these in the manuscript so that they can judge the internal validity of the findings. The exact models are not clear in all cases, but there is fairly consistent evidence of misfit in the models using Hosmer-Lemeshow’s test (while this test is not without its problems, some form of diagnostics are still needed).

Were any interactions/effect modifiers considered plausible and investigated? Interactions between AR and AS seem inherently plausible here and this is statistically significant for caries (p=0.003) with and without further adjustment. Further, by adding interactions, Table 2 will be much more useful with a direct test of effect modification included. At the moment, the reader is unable to determine simply from the information presented here whether or not effects differ by sex, urbanity, or income in most all cases.
Validity of the findings: It is traditional to begin the discussion with a short summary of the results, and I suggest adding such a paragraph at Line 190.

There is considerable over-interpretation of the study findings in my opinion. Because these are cross-sectional data, and I think there are missing confounders (see above and note your own discussion points in the manuscript), I would prefer the language to reflect this uncertainty. For example, describing AR is a risk factor in the title is claiming an actual causal association which I do not think can be justified here. AR might be a diagnostic/prognostic marker, but I cannot see a strong mechanistic explanation for the claimed causal association sufficient to reduce concerns that the results may simply reflect unmodelled confounding. The conclusion in the abstract (Line 56), for example, is an absolute statement that simply has not been justified here. This issue continues throughout the manuscript—causal claims can only be justified where all important confounding variables have been accounted for, which is an inherently difficult requirement in observational research. The discussion claims on Lines 203–204 are also overstated and the causal claim on Lines 252–253 cannot be justified in my view.

The potential confounding effect of AR on the AS->oral health association is still not clear to me despite being stated as a fact in the Discussion (Lines 208–209). How exactly would AR confound this association? Later in the Discussion, you soften this to “might be a [confounder]” (Lines 212–213).

While I appreciate the possible mechanisms suggested, I still feel that omitted variable bias (smoking, sugar consumption, engagement with the healthcare system, and other health experiences and behaviours could potentially be adequate explanations in themselves for the observed results) is a potentially important threat to the study’s internal validity. This isn’t to dispute that further research might not be worthwhile, but I feel that the observed associations, if they persisted, would have to be a speculative point and only after the issues with the statistical models are resolved.

The sample size (Lines 239–240) is not in itself a strength except insofar as it affects precision and stability of estimates. Related to the former point, I think more interpretation of the magnitudes of effects and 95% CI limits is needed. A major limitation would appear to be the lack of temporal sequencing in the exposure and outcome. If I have understood the data extraction process correctly, this was not a requirement, but please do correct me otherwise.
Additional comments: While the study has some interesting aspects, there are some important points to address, including a) providing a causal model to underlie the statistical analyses, b) addressing the limitations of the statistical modelling and/or reporting, and c) the over-interpretation of the study findings, particular in terms of causality.


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: ALLERGIC RHINITIS, RATHER THAN ASTHMA, MIGHT BE ASSOCIATED WITH DENTAL CARIES, PERIODONTITIS, AND OTHER ORAL DISEASES IN ADULTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the manuscript, Allergic rhinitis, rather than asthma, is a risk factor for dental caries, periodontitis, and other oral diseases in adults, Min-Sho Ku et al study association between oral disease and allergic rhinitis versus asthma in young adults.

Strengths: The manuscript is well written and discussion is appropriate. The data collected is robust in terms of number of subjects and timeframe of analysis. The statistically significant association of AR with oral disease is noted. The study does take into account age, sex, lifestyle (country v urban) and clinical visits.
Weakness:
The scientific rationale for studying oral disease’s association with AR or asthma has not been well described in the introduction.. They have a previous paper on similar topic in children yet they need to introduce why allergic diseases are relevant to oral diseases.
The association between higher income groups having more oral disease/AR is surprising. They need to discuss this better.
The number of clinical visit needs to be classified; meaning purpose of clinical visit should be taken into consideration.
Most importantly, the authors themselves state their weakness on lack of oral hygiene data. I think without that data, it is not reliable to make any clear associations between AR-oral diseases versus AS-oral diseases.
The level of IgA in oral samples/saliva and mucus should be taken into consideration as well.

Overall, the manuscript needs improvement on the weaknesses to be published.
Experimental design: Experimental design is mostly appropriate; Consideration of reason for clinical visit should be mentioned/taken into account. Oral hygiene must be accounted for. Use of mouth wash, brushing teeth (once v twice daily) etc are a major player in all oral diseases and should be considered.
Validity of the findings: no comment
Additional comments: Make the introduction better with details on why studying the connection between oral disease and allergic diseases are scientifically and biologically rational and important. State clearly the differences between asthma and allergic rhinitis.


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: ALLERGIC RHINITIS, RATHER THAN ASTHMA, MIGHT BE ASSOCIATED WITH DENTAL CARIES, PERIODONTITIS, AND OTHER ORAL DISEASES IN ADULTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The line numbers I previously listed as having language issues were only for the first few such lines. In the abstract, there remain language errors on Lines 38 (adult), 39 (remain), 44 (disease), 45 (list is not divided into sub-lists but refers to these categories in the final items), 46 (this is awkward), 47 (incidence), 50 (missing definite article), 51 (high), and 53 (missing word). I’m not listing the line numbers here to indicate specific errors and corrections, and I could in theory keep listing line numbers throughout the manuscript, but rather to support my suggestion that the manuscript would benefit from careful proofreading throughout.

 I still feel that the confounders adjusted for should be made clear in the abstract on Line 47 as it is difficult to interpret the findings without knowing at least the types of variables adjusted for here. Note also that these are just some of potential confounding factors and the statement here reads somewhat more definite than that to me.

Thank you for adding Table 1. I suggest looking at making this seven columns (possibly in landscape) so you can avoid repeating the first column for both variables. Also, I suggest “<0.001” for very small p-values (as you use in Tables 2 and 3, etc.) rather than “0.000” (the p-value is not actually zero). The capitalisation in Table 1 is inconsistent in the first column (e.g. “disease…” and “Obesity”). Finally, the table should indicate the test(s) used in the table in notes under the table so the reader can quickly find this information (and this should also be described in the statistical methods). This is what I meant by my previous comment: “All tables should indicate the exact statistical models used to produce the results presented there.” (Which you have done for Tables 2, 3, 4, and 5.)

In Table 2, the effects from the modified Poisson regression are relative risks and the reader will find it easier to follow with this indicated as “RR” rather than “IRR”. Same in Table 3 and throughout the text (e.g. Line 121 and 161).

In Table 2, it remains unclear to the reader which p-value is associated with the relative risks and CIs. Personally, I’d rather see all three sets of RRs, 95% CIs, and p-values so the effects of adjustment are more conspicuous; but at the very least, the reader should not wonder which p-value is attached to the reported effects. The same issue arises in Table 4, which uses a different layout, now separating the effect and CI into different columns rather than having them in a single column.

While you have added data for aphthae/stomatitis and improved the names of variables, the data continues to need a data dictionary. For example, as noted previously, it is unclear to me simply by looking at the data whether sex=1 or sex=2 represents males (I appreciate that this question can be answered by comparing the frequencies in the data with those in the manuscript, but I think that this should be apparent from the data alone). The same point applies to other variables, such as urbanization and income. A data dictionary for all columns needs to be available. I suggest using a second worksheet in the workbook for this purpose.
Experimental design: I feel that the causal model underlying the analyses still needs attention despite the additional text on this. Something being a risk factor for poor oral health is not sufficient for it to be a confounder. For example, if obesity is a consequence, more than as a result, of asthma (through a lack of exercise) and a consequence of poor oral health (through food choices given difficulties eating), this would make obesity a collider rather than a confounder for the association between asthma and oral health, i.e. a variable that must not be included in a model to estimate the total effect of asthma on oral health. On the other hand, if asthma led to obesity (which is also the case) and obesity led to poor food choices and so worse oral health, obesity would be on the causal pathway and again should not be included in a model to estimate the total effect of asthma on oral health. As I said last time, it is also plausible that obesity is indeed a confounder of this association, but this would need to be justified in the manuscript. I suggest starting with the definition of a confounder and establishing that this is more plausible than not for each of these variables. Epidemiology is seldom straightforward!

I’d asked if you could please explain in the manuscript how rhinitis is a confounder for the asthma->oral health association, and how rhinitis is a confounder for the asthma->oral health association. I cannot see any direct justification for your speculation that “AS might be an confounder when study the relationship between AR and oral disease, and AR might be an confounder when study the relationship between AS and oral disease.” (Lines 76–78). The second paragraph in the introduction doesn’t, for me, provide a reason to speculate this—two different mechanisms would not suggest that they might mutually confound one another in the relationship with poor oral health. I appreciate that you use “might be” on Line 238 for this possible confounding when looking at the literature, but I still cannot see precisely what would lead you to suspect this particular confounding in the first place. Again, I suggest starting with the formal definition of a confounder and considering these three variables in that context. I expect that answering this question will require expanding the causal model well beyond these three variables, with all the modelled variables here ultimately included, perhaps along with some that are not available here.

Thank you for adding information about model diagnostics, but I am confused as to how Hosmer-Lemeshow was used with Poisson regression. This is normally an option for logistic regression. Why did you use negative binomial regression (Line 162) rather than Poisson regression? What approach did you use for deciding between these options?
Validity of the findings: There are possibly some minor errors in the reported results (but note that I have only looked at a small number of results and not all presented values). The upper CI for caries and rhinitis in Table 2 should be 1.14 not 1.37 I think. I get p=0.101 (not 0.100) for the p-value for pulpitis in model (a) asthma. I get p=0.112 for gingivitis (not 0.118) for model (d). Finally, I get 0.99 for the lower CI limit for aphthae/stomatitis rather than 0.98 (my value was 0.985 so I suspect this is rounding). It is possible, but seems unlikely for such convention models, to get different results using different packages or, more likely, I’m misunderstanding some aspect of the model, so if your results are indeed as included in the table, I apologise and we can put this down to my error or a SAS/Stata difference in how these models are implemented.

While you mention looking for effect modification (and note that Breslow Day and MH both test homogeneity of odds ratios rather than relative risks and the questions here concern the fully adjusted models), you say there was no evidence for this, which, if true, would make the stratified presentation in Table 3 unnecessary. I’m not entirely sure how to reconcile Lines 174–175 with your later statements, e.g. Lines 189–193 where you note that some strata have higher RRs than others. However, based on my quick analyses, there is indeed statistically significant evidence of effect modification in the adjusted models looking at rhinitis for caries by sex (Wald p<0.001 for the rhinitis-by-sex interaction), caries by income (p<0.001), caries by urbanisation (p=0.002), periodontitis by sex (p=0.002), periodontitis by income (p=0.007), periodontitis by urbanisation (p=0.009), gingivitis by sex (p=0.004), gingivitis by urbanisation (p=0.003), and aphthae/stomatitis by sex (p=0.015). For the first of these, you can informally see this by the non-overlapping CIs (1.15–1.20 and 1.08–1.11) which indicates p<0.01 in this case, with a non-surprising p-value (p=0.015) for the very last given this rule and the fact that the CI limits just overlap.

I’m not clear on how “First, the data were collected over time (5 years).” (Line 266) is a study strength.  For strengths and limitations, I think you need to tease out how each is a strength or weakness. I’m not sure that the lack of data on sugar consumption needs to be mentioned twice on Line 275. What are the “laboratory results” on Line 276 referring to?
Additional comments: I think that the topic is worthwhile and the research question asked seem important in guiding future research. The manuscript is much improved from last time and with some very careful attention to the causal model, including effect modification, and the English, I think a useful article is possible here.


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

Input:
Title: HISTOLOGICAL CHANGES OF FEMALE REPRODUCTIVE ORGANS SUBJECTED TO DIFFERENT JUMPING EXERCISE INTENSITIES AND HONEY SUPPLEMENTATION IN RATS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article entitled 'Histological changes of female reproductive organs subjected to different jumping exercise intensities and honey supplementation in rats' possesses an interesting idea of research. But, it is not supported by valid experimental data. Several necessary information/data are missing. Authors are suggested to provide these data to support their hypothesis.
Experimental design: Authors should provide a few information/clarifications:

1. Please provide the animal ethical permission number with date.
2. Why authors have chosen 9-weeks old rats? Are these pubertal/adult rats? How would authors' like to justify the implementation of the findings in human females of same age group (pubertal/adult)? Please clarify.
3. Categorization based on estrous cycle phases are not clear. How authors have confirmed same estrous phase before initiating the study? Please mention.
4. Please provide the reference of using the honey supplement? Why authors have chosen 'Malaysian Tualang honey'?
5. What are also the basis of selecting 20 and 80 jumps respectively? Is there any reference supporting its usage as different intensities of exercise?
Validity of the findings: 1. Only histopathological sections and morphometric data are not enough to support the findings. What are the causatives for these changes? Authors are suggested to provide the hormonal data of different groups of rats.
2. 80E seems to be very much deleterious to the ovarian structure. What about its hormonal milieu? Do the authors have the data for oxidative damage? If yes, please provide.
3. Some basic data, like body weight gain (%), reproductive organ weights are missing. Please provide those data.
Additional comments: The article entitled 'Histological changes of female reproductive organs subjected to different jumping exercise intensities and honey supplementation in rats' possesses an interesting concept, but not supported by enough experimental data. Authors are suggested to provide these data to support their hypothesis.


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: HISTOLOGICAL CHANGES OF FEMALE REPRODUCTIVE ORGANS SUBJECTED TO DIFFERENT JUMPING EXERCISE INTENSITIES AND HONEY SUPPLEMENTATION IN RATS
Review round: 1
Reviewer: 2

Output:
Basic reporting: 	The manuscript is clearly written. The English is unambiguous and the grammar is correct.
	The introduction contains enough information to understand the purpose of the manuscript. However, it would be important, for a better understanding, for those who are not fully familiar with the histology of the ovary and uterus, that the authors incorporate a paragraph where they briefly describe the histological organization including the terms, which they will then use as primary follicle, cyst, haemorregia, blood vessels, etc.
	Authors are encouraged to carefully read the instructions for authors on how to cite the literature reference in the manuscript.
	The manuscript presents the format of "standart sections" of journal.
	With regard to the Figures, it is first suggested that they be mentioned in the results. On the other hand, it is strongly recommended to improve the quality of the figures. Some of them are out of focus (Fig. 1A, AC, 1E, magnificaction 10x) or very dark (Fig. 2D 4X, 10x) or have a background colour that prevents the structures from being seen clearly (Fig. 1F, Fig. 2B). It would be advisable that in the photos with lower magnification (4x) the area where the highest magnification (10x) is going to be photographed be indicated with a box.  Therefore, it is not necessary to include the magnification in each photo if there is a scale, which must be clearly added on the scale bar or in the legend of the figure.
	It is important that the authors clarify throughout the manuscript that when they use the term vessel they refer to blood vessels (lines: 120, 144, 157, 214. See document.doc).
	The authors should clarify in the manuscript, in the discussion section, the meaning of the abbreviation BPA (line 237).
Experimental design: 	In relation to the background on the subject, the proposal of the authors is very interesting and original. It tries to answer questions raised by the group as a result of previous work on the proposed theme.
	The research protocol was approved by an institutional ethics committee.
	As for the section on materials and methods, it is not necessary for the authors to clarify the magnification used to carry out the observations (Line 118).
	It is important that they explain in the methodology in detail how they counted the uterine glands, blood vessels, follicles, etc., in the histological slices and avoid counting the same structure in the slices. In addition, in how many histological slices the measurements were made for each rat and how many measurements per rat were made for all the structures analyzed statistically (Line 121-126).
Validity of the findings: The conclusions expressed are appropriate according to the results obtained and the question posed. However, it is important that the authors review the statistical methodology.
Additional comments: I consider that the work is very valuable and novel, it only needs some corrections (statistics, improve the quality of photos, etc.) so that the work done by you are even better appreciated by the scientific community.


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: HISTOLOGICAL CHANGES OF FEMALE REPRODUCTIVE ORGANS SUBJECTED TO DIFFERENT JUMPING EXERCISE INTENSITIES AND HONEY SUPPLEMENTATION IN RATS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Suggested corrections were made by the authors.

It is recommended that in the materials and methods section, the authors modify the way the fourth paragraph is written. Initially they mention the methodology used for processing the material for histological study and then mention the histological characteristics of the ovarian follicles and the uterus. I consider that they have to mention the characteristics of the different types of follicles and the histological organization of the uterus in another paragraph, explaining that these terms (types of follicles and layers of the uterus) are defined in order to have a histological criterion for later quantification.

The pictures of each figure have a better quality than the one initially presented.
Experimental design: The way in which some structures were measured was incorporated in the manuscript.
Modification has been made on the statement regarding ANOVA.
Validity of the findings: Modification has been made on the statement regarding ANOVA.
Additional comments: The modifications made in the manuscript will make this work appear by their scientific colleagues.  Very good work!


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

Input:
Title: DIETS WITH AND WITHOUT EDIBLE CRICKET SUPPORT A SIMILAR LEVEL OF DIVERSITY IN THE GUT MICROBIOME OF DOGS
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.	On line 177 please clarify that ‘100% operational taxonomic unit’ means ‘100% nucleotide identity’ among the region of the 16S rRNA gene you amplified. An ‘operational taxonomic unit’ is another term that needs to be defined so it’s best to just expand here on exactly what you mean and leave out ‘operational taxonomic unit’ considering you never mention this term in the manuscript again.

2.	On line 331, please clarify that the lack of ill effects was observed in another study – not this one.

3.	Table S6 is referenced on line 263, but a table S6 is not included in the supplementary materials.

4.	Some readers may not know that high fat, high protein diets are typically low in fiber. Please expand and include an appropriate reference that this is the case near lines 346-347. This will really emphasize the potential benefits of a diet with more fiber.

5.	Please write out inflammatory bowel disorder along with the acronym IBD on line 325 or include the acronym earlier in your manuscript so the reader will know what you are referring too.

6.	On line 207, you mention a cutoff of 0.7. Is there a name or variable for what value you are cutting off?

7.	On line 323, you describe the Lachnospiraceae [Ruminococcus] torques group is known to degrade mucin. Please expand on why this function connotes either positive or negative health consequences as you state in the intro sentence to this paragraph.

8.	Please expand the [Ruminococcus] sp. label in Figure to be  [Ruminococcus] torques group sp.. This is how you refer to this group in the text so keeping the labeling consistent will prevent confusion.

9.	On lines 69-70, could you expand on how dog and human gut microbiomes are more similar? Do they have more taxa in common? I’m curious if this similarity is based on taxa or bacterial function.

10.	The conjunction ‘but’ in the sentence on line 110-111 seems odd because it implies that just because chitosan is digestible by dogs its effects on the canine microbe should have been studied. I think this also undermines the great set-up you have for why you chose to study the association between the dog gut microbiome and chitosan/cricket meal. You might want to switch to another conjunction such as ‘and’.
Experimental design: 11.	The authors are inconsistent with how they filter their ASV table and if they use the rarefied table before an analysis. This seems odd to me. Could you clarify why you used different filtering thresholds across your analyses?

12.	On line 134 you discuss how the dogs were housed. Can you clarify if these individual pens are all in the same facility? This may be relevant for future reproduction of your results given facility effects seen in other gut microbiome studies.

13.	On line 146, can you include how long after the diet switch the initial fecal sample was taken? Including a lack of acclimation time as a caveat in your discussion was a great idea, but I also think that is why knowing the timeline of just how soon after the diet switch was made is important.
Validity of the findings: 14.	Consider using another description in the title other than “supports a healthy microbiome”. This language implies a cause and effect relationship that the study did not test. While there are ASVs increasing or decreasing that have been known to have health benefits in other studies, if these ASVs actually provided health benefits in this study’s dogs was not directly tested. Additionally, it may be best to avoid using the term ‘healthy microbiome’ as there is no consensus on what constitutes a healthy microbiome given that gut microbial composition among individuals that are considered healthy can vary greatly.

15.	When discussing the lack of difference between the Bacteroidetes:Firmicutes (B:F) ratio among dogs fed different diets, consider modifying the sentence that states the lack means ‘cricket diets are likely not obesogenic relative to standard diets’. This seems strongly worded to me given that we are still learning more about the relationship between obesity and the gut microbiome and the B:F ratio is not the end-all be-all to tell you if a microbiome is obesogenic or not. In fact, more current evidence suggests that the B:F ratio and obesity connection does not hold up in robust meta-analyses. This could be one of the reasons the B:F ratio is not different if you suspect one of the diets plays a role in obesity. Here is a reference that discusses this: https://mbio.asm.org/content/7/4/e01018-16

16.	On line 319, you write that the functional impact of ASVs with low abundance was “likely minimal”. Can you provide at least a reference to justify this statement? Especially because there are known examples of relatively low abundant bacteria that make important contributions to the function of the overall bacterial community.

17.	On line 348, stating that a decrease in abundance of Bacterodetes “is likely” beneficial to health is strongly worded. Consider switching that language to “may be beneficial to health”.

18.	Line 51 in the abstract states certain ASVs are “predicted to be beneficial to gut health”. Again, this seems strongly worded. You are not really ‘predicting’ that they are beneficial gut health, but you are mentioning it is a possibility given other literature. I would change this to “are associated with gut health benefits”.

19.	On line 339 you write “the overall increase of Catenibacterium in dogs consuming cricket was health-promoting”. I would switch “was” to “may be” because you did not directly test if it was health promoting in this study.
Additional comments: I enjoyed reading this manuscript by Jarrett et al. that reports specific ASV abundance changes in the dog gut microbiome after consumption of cricket meal. Of particular interest are the dose-response changes they observed in some ASVs that showcase the link between cricket meal and abundance changes in certain ASVs. Overall, the manuscript is well written and thorough. However, I do have some recommendations that should improve clarity for the reader and ensure the authors do not overstate their work. Most notably, the authors should consider eliminating the current implications made by the wording of the title.


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: DIETS WITH AND WITHOUT EDIBLE CRICKET SUPPORT A SIMILAR LEVEL OF DIVERSITY IN THE GUT MICROBIOME OF DOGS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript is well written and concise. More importantly, the level of detail reported is sufficient to assess the strength of their conclusions and to repeat their work. Literature review was sufficient and the majority of relevant studies in the area were cited. It would be nice to have see the characteristics (age/weight) of individual animals as well as to have final weight, food intake, and evidence of any gastrointestinal issues (diarrhea, constipation, or gas) reported.
Experimental design: This study wanted to establish the potential for inclusion of cricket as a novel and sustainable source of protein and fiber in animal diets. Towards this end, they conducted a 4-arm study with varying amounts of cricket included in the diet and assessed changes in the microbiota. As mentioned in the previous section, a more detailed reporting of the animal characteristics would have been helpful to establishing this. However, the design and analysis approach of the microbiota is solid and provides useful information- particularly that including even large amounts of cricket is unlikely to be disruptive of the microbiota.
Validity of the findings: The authors do not try to oversell their results and were very transparent in their analysis approach and interpretation. Very well done!
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: RITUXIMAB INCREASES THE RISK OF HEPATITIS B VIRUS REACTIVATION IN NON-HODGKIN LYMPHOMA PATIENTS WHO ARE HEPATITIS B SURFACE ANTIGEN-POSITIVE OR HAVE RESOLVED HEPATITIS B VIRUS INFECTION IN A REAL-WORLD SETTING: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript was written clearly. But the background should be more detailed.
Experimental design: The analysis was well designed and performed.
Validity of the findings: The data of this manuscript was well stated. It is very helpful to this field.
Additional comments: The authors analyzed the incidences and outcomes of HBV reaction in NHL patients in their hospital and found that the incidences of HBV reaction in the HBsAg-positive and resolved HBV infection population were not significantly different, and the late HBV reaction was not common. They also found that old age and advanced disease stage were independent risk factors for OS. So they concluded that regular monitoring of liver function after immunosuppressive therapy or after withdrawal of prophylactic is necessary. This retrospective analysis was well designed and performed. The manuscript would be suitable to be published, but it still need more efforts to proof-read 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: RITUXIMAB INCREASES THE RISK OF HEPATITIS B VIRUS REACTIVATION IN NON-HODGKIN LYMPHOMA PATIENTS WHO ARE HEPATITIS B SURFACE ANTIGEN-POSITIVE OR HAVE RESOLVED HEPATITIS B VIRUS INFECTION IN A REAL-WORLD SETTING: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: I commend the authors for their effort to submit a manuscript clearly written in professional, and unambiguous language. The manuscript contains sufficient scientific validity and thus suitability to join the scholarly literature.

I thank you for providing the raw data, however, your supplemental EXCEL file contains non-English characters in the column 'diagnosis date', which should be improved to ensure that an international audience can clearly understand your text.

Your introduction needs more detail. I suggest that you improve the description of the estimated prevalence of HBsAg-carrier or chronic hepatitis B among the general population and cancer patients in the real world (in Taiwan, particularly, Kaohsiung). The scope of problem is important to your paper.
Experimental design: Kaplan-Meier curves of overall survival should be given.
Validity of the findings: The result of HBV reactivation in the comparison group of 'HBsAg-negative, HBcAb-negative or -unknown' status should be reported in the results and mentioned in the Abstract. This will help the reader understand the impact of HBsAg-positive or HBcAb-positive status on the chance of reactivation.
Additional comments: Line 201, two, not 2.


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: RITUXIMAB INCREASES THE RISK OF HEPATITIS B VIRUS REACTIVATION IN NON-HODGKIN LYMPHOMA PATIENTS WHO ARE HEPATITIS B SURFACE ANTIGEN-POSITIVE OR HAVE RESOLVED HEPATITIS B VIRUS INFECTION IN A REAL-WORLD SETTING: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The topic is of interest particularly to gastroenterology consultants and researchers in the field. However, the writing is not clear and many times difficult to understand or to follow what the authors want to say. The whole manuscript needs to be reviewed by an academic whose English the mother tongue or an agent who could improve the academic writing.
Experimental design: The study design has several problems- small numbers in each group (tables 3 and 4), and different chemotherapies were used, and no proper follow up of patients.
Validity of the findings: The limitations in the methods will affect the results and it is difficult to make a generalisation in the presence of several variables and the small number of patients in subgroups (tables 3 and 4).
Additional comments: Rituximab increases the risk of hepatitis B virus reactivation in non-Hodgkin lymphoma patients who are HBsAg-positive or resolved hepatitis B virus infection in a real-world setting.

ID: #35793
Journal: Peer J

Thank you for asking me to review the above-titled manuscript which I read with great interest. However, there are several problems in the article.

The topic is of interest particularly to gastroenterology consultants and researchers in the field. However, the writing is not clear and many times difficult to understand or to follow what the authors want to say. The whole manuscript needs to be reviewed by an academic whose English the mother tongue or an agent who could improve the academic writing.

Abstract: Background: State the research question, under Materials: state what exactly was reviewed for patients with NHL. Results: First line is confusing. It is not clear what do the 62 and the 130 patients represent. Were the 130 patients negative for HBsAg and positive for HbcAg? Conclusion: not consistent with the reported results. How many patients developed late reactivation. The statement about regular monitoring of liver function tests is not consistent with what was reported in the abstract.

Introduction: Is too brief (about half a page) and did not prepare the readers to the purpose of the study. What was the rationale of the study, why this study was needed, what was the problem, what do we know about this area? The authors should justify the rationale for the study, and state their research questions. First two lines: Is Yeo et al the first author to report this reactivation? What were the recommendations of the EASL, and the AASLD? State a reference for the statement “however, prophylactic anti-HBV therapy is not prescribed routinely to patients with resolved HBV infection in clinical…”

Ethical approval for the study is a must. Please state the body/hospital/university/city/country granting the ethical approval and state the number/year of the ethical approval. What was approved exactly (line 84)? The sentence gives the impression that the institute approved that informed consent for the study was not needed because the study was retrospective!

Materials and methods: Not well described. The definition part could be placed in the introduction. The flow of writing and the formatting of the paper need improvement. What does the authors mean by “the upper limit of normal 40 IU/L at our hospital or an absolute increase >100 IU/L” which one was used? The study method could be improved by comparing prophylaxis used entecavir, tenofovir vs lamivudine. The study design has several problems- small numbers in each group (tables 3 and 4), and different chemotherapies were used, and no proper follow up of patients.

The methods need significant improvement to reflect the results outlined in tables 1 to 5. There is a need for suitable subtitles, and these subtitles should be mirrored in the results section.

Results: Lines 142-144, were these the authors results, or the results from Liue et al 2016 and Nakaya et al, 2016?
The results section needs organization and proper subtitles that mirror the methods and reflect the tables (1 to 5).

Discussion: Line 161, what do the authors mean by “the study provided real-world data”? Do other studies provide unreal world data? The limitations in the study design make it difficult to carefully interpret the results and make sound conclusions. The conclusions at the end of the study are not consistent with what was mentioned as conclusions in the abstract.

References: Several important references in the English literature were ignored such as Castelli R et al, 2016; Zhou X et al, 2017; Carrier P et al, 2015; Persico M et al, 2018 and others. The reference European Association (line 272) is not correct, why there is an electronic email address (Line 265)?, the journal “Jama” should be written “JAMA”, other similar errors were noted.

Figure 1- the description given in the abstract is not showing the grouping outlines in figure 1.


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: RITUXIMAB INCREASES THE RISK OF HEPATITIS B VIRUS REACTIVATION IN NON-HODGKIN LYMPHOMA PATIENTS WHO ARE HEPATITIS B SURFACE ANTIGEN-POSITIVE OR HAVE RESOLVED HEPATITIS B VIRUS INFECTION IN A REAL-WORLD SETTING: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 4

Output:
Basic reporting: In general, clear and professional English language is used throughout, the manuscript is well structured and well contextualised, and raw data is supplied. The figure is clear and well labelled. References are adequate.

However there are significant errors in the tables:

In Table 1, there is no p-value presented for the difference in median age between HbsAg-positive and HbsAg- negative groups.

In Table 3 and 4, units of measurements should be provided for HBV DNA.

In table 3, the inclusion of patients 2 and 4 in the column entitled “Time to HBV reactivation after treatment completion” is confusing, because they had reactivation on treatment. The authors should include them in a separate column indicating the length of time on chemotherapy before reactivation was detected (in addition to the number of cycles).

Similarly, in table 4, the inclusion of patients 6 and 7 in the column entitled “Time to HBV reactivation after withdrawal of prophylactic antiviral therapy” is confusing, because they had reactivation on treatment. The authors should include them in a separate column indicating the length of time on chemotherapy before reactivation was detected (in addition to the number of cycles).

Furthermore, in table 4, patient 7 does not have any data about the timing of his reactivation. The table just states “during lamivudine prophylaxis”, which is inadequate.

Similarly, these tables should indicate which patients met criteria for a hepatitis flare. Currently only objective ALT levels are provided, which is inadequate.

Table 5 should be presenting hazard ratios for mortality rather than survival. It currently seems to imply that an older age or stag III/IV cancer increases the risk of survival rather than increasing the risk of mortality. Similarly, in the results section of the abstract, the last sentence should state “An age ≥65 years and advanced disease 50 stage were independent risk factors for overall mortality” (or “for poorer overall survival”).
Experimental design: The research is within the scope of the journal. Data appears to have been rigorously collected and under appropriate ethical guidance. However it does not necessarily fill a knowledge gap and indeed similar data has already been presented by other larger studies, as per the discussion.

There are significant errors and omissions in the methods though:

Patients were recruited if they were initially either HBsAg- or HBcAb-positive: what is the definition of ‘initially’- is it within a short timeframe before commencing chemotherapy? If patients’ serology results were from a long time before commencing therapy, their serological status could have changed prior to commencement.

Similarly, the time of ‘baseline’ HBV DNA measurements is not clarified- is this the level on the day of first rituximab treatment?

The methods section should clarify how often HBV DNA and sAg status was checked while patients were undergoing chemotherapy, and afterwards in both sAg positive and resolved groups. It should also state how long (in median length of time) patients who were sAg positive received antivirals after the cessation of chemotherapy.

There is no data about the median length of time of follow-up of these patients after completing chemotherapy. Thus the data about their outcomes (dead or alive) as presented in tables 3 and 4 is not meaningful. Similarly, the Cox regression analysis cannot be well interpreted given there is no information about the specific time point used in the regression analysis to deem patients dead or alive.

More description should be offered about the treatment and virological outcomes after reactivation +/- hepatitis flare was detected. In those with previously resolved infection, did commencing antiviral therapy return the HBV DNA to normal, and return the ALT to normal? If so, how long did this take?

Similarly, in those with sAg+ positivity, what were the therapeutic switches of antivirals (this is presented in table 4 but not in the manuscript)- and did these switches return the HBV DNA to normal, and return the ALT to normal? If so, how long did this take?

Line 152 states the 5-year overall survival rate was 71.0%- this should be rephrased to emphasise this was an estimate reached by Kaplan-Meier analysis rather than an objective figure. Similarly, it is not stated when is the time-point to gauge 5-year overall survival: is it 5 years after commencement of chemotherapy? Or completion of chemotherapy?
Validity of the findings: There are significant omissions in the data and overly speculative conclusions are presented.

It is stated that rituximab containing regimen, older age (≥60 years), male sex, and advanced disease stage were associated with HBV reactivation. However there is no statistical analysis that presents these risk factors as statistically significant.

It is unclear whether patient number 5, who was sAg-positive and had reactivation after withdrawal of prophylactic antivirals, had an adequate length of time of prophylactic antivirals after ceasing chemotherapy. Thus it is unclear what conclusions can be drawn from his case, if there is a possibility that he was inadequately treated (e.g. if he stopped antivirals very soon within 6 months after ceasing chemotherapy). Furthermore, it is unclear as to the intervals at which his HBV DNA status and other blood tests were checked after cessation of antivirals. His reactivation detected at 11.2 months after cessation of antivirals may actually have commenced a lot earlier but maybe was not detected if blood tests were not done routinely. Without this information, it is uncertain if he can be truly classified as “late reactivation”, and thus the overall article’s conclusion that “late reactivation is not uncommon” is specious.

Patient 2 appears to have developed reactivation after 5 cycles of rituximab. However the manuscript elsewhere states that all patients with reactivation had at least 6 cycles of rituximab. Please clarify.

The authors state in the discussion that prevalent use of entecavir and tenofovir instead of lamivudine in their HbsAg positive patients could explain low HBV reactivation rates. However they offer no statistical comparison about the rates of reactivation in those using lamivudine and in those using other antivirals to back up this claim.

It is unclear why the difference in sAb status between sAg- positive and resolved groups is emphasised not only in the results section, but also in the abstract. There is no further analysis offered about the effect of sAb positivity on the risk of HBV reactivation. The authors go on in the discussion to speculate that a high proportion of sAb positive patients in their resolved HBV group could explain low rates of viral reactivation, and in the conclusion state that “the presence of HBsAb appears to be protective against HBV reactivation”. However actual statistical comparisons between their sAb positive and sAb negative cohorts should back up this claim.

The overall aims of the study are also unclear.

Initially it is stated that the aims are only to investigate the real-world occurrences of HBV
73 reactivation in HBsAg-positive and resolved HBV infection patients.

It is thus uncertain why analyses of 5-year survival rates and Cox regression models are being emphasised as they are not relevant to, and distract significantly from, the overall message of the study.  Instead of such analyses, it would be highly preferable if the authors could present statistical analysis about the risk factors for HBV reactivation (as above), and more importantly the risk factors for HBV flare. After all, it is HBV flare that is truly concerning to the clinician and potentially fatal to the patient, rather than just a rise in viral DNA.
Additional comments: There are a few unclear English language statements.

Line 152 states “The median overall survival of our NHL patients was not reached”. Please clarify what this means.

The abstract background should state “a common and potentially fatal complication”. Currently the phrase appears to imply that reactivation is invariably fatal, which is not the case.

In line 64, the phrase “This combination regimen has also been found to increase the
risk of hepatitis B reactivation” is redundant as it repeats what has been said in the previous sentence.


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: RITUXIMAB INCREASES THE RISK OF HEPATITIS B VIRUS REACTIVATION IN NON-HODGKIN LYMPHOMA PATIENTS WHO ARE HEPATITIS B SURFACE ANTIGEN-POSITIVE OR HAVE RESOLVED HEPATITIS B VIRUS INFECTION IN A REAL-WORLD SETTING: A RETROSPECTIVE STUDY
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