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: FACTORS ASSOCIATED WITH NON-ATTENDANCE AT APPOINTMENTS IN THE GASTROENTEROLOGY ENDOSCOPY UNIT: A RETROSPECTIVE COHORT STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors addressed very important questions about which are the factors associated with non attendance to endoscopic procedures. The article is very well written and I think this kind of articles allow us to reflect on parts of the health system that need to be improved.
This study has the objective to identify factors associated with non attendance to an endoscopic procedure. I think that the title should reflect the objective of the study and not the results of which factors were associated with non attendance in the study. I think a title like "factors associated with non attendance to... in ..." would be more appropriate as a title for this study.
The factors associated with non attendance are different considering different appointments, contexts and populations. Please specify in the introduction if all factors associated with non attendance are associated with non attendance to endoscopic procedures or not.
What are the differences in the non attendance rates from 3.6 to 67% in line 52 and from 12.8 to 20.5 in line 64? PLease add additional information to understand the differences between these 2.
Experimental design: In line 112 it says "Recurrent patient appointments were identified, and such patients’ last appointments were analyzed" why last appointment? why not first or all of them? I think it would be important to add a clarification here.
in line 115, Cancellations near the appointment within 48 hours were considered as non attendance. Non attendance and cancellation are usually very different conducts and usually do not have the same impact in the health systema. Could you add additional information for this decision?
In line 141 it says that after excluding inconsistent data, they analyzes 5938/11690. Almost have of the appointments were excluded becouse inconsistent data? what does this mean? >What was the definition of inconsistent data? how does this high exclusion rate affects the validity of the results?
Table 1. I suppose the p values correspond to the null hypothesis of equal distribution between atenders and non attenders. I would suggest changing the order of the columns and leaving them to total first. I would also suggest clarifying as a footnote what general hypothesis the p values are testing.
In table 1 all percentages are given for columns and not for rows. That does not allow to tell which is the percentage of nonattenders among men, or during the pandemics. I think this should be changed to the porcentaje within rows.
In table 1, please review ".001" if it corresponds to 0.001 or to <0.001
In table 1, it is extrange the way numeric variables are presented with mean and standard deviation in the "n" column and the min and max under the "%" column. Maybe this last information can be avoided.
In table 1, please provide the unit of quantitative variables like age and lead time.
The percentage in line 150 for example are discordant with the percentages presented in table 1. That is becouse of the difference between within row percentages and within column percentages. I would suggest to be homogeneous with this numbers. Probably it would be more informative to show percentages of non attendance with the different categories.
Probably it would be more clear not to use abbreviations for attenders and non attenders.
In line 154, I believe it is more cler to use standard deviation instead of +- symbol. Probably 1 decimal is more clear for these numbers.
In line 156 the porcentages 29 and 14 are not presented in table 1. This is becouse of the same problem if the authors should present within row or within column porcentajes. I believe that the more important porcentajes might be the percentage of non attenders within each category.
Please add the units for the travel distances in line 167
Please remove the extra "." in "21.2." in line 164
In my opinion, the part of the predictors of non attendance is the most important part of the results. I think it would be very important to provide all the OR of each relationship for each potential characteristic and non attendance. This is in my opinion much more important than the comparison in proportion provided in the previous section, that of course is also important. The association measurement provides much more information than p values.
In this particular part, I believe that there is some confusion. If the main objective of the study is to identify predictors, I think the authors should present bivariate association and avoid presenting multivariate association measurements (like using multivariate models).
If the authors objective is to generate predictive models to non attendance, I would suggest to follow the standard procedures to generate and validate predictive models like the method described by Towards better clinical prediction models: seven steps for development and an ABCD for validation Ewout W. Steyerberg* and Yvonne Vergouwe
I think it is very important to define if the objective of the paper is to identify potential predictors, or to generate and validate a predictive model. Because that would help to complete the results, methods and discussion section.
In table 2, there seem to be many factors missing. I think it would be important to complete the table with all missing factors. I believe that OR estimators should be bivariated and not multivariate to avoid table 2 fallacy.
Figure 1. Why is a distance under 4 km excluded? Is there a reason for that?
Figure 2. I think it is better to change the figure to a 2d figure. Usually 3d figures are less clear and more difficult to interpret
Figure 3 seems to assume that the number of risk factors to non attendance is related to the probability of non attendance. Since the effect of each factor may be very different, this figure probably needs additional clarifications.
Validity of the findings: In the discussion, I think it is very important to add that probably there is a selection bias affecting those endoscopies appointed during the pandemics since they may be reduced to only those procedures that, considering the nature of the condition, could not be postponed until the pandemics have gone. For example, maybe most screening studies could be delayed without consequences.
I think the interpretation in line 220 about sedation is at least mischieving. It is possible that the different types of sedation are related to different procedures. This interpretation should be taken with caution, since the nature of the study is not defined to address causality. The danger part of this kind of interpretation is to promote one kind of sedation to decrease non attendance rate. This kind of interpretations should be taken with caution.
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: FACTORS ASSOCIATED WITH NON-ATTENDANCE AT APPOINTMENTS IN THE GASTROENTEROLOGY ENDOSCOPY UNIT: A RETROSPECTIVE COHORT STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The writing appears to be clear and relative straightforward. There are a few minor issues with grammar and sentence construction which can be easily corrected. These are a few examples:

Line 72-74: The last word of that sentence should be infection rather than "contamination". Humans get infected with viruses while inanimate objects get contaminated.

Line 97-99: ....deep sedation "was applied with by".... The use of 2 prepositions back to back here is wrong. You either "apply with" or "apply by". In this context, "administered by" or "given by" seems more appropriate.

Line 89-91: I'm not sure what distinction the authors are trying to make here. The authors claim they intended to "explore the parameters associated with non-attendance to endoscopy appointments" and then go ahead to say "factors associated with Covid-19 was subject of another study". It appears this study also focused on appointments in Covid-19. In fact, about half of the study period was during Covid-19. A better clarification of what the authors mean by this statement is needed to avoid a potential Salami publication where similar data is presented as 2 or more separate publications.
Experimental design: The study design appears adequate, although the research question appears to have been previously explored in previous publications as cited by the authors with the major distinction in this article being the effect of the pandemic and deep sedation on appointments compliance. Despite being a single center study, this research provides a window to understanding how the pandemic affects utility of healthcare especially as it relates to GI procedures and helps identify target opportunities to improve or address non-attendance
Validity of the findings: With the aid of logistic regression, the authors identify various predictors of nonattendance including absence of deep sedation, female gender, type of procedure and referral physician. In the discussion, the authors go on to say "winter season, multi-scheduled appointments, and malign comorbidity" were associated with non-attendance (Line 257-258). These were however not mentioned in the earlier report of Predictors (Line 177-187). These variables were also not presented in Table 3 or referenced to any other table or figure. How did the authors arrive at these other predictors? They should be mentioned in the section 3.3 (Predictors of Nonattendance) and either included in Table 3.
Additional comments: Line 172 mentions "screening procedures of gastroscopy". Can the authors enlighten the readers what conditions are being screened for as screening gastroscopies is not universal like screening colonoscopies.

Overall, the article helps identify potential opportunities for intervention to reduce nonattendance. The finding of the impact of deep sedation is particluarly revealing. We need to do a better job at reassuring patients, allaying their fears and educating them on the use of conscious sedation. We also need to refine out technique to potentially reduce patient discomfort.


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: FACTORS ASSOCIATED WITH NON-ATTENDANCE AT APPOINTMENTS IN THE GASTROENTEROLOGY ENDOSCOPY UNIT: A RETROSPECTIVE COHORT STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: I have suggested considering the formatting of the title, the authors have provided major results in the title. I have a suggestion to please rewrite the title as Evaluation of Non-adherence to endoscopy appointments at a gastroenterology unit; A retrospective analysis

This manuscript is well structured, however; it lacks scientific writing at some points. I will suggest considering careful proof read after incorporating all the comments from reviewers.

The introduction section states that there is no study on this topic, but only colonoscopic data is available, can authors confirm their best search, and no other study, nationally or internationally has been done on this objective.
Experimental design: Can the authors explain why appointments for patients with age less than 18 years were not included in the study?

The heading no. 2 should only be "Methods".

Can authors explain on which grounds the variables were selected for a regression analysis? were they reported previously in other studies, or were they logically plausible with non-adherence, or did authors consider all variables to be run in univariate analysis? Please write dependent and independent variables in the analysis section

There is to define some terms in methodology i.e. what is meant by non-adherence? attenders etc.. were the attendees those who completed the procedure?
Validity of the findings: Authors have primarily compared between attenders and non-attenders and then evaluated various predictors of non-adherence to the procedure. Based on the rationale of the study, these non-adherence practices result in considerable financial loss as well as reduced trust/quality of patients. Authors have dug out various predictors, can they classify these predictors i.e. patient-related factors, hospital-related factors, healthcare-related factors. As gastroscopy is not related to the patient`s factor associated with non-adherence. Similarly, deep sedation is something related to the hospital.

There are many other factors that may associate with non-adherence i.e. comorbid conditions, psychological impairments, financial status, disease severity, health insurance status...... and so on. can author draw a firm conclusion without incorporating these factors in the model. Moreover, the exact cause of non-adherence is something more important than predictors. Authors should consider them while discussing the results.
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: FACTORS ASSOCIATED WITH NON-ATTENDANCE AT APPOINTMENTS IN THE GASTROENTEROLOGY ENDOSCOPY UNIT: A RETROSPECTIVE COHORT STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: I think the article improved significantly and all my concerns were clarified and improved significantly. In my opinion, the paper quality has substantially improved.
I agree with the exclusion criteria detailed in the responses point by point to the comment "In line 141 it says that after excluding inconsistent data, they analyze 5938/11690. Almost have of the appointments were excluded because inconsistent data? what does this mean? >What was the definition of inconsistent data? how does this high exclusion rate affects the validity of the results?". Please be sure these exclusion criteria are describe explicitly in the paper, allowing the reader to understand potential selection bias and validity of the results. The comment was directed to the external validity and not to the power of the study.
Experimental design: -
Validity of the findings: I still believe that the adjusted OR may represent here a Table 2 fallacy. Please see The Table 2 Fallacy: Presenting and Interpreting Confounder and Modifier Coefficients - Daniel Westreich and Sander Greenland. I think this can be acknowledged in the discussion, to interpret with caution the results of this adjusted OR if the authors decide to keep them in the table.
Additional comments: In my opinion, the paper quality has substantially improved.


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: FACTORS ASSOCIATED WITH NON-ATTENDANCE AT APPOINTMENTS IN THE GASTROENTEROLOGY ENDOSCOPY UNIT: A RETROSPECTIVE COHORT STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have addressed all my concerns very well. I have no more comments on the manuscript.
Experimental design: The authors have addressed all my concerns very well. I have no more comments on the manuscript.
Validity of the findings: The authors have addressed all my concerns very well. I have no more comments on the manuscript.
Additional comments: The authors have addressed all my concerns very well. I have no more comments on the manuscript.


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

Input:
Title: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING (LNCRNA) IN NILAPARVATA LUGENS’S ADAPTABILITY TO RESISTANT RICE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Sentence Structuring has to be improved throughout the manuscript. Please pay attention to words that have been used in the manuscript.  For instance, in line 49, Oryza should be italicized; in line 57, co-evolutionary should be co-evolution.

Line 58-59: Revise it to make sense. How come BPH can carry a resistance gene?
Experimental design: From where the BPH colonies were collected? And if the authors maintained them, then for how many generations? Did they check for the presence of rice-ragged stunt/grassy stunt virus in the BPH they used for the experiment? Please include the confirmatory results in the complementary file.
Validity of the findings: Results are interesting. However, some additional data, especially on the representation part can improve the manuscript. For instance, how many lncRNAs were shared in between the two libraries, and how many were exclusive to each? The authors can give a Venn diagram for the same.

Did the authors compare with a complete check (CK) library? It can show the basal lncRNAs which are there irrespective of the BPH interaction with rice.

Based on the findings of the study, I suggest the authors make a conceptual model of lncRNA-mediated rice resistance breakdown by BPH and include in discussion and also add it as a picture. This will be hugely helpful for the readers to understand and correlate the findings.
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: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING (LNCRNA) IN NILAPARVATA LUGENS’S ADAPTABILITY TO RESISTANT RICE
Review round: 1
Reviewer: 2

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: This manuscript by Wenjun Zha and his colleagues investigated the lncRNA expression profiles of two Nilaparvata lugens populations’ adaptability to susceptible and resistant rice by the RNA-seq method. The manuscript needs careful editing in English grammar.
However, several points should be addressed before acceptance.

Minor points:
Line 31, there should be spacing between “.” and “Altogether”,
Line 31-32, I suggest that the description at lines 31- 32 “this study proves that lncRNA may be involved in BPH’s adaptability to resistant rice.” could be changed to “it provided scientific data for the study of lncRNA regulation of brown planthopper resistance to rice.”
Line 43, deleted “-”,
Line 44, show should change to “showed”,
Line 45, there should be spacing between “resistance” and “(”,
Line 49, Oryza should be italic,
Line 50, I suggest that the description at lines 50-51 “rice-ragged stunt viruses and rice grassy stunt”, such as “rice-ragged stunt viruse and rice grassy stunt viruse”,
Line 52-53, it might be better to delete the description “less than four generations in”,
Line 54, there should be spacing between “,” and “0”,
Line 73 and 242, the brown planthopper was abbreviated as BPH hereafter. Why use “BPHs”?
Line 78, why did you choose “a moderately resistant rice variety (YHY15)”, Why not choose a high resistant variety?
Line 80, please modify the description “proof”, such as “a proof or proofs”,
Line 92, the brown planthopper was abbreviated as BPH hereafter, “N. lugens” should change to “BPH”,
Line 92, dose the brown planthopper have been reared on resistant varieties for a long time, or was it treated by the resistant varieties after several generations? Dose the physiology and behavior of BPH have changed?
Line 108-109, in the description, change the location of “size”,
Line 152, “®” should be superscript,
Line 180 and 186, lncRNA should be “lncRNAs”,
Line 189, deleted “identified”,
Line 193, LncRNA should change “lncRNA”,
Line 194, Mrna? It is “mRNA”,
Line 195, “cis-” should be italic,
Line 199, there are “-” between number and word (9-pair) in some paragraph, however, there are not “-” between number and word (9 pair) in some paragraph, please modify,
Line 243, there should be a spacing between “analyzed” and “(”,
Line 252, “insect” should change “insects”,
Line 253, lncRNA should be “lncRNA”,
Line 276, “P450” was not italic,
Line 277, “P450 gene” need not to be italic,
Line 278, “The” should be “the”,
Line 279, “cAMP-response element-binding protein” need not to be italic,
In the introduction, it needs more detail about the function of lncRNA.


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: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING (LNCRNA) IN NILAPARVATA LUGENS’S ADAPTABILITY TO RESISTANT RICE
Review round: 1
Reviewer: 3

Output:
Basic reporting: There are some typos and grammatical errors throughout the manuscript. Some examples,
Line 48: Nilaparvata lugens -> N. lugens.
Line 49: Oryza species -> Oryza (italics)

Line 241: worldwide rice plants -> worldwide rice cultivation.
Experimental design: I wonder on what basis only 10 genes were selected for qRT-PCR.
Author could use same RNA isolation method for both RNAseq and qRT-PCR. Any special reason for choosing different protocols.
Validity of the findings: From the overall results and discussion, we are not able to get which candidate genes are involved in the pest resistance. Apart from general GO and KEGG, key responsible genes information could be needed for readers to understand necessity to carried out this kind of works and future experimental design to be conduct on this area of research.
I would like to suggest author to emphasis significant differences and key regulatory genes/networks in both results and discussion.
Additional comments: No additional comments


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

Input:
Title: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING (LNCRNA) IN NILAPARVATA LUGENS’S ADAPTABILITY TO RESISTANT RICE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed my queries satisfactorily.
Experimental design: The authors have addressed my queries satisfactorily.
Validity of the findings: The authors have addressed my queries satisfactorily.
Additional comments: The authors have addressed my queries satisfactorily.


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: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING (LNCRNA) IN NILAPARVATA LUGENS’S ADAPTABILITY TO RESISTANT RICE
Review round: 2
Reviewer: 2

Output:
Basic reporting: The author has revised the manuscript completely according to the reviewer’s suggestions; therefore, I recommend the revised version of the manuscript can be accepted and published.
Experimental design: GOOD
Validity of the findings: GOOD
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: MICROBIAL COMMUNITIES ASSOCIATED WITH MOUNDS OF THE ORANGE-FOOTED SCRUBFOWL MEGAPODIUS REINWARDT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is clear, well written and the English of a high standard. The topic is well introduced and the background literature well covered. The terms ‘thermogenesis’ and ‘thermophilic’ need to be defined and distinguished in the introduction. The terms thermogenic and thermogenesis need to be used with extreme caution in reference to microorganisms - see the general comments above for reasons why. Figures and tables are well presented and are relevant. I did not see any statement where the raw data was available, so I could not confirm that raw data are available as is PeerJ policy.
Experimental design: The experimental design is straightforward and well described. The methods are easily followed. I’m not an expert on the methods used for determining microbe diversity and abundance and the statistical methods used to analyze this type of data. However, I do believe the methods and statistical analysis used are standard for this type of data.
Validity of the findings: The conclusions reached appear well supported by the data.
Additional comments: Specific comments
Lines 72-78: Also maybe mention there are also species that incubate their eggs in volcanically heat sand, and black sand beaches.

Line 91: Are there such things as ‘specialist thermogenic microorganisms’? The use of the term thermogenic implies that their major function in life is generating heat. But because such microorganisms, by definition are so small, individuals at simply not capable of generating sufficient heat to raise their temperature above the ambient environment, their surface area to volume ratio is such that any heat they generate would be rapidly dissipated to the surrounding environment. The only way these microorganisms can raise temperature above ambient is if they are clumped together by their millions, i.e. they combine together to form a ‘cooperative super colony’.  As suggest elsewhere these organisms are poor likely to be thermophilic, i.e. heat ‘loving’ or heat ‘tolerant’ as opposed to ‘thermogenic’. To be defined as ‘thermogenic’, which is a energetically expensive process, and therefore must have some other benefit to the organism because of this cost, this benefit must be explained. One possible explanation might be, that it gives these organisms a completive advantage, i.e. by raising the environmental temperature it kills off or excludes other species of microorganism that might also be using the organic plant material as a food source. So here the definition of ‘thermogenic’ and ‘thermophilic’ needs to be defined and the difference between the two pointed out.

Line 274-275: But previously the authors stated that the species distribution was not different between mounds and surrounding shallow soil, but there was a big difference in the relative abundance of different microbe types in these two environments. So this statement should be altered to be consistent with that in the previous text.

Line 279: Consider replacing ‘thermogenesis’ with ‘metabolic heat production’. As stated above, ‘thermogenesis’ has the connotation that heat is being deliberately produced for the sole purpose of raising the temperature of the organism, whereas it is far more likely that the heat is being produced as a simple by-product of routine metabolism in these microorganisms. Specialist heat producing metabolic pathways, the sole purpose of which is to produce heat have been demonstrated in animals (i.e. the H+ leak in the mitochondria of brown adipose tissue of eutherian mammals, and the Ca+ leak in the sarcoplasmic reticulum of the heater organ of billfishes) and plants, the alternative oxidative pathway in ‘heat producing’ plant organs. Until such metabolic pathways are demonstrated in microorganisms, the use of the terms “thermogenic’ and ‘thermogenesis’ should be avoided in reference to microorganisms.


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: MICROBIAL COMMUNITIES ASSOCIATED WITH MOUNDS OF THE ORANGE-FOOTED SCRUBFOWL MEGAPODIUS REINWARDT
Review round: 1
Reviewer: 2

Output:
Basic reporting: I did enjoy reading this well written and relatively well structured manuscript on an interesting topic.
Regarding the background provided in the introduction, I would have only liked to get a bit more information about the species ecology and in particular what is known about the mound:

-	L72-78: Is there anything known about the construction of the mounds? Who builds the mounds, male or female? Does one mound belong to one pair or are others involved in the process? Are there multiple eggs laid in multiple different chambers per mound?
Experimental design: The authors do present an original study well within the scope of the journal. The question from where the material and the microbes in the mound originate seems interesting and relevant, particularly given the unclear role of thermogenic/thermophilic bacteria in these mounds, that the authors highlight. I do however have several more questions and comments regarding the methods:

-	One criticism that I have is that I found it hard to follow what the sample sizes really were and how and which were used in the different analyses. I have made some detailed line-by-line comments on this below regarding that I was unclear where the faeces originated from, and that I was somewhat unclear about the rarefaction process and whether the samples excluded there were not used in any other analyses (see also comment on Fig. 2).

-	I found it not very clearly described anywhere how the multiple samples collected at some of the locations were dealt with (e.g., 3 soil samples from the same mound). It seems that they were perhaps just combined per mound in the analyses, but that does not seem to be explained anywhere.

-	L112-113: Why did the authors choose to sample 4 mounds within 1km?

-	L114-115: What time of the year and in what time window were all the samples collected?

-
-	L121: Could you tell if it actually originated from the owners of the respective mound? Around which mounds was the faeces collected? Later, in Table 1 I find it mentioned from 3 sites, in Fig2. there seem to be bacterial samples from 2 sites, and fungal samples from 1 site. This is somewhat confusing and unclear.

-	L127: “were” instead of “was”?!

-	L141-144: Can you describe the purpose and the chosen threshold in a bit more detail?

-	L154: What is SIMPER?

-	L190-191: How is this taking into account the different mound locations?
Validity of the findings: While some of the descriptive findings are certainly valid and meaningful, I do have some concerns about the details of some of the analyses and the conclusions drawn given a low sample size, but also the details of some of the analyses and my current lack of understanding some of the aspects.

-	What I had generally really hoped to see was a statistical comparison also of the different samples taken from the same sample type. The authors did take multiple samples from the same location, but, unless I missed it, neither analysed that nor specified what the purpose was otherwise. This might have perhaps been limited by the samples size, which is unfortunately rather low – but can still provide useful insides, I believe. Nevertheless, I would find the results presented in the manuscript, that basically all the microbial communities differed between categories and locations much more convincing if it was contrasted with something where we would expect a higher similarity, e.g. the difference within shallow soil samples. How the analysis was done, we do not really know what baseline level of similarity we would expect for samples from the similar source,

-	L151-153: Did you assess the fit of the data in the nMDS? What were the associated stress values?

-	L153-154/Fig.1: Is this correct, it seems that many of the phyla shown actually have a percentage of less than 1%. Also it’s very hard to make out which bacterial phyla the much more frequent sequences belong to, as there are too many similar colour shades and I’m also not able to count to order cause many of the bars are so low and the background grid doesn’t match the width of the bars. Maybe they could at least be numbered on the y axis. Otherwise, I’m not sure what information I am supposed to get from this figure.

-	- Fig.2: Why does the figure show unrarefied data? It seems however, that the samples that were described to have been removed in L141-144 are not included.

-	L163-164/Table 1: Is this averaged over the different samples collected from the different sites? This should be mentioned. Generally, the table might also be a good spot to add the number of samples per each site that were actually used in the analyses. Does Faeces B state an SD of 0 because it is only one sample? I do not think that it makes any sense to calculate an SD from one sample; this is misleading.

-	Given above mentioned concerns, limitations in sample size and statistical power, and the descriptive nature of the study, I would tune down some of the wording used in the discussion section to more careful interpretations. After the authors eagerly reject all hypothesis as for the origin of the bacteria, they do not present an alternative explanation for their source. Thus, I would recommend being a bit more careful with rejecting hypothesis and jumping to strong conclusions and give a bit more nuanced picture of what we can really say from the presented results.
Additional comments: I generally like the study, but the analyses lack clarity for me in the current form and I would not want to draw the presented conclusion from the data as it is presented.


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: MICROBIAL COMMUNITIES ASSOCIATED WITH MOUNDS OF THE ORANGE-FOOTED SCRUBFOWL MEGAPODIUS REINWARDT
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is a revision of the first version. The Authors have done an excellent job at addressing the comments raised by the editor and reviewers. I recommend acceptance for publication.
I noticed one minor typo no line 243: ‘significantly’
The article is well written, the English is clear and concise, the appropriate literature is cited, figures and tables are appropriate, hypotheses are well stated and tested.
Experimental design: Experiential and statistical design is appropriate.
Validity of the findings: The analysis and interpretation of data is appropriate and the conclusions made are well supported.
Additional comments: This is a revision of the first version. The Authors have done an excellent job at addressing the comments raised by the editor and reviewers. I recommend acceptance for publication.
I noticed one minor typo no line 243: ‘significantly’


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: MICROBIAL COMMUNITIES ASSOCIATED WITH MOUNDS OF THE ORANGE-FOOTED SCRUBFOWL MEGAPODIUS REINWARDT
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article is clear and well written. I think the manuscript has greatly improved from the previous version I have reviewed and the authors have addressed all my former points sufficiently.

I really enjoyed the additional information that was added on the ecology and behaviour surrounding the use of the mound. E.g., I previously hadn’t been aware that those mounds could exist for years or even decades and I think it’s an important detail to understand the distinct bacterial community within the mounds.
Experimental design: As stated in my previous review of this work, I think the experiment is sound and any concerns I had about regarding methodological aspects and data analysis have been addressed and corrected already.
Validity of the findings: All data have been provided, as far as I can see.

I appreciate the adjustments the authors have made during the revisions regarding the additional analysis and not overstating the conclusions that can be drawn.
Additional comments: I have no addititional 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: ADAPTATION OF A CLINICAL REASONING MODEL FOR USE IN INFLAMMATORY CONDITIONS OF THE LACTATING BREAST: A RETROSPECTIVE MIXED-METHODS STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: 1.	In phase 5, the author demonstrated that an iterative process was employed to determine factor inclusion. However, there are no clear criteria (numbers or qualitative information) about how to determine whether a factor should be included or not.  The author should provide statistics or qualitative statements about the qualification of individual factors in the adapted model.

2.	Given that all participants are from a mono-center study (a private physiotherapy practice in Melbourne, Victoria), some factors cannot be simply determined as “linked factors” to ICLB. For example, the authors need to justify whether the high socioeconomic status in this study is because the postal code around Melbourne is more likely to be above 6. If so, the high socioeconomic status actually reflects the economic advantage of the Melbourne area but has nothing to do with ICLB.
Validity of the findings: I suggest the author compare their model with the existing Breastfeeding Pain Reasoning Model in an irrelevant dataset to see if the adapted model performed better than the BPRM on ICLB.
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: ADAPTATION OF A CLINICAL REASONING MODEL FOR USE IN INFLAMMATORY CONDITIONS OF THE LACTATING BREAST: A RETROSPECTIVE MIXED-METHODS STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a well-design study evaluating the contributing factors of ICLB. Authors have aggressively updated the existing model on nipple pain i.e. Breastfeeding Pain Reasoning Model (BPRM). However, the rationale of the study is quite weak, the authors have described the confounding impact in the existing model but did not describe the extent and nature of such confounding during the rational statement of the study. However, the authors have provided many details on the significance and importance of this study in the introduction section which I believe should be discussed in the discussion section.
Experimental design: This study is well-designed and controlled in all aspects. However, there are a few things that should be considered in the method section. Authors should put a heading of operational definition and define the terms used throughout the manuscript.
The authors have discussed sample size estimation but did not describe the formula or equation used to estimate the sample. It's not clear what prevalence of ICLB was used to estimate the sample size. I am more concerned about the size as it is quite low. However, I agree that being a mono-centric study, a low sample size remains a barrier.
Consultation from physiotherapists is not common in various developing countries, it is needed to provide information on whether all patients with nipple pain are attended by physiotherapists at the study location. Moreover, it is suggested to please add more information about the study location in the method section.
I suggest describing the search strategies adopted to find the existing data on this topic as this data is used in the analysis and modeling.
Validity of the findings: The findings and results of this study are well presented in an adequate number of figures and tables. I have a query here; most of the demographic data are related to pregnancy outcomes. Can the authors explain why other social and clinical variables were not collected during the data collection process? For example, certain comorbid conditions may also affect the ICLB and their association with it is of utmost importance, particularly in endocrine disorders. Some other factors i.e. abnormal menstrual cycle, hormone replacement therapy, etc. may also contribute to pain. I am just suggesting considering the impact of these conditions on the model, as they may also confound the findings. I think the authors can discuss the same in the discussion section.
The authors have not discussed the low sample size as a limitation of this study.
The discussion section is very brief (hardly a few sentences). The authors did not discuss the relationship of the factors with ICLB. I can understand, the author cannot discuss each factor here but at least there should be information on how identified factors related to pain i.e. a brief plausible mechanism.
Additional comments: The conclusion is very general. Authors should state the number of factors included in the model along with the broad categorization of these factors.


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: ADAPTATION OF A CLINICAL REASONING MODEL FOR USE IN INFLAMMATORY CONDITIONS OF THE LACTATING BREAST: A RETROSPECTIVE MIXED-METHODS STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript describes a management tool of ICLB. This will largely benefit both clinicians and patients.  The manuscript is well written in professional English. The data provided in the manuscript explain the hypotheses clearly.

The author addressed all questions from the reviewer in an appropriate way.
Experimental design: The author provided modifications addressing the question from a reviewer.
Validity of the findings: The author provided additional explanations for the potential application of the ICLB tool and clearly stated the aspects that can be further improved in this ICLB tool.
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: ADAPTATION OF A CLINICAL REASONING MODEL FOR USE IN INFLAMMATORY CONDITIONS OF THE LACTATING BREAST: A RETROSPECTIVE MIXED-METHODS STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: I have no more comments on the manuscript.
Experimental design: I have no more comments on the manuscript.
Validity of the findings: I have no more comments on the manuscript.
Additional comments: I have no more comments on the manuscript.


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

Input:
Title: RECENT DETERIORATION OF CORAL REEFS IN THE SOUTH CHINA SEA DUE TO MULTIPLE DISTURBANCES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear and unambiguous, professional English used throughout - No

Literature references, sufficient field background/context provided - Kind of OK (see in comment to authors)

Professional article structure, figures, tables. Raw data shared - Kind of OK (see in the comments to authors)

Self-contained with relevant results to hypotheses - OK
Experimental design: Original primary research within Aims and Scope of the journal - Yes

Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap. - Not really (see in comments to authors)

Rigorous investigation performed to a high technical & ethical standard - Not really (see in comments to authors)

Methods described with sufficient detail & information to replicate - Kind ok OK (see in comments to authors)
Validity of the findings: All underlying data have been provided; they are robust, statistically sound, & controlled. - This part is OK

Conclusions are well stated, linked to original research question & limited to supporting results. - Not really (see the comments to authors)

Speculation is welcome, but should be identified as such. - NA
Additional comments: After reading the manuscript, I feel it is difficult to understand what authors want to say because the English is not clear due to grammatical errors and error in sentence.
This starts right from the abstract. Having said that, it is important to understand the dynamics and condition of reefs in remote atolls and islands. Hence this work should be encourage, but not before it is revised to have a more comprehensive introduction.

Introduction
The introduction is very simple and does not contain all the information necessary to make way for discussion. For example, information on the aspects of how, even remote, some atolls and islands cannot escape from natural and anthropogenic disturbances. Introduction does not have any information or comparison of other research conducted on remote atoll and island and hence fail to state why this work is important. There are information, but I feel they end and star abruptly without any hypothesis or question (there is in the last paragraph of the Introduction, but it is still lacking)

Materials and Methods
Experimental design is fine, however, authors need to give more details about the equipments used in videography including resolution
It is necessary to include the photos from which you extracted the data. Readers need to see those photos. Since authors have used the video transects to extract all the data they have mentioned it is necessary to be more clear how they did it. Did they freeze the video at every 10cm intervals to and then analyse the benthos?
Please provide representative photos for each of those indicators, especially coral recruits.

Results
Authors do not mention how did they identify coral species and to what level?
Also results have more really weird sentences - for example - Line 176,177 - "DIrecent of survey site SY2 at Yongle Atoll was illegal since no coral and recruit have been found"

Figures - Please provide map of China, which will help readers to know where in the South China Sea - Xisha is present. In its present form Figure 1 is not complete

Discussion
Needs lots of work. I cannot understand because many sentences are not properly written. Also, since the Introduction is not strong enough, the discussion suffers.

For example, Line 215-217- Authors state - "To sum up, a scene of prosperity spreads out, but when shift the
current assessment paradigm, a series of risks or impacts expose the nature of deterioration at Xisha Islands" don't underhand this. Does it mean the coral reef is healthy as of now, but due to temperature and COTS it will not be in the future? or it is not healthy at present, as per your DIrecent results and also contradicts next paragraph..

So, from the discussion, this is not the 1st record or highest record of COTS outbreak in Xisha? If so, this does not clear in the introduction, and is misleading. This study found only 163 individuals of COTS, previously it was 925?

I suggest complete revision of Introduction and Discussion such that the introduction is more detailed to include all the necessary information from previous studies in Xisha as well as comparative information. This will help to have a better discussion as well


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: RECENT DETERIORATION OF CORAL REEFS IN THE SOUTH CHINA SEA DUE TO MULTIPLE DISTURBANCES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a phenomenon-reporting manuscript of the current status of coral reefs in Xisha Islands, South China Sea (also known as Paracel by western countries). Some hypotheses were raised, but no further testings.
The explanations were reasonable.
English is generally OK, although I do have doubts about a few sentences. Some help from an English editor could take care of this.
High-quality figures, although more details are needed for some figures (notes in other sections.).
Experimental design: The basic design was to choose and survey 6 reefs, each with multiple transects and quadrats.
The quadrats were deployed randomly according to the text. That is unlikely in the real world. I suggest changing “randomly” to “haphazardly” or “systematically” whichever was the real case. The number of transects/quadrats was high and there was little doubt that the pattern found should be representative of 2020 in Xisha Islands.
The South China Sea has many atolls, most are difficult to access.
It would be nice if coordinates of those transects (no need for small quadrats) were mentioned. It makes temporal comparisons much practical.
Validity of the findings: The study is based on field works. Whereas dead/alive, small/large bleached/healthy are easy to judge underwater, hundreds of coral species are not easy to distinguish from one another underwater. The authors may want to write something about this issue.
I am not sure if the authors have uploaded all raw data. I do have suggestion/doubt about the statistical methods.
The authors need to justify using one-way anova to compare those indices. The raw data for the statistical procedures were 1) indices based on occurrence/frequency data, 2) relative frequencies, mortality, 3) percentages or densities. As a replacement, Resampling method could be considered.
Additional comments: Fig 2: Units are needed for every subfigure, e.g., coral bleaching, coral recruitment…
Fig 3: There were several sample reefs within each island. One has to wonder how are those reefs/sites arranged in the figure. Is there any meaningful way adopted? They should certainly be mentioned in the legends.
Fig 4: How were data of SST processes. What I really wonder was how come the frequency distribution of temperature were mostly “normal” within month, except two?
English is fine except some sentences needs revision to be clear. For example, I had problem with the following sentences.
1.Species distribution of hermatypic corals was not balanceable among different monitoring sites and regions.
2. DIrecent of survey site SY2 at Yongle Atoll was illegal since no coral and recruit have been found.


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: RECENT DETERIORATION OF CORAL REEFS IN THE SOUTH CHINA SEA DUE TO MULTIPLE DISTURBANCES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Although the English has improved from the previous version. I still find it difficult to understand, especially methods section

For example, Line 130 - "The transects (tapelines) were totally 50 m in length" - does this mean each transect was 50 m or total of 3 transects at 3 depths amounted to 50 m?

Another example, Line 131 - "If the actual distribution depth of corals was less than 15 m, the deepest transect can be adjusted appropriately" -- authors use "can be", should be "was"?

So, please check for English usage again
Experimental design: I do have comments now - previously i did not because of not clear writing

I don't agree with authors using DI to assess the stability and degradation of coral health since the equation for this index (even after the authors modify it) is ambiguous

For example, if DC = 10, LC=2 and RC = 1 and
DC =2, LC=10 and RC = 1 the DI will be same,

however, if you add 1 more recruit to either one, the value will change by half (increase or decrease)

This is also the reason you see that even with about 36% and 24 % of live coral cover, you still find some locations with high DI

Because the equation is biased towards "recruits or small corals". Even if you miss inadvertently 1 or 2 recruits during analysis or add 1 or 2 the health can shift from stable to degrading and vice versa

In table 1 you show the recruitment to be quite stable across locations except in Panshi Yu.

SO, I don't know how will you handle over or under estimation of recruit number
Validity of the findings: no comment
Additional comments: After reading the revised version of the manuscript, the authors have revised according to the comments and suggestions from both the reviewers. I feel the information presented in the manuscript is useful for researchers in the South China Sea area as well as ecologists elsewhere.

However, i do not agree with the usage of DI since it cannot present true picture and some times DI for stable and degraded reef can be same (See above - Experimental Design section)

Removing the DI part from the manuscript will not alter the relevancy of this report, since the data presented on coral reef health assessment and other parameters including COTS is important

I suggest authors to consider removing the DI part from the manuscript and revise accordingly


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: RECENT DETERIORATION OF CORAL REEFS IN THE SOUTH CHINA SEA DUE TO MULTIPLE DISTURBANCES
Review round: 2
Reviewer: 2

Output:
Basic reporting: Peer J review

This investigation reports coral status in Xisha Island (Paracel Island). Basic data, e.g., bleaching percentages, recent mortality percentages were provided in quite a few locations. These islands were off-limit to tourists or foreigners; they are nevertheless in the frontline of global changes.  A substantial amount of effort and resource is invested in carrying out this survey

•
Experimental design: Using atolls/islands as a unit is the way this study chose. The alternative is use habitats within each atoll/island since there are great difference among different habitats. This part, i.e., characteristics of surveying sites, need more details. Some significant patterns of bleaching and mortalities should emerge among habitats.
Validity of the findings: Given the snapshot nature of the investigation, and the fact that the sites are remote and protected, there could be little room to doubt the validity of the findings reported here. There is little justification for such doubt, either.
Additional comments: 4. General comments
How were surveying sites determined? This could easily “determine” or bias the results as variation among sites were high. For the same reason, the averages, e.g., coverage of 19.41%, needs to be accompanied by error ranges. In fact, using “mean” does not seem to make sense in this study, since the distribution of those numbers must differ from bell-shaped, , “median” should be a better choice. These error ranges of either means or medians, estimated by bootstrapping method, may not be symmetric, but they are nevertheless necessary to determine if difference among surveys of different years and sites are statistically significant.
Xisha Islands are known as Paracel in western world. Put this in the title, e.g., in parenthesis, could increase interest and a sense of relevancy.
“Recent dead corals (dead within a year)” needs to be better defined, so others could consider adopting it. Show some contrasting pictures distinguish Recent dead and other dead corals may be helpful.
“DI is a reliable criterion and efficient tool for assessing health of coral communities, and it can provide a comparable quantitative indication for the deteriorative process and its intensity. “ I agree with the part of  “quantitative”, other parts belong in Discussion.
“DIrecent better reflects the real recent coral reef development. “ Better than what? This statement does not belong in M&M, anyway.
Some statements, e.g., “More precisely, coral reefs have been in a cycle of disturbance and recovery.” seem to be based on believes without data or proper citations.
“Based on 15 years of monitoring data, Li et al. (2019) showed that the cycle of CoTS outbreaks in the Xisha Islands was about 15 years…” 15-year cycle based on 15 years of data? This sentence needs change.
What does “full-scale coral reef health reports” mean? What could it accomplish that this study could not? How could the “full-scale …reports” be implemented, and help reversing the declining coral reefs? Give some examples of how “full-scale…” data could help.
Rather than focusing on comparison within Xisha Islands, more effort should be spent on comparisons with other parts of the world. It may reveal the factors impacting the reefs in SCS or under Chinese management.
The title implies that there are linking between the decline of coral reefs and multiple factors. The authors provided some subjective opinions, whereas most are in the stage of “reasonable doubt”. It would be more convincing if the multiple factors mentioned also have a temporal trend. Which of those environmental factors played a dominant role, for example. It would be more valuable if some evidence in these directions are available.


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: RECENT DETERIORATION OF CORAL REEFS IN THE SOUTH CHINA SEA DUE TO MULTIPLE DISTURBANCES
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I commend the efforts the authors have put to revise the manuscript and also answer the comments of the reviewers.
With respect to the explanation given by the authors about the usage of DI to determine the health of the coral reefs is still not satisfactory.

While I get the point, still think that the results obtained by using the formula can be very biased against or depending on many factors - for example - what happens if another transect is laid adjacent or a few meters to the location of the transect in this work? there is every chance it will skew the results as even an addition or reduction of 1 can change the result. I did mention this and the authors say that this is a kind of extreme example. I don't think so. Even what you see on a transect laid at any location is random, the observation bias, as well as community dynamics in a given location (on a wide scale and not just that seen on the transect), will result in this method questionable

The authors mention that since they did 3 transects at each site ("In this study, we calculated the coral recruits of 10 quadrats in a transect, and in general, SC is large enough and tolerance, one more or one less recruit could not change the general situation. What's more, we did three transects (30 quadrats totally) in a survey site")...yes but this is not 3 replicate transects at each depth, but rather an independent single transect at 3 different depths. Dynamics can vary with depth as well as at each depth with distance. This is exactly why I say that the results using the equation for DI can be biased unless there are enough replicates with surveys done across and time.

I wonder why this method is not popular and used generally by coral reef ecologists if it is effective?

So, I suggest that the authors put a disclaimer and mention that this way of assessing the health has its own caveats and the readers need to be very careful when interpreting the results of the work and also pay attention if they want to use this method.

Other than this, I don't have any more comments on this manuscript


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

Input:
Title: RECENT DETERIORATION OF CORAL REEFS IN THE SOUTH CHINA SEA DUE TO MULTIPLE DISTURBANCES
Review round: 3
Reviewer: 2

Output:
Basic reporting: Professional English. I marked some sentences that needs clarification.
This is a report of surveys, not a hypotheis-testing article.
Experimental design: no comment
Validity of the findings: See 1. Basic reporting
Additional comments: no


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: INSIGHTS ON THE EVOLUTION OF CORONAVIRINAE IN GENERAL, AND SARS-COV-2 IN PARTICULAR, THROUGH INNOVATIVE BIOCOMPUTATIONAL RESOURCES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Figure 1 could be improved if some animal hist notations could be placed next to some of the nodes of the tree, In this way,, evolution of CoVs among its animal hosts can be observed.
Experimental design: This is an interesting paper that introduces a novel methodology to phylogenetic studies.
The authors did, however, applied to just one of the many problems involving the use of phylogenetic studies in COVID-19 related. The paper attempts to address the problem pf chimerism especially with respect to the possible lab design of the virus. While this is a important problem, there are, however, many other unsolved problems.

A glaring example is the search for the intermediary animal host. Pangolin and bats have been cited as possible intermediaries. Many are not convinced that pangolins are the intermeidary for two reasons. Firstly, the sequence similarity between pangolin-cov and SARS-CoV-2 is about 90%, which some people believe to be insufficiently close. Secondly, there are much confusion about the phylogenetics:
https://pubmed.ncbi.nlm.nih.gov/32407364/
As seen in the article above, the phylogenetic study using genome-wide is unable to conclude that SARS-CoV-2 came from pangolin-cov. Goh et al suggested that much of the confusion arose because the existing phylogenetic algorithms is not able to handle recombination well:
https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00001
https://pubmed.ncbi.nlm.nih.gov/11114432/
They suggested that the best phylogenetic tree can be obtained by using only the M protein as the M protein is highly conserved among all COVID-19 related viruses because the COVID-19 M protein is among the hardest within the CoV family. Indeed, the COVID-19  phylogenetic study using M protein shows a tree that is different from those using other proteins or entire genome:
https://zenodo.org/record/6355263#.YkYbvh0RXUr
I was looking to see if there is any resulting difference between the approach used by this paper and the studies already done especially with respect to this issue. I am not able to see the difference as the paper did not include sufficient samples of COVID-19 CoVs. It would have made the paper stronger if the authors are able to demonstrate the differences.
Validity of the findings: The approach is novel interesting and perhaps good but the authors need to make their case stronger as mentioned above. The paper needs to show if it can handle recombination better than current phylogenetic software available.
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: INSIGHTS ON THE EVOLUTION OF CORONAVIRINAE IN GENERAL, AND SARS-COV-2 IN PARTICULAR, THROUGH INNOVATIVE BIOCOMPUTATIONAL RESOURCES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors constructed a proximity network based on the 4 major structural proteins in coronavirus. Through this, the authors explored the relationship between host-phylogeny and viral proteomic distance. They also investigated the potential of generating feasible chimeras in nature from loosely related hosts through simulation.
Experimental design: The concept of the study is novel and interesting. Given the methods used in the study is atypical, a clear explanation of the methods is paramount. Unfortunately, it is not well written, which made following the methods, let along replicating it, particularly difficult. I cannot confidently give a more in depth review or feedback.
Validity of the findings: The methodology sections of the study needs to be better written. I am unable to replicate the study as it is.
Additional comments: Line 130-139. I appreciate the authors have in depth discussion on how this analysis was calculated, but it is not clear to me and I would not be able to replicate this. A few terminologies are unclear to me, such as “pertinent phylogenetic node”. The sentence - “the phylogenetic diversity associated with a set of taxa was derived from the average value of pairwise patristic distances” – what does “a set of taxa” refer to? “Match any available host with the pertinent phylogenetic node, either a terminal or an inner node” – are the nodes referring to the viruses? How was that used to calculate the phylogenetic distance between hosts (isn’t that calculated using patristic distance mentioned in line 131)?
Line 150. “So, for two heterotopic proteins, the chance of being amalgamated increases if both are similar to the respective partners in the actual assembly where the alter occurs.” This sentence does not make sense to me.
Line 154. “As a corollary of this statement, chimeras derived from the assembly of proteins coming from slightly akin viruses hardly proceed in a natural way.” Not sure what the sentence means.
Line 157. “Using combinatorial simulations, we study the behavior of the coefficient of chimerality in mixtures of proteins randomly drawn from the empirical sets already compiled by us.” As in compiled in the earlier section of the method? Or in-house pre-compiled set? If the latter, how was the compiling done?
Line 171. “Basic information about amino acid sequences of every kind of protein” sounds a little informal – perhaps use terms like “Basic information about amino acid sequences of the major structural proteins”
Line 172. “Lengths of sequences vary across ranges that never overlap when comparing among 173 them (Table 2)”. I am not sure what the sentence mean. The length of sequence are not identical in any of the 4 proteins for any of the 173 genomes?
Line 175. “suggesting that the information held by the structural proteins is rather concordant.” I am guessing what the authors meant by information, they meant “cross-genome variation in structural proteins”, but it is not clear and the sentence does not really make much sense as it is (what is “the information” held by structural protein?).
Line 176. “This finding makes the average distance between proteins a good choice to assess the dissimilarity between virions as a whole.” I agree that it is a good proxy, but more rigorously analysis, such as whether if the variation occur in conserved regions, would be required to claim this to be a good choice. Also, I would change the language from “makes the average distance…” to “suggests the average distance…”.
Line 179. “perfect connected components after removing the only inter-genera links.” It is unclear to me what perfect connected component means.
Line 180. “All the shortest paths between β-coronavirus and γ- and δ-coronavirus necessarily pass through representatives of α-coronavirus.” Please rewrite the sentence.
Line 183. “SARS-CoV-2 is located at the frontier of the network” What do you mean by “frontier of the network”? It’s not a terminal node, is frontier a special terminology used in network analysis?
Line 187. I am not entirely sure I follow the reasoning for Figure2. Am I correct in thinking that the authors are attempting to show that two nodes with a link between are more likely to bridge more similar virus than less similar virus? But isn’t that the whole point of the network? The majority of the edges would be between viruses within the same genera, with the occasional cross-genera edge that will have large parabolic arcs.
Line 187. “By focusing exclusively on the network links of Figure 1, and tagging nodes with the respective host, we track the phylogenetic relatedness between pairs of hosts across the total set of links (Fig. 2).” It is not clear to me why relatedness between pairs of hosts across total set of links were only done on the network links in Figure 1 rather than an all-to-all comparison. If there is a reason for this, please clarify this in the text.
Line 189-193. Please be more specific (e.g. include the percentages or definition) with the terms “minor proportion”, “frequently associated”, “weakly related hosts”.
Line 191. “Viral endpoints of links”. I am unsure what this refers to.
Figure 1. It may help readers to explore potential relationships of host organisms within the network if the nodes were outlined by a second colour indicating the host organism. Can edge thickness be used to indicate the distance (such as thickness correlates to the invert log distance) between the connected nodes?
Figure 1. Are the two grey circles with question marks the two unknowns? If so, please indicate in figure legend.


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: INSIGHTS ON THE EVOLUTION OF CORONAVIRINAE IN GENERAL, AND SARS-COV-2 IN PARTICULAR, THROUGH INNOVATIVE BIOCOMPUTATIONAL RESOURCES
Review round: 2
Reviewer: 1

Output:
Basic reporting: All requirements met as far as I can see. Improvements made since last review
Experimental design: Improvements made since last review
Validity of the findings: Improvements seen since last review
Additional comments: No additional comments


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

Input:
Title: IDENTIFYING DUSP-1 AND FOSB AS HUB GENES IN IMMUNOGLOBULIN A NEPHROPATHY BY WGCNA AND DEG SCREENING AND VALIDATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comment
Additional comments: WU et al. found key 2 key genes related to IgA nephropathy through WGCNA analysis and differential analysis using GEO database, and verified their expression through other data sets and clinical samples. However, this paper still has the following deficiencies:
1. The author used a total of three data sets for analysis. Why does the WGCNA analysis and difference analysis only focus on data set GSE93798?  The author claimed to have found two key genes related to IgA nephropathy, but the analysis of these two genes was based on data set GSE93798. Then, are these two genes also key genes related to IgA nephropathy in the other two data sets?
2. The author's description of the immunohistochemical process is too simple. It only introduces the source of primary antibody, but does not introduce the thickness of wax block section, what tissue repair solution is used, the source and concentration of secondary antibody, and the number of immunohistochemical repetitions.
3. In fact, the author only analyzed functional enrichment without pathway analysis, which is inconsistent with the description in the paper. Why did the author only enrich the genes obtained by WGCNA analysis while not enrich the genes obtained by difference analysis when conducting functional enrichment? At the same time, Figure 4A and Figure 4B are the enrichment results, one is the enrichment results of the first 6, the other is the enrichment results of the first 9, whether there is duplication?
4. The numbering of pictures in Fig. 5 should be carried out in sequence. Why there is only IgAN in Fig. 5B, and what blue represents needs to be explained. Fig. 6 About the Immunohistochemical results, there were 2 images of each gene in the control group and IgAN group respectively, while the author used 3 pairs of samples, which need further explanation. At the same time, the control group of patients was normal during data set analysis, but the control group was para-cancer samples of patients with renal cancer when clinical samples were used for verification. Please explain.  In Fig. 6, the E is shown in the annotation, but not found in the picture. The AUC of FOSB gene of GSE93798 in Fig. 7 is significantly lower than 1, however in this figure, the AUC is marked as 1. Please explain.
5. There are many punctuation and formatting errors in the article, and grammar polishing is needed.


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

Input:
Title: IDENTIFYING DUSP-1 AND FOSB AS HUB GENES IN IMMUNOGLOBULIN A NEPHROPATHY BY WGCNA AND DEG SCREENING AND VALIDATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: IgAN is a common health issue that needs to be understood.  The authors used bioinformatics approaches to identify key hub genes for IgAN and validated their findings in clinical samples. This will provide critical insight for other researchers to further study this disease. The results in the manuscript are well-related to the hypothesis.

However, this manuscript is poorly written in unprofessional English with numerous grammar problems and missing parts.  This needs to be corrected before the manuscript can be accepted.

For example,
in line 27: specimens. used receiver operating characteristic (ROC) curve to evaluate the diagnostic efficacy.  (missing the subject)

In line 123: Set the power value (β)  to 8 and the scale independent value was 0.85.(Figure.2B, C),There was negative correlation between the logarithm log(k) and the logarithm log(P(k) and the correlation coefficient is greater than 0.8, c. (wrong uppercase,  a space is needed after a period, the last "c" is meaningless.)

Other small errors also need to be corrected, such as using "et al." instead of "et al".
Experimental design: The experiment in the manuscript is well-designed. The authors used one dataset to draw the conclusion and validated it in another two datasets and clinical samples.

Additional information about the methods needs to be provided: Since the analysis is using publicly available tools, the authors need to provide the date when they performed their analysis, as well as the version of code/package/software they used for their analysis. This is essential for other researchers to replicate the study in the manuscript.
Validity of the findings: The conclusion is well stated in the manuscript. The authors provide sufficient samples to validate their findings.

A minor point: in line 222 all the databases that include glomerulus tissue of IgAN to make bioinformatics analysis as glomerular biological information analysis could better identify candidate biomarkers and therapeutic targets contributing to a more comprehensive understanding of IgAN. (This is an overstatement since the author needs to justify that ALL the databases including glomerulus have been used in this study. This is almost impossible)
Additional comments: No additional comments


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

Input:
Title: IDENTIFYING DUSP-1 AND FOSB AS HUB GENES IN IMMUNOGLOBULIN A NEPHROPATHY BY WGCNA AND DEG SCREENING AND VALIDATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: This article provides a good idea, and the author has a strong ability of bioanalysis and basic experiments, but the author does not seem to be very serious. Such as, after revision, in Figure 7A, it is clear that THE AUC of DUSP1 is higher than that of FOSB, but the notation shows that DUSP1 is lower than FOSB.


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

Input:
Title: IDENTIFYING DUSP-1 AND FOSB AS HUB GENES IN IMMUNOGLOBULIN A NEPHROPATHY BY WGCNA AND DEG SCREENING AND VALIDATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: IgAN is a common health issue that needs to be understood. The authors used bioinformatics approaches to identify key hub genes for IgAN and validated their findings in clinical samples. This will provide critical insight for other researchers to further study this disease. The results in the manuscript are well-related to the hypothesis.

The authors have modified the manuscript with improved written English. The manuscript is clear and easy to understand.

There are still some minor errors that need to be corrected:
line 172: and the two validation datasets, GSE104948 (Figure 6A) and GSE37460 (Figure B). The second figure label should be (Figure 6B)
Experimental design: The experiment in the manuscript is well-designed. The authors used one dataset to draw the conclusion and validated it in another two datasets and clinical samples.

Following the suggestion from the reviewer, the author provided the date and versions for all datasets and methods that are used for this manuscript.
Validity of the findings: The conclusion is well stated in the manuscript. The authors provide sufficient samples to validate their findings.

The author corrected the statement regarding glomerulus databases.
Additional comments: No additional comments


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

Input:
Title: IDENTIFYING DUSP-1 AND FOSB AS HUB GENES IN IMMUNOGLOBULIN A NEPHROPATHY BY WGCNA AND DEG SCREENING AND VALIDATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The author has carefully revised it.


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

Input:
Title: FOREST TREE SPECIES DISTRIBUTION FOR EUROPE 2000–2020: MAPPING POTENTIAL AND REALIZED DISTRIBUTIONS USING SPATIOTEMPORAL MACHINE LEARNING
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study is useful and innovative in combining remotely sensed and other types of variables for tree species mapping, and in developing temporally dynamic maps (for 4 year time steps). The temporal mapping is a very nice contribution of this study.

I am not really sure how useful it is to use realized distributions to evaluate the predicted potential distribution. I mean, it is not surprising that the accuracy is lower.

I think the background section on SDM theory lines 158-218 could be greatly condensed to highlight just the two relevant points – potential versus realized (although as noted above, I am not sure the ‘potential’ modeling is a very informative part of this paper) and the issue of presence/absence data (a great strength of your study is that you have p/a data, and many do not).

I think you missed this opportunity because the paper is couched too much in the framework of SDM (high spatial resolution data have been underrepresented as predictors in SDM). I think this is because tree species mapping studies have been represented more in the remote sensing image classification literature – where one could say that non-image predictors are underrepresented! Terrain and some other non-image data have been incorporated into image classification, however, since the 1980s.
Experimental design: I am surprised that you did not test convolutional neural networks because they seem to be promising for tree species identification from hyperspectal high resolution and lidar data. Perhaps other ML approaches are something you could discuss in your paper even if you did not test them.

Fricker, G. A., Ventura, J. D., Wolf, J. A., North, M. P., Davis, F. W., & Franklin, J. (2019). A convolutional neural network classifier identifies tree species in mixed-conifer forest from hyperspectral imagery. Remote Sensing, 11(19), 2326.

I also feel that your paper needs more extensive comparison with other studies using ML to classify forest tree species (especially in Europe). That would really help put your results in context. This one looks relevant:

Raczko, Edwin, and Bogdan Zagajewski. "Comparison of support vector machine, random forest and neural network classifiers for tree species classification on airborne hyperspectral APEX images." European Journal of Remote Sensing 50, no. 1 (2017): 144-154.
Validity of the findings: I do not really like your use of non-forest land cover as absences – you should really use locations of other species (other than the target species) if you are trying to discriminate tree species.

I appreciate the reporting of hyperparameters.

Logloss might be robust but nobody uses it to report accuracy in SDMs.  In order for your results to be more useful and the paper to be read and cited you should report a more widely used accuracy measure.
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: FOREST TREE SPECIES DISTRIBUTION FOR EUROPE 2000–2020: MAPPING POTENTIAL AND REALIZED DISTRIBUTIONS USING SPATIOTEMPORAL MACHINE LEARNING
Review round: 1
Reviewer: 2

Output:
Basic reporting: see additional comments
Experimental design: within scope; relevant interesting study; see additional comments on methods
Validity of the findings: see comments
Additional comments: Review of Peerj 69672-v0
Overview
This manuscript reports on an effort to map the actual and potential distributions of 16 European tree species. A single potential distribution map for each species was generated for the 2000-2020 period, while maps of actual distribution were generated for every 4th year, resulting in a 6-map time series over this period. The study employs an impressive state-of-the-art modelling approach that features: 3 million occurrence locations, six machine learning algorithms, a stack of >500 explanatory variables (including climate, soil, spectral reflectance, and biotic variables), and generation of ensemble models using a meta-learner for each species. The resulting maps provide high-resolution (30 m) occurrence probabilities for each species across the European study area, with the following key findings: high-resolution inputs and outputs significantly improved map accuracy, predictor variable importance varied across species and models, and ensemble models tended to outperform individual models. This study employs high technical standards to address an important topic for a variety of ecology-related fields. Below we make a number of suggestions to improve the manuscript.
Main Comments
1. The authors purport to model species’ potential distributions by: 1) carefully selecting absence points for each species (i.e., only points falling outside both human-altered land cover types and existing tree atlas range boundaries), and 2) including only certain environmental predictor variables in the modelling process (i.e., no biotic variables or Landsat imagery). At line 182, they define the potential niche as “that portion of the fundamental niche that exists in the study area at the time of the study (Peterson et al., 2011)” – in other words, anywhere the species could become established in the study area. If this is truly what they are attempting to model, then they are surely not accomplishing it by controlling absence locations and predictor variables. As the authors point out at lines 178-181, true potential distribution cannot be modelled using a correlative approach; this is more the realm of mechanistic models. Thus, it would seem that the products produced here are a hybrid between actual and potential distributions. The authors should further clarify the exact nature of their potential distribution maps.
2. Multiple studies have suggested that the study area from which absence or background points are selected should be carefully considered as it has important implications for model outputs. For the current work, the study limits include the entire European continent, but there is no discussion of the implications this may have on the resulting models.
3. The spatial distribution of presence/absence points is an important aspect of species distribution modelling. In the current study, the very short description of the ‘thinning operation’ that was applied to occurrence locations (lines 444-448) is simply not detailed enough to allow readers to assess this key aspect of the study.
4. In Section 4.3 of the manuscript, there is considerable discussion around the relative importance of the various explanatory variables in determining species distributions. A well-known challenge of such efforts is that correlations between explanatory variables make it difficult to attribute causation to any particular variable(s). The authors should at least provide a caveat that recognizes this inherent limitation of correlative modelling approaches.
5. The quality of the writing throughout the manuscript is generally fine, but there are a large of grammatical improvements that could be made. I have suggested a number below, but further efforts in this area would be beneficial. Perhaps an English editor could have a close look? Even the last sentence in the manuscript as written is awkward/not grammatically correct and requires an edit: Scaling up approach described in this paper to help produce  objective predictions and help monitor forest dynamics and support re-forestation efforts across globe is our next frontier.
6. Stylistically, the number of lists could be greatly reduced, which could potentially shorten the manuscript by several pages. Examples include: 1) bullets of time periods at lines 236-242; 2) numbered list of 16 species at lines 258-274; 3) bullets of forest types at lines 298-304; 4) bullets of land cover types at lines 314-322; 5) bullets of ML algorithms at lines 482-490; see also lines starting at 574. These are just a few examples. The large number of lists and bullets throughout the manuscript take up unnecessary space and, in my opinion, make it feel more like a report than a scientific article.
Specific Comments
Line 19; replace ‘Paper…’ with ‘This paper…’ .
Line 40; acronyms NDWI and NDVI have not yet been defined.
Line 44; acronym EO has not yet been defined.
Line 49; replace ‘restauration’ with ‘restoration’.
Line 54-56; this sentence seems to be a bit of an overstatement – if we could ‘anticipate and minimize climate change impacts’ simply by knowing where tree species occur, I’d be a lot more optimistic about the future of our forests!
Line 73; insert the word ‘an’ between ‘ML’ and ‘increasingly’.
Line 74; replace the word ‘an’ with ‘a large’.
Line 78; replace ‘presence-absence we find’ with ‘for presence-absence modelling are’.
Line 100; replace ‘effect’ with ‘effects’.
Line 109; never heard of ‘auto-ecology’… do you mean autecology?
Line 114; insert the word ‘are’ between ‘that’ and ‘potentially’.
Line 116; replace ‘Earth Observation’ with ‘EO’ as you have already defined it at Line 93.
Line 121; insert the word ‘that’ between  ‘fact’ and ‘the’.
Line 156; replace ‘whole of’ with ‘the entire’.
Line 177; the acronym ‘BAM’ should be defined – e.g., Biotic-Abiotic-Mobility (BAM) diagram.
Line 195; replace ‘vegetation’ with ‘plant’.
Line 195; replace ‘owing to’ with ‘by’.
Line 197; replace ‘just temporary’ with ‘temporarily’.
Line 198; remove the word ‘of’.
Line 311; replace ‘was’ with ‘were’.
Line 312; remove sentence starting ‘As for the occurrence points…’ as it is redundant with sentence starting with ‘Each unique combination…’ at Line 306.
Line 340; the acronym ‘GLAD’ has not been defined.
Line 344; replace ‘period’ with ‘periods’.
Table 1, column 1, row 3; replace ‘Soild’ with ‘Soil’.
Line 353; replace ‘have’ with ‘generate’.
Line 459; replace ‘metric’ with ‘metrics’.
Line 495; replace ‘an hyperparameter’ with ‘a hyperparameter’.
Line 504; replace ‘educes’ with ‘reduces’.
Line 528; replace ‘towards’ with ‘regarding’.
Line 537; replace ‘performances’ with ‘performance’.
Line 574; consider removing the raw R outputs associated with the final fitted ensemble model. Is it really necessary? Could it be presented in a table or in the supplementary material?
Line 697; replace ‘underestimations’ with ‘underestimation’.
Line 699; correct the term ‘datacube cube’.
Line 731; consider replacing ‘not tuned’ with ‘untuned’.
Line 768; replace ‘come as’ with ‘are the’.
Line 771-774; replace:
‘Which environmental variables and their relative importance as limiting factors are still unclear for many tree species and few peer reviewed studies focused on investigating the importance of different environmental predictors on potential distributions are available.’
With:
‘Few peer-reviewed studies have reported on the importance of various environmental predictors in shaping species' potential distributions.’
Line 788; not clear why mangrove distributions are being referenced here?
Line 791; remove ‘For realized distribution…’ from the start of the sentence as it is repeated at the end of the sentence.
Line 820; replace ‘…regardless of the terrain data high resolution,…’ with ‘…despite the high resolution of the terrain data,…’
Line 822; replace ‘on’ with ‘at the’.
Line 832; please clarify the meaning of: ‘The opposite approach could be used by conservation planners’.
Line 835; replace ‘have greater performances’ with ‘productive’.


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: FOREST TREE SPECIES DISTRIBUTION FOR EUROPE 2000–2020: MAPPING POTENTIAL AND REALIZED DISTRIBUTIONS USING SPATIOTEMPORAL MACHINE LEARNING
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed all of the substantive criticisms to my satisfaction. I think overall that the revised manuscript is now suitable for publication. This is a valuable and exciting study and an impressive amount of data processing.

The introduction, although the content and focus is much improved, is a bit choppy. All the right parts are there but the connections between the parts do not flow. For example the 2nd paragraph, line 57-, is not really a paragraph and should be integrated with the 3rd.  The paragraphs jump from 1. Importance of forests and mapping them, 2. What is SDM, 3. Spatio-temporal and EO data have not been used much in SDM (these are both important points, and maybe deserve more detail – much temporal remote sensing is used for phenology and not for high-resolution mapping), 4. Ensemble and ML modeling. It needs smoother transitions or connectors. I really recommend the following book for helping scientific writers follow s story arc, introduce the main characters, etc.
Schimel, J., 2012. Writing science: how to write papers that get cited and proposals that get funded. OUP USA.

The manuscript may require a careful final editing to catch all remaining minor grammatical errors and typographical errors.
Experimental design: Good
Validity of the findings: Good
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: THE DETERMINANTS OF PATIENT CARE MANAGER ROLE AND THE IMPLEMENTATION OF COVID-19 CLINICAL PATHWAY: A CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1.	In Abstract, the authors wrote that the aim of the study was to determine the factors associated with patient care manager role and the implementation of the clinical pathway among nurses in private hospitals.

In Conclusion, the authors wrote: The role of patient care manager and compliance with COVID-19 clinical pathways correlated significantly

There is no correlation between the aim and the conclusion (the aim and conclusion not in line). If the aims of the study is: to determine the factors associated with patient care manager role….. , the authors should mention what are the factors.

2.	In Abstract:
Objective. The aim of this study aims to determine the factors associated with patient care manager role and the implementation of the clinical pathway among nurses in private hospitals.

In Introduction:
Therefore, this study aims to measure the role of nurse managers and their relationship to the COVID-19 clinical pathway.

The aims of the study in Abstract and Introduction are different, which one is true?

3.	Introduction is too long. The authors should write introduction briefly that contains four main components: general background information, specific background information, an explanation of the gap in our knowledge that the study was designed to fill, and a statement of study objective.

In this Introduction, we could not find  what is the problem/background of the study and why is it important ?

4.	In Material and methods.
	In study setting and participants. Why the authors choose a private hospital ?

5.	In Discussion
a.	The authors stated that: The results showed that the high factors affecting the level of clinical pathways implementation were the length of service above ten years….
How about : age (25-35 years), Gender, and educational level????
b.	In Results, the authors stated: Based on the analysis, three factors dominate the high role of nurses in the clinical pathway application namely facilitating communication and coordination between members of the health care team (95.8%), educating COVID-19 patients (94.6%) and empowering the patients to solve problems (92.9%).
Why the authors did not discuss/analyze factor empowering the patients to solve problems (92.9%) in Discussion section???


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

Input:
Title: THE DETERMINANTS OF PATIENT CARE MANAGER ROLE AND THE IMPLEMENTATION OF COVID-19 CLINICAL PATHWAY: A CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is written well. However little grammar and spell check needs to be done
Experimental design: yes, it is an original research and the study design is cross-sectional
The sample size is not sufficient for this nature of research. Few changes required is marked in the draft
Validity of the findings: Some more statistical support is required. My comments are marked in the draft
Some information on the validity and reliability of the Indonesian version of the scale is required
Additional comments: The research is performed well and written properly. However some changes to be done.


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: WEDELOLACTONE FACILITATES THE EARLY DEVELOPMENT OF PARTHENOGENETICALLY ACTIVATED PORCINE EMBRYOS BY REDUCING OXIDATIVE STRESS AND INHIBITING AUTOPHAGY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The article must be written in English and must use clear, unambiguous, technically correct text. The article must conform to professional standards of courtesy and expression.
2. The title should be change to the interesting topic.
3. Abstract
- What is a couma ether compound extracted? (no mention in the manuscript)
- "in vitro" this word should change into italic letter in all of manuscript
- In abstract should be write the conclusion in the last sentence.
4. Introduction :
- more review about Nrf2/ARE signaling pathway in embryo development
- No research aims and scope
Experimental design: 1. No subtopic of experimental design. The submission should clearly define the research question, which must be relevant and meaningful. The knowledge gap being investigated should be identified, and statements should be made as to how the study contributes to filling that gap.
2. line 59-60 move to combine with subtopic "Animals and chemicals"
3. Why some assay was done on day 6 and day 7 of embryo, should explain?
Validity of the findings: 1. line 173-175 : should rewrite because redundant writing in 2 sentences.
2. line 189 : what is NC group? no mention before
3. line 249-250 : the unit of measure was difference, how to compare it?
4. line 253-255 : should give more reason the support this data
Additional comments: Please double check the correctness of references.