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: USING HISTORICAL DIP NET DATA TO INFER ABSENCE OF FLATWOODS SALAMANDERS IN STOCHASTIC ENVIRONMENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, this is a very well written article, and the basic reporting is good. The introduction is well structured, but does not introduce the focal species. The discussion is too long for my taste. I suggest moving some of the life history information and previous work on the focal species into the introduction. I have some questions about the methods, including the supplementary script, that I elaborate on in the experimental design section of this review. I found the results clearly presented and easy to understand, with the exception of use of credible intervals, confidence limits, and quartiles. All three are used to summarize findings, and I found this a little confusing. The figures support the findings, and are well designed. I would like to see the authors reiterate a clear recommended survey scheme for their focal species in the conclusions section, if possible.

I have a few very minor comments for the Abstract and Introduction.
Line 30: detection probability is referring to aquatic juveniles and subadults, I think.

Line 34: Is a suitable site for reintroduction any site that is truly absent? If so, I’m not sure this is a major takeaway of your study.

Line 58: Comma after detectability

Line 75: Comma following i.e., throughout the manuscript

Line 88: This paragraph needs to be limited to just thesis statements and hypotheses. Introduction of the focal species should come before here.

Line 89: It seems 8 year’s of detection probabilities are given from the previous study, and subsampled into 10 “years” worth of data. I think maybe some distinction needs to be made between these two things. Maybe the term “pseudo-years” if that isn’t too obnoxious?
Experimental design: This article presents original primary research within the scope of PeerJ. The research questions are relevant to conservation of species that have multiple life stages, with heterogeneous detection probabilities. The investigation was performed to a high ethical and technical standard. The methods were described in enough detail to replicate them, but could benefit from some additional clarification.

Line 112: regarding research approval declarations. Is this declared in the original Brooks et al 2019 article? If so, is it necessary to repeat here, given this study refers only to previously published data? Further, if an IACUC statement is needed, are federal and state permit numbers also missing here? Personally, I think you could get rid of this statement, and refer readers to the previously published work.

Lines 129-131: Does line 52 of the R script demonstrate this? Why is only the first column of each sampled year used here? What are the other 19 for?
In the creation of Pstar1 etc, columns 2:19 seem to refer to repeat sampling? If this step is done here, on randomly drawn samples, why perform this calculation again at lines 56-58 for example? I may be misunderstanding the approach used, but this seems to be where the (1-p)^n formula is first implemented.

Line 134: The investigation of repeat surveys within a single year uses 1000 draws. Your script indicates 2700 draws were conducted for the multi-year simulation.

Lines 134-138: Is this right? or is this meant to be Occupancy probabilities? The wording of this sentence has me totally confused. I think the step referred to in this sentence deserves more explanation. Further, Is there a precedent for this approach available that could be cited here to give readers a deeper understanding of why this is true?

Line 142: R script indicates a 90% credible interval here, and I think that should be stated explicitly.

Regarding the supplementary script. I would like to see some notes spelled out more clearly. There’s a lot of loops used to populate subsamples, I’d like to see some more information given about each step in the process as comments in the script. For example, at lines 49-55 of the script, slightly more information could help a reader move through this supplement faster, making it more useful to novice coders (which I might qualify as!). Here’s what I mean:

I_ran = matrix(nrow = 10, ncol = nreps)  #creates 10x1000 matrix
for (i in 1:10) {                                          #populates rows
  for(j in 1:nreps) {                                    #populates columns
#each sample is the mean of the first column of a random year
    I_ran[i,j] = colMeans(ps[[sample(1:8, 1)]])[1]
  }
}

The Rdata file “supp_1” loads an object titled “dat”, but the supplied script utilizes an object titled “outAB”. This wasn’t immediately obvious to me, and it would probably benefit readers to modify one or the other of these supplemental files so they match.

At line 67 the function rowMedians is used. This requires the package matrixStats. I think it’s helpful if readers are given code that initializes all necessary packages to execute example code, at least something like library(matrixStats) or install.packages(“matrixStats”) to tip them off to this type of thing.

I may be missing something, but as near as I can tell, there are sections of code at lines 18-24 and 92-95 that can be removed. These “x” objects don’t seem to be used anywhere else in the script, and they are overwritten by the use of “x” in the generation of your figures starting at line 158.

At line 101, the median of a single number is taken. I think it’s worth removing this for clarity towards the readers. If this method is applied to a group of values elsewhere in the script, then I think it’s alright to keep, but I didn’t notice it being used elsewhere.
Validity of the findings: Without question, the data utilized by the authors is robust and statistically sound. This is a simulation-based study, stemming from previously published observational data, and thus controls are not of concern. The authors have made their data available and for the most part it is reproducible quite easily (although some improvements to the supplementary script are proposed in the previous review section). The conclusions are generally supported by their findings, but may be overstated some. The authors repeatedly refer to identifying suitable reintroduction sites for their focal species, however, their data only enable identifying a method for calculating how much effort is required to determine the species is absent from a site. If absence from a site is all it takes to be suitable for reintroduction, then that’s worth stating in the discussion, but I do not see this as the primary finding of this study.

Regarding the Results section, I have some specific comments.

Line 150: “high detection probability.” This is a vague term (which I have been criticized for using often, myself!). I suggest rewording this to be explicit about what needs to be achieved, whether that’s mean detection probability of above 0.99 or otherwise. If it’s not clear what the goal detection probability is, then this idea needs further explanation.

Line 154: Here you call it a quartile (and I think that makes sense), but in the figure caption it’s called a 75% credible interval, and I don’t think those are the same thing. But, if they are the same thing, use the same name when referring to them throughout the manuscript. Additionally, the R script seems to be calculating a 50% interval in any case.

Lines 155-156: 95% confidence limit. I do not see example of this being calculated in your script. I also think that if you’re going to refer to the 95% confidence limit here, that should also be demonstrated in the figure. Which is more useful for management of the species, or determining the necessary survey effort, quartiles or the 95% confidence limit (or credible interval)? These terms are not interchangeable to my knowledge, and I think if you streamlined your use of them it would spare readers some confusion.

I mentioned in a previous section that I believe the discussion is too long, and could benefit from moving introductory information about the focal species to the introduction. That is my only concern regarding the discussion section.

I have one minor comment at line 245-246: The information here regarding fire-ants sounds like an anecdote from a related study, and if that is the case I would like to see a citation provided.

At line 236 “Conlisk et al, 2008”, is given as 2009 in your reference list.

These articles are not cited in text but appear in your references. Alford 1999, Berven 1990, Chesson and Warner 1981, Dodd 1993, Endangered Species Act, Green 2003, Lande and Barrowclough 1987, Lande 1993, Mehta et al 2007, Nielsen et al 2005, Pechmann et al 1991, Pechman and Wilbur 1994, Rhodes et al 2006, Rhodes and Jonzen 2011, Salvidio 2009, Semlitsch 1983, Semlitsch 1987, Semlitsch et al 1996, Semlitsch et al 2014, Vucetich and Waite 1998, Whiteman and Wissinger 2005.

Finally, the caption of Figure 1 indicates a 75% credible interval, but the R script demonstrates 50% (0.25 and 0.75 quantiles). Likewise, Figure 2 indicates 95%, but quantiles used in the R script are 90% (0.05, 0.95).
Additional comments: I really enjoyed reading this article. It is well written, timely, and focuses on a topic of critical importance to conservation of endangered species. I apologize for agonizing over your provided script, but I found this to be a hugely useful tool for understanding your work. I believe simulation studies of this nature are invaluable towards identifying the best available methods for achieving success in determining the presence and abundance of endangered species within their given landscapes. Congratulations on a wonderful study.


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

Input:
Title: USING HISTORICAL DIP NET DATA TO INFER ABSENCE OF FLATWOODS SALAMANDERS IN STOCHASTIC ENVIRONMENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In general, I found this to be a fairly well written manuscript that made use of sufficient background information and citations, used clear and professional English, and adhered to a proper article structure.
I caught a few minor issues with the tables and the textual citations of the second figure.
o	Please elaborate on why 75% CIs are used in Figure 1.
o	Should Line 180 refer to Figure 2 instead of Figure 3? If not, I was not provided with any Figure 3.
o	The caption for Figure 2 requires more detail. Please explain what the dot and whisker lines along the bottom of each panel represent.

I appreciate that the data were shared, and am especially impressed that the code was shared as well. I did, however, find that some necessary details were omitted from the supplemental code document. Namely, the data file was not loaded with the name that was used later in the coding, nor were packages required to run certain functions named. I believe that this would require a simple fix. Adding a setup section to the provided code to a) name the data file as it is read into the work environment and b) load the required packages would greatly improve the access to these supplemental materials. Additional comments would also be useful to align with the methods described in the text.

For the most part, I found this paper fairly clearly written. I would like to call your attention to a handful of places that I found inaccurate or difficult to interpret:
o	Line 28-30: Initially I did not follow the logic of this statement. I believe it would be helpful to explain somewhere in the abstract that this is a situation that arises because monitoring of the breeding population occurs indirectly through surveys of a different life stage of the organism.
o	Line 218: Should this refer to “time since the species was last observed?” If not, I need more clarification because “the time the species was last observed” is unclear to me in this context.
o	Line 242: Does obtaining genetic samples require multiple captures? I can see how growth rates (or possibly checks for disease/parasites) can require multiple captures, but to my knowledge genetic samples are generally collected from an individual organism just once as genetic material should not change over time.
Experimental design: This work is well aligned with the aims and scope of the journal. The stated research question is to present a procedure for developing an appropriate monitoring scheme for a species of salamander that incorporates environmental stochasticity so that confidence in non-detections is sufficiently high that conservationists can select unoccupied sites for reintroductions. The authors also have the goal of developing a procedure that can be adapted for any species with sufficient detection data over a series of years that include a representative sample of environmental conditions.

The information gap that the researchers are seeking to fill is the need for approaches to confidently predict the site status and determine outcomes of reintroduction, given the variability of environmental conditions. This work clearly demonstrates the high degree of uncertainty in detection probability that can result from environmental stochasticity for a species of conservation concern with a highly complex life cycle. This study demonstrates that repeated surveys are required over a number of years for the focal species, and demonstrates how long-term monitoring data can be used to identify the number of surveys per year and years of monitoring required to reach an acceptable level of confidence in site status.

The authors use a robust, hierarchical analysis procedure.  I appreciate that the code and data have been shared. The ethical standards were approved by the home institution of the researchers.

While I followed what they did in the code, I would appreciate some additional explanation for Lines 129-131. I could not replicate this from the text alone (say if the link to the supplemental material was broken).
Validity of the findings: The underlying data have been provided and come from many years of monitoring data.
o	Please clarify in the text whether you used detection data from 2018 and 2019. You report in the methods that the study lasted from 2009-2019, but the Brooks et al. paper reports year-specific detection probabilities only for the period from 2009-2017. I believe that this 8 year sample provides a sufficiently robust dataset for your bootstrapped analysis, but it needs to be explicitly stated how many years of detection probability data are used.
o	I have some concerns about the range of wetland sizes (0.1-20.9 ha). You used a similar amount of sampling effort (30 minutes per visit) at all wetlands, but I would be far more confident calling a non-detection from a 0.1 ha wetland a true absence than a non-detection at a 21 ha wetland.

The conclusions are appropriate and well founded based on the results. However, I found that the discussion of the results was insufficient to match the aims laid out in the abstract and introduction. I would suggest that you spend more time in the discussion section explaining how other researchers can apply this approach to their own species of interest. What are the necessary steps (could you list or label them more clearly)? Is it important to both determine how many years are necessary with one survey per year AND how many years it will take them if effort is increased? How should they decide on a threshold of detection probability that is appropriate for their species? And finally, how will this help you moving forward with monitoring for Reticulated Flatwood Salamanders, and with reintroductions of this species? You state that intensive, long-term sampling is necessary (Line 227), but does that mean that you will recommend 4 surveys a year for five years? Or stick to 2-3 surveys for a longer time period. How can you (and others) weigh the trade-offs of more visits vs. more years? How should researchers respond if they hit a series of bad years mid-project? Addressing some of these questions would greatly increase the utility and usability of your manuscript.
Additional comments: Dear authors, it was a pleasure to read your manuscript. You clearly stated your research question, and wrote persuasively about the need for better monitoring schemes to account for environmental stochasticity, especially in the context of conservation reintroductions. It is an interesting case study of a species with an environmentally-mediated life cycle, and indirect monitoring procedure for the adult population, and a long-term monitoring dataset. You made good use of bootstraping and a hierarchical approach to simulate the amount of monitoring required to achieve confidence in site status, which is an ongoing issue in conservation and monitoring. I would love to see more in the discussion section regarding how this approach can and should be implemented by others, since you state that that is one of your main goals.


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: RAPID AUTHENTICITY TESTING OF ARTIFICIALLY BRED GREEN TURTLES (CHELONIA MYDAS) USING MICROSATELLITE AND MITOCHONDRIAL DNA MARKERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The raw mitochondrial haplotype data and microsatellite allele data are provided.

A figure illustrating the possible Australasian sources of these turtles would be helpful, rather than having to refer to other manuscripts for context.

I would recommend restructuring some of the information currently contained in the tables/supplemental tables.

Table 1 is unnecessary as it stands. I would recommend naming these loci and referring to the original development note and simply stated the dye used in the methods text. It might be more helpful to readers to treat this as a supplemental table and include more specifics of primer concentrations used in the multiplex PCR analysis.

The data presented in Table 3 might be better presented in a supplemental table with haplotypes as rows and captive adults and juveniles as separate columns, along with all of the rookery and foraging ground data available for this region. It should be fairly easy to append these data to an existing excel file from recent analyses. Alternatively, you could retain Table 3 but have separate columns to summarize the adults and juvenile haplotype counts from the present study and exclude the area of origin and frequency portion but refer to a supplemental table with these data.

Table 4 might be best treated as a supplemental table as well.
Experimental design: More details on the mitochondrial sequencing (or at least a reference to a previous study that used the same approach) are needed.

More details on the multiplex genotyping would also be helpful for authors interested in replicating this study.

Line 94 in materials and methods. I don't think skin biopsies qualify as noninvasive. I would recommend removing this descriptor.

For the mixed stock analysis, were only the 16 juveniles used or a mixture of adults and juveniles? It's not clear from the methods or results, given some haplotype overlap between groups. Please clarify. I would recommend only the juveniles be used or that they be treated separately.

There are several references to "paternity" testing when I think the authors are analyzing both parents. I would recommend referring to these as "parentage" analyses. Paternity specifically refers to potential sires/males.

Line 208/209: I would recommend referring to these as "trinucleotide" and "tetranucleotide" loci to follow standard nomenclature.
Validity of the findings: The loci used were sufficient in this case to discriminate between candidate parents and the randomly selected juveniles. However, as noted by authors, only two loci may not be enough in many other circumstances. I would recommend running many more loci to increase confidence that exclusion will be certain and also to help clarify potential relationships among juveniles of unknown origins.

There are existing resources for multiplex genotyping of green turtle microsatellite loci. The authors don't appear to have considered the available data. Previous studies have successfully employed mutiplex PCR reactions to provide data on multiple paternity and relatedness analysis (Wright et al., 2012, 13 well behaved loci in 2 multiplexes) and Barbanti et al. 2019, a different set of 13 loci in 2 multiplexes). Wright et al. 2012 previously demonstrated that D105 used in the present study had amplification/scoring issues and was an unreliable marker. I would recommend making use of these existing multiplexes that contain additional loci and recommending their use in the discussion section.

The authors successfully demonstrate the primary objective of excluding the adult farm turtles as the parents of the juveniles. However, this represents the bare minimum of meaningful treatment of these samples, particularly given that only 16 of several hundred juveniles were analyzed. I appreciate that resources are limited, but relatedness analysis of at least the randomly selected juveniles already using either set of the 2 multiplexes above could provide important additional context on their potential source(s). Are the juveniles that share haplotypes siblings or half siblings or more likely unrelated? If this is beyond the scope of the present study, I would recommend running additional loci and additional samples in the future.
Additional comments: Rather than referring to the mitochondrial sequences and microsatellite loci analyzed as "genes" I would simply call them sequences/haplotypes or microsatellite loci.


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: RAPID AUTHENTICITY TESTING OF ARTIFICIALLY BRED GREEN TURTLES (CHELONIA MYDAS) USING MICROSATELLITE AND MITOCHONDRIAL DNA MARKERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are some key papers that can add crucial context to this study.

Shi et al. 2007. Farming endangered turtles to extinction in China. Conservation Biology 21(1):5-6.

This study discusses a related problem for farming freshwater turtles in China. Given the parallels with this study the authors should include the direct comparison. One of the key points is that farms are often the biggest purchasers of wild turtles.

As part of this, the bushmeat phenomenon and false localities of Chinese turtles led to a series of studies that talked about false claims of provenance.

Parham, J.F., and H. Shi. 2001. The discovery of Mauremys iversoni-like turtles at a turtle farm in Hainan Province, China: The counterfeit golden coin. Asiatic Herpetological Research 9:71-77.

Parham et al. 2001. New Chinese turtles: Endangered or invalid? A reassessment of two species using mitochondrial DNA, allozyme electrophoresis, and known locality specimens. Animal Conservation 4(4):357-367.

Li et al. 2021. Sea turtle demand in China threatens the survival of wild populations. iScience 24(6):102517.

This recent study on the plight of captive sea turtles in China discusses faux-farming situations (aka ranching) and should be cited as it directly relates to the current study (both specifically and in general).

-----------------

Line 22: “which further aggravates the already endangered species” is awkward as it sounds like it makes the species angry. I suggest a different phrasing “which adds another threat to an already endangered species”
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I think this is a really simple and straightforward, but also elegant and important, study. I provide some citations that can help better-frame the study,


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

Input:
Title: RAPID AUTHENTICITY TESTING OF ARTIFICIALLY BRED GREEN TURTLES (CHELONIA MYDAS) USING MICROSATELLITE AND MITOCHONDRIAL DNA MARKERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This version of the manuscript looks much better.
Experimental design: The revised version rectified most potential issues with methodology and analyses. The one glaring remaining issue is with the mixed stock analyses. Despite the small sample sizes, the haplotype frequencies between the adults and juveniles looked like they might be differentiated to me. I ran the frequencies through Arlequin. The FST comparison was not significant, but the exact test did indicate significant differentiation (p = 0.025). It is inappropriate to combine these groups for mixed stock analyses given this signal of differentiation and the nuclear data that exclude them as parents. Analyzing small sample sizes through MSA will certainly lead to broader credible intervals, which rightfully indicate greater uncertainty given potential for sampling error with smaller data sets. But that would be better than combining disparate samples and potentially getting illegitimate signals about their sources. I would recommend splitting these into 2 groups and rerunning the analyses. It should only take an hour to create 2 separate DEC files and run them both through BAYES with all of the existing base and control files you already have.
Validity of the findings: No comment.
Additional comments: No additional comments


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

Input:
Title: PSYCHOMETRIC EVALUATION OF AN ITALIAN CUSTOM 4-ITEM SHORT FORM OF THE PROMIS ANXIETY ITEM BANK IN IMMUNE-MEDIATED INFLAMMATORY DISEASES: AN ITEM RESPONSE THEORY ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In general, the paper is well-written, however it would benefit from a careful read-through and editing by a native English speaker  (e.g., line 129: "permits to assemble")

It would be nice to see actual anxiety level data shown for the patient versus control groups, and patient subgroups, to illustrate degree of anxiety relative to the general population, and have more text to this effect. Unless i missed it, after reading the manuscript, one has no idea how anxious patients to inflammatory diseases are relative to one another or the general population, or the control sample.  This seems odd to me.  please provide at minimum the mean T scores and standard deviations around those means. Some of the
Experimental design: The logic of the study is clear, and the methods used are state-of-the-art, with appropriate software documentation. all-in-all, it is clear the 8-item anxiety measure fits a 1PL model which affords it some potential advantages in application. To some extent, the authors get a little lost in this explanation regarding 1PL vs 2PL GRM results, and might consider scaling that back in favor of more information about the nature of anxiety in the inflammatory diseases studied.
Validity of the findings: The authors state that they translated the 8-item anxiety short form, but do not report whether this translation has been recognized and approved by the PROMIS Health Organization (PHO) or Northwestern University, acting on behalf of the PHO.  It is also not clear exactly which 8-item version was translated.  the specific version name, as specified at http://www.healthmeasures.net, should be provided. in the method section, after which a 'shorthand' referencing may be applied.

I have some concern about this issue in the discussion: "Finally, the inspection of the assumption of local independence suggested that one of the items (either "I felt anxious" or "I felt tense") could be removed as they semantically overlap with other items ("I felt uneasy"). Overall, these results suggest that this item bank could be reduced to six items in future studies, making the instrument even more agile for testing clinical populations."  First, the authors did not study a bank; they studied an 8-item short form drawn from a larger bank. Second, the words "anxious" "tense" and "uneasy" are not very overlapping in English. perhaps the Italian translations were more overlapping, causing the observed result. Thus, it is reasonable for them to conclude that the Italian (but not necessarily English) version of this short form could be reduced to 6 items without much loss of information.
a related concern is the return to this finding in the short conclusion. As the authors themselves point out, an item bank affords multiple assessment options, from fixed short forms of varying lengths, to computerized adaptive testing.  this paper studies one particular short form, and concludes that (in Italian version) the six-item version may work as well as the 8-item version. I would think that the short conclusion would be borader than this narrow finding; for example stating the multiple sources of support for the Italian PROMIS Anxiety 8-item short form.
Additional comments: Minor comments:
throughout:  the ® in PROMIS® need only be used in the title and first use of the term in abstract and body

Line 88: "married" should be "marital"
Line 87 gives "RA" as abbreviation for rheumatoid arthritis, and then line 102 flips it to "AR".  use "RA throughout
line 103: 'the definition of a "core set" of eight results' - results is not the right word here
line 111: Conley et al., 2017 is not the correct reference for PROMIS.  Use cella references here


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

Input:
Title: PSYCHOMETRIC EVALUATION OF AN ITALIAN CUSTOM 4-ITEM SHORT FORM OF THE PROMIS ANXIETY ITEM BANK IN IMMUNE-MEDIATED INFLAMMATORY DISEASES: AN ITEM RESPONSE THEORY ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors have performed a validation study of an Italian translation of a PROMIS Anxiety Short Form.
Unfortunately, the authors did not use an approved translation. Translation of PROMIS measures is not allowed without prior written permission from the provider, see the PROMIS terms of Use
https://www.healthmeasures.net/images/PROMIS/Terms_of_Use_HM_approved_1-12-17_-_Updated_Copyright_Notices.pdf

I recommend the authors to contact the PROMIS language coordinator at translations@HealthMeasures.net to request for approval of the translation. Without approval this paper cannot be published. Note that an official 8-item Italian translation of PROMIS Anxiety does exists. It has to be checked whether there is no overlap between the translations to prevent two different translations of the same items.

Caroline Terwee
President PROMIS Health Organization
Experimental design: I have not further reviewed the paper
Validity of the findings: I ahev not further reviewed the paper
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: PSYCHOMETRIC EVALUATION OF AN ITALIAN CUSTOM 4-ITEM SHORT FORM OF THE PROMIS ANXIETY ITEM BANK IN IMMUNE-MEDIATED INFLAMMATORY DISEASES: AN ITEM RESPONSE THEORY ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I have one major concern about the current paper. It is not clear to me whether the conversion table used for scoring (Appendix 1) was created using the item parameters from the original US calibration sample. This could be done by using the HealthMeasures Scoring Service tool. This should be confirmed because it is not allowed to create T-score tables based on local item parameters. Also, all T-scores for the study population, presented in the paper, should be based on the US item parameters (again, T-scores can be obtained through Scoring Service). See the PROMIS reporting guidelines (Hanmer et al, JPRO 2020;4:21).

Some other comments for further improvement of the paper:

1.	The word ‘adaptation’ can be removed from the title because the word ‘custom short form’ is sufficient and common ‘PROMIS language’. It is also not necessary to mention the 8-item short form in the title, referring to the item bank where the 4 items originate from would be more clear. The domain name of the item bank should be presented with capital A (Anxiety). Suggested title: “Psychometric evaluation of an Italian custom 4-item Short Form of the PROMIS Anxiety item bank in immune-mediated inflammatory diseases: an item response theory analysis.”
2.	The aim in the abstract should refer to the custom short form, not the original anxiety items. Suggestion: “The aim of this study is to test the psychometric properties of an Italian custom 4-item Short Form of the PROMIS Anxiety item bank in a cohort of outpatients with IMIDs.”
3.	The first sentence in the methods section of the abstract should also be rewritten because it still refers to the original 8 items and suggests that 8 items were tested. I suggest to state that 4 items were selected from the standard 8a Short Form. Suggestion: “We selected 4 items from the Italian standard Short Form Anxiety 8a and administered them…..” I suggest to make the same change to line 170-172, 222-223, and 388-389.
4.	Line 224-227: the comment about the back translation can be removed. It should be stated that 4 items from a previously approved translated version are being used. Also, line 398 should be corrected as translation of these 4 items was not performed in this study.
5.	I wonder if the term “Test Reliability Curve” shouldn’t be “Test Information Curve”. The latter term seems more common.
6.	The last sentence of the abstract (“It is advised to compute T-scores based on the estimated latent trait in order to compare different groups”) seems to suggest that are also alternative ways to compute scores (e.g. raw scores), but that is not the case. It is required to present PROMIS scores as IRT-based T-scores, not raw scores (see PROMIS reporting guideline). Please rewrite this sentence. Also lines 426-427 and lines 440-441 seem to suggest that raw scores can be used. These lines should also be rewritten.
7.	Line 175: I suggest to change the phrase “change for different levels of the latent trait” into “differ between different levels of the latent trait”
8.	Line 132-133: “physical appearance” should be “physical health”
9.	Line 169-170 seems to suggest that you will be comparing a Rasch model and a 2PL model in this study, this sentence is a bit confusing. It would be helpful to clarify that PROMIS was developed using a 2PL model and you will therefore also use this mode for testing the 4-item short form.
10.	Line 245, the phrase “we conducted an Item Response Analysis by Exploratory Factor Analysis” is confusing because EFA is not an IRT analysis. The IRT analysis is described in the next paragraph. Please remove “Item Response Analysis by” from this sentecnce.
Experimental design: 1.	It seems that two samples were used for calibration, 286 were patients, and 280 were healthy
controls. It is not clear if it is appropriate to combine two different samples into one study. Smits for example, showed that “ignoring the addition of extra clinical respondents leads to bias in item and person parameters“ (Smits Qual Life Res 2016, DOI 10.1007/s11136-015-1199-9).
2.	Methods, line 235 and further. I do not understand why it is stated that unidimensionality and IRT analyses were perform “for each subscale”. Isn’t there only one scale?
3.	Why was MAP used for score estimation instead of EAP as used by PROMIS?
Validity of the findings: 1.	DIF between patients and controls was found for three out of the four items. It would be helpful to present an indication of the magnitude of the DIF (e.g. MacFadden’s R2change) and to analyze the impact of DIF on total scores (this can be done e.g. with the lordif package in R), to see whether this DIF is problematic or not.
Additional comments: I appreciate the efforts that the authors took to collaborate with PHO and Northwestern University to obtain permission for a 4-item custom short form. I am happy to see that the translation issue has been solved and that this 4-item custom short form has now been validated. Since all short forms originate from the same item bank and are assumed to measure the same construct, information on the performance of this 4-item custom short form may also be relevant for the application of other Italian short forms from this item bank. Therefore, the paper is a relevant contribution to the literature.


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

Input:
Title: POLYCAPROLACTONE NANOFIBERS AS AN ADJUVANT STRATEGY FOR TAMOXIFEN RELEASE AND THEIR CYTOTOXICITY ON BREAST CANCER CELLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: a.	The language in the article is generally clear and simple, but a thorough grammar check is needed throughout the manuscript to address issues that could cause confusion because of unclear language. Sentence structure should be revised as well. In general, the article text is technically correct.
b.	The article is well cited and demonstrates good mentions of previous work and current understanding in the literature.
c.	In general, the figures are well represented. However, figures 6 and 7 need to display error bars and sample size. It would be helpful to include the statistical analysis from the supplemental files directly on the graphs to point to statistical significance in the form of p-values (*). In figure 7, data are not presented clearly and could benefit from rearranging or even breaking up into 2 parts unless statistical tests are to be included comparing certain groups. The Raw data excel files need more annotation for better readability.
Experimental design: a.	The article is well within the scope of the journal. The article clearly defines the research questions, and the experiments are proposed in attempt to answer the defined questions.
b.	In general, the experiments and investigations are rigorous and are technically sound. The nanofiber material characterization is thorough and provides good insight on the effect of tamoxifen loading. Quantification of loading amount is needed. Good attempts to assess cytotoxicity for breast cancer cells. Results on nanofiber effects on lymphocyte cytotoxicity is not clearly presented or discussed. Information on amount of nanofibers dosed for cytotoxicity studies is needed.
c.	The methods described in the article are clear and are repeatable. As mentioned above, dosing concentrations should be included in the methods.
Validity of the findings: a.	In general, the data presented in the manuscript is robust and is a solid base for the conclusions. Statistical analyses are adequate, but more robust comparisons may be helpful including ANOVA tests for cytotoxicity studies and more discussion of statistical results. In general, experimental controls are present. For cytotoxicity experiments, free (bulk) Tamoxifen dosing at amounts comparable to nanofiber loading amounts are helpful as an additional control.
b.	The conclusions from the studies are well presented and discussed.
Additional comments: 1.	Have you looked at range of concentrations for the nanofiber dosing? What amounts are being treated to cells?
2.	What tamoxifen amounts are present in the nanofibers after loading? Is there a way to tune those amounts?
3.	How are you ensuring that cells from buffy coat are purely lymphocytes? Flow cytometric analysis or potentially FACS may be helpful to ensure no contamination from other leukocytes that are usually present in the buffy coat from density gradient separations.
4.	Figure 7 cell viability shows >250% cell viability; this needs more explanation and potentially different representation.


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: POLYCAPROLACTONE NANOFIBERS AS AN ADJUVANT STRATEGY FOR TAMOXIFEN RELEASE AND THEIR CYTOTOXICITY ON BREAST CANCER CELLS
Review round: 1
Reviewer: 2

Output:
Basic reporting: A well written paper with Authors have reported use of tamoxifen citrate (TMX) loaded nanofibers for treatment of breast cancer. Following are some minor changes in reporting. Sufficient literature has been reviewed and cited. Data has been sufficiently reported in form of table and figures.

a. Some mistakes in sentence structures have been observed and should be fixed before final submissions.
b. Grammatic mistakes have been observed frequently in the manuscript.
Experimental design: The studies presents original results obtained from rigorous experimentation, keeping in view the technical and ethical standards. All methods have been described sufficiently. However, shortcomings of use of TMX (i-e the research gap) needs to be elaborated further.
Validity of the findings: Novelty of study lies in use of TMX, in conditions where it can't be used with conventional methods, thanks to the electrospinning process and nanofibers produced thereof. Underlying data has been provided adequately. The samples have been characterized to required level using a number of techniques that are well known in subjected domain. However, following observations were made:

a. The gap (i-e inappropriateness of TMX or shortcomings of TMX for which it was incorporated in nanofibers) has not been related to results. Authors reported interesting findings which need to be related to the research gap in more detail.
b. The conclusion section needs to be improved and linked to original research question.
Additional comments: The study presents an important application of electrospun nanofibers for treatment of breast cancer and seems worth publishing once the minor changes mentioned above have been addressed.


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

Input:
Title: POLYCAPROLACTONE NANOFIBERS AS AN ADJUVANT STRATEGY FOR TAMOXIFEN RELEASE AND THEIR CYTOTOXICITY ON BREAST CANCER CELLS
Review round: 1
Reviewer: 3

Output:
Basic reporting: - The English needs review (I highlighted below a few examples of sentences with grammatical errors, but I found many others in the text).

- The introduction was too long. Also, it does not bring any information about the polycaprolactone nanofibers, in specific.

- The reason for choosing the polycaprolactone nanofibers as delivery material was not clear.

- The references should be updated. There are too many old references, some of them over 20 years of publication date.
Experimental design: - The paper follows the scope of the journal.

- I believe the authors presented well the importance of the nanofibers in general therapies, however, they should focus on the specific material they've chosen. Also, it would be interesting to show some data on the use of polycaprolactone nanofibers in other diseases, explaining the rationale why it must be a good option for TMX.

- The statistical analysis should be another subtopic.
Validity of the findings: - The statistical results were almost not presented in the text.

- The conclusions match the objectives of the study and the results are well stated.
Additional comments: - Abstract. The authors could make a better description of the in vivo results.

- Introduction. Lines 36-38. Where is the reference?

- Introduction. Lines 46-48. In the sentence "Anti-estrogens such as tamoxifen is widely accepted drug for the treatment of hormone receptor-positive (ER+ and PR+) breast cancers", the pronoun must be in the plural: "Anti-estrogens such as tamoxifen are widely accepted drugs for the treatment of hormone receptor-positive (ER+ and PR+) breast cancers".

- Introduction. Lines 52-53. The sentence "It is an agonist in the liver, uterus and bones, and as an antagonist in the brain and mammary gland." should be: ""It is an agonist in the liver, uterus and bones, and an antagonist in the brain and mammary gland."

- Introduction. Lines 76-78. Exclude the sentence "Nanotechnology in recent years has produced various kinds of nanodevices with applications in many fields; one of the most benefited has been that of medicine. In particular, the release of local medicines using controlled systems is of great interest."

- Conclusions. Lines 462-464. In the sentence "These results suggest that the PCL-TMX nanofibers have potential as a drug delivery system as adjuvant to treat solid tumors or breast cancer", I suggest trading "or" for "including".


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: POLYCAPROLACTONE NANOFIBERS AS AN ADJUVANT STRATEGY FOR TAMOXIFEN RELEASE AND THEIR CYTOTOXICITY ON BREAST CANCER CELLS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The language has been improved. Sufficient literature has been cited.
Experimental design: Experimental design and its execution is as per standard research requirements. Research question has been defined and answered in a better way compared to previous version.
Validity of the findings: The validity of results seems to be acceptable.
Additional comments: The manuscript may be proceeded for publication.


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

Input:
Title: LAND-USE CHANGE INFLUENCE SOIL QUALITY PARAMETERS AT AN ECOLOGICALLY FRAGILE AREA OF YONGDENG COUNTY OF GANSU PROVINCE, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: Experimental design; rewrite it to make it easy to follow, you can use illustration of figure to present your experimental design
Validity of the findings: The abstract is well written and clear to the reader, congratulation for good job.
Introduction: Well structured and well written with enough background information
Additional comments: 1.	Abstract:  The abstract is well written and clear to the reader, congratulation for good job.
2.	Introduction: Well structured and well written with enough background information
3.	Materials and Methods
4.	Line 111 to 112; present degrees Celsius by using symbol
5.	Line 130: the area is 15.3hm2, it is not clear
6.	Line 130 and other places in the Ms i.e., plants spaced 7m leave space between value and unit
7.	Line 135; Table 1 summarizes the fundamental characteristics of each land-use type, you presented the table caption but the table itself is not located in a particular location. I understand figures and tables are at the end of the document, thus in the text just cite the figure or table without full figure or table caption.
8.	Line 137 to 147: Experimental design; rewrite it to make it easy to follow, you can use illustration of figure to present your experimental design.
9.	Line 151; How did you determined the soil moisture? Did you use soil core to take the soil samples for moisture content?
10.	Line 216: why you decided to use spearman’s correlation? and not Pearson?
11.	What is the recommended SOC ad Total N in the area for agricultural productivity?
12.	Conclusion: acceptable


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: LAND-USE CHANGE INFLUENCE SOIL QUALITY PARAMETERS AT AN ECOLOGICALLY FRAGILE AREA OF YONGDENG COUNTY OF GANSU PROVINCE, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: This paper has high standard interms of original research, experiments conducted and results presented by the authors. This paper addresses issues in dry land, abandoned land and other types that are critical for food sustainability.


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: LAND-USE CHANGE INFLUENCE SOIL QUALITY PARAMETERS AT AN ECOLOGICALLY FRAGILE AREA OF YONGDENG COUNTY OF GANSU PROVINCE, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: I thank the authors for their extensive dataset (figures and tables) as well as the raw data that they helped to track the statistical analysis collected from detailed field studies. The articles are written in English at a high level, In addition, the manuscript is clearly written professionally, but requires revision. Such as references for literature that need to be finalized.
Hypotheses is consistent with the results obtained. All notes are given in the text of the article.
Experimental design: The goals and objectives are reflected in this work within the goals of the journal. The research question is clear, relevant and meaningful. Shows how research fills the identified knowledge gap.
The methods are described with sufficient detail and information to reproduce, but there are minor issues with the use of methods for thinning such as soil texture. See comments in the pdf file.
Validity of the findings: All basic data were provided; they are reliable, statistically reliable and controlled.
Conclusions are well articulated, related to the original research question, and limited to supporting results.
Additional comments: The structure of the article is written at a high level, but needs improvement. All remarks are given in the text of the article. Determining the type of soil texture is of particular concern to scientists when talking about the quality of soil parameters.

I commend the authors for their extensive data set and also the raw data they helped track the statistical analysis, compiled over of detailed fieldwork. In addition, the manuscript is clearly written in professional. If there is a weakness, it is in the methodology (as I have noted in text) which should be improved upon before acceptance.


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: LAND-USE CHANGE INFLUENCE SOIL QUALITY PARAMETERS AT AN ECOLOGICALLY FRAGILE AREA OF YONGDENG COUNTY OF GANSU PROVINCE, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Good
Experimental design: well presented now
Validity of the findings: Acceptable
Additional comments: The authors have followed and worked on all comments and suggestions provided and the manuscript quality and clarity are impressively improved. ACCEPT FOR PUBLICATION


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

Input:
Title: LAND-USE CHANGE INFLUENCE SOIL QUALITY PARAMETERS AT AN ECOLOGICALLY FRAGILE AREA OF YONGDENG COUNTY OF GANSU PROVINCE, CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I thank the authors for their extensive dataset (figures and tables) as well as the raw data that they helped to track the statistical analysis collected from detailed field studies. The articles are written in English at a high level.
Experimental design: The goals and objectives are reflected in this work within the goals of the journal. The research question is clear, relevant and meaningful. Shows how research fills the identified knowledge gap.
The methods are described with sufficient detail and information to reproduce.
Validity of the findings: All basic data were provided; they are reliable, statistically reliable and controlled.
Conclusions are well articulated, related to the original research question, and limited to supporting results.
Additional comments: The structure of the article is written at a high level.


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: AGE AND LUNAR CYCLE PREDICT HARBOR PORPOISE BYCATCH IN THE SOUTH-WESTERN BALTIC SEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The authors clearly defined their question and motivation.
2. There are some places where the English could be improved, like
line 44: bycatch is not the "main" cause of death of marine mammals, although it may be the main human-induced cause of death.
line 54: "severely affected" needs to be changed.
many places: the term “influencing bycatch” is not totally correct.  Consider using terms like “correlated” or “associated”. Although the factor may truly drive (influence) more bycatch, you are actually looking for statistically significant correlations in the data.  Do you see the fine difference in terms.
3. The figures look pretty.
4. The discussion section rambles on a bit and is too long (in my opinion). The results section was 24 lines long and the discussion was over 130 lines long.
Experimental design: This manuscript is interested in identifying biotic and abiotic factors that correlate to harbor porpoise bycatch levels, which could be used to inform management actions to reduce bycatch. This is a worthwhile goal, especially for the small Baltic stock.

Unfortunately, the authors need to do more statistical work to actually address this question and thus provide useful information for their managers.  Some specific additional analyses and questions about what was done are below.
1)	If there were no recorded bycatch from fishermen during 2005, 2010 and 2014 and there was fishing in these years, then these years should be removed from the analyses because it is highly unlikely there were truly no bycatch. As the authors mentioned, the fishers may not have been cooperative those years.
2)	Lines 149-150: What was the purpose of developing a polynomial regression line of the time series of annual numbers of bycatch? The real question is why is there interannual variability? Was it because of some biotic or abiotic factor that managers could use to develop a management action?
3)	The authors should consider developing a model of the bycatch rate (number of bycatches /100 fishing days at sea) say by month-year (and 10x10 km2 grid cell maybe) as it relates to year, month, age group (perhaps <4 years versus >4 years old), area, sex, wind speed, precipitation, and lunar phase. A generalized additive model would provide the most flexibility. You could look at each variable individually to get a better feel of the relationships. Then you could build a multi-variable model to see which combinations of variables are needed to explain the bycatch patterns. Since many of the factors are related to each other you should check for aliasing.
4)	Figure 3 is great, now you need a complimentary map of the fishing effort and of the abundance estimates.
5)	You mentioned abundance estimates of the porpoises, but I don’t think you used this information.
6)	You mentioned stranding increased, especially in years with low fisherman delivered bycaught animals.  You could consider adding the numbers of stranding to the observed bycatch.  However, some of the stranded animals did die of other causes.
7)	You said you wanted to help managers but most of these variables would be difficult to develop a management action.
8)	Lunar phase appears to be important, so it would be very informative if you dove more into why.  But perhaps if you used bycatch rate then this would not be important if more fishing is occurring at this time.
Validity of the findings: 1. All of the bycatch underlying data were provided. Although the fishing effort data were not

2. Stated conclusions follow from the analysis, but as discussed above, the analysis is very limited and I bet there is more in the data that should be shared.
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: AGE AND LUNAR CYCLE PREDICT HARBOR PORPOISE BYCATCH IN THE SOUTH-WESTERN BALTIC SEA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see "General comments for the author" section below for my review.
Experimental design: Please see "General comments for the author" section below for my review.
Validity of the findings: Please see "General comments for the author" section below for my review.
Additional comments: Review of “What influences harbor porpoise bycatch in the
south-western Baltic Sea?”

Summary
This paper is an interesting summary of ~30 years of harbor porpoise bycatch data in Baltic Sea gill nets. There are several important findings here that are work reporting in the primary literature. In my estimation, those key points are: 1) 90% of all bycaught animals were four years or younger 2) 69.3% of all porpoises were bycaught from July to November 3) The majority of bycatch (28.6%) occurred during the lunar phase 5. Also, possibly (but not definitely) that this bycatch has declined since 1996. However, there are some major issues I have with the manuscript and therefore cannot endorse its publication at present. Please address those comments and I would be happy to reconsider the paper.

Major points:

•	I tend to think paper titles are best when presenting the main finding. Consider changing title to “Age of individual and lunar cycle predict harbor porpoise bycatch in the south-western Baltic Sea” or something along those lines.
•	For the meteorological data analyzed were you able to get information on local cloud cover or just wind-speed. Cloud cover would be an important factor to consider as it could negate the luminosity provided by a full (or nearly full) moon.
•	For the vessels considered (boats >8m), were fishermen required to report bycatch, and/or were there independent fisheries’ observers on-board? If neither is true how can you be sure that bycatch was reported honestly and accurately? At minimum this should be specified in the methods section.
•	Statistical analyses are only briefly described and therefore challenging to determine whether the approach taken was appropriate. My initial thought is that a simple ANOVA is overly simplistic for these data, and that a mixed model approach would be more suitable. Please justify your current statistics better (e.g., cite/describe other bycatch studies that used similar statistics) or use a different statistical approach with better justification.
•	Lines 167-168: “The majority of bycatch (28.6%) occurred during the lunar phase 5”. This is an interesting and useful finding, please conduct and report statistics on this finding.
•	Lines 176-178: I agree this is a key finding, but your vague discussion of “Within this critical time period, mitigation measures should be applied” is unhelpful. What critical time period? The animals are juveniles for ~4 years with overlapping generations. Do they (the juveniles and adults) spatially segregate? Are there any specific ideas you can point to that would reduce bycatch risk to this vulnerable life-stage?
•	Lines 182-193: this is an important issue (voluntary fisherman reporting) that calls into question a potential key finding (bycatch numbers declining post 1996) of your work. Is there any data from other regions (ideally NE Atlantic) that suggests that marine mammal/gill-net bycatch declined from pre-mid-1990s to post-mid-1990s? I understand that you cannot say for sure whether this change has to do with a difference in reporting by fisherman, which is unfortunate, but here would be helpful to draw on other studies from the same region that are better controlled for reporting.
•	Figure 4B I recommend a log-scale (or some form of data transformation/visualization technique) where the reader will be able to see the majority of the data more easily.
•	One of the most interesting points of the paper is your claim that a statistically significant portion of bycatch events happened during bright moonlight. In addition to not tracking cloud cover (which may have been impossible, but seems important to make this claim), in Figure 5 your data show that yes, the most bycatch happened during full moon conditions; however, the second most bycatch events happened during new moon conditions without moonlight. How do you explain that?

Minor points:
Passive voice should be changed to active voice when possible. Several examples:
•	Lines 90-91: “a long-term data-set… was analyzed”
•	Line 93: “it was examined”
•	Lines 112-113: “data from dedicated aerial surveys… were used”
•	Lines 295-296: “how bycatch… is affected by”
Imprecise language at points that could be made more professional. Several examples:
•	Lines 44-45: “gill nets, which is the main cause of death in marine mammals,” may be true for pinnipeds and odontocetes, but not for mysticetes.
•	Line 67: describing bycatch rates as “way above”. How much greater?
•	Line 256: “way lower” How much lower? Be specific.
Lines 207-208: “During necropsies at ITAW over the last 30 years, only single animals showed scars indicating a previous bycatch situation.” This sentence doesn’t make sense as is, please reword.
Line 288-289: “of two captive showed” I believe the word “porpoises” is missing?


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: AGE AND LUNAR CYCLE PREDICT HARBOR PORPOISE BYCATCH IN THE SOUTH-WESTERN BALTIC SEA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed my concerns and I consider this paper acceptable for publication
Experimental design: The authors have addressed my concerns and I consider this paper acceptable for publication
Validity of the findings: The authors have addressed my concerns and I consider this paper acceptable for publication
Additional comments: The authors have addressed my concerns and I consider this paper acceptable for publication


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

Input:
Title: AGE AND LUNAR CYCLE PREDICT HARBOR PORPOISE BYCATCH IN THE SOUTH-WESTERN BALTIC SEA
Review round: 2
Reviewer: 2

Output:
Basic reporting: See general comments to the authors.
Experimental design: See general comments to the authors.
Validity of the findings: See general comments to the authors.
Additional comments: Review of “Age and lunar cycle predict harbour porpoise bycatch in the south-western Baltic Sea.

Overall: This manuscript makes use of a long-term data set on bycatch in the south-western Baltic Sea to attempt to gain more information on the impact of environmental and anthropogenic factors on the chances of bycatch. This information is important and much needed. Overall, the manuscript is well written. Unfortunately, there are a number of areas where a lot of clarification is needed before this manuscript is ready for publication. My main concerns are highlighted below followed by more specific comments on the sections of the manuscript.

Main concerns:
-	The Baltic region has three distinct populations of harbour porpoises, with very different conservation statuses, that all exhibit distinct seasonal movement patterns. I think the interpretation of the results could benefit from a clearer explanation of how porpoise presence in this region is influenced by the movement patterns of the two populations likely to utilise the area observed, and how this may influence the seasonal pattern in bycatch rate reported. i.e. Belt Sea population mainly uses the area in summer, yet Baltic Proper population is thought to move into the area over the winter months. Making it clear how these results likely relate to which porpoise populations is important from a management perspective.
-	Linked to this, there needs to be consistency in when the author is referring to a specific population, or all porpoises in the Baltic region. For example, in the abstract “a decline in Baltic porpoises”- is this in relation to the Baltic Proper population, or all porpoises in the Baltic region. This should be checked and clarified throughout. As far as I understand, none of the bycaught animals have been tested genetically to assign population ID, so it is not possible for the authors to say for sure which population the bycaught animals belong to- but this should at least be discussed as a factor to consider.
-	In regards to lunar influences, I wonder why the lunar cycle at the locations was not calculated (e.g. using the simple “lunar” package in R), rather than relying on values from a single station? Also, in order to reduce the number of factors/levels in the analysis (which is always a good thing), I wonder whether it would have been clearer to lump phases of the lunar cycle with similar illumination level (e.g. waxing and waning) together? For example, in Figure 6 with the histogram of lunar phase and bycatch, it would have shown a clear trend across five bars of lunar illumination level. Also, studies showing the impact of light on bycatch should probably be discussed. Here is an example for birds (Field et al. 2019- High contrast panels and lights do not reduce bird bycatch in Baltic Sea gillnet fisheries). There is also a lot of literature showing light reduces fish bycatch. I am unsure what exists for harbour porpoises, but it should be discussed given the findings surrounding higher bycatch during the full moon (higher light levels).
-	Exclusion of years with no bycatch (2005, 2010, 2014) as it was unlikely that none occurred in those years makes it seem as though a different assumption was applied to these years relative to the other 27. In other years you don’t account for bycatch that was likely not reported either…
-	Fishing effort data is only for a short time period (3 years). This detail should be made clearer, as it is not a 30 year data set for this analysis.
-	The analysis section of the methods needs a lot more detail added. As I understand, you plan to compare days with and without bycatch, yet this would likely result in a lot of zeros (thousands of days over 30 years with no bycatch). However, in figures 4 and 5 I see that you only compared to 60 or so days with no bycatch? How were these selected? And why were the number of days with bycatch different between the wind and precipitation analysis?
-	Chisquared tests were used, but no definition of the expected outcome was given, or justification for why this was the assumed expected outcome. This information is essential.
I also have some more specific comments, including:

Abstract:
Line 46: There was “a” significant….
Line 49: During “a” full moon. Check throughout. Should be “a full moon” or “the full moon” depending on sentence context.

Introduction:
Line 64-67: Long convoluted sentence: suggest changing it to “For all three populations in the Baltic region, assessed…” Could also be built into more detail on the three populations and their movements as highlighted in concerns above.
Line 70-72: Also use of alternative gear is another option- (see Königson et al 2015. Cod pots in the Baltic. Are they efficient and what affects their efficiency? )
Line 84-87: Lunar influence on cetaceans has been seen also. E.g. The echolocation of indo-pacific humpback dolphins (Wang et al. 2015- Passive Acoustic Monitoring the Diel, Lunar, Seasonal and Tidal Patterns in the Biosonar Activity of the Indo-Pacific Humpback Dolphins (Sousa chinensis) in the Pearl River Estuary, China) and pilot whales changed the dive behaviour and spatial area use (Owen et al. 2019- Lunar cycles influence the diving behavior and habitat use of short-finned pilot whales around the main Hawaiian Islands). This should be mentioned here, not just that it influences fish, and may influence porpoises.
Line 92: Should be made clear here that you mean harbour porpoise abundance.

Methods:
Line 104-106: Should be split into two sentences for clarity. Option 1 was age using teeth. Option 2 was based on length. Right now it reads as though the length option was a second step of option 1…which I don’t think is right. Please reword.
Line 111: delete the comma.
Line 115-117: This sentence is not clear and needs a reword. What was it monthly averages of? Fishing effort?
Line 120: change “whether” to “if”- flows better than “whether weather”.
Line 123: What was the temporal scale that precipitation data that were used ? Daily mm? Same for cloud cover. Was it daily average for the day of the bycatch event?
Line 127-130: Why was a single location used for lunar data? It is possible to obtain information on lunar cycles for exact locations and times. E.g. using the “lunar” package in R.
Line 131-134: In analyses the levels of factors can influence results, with it typically being better to minimise levels as much as possible. I wonder if it would have been clearer to lump lunar phases with similar illumination levels (e.g. waxing and waning gibbous), or if there is a reason why you did not do this?
Line 138: Make it clear that the abundance assessment is not over the full 30 year period.
Line 142: It is not clear that multiple models were run, and that model selection was needed? Also, it is not common to use statistical significance as an assessment of model fit. I think the explanation of which models, and model structures were actually tested, as this section is not clear.
Line 143: “days with and without bycatch”. You only had 140 bycatch events over 30 years, so this implies that you had 10,810 days without bycatch. This would result in a massive zero inflation problem and a very unbalanced sample size, and it is not clear how you got around this problem. I see in figure 4 and figure 5 that a much smaller sample size (n around 60) is given, but it is unclear how you reached this number and which days were selected. Also why less days are considered than were available for days with bycatch?
Line 144: Chi squared tests require a comparison between an expected and observed outcome. It is essential that you define what your expected outcomes were in these tests, and what you based these assumptions on.

Results:
Line 154-155: delete the sentence starting with “in 2005, 2010...” as this information is already given above. See comment above on the validity of this.
Line 155-156: This increase to 8 per year seems higher than the mean of 7.4 in the first decade. Potential reasons for this increase in recent years should be discussed.
Line 161: Is this 73% of the 90% mentioned above? These % and differences are a little unclear. Consider re-wording for clarity.
Line 164: “no significant difference”- give the statistic results.
Line 177-178: This result goes in line with my suggestion above to lump all lunar phases with similar illumination levels.

Discussion:
Line 189-191: See comment above on the increase in bycatch to 8 animals a year after 2015 and the need to discuss this.
Line 194: What mitigation measures in EU waters are you referring to? This should be specified here for the reader. Was there something specific in the mid 90s (other than a reduction in bycatch reporting) that could have reduced fishing effort/bycatch? Also consider indirect measures, e.g. cod ban in recent years that could have influenced fishing effort.
Line 195: catch limits of what?
Line 206: change word “demand” to “imply”. This sentence seems quite speculative and should be made clear that this is the case. You could similarly speculate that they have seen other animals bycaught and understand the danger.
219: Could be good to include information on when young animals likely separate from their mother, and whether juvenile animals move around alone, or in mixed age groups.
Line 223-225: So does this mean that juveniles potentially aren’t at higher risk than adults, it is just that the age distribution of the animals bycaught matches the age distribution of the animals out there.
Line 236: add ‘s’ to the end of ‘occur’. Make it clear that it is the monthly distribution in this specific area. As it is likely different in other areas depending on fishing effort/porpoise movement patterns.
Line 239: Again- make it clearer this is only in your area. There are plenty of areas where porpoise density is highest in winter and overlapping with areas used for gillnet fishing.
Line 245-249: I think the fact you only used 3 years of fishing effort data should be addressed here. It is possible that the distribution of fishing effort changed over the 30 years, and that a larger overlap of fishing effort with the time that porpoises are present in the area leads to higher bycatch.
Line 256: delete the word prey.
Line 260: noise from factors such as shipping has been shown to reduce the echolocation of porpoises and cause fleeing behaviour (Dyndo 2015, Wisniewska et al. 2018- already in the reference list)- reduced echolocation could lead to less nets detected.
Line 275: why would they be more active during a full moon? I don’t follow. Porpoises need to forage continuously so it is not as though they can stop foraging outside of a full moon period? Active in what way?
Line 276: you ruled out an impact of weather on bycatch, so it is unlikely that weather influenced this. Or is this why you found an influence? i.e. nets only set in low wind and no rain- so the lack of influence is due to only sampling one end of the range of possible weather? Was there an interaction between weather and fishing effort?
Line 277: You have fishing effort data and lunar cycle information. Did you see this interaction in the data?
Line 278: give more specifics of what you mean by “clear lunar activity patterns”
Line 283: Captive porpoises are not subjected to the possible influence of lunar cycles on their prey, so it makes sense that they would not display lunar differences.
Line 295: The sentence is not clear and needs a reword.
Line 298: delete the ‘s’ off the end of ‘results’.

Figure 1: Change “bycatches” to “bycatch events”- change throughout the manuscript as “bycatches” is a weird word in English, and it is better to be consistent throughout the document (e.g. with figure 4 and 5).

Figure 2 and Table 1: that some bycatch events were excluded from the analysis should be made clear in the methods/results section, not only in the figure.

Figure 3: If I interpret this correctly, the highest fishing effort was in 37G1, where there was hardly any bycatch. This should also be discussed, particularly in light of the distribution of the 2 populations in this area. What was the fishing effort in 38G1, 37F9 and 38F9?

Figure 4: how were the number of days with no bycatch determined? Why were these 52 or 68 days selected out of the 10,800 ish available with no bycatch, and why were there less days with bycatch than 140 (i.e. precipitation n =115 days with bycatch, but wind speed n = 75 days with bycatch)? This should be explained in the methods/results too.

Figure 5: Seems to be a weird repeat of part of figure 4B?


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: AGE AND LUNAR CYCLE PREDICT HARBOR PORPOISE BYCATCH IN THE SOUTH-WESTERN BALTIC SEA
Review round: 3
Reviewer: 1

Output:
Basic reporting: Line 67-71- I feel it is worth noting that for the Critically Endangered Baltic Proper population it has been estimated that a maximum bycatch of 0.7 individuals is able to be sustained- meaning that bycatch of this population should be at zero.
Experimental design: The authors have done an excellent job of clarifying the statistics. I have one remaining question, and that is whether zero inflation can be an issue with chi squared tests, or the regression analyses? The data set used were heavily zero inflated, and while I am not sure if this is an issue with the tests used, it should be clarified/stated in the text what (if any) issue it is likely to create, and how it was dealt with.

Figure 4: it is still unclear why 75 bycatch events were analysed for wind speed, but 115 for precipitation. Yet the methods say only "Five animals were excluded from the spatial analysis due to unknown bycatch location". And the methods also say there was a total of 140 bycaught animals. I am also a little confused about how you tested "for significant differences between wind speed and precipitation during days with and without bycatch, we used ANOVA Chi-squared tests"? What was your expected wind speed against measured wind speed? I assume these data would have been better suited to the polynomial models mentioned above? Is this a mistake in writing?
Validity of the findings: I also have concerns on the management recommendations in the conclusion. "To reduce bycatch, fishing efforts could be reduced seasonally between e.g., July and November, especially in areas with high bycatch of juveniles and neonates, such as Eckernförde Bight and Schlei". Based purely on bycatch data I can see why this would be recommended. But as I mentioned previously, I think the authors need to be careful with what is recommended here, as the area may be used by the Critically Endangered population of harbour porpoises during the winter months (we don't currently know how far west they go in the winter, and there is no genetic data on which animals were bycaught (great that this is now highlighted!). Even one bycaught harbour porpoise from the Baltic Proper population is a massive issue for this population. I think this issue should be mentioned in the discussion, and again in the conclusion. (i.e. that the potential for the critically endangered population to use the area in the winter months should be taken into account).
Additional comments: The authors have done a good job of incorporating most of my concerns/comments and I congratulate them on pulling it together.


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: IN VITRO INDUCTION AND IDENTIFICATION OF POLYPLOID NEOLAMARCKIA CADAMBA PLANTS BY COLCHICINE TREATMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors reported colchicine-induction of polyploids of Neolamarckia cadamba here. In vitro regeneration, in vitro and on soil growth, and morphological characters were also compared between the original tetraploids, induced octaploids and mixaploids.  The data are clear and described in detail. Discussion part is a little bit too wordy, and could be reduced in length, but overall contents are well prepared. Specific comments are as follows:
Introduction.
1) In line 50, the authors are better to mention to the synonym Anthocephalys cadamba Roxb,, that will be referred in Line 362. Unless readers cannot understand the part around the Line 362 of Discussion part.
2) It is strongly recommended to mention to the original ploidy level (tetraploid, 2n = 4X) first in the Introduction. Unless, as myself, readers would misunderstand that the authors obtained tetraploids and octaploids from diploid original until the Discussion part.
3) Line 63, colchicine is NOT "anti-microtubule" drug, but inhibits polymerization of the tubuline.
4) LIne 99-100, "Machine" is not appropriate here. Just "FCM" is better.
5) Line 100-102, while FCM is high-throughput to examine the ploidy level, it is hard to detect aneuploidy. Therefore combination of FCM and karyotype examination is the best way. The authors have to mention to the above here.   In many past studies, colchicine-induced doubling of the ploidy often cause aneuploidy, too. Did not authors find such case here?
6) Line 111 "there is no published..." is better to be said as "this is the first report..."
Materials and methods
7) Line 126, how much was the sucrose concentration ?
8) Line 142 "5-days-old": from when? 5 days after the transplantation?
9) ibid. "between 9 00 to 10 00 am": this is not informative and no need.
10) Line 213 "SPAD": at the first appearance this type of abbreviations should be written in a full spell.
Results
11) Line 287-288, such as "94.44%". These figures are too fine. Please re-examine the significant digits. This is also the case for Line 298-300 as "0.247 mm" (or is this 247.0 micrometer?). Please check the significant digits also for the tables 2 and 3.
Discussion
12) Something was lost between line 368-369.
13) In overall meaning, the Discussion part is too wordy. For example the paragraph from line 394-408 could be omitted, because this is too general matter.
14) Line 446, "PGR":  at the first appearance this type of abbreviations should be written in a full spell.
15) Line 576 "Arabidopsis" should be "Arabidopsis thaliana". For your reference, Tsukaya (2008) doi:10.1371/journal.pbio.0060174 referred to a "high-ploidy syndrome" in the octaploid of Arabidopsis thaliana.
References
16) Order should be re-examined. For example, Sharma and Sen should be after the Sen et al.
Figures
17) Some could be combined, for example Figures 3 with 4 and 5, or 9 with 10.
Experimental design: Well designed. Minor points were raised above.
Validity of the findings: Well confirmed.
Additional comments: Detailed comments are available above "1 Basic reporting".


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: IN VITRO INDUCTION AND IDENTIFICATION OF POLYPLOID NEOLAMARCKIA CADAMBA PLANTS BY COLCHICINE TREATMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript nicely documents chromosome doubling and associated morphological changes in a Malaysian timber species. The methods and results are well-presented, the figures and tables are appropriate. Some critical information is missing from the introduction – detailed below. The discussion includes an abundance of general background information and is much too long for the results described here – sections that can be deleted are listed below. Some potential outcomes of this study are presented as facts – these need to be rephrased. For example, the morphological changes documented here may contribute to increased photosynthetic capacity, but this remains to be evaluated. Likewise, the octoploid may be valuable in cultivation, but this remains to be determined.
Experimental design: no comment
Validity of the findings: see section 1.
Additional comments: Line 28: It is premature to state that polyploidy “has become a valuable breeding strategy” since you are reporting it for the first time here.
Line 28: Please provide the family and describe that Neolamarckia cadamba is a tetraploid with 2n=44. Cite the previous chromosome counts.
Line 34: Define mixoploidy as mixed tetraploid and octoploid cells, when first used in abstract and text.
Line 39: “grew” not “reported growing”
Line 42: Morphology is not “improved”. It changed and resulted in traits that are predicted to increase phyotosynthetic capacity”
Line 50: Please provide the family and state that Neolamarckia cadamba is a tetraploid with 2n=44.
Line 54: that is easy to work…
Line 69: delete “still”
Lines 83-84: sentence can be deleted
Line 97: define mixoploid
Line 102: straightforward
Line 111: change “there is no published report on the polyploidization study of N. cadamba” to “there is no previous report of polyploidization in N. cadamba”
Line 260: replace “caused lower renderability” with “resulted in higher mortality”
Line 312 “possess” not pose
Lines 341-346: The description of explant mortality needs to be moved to the results.
Line 362: Please add that Anthocephalus cadamba is the same as Neolamarckia cadamba.  Better yet add this to the introduction, and then you say “N. cadamba (reported as A. cadamba)” here.
Lines 369-464. Most of this is general background information or repeats the results, and can be deleted. Please keep the citations of previous chromosome counts, but move these to the introduction.
Line 547: replace “The stomatal study” with “stomata morphology”
Line 559-599. General background information on stomata can be deleted.
Line 632: replace “have” with “are predicted to have”
Line 646: delete “were more superior compared with the tetraploid; the former”
Line 652-654: very speculative and best deleted


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: IN VITRO INDUCTION AND IDENTIFICATION OF POLYPLOID NEOLAMARCKIA CADAMBA PLANTS BY COLCHICINE TREATMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: I found that the authors adequately revised their text and figures, except for a few points.

1) Line 125. The authors added "2% sucrose". Here they must precisely write it as "2% (w/v) sucrose", perhaps.

2) Literature.  Li, Q. et al. must be before the Li, S. et al., I think.

Figure combinations are now quite improved.
Experimental design: Good.
Validity of the findings: Enough good.
Additional comments: As mentioned above in the basic reporting, a few minor points should be fixed.


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: IN VITRO INDUCTION AND IDENTIFICATION OF POLYPLOID NEOLAMARCKIA CADAMBA PLANTS BY COLCHICINE TREATMENT
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have appropriately addressed all reviewer comments. The revised figures are much improved.
Experimental design: blank
Validity of the findings: blank
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: ESTROGEN RECEPTOR—POSITIVE BREAST CANCER SURVIVAL PREDICTION AND ANALYSIS OF RESISTANCE–RELATED GENES INTRODUCTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: line 42-43. endocrine resistant -> endocrine resistance

line 63 The Cancer Genome Atlas

line 135 was -> were

line 148 I would remove the term “Regrettably”
Experimental design: I would have included to the supplementary materials an R script with all commands used to produce figures and analysis reported in this paper.

For example:

# dataset 1 has been downloaded from (link to the file), file name is "RNAseq.txt"

RNA.dataset <- read.table("RNAseq.txt")

#  now make plot of PCA

library(packageX)

png(plot1.png)
plotPackageX(RNA.dataset, makePCA)
dev.off()
Validity of the findings: There are several critical points in this paper.

The first is related to model quality,  in line 157 authors specify that AUC was between 0.686 and 0.714, suggesting that the four-gene risk signature had high sensitivity and specificity. In principle a value of AUC over 0.7 is considered acceptable [1], while a lower value is computed in most of the datasets used in this work (figure 3) . The AUC lower than 0.5  for single genes shows that their performance is a little worse than random, hence it’s difficult to support a method based on these predictors, even if some mathematical transformation is performed on them.

For multivariate cox analysis (figure 2 B),  only WLS has a  p-value < 0.5 and they all show a protective effect (according to the Hazard ratio) that doesn’t make sense at a first glance, maybe it should be better explained.

Figure 2, panel D, doesn't show a clear distinction between "Recurred/Progressed" and "DiseaseFree" patients.

In line 147 authors  claim that WLS and SCUBE2 are protective factors. This is strange, it doesn’t fit with what is reported in literature, for example [2]

References

[1] Mandrekar JN. Receiver operating characteristic curve in diagnostic test assessment. J Thorac Oncol. 2010 Sep;5(9):1315-6. doi: 10.1097/JTO.0b013e3181ec173d. PMID: 20736804.

[2] Stewart, J., James, J., McCluggage, G. et al. Analysis of wntless (WLS) expression in gastric, ovarian, and breast cancers reveals a strong association with HER2 overexpression. Mod Pathol 28, 428–436 (2015). https://doi.org/10.1038/modpathol.2014.114
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: ESTROGEN RECEPTOR—POSITIVE BREAST CANCER SURVIVAL PREDICTION AND ANALYSIS OF RESISTANCE–RELATED GENES INTRODUCTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The title, abstract, introduction, methods, results and discussion are appropriate for the content of the text. Furthermore, the article is well constructed, the experiments are well conducted, and analysis is well performed. The figures are relevant, high quality, well labelled and described.
Experimental design: The experimental design is original and the research is within the scope of the journal. Research question is well defined, relevant and meaningful. The methods are highly technical, ethical and logistical.
Validity of the findings: All underlying data have been provided in detail. The findings are meaningful. The conclusions are well stated and relevant to the research questions.
Additional comments: This paper investigates the reliable prognostic signatures for ER+ and HER2- breast cancer
using TCGA dataset as discovery dataset, and GEO dataset as validation dataset. The authors identified 4 drug resistance-related genes as potential tools for ER+ and HER2- breast cancer risk stratification by developing a nomogram to predict the overall survival. Furthermore, the authors demonstrated the strong correlation between immune infiltration and the expression of these 4 genes or risk groups.

Editorial Criteria
BASIC REPORTING
The title, abstract, introduction, methods, results and discussion are appropriate for the content of the text. Furthermore, the article is well constructed, the experiments are well conducted, and analysis is well performed. The figures are relevant, high quality, well labelled and described.
EXPERIMENTAL DESIGN
The experimental design is original and the research is within the scope of the journal. Research question is well defined, relevant and meaningful. The methods are highly technical, ethical and logistical.
VALIDITY OF THE FINDINGS
All underlying data have been provided in detail. The findings are meaningful. The conclusions are well stated and relevant to the research questions.

Overall, I think this paper is novel and will be of interest to the community of breast cancer genetics, especially ER+ and HER2- breast cancer. The statistical part is valid and makes sense. The authors make it comprehensive by integrating analysis of multiple sources including GEO, TCGA. The main strengths of this paper is that it addresses an interesting and timely question, finds a novel solution based on a carefully selected set of rules and filters. As such this article represents an excellent and elegant bioinformatics study. Some of the weaknesses are the lack of in vitro or in vivo validation experiments. In general, the work is convincing except some major and minor comments below:

Major Comments:

I’m wondering if there are any ongoing clinical trials focusing on the 4 genes identified in this study in breast cancer? It will be very strong evidence for the significance of the current study if so.

I strongly recommend the authors to incorporate more data into their discovery datasets. The authors may also check if there are some consortiums focusing on breast cancer. I know a famous breast cancer dataset hosted in EGA: METABRIC (Molecular Taxonomy of Breast Cancer International Consortium https://ega-archive.org/studies/EGAS00000000083 ).

The Results of the Abstract didn’t mention the strong correlation between immune infiltration and the expression of these 4 genes or risk groups. However, it was mentioned in Methods in Abstract. I would recommend to add the results in the results as well.

Minor Comments:
It is great that a session of abbreviations was there to list all the abbreviations for the database names. I would recommend to also include abbreviations like IDC, ILC, TIL, DFS etc in that list.

All the gene names should be italic for all the gene names.

Figure 6 typo:  replace “t he 22 immune cells” with “ the 22 immune cells”.

Paragraph from line 290: please include the lack of in vitro and in vivo validation experiment as one of the limitations.

Figure 1: replace “37DEGs” with “37 DEGs”.


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: ESTROGEN RECEPTOR—POSITIVE BREAST CANCER SURVIVAL PREDICTION AND ANALYSIS OF RESISTANCE–RELATED GENES INTRODUCTION
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1.	Figure legends for the supplementary figures are missing.

2.	Line98-99, how were the coefficients for each gene computed? Providing more information for clarity. Also elaborate on how a concordance index is used to discriminate and calibrate nomograms in the methods (Line109-110). The global p value for the best model shown in Fig2b should also be reported.

3.	In Figure3, the survival plot figures should include more description, for example, what is the median survival for high risk and low risk?

4.	Line113-114, and Line187, what is specifically the statistical test used to for the pathway analysis? Is it over-representation analysis or gene set enrichment analysis? Need to specify. Also it would be interesting to report what genes/gene sets are altered in expression that led to the altered pathway activity. Were any of the four genes in the signature in any of these significant pathways?

5.	The figure5 needs to show the statistical test used in each case and the number of samples in each group.

6.	How were the columns of Fig6A ordered? Was it ordered randomly or based on the low/high risk group?

7.	The author should elaborate on the interpretation of nomogram and how it can be used to predict the survival of patients.

8.	The r packages used for the analysis should also be cited, such as "rms", "clusterProfiler", "corrplot", etc.
Experimental design: 1.	In this study the authors did a very nice study of breast cancer prognostic biomarker discovery. They first identified genes that are differentially expressed between resistant cell lines and parental cell lines and then they established a link between these genes and survival probability of patients who are ER+ and HER2- . They demonstrated the independent prognostic value of the four-gene based signature and constructed comprehensive models to predict patients DFS. Very well done overall.
Validity of the findings: 1.	For the results presented in Fig6 B, since there are multiple tests for significance, are the P values reported after correction for multiple-testing? It is not mentioned in the body of the text nor legend.

2.	In the multivariate models Fig7 b and Fig7 C, the relative importance of each variable is different, can the authors explain the discrepancy? Also what is the statistical test used to calculate the p values?
Additional comments: 1.	Overall very nice work. Just need to add more description to the figure legends and methods section as suggested above, as well as adding legends for supplementary figures.


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: ESTROGEN RECEPTOR—POSITIVE BREAST CANCER SURVIVAL PREDICTION AND ANALYSIS OF RESISTANCE–RELATED GENES INTRODUCTION
Review round: 2
Reviewer: 1

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