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: ASSESSMENT OF THREE RISK EVALUATION SYSTEMS FOR PATIENTS AGED ≥70 IN EAST CHINA: PERFORMANCE OF SINOSCORE, EUROSCORE II AND THE STS RISK EVALUATION SYSTEM
Review round: 2
Reviewer: 2

Output:
Basic reporting: While I appreciate the authors’ point about the participants aged under 70 being a comparison group, and this would justify their choice of title for the manuscript, this needs to be made clearer to the reader in the abstract, e.g., “Patients were divided into two subsets according to their age: elderly group (age≥70) and younger group (age<70).” could be “Patients were divided into two subsets according to their age: elderly group (age≥70) with a younger group (age<70) used for comparison.” (this could also be made clearer in the methods later in the manuscript) and this should then be reflected in the amount of space the manuscript dedicates to discussing the elderly, younger, and overall results. If the younger group is used for comparison purposes, as the title and authors’ comments suggest, I would expect the results related to them to be secondary in the abstract and manuscript body. At the moment, the entire cohort results are reported, then the elderly, and finally the younger (with approximately equal space for each). If the elderly group is central, they should be reported first and then the younger age group for comparison purposes. I’m not sure that results about the entire cohort are at all meaningful if the focus is on the elderly (e.g., the overall median age of 66 doesn’t make sense to me in this context).

There are still some instances of awkward or unusual wording (e.g. in the abstract “The outcome endpoint of this study was in-hospital mortality.” could written more conventionally as “The outcome of interest in this study was in-hospital mortality.” or similar; “receiver’s” should be “receiver”, see also this typo in the methods). The methods start with “Form January…” Some careful proofreading should fix these as the intended meaning of the text is generally clear. Some typos have also crept into the manuscript with the edits, e.g. “paticipation” and “SionSCORE” in the methods. I won’t list all of the typos here.

My comment that sometimes I was not sure what particular values represent remains, e.g. “an median age of 66.00(60.00,71.00)” might be showing the 25th and 75th percentiles (note that the IQR in this case would be 11 years; this is a single number summary of the variability and not two separate numbers, see: https://en.wikipedia.org/wiki/Interquartile_range) but this is not made explicit.

It’s important that readers with a wide variety of backgrounds can understand most if not all aspects of the manuscript even if things might be obvious for those with a particular background.

By the way, I’m not sure that this information about age should be repeated in both the methods and results (I would suggest that the latter would be more appropriate, although I can see an argument that the methods refer to the database available).
Experimental design: Note that “Mann-Whitney-Wilcoxon test” is not a test “for categorical variables” (see the methods) but a test for ordinal or continuous variables that do not satisfy the assumptions required for a t-test or where a t-test is not desired for other reasons. I appreciate the addition of the level of significance to the methods, and, while pedantic, would also like it made clear that this is a two-sided level of significance (I am assuming this is the case here).

I still have to disagree with “A well-calibrated risk evaluation system gave a P-value greater than 0.05.” as Hosmer-Lemeshow’s test is looking for evidence of misfit and absence of evidence cannot be interpreted as evidence of absence (i.e., a non-significant test does not mean that there was no misfit or that the model is well calibrated, merely that there was no evidence against this hypothesis). Statement such as “SinoSCORE, EuroSCORE II and STS risk evaluation system all showed good calibration in predicting in-hospital mortality (H-L: P=0.411, P=0.113 and P=0.230, respectively)” are misinterpreting the non-significant test result as a positive test result for good calibration.

Again, being pedantic, the number of groups used in the H-L test should also be made clear in the methods.

Note also that “Discrimination (statistical accuracy) was tested by calculating the area under the receiver’s operating characteristic curve (AUC)” isn’t strictly true if the AUC is being reported in isolation—in that case the AUC merely describes an estimate of the model’s discrimination ability.

I would prefer to see false positives and false negatives given much more focus (rather than just in the DCA, which is only very briefly mentioned in the results) as I suspect these are more readily interpretable to clinicians than AUCs (while the AUC does have a precise probabilistic interpretation, this is not well understood, in my experience, among clinicians). This would also support a more health economics interpretation of the results and should broaden the usefulness of the presented results (false positives and false negatives have different implications for both patients and the health system).

A problem with the SDs in the results (e.g. “Expected mortality rate of SinoSCORE, EuroSCORE II and STS risk evaluation system for the elderly group were 1.81±3.50% (95%CI 1.54-2.08), 2.61±1.66% (95%CI 2.48-2.74) and 1.66±2.08% (95%CI 1.50-1.82), respectively.”) is that the SD suggests a 95% reference range that includes negative values. This makes it clear that the expected mortality rates are positive skewed, which is entirely expected, but then contradicts the statement in the methods that “If continuous variables satisfy the normal distribution, then variables were expressed as mean±standard deviation, else variables were expressed as median and interquartile range (IQR).”
Validity of the findings: I remain unconvinced by the statement in the abstract that “SinoSCORE, EuroSCORE II and STS risk evaluation system all achieved positive calibrations in the entire cohort and subsets.” as my interpretation of the results is that all three systems performed poorly and the authors seem to agree with that interpretation in their rebutal. While they are all statistically significantly better than chance, I would have substantial concerns about using these systems in clinical practice given their (to me) poor performance in this population. Perhaps I am misunderstanding exactly what “positive calibrations” means in this context but the next sentence is “The three risk evaluation systems showed good discrimination and calibration in the entire cohort.” and this seems at odds with my interpretation and the authors’ comments in their rebuttal as does the first sentence of the conclusion at the end of the manuscript: “The three risk evaluation systems showed good discrimination and calibration in the entire cohort.”
Additional comments: Overall, I appreciate the authors making several changes in response to some of my comments and I feel the manuscript has improved but I still have concerns about the relative focuses on the entire cohort, elderly subgroup, and younger subgroup and even stronger concerns about the poor performance of the risk evaluation systems being described in such positive terms. I feel that a reader could come away from reading such a manuscript with an overly favourable interpretation of these systems.


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: ASSESSMENT OF THREE RISK EVALUATION SYSTEMS FOR PATIENTS AGED ≥70 IN EAST CHINA: PERFORMANCE OF SINOSCORE, EUROSCORE II AND THE STS RISK EVALUATION SYSTEM
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Thank you for your revisions. I just have two very minor comments to correct what appear to be typos introduced in the latest version of the manuscript.

First, in “Statistical analysis was performed by t-test for continuous variables, Mann-Whitney-Wilcoxon test and Fisher’s exact test or c2 (chi-square) test for ordinal or continuous variables that do not satisfy the assumptions required for a t-test or where a t-test is not desired for other reasons.” the reader might be confused by the order of the material and perhaps something like the following might be clearer: “Statistical analysis comparing groups was performed using t-tests for continuous variables, Mann-Whitney-Wilcoxon tests for ordinal or continuous variables that do not satisfy the assumptions required for a t-test, and Fisher’s exact or c2 (chi-square) tests for categorical variables.”

Secondly, in “The H-L statistic measured the differences between expected and observed outcomes. P-value greater than 0.05 means there is no evidence that this risk evaluation system is bad calibrated.”, I’d use “poorly” rather than “bad”, so “The H-L statistic measured the differences between expected and observed outcomes. P-value greater than 0.05 means there is no evidence that this risk evaluation system is poorly calibrated.”


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: ASSESSMENT OF THREE RISK EVALUATION SYSTEMS FOR PATIENTS AGED ≥70 IN EAST CHINA: PERFORMANCE OF SINOSCORE, EUROSCORE II AND THE STS RISK EVALUATION SYSTEM
Review round: 4
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Thank you for making these minor revisions. I have no further 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: CONSERVATIVE TREATMENT FOR PATIENTS WITH SUBACROMIAL IMPINGEMENT: CHANGES IN CLINICAL CORE OUTCOMES AND THEIR RELATION TO SPECIFIC REHABILITATION PARAMETERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: First of all, the trial evaluates an interesting research question. Its design is be able to evaluate the basic research questions the authors are trying to answer. However, several limitations make the trials results partly invalid.

In general the manuscript is acceptably well written. However, as I am not native English speaking, I would recommend review from a native on this point, as some phrases could be optimized.

In line 28+39, a statement regarding 50% lack in strenght is reported for SIS patients based on ref 3 and 4. When reading reference 3, and 4, I can´t find where the 50% is reported.In general I can only find defiencies up to 37% in ref 4 and 33% in ref 3. Furthermore, reference 4 is based on a biased population of healthy participants working in a healthcare setting, and thereby not equal to a “normal” patient population. As this is a primary argument throughout the article, that patients lack 50% strength in general, and often minor strength gains are obtained in clinical trials, I worry the rationale for the discussion is screwed towards questioning the effect in clinical practice based on a unvalid claim.

Line 164 delete “AND” in “recovery and was collected…”
Experimental design: Line 86-88: I suspect that 10 min. interviewes performed 6 months post baseline, regarding amount of physiotherapy sessions and time spent on exercise, is highly influenced by recall bias. Especially as most patients will have been treated by physiotherapy closer to the baseline measurement then the follow-up time. It could be suspected that in many cases a 3-4 months recall period may influence the data. This should be considered a major limitation of the study results, probably overestimating the number of sessions/minutes performed for gains in function, as patients will tend to overestimate the amount of exercise performed and number of treatments by physiotherapy. This is discussed in the article, however, the potential influence on the results could to be furthere discussed in the article.

Line 92-93: It seems that a new group of testers performed the follow-up testing. Even though the authors present their methods for strength and ROM measurements as being reliable, it would be expected that some inter rater variation could have been introduced. Especially as the raters are students. The authors describe that all raters have trained with the PI. However, I wonder why the healthy arm have not been measured at the follow-up also, in order to minimize this effect, by looking at between arm differences.
Validity of the findings: I am not a statistical expert, but I was wondering if the multiple regression model described in line 193-199 is the optimal method for answering if there is an association between nr of sessions /time spent on exercise results and effect on PRO/Strength/ROM/Pain. It could be speculated that chronicity could have an impact, and maybe duration should be included as a covariate. A scatterplot of change X time/nr of sessions would be helpfull to support the findings from these multiple regressions.

Line 200: A significance level of 0.05 is used. However with the amount of different tests, an ”0.05/number of analysis performed” correction (Bonferroni correction) could be applied, in order to minimize the risk of finding a statistical significant effect by chance.

Line 203-204: What is the reason for not including all 157 patients from the original consecutive cohort?

line 206: The authors report that 63% of the population is participating in the follow-up. This is 63% of the 98 patients treated conservatively. Why not present the actual percentage the sample consist of from the included patients (48%).

Line 290-294: I find it a bit one-sided only to discuss the lack of strength/ROM gain to be an effect of placebo. Several other causes could influence this (e.g. indurance training VS strength training; Remaining amount of pain; Chronicity).

Line 305-316: A 19 points change in SPADI – how is this somewhat disappointing. Several other factors could have influenced this trial results (e.g type of training/amount of training/degree of chronicity in the population) to expect a change in strength. I would recommend minimizing the focus on the lack in strength gains as a consequence of the physiotherapy intervention, when there are so many uncontrolled reasons for why the small population included hasn’t changed. Physiotherapy rehab is much more than giving strengthening exercises – maybe a major proportion have been instructed in performing less work with their shoulder in general, to decrease a potential overloaded shoulder and so on.

I lack an explanation for why the entire group has not been included from the original cohort. When presenting the results from the patients undergoing the telephone interview and the group participating in the follow-up tests, I lack a separate presentation on the group of patient declining from participation in the follow-up (35 patients treated conservatively) – the way the groups are presented now makes it difficult to confirm the statement in line 322-326.

Line 348-349: In general this conclusion is not well supported by this trial, based on the issues mentioned earlier.
Additional comments: Line 239-240: Presenting it as “Surprisingly” that no change is seen in the objective measures is maybe an overstatement. In the trial population, a large percentage does not recover completely, and as long as there is some degree of pain, a significant change in especially strength cannot be expected, as pain will inhibit the MVC. Furthermore, the exercises performed in rehabilitation cannot be expected to focus on strength gain. The authors could maybe have looked at endurance instead of max strength.

Line 251: 50% is used as percentage on how much patients in general lack in strength/ROM. As mentioned previously, I can’t see this statement is not supported by the reference used.

Line 259-261: I would suggest to delete this phrase, as the information is included in the sentence line 255-257.

I would recommend to change the wording to “…findings from ours and some of the previous studies…”

Line 333-336: Please consider to rephrase – I don´t completely understand the point trying to be made.


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: CONSERVATIVE TREATMENT FOR PATIENTS WITH SUBACROMIAL IMPINGEMENT: CHANGES IN CLINICAL CORE OUTCOMES AND THEIR RELATION TO SPECIFIC REHABILITATION PARAMETERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Not clear in many areas.
See separate comment sheet.
Experimental design: Methods need more detail.
Literature review on previous clinical trials looking at strength and needs to be more detailed.
See separate comment sheet.
Validity of the findings: Data collected was lacking key information to make the types of statements made about conservative treatment weak.
See separate comment sheet.
Additional comments: Overall, I can see the value and importance of their main research questions.  However, I think a lot revisions are needed.  The language was not clear and would benefit from a native English speaker to help with awkward phrases and word choices.  I tried to assist with providing examples.

Methods need to be clearer.  Referencing a methodology used in a previous paper may be acceptable but not on key pieces of information that define the patient population being studied.  When making comparisons to previous clinical trials and their data, and when discussing the variability of findings from previous trials,  the authors need to present a stronger case by outlining the types of reviews these were (design, sample size, perhaps provide a summary table).  This would strengthen their paper.

I thought they needed to capture more details on the types of treatments their patients received for the SIS.  The number of hours and sessions doesn't tell you anything about the quality of the treatment and content.  Exercises can mean a huge range of things and so capturing time doing "exercise" can't be translated to all types of practices.  They say that the nature of exercises likely differs between subjects but there is a huge range in what "exercise" could be defined as by a patient's perspective and also by therapists level of training, experience, practice setting etc.

The generalizability of their findings is limited.


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: CONSERVATIVE TREATMENT FOR PATIENTS WITH SUBACROMIAL IMPINGEMENT: CHANGES IN CLINICAL CORE OUTCOMES AND THEIR RELATION TO SPECIFIC REHABILITATION PARAMETERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Table 2:
Title: ”….Assessment those who did not”. I would recommend to add ”And” between assessment/Those.

In general it can be misunderstood when the group who did not participate in follow-up is called “Conservatively treated” – it makes you wonder what the other group (who participated in follow-up) received. Use the same label as in table 4.

Question: “Duration at baseline” – Duration of what?

Table 4:
There is a mismatch between the n in “physiotherapy, %yes” and “Grouped by number of Physio-Sessions” for the “Participants in follow-up assessment” answering “0 Sessions” (16 answering “NO” to physio and 17 answering “0” Physio sessions)
Baseline values: “n=XX” is shifted so the numbers is on two lines.
Experimental design: No comments
Validity of the findings: Answer to my precious "Comment 13":
I would recommend adding that patients declining to participate in follow-up test, probably/might are those who have had the largest positive change. This means that, the significantly less time they have exercised would have an impact on the regressions analysis’s, and this should be pointed out in the discussion section, and not just be rejected as not influencing the results or the validity of the results. (Line 358 to 361 in revised manuscript)
Additional comments: Thank you for considering my previous comments, and acting accordingly. I have no more comments to the manuscripts then the above mentioned.


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: CONSERVATIVE TREATMENT FOR PATIENTS WITH SUBACROMIAL IMPINGEMENT: CHANGES IN CLINICAL CORE OUTCOMES AND THEIR RELATION TO SPECIFIC REHABILITATION PARAMETERS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I had a chance to review this manuscript initially and it has improved sufficiently since then. Most of my concerns were brought to the authors' attention through reviewer #1.  I feel the authors have sufficiently address the concerns.


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

Input:
Title: GENOME-ENHANCED DETECTION AND IDENTIFICATION (GEDI) OF PLANT PATHOGENS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The ability to correctly identify and differentiate between fungal and oomycete species is very important, with significant implications for monitoring pathogens, latent pathogens, and potential pathogens. ITS comparisons alone do not provide nearly enough information to correctly separate closely related species or species complexes, as the authors discuss. As such, use of multiple loci or equivalent screens provide a more accurate tool for differentiating species. The manuscript by Feau et al., describes a detailed pipeline that can be applied to identify taxa and/or clade specific protein-encoding sequences. It is proposed that these sequences can be used to generate qPCR markers that can be used to differentiate species. The computational analysis is supported by application of the generated qPCR primers on a wider range of isolates, supporting the claimed robustness of the assay for the species tested.

As pathogen identification and differentiation is so crucial, designing new methods is important, even if merely to open up discussions among the community about how best to advance/move away from reliance on ITS, beta-tubulin, etc. As such, and as the pipeline seems thorough and well detailed it should be considered for publication after minor revisions. However, I have some concerns and reservations that I believe should be addressed/given some thought during revisions. I outline my opinions on this matter in “general comments for the author” section below.

In general, the manuscript is clear and professional in language

Specific points:

I would remove most of the paragraph from line 73-82. Personally, I don’t think that level of detail needs to be given to outlining PCR (not even sure the acronym needs to be spelt out). Perhaps move the line “DNA detection methods have provided…. Monitoring of invasive species” down to the next paragraph, and start the next sentence along the lines of “However, …”.

Line 145: remove comma after e.g. --- (e.g., same genus…)  (e.g. same genus…)

Line 152 to 157: Confusing/convoluted sentence. I got a little lost with linking the ideas after that semi colon (line 155). Perhaps break these into two sentences, something like “de novo genome assemblies … such as ABySS (etc…)(etc…). Programs such as Augustus can provide a fast way … Gene/protein model predictions from these de novo assemblies.

--- > Further: Perhaps consider re-ordering the module outline. Almost seems that the back paragraphs are the introduction paragraphs. Or perhaps shift a few of the sentences to the front to. E.g. Next-generation sequencing (NGS) techniques constitutes…. In order to maximize the accurate….
	This is stylistic, and can be ignored if the authors do not agree.

Line 172: "with a similarity cutoff defined by a e-value" --> " with a similarity cutoff defined by an e-value"

Line 194: add a comma. “unique, i.e. specific to the target…”

Line 198: add a “to”. “annotation error in target genome or due to gene…”

It is nicely spelt out in line 240 -241 “we obtained the genomes of eight non-target taxa …”. Perhaps similarly spell that out also for the dothideomycetes and rusts. E.g. obtained 39 non-target dothideomycetes.

Line 275: “five ng of DNA” change to “5 ng of DNA” in order to be consistent with the text below e.g. “concentration was at 1 uM”.

Line 287: Filtering simulations: I feel that this section lacks a little clarity. Although these results are listed in detail in the supplementary text, I think the key points summarised here could be more informative than it currently is. For example, it is slightly confusing in the first sentence starts “BLASTn and BLASTp filtering…” but then only BLASTp was mentioned later in the sentence. Since BLASTn was mentioned at the start of the sentence, it should be raised again. If you aren’t interested in discussing BLASTn results, split the sentence in two. E.g. Simulations with BLASTn and BLASTp filtering were conducted on a set of 13 Phytophthora …”. “This analysis demonstrated that BLASTp e-value cuttoff…”

Line 293: “rejected the most potential false positive”  might just be me, but that sentence doesn’t sound right. Perhaps re-word?

Line 313: Perhaps be a little more verbose here and actually state which statistics without going into too much detail (for example N50, completedness, etc.)

Check spelling of Melampsora throughout. Quite a few instances of Melamspora. E.g. in the tables.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: In the discussion, there is a heavy focus on the flaws of using ITS alone. Although true, the use of ITS alone is no longer the norm. As such, it is my opinion that the paragraph discussing the negatives of ITS alone should be condensed.

When I first read the abstract, I initially interpreted lines 36-38 to mean that the authors would take the two polar approaches: 1) to look at taxa specific genes 2) to look conserved genes that could be used as more universal markers. The authors explain their intentions at the end of the introduction (110-113) much more clearly. E.g. I found that “to identify genome regions specific to targeted taxa or groups of related taxa” was clearer than “to identify unique taxon-discriminating genome regions as well as regions conserved across taxa”. Perhaps alter the abstract wording to be clearer.

I have a few major reservations with the outlined approach. These might be based on my misinterpretation, and so I would appreciate a response to these concerns or clearer discussion about potential limitations.

1)	If the approach was used to screen for environmental samples, and resulted in positive amplification of the target genes, can you be sure that the sample isn’t a closely related species that has not been previously not been characterized, and with no associated genomic data? At this stage you would have to amplify and sequence other genes/sequence the genome, and by doing so, would this make the whole method redundant?
2)	Gene loss is quite frequent, and so not having a gene may not actually indicate that an isolate belongs to a different species. Would there be a way to account for this/design an expected species amplification threshold for a given species? Hypothetical analysis with threshold marker; we multiplexed X number of taxon-specific genes, and successfully amplified 80% of these, which is within the acceptable range observed for trial analyses on a diverse range isolates of this species. The pipeline proposed by the authors might work for the tested species, but I wonder how it would work on a species with a high level of genetic diversity/intraspecific gene variation. For example, how would the pipeline work for a related septoria species such as Zymoseptoria, which has an incredibly high level of diversity? This is a species with a lot of genomic data available, so perhaps it could be possible to trial the robustness of the pipeline and see if it holds up on such a species?


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

Input:
Title: GENOME-ENHANCED DETECTION AND IDENTIFICATION (GEDI) OF PLANT PATHOGENS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I found the manuscript very carefully crafted and written.
Raw data can be retrieved from NCBI and other public genome repositories cited in the manuscript. Figures and tables are helpful and done well.

Table 2: « Number of species and genus-specific protein models found after clustering with OrthoMCL and filtering with BLASTn »
Shouldn’t it be « Number of species(…) with BLASTn and BLASTp » ?

L353: polymorphism usually refers to differences within species, not between species (usually called ‘divergence’)
Experimental design: The research question is clear, methodology is sound and well described.
Having read the first sections of the manuscript, I had several concerns with the experimental design, but I found answers to my questions in Text S1.

I have only one minor comment: Orthologous gene clusters are identified using OrthoMCL (L167). I am not a specialist such orthology analyses. But is there any reference that would support the use of OrthoMCL over other orthology analysis tools? Is there any method that could be used in place of OrthoMCL? a method that could even make the filtering steps of Module 3 unnecessary?
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: GENOME-ENHANCED DETECTION AND IDENTIFICATION (GEDI) OF PLANT PATHOGENS
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This manuscript describes in great detail a pipeline which can be used to develop diagnostic PCR assays for a large number of fungal and oomycete plant pathogens, deriving from full genome sequences. The bio-informatics analysis appears robust and is well described. The outcome was the development of a number of PCR assays which can detect a large number of important plant pathogens. Overall the approach is logical and these types of diagnostic assays are a useful resource for field detection of disease, and for early warning of likely disease incidence. I have only a couple of significant criticisms / questions that the authors may need to address.
1. I could see no evidence whatsoever for the functionality of the PCR assays. No gel pictures are included? I think this is necessary to support the stated conclusions, at least as supplementary material.
2. The authors have done a good job in identifying diagnostic regions of genome sequences which can distinguish different fungal species. But I could not determine whether the authors checked that these regions were conserved in the genomes of additional strains of any given species. This is important for them to be truly useful in the face the large genetic diversity (snps etc) which can be detected between different individuals of the same species. Could the authors comment on whether this was done? Or whether they believe this to be important? Perhaps some gels showing the amplicon obtained from different strains of a given pathogen would be useful?


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: 16S RRNA GENE SEQUENCING REVEALS EFFECTS OF PHOTOPERIOD ON CECAL MICROBIOTA OF BROILER ROOSTERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study conducted by Wang et al. describes the impact of three different light regimens on the cecal microbiota profiles of Broiler Roosters. Overall, the topic is very interesting. However, the way the microbiota data has been analyzed, presented, and interpreted, as well as the shallow depth of the introduction and discussion sections, raise many concerns.  English language also needs to be improved. Please find below my specific comments.

Abstract:

- Abstract should be self-explanatory. Define the abbreviations for the treatment groups (LD, CTR, SD, what do they stand for?)

Introduction:

- line 48: Consider paraphrasing  " most of pivotal roles". You mean different aspects of the physiology?

- lines 55-56: photoperiod alters with the community structure of gut microbiota???

- line 57: Gut microbiota is not only made up of bacterial species, but different groups of archaea, fungi, viruses,,,,

- line 63: delete "the role of".

- line 64: most functions of what?

- Line 65: knowledge is limited? So, do you mean there is any other manuscript published in this field? If yes, it should be mentioned in the introduction. If not, then it is a knowledge gap, not limitation.

- Lines 65-67: not common to say "the role of something in the abundance of something else"

- line 66: this study is not evaluating the functional differences. It should be clearly mentioned that "predicted functional properties or genes" have been evaluated. Acknowledge the limitation of prediction in first place. Second, the authors should keep in mind that even if they have done actual metagenomics (shotgun sequencing), changes in functional properties (genes) do not necessarily translate to changes in the functions of microbiota. Interpretation of PICRUSt data should be practiced very carefully in order to avoid provision of misleading information to the general audience of this manuscript that are not familiar with microbiome science.

Overall, the introduction is poorly written, scientific-wise and language. There is no clear link between different sections of the introduction. The authors should identify potential mechanisms by which photoperiod may modulate the composition of gut microbiota. Doing a brief search suggests that in other species (e.g. mice) hormonal changes and gut-brain-axis can play role. The most important link, particularly in broiler, would be the photoperiod-mediated shifts in the feed intake. Of course diet and availability of nutrient are the most important contributing factors to the overall structure of gut microbiota. There is a wealth of knowledge available regarding the influence of photoperiod on the production/performance parameters of broilers (feed intake, FCR, weight gain, etc.) that is being ignored throughout the introduction, and how they can be associated with shifts in the composition of microbiota.
Experimental design: Materials and Methods:

- Lines 69-70: there should be a protocol number or precise reference number for this approval.

- Lines 74-78: Why "LD" is used for Short Day and "SD" for Long Day???

- Lines 79-81: How many broilers in each cage? Does this mean that the feed intake for all broilers has been equal throughout experiment? This needs to be clarified in order to help interpreting the data. If feed intake and feed composition has been equal for all, then compositional shifts in the microbiota can be linked with other factors (e.g. hormonal, gut-brain-axis, etc.).

-Line 80: what is the composition of this "commercial diet"? It should be provided as a table (at least supplementary file). This will be a required infromation for future comparisons of the result of this study with others.

- As a general note, why performance parameters are not accompanying the microbiota data? Weight gain and FCR should have been measured for these broilers. This can improve the analysis/presentation of the microbiota data as well (correlation analyses between performance parameters and microbiota composition/predicted functions).

- line 86: " refrigerator" change to freezer.

- line 96: change 35 to 25

- Lines 111 & 121: Sequence analysis is done using Bioinformatics. Methods should be presented as one section for "Sequence analysis and Bioinformatics" and another section for " Statistical analyses". Or you can combine both.

- Line 126: weighted or unwieghted UniFrac?

- Line 133: "Predicted functional genes"  instead of "microbial functions"

- Lines 111-120: What OTU picking strategy was used? Reference-based or De-novo? If reference-based (closed-reference) script of QIIME, then what percentage of reads were not mapped to database and discarded? This is the main criteria to be considered for validity of PICRUSt data.

- Why not using PCoA or NMDS for visualizing the beta-diversity of microbiota?
Validity of the findings: Results:
-Line 138: Why about?

-Lines 139-141: Not informative. Instead of total and per group reads, the sequencing depth should be specified based on "average number of reads per sample within each treatment group".

-Lines 143-145: these are material methods rather than results.

-Lines 146-147: What is the benefit of reporting per sample data without performing among groups comparisons???

-Line 151: bacterium? change to bacterial phyla.

- Line 161: the other abundant genera,,,

- Line 163: 10 genera, line 165: 5 genera , fix this throughout the text.

-Line 174: why heatmap of genera is reported here in the PICRUSt result?

_line 172: again, these are not functional differences. This should be fixed throughout the manuscript, specifically the discussion.

Discussion:

Discussion in general is very descriptive, repeating the results in most parts. Lots of speculations and non-relevant comparisons between different species of animals.

-Lines 204-207: this is a very loose speculation, changes in the proportion of one genus cannot be translated to change in the metabolite profile of the gut.

- Line 208:  Indicate that you are comparing this with swine studies, etc. And, what is the relevance?

-Line 212: Lactococcus as a metabolite??? There is for sure better way for describing the beneficial role that lactic acid bacteria can play in gut health.
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: 16S RRNA GENE SEQUENCING REVEALS EFFECTS OF PHOTOPERIOD ON CECAL MICROBIOTA OF BROILER ROOSTERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The study investigated impact of three different photoperiod regimes on cecal gut microbiota in rooster broiler chickens. It is admirable that the authors investigated an important aspect that has not been greatly explored in the past. However, that said, I have several major and minor concerns with details of the manuscript, and with the author’s interpretations. Some of these concerns are highlighted here and in the sections that follow.

The English language is a major concern I have with this manuscript, particularly in the introduction section, discussion and in other sections as well (some specific areas are indicated below). This has a major impact on the flow of the text and needs to be improved. For example, the authors can utilize the services of English editors.

The introduction does not clearly and adequately capture the existing literature and clearly state the knowledge gap in the topic of the study. English language is also a major weakness in this section and should be improved. This to some extend applies to the discussion section, which should be improvised as it is not well detailed in relating the current results with literature.

The structure of the manuscript is adequate and the figures are of high quality; however, table 1 should be revised to report statistically analyzed data.
Experimental design: Presentation of the study design is okay but it could have been improved by providing detailed descriptions on various aspects of the study. Specific areas that needed to be improved are shown in general comments section. However, the research question is clearly stated and the study addresses an important area of research.

The authors collected luminal contents from the cecum only. Could they explain why mucosal samples from the same section were not collected/analyzed?  Interpreting temporal changes found in the luminal contents, in the absence of mucosal changes, especially when the birds were indeed slaughtered can be weak without a justification.

The methodologies and statistical analysis used in this study are commendable. However, there are several areas that needs to be improved upon, regarding reporting and presentation of the information (see my comments below). I find some of the description of the analysis methods/ techniques used inadequate and or unclear
Validity of the findings: My concern is the over-interpretation of the data in two primary regards. One, there is no evidence whether the changes observed at phylum level, and at genus levels are indeed due to the light regimes because these could be temporal changes related to diet, housing or generally the management, as there was no baseline analysis that were done in this study to prove that the birds had a similar microbiota profile before the start of the experimental procedures. Second, the interpretation of the data at functional level is to some extent overstated given that very minor changes were observed at this level.

Part of the literature cited in the discussion is not clear how it relates to the current results and may not apply to the current study (e.g Line 213 Fusobacterium in humans).  Line 219 – 220, the rainbow trout study doesn’t mention changes in gut microbiota. However, the authors have acknowledged that these kind of speculations needs further investigations

The abstract conclusion is quite broad and doesn’t clearly capture the main message or conclusion of the study, given its scope. However, this is somehow corrected in the overall conclusion of the discussion section. I suggest that the abstract conclusion be revised to be in line with the overall conclusion of the results reported in this study.
Additional comments: Line 32: Even though the descriptions of the different light regimes used in this study are clearly indicated, the authors did not provide the full meaning of the abbreviations used, as this is the first time they appear in the paper (LD, CTR, SD)

Line 42 – 43: The way this sentence is written is confusing and not clear. It can be improved by revising the sentence structure/grammar

Line 43 – 44: Based on the scope of this study, the abstract conclusion is quite broad and doesn’t clearly capture the main message or conclusion of the study

Line 50: It is not clear what message the authors are trying to put across here. Revising the English language here can improve the sentence

Line 55 – 56: Photoperiod may be,,,,,,,(modify, move or delete this sentence). As it is, it doesn’t have a good connection with the previous or succeeding sections and hence, it interferes with the flow

Line 57 – 65: This section is very confusing and difficult to understand. There is need to improve on the English language (sentence structure, choice of words, flow, etc), as well as on the message the authors are trying to put across.

Line 74 – 76:  The abbreviations for the different light regimes are confusing (long day photoperiod; SD, and Short day photoperiod; LD. Why not the other way?

Group II: Long day photoperiod (SD; 16 h Light: 8 h Dark, i.e. lights on at 04:00 p.m. and lights off at 08:00 a.m). why were the lights not switched on at 8: 00 am as in the other two groups? Also, please explain how was darkness maintained in this group given the fact that the lights were off during the day time?

Line 79: Were the birds housed in individual cages or group? If in group cages, how many birds per cage? Was the 115g/day per bird (in case of individual housing) or per cage (in case of group)

In line 73, the authors mentioned that the birds were kept for 5 weeks, but in line 80, they talk of 20 weeks. Was 20 weeks the period prior to the experiment? Please clarify this. Also, clarify the fact that the feed intake was increased by 5 g every week. Did the increase start after 20 weeks of age (during the experimental period) or when exactly did it start and until when?

Line 83: The authors here mention that the roosters were slaughtered at about 24 weeks of age, which kind of contradicts lines 72 – 73 where they mention 20 weeks of age and 5 weeks photoperiod regime. Please clarify

Line 87: 16S rDNA is mentioned here but everywhere else 16S rRNA gene is used. Try to be consisted and correct this to 16S rRNA

Line 93: gene, not genes

Line 107: The authors mention that Illumina Miseq platform was used for sequencing; however, earlier they indicated that pyrosequencing was used (line 67). Please clarify

Line 122 – 127: Here and in other sections of the manuscripts, the word ‘the’ is overused

Line 138 – 141: Also, include the average number of sequences per sample

Line 142: the subtitle (Validation and structure of the sequences) doesn’t agree with the message communicated in lines 143 – 147. Here the authors mention diversity analysis, which explains microbial community composition/structure as well as diversity indicators such as richness and evenness, which could not be necessarily a validation or structure of sequences.

Also, the authors mention significant differences in data distribution (P<0.01) under unweighted Unifrac distance, but there are no figures/data in support of this e.g PCoA plots that could be associated with the ANOSIM P-value provided here.
It is also not mentioned whether the data is shown or not, because Table 1, which is quoted here shows data for alpha diversity but not Beta diversity.

It is possible that the significance difference reported here could be due to the housing/cage effect, and without the data and or clear statistical analysis reporting it is difficult to attach any significant impact to this kind of results.

The authors need to be clear on the diversity measures that they used. As it is now, they don’t seem to understand the distinction between different diversity measures (e.g beta diversity and alpha diversity)

Table 1: The title should be improved to clearly state the message in the table. Also, the table only shows raw data of the different diversity indices used for each sample, but does not indicate any statistical analysis.

Line 148: at the phylum level
Line 149 and 159: the word occupying is inappropriate
Line 158: at the genus level

Line 173: at functional level

Line 173 – 174: “A heat map indicating significantly expressed genus is shown in Fig.5”. This section is reporting functional level differences but not changes at genus level. Move this sentence to the previous section

Line 202: ,,,some bacteria in rooster gut. As such,

Line 206 – 209: Revise grammar in this section and restructure the sentences


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: 16S RRNA GENE SEQUENCING REVEALS EFFECTS OF PHOTOPERIOD ON CECAL MICROBIOTA OF BROILER ROOSTERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Figure 1 and 2, legends: "Samples are presented along with the horizontal axis and relative abundance at the vertical axis" this description is totally wrong. Please refer to literature to find out more about the definition of these axes and how to describe nMDS and PLS-DA analyses.

Line 180: the most abundant ,,,

Lines 163-165: "The alpha-diversity indices (chao1, Simpson and Shannon index) are reported in Table 1. The results of the beta diversity analysis and the PLS-discriminant analysis are shown in Fig. 1and 2, respectively." You need to report important findings of these table/figures. The table itself is not associated with any descriptive caption. It also does not statistically compare the indices of alpha-diversity among groups.

Lines 224-227: " With the exception of Firmicutes and Bacteroidetes, our results suggest that different photoperiodic regimes could dictate the abundance of some bacteria in broiler rooster gut microbiota. It was noted that Megamonas was significantly more abundant in CTR group as compared to LD and SD groups." Isn't Megamonas a Firmicutes genus? Then why "with the exception of Firmicutes" ? Many of bacteria that you have reported to shift in response to photoperiod belong to Firmicutes and Bacteroidetes.

Lines 253-257: " These findings provide a baseline to be used in further investigation of the factors that may be detrimental in the regulation and control of the functional properties of the gut microbiota. To the best of our knowledge, this is the first report on the effects of photoperiod on chicken gut microbiota which may shed some light on future studies in the field. " these sentences do not add value to the discussion, too vague.


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: 16S RRNA GENE SEQUENCING REVEALS EFFECTS OF PHOTOPERIOD ON CECAL MICROBIOTA OF BROILER ROOSTERS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors addressed all comments adequately
Experimental design: Required details and clarifications were provided
Validity of the findings: Missing information was provided and all concerns addressed
Additional comments: The authors did a good job in revising the manuscript


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

Input:
Title: EVOLUTIONARY RADIATION OF EARLESS FROGS IN THE ANDES: MOLECULAR PHYLOGENETICS AND HABITAT SHIFTS IN HIGH-ELEVATION TERRESTRIAL BREEDING FROGS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The paper needs to be more clearly written throughout to explicitly state the questions and hypotheses tested, the rationale behind testing these hypotheses in this group, the conclusions that can be drawn from these results (within this specific group), and the interest to a broader readership.
Validity of the findings: In general, the manuscript adds to the general knowledge of species’ relationships and how habitat and morphology can shift among closely related species.
I enjoyed the presentation of data but had some trouble deciphering the overarching questions and hypotheses.
The rationale and benefit to the literature need to be more clearly stated in both the introduction and discussion.
Additional comments: Specific notes below:

Throughout the paper the authors sometimes put “eared” and “earless” in quotations and other times do not. Please watch this and be consistent.

The term ‘earless’ has been used to describe complete loss of all middle ear structures by some authors and is also commonly used to indicate only a lack of tympanic membrane. Please define earless for your paper and be consistent in using it only when appropriate for your definition.

Throughout the paper watch consistency of putting et al. in italics or not.

Introduction:
Line 46: Please specify that “the tympanic membrane aids in transmission of” airborne vibrations. A separate system (not including the tympanic membrane) is used for substrate borne vibrations.

End of first paragraph: The opening paragraph ends with an unanswered question regarding middle ear loss, however, this question is not addressed with the data in this paper. It would be better to specifically introduce the questions and hypotheses addressed by these data (including morphological evolution more broadly and habitat shifts).

Line 75-77: There is a lot of evidence to suggest that some alternative hearing pathways are ancestral to anurans and have not evolved in response or association with loss of the tympanic middle ear. Regardless, we cannot currently be sure that extratympanic pathways have evolved in concert with tympanic middle ear loss. All we know is that low frequency hearing is retained in most earless species and in a few earless species there are clearly alternative hearing mechanisms that allow high frequency hearing.

Line 77: Please rephrase “evolved… to” because structures are not evolved “to” do anything.

Line77-78: references appear out of order

Paragraph that starts on Line 98: The body size and other morphological data come out of nowhere and the questions associated with these hypotheses should be presented towards the forefront of the paper instead of only focusing on middle ear loss at the top of the manuscript.
Do these morphological analyses tie into your middle ear loss predictions?

Methods:
246: The ancestral tympanum condition is not determined by stochastic character mapping. The result of this analysis is simply a hypothesis of tympanum evolution for the group.

Line 251: “we used phylogenetic principle components analysis...” Again, body size and other morphology analyses come out of nowhere and the term “morphological data” is vague.

Line 253: The morphological traits should be corrected for body size in a way that controls for phylogeny (see Revell 2009 - SIZE-CORRECTION AND PRINCIPAL COMPONENTS FOR INTERSPECIFIC COMPARATIVE STUDIES).

Results:
Line 305: for the PCA analyses you should quantify shape differences (or lack of shape differences) between eared and earless species and among habitats.
You could do this by comparing morphology among groups (different averages or medians) and/or comparing evolutionary rates of morphology (different amounts of shape change).
Also – you did not set up in the introduction why you would expect different morphologies among eared and earless species. This test should be justified or removed.

Line 321: which of these relationships are significant when controlling for phylogenetic relationships and which are no longer significant? Given some of your relationships do not hold when controlling for phylogeny it is best to be clear what relationships you are confident in (always show a relationship or show a relationship in the most supported model (lowest AIC)) and which relationships are less reliable.

Discussion:
Line 368: This paragraph does not clearly explain what the relationship between habitat, elevation distribution, and body size mean. The paragraph itself jumps around and ends on a note that leaves the reader wondering if the relationships among these craugastorids matters.

Line 386-387: Again, when discussing which morphological associations with elevation it would be best to only point out the relationships that are supported by either all models or at least the best supported model.

Line 412: why would including terrestrial breeding frogs matter? Would you predict terrestrial breeding frogs would follow Bergmann’s rule more so than other frogs? Why?

Supplemental materials:
Some of your museum prefixes in the museum numbers column are not defined in the legend.


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

Input:
Title: EVOLUTIONARY RADIATION OF EARLESS FROGS IN THE ANDES: MOLECULAR PHYLOGENETICS AND HABITAT SHIFTS IN HIGH-ELEVATION TERRESTRIAL BREEDING FROGS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In accordance.
Experimental design: In accordance.
Validity of the findings: In accordance.
Additional comments: Here I return my review of the manuscript entitled “Evolutionary radiation of earless frogs in the Andes: molecular phylogenetics and habitat shifts in high-elevation terrestrial breeding frogs” by Rudolf vom May, Edgar Lehr, and Daniel L. Rabosky. The authors present a new phylogeny of the genus Phrynopus with 11 species never tested before in a phylogenetic context, including the type species, P. peruanus. The authors find that Phrynopus is monophyletic and includes a clade of “eared” and a clade of “earless” frogs, and based on their topology propose P. curator Lehr, Moravec & Cusi, 2012 and P. nicoleae Chaparro, Padial & de la Riva as junior synonyms of P. tribulosus Duellman & Hedges, 2008. Another interesting finding is that members of the genus Phrynopus increase their SVL, and decrease their forelimbs, hind limbs, and snout sizes with the increase of the elevation. The CT scan figures are amazing and the authors show the absence of tympanum membranae and annulus are connected to the loss of columella in at least one species of the genus, P. montium.
The manuscript is a great contribution, it is well-written and I suggest the acceptance considering the following changes:

(1)	The authors must take off the last sentence from the abstract (Lines 32–34) because they do not talk about it anywhere else in the manuscript and also because one cannot predict what clades future analyses will reveal without any evidence.
(2)	The proposed taxonomic change must be in the body of the manuscript, and not as an Appendix. The authors also must talk about these species on the introduction.
(3)	The authors make some confusion in the Materials and Methods part, writing on it part of the Results section (lines 208–215, 217–218, 221–222, 236–238)
(4)	The authors use the substitution rate of 16S as 0.01 bp per million years and they do not say from where they took it. It is the highest mutation rate I have ever seen for frogs and they can either explain from where they took it or take another rate from the literature (e.g. Gehara et al. 2017, phylogeography of I. parva).
(5)	There are many parts in the Conclusion section which are copies of the Discussion section, the authors should take a closer look at it.
(6)    Some museum abbreviations are not explained in the text, so the reader has to guess what does the acronym mean. Additionally, there are a few specimens that are not housed in any museum collection, and only the name of the collector is provided. Is this in accordance with the collection permits? Other Scientists should be able to track the studied specimens after you publish your work, as they will do with your sequences, for example.

These and other minor suggestions and misspelling checks are directly in the pdf.


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

Input:
Title: FUNCTIONAL OUTCOMES AND QUALITY OF LIFE AFTER A 6-MONTH EARLY INTERVENTION PROGRAM FOR ORAL CANCER SURVIVORS: A SINGLE-ARM CLINICAL TRIAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall the manuscript is written using appropriate scientific language in the English language. There is a sufficient list of supportive references. The standard sections and subheadings are used throughout the manuscript as suggested by the journal.
However, the manuscript lacks clarity throughout, and is repeatedly ambiguous. Listed below are several suggestions to improve the manuscript:
1.	The abstract does not clearly describe what exactly the study involves and its subsequent aims. Stating it is exploring an “early rehabilitation program” is ambiguous and fails to report what exactly is meant by “rehabilitation” and what physical areas it encompasses.
2.	Ensure the tense is consistent throughout. Suggest not using the term “was” to report previous literature in paragraphs between lines 67 and 75.
3.	“Advanced treatment technology” lines 49-50 is ambiguous. Does this mean treatment of advanced cancer?
4.	Suggest delete word “cosmetics” line 51 and replace with “appearance”
5.	Suggest exclude “..along with the usual sequelae of oral cancer treatment” Line 52– it is ambiguous and does not add to the sentence.
6.	Line 54 “.. advanced stage..” please describe if it is meant advanced stage of cancer or treatment. Also provide an example of donor site-related impairments.
7.	Remove “.. sublevel IIB neck dissection..” lines 61-62 for same reason given in point 5.
8.	Suggest delete paragraph starting with “Additionally.. “ line 62 as the reason that spinal accessory nerve sparing procedures may experience ANSD is not related to innervation of trapezius from C2-4 cervical branches, but rather that varying degrees of nerve injury can occur with an intact nerve (i.e. neurapraxia, axonotmesis) Please refer to refs 4-6 in your manuscript.
9.	Paragraph from line 67-75 lacks clarity.  This paragraph lists an entire range of possible post-treatment sequelae which aren’t all relevant to the rehabilitation program of the study (for example “.. increased xerstomia..” line 73, “.. speech and social eating” lines 73-74). Instead this section needs to outline what specific physical issues relating to health-related quality of life the study is aiming to address. Suggest replace “.. residual..” in line 68 with “treatment-related morbidity”. Also in this line delete remainder of sentence from “.. ANSD..” and replace with “physical issues”.
10.	Colloquial terms in line 76 “In light of..” and “.. we decide”.
Experimental design: I commend the authors for the effort associated with recruiting such a challenging group of research participants. There is a broad range and large number of outcome measures that were assessed during the study, which overall were well supported with references.
Unfortunately the study design has major design flaws, which mean that subsequently the validity of the findings is inaccurate. These substantial methodology issues are as follows:
1.	The aim is not specific enough in lines 80-85. The term “.. early-intervention program..” needs further description. There is no outline of what therapy discipline the program is entailing and what specific issues. If the program is multi-faceted, then this needs stating.
2.	Further description of participants needed such as location and setting, method of recruitment, area of tumour (please add this to Table 1).
3.	Poorly defined as to what exactly were the physical limitations encountered by the study population in lines 108 “.. the problems suffered as a result of the surgery..” and again in line 129 “.. impairment suffered from the surgery or radiation therapy..” .
4.	The interventions are poorly described in the Methods section, and there is no specific dosage as to the rehabilitation received which is essential when investigating any rehabilitation intervention.  For example what does “.. pain management, edema control etc..” lines 109-110 entail? What is “.. electrical stimulation..”?
5.	There are no supporting references to justify the huge array of therapy undertaken. Additionally, there is poor evidence and clinical reasoning for this program.
6.	No mention of assessor blinding, means there is a risk of bias with this study if the assessor was aware of what follow up time point participants were at the time of assessment.
Validity of the findings: As outlined above, the methodological issues mean that the conclusion of the study cannot be support.
1.	Lack of a control group means that the study lacks the internal validity to aim for evaluation of outcomes due to a rehabilitation program because of potential confounders such as natural recovery. This and methodological flaws mean that the study’s conclusion that rehabilitation is “necessary for oral cancer survivors” is inaccurate.
2.	Recommend providing data as to the type of surgery and tumour site (eg. Tongue, Mandible) in the Results section and corresponding Table.
3.	Please provide reason(s) why 13 participants decided not to enrol.
4.	The drop-out rate of 34% reported is reasonably high.  Data contained in Table 1 reports that 37 participants out of the 65 included participants received radiation therapy. With 30 out of that number dropping out due to the “discomfort caused by RT”, as the CONSORT diagram in Figure 3 indicates, this would mean that for 81% of participants receiving radiation therapy this rehabilitation was not feasible. This result would be an interesting outcome to explore and describe, particularly as there is limited evidence as to the effect of rehabilitation during radiation therapy.

There are some interesting findings from this study such as the feasibility of a generalised rehabilitation program during radiation therapy and changes on a large range of outcome measures (and physical issues) over a 6 month time period. Furthermore, the data collected on return-to-work could be analysed further to potentially provide any association between return-to-work status and vocation type (as per data collected in Table 1) which may be of predictive value and therefore clinically useful information. If any data was collected as to reasons for not being able to return-to-work, would again be of clinical benefit. I suggest the manuscript be re-written to change its focus towards this data, of which a single-arm pilot study can provide valid and clinically-useful data.
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: FUNCTIONAL OUTCOMES AND QUALITY OF LIFE AFTER A 6-MONTH EARLY INTERVENTION PROGRAM FOR ORAL CANCER SURVIVORS: A SINGLE-ARM CLINICAL TRIAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: The outcome measures are well chosen and relevant. And I want to commend the authors for the long follow-up time in this study. If there is anything new in the intervention itself (which there doesn’t have to be!) compared to ‘normal practice’ that could be more clear.
Figures are relevant and of high quality – the photos are very informative.

The following sequences need linguistic editing:
Line 71 – ROM – please note, that ROM is not explained until line 110.
Language in line 76-77
Line 84 instead of  ”the early and the advanced period” I suggest “the early and the advanced stage population eligible for surgery” otherwise it is a quite unclear what you mean.
Language in line 388-89.
Experimental design: Methods are very well described with sufficient detail & information to replicate. Well done!
Validity of the findings: As far as I can see the raw data from the questionnaires is not provided – or perhaps just not labelled in a comprehensive manner?

33 out of 98 discontinued and the intervention is quite demanding. I believe some thoughts on feasibility are required? If you have the possibility to present whether there were any differences in baseline-characteristics of the dropouts compared to the ones who completed the intervention that might help the reader in deciding who the intervention is most suited for.
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: FUNCTIONAL OUTCOMES AND QUALITY OF LIFE AFTER A 6-MONTH EARLY INTERVENTION PROGRAM FOR ORAL CANCER SURVIVORS: A SINGLE-ARM CLINICAL TRIAL
Review round: 4
Reviewer: 1

Output:
Basic reporting: The points raised in the Reviewer comments have been sufficiently addressed and changed.
Experimental design: The points raised in the Reviewer comments have been sufficiently addressed and changed.
Validity of the findings: The points raised in the Reviewer comments have been sufficiently addressed and changed.
Additional comments: The points raised in the Reviewer comments have been sufficiently addressed and changed.


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: FRUIT AND VEGETABLE CONSUMPTION AND ANEMIA AMONG ADULT NON-PREGNANT WOMEN: GHANA DEMOGRAPHIC AND HEALTH SURVEY
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. I would like the introduction to make it clear why the particular hypothesis being tested (that there is an association between fruit or vegetable intake and anemia) is worth examination. It seems that a more general exploratory exercise of examining which characteristics are associated with anemia in this population might have been more easily justified than specifically looking at fruit and vegetable consumption (in the absence of any other dietary data) on anemia. Then the purpose of the study would be to examine where the burden of anemia lies (i.e.: with whom) and behavioural correlates. Because you have no other components of diet, it is very difficult to be sure that any association between fruit or vegetable consumption and anemia is actually specific to this aspect of the diet, or whether fruit or vegetable consumption are just markers of diet quality (and perhaps those eating more fruit are also eating more meat, a more varied diet, or more food in general).

2. Throughout you refer to fruit and vegetable consumption. But you actually looked at fruit consumption and vegetable consumption separately so I think much of your manuscript needs you to address this by changing "fruit AND vegetable consumption" to "fruit OR vegetable consumption"

3. The introduction needs attention in order to improve the English. Specifically, the grammar is confusing.

4. I believe Tables should be standalone- ie: In Table 1 you need to state what the p-values are referring to, either in the table or in the legend. In Table 5, you need to make it clear in the table or legend that the first row is urban women and the second row is rural women (as can be deduced from the text). (Otherwise my assumption would be that the first row was reporting an unadjusted model and the second row was reporting an adjusted model).

5. Line 66 should read "increased exposure *to* pregnancy related complications".
Experimental design: This is an original primary research article within the Aims and Scope of the journal.

The research question needs to be better defined and justified in the introduction (see above).

The methods require more detail and some decisions are not justified.
1. I assume that "a portion" was defined as 80g in order to match the WHO recommendation (ie: of 400g per day)? Please state this clearly if so. Were women told how to estimate a portion, or did they give natural portions and these were converted into 80g portions later?
2. I am not sure why fruit intake and vegetable intake have been examined separately- is there justification for this (e.g.: evidence of a differential effect)? Note that the WHO recommends 400g of fruit *and* vegetables- so describing women's intake as inadequate based on just one of these needs further explanation. If possible a variable which described <5 and >5 portions of fruit and vegetables would be more meaningful (unless there is justification for examining these separately).
3. Given that the DHS collects data on pregnancies/births- I am surprised that you didn't consider this an important variable to examine with respect to risk of anemia (given as you say in the introduction that child-bearing is one of the reasons that anemia is important in women). Parity could have been included as a variable in the multivariate analysis?
Validity of the findings: 1. Findings must be more carefully described
eg1: "the majority of women were aged between 15 and 19" (line 218). This is not true. 21.7% of the population were in that age category according to Table 1, so you can say "the modal age category was 15-19" or "the majority of women were aged 15-29" (because more than 50% of your sample are in those 3 age-categories).

eg2: "considerable difference in participation was observed from poorest and richest households between urban and rural women" (line 227-228). I don't think this is accurate. You are not reporting participation rates here. Do you mean that the richest quintile are over-represented (probably because they are more likely to live) in urban areas, while the poorest quintile are over-represented (probably because they are more likely to live) in rural areas (that is how I interpret Table 1). By using the word participation it suggests that in urban areas poorer women were less likely to participate- but I don't think that is what you mean.

2. All of the variables examined were significantly different between Urban and Rural groups. This could justify why you have stratified your later analyses by place. I think this should be explicitly stated (instead you have only commented on wealth and BMI as significantly different between urban and rural groups).

3. In your multivariate analysis I think it would be useful to see unadjusted, adjusted (as you have presented) and fully adjusted models (including all the variables you considered as possible confounders- because although smoking may not have come out as associated in bivariate analyses, might this be because it was confounded by wealth status in these analyses, but it may still be important in multivariate analysis). I am particularly interested in comparing the unadjusted model to the model after adjusting for BMI (see below...).

4. I feel strongly that the most obvious explanation for your findings is that F/V intake is simply a signal for dietary quality and that this makes it more likely that there is something else about the diet that is the real reason for differential anemia prevalence. I think examining the OR for F+V and for BMI with anemia might suggest that diet quality is associated with anemia and that is a more justifiable conclusion that the one you currently draw. I am keen to know whether the adjustment for BMI had a large effect on the OR for fruit and/or veg consumption and anemia as I think you are more likely seeing an effect of diet quality on anemia.
Additional comments: It is not clear why this particular hypothesis is being tested from your current introduction. Given that this is your hypothesis, I think a variable that looks at fruit AND vegetable consumption is really important.

I look forward to seeing the revised manuscript in due course.


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: DIVERSITY IN ROOT GROWTH RESPONSES TO MOISTURE DEFICIT IN YOUNG FABA BEAN (VICIA FABA L.) PLANTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English is satisfactory and the professional article structure was followed.
Experimental design: The topic of the research is crucial and fit within the scope of the journal.

•	The main concern regarding this experiment is the method used for selecting the potential drought susceptible and resistant accessions. The authors screened a panel of 89 accessions in a well-watered condition and based on the physiological responses like stomatal conductance, leaf temperature, chlorophyll content root/shoot dry matter, eight accessions were selected for further root architecture phenotyping. Although these traits are important, they do not necessarily translate to the ultimate drought resistant phenotype. The drought resistant cultivars can use different strategies according to Levitt (1980) and one of them is increasing the root architecture (mainly observed in water spenders as a avoidance strategy). These complexities of drought tolerance should be acknowledged in the experiments addressing the drought stress. I would also recommend to choose the drought resistant/susceptible accessions directly by evaluating the panel (89 lines) under drought condition and compare the results with the well-watered treatment.

Minor comment:
•	In Line 101 please indicate the type of checks: tolerant or susceptible checks?!
•	Line 102: the final number of accessions were 89 so please simply mention the origin of these 89 lines. What portions is from wet/dry origin? How many from Ethiopia and Europe?..
•	Please mention the growing condition of the 89 accessions. Did you have different treatments (control vs drought)?!
•	Line 117: please use “leaf surface temperature” instead of “canopy temperature” for this sentence and the whole manuscript.
•	Line 117: Instead of “days after sowing” please indicate the developmental stage of the plants. It is difficult to interpret the developmental stage from days after sowing since growing rate depends on several environmental and genetic factors.
•	Line 209: Please put a space in “Chlorophyll concentration was”
•	The structure of Table 5 is confusing. For instance “Well-watered”/”water limited” were repeated in both columns and rows. Why not to replace them with “overall” in the row?!
•	Please explain the abbreviations for each table like SE and LSD.
•	Line 290: Please replace “genotype by environment interaction” with “genotype by treatment interaction”. Environment is usually refer to source of variation in the experiment with random effects.
•	In table 2 and 4 please indicate the values of two checks. Also in Figure 1 highlight the checks.
Validity of the findings: •	It is crucial to assess the correlation between greenhouse results and the phenotypes in the field. Root architecture is highly dynamic and affected by the environmental factors. Using the root architecture parameters as markers in the selection process by breeders is applicable if it is confirmed in the field.
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: DIVERSITY IN ROOT GROWTH RESPONSES TO MOISTURE DEFICIT IN YOUNG FABA BEAN (VICIA FABA L.) PLANTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I believe this experiment was a good use of available resources with the goal to use an advanced root phenotyping technique to identify traits for comparing previously described as being from “dry” and “wet” regions of the world.

1.	Basic Reporting
 Overall, this manuscript is not clear in many areas of the paper and needs to be improved structurally and grammatically. Often, terms are used without being defined or with a reference which makes it difficult to read. For example, not
Line 15: 89 accessions from wet and dry growing regions of the world
	It’s not clear why you chose these accessions, what you mean by wet and dry growing or what regions of the world that would cover. It would be clearer introducing FIGS as early as possible to clear up the confusion.
Line 45 -51: The term fava bean and “crop” is often used but it is not clear if these are interchangeable with fava bean or if “crop” is a more general use.
	You could break up the paragraph by fava bean and other important crops to improve the structure
Line 55 – Define dry and wet regions of the world
Lin 58 – This is an example of structure how you could highlight the importance of your work and have a transition. Here instead you could write the following in your own words.
The fact is that breeders don’t breed directly for root traits traditionally and often focus on yield or resistance to biotic and abiotic stress. FIGS study is a great example of how the important underground structure of a crop is often overlooked, a major factor being the low-throughput and destructive nature of the process. To address this lack of knowledge of below ground contribution to drought stress adaptation, we incorporate high-throughput non-destructive methods.
86 -90 – Needs restructuring

I can’t go line for line throughout the paper but I recommend revisiting the paper and improving the structure and grammar.
Experimental design: 2.	Experimental Design
The experimental questions and design was well defined overall and had useful details so I could compare to previous similar studies.

There were a couple parts that I ask for improvement.

The germplasm was grown at separate times because of a limitation of space. Were there any temperature, humidity or other measurements taken over this timeline? What sort of variation was found between the experimental blocks? Where the blocks randomized within a growing interval or across the intervals. For example, was an accession represented within at each sowing time point?

Improve consistency of the terms such as days after sowing or days after treatment, but in some cases use terminology like “5th week” (Line 18) or “one week later (Line 188)

		Planting and treatment management (portion)
			Were there any rhizobacteria inoculation? Ex Rhizobium leguminosarum
The FIGS paper was referenced when choosing dry-adapted or wet-adapted. Maybe reference table 4 or outline major traits you based your selection for the 89 accessions.
Making the comparison of the automated acquisition of data with wash and preserved roots manually was a very useful comparison to estimate the accuracy of the high throughput technique.
Validity of the findings: 3.	Validity of the findings
The provided data analyses were acceptable, however, there were several opportunities to dig deeper into the data. I suggest reading some papers on high throughput phenotyping.
Dissecting the Phenotypic Components of Crop Plant Growth and Drought Responses Based on High-Throughput Image Analysis
The Plant Cell Dec 2014, 26 (12) 4636-4655; DOI: 10.1105/tpc.114.129601
A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria
Fahlgren, Noah et al. Molecular Plant, Volume 8, Issue 10, 1520 - 1535

Not much detail on the handling of the data, such as a test for normal distribution before using Independent samples test. Any outliers removed? A number of samples equal among all samples?

Germplasm Survey
It was not clear if DAS or DAT were the values taken?? What day were the data collected?

Table 2: Not clear if significant difference were found between wet- and dry- accessions or an ANOVA was used to compare all three. Was the mean take of all replicates first, and how much variation was found within the replicates?

Line 209: Use numbers in the results. A negative correlation is too general of a description, especially when the negative correlation was -0.04

Table 3:
	This should be a matrix with scatter plots and fit line

Line 214: Could use total dry weight by adding root and shoot dry weight

Root Phenotyping

Line 228: DS70622 had the longest 2nd order roots in well-watered treatment, so it is not surprising it has the smallest difference. The same table with percent change would tell us what plant had the smallest change regardless of size in well-watered. How do you determine which number is more useful for drought resistance or avoidance?

Line 236: Were these numbers for all plants, only well-watered or less-watered

Line 238: At the end of the treatment period for all treatments? (or less or well-watered)

Line 248 – 251: How does the author face the difference between well-watered and water-limited lines represented in the rhizotron? Differences between visible roots from each treatment could be significant.

Additional data analysis

Having multiple traits, the author should consider using principle component analysis and other multivariate methods to revisit all of the data.  There is discussion of the time series of the experiment but no figures with days and trait measurements.

Results
Concentrated on outliers as sources for future studies. The figures don’t visually depict the outliers well. The author lists some outliers as max. or min., but it’s too difficult for the reader to make their own comparisons. I suggest ordering accessions by rank either with transformed data or raw data.
Line 279: “The outliers above regression line (Fig. 1)….” This is a great example of when this would be useful, however there is no regression line in the figure.
Overall structure of Results needs work, for example;
Line 272: The first sentence mentions chlorophyll concentration, but discusses root mass fraction in other papers to back up the possibility that RMF as potential source for breeding.
What is more important RMF at well-watered and dry conditions? Less of a root mass reduction in limited-water or percent change of root mass from well-watered to less-watered? It’s not clear why RMF is the major trait focused on except for the fact it was an outlier. More citations of the physiological uses of having higher root mass fraction would help the case. Citations of other correlations in useful, but citations of physiological connection is more powerful similar to Line 294. However, this acknowledge deeps roots is a benefit, not so much root mass overall.
Additional comments: There is no doubt that roots are far behind in the field of plant phenotyping and this paper will add useful results for an important crop combating common issues such as water stress. This paper uses previously defined groups of fava bean with a new high-throughput, non-destructive technique and identifies useful traits for further breeding.
Overall, I think there should be some major changes in the paper which I hope will improve the overall quality of the paper to its highest potential before publishing.


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: DIVERSITY IN ROOT GROWTH RESPONSES TO MOISTURE DEFICIT IN YOUNG FABA BEAN (VICIA FABA L.) PLANTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
Additional comments: I would like to thank the authors for the improvements they have made for the manuscript. I think that is a good idea to look at these results as a root diversity survey instead of direct use in breeding. I still believe the major limitation for this experiment is the lack of germplasm survey (88 genotypes) in water-deficit condition. Stomatal conductance, canopy temperature, chlorophyll concentration and shoot dry weights were measured at well-watered condition. These traits in water-available condition might be independent of the root architecture. Thus using these criteria to choose a subset of potential drought tolerant/susceptible genotypes for root phenotyping is not a very convincing approach. I highly encourage the authors to screen the 88 genotypes in the water-deficit conditions and then choose the drought tolerant/susceptible genotypes based on those results. I highly appreciate the author’s efforts to shed lights on the root architecture, as this is one of the bottlenecks in agricultural researches.


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: DIVERSITY IN ROOT GROWTH RESPONSES TO MOISTURE DEFICIT IN YOUNG FABA BEAN (VICIA FABA L.) PLANTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Overall, this manuscript is very clear in its all subjects under the basic reporting requirements. I have only a few suggestions below:

Line 53: For example, line…. (example of experiment)
Line 193: Could put all traits and descriptions in table format
Line 205: example images in supplementary may be useful (never mind for the rhizo images but could include scan images)
Line 242: Sentence is not clear at first, maybe introduce the concept of a, t x a
Line 245: What percentage on average and did it change for each treatment? Could contribute fewer resources to laterals. You have said you did check this and didn’t find a change, but no change is also interesting
Experimental design: Meets the standards of the aims and scopes for this journal and as a reviewer. The question and hypotheses were well defined and the methods of the project were spelled out in detail and easy to follow their logical approach to test their hypotheses.
Validity of the findings: no comment
Additional comments: The improvements to the paper met and sometimes exceeded expectations.