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: CONFORMATIONAL HETEROGENEITY OF SAVINASE FROM NMR, HDX-MS AND X-RAY DIFFRACTION ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is well written and highly intelligible, with an introduction that clearly and interestingly focuses on the research question with exhaustive references to previous studies and to the techniques implemented. I would only suggest minor adjustments:
1. Specify that room temperature is 25°C for HDX-MS experiments (line 129) since for diffraction experiments it is set to a different value, namely 297K, i.e. 24°C (line 185).
2. When first using the abbreviation RT (line 182), you could specify that it stands for “room temperature”.

Thanking you for providing the raw data following the recommendations stated by Masson et al. (2019), I have to highlight that they show a couple of inconsistencies:
1. In Table S1, the number of replicates is set to 3 while the paper states that (local) HDX experiments were performed in tetraplicate (line 166). In second place, please specify in Table S1 that the units of HDX time course is minutes and correct the sequence coverage (one extra % is present).
2. In Table S1 the number of peptides is set to 106, while in Table S2 110 peptides are present and 112 peptides are declared in the manuscript for the uninhibited enzyme (line 252).
3. In Table S2 the last 32 peptides do not have associated values in the columns “Uptake – Control Sample (D)” and “Uptake error (SD) – Control Sample (D)”. Moreover, it could be nice to have a uniform value for non-performed measurements: in fact, sometimes an empty space is left, other times “NA” or “NaN” are used.

Figures are clear and well captioned, the only typo to be corrected is in the caption of Figure 3-C (it is referred as B instead of C).
Experimental design: No comment.
Validity of the findings: I would strongly suggest inserting the plots showing the results of the analysis described in lines 231-233 of the manuscript.

I disagree with the statement in lines 256-257: “In the most parts of the sequence, exchange occurs on the minute time scale”. I would remove the "most" since looking at Figure S2 the “no exchange” and the “minute time scale” situations are comparable in terms of probability to occur (maybe the "no exchange" situation is even more probable). As no exchange occurs for segments 119-122 and 217-227 (line 264), I would say that no exchange occurs even for other segments like 1-30, 1-31, 1-41, 2-31, 3-31. Anyway, this does not influence the overall conclusion.
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: CONFORMATIONAL HETEROGENEITY OF SAVINASE FROM NMR, HDX-MS AND X-RAY DIFFRACTION ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: In this study, an important enzyme for biological washing applications – savinase – is analysed to answer the hypothesis that it has a specific conformation which confers activity. Multiple biophysical approaches are brought together to yield sub-molecular resolution of structural- and thermo-dynamics: X-ray crystallographic structural models, 1-D and 2-D NMR and hydrogen/deuterium-exchange mass spectrometry. The study provides two alternative active and inactive conformations of the savinase structure and these are annotated with detail of the extent of conformational dynamics, resulting from covalent inactivation by PMSF irreversible inhibition. The conclusion of the study is that there are no significant differences in local or global structure to support the hypothesis that there is an alternative active conformation of savinase.

Communication is excellent.
The study is well connected to the immediate and wider literature. Citations were full and complete, as fast as I could determine.
Enough raw, or processed data has been shared.
Experimental design: The authors perform Student t-tests per peptide per timepoint, which is a very robust statistical treatment of the data. This is crucial to the overall objective here of sensitively comparing two states of a highly stable enzyme and, in particular, to support the finding that there are no significant differences. The study has been performed experimentally and data statistics performed to a high level.

Detail of methods is absolutely fine, as far as I can tell. Certainly enough experimental detail is provided that the experiments could be replicated successfully.
Validity of the findings: Conclusions are supported by the data, with only minor comments (see below note).
Additional comments: Major comments:

No major criticisms found.

Minor Comments:

1.	The NMR and MS methods employed here are ensemble methods. Please can the authors comment on the extent that their measurements conclusively refute the existence of a sub-population of the alternative conformation that was indicated by NMR relaxation data. What fractional population would be required in order to be detected above noise in this dataset?

2.	I recommend adding a volcano plot of the HDX-MS data, as this would make for a simple communication of the hybrid significant differences between the savinase states – or lack thereof. This was shown to great effect in Hageman & Weis which the authors have cited here.

3.	HDX data for some peptides is absent or incorrectly isotopically assigned for the PMSF state in S2:
•	208-226
•	209-226
•	209-227

4.	Page 14 line 289: Quantify “major differences” between crystal models. Is there a threshold of Å displacement that qualifies as a major difference?

5.	Mentioned in a few places (e.g. Page 13 line 233): What was the non-linear model used in the F-test? Can the authors please provide a supplementary figure that locates the pseudo-random distribution of these deviating residues (e.g. highlighted on the structure)? Perhaps it is meant to be clear from Fig. 1, but I didn’t find this the case.

6.	Figure 3 Legend: “side-chain ꭓ1 dihedral angle” formatting error.


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: CONFORMATIONAL HETEROGENEITY OF SAVINASE FROM NMR, HDX-MS AND X-RAY DIFFRACTION ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Everything I asked for has been updated I have no further issues
Experimental design: Everything I asked for has been updated I have no further issues
Validity of the findings: Everything I asked for has been updated I have no further issues
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: CONFORMATIONAL HETEROGENEITY OF SAVINASE FROM NMR, HDX-MS AND X-RAY DIFFRACTION ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Communication in the paper is optimal: the article is highly intelligible and well referenced.
About HDX-MS raw data (Supplementary Table S2): the fully deuterated reference sample is missing for the last 32 peptides. I strongly recommend to insert these data, otherwise such peptides could not be used by an external user. In fact, normalization expressed in line 179 would not be possible.
Experimental design: The research question is well defined and opportunely addressed in lines 89-97, providing further proof of the clarity of the paper.
The different methods implemented to probe Savinase testifies a rigorous investigation of the protein's dynamical behaviour.
Validity of the findings: The conclusions are well stated and the findings are supported by a sufficient amount of data.
Additional comments: The paper is well written, the research question is clear and well addressed.
The only critisism I have is about HDX-MS data (Supplementary Table S2) since uptake values for the reference samples are missing for the last 32 peptides. Once these values have been added, the paper deserves to be published.


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: CONFORMATIONAL HETEROGENEITY OF SAVINASE FROM NMR, HDX-MS AND X-RAY DIFFRACTION ANALYSIS
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I recommend that this manuscript is acceptable for publication following the amendments.


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: QPCR MULTIPLEX DETECTION OF MICRORNA AND MESSENGER RNA IN A SINGLE REACTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: In general, the reading of the article flows, thanks to the quality of writing, the manuscript is clearly written and the length of the article is good. Perhaps, a few words in the scientific context could be improved; for example, the word “patriarch” in line 49, and the word "governing" in line 61, could be changed for other words more correct. Moreover, I advise using keywords that do not appear in the title of the article, to take better advantage of search engine efficiency. Other minor observations, at lines 58 to 71, I noticed a lot abbreviates in the same paragraph that rest clarity to the sentences, I advice to rephrase them.

On the other hand, I think the introduction needs new recent references, the newest reference cited is from 2015, is five years old. The Structure of the paper was according to the PeerJ standards, discipline norm, but can be improved for clarity. I consider that the figures are relevant, have high quality, are well labelled & described. Lastly, I found that raw data supplied is enough and necessary.
Experimental design: It seems to me that the content and theme are congruent with the contents presented in your magazine. The question of investigation, hypotheses and objectives are easily identifiable, although they are not preceded by declaratory phrases such as: "the objective of this investigation was ..."

The validating technique is novel and useful to increase the knowledge of the study area. I could see that they have clarified having made 3 technical replicates per analyzed sample, complying with the sampling requirements to reduce the variability of the data and to confirm their validity. However, I recommend improving the phrases or sentences of lines 144 to 151 to clarify the way in which the experiments were related.
Validity of the findings: I consider that the data is sufficient to validate the findings reported and the speculations made by the authors are mentioned as such in quantity within the permissible limits. All underlying data has been provided; they are robust, statistically sound, & controlled. Conclusions are well stated, linked to original research question & limited to supporting results.
Additional comments: The manuscript is useful in a rising research area within gene expression regulation by small RNAs. One question about the biological samples, do you have informed consentiment forms for all of them? I noticed only one is shown. Why did you named the approach RNAmp? could you describe the meaning at the paper? Did you sequenced the PCR products?


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: QPCR MULTIPLEX DETECTION OF MICRORNA AND MESSENGER RNA IN A SINGLE REACTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: I commend the authors on the clear and unambiguous, professional English that was used throughout the article. Sufficient background/context was provided and appropriate literature was cited throughout. The article was of professional structure and the raw data and tables provided were clear and transparent. While the hypothesis is very clear, some additional information on how this research is useful to the wider field would be beneficial. Some sections that require modifications or additional clarity are listed below:
Line 31-32: Please consider rephrasing this sentence. A Suggestion: “Our approach termed RNAmp enabled parallel measurement of miRNA and mRNA expression from various cell lines”.
Lines 36-37: Please reconsider the use of the word “sensitivity”. See general comments in Section 4 below.
Lines 58-71: Although you have mentioned that this process requires cDNA synthesis followed by qPCR. I think it is important to highlight that this is a two-step process (i.e. two separate reactions performed in two separate reaction tubes, requiring different reaction components etc.). It would be very convenient if these could be performed together in a single reaction vessel (similar to regular RT-PCR). Is there possibility for this in the future? If not, what are the limiting factors? This could possibly be discussed in the discussion/future work section.
Lines 68-70: You have mentioned one difference between miRNA and mRNA cDNA synthesis (i.e. different primer technologies). Could you please also highlight some of the other differences (e.g. different temperature and enzyme concentration requirements). Do you know why they currently have different requirements?
Lines 72-78: Please explain why it’s important for researchers to detect miRNA and mRNA in parallel? What information does this provide?
Lines 79-87: How do the hydrolysis probes work for miRNA and mRNA? Are the miRNA and mRNA detected using the same probes and in the same fluorescent channel (is it an accumulative signal when miRNA and mRNA are analyzed together?) or are they differentiated? i.e. miRNA and mRNA each produce signal in a different colour channel.
Experimental design: This manuscript is original and is within aims and scope of the journal. The research question is well defined, relevant and meaningful. The authors state how this research fills an identified methodologies gap, however additional information on why researchers use these methodologies would be beneficial. The authors demonstrate rigorous investigation, performed to a high technical & ethical standard. The methods are described with sufficient detail. Some sections that require minor modifications are listed below:
Line 100: “Serum samples were cancer patients and healthy …” Suggestion: “Serum samples were from cancer patients and healthy…”
Line 117-135: My recommendation would be to include this table in the main text and remove the in-text description (Lines 124-135). The in-text description could instead include a broader description about the three cycling conditions and what each of them are used for (please see an example below).
Example for broader in-text description: Three different cycling conditions were performed and are described in Table X. Cycling condition 1 uses stem loop primers for miRNA synthesis as per manufacturer's protocol (Applied Biosystems). Cycling condition 2 uses random primers for coding gene synthesis (i.e. mRNA) as per the manufacturer's protocols (Applied Biosystems). Cycling condition 3 uses a combination of random and stem-loop primers for simultaneous duplex detection of mRNA and miRNA in a single reaction.
Line 138: Please include an introductory sentence to let the readers know why you are testing different reaction volumes.
Line 138: What did you use to dilute the cDNA? Was it dH2O?
Line 140: Again, my recommendation would be to include this table in the main text. These tables are very clear and informative and are easier to follow than the text. You could instead include more generic text about why things are being done. E.g. Why is only 0.8x master mix used for 2.5 uL reaction when 1x master mix is used for all other volumes?
Line 141: Perhaps a table outlining which fluorophore belongs with each target and which targets are duplexed together? I sometimes have trouble following this.
Line 144: Please change “1x volume of Taqman Universal…” to “1x concentration of Taqman Universal…”.
Line 183-191: Please clarify here if Cq was determined using LinReg analysis methods?
Validity of the findings: The authors demonstrate meaningful replication by testing with a range of different mRNA and miRNA biomarkers.  The authors have provided all underlying data which are robust, statistically sound, & controlled. The Conclusions are well stated, linked to original research question and are limited to supporting results. I would like to remind the authors that speculation is welcome as long as it is identified as such. Some sections that require minor modifications or additional clarity are listed below:
Lines 197: Please reconsider the use of the wording “increase in qPCR sensitivity”.
Line 206: See above comment
Lines 209-217: Please include a generic statement that highlights this is duplexing two miRNA as opposed to multiplexing miRNA and mRNA (which is discussed later).
Lines 227-235: Can you comment on whether this is an expected finding for qPCR of miRNA and mRNA? Are there any references in the literature to support these findings? Do you have a theory or any speculation as to why this could be? What exact reaction volume was used for these experiments? I can only see that it says “low volumes”.
Lines 237-254: Very interesting. Do you have any theories as to why it was improved using RNAmp? Also, which genes are the miRNA machinery genes?
Lines 248: Wording regarding increase in “sensitivity”. (See general comments below).
Line 250: See comment above.
Lines 360-363: Could you please elaborate on this comment. As far as I am aware, most PCR machines are limited to 5-6 fluorescent channels. Are there other machines with 12 fluorescent channels? Or are you able to detect multiple miRNAs/mRNA/ncRNAs per channel?
Table 1: Perhaps indicate that these PCR efficiencies are for singleplex qPCR reactions.
Table 2: Are these PCR efficiencies for singleplex or multiplex qPCR reactions?
Figure 1: Wording around sensitivity. See general comments. Are the results in Figure 1 singleplex or Multiplex reactions? Please include the amount of RNA added to reactions.
Figure 2A and 2B: Should these graphs say “Reaction Volume” or “Starting template Concentration”? What volume were these reactions performed at? The methods say low volumes, but not exactly which volume.
Figure 4: For the Figure legend, perhaps you could include in brackets which channel was used for JAG-1 and mir-21?
Additional comments: 1.	Throughout the article you discuss that using a lower reaction volume results in an earlier Cq which suggests increased sensitivity. In PCR, sensitivity represents the smallest amount of substance in a sample that can accurately be measured by an assay. Do you have any data demonstrating that lower reaction volumes improve the limit of detection (LOD)? By this I mean, can you detect lower concentrations of miRNA/mRNA using these lower volumes? If not, my recommendation would be to change the wording of ‘improved sensitivity’ throughout the manuscript. The lower Cq values indicate an earlier or faster detection. However, without testing lower target concentrations and determining the LOD at each volume, I am not sure if it can be assumed that using a lower reaction volume results in better sensitivity.

2.	Supplementary Tables 2 - 4 are clear and informative and my recommendation is to include these in the main text. Furthermore, the in-text descriptions could be removed/modified.

3.	For the raw data, it looks like technical PCR replicates were performed in triplicate? Could you please confirm this in the methods section?


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

Input:
Title: SEARCHING FOR A SIGNATURE INVOLVING 10 GENES TO PREDICT THE SURVIVAL OF PATIENTS WITH ACUTE MYELOCYTIC LEUKEMIA THROUGH A COMBINED MULTI-OMICS ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Complete review submitted under "General comments to the author."
Experimental design: Complete review submitted under "General comments to the author."
Validity of the findings: Complete review submitted under "General comments to the author."
Additional comments: By employing data garnered from public databases, the group describe establishment of a predictive 10-gene signature profile for over-all survival in acute myeloid leukaemia.
The findings are consistent with previously published data, with minor progress in understanding within the field.

Major points
Several major comments which require either supporting data and/or written clarification before acceptance for publication are:
1/ A fundamentally important criteria is the establishment of cut-off values in categorising low v high expression and hence low v high risk.
Line 189: “The training set samples were divided into high and low expression groups according to the medium expression of these 10 genes, ...”
This is unclear.
The authors need to explicitly justify the cut-off criteria and explain the imbalance of the dataset between the training versus test sets – high-v-low risk Fig5 57v45, Fig6 70v57, Fig7 37v35 and Fig8 66v58 (which may have introduced bias within the analyses.)
Other arbitrary cut-offs are applied with WBC (set at 20) and staging (M0-M3 v M4-M7)

2/ Similarly, the authors fail to rationalise why comparison to the other models is made at 80-months and beyond (Figure 14). Given the patient and disease evolution biology, it is unlikely that diagnostic material from 6 years previously will be used in patient management strategies.
3/ Although data may be limited, substantial knowledge may be gained if the gene signature was determined as a measure of relapse/resistance to therapy.

Minor points
Given the central point of this report, the construction of the 10-gene signature requires further elaboration, with more detail of the steps employed in the R-package as well as analysis applied in accordance to the AIC.
Although the reporting is on the whole clear and systematic, with supporting explanations; the manuscript requires re-writing by a native English speaker with scientific knowledge in the field. Apart from the abstract, several phrases and reference points are inconsistent and ambiguous e.g. Lines 61-62, 214, 216, 235, 285 and throughout the ‘Discussion’.

Figure labels lacking:
Figure 5-8
A: lower chart referring to overall survival: X-axis label is lacking. Is this log or linear expression value? Can the heat-map be segregated into low v high risk strata?

Although informative, all 14 figures do not need to be within the main body of the manuscript. Some of the figures (for example from Figures 5-8) could be migrated to the supplementary sections.

What are the units for WBC?


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: SEARCHING FOR A SIGNATURE INVOLVING 10 GENES TO PREDICT THE SURVIVAL OF PATIENTS WITH ACUTE MYELOCYTIC LEUKEMIA THROUGH A COMBINED MULTI-OMICS ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language used needs significant editing. Although the text is understandable, it contains unusual word usage, grammar errors, typos, and long, complicated sentences. Already in the title:

Title “survival for patients” => “survival of patients”
Title “through the combined” => “through a combined”
Line 19 “multi-omics datas” => “multi-omics data”

The background is properly referenced and previous similar signatures are discussed. However, the paper contains an extensive number of figures, that are unnecessary and some of most of them are unreadable. Figure 1 and 2 are summaries of already existing results from TCGA. This is unnecessary. Figure 3 is almost unreadable and the colors are hard to see. Figure 4 doesn’t add much information to the paper, Figure 5 – 8 have exactly the same layout and data type showing different datasets. These last 4 figures should be summarized into a single figure, showing the most important finding. Figure 9 should be a supplementary material figure. Figure 10 and 11 contain 13 KM curves. Again, these should be condensed into a single figure/panel showing the most relevant information, illustrating the paper’s results. Figure 12, 13, and 14 are probably the most important results, but they also have a low resolution, with hard to read text.
Experimental design: The experimental design is acceptable, even if the paper only uses already published data, it is analyzing this data in a new way. However, the methods used are unclear.

-	When did the authors download the data, and exactly which version?
-	What does “TCGA RNA-Seq data of SNP 6.0 chip” on Line 96 mean? Are the authors talking about RNA-seq data or SNP chip data?
-	How did they process the GEO datasets? Apparently, these GEO datasets contain raw CEL files, and the authors do not describe any data processing steps for them.
-	What does “those with marked correlation with patient overall survival” on Line 106 mean?
-	On Line 104: how was the analysis carried out. OS was correlated with what? Mutation status? Expression level? Something else?
-	The description of methods is confusing at times. For example, the authors write in Line 109 “this study used the GISTIC 2.0 software”. Did the authors use GISTIC themselves, or only refer to the methods used by TCGA?
-	The above question is true for the Mutsig analysis.
-	On Line 119 and 126 the authors write several times “… function of R package”. What does this mean? There is no general “R package”. The text needs to be clarified, to include the specific functions used from specific R packages.
-	The functional enrichment analysis is not described in detail.
-	How was high-risk and low-risk defined?
-	The results section also contains some information that should go into the Methods section, for example Line 148, 196, 235, 272.
-	The exact version of the various R packages is missing.
-	On Line 196, what does “z-score processing” means?
-	Unclear how the stromal, immune and estimate scores were calculated for Figure 2. Line 235 mentions an “estimate function of R package” but there is no such function in R.
-	On Line 272, how was the GSVA score calculated and how were the signaling pathways defined?
Validity of the findings: It is hard to assess the validity of these findings, as the Methods section lacks important information and the included descriptions are unclear. The large number of Figures, without highlighting the most important details, is also confusing.
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: SEARCHING FOR A SIGNATURE INVOLVING 10 GENES TO PREDICT THE SURVIVAL OF PATIENTS WITH ACUTE MYELOCYTIC LEUKEMIA THROUGH A COMBINED MULTI-OMICS ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have sufficiently addressed all major concerns and have significantly improved the manuscript to the level fit for the journal.
Experimental design: Consistent with the standard protocols and described with the necessary detail.
Validity of the findings: Sufficiently addressed in the rebuttal.
Additional comments: 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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The manuscript was written in clear and unambiguous, professional English used throughout but authors should correct syntax errors in the following part of the manuscript:
a) Line 49: The use of 'diseased people' is generic in the context which authors used it. Authors should clarify if this description encompasses people with other transmissible diseases such as HIV, Hepatitis B virus etc, as they also come under the category of 'diseased people' as used by the authors.
b) Lines 162-163: '......where we found that....more an airport shows closeness centrality.....'

2. Although, authors provided sufficient introduction and background to demonstrate how the work fits into the broader field of knowledge. However, various statements in the introduction were not referenced. Authors should provide appropriate references to the following sections highlighted in the reviewed manuscript:

a) Line 41: Nigeria has a population of 206 million, similar to that of Brazil (209 million)

b) Lines 42-46: The use of 'claim' in the sentence sounds judgmental and may imply that the authors had pre-conceived bias as they did not believe the actions reported by airport authorities in India and Nigeria, but believed the Brazillian authorities. This becomes relevant because the findings of the study contradict the position/views of the authors. Authors should consider backing up this statement with appropriate references.

c) Lines 306-312: Authors should cite these URL with appropriate references properly, including the accessed dates
Experimental design: 1. The article described original primary research which aligned with the scope of the journal. Authors should include in relevant section of the manuscript that 'ethical approval was not obtained or required because human participants were not involved in the study'.

2. Although the analysis reflected acceptable scientific rigour, the assumptions made in modifying the SIR model would benefit further explanation and justification:
a) Lines 94-95: This statement is not consistent with known aetio-pathogenesis of COVID-19 transmission. Usually, the index case or first occurrence is imported into the country via air travel by a person who visited an affected area. When the index case arrives their destination, transmission occurs by air droplets from the index case via coughing, sneezing, touching the infected surface areas, social interactions such hand-shaking etc. Authors should kindly check the following references and consider revising the assumption on which the modified SIR model was based: https://www.cdc.gov/coronavirus/2019-ncov/prepare/transmission.html;
https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.8.2000097

b) Lines 109-110: Authors described the first modification of the two modification of SIR model, but it is difficult to locate the description of the second modification in this section. Authors should clarify if the linear model described in the method section is the second modification of SIR model. If not, authors should describe the second modification clearly.

3. Line 39: This statement is debatable because COVID-19 was first reported in Egypt on 14 Feb 2020, ahead of Nigeria which was reported on 27 Feb 2020. Author should consider revising the sentence to read that Nigeria was the first country in sub-Saharan Africa to detect COVID-19.

4. Line 133: Assumptions in mathematical modelling usually mirror realistic estimates as much as possible. In real life, disease expansion for a highly contagious SARS-nCoV2 is much shorter than 90 days. For the conclusions of this study to benefit and shape public health policy, authors should consider re-visiting the estimated disease expansion or provide further justification to use 90 days in the context of a very rapidly expanding COVID-19.

5. Lines 135-136: This hypothesis has been recently disproved because about 14% of people who recovered from COVID-19 still carry the virus and can potentially infect other people. This does not support the theory of resistance being argued by the authors.
Authors should kindly refer to these reports and revise the hypothesis accordingly: https://jamanetwork.com/journals/jama/fullarticle/2762452
https://onlinelibrary.wiley.com/doi/full/10.1002/jmv.25685
https://www.forbes.com/sites/brucelee/2020/03/15/can-you-get-infected-by-coronavirus-twice-how-does-covid-19-immunity-work/#6b0f9e115c0f
Validity of the findings: The criteria for this section were satisfactorily met
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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see the review.pdf attached
Experimental design: Please see the review.pdf attached
Validity of the findings: Please see the review.pdf attached
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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 1
Reviewer: 3

Output:
Basic reporting: It would be great for the authors to highlight any existing measures already put in place at the airports and the gaps identified which then should form the basis of their model.

Line 26 and 27: there is need for a reference and suggestions below for the authors to consider; Novel Coronavirus (2019-nCoV) SITUATION REPORT - 1 21 JANUARY 2020
https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200121-sitrep-1-2019-ncov.pdf?sfvrsn=20a99c10_4 and A Novel Coronavirus from Patients with Pneumonia in China, 2019 https://www.nejm.org/doi/pdf/10.1056/NEJMoa2001017?articleTools=true

Lines 30-33; There is need for a reference as well since the authors are highlight data that should be publicly available. By not citing, they make it difficult for the reader to try and look it up.

Line 39: This statement is inaccurate;  “Nigeria, since it was the first country to detect a COVID-19 case in Africa” The following is what is correct and the authors should consider revising it and I have included references for the same. Nigeria was the 1st country in sub-Saharan Africa to report a COVID19 confirmed case but third in the entire continent after Egypt and Algeria. COVID-19, Situation 1 update for WHO African Region https://apps.who.int/iris/bitstream/handle/10665/331330/SITREP_COVID-19_WHOAFRO_20200304-eng.pdf and Coronavirus disease 2019 (COVID-19) Situation Report – 26 https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200215-sitrep-26-covid-19.pdf?sfvrsn=a4cc6787_2

Line 40; For this statement, “Nigeria displayed less than 10 confirmed cases during the same period of time”, cconsider referencing this Nigeria Centres for Disease Control link for that information. https://covid19.ncdc.gov.ng/

Line 47-49 : “For this statement the government decided to control the airports, avoiding the entrance of people coming from Europe or Asia” By writing “avoiding” do you mean do you mean entry of passengers was stopped from these 2 continents? If so, please consider changing the word to ‘restrict’.

In line 48: What are these control measures? Were any existing before. May be good to give the reader an idea of what was done.

Line 49: Consider changing this statement “Hence, the entrance of diseased Brazil has been occurring” to “Hence, the entrance of potentially exposed passengers to SAR-COV-2 to Brazil has been occurring’. As written, it denotes occurrence of the disease withing the country, yet I believe the message being conveyed is the arrival of passengers who may be already exposed to COVID-19

Line 52: Consider changing “his/her living networks” to ‘potential contacts’ to underlie that monitoring needs to happen at the very of the case and contacts which is crucial in determining transmission dynamics and to put in place measures to disrupt transmission or contain the disease.

Line 53: Consider deleting “that with which were are living with”. It is confusing and without it the message remains unchanged and is clearer.

Line 79: Consider the word ‘introduction’ instead of the used one “invasion”
Experimental design: 154: The authors meant from the statement ‘fast’ instead of what is written “first”. Kindly correct.

162” Add the word ‘the’ to make the statement complete.

175: There needs to be a reference of where you obtained the information about Manuas being the 1st Amazonian city with confirmed cases as of 17th March.
Validity of the findings: It would have been a good idea to summarise the model results in the first statement before stating the statement in 186. The message really is that there will be an exponential rise in cases by more than 50% within 3 months perpetuated by lack of intervention measures at the airports.

189-195: The authors need to add the reference. It makes it easy for a reader to look it up and these are data that has been generated by the relevant instructions thus should be available.

Line 199-203: It may be helpful to give the specifics of what India was doing different to Brazil for their case count to be low as described in the statement. What is written is general thus does not provide the reason why India was deemed to manage the situation better than Brazil.

Line 211-213: Is it really that majority were asymptomatic, or they have entered the country at the early stages of incubation period even before the latency period was over?  Kindly look at these manuscripts below talking about CODID19 asymptomatic carriage. Asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Facts and myths. https://www.ncbi.nlm.nih.gov/pubmed/32173241 and Presumed Asymptomatic Carrier Transmission of COVID-19 https://jamanetwork.com/journals/jama/fullarticle/2762028

Line 227: Consider using ‘account for’ instead of “quantify” so that the statement reads; “Another weakness of the model is that it cannot account for a great number of small airports not registered for commercial flights”.
Line 232: Delete “as”.

Figure 1. It may be helpful to show the main international airport as a reference point for the reader who is not conversant with the region. In line 146 reference is made to São Paulo and Rio de Janeiro airports as main hubs. This could be indicated in the figure.
Additional comments: Thank you for the opportunity to review the paper

This is a great paper trying to project the magnitude of COVID19 in country following introduction through air transport. It is a vital piece of analysis that can help policy makers and those in charge of the Response team to make timely and objective decisions. Thank you for putting it together. Find my comments below.

There is a lot of factual information cited but not referenced. Kindly ensure this is done. I have tried to include references in the specific comments for your consideration and feel free to use others sources that you are comfortable with.

Different fonts and size used in the narrative. i would imagine this would be handled during when setting the manuscript for publishing if approved.

The authors use Nigeria and India as comparison for the measures put in place but they do not mention specifically what was done in those countries and further in the discussion provide different scenarios of the outcomes if some of these measures are put in place.

The reference list in line 306-312 should be inline where cited. As current structured, it is a bit confusing and time consuming for one to figure out where they are used.

In the conclusion in the first paragraph, it may be good for the authors to provide specifics of the measures that need to be undertaken and how that relates to the model.


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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 2
Reviewer: 1

Output:
Basic reporting: Satisfactory
Experimental design: Satisfactory
Validity of the findings: Satisfactory
Additional comments: Authors have addressed concerns raised by the reviewer and made necessary corrections. Nevertheless, authors are encouraged to correct the following items and the Editorial team should kindly confirm these are done before publication of the manuscript:

Line 26: The opening statement (In the last few weeks) is currently not consistent with time evolution of COVID-19 pandemic. Authors should consider revising the phrase to reflect the COVID-19 timeline.

Line 27: 'Stealth transmission' has ceased to be the main route of COVID-19  transmission. Despite strict lockdown and restrictions placed on air travels in most parts of the world, COVID-19 transmission has not only remained unabated but is increasing at an exponential rate with Ro greater than 1 in several parts of the world. Authors should consider revising this statement to reflect the current transmission dynamics of SARS-CoV-2

Line 267: Author should consider supporting the sentence (Nigeria, a country poorer than Brazil) with a reference


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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 2
Reviewer: 2

Output:
Basic reporting: In this paper, the authors investigate a scenario of COVID19 spreading in Brazil through the air-transportation network for 90-days after the first incidence. They use an SIR compartmental model where the country is divided into subpopulations served by airports. They find that closeness centrality of the different airports is what drives the epidemic spreading.

I find the authors edits after the reviews sufficient and therefore I believe that the study can be accepted for publication in PeerJ. I would suggest that the authors reconsider doing the following before the very final acceptance.

Major:

The authors believe that the size of the subpopulation does play a very minimal role in their model. However I believe it is misleading having in a model same population for Rio Airport and a small regional airport. If you see the equations you are evolving in time, the subpopulation size N appears in the denominator and therefore plays a role. If the authors consider running a robustness check with heterogeneous population size across Brasil, this will definitely strengthen the paper!

Minor:

There are some references appear in the text but not in the reference list. Please double check.
Experimental design: All my comments are above
Validity of the findings: All my comments are above
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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 2
Reviewer: 3

Output:
Basic reporting: Line 28. Put a semi colon between the first and second references
Line 41. Consider replacing “displayed exactly” with “reported”.
Line 44 the United Nations 2019 reference is ambiguous. As currently stated, one will take time to find it. Kindly make it specific. Refer to the journal reference guidelines.
Line 46. ‘Ensured’ instead of ‘ensure’.
Line 51-52. For clarity you could consider changing the following statement “the government decided to impose 52 some limiting in the number of flights coming from Europe or Asia.” to “the government decided to limit the number of flights coming from Europe or Asia.
Line 60. Consider changing “social isolation” to “social distancing”
Line 63. Is the main form of transmission through direct contact or droplet infection? Of course, I am not negating the role of direct contact.
Line 69. Do you want to consider stating the current estimated R0 with a corresponding reference? Some papers here for an idea. Ranges from 1 to 3.5 depending on the literature one looks at and time period. Early phylogenetic estimate of the effective reproduction number of SARS-CoV-2. https://www.ncbi.nlm.nih.gov/pubmed/?term=Early+phylogenetic+estimate+of+the+effective+reproduction+number+of+SARS%E2%80%90CoV%E2%80%902
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. https://www.ncbi.nlm.nih.gov/pubmed/32081636
Line 90. Is it meant to be “showed” or “show” since this is still in the introduction section and is part of what your paper seeks to establish through the model?
Experimental design: A speculative question; Why `γ' presumed to be '0' given that recoveries are expected even from the already available of more than 60% recovering from SARS-COV-2 infection? Brazil, Out of  233 142 about more than 100, 000(42.9%) of the confirmed cases have recovered. https://www.worldometers.info/coronavirus/country/brazil/; https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200518-covid-19-sitrep-119.pdf?sfvrsn=4bd9de25_4) Of course your next statement points to the artificiality of the statement
Validity of the findings: Line 189-195 in the first manuscript and now 241-247 in the revised one, the authors, in their rebuttal wrote they have included the reference. However, I could not see it. Could they confirm it is referenced and did not include it?
Line 235 change “raise” to “rise”.
Line 258. Than as currently described, “Nigeria, a country poorer than Brazil but with a similar population” This comes out as a bit subjective, would you consider using a measurable indicator? E.g GDP, infrastructure etc.?
Line 260. Add “wearing of” before “face masks”.
Line 263-265. The statement is unclear. I guess the message you are passing here is that the Nigerian authorities had in place precautionary measures to be adhered to by inbound passengers. If so, kindly rephrase the statement for clarity.
Line 269. Consider changing “drop down” to “reduce” and “refrains” to “restrict”.
Line 280. Consider changing “a more precise counting” to “enhanced case detection”. This is because the message you are passing here is increasing the ability to determine COVID19 cases.
Line 293. “Social isolation” or “Social distancing”. Given that “isolation” is largely used to for confirmed cases.
Line 327. Change “distributed” to “spread”.
Line 350. Comment similar to the one in Line 293.
Additional comments: Thank you Prof. Aristoteles and team for taking time to respond to the issue raised which only makes the manuscript better and enhances its veracity.
Find above few comments to address.
The conclusion seemed a bit long and cold be shortened.
The Lines references noted above are based on the version which i will attach as well with a few comments in it.
All the best.


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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 3
Reviewer: 1

Output:
Basic reporting: Satisfactory
Experimental design: Satisfactory
Validity of the findings: Satisfactory
Additional comments: I am pleased to confirm that authors have addressed the concerns I raised in my previous reviews.


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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 3
Reviewer: 2

Output:
Basic reporting: Satisfactory
Experimental design: Satisfactory
Validity of the findings: Line 241-242: Delete ‘be’ “in this sentence “…….if nothing is be done to avoid it….” so that it reads ‘if nothing is done to avoid it’
Line 276-280: “The Federal Airports Authority of Nigeria (2020) have strict instructions for travelers in their page, from how to be conducted in front of the precautionary measures in the entrance to the hygienic behavior. The equivalent Brazilian agency just says “there is currently no restrictions for domestic or international flights” (ANAC 2020)” This was raised in the second review in which then it in line ‘Line 263-265” and the reviewer comment was: “The statement is unclear. I guess the message you are passing here is that the Nigerian authorities had in place precautionary measures to be adhered to by inbound passengers. If so, kindly rephrase the statement for clarity”. In their rebuttal, “Exactly, the sentence was re-written for sake of clarity” the authors stated they have addressed it but it still remains as in previous versions. For clarity it may be good to rephrase the sentence.

Line 287- 289. You may consider choosing the data from WHO or Nigeria CDC instead of having both. The variations in the data is because of when Nigeria CDC reports to WHO. In essence it is same data hence can opt for one of them whichever is latest by the of referencing.

Line 294: Change “SARS-Cov” to ‘SARS-C0V-2’

Lines 427 and 529; same comment as in line 294.
Line 346-347 Add “on” between ‘be’ and ‘lockdown’ “it should be lockdown right now”.
Additional comments: Dear Prof. Aristoteles and team, tyou have made great strides in addressing the comments raised by the reviewers. Minor comments from me.

Thank you

All the best


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: SEVERE AIRPORT SANITARIAN CONTROL COULD SLOW DOWN THE SPREADING OF COVID-19 PANDEMICS IN BRAZIL
Review round: 4
Reviewer: 1

Output:
Basic reporting: Could the word ‘pandemics’ in the title and in line 28 be changed to ‘pandemic’?
Experimental design: Satisfactory
Validity of the findings: Line 292: ‘o’ is missing in ‘SARS-CV-2. It seems to have been deleted by mistake by the authors in the tracked changes.
Additional comments: Dear Prof. Aristoteles and team, you have made great strides in addressing the comments raised by the reviewers and the manuscript it is at stage to be considered for publication decision by the journal. Two errors noted above likely made during the editing process. It was a privilege to review your work.

One more general comment;

Line 378: Removes ‘s’ from “We thanks”

Thank you

All the best


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: OCEAN WARMING IS THE KEY FILTER FOR SUCCESSFUL COLONIZATION OF THE MIGRANT OCTOCORAL MELITHAEA ERYTHRAEA (EHRENBERG, 1834) IN THE EASTERN MEDITERRANEAN SEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: THe language is correct and clear
The references are appropriately cited
The manuscript is well written
The question is clearly formulated
The conclusions are congruent with the results
Experimental design: The applied methods are well described
The described research is rigorous
Results are interesting
Validity of the findings: The story is new and interesting
as already reported conclusions are congruent
Additional comments: This is an interesting paper that can be published as it is
I have only a criticism. If spicules of the mediterranean species are different from those of the red sea ones, while authors do not take in consideration the hypothesis that the mediterranean specimens belong to a different species? I think that this idea have to be at least discussed


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: OCEAN WARMING IS THE KEY FILTER FOR SUCCESSFUL COLONIZATION OF THE MIGRANT OCTOCORAL MELITHAEA ERYTHRAEA (EHRENBERG, 1834) IN THE EASTERN MEDITERRANEAN SEA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Manuscript Number: PeerJ 45922

Title: Warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea in the Eastern Mediterranean

Article Summary:
This manuscript seeks to test the hypothesis that the increase in water temperature in the Eastern Mediterranean, and thus, global climate change, has determined the colonisation success of the Indo-Pacific octocoral Melithaea erythraea (Ehrenberg, 1834). The authors have used stable isotope analysis of oxygen and carbon of the sclerites of this and a comparative species, Melithaea biserialis (Kükenthal, 1908). They have also compared their results with water temperature, although these measurements were taken at depths significantly deeper than the specimens collected for analyses.

Article Review:
Overall, this is a very interesting study and highlights some key results with regard to the subsequent success of migrating species as a consequence of global climate change. This study is worthy of publication, and I enjoyed reading it, thank you. There are key points that need to be addressed prior to acceptance for publication.

Key Points to Review:
1. Foremost, this manuscript requires the thorough review of a native English speaker who regularly writes and reviews publishable text in the English language. There are many confusing sentences and grammatical errors throughout the text, which reduce the quality of the message in the paper.

2. It would benefit the manuscript to define the terms 'introduced', 'invasive', ‘migrant’ and then how they relate to this study. At present, the terms used suggest that the octocoral Melithaea erythraea is detrimental to the marine ecosystems of the SEMS, however, there appears to be no published or presented data to support this.

3. Both the abstract and introduction would benefit from being re-written and structured so that the reader can be clear on the message that the authors are trying to portray, as well as providing the sufficient back ground on the information such as introduced vs. invasive. The hypothesis and objectives were not laid out well. Suggestions have been made throughout the text in the attached pdf.
Experimental design: Research was good.

Research question is not well defined. I think that this is due to English not being the native language of the author(s) and consulting someone who is would help re-define the manuscript significantly.

I don't recall seeing any sample replicate numbers. The number of test samples needs to be specifically stated in the text.

Methods fairly well described.
Validity of the findings: The findings would be clearer and appear more meaningful with the assistance of a native English speaker.
Additional comments: Manuscript Number: PeerJ 45922

Title: Warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea in the Eastern Mediterranean

Article Summary:
This manuscript seeks to test the hypothesis that the increase in water temperature in the Eastern Mediterranean, and thus, global climate change, has determined the colonisation success of the Indo-Pacific octocoral Melithaea erythraea (Ehrenberg, 1834). The authors have used stable isotope analysis of oxygen and carbon of the sclerites of this and a comparative species, Melithaea biserialis (Kükenthal, 1908). They have also compared their results with water temperature, although these measurements were taken at depths significantly deeper than the specimens collected for analyses.

Article Review:
Overall, this is a very interesting study and highlights some key results with regard to the subsequent success of migrating species as a consequence of global climate change. This study is worthy of publication, and I enjoyed reading it, thank you. There are key points that need to be addressed prior to acceptance for publication.

Key Points to Review:
1. Foremost, this manuscript requires the thorough review of a native English speaker who regularly writes and reviews publishable text in the English language. There are many confusing sentences and grammatical errors throughout the text, which reduce the quality of the message in the paper.

2. It would benefit the manuscript to define the terms 'introduced', 'invasive', ‘migrant’ and then how they relate to this study. At present, the terms used suggest that the octocoral Melithaea erythraea is detrimental to the marine ecosystems of the SEMS, however, there appears to be no published or presented data to support this.

3. Both the abstract and introduction would benefit from being re-written and structured so that the reader can be clear on the message that the authors are trying to portray, as well as providing the sufficient back ground on the information such as introduced vs. invasive. The hypothesis and objectives were not laid out well. Suggestions have been made throughout the text in the attached 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: OCEAN WARMING IS THE KEY FILTER FOR SUCCESSFUL COLONIZATION OF THE MIGRANT OCTOCORAL MELITHAEA ERYTHRAEA (EHRENBERG, 1834) IN THE EASTERN MEDITERRANEAN SEA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea in the Eastern Mediterranean

Basic reporting
Grossowicz et al. investigate the octocoral Melithaea erythraea, endemic in the Red Sea and since 2002 documented as newly introduced species in the south-eastern Mediterranean Sea (SEMS). The authors argue that rising winter water temperature in the SEMS facilitated successful establishment of colonies and that changing trophic levels may play a further role to their advantage. Sclerite morphology and mineralogical composition (XRD) are combined with bulk oxygen isotopes (d18O) and stable carbon isotopes (d13C). The latter are used to reconstruct temperature at the time of calcification from d18O and the degree of metabolic carbon uptake from d13C.

The language is generally clear, but shows a minor albeit systematic issue with use of plural, that needs a second look throughout the document (e.g. “sclerites morphometrics, sclerite morphometrics, sclerite’s morphometrics”). Context of introduction and background are well tailored and simple to follow. Structure and standards of PeerJ are met. But the manuscript would benefit from major revisions prior to publication, including a more in-depth discussion on the validity of the conclusions drawn from the geochemical and mineralogical data. All provided Figures are relevant and necessary, ameliorations to content and captions are given below. References are complete, but would need a format polishing, see detailed line by line comments below. The raw data are all supplied. In the supplementary files the units are missing in the column headers of most parameters (percent, permille, µm, °C, etc.). These data columns need some more description.
Experimental design: Experimental design
The current work provides original data that are worthwhile to be published with PeerJ. Methods are described with sufficient detail for replication and research questions are clear. But data interpretation lacks rigor and relation to other geochemical work on octocorals. In particular the aspect on reconstructed temperature at time of calcification needs a careful look, with respect to sclerite deposition (season, precipitation velocity, ontogeny, vital effects). At the current stage the argumentation remains somewhat circular, with reconstructed temperatures accepted as correct and result in the claim that corals can hence prevail in the basin.
Validity of the findings: Validity of the findings
All underlying data are provided, statistics look sound, and data provide an important mosaic stone for octocoral calcification research. Their impact and novelty with respect to other research still needs to be fathomed, and some references (e.g. Taubner et al., 2012; Vielzeuf et al., 2018) are suggested to build a more in-depth discussion.
Additional comments: General comments
Introduction
Sclerite morphometric data, bulk stable isotopes and mineralogical characteristics are employed to solve how well the newly invaded species can cope with the conditions in the SEMS, with temperature and trophic state as the two key variables. While few would argue that rising winter temperatures would make conditions more suitable, this aspect is not fully followed through. Are the conditions with 21 to 28°C in the Gulf of Aqaba at Eilat representative for the temperature range this species can live in? If there are M. erythraea sites prevailing at colder conditions in the Red Sea, eventually at deeper settings, this would then hence be less surprising for their colonization success?
What about the second variable - trophic levels? It is mentioned that the trophic conditions are changing in the SEMS. It would be easier to follow to compare first the natural trophic level between the Red Sea and SEMS first and then move to temporal changes. Is Eilat more eutrophic?

Material and methods
In the Material and Methods it is not always clear, when you talk about M. biserialis or M. erythraea. For instance, in Lines 127 to 131 – I’d presume this specimen is from Hadera 2002 and hence M. erythraea?
It would be good to add some more information on the sampled colonies. How high were they? Have the distal branches been sampled or the basal stem? Sclerites may form fast, but could continue to add layers for longer time periods. This is an important aspect for the discussion of reconstructed “calcification temperatures” and vital effects. Was there a conspicuous difference in colony morphology between SEMS and the Eilat specimen?
Lines 137 ff, the ADCP unit captures the Hadera port, the Nasholim Bay an Eilat/Aqaba SSTs are derived from a web-source this should be mentioned either here, or put a link to the supporting online material and direct to Fig. 1.
Section 2.2 on Sclerite morphology can be combined with Section 2.7 on Statistical analyzes, since all tests refer to morphometric measurements.
Line 159 this aspect on how d13C are expected to reflect responses to oligotrophic condition needs some more explanation – either here or in the Introduction and Discussion parts. Temperature and trophic level are the key aspect of the paper. While the temperature part is easy to follow, this second aspect is relatively underrepresented in the argumentation.
Section 2.3 mention that for all sites two stable isotope samples have been measured.
Section 2.4 seawater values are given against VSMOW? Needs to be added behind both values (lines 178/179). If seawater values remain within 0.5 ‰ variation, then the temperature uncertainty range (lines 183/184) would be 2°C instead of 0.5°C?
Section 2.6 XRD, you might want to mention the calculation of the %Mg here (for now these values are only in the online material but would be important for the discussion). You could use Titschack et al. (2011) if it was calculated via Rietveld methods, or another reference for 104-calcite peak calculation.

Results
Section 3.1 It might be better to give an overview of the raw measurements first, before moving to “significance of differences” – this would make this paragraph easier to read. It is not immediately clear that M. biserialis has a complete overlap with the field of length/width of M. erythraea and is hence not shown in Figure 3A.
Section 3.2 (Line 246f.) why are both species presented with pooled isotope range? They may have different strengths of the metabolic effect.
M. biserialis misses XRD – can these measurements still be done? This could be interesting because the d13C does not fall onto the same regression as axis length vs d13C as in M. erythraea (Fig. 5). Why is that? According to the calculation its metabolic carbon uptake in percent would be similar to M. erythraea, despite strongly differing sizes.
It would be good to present the calculated Mg-content based on FWHM or d, as well as to point out its correlation with d13C. This could be an indication for a vital effect, since Mg/Ca and d13C are correlated in bamboo corals and also in scleraxonian corals like Corallium rubrum.

Discussion
Sclerite morphometrics need to be discussed also with respect to ontogenetic growth and timing of sclerite deposition. What is the normal known size variability of sclerites in the Red Sea? If there are other taxonomic/morphometric studies from the Red Sea – is the single specimen of M. erythraea from Eilat representative? Is there an ontogenetic effect on sclerite morphology? It would be good to relate this to colony size are the longer and slender types encountered in the SEMS and expression of juvenile colony stage and fast growth? It is important to distinguish when M. erythraea or M. biserialis is meant, in several occasions (e.g. Line 276) both are combined as “Red Sea specimens”.

For the stable isotope discussion, it would be beneficial to dwell on some basic questions first, like: When exactly are sclerites formed? Is there a specific season of deposition? How fast are they formed? Do they continue to grow for extended periods after initial deposition? Can they be multi-annual? These questions are important because they relate to growth rates and vital effects, which affect the isotopic composition, while on the contrary the necessary bulk sampling of multiple sclerites to generate enough sample powder would iron out some of these effects. The aquaria culturing work by Taubner et al. (2012) would be a good starting point to address these questions and implications for the current work.
At the current state the oxygen isotopes are directly used to calculate temperatures at the time of deposition and since the values fall into the measured temperature range they are accepted as correct. Most octocorals have massive vital effects both in there calcareous skeletons and in the sclerites that can confound this interpretation. It would be better to start from the expected calcite d18O at equilibrium based on water temperature and seawater d18O composition, for each sclerite batch and measured temperature, and rigorously see if they coincide or by how much they are offset. Figure 5 is the most interesting in this aspect since both FWHM and d13C are correlated to sclerite axis length. FWHM is however also an expression of Mg-content – bring these data from the online materials to the results and introduce them in the discussion. These data have the potential to evaluate the degree of the present metabolic and kinetic vital effect. The Mediterranean C. rubrum would be indeed a suitable model organism for a comparison, as it has the same high-Mg calcite mineralogy and potentially similar Mg/Ca to d13C systematics (Chaabane et al. 2016, 2019; Le Goff et al. 2017; Taubner et al. 2012; Vielzeuf et al., 2018; Weinbauer et al., 2000). In Corallium rubrum juvenile fast grown skeletal axis (medullar zone and initial parts of annual growth rings) tend to have higher Mg-content and depleted d13C and d18O (Chaabane et al. 2016, 2019). Vielzeuf et al. (2018; see their Fig. 9) demonstrated further a systematic geochemical offset between skeleton and sclerites for Mg-content. It is hence conceivable that similar vital effects act also in the sclerites of M. erythraea. For comparison with Corallium rubrum sclerite isotopes see also Le Goff et al. (2017), and Taubner et al. (2012) for cultured alcyonarian sclerites. Weinbauer et al. (2000; Mar. Biol 137, 801-809) attempted a Mg-Temperature calibration in C. rubrum, this attempt has been used with mixed-success by Matsumoto (2007) in Primnoa pacifica. However, they observed that the sclerites collected at 0.65°C had similar compositions than the Mg-content in skeletons of Mediterranean C. rubrum collected at ~15°C, potentially impeding a temperature calculation. With your data and the systematic offset (skeleton to sclerites) observed by Vielzeuf et al. (2018), can actually provide an important mosaic stone to address these questions.
Overall, your data and direct interpretations with reconstructed temperature and degree of metabolic effects require a more rigorous discussion.

Suggested additions to references:
Chaabane, S., López Correa, M., Ziveri, P., Trotter, J., Kallel, N., Douville, E., McCulloch, M., Taviani, M., Linares, C., Montagna, P. (2019): Elemental systematics of the calcitic skeleton of Corallium rubrum and implications for the Mg/Ca temperature proxy.- Chemical Geology 524, 237-258. doi:10.1016/j.chemgeo.2019.06.008

Chaabane, S., López Correa, M., Montagna, P., Kallel, N., Taviani, M., Linares, C., Ziveri, P. (2016): Exploring the oxygen and carbon isotopic composition of the Mediterranean red coral (Corallium rubrum) for seawater temperature reconstruction.- Marine Chemistry 186, 11-23; doi:10.1016/j.marchem.2016.07.001.

Le Goff, C., Tambutté, E., Venn, A.A., Techer, N., Allemand, D., Tambutté, S. (2017): In vivo pH measurement at the site of calcification in an octocoral.- Scientific Reports 7:11210; doi:10.1038/s41598-017-10348-4.

Taubner, I., Böhm, F., Eisenhauer, A., Garbe-Schönberg, D., Erez, J. (2012): Uptake of alkaline earth metals in Alcyonarian spicules (Octocorallia).- Geochimica et Cosmochimica Acta 84, 239-255.

Titschack, J., Goetz-Neunhoeffer, F., Neubauer, J. (2011): Magnesium quantification in calcites [(Ca,Mg)CO3[ by Rietveld-based XRD analysis: revisiting a well-established method.- American Mineralogist 96, 1028-1038.

Vielzeuf, D., Gagnon, A.C., Ricolleau, A., Devidal, J.-L., Balme-Heuze, C., Yahiaou, N., Fonquernie, C., Perrin, J., Garrabou, J., Montel, J.-M., Floquet, N. (2018): Growth kinetics and distribution of trace elements in precious corals.- Frontiers in Earth Science 6:167; doi:10.3389/feart.2018.00167.

Weinbauer, M.G., Brandstätter, F. & Velimirov, B. (2000): On the potential use of magnesium and strontium concentration as ecological indicators in the calcite skeleton of the red coral (Corallium rubrum).- Marine Biology 137, 801-809; doi:10.1007/s002270000432.

Detailed comments
Figures
Figure 1: Inset Map – You might want to zoom to show the Eastern Mediterranean and the Red Sea, marking the distribution of Melithaea erythraea? Please add a km-scale.
Figure 1: Caption – mention where M. erythraea and where M. biserialis has been sampled. Mention SST-data source for Tel Aviv “Hadera” and Aqaba “Eilat”.
Figure 2: Are the Eilat sclerites in (A) from another M. biserialis specimen or from a thick morphotype of M. erythraea? Not immediately clear that the latter is the case - use letters (A) to (E) in caption.
Figure 2: Caption – change “sclerites morphologies” to “sclerite morphology”. Make caption more informative, pointing out thicker and shorter Red Sea sclerites with respect to slender Mediterranean forms. Point out also differences in wart-density.
Figure 3: In (A) only M. erythraea data are shown. M. biserialis is mentioned in the caption, but not plotted, this is not immediately clear. I presume the M. biserialis data have been omitted in (A) due to complete overlap with the M. erythraea data from Nasholim and Hadera? It would however be good to add them in (B) and (C).
Figure 4: change “EMS” with “SEMS”. It will be better to show raw sclerite δ18Osc values on the x axis, maybe with seawater δ18Osw correction – but putting “temperature of calcification” is an over interpretation of the data, since vital effects are rather common in octocoral calcite. An expected equilibrium range for high-Mg calcites for SEMS and Red Sea areas could be given instead?
Figure 5: (B) change y-axis label “δ13C” to superscript “δ13C”.

Raw Data Tables
Please introduce units in each column header.

Title/Abstract
Line 15: change “Correspondent” to “Corresponding”.
Line 31: change “of” to “for”.
Line 34: change “indigenous” with “endemic”.
Line 35: change “sclerites” to “sclerite”.

Introduction
Line 59: change “Hewitt et al., 2002” to “Hewitt and Hayes, 2002”.
Line 66: change “Bethoux” with “Béthoux”.
Line 69: change “Chevaldonne” with “Chevaldonné”.
Line 71: “tropicalization” lower case.
Line 73: check year “Peleg et al. 2020” – given as “2019” in references.
Line 77: change “Sisma-Ventura Yam” to “Sisma-Ventura, Yam”.
Line 86: change “zooxanthellae” with “zooxanthellate corals”.
Line 90: change “(Grossowicz et al., accepted)” to “(Grossowicz et al., 2020)”.
Line 91: change “might contributed” to “might have contributed”.
Line 94ff: you might want to support sentence with reference on sclerites.
Line 95: change “octocoral” to “octocorals”.
Lines 94 to 96: sentence needs a supporting reference (e.g. Taubner et al., 2012, GCA)
Line 96: change “Sclerites features” to “Sclerite features”. (check this plural issue throughout)
Line 100: change “M. erythraea’s” to “M. erythraea” (Italics).
Line 101: change “octocoral’s physiological traits” to “physiological traits of each octocoral”
Line 111: remove “soft”, distal axis is organic, but the basal stem turns into a massive calcitic stem.
Line 111: change “where magnesium” to “where the magnesium”

Methods
Line 121: change “sclerites” to “sclerite”.
Line 129: rephrase sentence. Mention species of 2002 specimen and collection site (not clear if Eilat or SEMS).
Line 134: change “debris were removed” to “debris was removed”.
Line 152: what is IRMS? Spell abbreviations out at first mention, check throughout text.
Lines 160/161: rephrase “at the stable isotope laboratory of the”.
Lines 160/161: change “Max-Planck institute” to “Max-Planck Institute”.
Line 163: change “70 degrees Celcius” to “70°C”.
Line 194: change “Sisma-Ventura, Yam and Shemesh, 2014” to “Sisma-Ventura et al., 2014”.
Line 200: FWHM – spell abbreviations out at first mention.
Line 200: These are geometric angles, remove Celsius from the unit.
Line 206: change “Site” to “site”.

Results
Line 215: change “sclerites” to “sclerite”.
Line 216: change “sclerites axis” to “sclerite axis”
Line 222: change “comparing” to “compared”.
Line 252: change “ranges” to “ranging”.

Discussion
Line 275: lower case “sclerite”.
Line 307: change “Maier, Paetzold,...” to “Maier et al.”
Line 309: “samples of 2016”, please state if they are from Hadera and/or Nasholim.
Line 316: change “Maier, Paetzold,...” to “Maier et al.”.
Line 323: change “(Grossowicz et al., accepted)” to “(Grossowicz et al., 2020)”.
Line 330: Aspect of crystal size needs to be explained in Material and methods already.
Line 331: “higher density” – density of warts on sclerite surface?

Conclusions
Line 339: change “Sisma-Ventura, Yam and shemesh, 2014” to “Sisma-Ventura et al., 2014”.
Line 339/340: change “Amitai et al., in review” to “Amitai et al., 2020”.

References
Line 361ff: Update reference to: “Amitai, Y., Yam, R., Montagna, P., Devoti, S., López Correa, M., Shemesh, A. (2020): Spatial and temporal variability in Mediterranean climate over the last millennium from vermetid isotope records and CMIP5/PMIP3 models.- Global and Planetary Change 189, Article #103159; doi:10.1016/j.gloplacha.2020.103159.”
Line 366: replace “(2007.)” by “(2007).”
Line 383: replace “Chevaldonne” with “Chevaldonné”.
Line 385: replace “D.” with “D.S.”
Line 386: replace “Methids Researc” with “Methods Research”
Line 399: update reference to “Grossowicz M, Shemesh E, Martinez S, Benayahu Y, Tchernov D (2020). New evidence of Melithaea erythraea colonization in the Mediterranean. Estuarine, Coastal and Shelf Science 236; doi:10.1016/j.ecss.2020.106652.”
Line 403: replace “Chemical Geological” with “Chemical Geology”, remove “Isotope Geoscience”
Line 410: add page numbers, or “doi:0.3389/fmars.2018.00001”.
Line 412: replace “europe” with “Europe”.
Line 432: remove “676”.
Line 448: replace “Paetzold” with “Pätzold”.
Line 452: replace “Porites Lutea” with “Porites lutea”.
Line 458: check year “Peleg et al. 2019” – as “2020” in text.
Line 459: replace “ecology” with “Ecology”.
Line 464f: add reference for “R Core Team, 2014” mentioned on line 212.
Line 465: remove “et al.” add authors “Teocharis A and Papathanassiou E”.
Line 478: check page numbers
Line 503: Italics “Acabaria biserialis”.

Review by M. López Correa (CNR-ISMAR, Bologna, Italy)


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: OCEAN WARMING IS THE KEY FILTER FOR SUCCESSFUL COLONIZATION OF THE MIGRANT OCTOCORAL MELITHAEA ERYTHRAEA (EHRENBERG, 1834) IN THE EASTERN MEDITERRANEAN SEA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is now ready to be published
Experimental design: The manuscript is now ready to be published
Validity of the findings: The manuscript is now ready to be published
Additional comments: The manuscript is now ready to be published


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: OCEAN WARMING IS THE KEY FILTER FOR SUCCESSFUL COLONIZATION OF THE MIGRANT OCTOCORAL MELITHAEA ERYTHRAEA (EHRENBERG, 1834) IN THE EASTERN MEDITERRANEAN SEA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The work by Grossowicz et al. on the octocoral Melithaea erythraea has carefully incorporated the comments by several reviewers, seen language polishing, and has significantly ameliorated and can now be recommended for publication with PeerJ in its current form.
Experimental design: Review comments have been accomodated.
Validity of the findings: Review comments have been accomodated.
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: EFFECTS OF STELLERA CHAMAEJASME REMOVAL ON THE NUTRIENT STOICHIOMETRY OF S. CHAMAEJASME-DOMINATED GRASSLANDS IN THE QINGHAI–TIBETAN PLATEAU
Review round: 1
Reviewer: 1

Output:
Basic reporting: This artical met the standards of PeerJ. This work would be improved by concepting a core idea. Authors would be benefitted to read several related papers which reported the stoichiometric responses of different levles ranging from species to community.
For instance, Hu et al. 2019. Legacy effects of nitrogen deposition on plant stoichiometry in a temperate grassland. Plant and Soil.
Hou et al. 2019. The relative contributions of intra- and inter-specific variation in driving community stoichiometric responses to nitrogen deposition and mowing in a grassland. Science of the Total Environment, 666: 887-893.
Wang et al. 2018. The impacts of nitrogen deposition on community N:P stoichiometry do not depend on phosphorus availability in a temperate meadow steppe. Environmental Pollution, 242: 82-89.
Lu et al. 2018. Intraspecific variation drives community-level stoichiometric responses to nitrogen and water enrichment in a temperate steppe. Plant and Soil. 423: 307-315.
Hou et al. 2018. Consistent responses of litter stoichiometry to N addition across different biological organization levels in a semi-arid grassland. Plant and Soil, 421:191-202.
Han et al. 2014. Hierarchical responses of plant stoichiometry to nitrogen deposition and mowing in a temperate steppe. Plant and Soil, 382: 175-187.
Experimental design: Experimental design is well.
Validity of the findings: Findings are valid and important.
Additional comments: The paper from Song et al. reported the ecological stoichiometric responses of plants from species level to community level to a weed removal in an alpine grassland. Findings from this work would improve our understanding of the grassland resotration processes. While the experiment is well carried out and data were well analyzed, the mnuscript would be improved by further revision.

First, the hypotheses should be improved because they are not clear at the present version. Further, the article should be written with hypotheses as the main core. The Introduction section should be provide direct background information for each hypothesis.

Second, the Introduction section should be rewritten as there is too much too general information about what is stoichiometry and the importance stoichiometry. In contrast, the introduction should be more specific and focus on the particular question you want to answer in this study.

Third, the discussion is too long. You don't have to mention every result found in this study. Instead, you should focus on the most important one and those are directly related with your hypotheses.

I hope the literature I suggested could help authors to learn how to organize the writing of your paper.


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

Input:
Title: EFFECTS OF STELLERA CHAMAEJASME REMOVAL ON THE NUTRIENT STOICHIOMETRY OF S. CHAMAEJASME-DOMINATED GRASSLANDS IN THE QINGHAI–TIBETAN PLATEAU
Review round: 1
Reviewer: 2

Output:
Basic reporting: I would suggest choosing only a handful of all figures presented, as they are many. Pick the most important ones, and place the others into the supplementary files section. Also consider unifying the tables, in cases where it makes sense, and also move some of them into the Supplementary section.
Experimental design: Lines 118-121: I find the formulation of the hypotheses a little bit vague, and very general. I would suggest formulating the hypotheses a little bit more specific. For instance in the case of the first hypothesis: how do you expect the stoichiometric traits in foliar biomass to change, exactly?

I have general concerns about the presentation of the experimental design, as from the written description it has not become completely clear to me, how the sites were located relative to each other. First, it does not become clear whether the three study sites of 60x40m were located on three different pastures, or on the same one. Second, it did not become clear to me why the four subplots per plot-half were chosen (were the entire half plots treated by Stellera removal, or only the four suplots? And where exactly were the three sub-sub-plots for biomass and community diversity assessment located? Three per each subplot, meaning 12 per half-plot? Or three per half-plot? For this, I would suggest providing both a figure of the general location of the study sites in the Tibetan Plateau or China (optional, but would be nice) on one hand, and a Figure depicting the experimental study design for clarification (definitely important if someone wants to replicate this experiment).
Furthermore, I do not understand how the surveyed plots were exactly analyzed, or pooled. If there were three plots per half-plot, in the RDA or PCA analysis there should be 9 points per treatment visible. If there were three sub-sub-plots per subplot per half-plot, there should be 36. However, there are only 6 points visible. How was the data assessed here, pooled?
Validity of the findings: The conclusions section is basically just a repetition of all results; but the exact meaning or the utility of the results is not made clear. The use of this study in the terms of conservation and preservation of grasslands and species richness, as introduced in the abstract, is lacking though. Maybe use the conclusions for the elaboration of the possible application of your results rather than repeating results.
Additional comments: Dear authors,

I found this manuscript very interesting and very well written. I congratulate the authors on their excellent introduction to this complicated subject, rendering this subject easily understandable even for people unfamiliar with Ecological Stoichiometry.
Overall, I believe this study makes a good contribution on basic research of grassland ecology, both on a local or regional scale (alpine grasslands in the Tibetan Plateau) as well as on global scale. It makes a good contribution to studies assessing the underlying mechanisms driving species occurrence and performance, as well as community dynamics, considering the impact of dominant toxic weeds invading heavily grazed grasslands.
All underlying data has been provided and seems sound and well funded. This research was very well referenced to literature; results and conclusions were sound and well supporting each other. Figures and tables are relevant and supporting the presented study. Conclusions were well stated, linked to the original research questions and limited to the supporting results.
However, I have some suggestions and concerns regarding the formulated hypotheses and research questions, the experimental design and the overall conclusions posed by the authors, as stated below. I believe that this manuscript well fits the scope of the PeerJ Journal, and will be fit for publication once the issues presented below are addressed.

General comments:
Abstract:
Line 14 and 28: “Controlling Stellera chamaejasme is one of the main methods used to recover degraded grasslands in the Qinghai-Tibetan Plateau. …. In addition, examination of plant performance showed an increase in biomass and decline in community diversity after S. chamaejasme removal.” In the abstract, it does not immediately become clear why, considering biodiversity conservation, one would want to control a species in grazed grasslands that maintains or increases community diversity if present. When reading the introduction (Line 94), it becomes clear that these grasslands are used by herders to maintain sheep, and that the recovery of these more species rich grasslands by removing Stellera has predominatly economic reasons. I think it is necessary to elaborate why this recovery, i.e. removal of this toxic weed, is of interest, even if it causes species diversity to decrease.
Introduction:
Lines 118-121: I find the formulation of the hypotheses a little bit vague, and very general. I would suggest formulating the hypotheses a little bit more specific. For instance in the case of the first hypothesis: how do you expect the stoichiometric traits in foliar biomass to change, exactly?
Material and Methods:
I have general concerns about the presentation of the experimental design, as from the written description it has not become completely clear to me, how the sites were located relative to each other. First, it does not become clear whether the three study sites of 60x40m were located on three different pastures, or on the same one. Second, it did not become clear to me why the four subplots per plot-half were chosen (were the entire half plots treated by Stellera removal, or only the four suplots? And where exactly were the three sub-sub-plots for biomass and community diversity assessment located? Three per each subplot, meaning 12 per half-plot? Or three per half-plot? For this, I would suggest providing both a figure of the general location of the study sites in the Tibetan Plateau or China (optional, but would be nice) on one hand, and a Figure depicting the experimental study design for clarification (definitely important if someone wants to replicate this experiment).
Furthermore, I do not understand how the surveyed plots were exactly analyzed, or pooled. If there were three plots per half-plot, in the RDA or PCA analysis there should be 9 points per treatment visible. If there were three sub-sub-plots per subplot per half-plot, there should be 36. However, there are only 6 points visible. How was the data assessed here, pooled?
Just out of interest, I was wondering about the stoichiometric regulation of plant species. The authors elaborate about species-specific nutrient uptake and use efficiency by comparing mean values of nutrient content and nutrient ratios. Why did they not calculate the 1/H homeostatic regulation coefficient, which is the slope of the log (nutrient in plant biomass) ~ log (nutrient in soil) relationship, and which directly allows the estimation of excess nutrient uptake, degree of C assimilation relative to nutrient content and degree of nutrient homeostasis is species? This might be a nice addition to this study.
Also, I would suggest choosing only a handful of all figures presented, as they are many. Pick the most important ones, and place the others into the supplementary files section. Also consider unifying the tables, in cases where it makes sense, and also move some of them into the Supplementary section.

Conclusions:
The conclusions section is basically just a repetition of all results; but the exact meaning or the utility of the results is not made clear. The use of this study in the terms of conservation and preservation of grasslands and species richness, as introduced in the abstract, is lacking though. Maybe use the conclusions for the elaboration of the possible application of your results rather than repeating results.

Introduction:
Lines 61, 103: Authors mention “scholars” having examined different aspects of the surveyed grasslands. I find this terminology unsuitable, as I suppose these studies are research studies well supporting the presented one. Better refer to them as such.
Line 83: ….(water, light and nutrients)….
Line 87: …, there has this far been little attention….
Line 92: …. , and CO2, they are fierce competitors (Baker…..)” … Competitors to what? Each other? Other plants?
Line 107: “….. Most research on S. chamaejasme has focus on population spread dynamics….” I find this formulation unusual. Population expansion maybe?
Line 109: “… and the use of its extracted flavonoids”….  – what does this mean, I do not understand this? Does this mean that flavonoids have been extracted from this species´ plant biomass and spread on other plants, in order to assess their response?
Line 109: …Little is therefore known about the effects on S. chamaejasme removal on ecological stoichiometry. “ – I would consider changing the wording here to clarify this sentence. Maybe like this: Hence, although the effects of removal on plant communities has been studied before, the effects of CNP community stoichiometry have not been studied before. The information resulting from this research might aid in understandig this species role in ecological protection...

Material and Methods:
Line 129: “….Vegetation is typical of an alpine grassland, with Kobresia and Elymus species…”  - add a comma
Line 131: “…Kobresia humilis, Carex atrofusca, and Lancea tibetica. ….” – remove comma
Lines 135-136: “… Field experiments were approved by …” – I think this is not a good place to state the approval of the Haiyan County grassland Station. Usually, one states the grants and fundings of a study at the end of the manuscript, at the end of the Acknowledgement-Section.

Line 147…”Heights of all living plants…”  - I believe you refer to average vegetation height? Better change wording
Line 150: …”Biomass was harvested by hand clipping to ground level, sorted by species, oven dried….” . Do you refer to all species in the entire 0.5 x 0.5 m square, or only to those dominant ones that were later on analyzed?
158: …” 30 consistent leaves of each species were collected and mixed as one sample…” – I believe the correct wording here is “ were collected and pooled”. You sampled the 30 leaves from different individuals, I suppose? Clarify.

Line 191: …” and N:P in different species or functional groups was performed.” Incomplete sentence

Results
Line 200: “ Plant aboveground biomass in SR…” You refer to the total aboveground biomass of the sampled species? Or total aboveground biomass of the entire community?
Line 204: “…. On a species level, the aboveground biomass….”
Line 207: “…. K. humilis, and C. atrofusca was not different between CK…”
Line 209: “…. Shannon-Wiender index and Simpson index, respectively.”
Line 213: “… On a species level, total C content….”
Line 216: ”… but only species richness significantly altered….”
Line 223: “.. Hovewer, species diversity and treatment both….”
Line 279: “…. Across the sites for all eight species, with P. crymophila…”
Line 298: “… Besides K. humilis and C. atrofusca, all importance values of the other studied species increased…..”  - what are these “importance values”? What do they mean and how are they calculated or assessed. I believe this was not explained or mentioned in the Methods section.
Line 301: “...  S. chamaejasme removal may significantly enhance the competitive potential of these species via increasing available, space, which allows them to inhibit the growth of their competitors.” This may need a bit more explanation, maybe like such: “Stellera removal causes open gaps in the vegetation, which is quickly occupied by Species XX; leading to competitive exclusion of the other co-occurring species.”.
Line 314: “…. This result may help explain the increased dominance of these six species and also suggests that they may have developed a N storage strategy in response to neighbor removal, in which more N is transported to….” – This is speculative. The results do not suggest this, but this may be a possibility to explain the observed patterns. It furthermore could possibly be that species to not only store nutrients, but that they also take up more nutrients than needed (excess uptake). This entire section must be formulated in a way that clearly identifies this as speculative. “Suggest” is, form my point of view, more that speculative.
Line 323: …” N is limited, rather than P, in this alpine grassland. “ This could also indicate that these species reach dominance because they have lower N needs than the others under N limited conditions.
Line 328: … This could partly explain the increase in the P content of P. crymophila and the decrease of P content in….” - This aspect is unclear to me. Nutrient limitation is apparently species specific.
If one species takes up phosphorus under Stellera removal and increases nutrient content in its biomass -  and the other species does not…  how is this indicative of nutrient co-limitation? In the case of P. crymophila this seems reasonable - P. crymophila takes up P and incorporates it directly via C assimilation, maintaining high CP values. But C. atrofusca does not. Wouldn’t a species take up P and N simultaneously and proportionally under NP co-limitation?
Line 340: “…. The growth of forbs may be inhibited by Graminae plants because of their greater competitive ability.” – How could this protective mechanism work? Why could graminoids be less sensitive to environmental factors than forbs? Maybe explain this a little.
Line 405: “… From the population level to the functional group level…” – you mean species level?
Line 407: “… may relate to grassland ecosystem homeostasis, …“ – I am unsure about using this terminology here. A species can be homeostatic about its internal nutrient content, but can a whole community?
Line 410: “… Stoichiometry may be inhibited by inertia effects. “ – This is not explained properly, what does this mean?
Lie 413: “…increasing number of reports that show that the nutrient traits of plants ….”


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: EFFECTS OF STELLERA CHAMAEJASME REMOVAL ON THE NUTRIENT STOICHIOMETRY OF S. CHAMAEJASME-DOMINATED GRASSLANDS IN THE QINGHAI–TIBETAN PLATEAU
Review round: 2
Reviewer: 1

Output:
Basic reporting: The quality of this work has substantially improved after revision. I suggest this work could be accepted after minor revision.
Experimental design: The experiment was well designed and carried out.
Validity of the findings: The novelty of results in this study is high.
Additional comments: Findings from this study help improve our understanding of stoichiometric changes of grassland ecosystem to invasive species removal. The quality of this paper has been improve during the revision. I suggest authors do minor revision before this paper could be accepted for publication.

1. Lines 13-16 It is important to show why studies on ecological stoichiometry are important.
2. Line 17 'We' instead of 'This study'
3. Line 21 delete 'Our results showed that'
4. Line 25-26 delete 'when compared to those at the control  site (CK)'
5. Line 29 delete 'Overall, this study found that'
6. Line 33 'could' instead of 'will'
7. Line 62 'in response to'
8. Line70 'species-specific'
9. Line 167 'At species level'
10. Line 174 did you use 'species diversity' as an variable in your experiment?
11. Line 176 'to affect' instead of ', affecting'
12. Line 183 'At the functional group level'
13. Line 185 'in affecting C content'
14. Line 187-188 'Legume had the highest N content among all the functional groups.'
15. Line 199-200 'At the community level, SR significantly reduced plant total N content and increased C:N  ratio.'
16. Line 217-219 this sentence could be deleted without any loss of information.
17. Line 220 'at different biological organization levels'