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: HIGH THROUGHPUT SEQUENCING-BASED ANALYSIS OF THE SOIL BACTERIAL COMMUNITY STRUCTURE AND FUNCTIONS OF TAMARIX SHRUBS IN THE LOWER REACHES OF THE TARIM RIVER
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: This in an interesting report, evaluating the microbial communities associated to Tamarix shrubs found in nekhabs dunes and in no dunes, and although the experimental procedures are well explained and in my opinion valid, I have some questions:

1) Why not control samples for the analysis of the microbial community composition not associated with the shrubs was done? is it enough with the samples taken from the edges of the shrubs and canopies?

2) The weather of the sampling site (temperature, precipitation, etc) was very variable, when exactly were the samples taken? Do you expect significant changes in microbial composition in different seasons?

3) although the microbial communities in shrubs of similar sizes were analyzed are there morphological differences between the ones in nekhabs and the ones in no nekhabs?
Validity of the findings: I think the findings are valid, although I have some doubts about the experimental design.
Additional comments: it is an interesting and informative work, but I have some concerns already stated, related to the experimental design and also some minor points:

1) abstract mentioning "very significnatly" possitive or negative correlation is not necessary, better is to mention the p values.

2) in several parts of the text there are extra spaces between words and some words with no spaces between them. e.g. L 36 "well as    Bacteroidota", L 263 "analysis(Figure 5).", etc, please correct this and "justify" the text.

3) L 313 "human diseases (0.8%)," do you mean genes encoding virulence factors?

4) L. 341 "functiona"?

5) L 407 "had obvious affection" what do you mean?

6) more informative figure legends are needed.


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

Input:
Title: HIGH THROUGHPUT SEQUENCING-BASED ANALYSIS OF THE SOIL BACTERIAL COMMUNITY STRUCTURE AND FUNCTIONS OF TAMARIX SHRUBS IN THE LOWER REACHES OF THE TARIM RIVER
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: An important problem I encounter is whether there are differences in the microbial communitiesin the  nebkhas and no-nebkhas Tamarix shrubs, the results (269) shown ""It indicated that the diversity of bacterial community structure in nebkhas Tamarix shrubs was greater than that in non-nebkhas Tamarix shrubs" but in the discussion says (389)"Alpha diversity of soil bacterial communities in Tamarix shrubs, calculated using Shannon,Simpson, Chao1, and ACE indices, was not significantly different in nebkhas and non- nebkhas Tamarix shrubs. It indicated that nebkhas had an insignificant effect on soil bacterial community diversity and abundances" However in Halobacterota there are differences (figure 3).is enough to say that the microbial communities are different in nebkhas and no-nebkhas Tamarix shrubs?
Additional comments: This study describes the results of massive sequencing and physicochemical characteristics of two types of soils in the lower Tarim river basin in China, particularly in a type of soil called nebkhas which contains shrubs of a genus called Tamarix, This paper can be published in Peer J as an article after solving some questions and correcting some typos.

106: for a clearer understanding for the reader, it would be desirable to visualize the distinction between "the nebkhas (X) and three non-nebkhas Tamarix shrubs (F)", as shown in the  figure 2 from paper: Plant Soil (2011) 347:79–90  or in the figure 4 from GEOMATICS, NATURAL HAZARDS AND RISK 2019, VOL. 10, NO. 1, 1176–1192.

by way of the figure legends could be more detailed for a better understanding of the figures.

In table 1 and 2  it is confusing to determine the statistical significance with the nomenclature proposed by the authors, I suggest an additional table showing the statistical significance.

179: the Authors say: "The pH of nebkhas Tamarix shrubs was significantly higher than that of non-nebkhas Tamarix shrubs"  the values are 7.88 vs 7.59", that values are statistical significant, Ok, but,  has this difference some biological consequence?

185,187 : similar to the case of pH, the values of TK and NH4+ were significantly different in nebkhas and no-nebkhas tamarix shrubs,has difference some biological consequence? or is only statistical

257: the analysis NMDS is not clear, What does it mean in this analysis? What does it mean "NMDS can analyze the differences between samples in low dimensions"  and define the term "bacterial community structure" because in 266 :These results indicated differences in bacterial community structure between nebkhas and non-nebkhas Tamarix shrubs" what does it mean?

326: please clarify, how to explain?: "Therefore, it can be inferred that most of the soil bacteria in Tamarix shrubs had active growth and metabolism processes", Finding more genes related to metabolism does not mean that there is an active growth in these soils, it is possible that in the genomes of these bacteria this group of genes is just overrepresented.

360 and 468: how was determined that Tamarix nebkhas shrubs formed recently?

380 :could you please name some members of this plhylum Halobacterota?

typo: table 1 PH is pH

233: typo: FC is Fc

245:explicitly define LDA

248: typo: FC is Fc

338: typo: FC is Fc

356: typo: PH is pH


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: HIGH THROUGHPUT SEQUENCING-BASED ANALYSIS OF THE SOIL BACTERIAL COMMUNITY STRUCTURE AND FUNCTIONS OF TAMARIX SHRUBS IN THE LOWER REACHES OF THE TARIM RIVER
Review round: 2
Reviewer: 1

Output:
Basic reporting: it is OK
Experimental design: it is OK
Validity of the findings: it is OK
Additional comments: Thanks for addressing my 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: HIGH THROUGHPUT SEQUENCING-BASED ANALYSIS OF THE SOIL BACTERIAL COMMUNITY STRUCTURE AND FUNCTIONS OF TAMARIX SHRUBS IN THE LOWER REACHES OF THE TARIM RIVER
Review round: 2
Reviewer: 2

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


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

Input:
Title: WHOLE-GENOME COMPARATIVE ANALYSIS AT THE LINEAGE/SUBLINEAGE LEVEL DISCLOSES RELATIONSHIPS BETWEEN MYCOBACTERIUM TUBERCULOSIS GENOTYPE AND CLINICAL PHENOTYPE
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper, the authors downloaded publically available whole genome data from Mycobacterium tuberculosis (Mtb) clinical isolates to search for possible associations between Mtb lineage/sublineage and the form of tuberculosis (TB) disease (i.e. extrapulmonary (ETB) versus pulmonary TB (PTB) and antibiotic resistance. They used all available ETB genomes (N=245) and matched these with an equal number of PTB genomes. The find Mtb Lineage 2 (L2) associated with PTB and L1 associated with ETB. Moreover, they find L3 to be associated with multidrug-resistant TB (MDR-TB) and the modern Beijing sublineage of L2 associated with “antibiotic resistance”. My comments are the following:

1) The manuscript would greatly benefit from input by a native English speaker, as there are several instances where the wording is rather awkward.
Experimental design: 2) All available ETB genomes were used, but how was the subset of PTB genomes selected?

3) There are insufficient details in the Methods to understand analyses the authors have carried out; this is particularly true for the logistic regression models mentioned. For example, what were the outcome variables; i.e. how where the different lineages and sublineages compared (all against all, or grouped on some way etc.)?

4) Where “clustered” genomes excluded from the analysis? Inclusion of multiple representatives of the same strain might be biasing the analysis.

5) The authors mention a large number of odds ratios in the text but I could not find any table where all these data are properly presented, including the proportion of the different categories that have been analyzed, p-values etc.
Validity of the findings: 6) The authors mention correctly in the Introduction that allowing for confounding factors when carrying out these kind of analyses is important. However, it seems that the only patient variable the authors were able to control for was HIV co-infection (i.e. by choosing available genomes from HIV-negative TB patients only). What about variables such as age, sex, other comorbidities, all of which could influence the presentation of TB?

7) Following from the previous comment, one important aspect, which the authors completely ignore, is the potential impact of host genetics. There are indications that populations from South Asia and North Africa (and perhaps elsewhere) might have a higher risk for ETB, completely independently from the infecting Mtb strain. At the same time, and as the authors correctly acknowledge, the Mtb populations are strongly geographically structured. Hence, without considering the host genetic background, the associations with Mtb lineages might be a more consequence of the geographical association between host populations and Mtb lineages. This possibility should at least be discussed.

8) In the abstract the authors state that these association with E/PTB where with “ancient” and “modern” lineages but in the main text they clearly show that this refers to L1 and L2 which is not the same as saying “the ancient and modern lineages”.
Additional comments: 9) On multiple occasions, the authors argue that their study is more robust because a lack of potential bias based on their genome selection. This might be partially true. However, by relaying on previously published genomes that were generated for other purposes, new types of (e.g. sampling) bias can emerge, which the authors cannot control for because they are essentially blind to how and why these strains where collected and sequenced in the first place.


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: WHOLE-GENOME COMPARATIVE ANALYSIS AT THE LINEAGE/SUBLINEAGE LEVEL DISCLOSES RELATIONSHIPS BETWEEN MYCOBACTERIUM TUBERCULOSIS GENOTYPE AND CLINICAL PHENOTYPE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Negrete-Paz et al investigated the statistical associations between the types of tuberculosis (pulmonary and extrapulmonary) and lineages / sublineages, in addition to genetic predictors of drug resistance.

Since the study is mainly focused on the analysis of lineages and types of tuberculosis (pulmonary or extrapulmonary), the corresponding rates should be established worldwide or by regions, in such a way that they help to better demonstrate their situation and hence the importance of present study.
Experimental design: The present study does not specify how the selection of strains included in the analyzes was carried out. It only mentions that equal amounts of strains obtained from pulmonary and extrapulmonary tuberculosis were included.

The eligibility criteria that were taken into account should be clarified in the corresponding section. On the other hand, in the methods or discussion section it should be clarified why an adequate proportion of strains obtained in the continents of Africa and America was not included.

It must also be supported why 91% of the strains included in the analysis only come from three countries (Russia, Indonesia and Thailand).

The quality of the reads used in the analysis is not clear. The authors only mention that they were filtered with a Phred score greater than 30. However, in the results section, the authors do not specify the percentages of the reads that were finally filtered or if these reads had good genomic coverage.

All programs must show the version used, since through the years the programs vary due to improvements that may include changes in the internal analysis algorithms. An example of this is that the TBprofiler program used is version 0.2.1, when at present this program is in version 3.0.4. The version used includes a base of 1325 mutations while the last update of this program includes up to a total of 1541. This could affect the prediction of resistance and the consequent association with lineages and sites of infection. Finally, the latest version of the TBprofiler also uses a total of 90 SNPs for the determination of lineages compared to the 62 initially established.

Regarding the obtaining of variants used for the evolutionary reconstruction by the phylogenetic tree and the in-silico determination of drug resistance, the authors only mention the programs used, however it is not specified whether they used the default values of the different options of the same or if these were determined by criteria of the researchers. For example, given that evolutionary inference requires the use of variants that have been fixed in the genome, variants with allelic variants greater than 75% should be considered.
Validity of the findings: In Figures 1 and 2, the name of the figure should be mentioned in their description, as well as that the bootstraps values are established in the respective branches. Also, it is not specified whether any external groups were used to root the tree. In case you have used, it would be appropriate to mention the sequence name (or GenBank accession number). Likewise, in figure 2 it is observed that the ancestral node has up to three Bootstraps values. Is it a mistake or do you have any explanation?

Figure 1 mentions the categories: sensitive, drug-resistant, MDR and XDR. However, the exact definition of them is not clarified in the text. In addition, these 4 categories are considered as "drug resistant phenotype" when in reality the determination of these categories are obtained in silico. In any case, you could be defined as drug-resistant genotypes, since the word phenotype is associated more with a behavior demonstrated in microbiological cultures. In the same figure, it is observed that the labels of some sequences have a yellow background, which is not clarified anywhere in the text.
The statistical values obtained from the main results are mentioned; however, since the statistical association analyzes are a strong component of the study development, the other statistical results obtained from the other variables analyzed should be specified in a supplementary section.
Additional comments: Negrete-Paz et al investigated the statistical associations between the types of tuberculosis (pulmonary and extrapulmonary) and lineages / sublineages, in addition to genetic predictors of drug resistance.

In general, the work is good and detailed, however the recommendations must be taken into consideration in such a way that an improvement is noticed in it.

Finally it is important to mention that a  limitation of the study would be the fact that there was no information on phenotypic drug resistance in vitro obtained by any microbial culture method. Instead ofi t, the determination of drug resistance was only inferred by detecting genetic markers in target genes.

Different bioinformatics programs use sets of bases of mutations associated with drug resistance that can vary from one another. This produces a variation in the drug resistant genotypes obtained with the consequent risk of over or under estimating the true drug resistant behavior of the strains analyzed, as well as the statistical inferences that depend on this determination (eg association of drug resistance with affected organs or mycobacterial lineages)


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: WHOLE-GENOME COMPARATIVE ANALYSIS AT THE LINEAGE/SUBLINEAGE LEVEL DISCLOSES RELATIONSHIPS BETWEEN MYCOBACTERIUM TUBERCULOSIS GENOTYPE AND CLINICAL PHENOTYPE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed all my comments. I have only 1 small additional comment:

In the Introduction the authors refer to L8 as "M. africanum", which is incorrect. Please remove this statement. Based on the current limited knowledge, we just don't know what the host tropism of L8 is and thus whether to refer to it as  "M. tuberculosis sensu stricto" or anything else. It clearly is a member of the Mtb complex though.
Experimental design: ok.
Validity of the findings: ok.
Additional comments: ok


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: APIS MELLIFERA PROPOLIS ENHANCES APOPTOSIS AND INVASION INHIBITION IN HEAD AND NECK CANCER CELLS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript has some originality, technical quality, clarity of production and it is important in its field.
The “introduction” has background, describe a problem, shows what currently exists and proposes solution, with current literature references.
A revision of the English language can improve the quality of the work.
Experimental design: The methodology is well described and reproducible.
Validity of the findings: Conclusions are well stated, linked to the original research question & limited to supporting results.
Additional comments: Major points: The strongest point of the work was the use of two pairs of isogenetic HNSCC cell lines representing both primary and metastatic disease from the same patient.

The use of doses with low cytotoxicity can somehow compensate for the lack of use of non-tumor cells, which would assess the selectivity of treatment for tumor cells.
Also, the evaluation of other secondary compounds that might be present in the EAEP should have been done.
The work's weakest point was the lack of any in vivo testing. It was written in an understandable language, but it still needs language revision to improve clarity.


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: APIS MELLIFERA PROPOLIS ENHANCES APOPTOSIS AND INVASION INHIBITION IN HEAD AND NECK CANCER CELLS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is interesting and provides information about anti tumor activity of a especific fraction of propolis from Tai Apis mellifera.
However, this revisor would like to understand the reasons why only EAEP was studied and not the first extract obtained, and either, why not galangin and apigenin as isolated compounds as the authors are attributing the activities found in these two substances.
Experimental design: About the experimental design, I have some points to the authors answer:

1. I would like to understand the reasons why the authors used 72 hours to measure citotoxicity. Isn't it to high for cell culture citotoxicity evaluation?

2. The authors used 24 hours for flow citometry measure, 48 hours for MMP activity determination and 72 hours for cell viability. Please, justify the reasons.

3. The authors atribute the anti tumor activities to galangin and apigenin. However, the EAEP fingerprint observed in the figure 5 b, showed other important peaks around the minutes 43-45. Galangin and apigenin are easily available in the market and the authors used them to construct the calibration curve. Why the author didn't used the isolated compound to test their hypothesis?

4. Considering that the authors possess an HPLC-ESI-TOF-MS, why don't identify the other peaks present in the EAEP? Especially considering that other compounds maybe be present in amounts closer to galangin and apigenin in the fraction (figure 5b), and probably can contribute the the findings, it is important to identify then.

5. Considering the solvents used in the extraction process, can the authors provide evidences about the lack of solvents residues in the samples tested? Or, the controls involved the presence of these solvents?

6. In the lines 142-143 the authors inform that ethyl acetate is used as a polar organic solvent. In the lines 143-145, the authors says that is a medium polarity solvent and with minimal toxicity. Can the authors inform the reference for both information? Especially the minimum cell toxicity?

7. Considering that the authors atribute to the EAEP powerful citotoxicity in tumor cells studied, can the authors support that this EAEP extract is safety to the normal cells? Is is very important to check the citotoxicy in at least fibroblast cells in order to attribute to this EAEP extract a powerful candidate for future in vivo studies.
Validity of the findings: In the conclusions, the author attribute to the extract obtained a powerful candidate to anti tumor activities. Also, the authors discussed that other authors considered galangin and apigenin this activity. Can the authors discuss the concentration of these substances in the EAEP obtained, the scientific literature already published with these compounds to the same activity, and the dosages found as effective in the paper to support "powerful candidate" term in the 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: APIS MELLIFERA PROPOLIS ENHANCES APOPTOSIS AND INVASION INHIBITION IN HEAD AND NECK CANCER CELLS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors reviewed, edited, and answered all questions in a satisfactory manner.
Reviewers' comments helped the authors improve the text, and the manuscript was revised by a native speaker. I think that it deserves to be published.
Experimental design: The experimental design was revised.
Validity of the findings: The modifications met the requested criteria. Information added in the discussion item clarified the text.
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: APIS MELLIFERA PROPOLIS ENHANCES APOPTOSIS AND INVASION INHIBITION IN HEAD AND NECK CANCER CELLS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript was improved with the points previously requested. The manuscript is clear, with professional structure, good background and english.
Experimental design: The questions previously done were properly answered.
Validity of the findings: The limitations was identified clearly in the manuscript.
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: PROBABILISTICALLY SAMPLED AND SPECTRALLY CLUSTERED PLANT SPECIES USING PHENOTYPIC CHARACTERISTICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: There contains grammatical errors and typos in the manuscript. The authors should re-check and revise carefully.

The authors listed a lot of references in the literature review. However, in my opinion, they are listed one by one. It is better if the authors could group the literature review according to the methods or data.
Experimental design: Equations should be assigned to their numbers.

There are a lot of paragraphs that should be in the "Methodology" section, but they are in "Results" now. For example, "Sampling Discussion" part, "Clustering setup", etc.
Validity of the findings: Table 1 did not contain any meaning if you only listed a few phenotypes. It is necessary to show all phenotypes, maybe in supplementary.

How did the authors convince that their methods could be applied to any phenotype? It needs some evidence.

Is there any statistical tests had been performed for comparison among different methods?

The authors should compare to previously published works/methods on the same dataset.

The authors should have some validation data.
Additional comments: No comment


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

Input:
Title: PROBABILISTICALLY SAMPLED AND SPECTRALLY CLUSTERED PLANT SPECIES USING PHENOTYPIC CHARACTERISTICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The author’s use of English was generally competent, although the sentence structure could be tightened. Specific instances where I disagree with author word usages are detailed in the general comments below. Background intended to show the context of this work in relation to plant breeding lacks relevant detail, and so is sometimes misleading. The literature review is repetitive and relevant literature could be grouped where similar.
Experimental design: The research question was clearly stated. The experimental design appears appropriate to the objectives. However, the set of analyses performed and what hypothesis each was intended to test is not clearly presented.
Validity of the findings: The authors should be more candid when comparing their methods to other methods. There is no way of knowing, for example, which silhouette values are statistically different from one-another. Is the contrast between silhouette values .2152 and .2105 (Euclidean distance with k=10) really different compared with the contrast of .3367 and.2582 (correlation with k=10)? Data comparing computational complexity of the various methods is not presented, yet the authors conclude that their method is faster. They should present some data.
Additional comments: line 23: Genome data should more properly be called genotypic data – referring to sets of genotype calls. The authors have a nomenclature problem. By referring to individual soybean pure lines as genotypes, they were forced to use the incorrect ‘genome data’ term. Genotype is often used as a generic term for pure lines (or clonal lines or hybrid lines), but the two are confusing together.  I suggest that they either specifically define the meaning of the term plant genotype in the context of this paper or use a different word to describe an individual or leave genotypic data out of the introduction altogether.
lines 35-37: The relationship between breeding progress and genetic diversity is much more complicated than stated. For a more nuanced review I suggest (among others): Louwaars, NP. 2018. Plant breeding and diversity: A troubled relationship? Euphytica 214,114. For a better defense of the role of genetic diversity in plant breeding: Swarup, S., Cargill, E.J., Crosby, K., Flagel, L., Kniskern, J., and Glenn, K.C. 2020. Genetic diversity is indispensable for plant breeding to improve crops. Crop Science. https://doi.org/10.1002/csc2.20377
lines 38-40: Incomplete. I presume the authors are referring to genotype-by-sequencing methods of acquiring genotypic data on hundreds of thousands of SNPs for hundreds of samples. This is something different from genome sequencing. They should use more specific language.
line 41: I suggest you say “Plant genetic diversity can also be studied…”
line 51: I wasn’t sure what you meant by “genotypes of the same plant”, please clarify.
lines 91-92: Please avoid phrasing correlation in a way that implies causation – your example comes too close to this. Also “lower” not “less” here and throughout.
lines 112-114: when you say “activity on” do you mean “correlation with”? If not, then more detail on how the authors proved causation should be included.
lines 118-119: I don’t know what you are trying to say with this sentence. Wheat breeders are people, therefore diverse rather than related (except in a few well-noted cases). Were you trying to talk about genetic distance within and between wheat breeding programs?
line 137: Not “catered”, perhaps “addressed”?
line 250-251: should be “…since the better the matrix quality, the better the clustering accuracy”.
Line 315: Did you convert non-numerical values into numerical values or did you remove traits with non-numerical values?
Line 360: “lower” not “lesser”
Table 4 legend: define the meaning of * here as well as in the text.
Line 433: Sine you state above that your method worked well, why do you propose replacing Pivotal Sampling?


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: PROBABILISTICALLY SAMPLED AND SPECTRALLY CLUSTERED PLANT SPECIES USING PHENOTYPIC CHARACTERISTICS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The introduction was succinct and the related literature well-reviewed.
Based on the methodology of this study, it will be interesting to see the result of spectral clustering on the complete samples in the population without prior application of sampling. If we have a less significant difference in the results this will reduce the time and design complexity of the experiments.

Deviation property of the genes was used as the inclusion criterion of the pivotal sampling, can you specify the threshold chosen for the selection and rejection step in line 162-169?
Experimental design: I think this study is purely computational and not require experimental design.
Validity of the findings: Line 395-400: Further information from the validation done will be required to justify the conclusion about the skewness of the clustering distribution not being a true representation of the samples. The segregation of the samples in a few clusters might be expected since all genotype belongs to the same plant. Kindly include these details in the manuscript.

In addition to the normalization performed in the data preprocessing phase, the one-hot encoding of the categorical variables (EPV and LS) can be performed in future studies since the number of attributes are few.
Additional comments: In general, the manuscript is well written.


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: PROBABILISTICALLY SAMPLED AND SPECTRALLY CLUSTERED PLANT SPECIES USING PHENOTYPIC CHARACTERISTICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: My previous comments have been addressed.


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

Input:
Title: PROBABILISTICALLY SAMPLED AND SPECTRALLY CLUSTERED PLANT SPECIES USING PHENOTYPIC CHARACTERISTICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I have gone through the revised manuscript, all the issues raised have been attended to by the authors.
I am just suggesting in the "Results and Discussion" section if the "Discussion" part can have a separate section would be fine.

Aside from this, it is highly recommended 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: POTENTIAL APPLICATIONS OF PERSONALITY ASSESSMENTS TO THE MANAGEMENT OF NON-HUMAN PRIMATES: A REVIEW OF 10 YEARS OF STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The review “Potential applications of personality assessments to the management of non-human primates: A review of 10 years of study” summarizes the literature published between 2010 and 2020 across various fields of research including psychology, animal management, zoology, behavioural ecology, veterinary medicine, and conservation and thus has a broad impact. The review is within the scope of the PeerJ and meets the requirements of the journal. There are however, several issues (or rather suggestions for improvement), which I would like to address.

It has been 11 years since the critical review of Freeman & Gosling (2010) which set the direction and profoundly influenced the field of primate personality. One of the gaps suggested by Freeman & Gosling (2010) was the implementation of the knowledge of individual differences in behaviour of primates into animal management and welfare (3 main areas – enrichment, group composition, reintroduction). The current review reappraises the state of research on the practical implications of primate personality in management practices since the review of Freeman and Gosling (2010). Authors identified and discussed 5 most studied areas of personality applications in primate management (social management, environmental enrichment, training protocols, health and welfare monitoring, and conservation planning). New reappraisal of the field is timely as the last attempt to review this topic was made by Kristine Coleman in 2012 (Coleman K. 2012. Individual differences in temperament and behavioral management practices for nonhuman primates. Appl Anim Behav Sci 137: 106–113) who identified similar areas of interested and suggested recommendations for implementation. Authors might wish to acknowledge the study of Coleman (2012) in their review.

The review is well written and broad. Authors state (L105-107) that the review primarily focuses on zoo management (with applications also in other captive facilities). However, focusing on methods of personality assessment potentially obstructs seeing the progress in the field and the practical implications. The review would benefit from focusing more on the research of practical implications (than on methods) and more in detail on the specific topics of practical implications. Suggesting specific recommendations tailored for zoo (and other captive) management could provide guidelines for the future research and help in management decisions. These issues are addressed and discussed in detail in the following 2 parts.
Experimental design: The current review revealed and the authors state that “the majority of studies (31%)” (L29-30)  and that “method validation dominated the literature” (L184-185). This result might seem worrying. However, taken together, studies on animal personality and practical implications (management, welfare, health, conservation) accounted for 45% (69% including social behaviour) (Tab 3). Thus, the opposite is truth, which should be acknowledged.

For their search, the authors used a combination of words “primate” AND (temperament OR personality) AND (welfare OR management OR conservation) and then discarded papers that were not relevant resulting in the list of 58 articles. In this list, there are, however, articles that are not directly connected to welfare, management or conservation. These articles might mention potential implications for welfare, management or conservation, but they don´t evaluate them empirically (8/58 studies describing method of personality assessment: Freeman et al. 2003; Highfill et al. 2010; Úbeda and Llorente 2015; Šlipogor et al. 2016; Martin and Suarez 2017; Weiss et al. 2017, Hopper et al 2018; Masilkova et al. 2018; 3/58 studies describing personality structures: Koski et al. 2011; Morton et al. 2013a, Baker et al. 2015). These studies might be interesting for evaluating the spectrum of species that were studied in captivity (and thus set priorities for future research) but cannot inform about practical implications. Studies on wild primates were also included (12/58 studies covering various topics: Dammhahn and Almeling 2012; Konečná et al. 2012; Seyfarth et al. 2012 Carter et al. 2014; Carter et al. 2012; Pritchard et al. 2014; Seyfarth et a.l 2014; Eckardt et al. 2015; Molesti and Majolo 2016; Blaszczyk 2017; Ebenau et al. 2019a; Ebenau et al. 2019b). Although studies on wild populations can be informative about potential implications (although not tested yet in captivity), they might skew the overview of studied species and general research focus. Moreover, including not relevant studies can cause this relatively high percentage (31%) of methodological studies. Therefore, the authors might wish to revise the selection of the relevant articles (e.g. focusing only on captive species and/or only on topics relevant to practical implications).

	It would be also beneficial for the researchers and the field in general to see whether the research on practical implications changed and how since Freeman and Gosling (2010). Specifically, authors could compare the number of studies on primate personality and practical implications (welfare, conservation, management) between 2 periods (2000-2010 vs. 2010-2020) to see whether there is actually a decreasing or increasing trend to study this issue nowadays. Moreover, the authors could evaluate which topics are currently studied and which are understudied and how the field developed (e.g. by comparing the information to Coleman et al. 2012 who introduced very similar areas). New topics are e.g. the social networks, psychological well-being and missing are studies on interactions with caretakes. Thus, authors could give more specific recommendations to set the future direction of research.

For the researchers as well as people involved in the management of zoo populations would be also interesting to see the proportion of studied primate species (and families) in captivity (either in general regarding any personality aspect or specifically in the connection with practical implications) from all primate species in captivity. The authors could easily identify families or groups that are not represented in the research (e.g. gibbons, lemurs, howler monkeys, …) and explain why is that (i.e. difficult to study in captivity due to low numbers, difficult to handle them in zoo settings, or recognize them individually without marking, … ). The authors could specifically mention which groups shall the further research focus on.
Validity of the findings: The review would benefit from focusing more on the practical implications as mentioned above:

One suggestion would be to move the Tab 2 to Supplement (similar table published in Freem and and Gosling 2010 and in Koski SE 2011. How to Measure Animal Personality and Why Does It Matter? Integrating the Psychological and Biological Approaches to Animal Personality. In: Inoue-Murayama M, Kawamura S, Weiss A (eds) From Genes to Animal Behavior. Springer Japan, pp 115–136).

Another suggestion is to include the names of personality dimensions (i.e. Boldness, Sociability, …) and their exact relationship (e.g. +, -, 0) with the response variables in tables 3-7.  To safe space, the Setting and Personality measure could be replaced by abbreviations (i.e. Z = zoo, L = lab, …). I suggest to rename “Personality measure” to a more straightforward “Method of personality assessment” or “Personality assessment method”. Knowing that the definition of particular personality dimensions might depend on the method used, the information about which dimensions and how exactly they relate to the animal welfare, conservation, health, … measures could be used to inspire further and more detailed research and could be more easily implemented into the current management practices by captive facilities. Based on this overview, it will be also possible to conclude which personality dimensions are the most important predictors or animal management issues (although generalization should be treated with care).

Finally, I would like to encourage the authors to include a paragraph on possible other (specific) implications relevant to the zoo and other captive management, either based on research done on other non-primate species in captivity or on their professional opinion (based on their practical experience). These implications could inspire further research. Below are some tips:

1.	Personality has been connected to reproductive success (e.g. litter size and offspring survival) – this knowledge could be used to increase reproductive success in critically endangered or difficult to breed species. Reproductive success is easy to assess in captivity because of the detailed records - studbooks, breeding reports, pedigree info from ZIMS. See e.g.
Wielebnowski NC (1999) Behavioral differences as predictors of breeding status in captive cheetahs. Zoo Biol 18:335–349
or studies on wild primates (Seyfarth et al., 2012).

2.	Personality can affect reproductive partner choice and compatibility.
Martin MS, Shepherdson DJ (2012) Role of Familiarity and Preference in Reproductive Success in Ex Situ Breeding Programs. Conserv Biol 26:649–656. https://doi.org/10.1111/j.1523-1739.2012.01880.x

3.	Further ideas might be: personality could help to identify which individuals are suitable to house in mixed-species exhibition, walk-through exposures (e.g. to prevent visitor-animal conflicts), suitable for exposition purposes, suitable for the standard method of capturing (via nets) versus less stressful box capturing, which individuals will habituate faster to new environments, …

4.	To encourage research on the link between primate personality and animal welfare, management, etc. authors could suggest methods that could be easily applied in captive facilities and that could promote the research, such as shorter forms of personality questionnaires (such as e.g. in Robinson et al. 2018), installing cameras to for behavioural coding, easy and short form psychological well-being (Weiss et al. 2009), using body scoring form to assess body condition, etc.

The third recommendation in the Conclusion reads as “Future study should address key gaps in the primate personality literature; particularly (i) regarding taxa which are currently underrepresented in studies and (ii) exploring the links between personality and health, welfare, social management, and other practical areas of interest in greater detail.“  The authors can be specific and identify underrepresented taxa and other areas based on their review.

Finally, there are some minor issues within the manuscript:
L150: replace “popular” by “studied”
L154-157: “It is worth noting that“ redundant
L248: please delete “counterintuitively“
L279: “less” should not be in italics
L364-365: please, rephrase so it reads “… high scores on Activity, … “
Additional comments: I wish the authors all the best and I hope that the suggestions above will help to improve this review and spark future research and discussion on the links between personality and welfare.


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: POTENTIAL APPLICATIONS OF PERSONALITY ASSESSMENTS TO THE MANAGEMENT OF NON-HUMAN PRIMATES: A REVIEW OF 10 YEARS OF STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Review of Potential applications of personality assessments to the
management of non-human primates: A review of 10 years of study
(#56138)

The manuscript was a review of work on personality in nonhuman
primates since 2010. The review focused largely on the utility of
personality assessments of various sorts in the management of captive
primates and, to a lesser extent, primates reintroduced into the
wild. Seeing as 10 years have passed since the previous, more general,
review by Freeman and Gosling, the overall goal of this review is to
be lauded. It's important to review the state of the field, especially
given that work in the area is beginning to move into applications of
these measures.

Before saying anything else, I apologise for taking longer than
expected to complete the review. I recently welcomed another child
into the world, and so things are a bit less settled than they usually
are around here.

I had a few moderate comments and several minor ones that I hope the
authors can address. I'll begin with the former.

1. The review seems to have missed some papers, which I thought should
be there. Perhaps these fell outside the scope of the literature
search, and if so, the search should have been described more clearly,
or they weren't missed by the authors.

One such paper was by Altschul et al. (2017):
https://royalsocietypublishing.org/doi/full/10.1098/rsos.170169

Another was by Weiss et al. (2015)
https://doi.org/10.1177%2F0956797615589933

And there have been empirical papers published by Uher:
http://dx.doi.org/10.1016/j.jrp.2016.02.003
http://dx.doi.org/10.1016/j.jrp.2013.03.006
https://doi.org/10.1016/j.jrp.2013.01.013

I suspect there are other papers, but I will leave the task of finding
them to the authors, unless, of course, these and the other papers
were omitted for reasons that were not made clear (to me).

2. In lines 170-171, the authors cite King and Figueredo as the
originators of the Hominoid Personality Questionnaire (the HPQ). The
HPQ is based on the questionnaire used in their 1997 paper (the
Chimpanzee Personality Questionnaire) in that it is an extension of
this questionnaire. However, the references for the HPQ are:

a). Weiss A. et al. Am J Primatol. 2009. https://doi.org/10.1002/ajp.20649
b). Weiss A. 2017. https://doi.org/10.1007/978-3-319-59300-5_2

Note that the latter reference is a book chapter which outlines the
questionnaire's history and development. I have attached it to my review.

3. In lines 266-272, and perhaps further, the authors refer to
sociability. Here the writing would lead a reader to believe that
sociability is the same as extraversion. This blurs some distinctions
that have been noted, both in the key papers, but also in a review of
the field by Weiss (2017, J Pers. https://doi.org/10.1111/jopy.12310.

Specifically, depending on the species, a single factor (sociability)
loads on social traits or two factors comparable to the Big Five
factors of extraversion and agreeableness load on these traits,
although bonobos (see the 2015 paper cited above) show a different
configuration. I don't think the authors need to get into the nitty
gritty of it all, so they could simply refer to personality factors
associated with social traits, and then just name the different
factors when citing the relevant studies.

4. In line 339 the authors refer to "facets", but it is not clear to
what they are referring to. Are they referring to what are known as
factors, domains, dimensions, for example, extraversion or one of the
other Big Five dimensions in humans, or do they mean lower order
constructs, such as the facets of each of the Big Five, e.g., the
"warmth" facet or extraversion?

Whatever the case may be, the authors need to be consistent in their
terminology here, maybe every so briefly defining any new term.

A helpful reference, by the way, about facets is a 1995 paper by PT
Costa and RR McCrae published in the J Pers Assess, http://doi.org/10.1207/s15327752jpa6401_2

My minor comments are as follows, and I refer to line numbers where I can:

1. In the Abstract, I think I would delete "widely", which is true,
but it is implied by the the rest of the text. In fact, it's a
good idea to omit as many *ly words as possible.

2. I've always known "non-human" to be spelled without a hyphen,
namely as it's not a compound word.

l 42. I would omit "it be"

l 44. "incorporation" -> "incorporating"

l 47. Here and elsewhere the authors use causal language
("predicted"), which is a problem when studies are anything other than
true experiments. I would be more modest and would use terms like
"associated" and "related" instead.

l 55. The authors will want to note that these measures are reliable
and validated. Here I think the authors ought to provide definitions
from the literature on psychometrics and construct validity. A 1955
paper by Cronbach and Meehl (https://doi.org/10.1037/h0040957) and a
1959 paper by Campbell and Fiske (https://doi.org/10.1037/h0046016)
are good for defining validity, but many textbook treatments will be
fine. Reliability has been discussed extensively, too.

l 58. I would omit "existing".

l 59: Is the word "animal" needed here?

l 64: Is the word "validated" necessary here?

L 82: I think the word "numerous" is redundant; it can be omitted.

l 92: Consider omitting this line.

l 97: I would omit the word "then".

l 106: I would change "have generality" to "generalize". Here, too, a
definition would be nice.

l 149: I would omit the word "different".

ll 173-174: I would revise the text so that it reads "...and each has
its benefits and drawbacks" and "which we have outlined".

l 189: If the authors could cite an example cite here, that would be good, too.

ll 214-216: Some examples here would be helpful.

l 217: I think there could be a a better transition sentence at this
point.

l 241: Please cite who proposed this idea.

l 250: I would not refer to "types" when personality traits, factors,
etc. are better thought of as being on a continuum. Thus, refer to
"individuals higher or lower in..."

l 254: Might it be worth considering what the human literature shows?
Is this a promising avenue for future work, in other words?

ll 298-299: I would use the active voice here and throughout.

l 306: I would rewrite this sentence without the text "take a holistic
approach which"

l 326-330: Please shorten or split this sentence.

l 334: I'd rephrase this as "the shy-bold continuum".

l 337: Here I would strive to be consistent in labels that are
used. So if "shyness-boldness" is referred to before, just use that
label again.

l 351: What do the authors mean, in particular, by "in-depth"? That
is, what aspects need to be looked at in more depth?

l 358: I would rephrase to "voluntarily participate".

ll 488-494: I think this section could do with some reference to the
fact that heritable personality variation is the norm and provide some
indication of what mechanisms might support this in wild
populations. That's going to be key with regards to reintroduction
programs and breeding, etc.

l 496: I think the word "some" could probably be deleted.

ll 538-539: For clarity, it's best to phrase this kind of thing as
"shifting" from something "to" something else.

Thank you for asking me to review this interesting paper. I hope the
authors find my comments helpful.

Alexander Weiss [I sign my reviews]
Experimental design: See above.
Validity of the findings: See above.
Additional comments: See above.


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: POTENTIAL APPLICATIONS OF PERSONALITY ASSESSMENTS TO THE MANAGEMENT OF NON-HUMAN PRIMATES: A REVIEW OF 10 YEARS OF STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
Additional comments: Review of 56138v2: Potential applications of personality assessments to the management of non-human primates: A review of 10 years of study
This is a revised version of a manuscript that I had previously reviewed. I thought it was a useful review and most of my comments were minor. The authors did a good job in responding to these comments and this version of the manuscript is a clear improvement. I only had some minor comments remaining, most having to do with writing. I list these below in no particular order.
Can omit “disparate and” from the Abstract.
 “since 2010”: Note this comes after an earlier review
“increased progression” -> “progression”
“existing animal” -> “animal”
l 46: Perhaps just spell out “for example” throughout but be sure to have it followed by a comma in any event. Same with “i.e.”
l 49: delete “well”.
ll 60-65: Refs to show the validity and reliability studies?
l 89: “carried out” (omit)
ll 104-113: The word “will” comes up many times. Is it needed?
l 144: Is “further” needed?
l 174: Some duplicated text (“, to name a few”)
l 189: Is “observer” needed?
l 205: Insert “single”?
ll 241-242: Omit “an area of research”
ll 305-308: A bit confusing as written. Suggest that it reads “A study by Morton et al. (2015) found that captive capuchin (Sapajus spp.) dyads who were more similar in the Sociability dimension, had higher-quality relationships.”
l 351: “common squirrel monkeys”
l 364: Omit “more”.
l 373: The word “facets” is used here.
l 374: Insert “studying” before “the interaction”
l 375: Delete “approach”?
l 381: The word “type” should be omitted.
l 399: Wouldn’t the Altschul et al. 2017 study fit into this? Same goes for Altschul et al. 2016. (doi: 10.12966/abc.02.04.2016).
l 463: The apostrophe is in the wrong place.
l 498: Can omit “different”.
l 527: In cases like this, shouldn’t an “e.g.” precede the references as this is not an exhaustive list?
ll 526-529: The 50% heritable number comes from a lot of studies on animals, which these authors cite. Also, the statement “is attributable to additive genetic variation and is thus heritable” is somewhat redundant as to be heritable means that variance is due to additive genetic effects. I would just say “is heritable”.
ll 536-537: “a number of” -> “several”.
l 540: The species is cited earlier (line 429) but it’s only now that the scientific name is given. I would move the scientific name to the first reference of this species.
l 551: “approach” not “theory”.
l 567: I believe what was concluded was that one of the assays could not have been measuring boldness.
l 577: Delete “of these”
l 606: Delete “The”.
ll 614-616: I’d be cautious about endorsing short questionnaires. They have numerous problems associated with them, which I won’t go into. Suffice it to say, they may not cover all aspects of some trait and thus their use may provide misleading results (see, e.g., Weiss & Costa 2014, doi: 10.1093/aje/kwt300).
Thank you for asking me to review this interesting manuscript. I hope the authors find my comments helpful.
Alexander Weiss [I sign my 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: IDENTIFICATION OF IMMUNE RELATED CELLS AND CRUCIAL GENES IN THE PERIPHERAL BLOOD OF ANKYLOSING SPONDYLITIS BY INTEGRATED BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is clearly written but with some mistakes in typewriting, e.g., line 117, 203 and 207, et.al., which should be carefully checked and corrected.
Experimental design: The authors should state why the two datasets GSE25101 and GSE73754 were chosen for analysis, with other datasets from AS patients’ peripheral blood available, such as GSE18781. What’s the criteria of including and excluding datasets? And how these criteria would affect the results?
What’s the disease activity of the 6 AS patients and what medications they were receiving at the time sample collected?
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: IDENTIFICATION OF IMMUNE RELATED CELLS AND CRUCIAL GENES IN THE PERIPHERAL BLOOD OF ANKYLOSING SPONDYLITIS BY INTEGRATED BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I think this is an epoch-making treatise that comprehensively analyzes the genetic pathology of ankylosing spondylitis, which has not been completely elucidated yet.
However, I have to say that the pursuit of research is insufficient to conclude from this treatise.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The detailed patient background of ankylosing spondylitis is not fully considered.
For example, there is no mention of the duration of illness, treatment details, involvement of underlying diseases other than ankylosing spondylitis, etc., and their effects cannot be ignored.
Consideration should be given to the patient background.
If it is difficult to present a list of patient backgrounds, it is necessary to consider picking up AS patients excluding major diseases such as diabetes, collagen disease, and cancer. Is such an operation done?

Further verification is needed to determine whether this gene expression is completely linked to the pathogenic factors and pathophysiology of ankylosing spondylitis.

The authors are only conducting gene analysis, but do you confirm the protein expression level? If you have any data, please show it.
Also, are there any plans for in vitro cell-based research, in vivo animal experiments, confirmation with knockout mice, etc.? I think it is desirable to describe in the consideration part that the verification is necessary.

Also, the expression "useful for treatment" in the discussion department and conclusions is an overstatement. In other words.
As an additional study, it is necessary to analyze peripheral blood leukocytes in patients whose pathology can be controlled by intervention and those who do not. If you have data, please consider adding it.


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

Input:
Title: IDENTIFICATION OF IMMUNE RELATED CELLS AND CRUCIAL GENES IN THE PERIPHERAL BLOOD OF ANKYLOSING SPONDYLITIS BY INTEGRATED BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: There are a lot of grammatical errors, typos, or ambiguous parts in this manuscript, for examples:
- ... other elements may also play an critical role ...
- the comprehensive analysis may shed light on further insights regarding AS development and facilitate to provide new diagnostic and immunoregulatory therapeutic targets for AS.
- ... the GSE25101 and GSE73754 dataset ...
- ... with reference of KEGG gene sets ...
- the cut-off criteria as nominal nominal p value ...
- ...
Therefore, the authors have to re-check and revise carefully. It is better to be checked by a native speaker or an English editing service.

More literature reviews on bioinformatics-based ankylosing spondylitis studies should be added.

The part from line 70 to 83 should be in section "Methodology" or "Result".

There are some inconsistency in font format.
Experimental design: - A critical concern is the use of a very small dataset (only 36 normal and 68 diseased specimens). This number cannot be considered as enough as a comprehensive analysis.
- Methodology should be explained in more detail.
- GO database or analysis has been used in previous studies i.e., PMID: 31277574 and PMID: 31921391. Therefore, the authors are suggested to refer to more works in this description.
- Why did the structure of "Methodology" and "Results" look similarly? At least the authors should present the "Results" section in a different way, not list alike the method.
Validity of the findings: - The authors should compare the predictive performance with the previous studies on the same problem/data.
- The authors should have some validation data.
- What is the significant level of KEGG analysis?
Additional comments: No comment.


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

Input:
Title: IDENTIFICATION OF IMMUNE RELATED CELLS AND CRUCIAL GENES IN THE PERIPHERAL BLOOD OF ANKYLOSING SPONDYLITIS BY INTEGRATED BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 4

Output:
Basic reporting: 1. Citations for cell-specific expression of Granzyme expression in CTLs and NK cells to ascertain the RT-PCR findings are not contributed from other mononuclear cells.

2. Should also address what was missing in the original report of the GEO dataset generation and how this analysis generates different insights.
Experimental design: 1. A detailed distinction in age, sex, education, and comorbidities of the participants in the GEO datasets should be factored into a demographic analysis to effectually address if any other factor could have affected the DEG comparison.

2. Brief description of the GEO datasets referenced - cells used, isolation procedure, storage conditions, RNA isolation procedure, and microarray analysis to directly compare the results with the RT-PCR analysis.

3. The above comment also applies to the RT-PCR analysis.

4. Detailed methods of peripheral blood analysis - such as a citation for the procedure of mononuclear cell isolation and methods used.
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: IDENTIFICATION OF IMMUNE RELATED CELLS AND CRUCIAL GENES IN THE PERIPHERAL BLOOD OF ANKYLOSING SPONDYLITIS BY INTEGRATED BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: After revising, the paper is much more readable, but still needs to be re-checked carefully throughout, such as “Figure 7” in line 237. The ABSTRACT section should also be revised, especially the part of Results, to make it stand alone without the full paper.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: IDENTIFICATION OF IMMUNE RELATED CELLS AND CRUCIAL GENES IN THE PERIPHERAL BLOOD OF ANKYLOSING SPONDYLITIS BY INTEGRATED BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Thanks for addressing my previous comments. However, in my opinion, some comments were not addressed well as follows:
- More literature reviews (related works) on bioinformatics-based ankylosing spondylitis studies should be added.
- The authors should compare the predictive performance with the previous studies on the same problem/data.
- The authors should have some validation data (the data with the same characteristics, not validation the protein expression)


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: IDENTIFICATION OF IMMUNE RELATED CELLS AND CRUCIAL GENES IN THE PERIPHERAL BLOOD OF ANKYLOSING SPONDYLITIS BY INTEGRATED BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 3

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


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

Input:
Title: IDENTIFICATION OF IMMUNE RELATED CELLS AND CRUCIAL GENES IN THE PERIPHERAL BLOOD OF ANKYLOSING SPONDYLITIS BY INTEGRATED BIOINFORMATICS ANALYSIS
Review round: 3
Reviewer: 1

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


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

Input:
Title: INVESTIGATION OF MULTIPLE SCLEROSIS-RELATED PATHWAYS THROUGH THE INTEGRATION OF GENOMIC AND PROTEOMIC DATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors used combinational omics approaches to reveal functional pathways of Multiple sclerosis and such an approach is demanded in the field. Nevertheless, the main message of the work should be more widely disclosed.
English - suitable.
Cited references - suitable.
Fig. 1 needs to be improved. No blue threshold line indicated.
Experimental design: Methods part is well described; investigation performed according to the ethical standards. I missed the visualization of the main findings, where the protein level and SNP data would be shown in a single figure. The possible association between SNP and protein expression is described in the text, nevertheless, the additional figure would let to better reveal the association and translate the main message of the analysis. Since narrowing down analysis enabled the selection of the most important targets possibly associated with MS, these can be deeper analyzed revealing protein level and SNP link.

The authors are comparing two distal biological elements - initial: DNA code changes (SNPs) and final - protein level, nevertheless, there are numbers of intermediate regulation between these elements. It would be very beneficial if authors could analyze for example mRNA level of selected targets in selected samples. If it is not possible, the possible impact should be considered in the discussion part.
Validity of the findings: Since the idea to compare different biological elements data (SNPs, and protein expr.) itself is great, the result should be treated with cautions, since there are many intermediate biological elements, which are not measured. Such design might generate false-positive associations between SNP-proteil level- and MS.
Additional comments: Comments are given in the section above.
Why you selected only 11 patients for the analysis since you have a bigger cohort?
Are you the first who analyse protein level and SNP association in MS?
Why only a qualitative comparison of MS and molecular features were made, does the "disease progress" for all the patients was similar? It would be worth including the clinical characteristics of patients when comparing molecular data as well.


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

Input:
Title: INVESTIGATION OF MULTIPLE SCLEROSIS-RELATED PATHWAYS THROUGH THE INTEGRATION OF GENOMIC AND PROTEOMIC DATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: One main suggestion from my side would be to broaden the Introduction. The discussion part sufficiently covers all the questions raised during the given study, but I would suggest moving the first paragraph of the Discussion (L193 – L201) to the Introduction section.
Experimental design: The experimental part is flawlessly designed, and the Materials and Methods section covers all the necessary information. The ethical aspect is described in the Study group subsection.
Validity of the findings: The current pool of MS genetic data is relatively small. So far, there is little evidence to correlate MS genetic data with the clinical phenotype. But recent studies confirm that MS genetics may indeed describe the severity of the disease. The authors did a great job attempting to fill in the knowledge gap within the genetic aspect of MS.
Additional comments: General suggestions:
L2 – “the” before “integration”
L46 and L80 – comma after “independent”
L81 – split into two sentences. “…were conducted. The two datasets…”
L126 – perhaps “corrections” instead of “correction”
L132 – change “analyses” to “studies”
L157 – comma after “rs7873”
L158 – cut-off
L202 – The complement
L211 – CCC component
L228 – L229 remove “found to be”
L236 – re-phrase as “actin cytoskeleton regulation”
L244 – comma instead of semicolon
L258 – comma instead of semicolon
L259 – also occur
L278 – dot after “associations” and remove “whilst”
L280 and through the text – remove “very”. Consider not using “very” at all or replace with “rather, relatively, considerably…”
L281 – L283 consider rewriting as “Therefore, we aimed to include both false-positive SNP associations and prevent missing out…”
L287 – change “be effective for representing” to represent
L290 – change “at the time” to “when”
L301 – “agreed” instead of “accepted”


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: INVESTIGATION OF MULTIPLE SCLEROSIS-RELATED PATHWAYS THROUGH THE INTEGRATION OF GENOMIC AND PROTEOMIC DATA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Thw paper by Everest et al. presents a pathway enrichment analysis on merged genotyping and proteomic data.
The paper is clearly writter and clearly presented.
Experimental design: The experimental design involve the analysis of a previously released proteomic dataset and of a new genotype dataset.

Enriched pathways obtained by the merging of the two datasets are presented and contrasted with those obtained from the anaysis of the proteomic dataset. The comparison should be better shown and it would be interesting to compare with results obtained using genotype data only .

The procedure of analysis, particularly for genotype data, involves the adoption of many external resources (e.g. SPOT, human PPI network) and some of them seems a bit outdated. Are they critical for the analysis and the drawn conclusions? In particular, "the gene on which the SNP has the most important functional effect" is a quite general sentence for a very complex association and it deserves more comment, in my opinion.

If possible, results could be corroborated by adopting alternative methods (but I undestand this can be time consuming and not essential in the economy of the paper)
Validity of the findings: I cannot comment the medical and clinical significance of the findings. On the point of view of the analysis, I think that the statement " We conclude that integrating multiple datasets of the same patients helps reducing false negative and positive results of genome-wide SNP associations and highlights the most prominent cellular players among the complex pathophysiological mechanisms" would be strengthened by a more thorough comparison of the pathways enriched with proteomics and genotyping data, separately, and with the merged dataset
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: INVESTIGATION OF MULTIPLE SCLEROSIS-RELATED PATHWAYS THROUGH THE INTEGRATION OF GENOMIC AND PROTEOMIC DATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I am fully satisfied with the revision. All suggestions were taken into account. No further comments from my side.


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: INVESTIGATION OF MULTIPLE SCLEROSIS-RELATED PATHWAYS THROUGH THE INTEGRATION OF GENOMIC AND PROTEOMIC DATA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The current version of the paper basically addresses all previously raised concerns
Experimental design: The only point possibily deserving deeper (although optional) discussion is the fact that a quite outdated protein-protein interaction network is adopted, while more than 10 years later the picture is probably changed.
Validity of the findings: No further comment
Additional comments: No additional comments


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

Input:
Title: A HIGHLY EFFECTIVE AND SELF-TRANSMISSIBLE CRISPR ANTIMICROBIAL FOR ELIMINATION OF TARGET PLASMIDS WITHOUT ANTIBIOTIC SELECTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper, Wongpayak et al. demonstrate a CRISPR-based approach to plasmid elimination in target cells, with the aim of combating antimicrobial resistance (AMR). The authors include a sufficient amount of raw data as supplementary information.

The paper is well-structured and well-referenced. Sufficient context for the work is provided in the Introduction, particularly highlighting specific problems with existing literature in the field in a convincing manner, clearly providing a good rationale for this study. The paper is self-contained and the authors write in clear and appropriate English throughout, though there are some instances of incorrect tense (e.g. line 23, “suffer” rather than “suffers”) and missing words (e.g. line 27, “targeted plasmid” should be “the targeted plasmid”) throughout the document. The manuscript would therefore benefit greatly from being proofread by a native-level English speaker.

The data presented are complex and the authors make good use of colour to distinguish strains and cell types in their graphs. However the authors tend to switch between different nomenclature for their plasmids (using what I assume to be a general term, e.g. pCRISPR, and a specific term, e.g. pgNDM1) throughout the manuscript – even from one sentence to the next within a single experiment. This is presumably done in order to reduce jargon, however I found that it actually made things harder to understand. The manuscript would be more readable if a consistent naming approach was maintained throughout (e.g. drop the generalised terms and use the actual plasmid names in all cases).

MINOR ERRORS
General: consider defining the CRISPR acronym upon first mention in the abstract and main text
Line 48: consider a more precise word than “breaks”, e.g. “cleaves”
Line 51: there is some kind of formatting error on this line
Line 56: there should be a comma before Staphylococcus
Line 74: Have the authors considered the presence of pre-existing surface exclusion factors that prevent conjugation?
Line 114: plasmid “pgEMPTY” is given later as “pEMPTY”, presumably this is a typo
Line 150: “1.5 tube” should presumably be “1.5 mL tube”
Line 270: Typo in pCRISPR
Line 273: “incompability” should be “incompatibility”
Throughout: “resistant” should be “resistance” in a few places
Throughout: there should be a space between “E.” and “coli”
Throughout: please use the symbol μ rather than u where appropriate (e.g. μg/mL, μL)
Throughout, including figure legends: genes and DNA sequences should be italicised
Results: I felt that subheadings would improve the readability of this section, if appropriate to the journal style
Figure 2B: there is a colour discrepancy between the key and the graph itself
Figure 4: formatting errors (the figure labels A/C have been cut off)
Experimental design: The design of the conjugation experiments themselves seem appropriate and the authors have included several steps that are fully reproducible from the instructions given; e.g. the number and amount of time that samples were vortexed. This is commendable.

Line 145-146: Donor and recipient cells were adjusted to OD600 ~ 0.3 prior to mixing, but it is unclear whether the cells are actually present at an equal concentration (i.e. CFU/mL). The authors do say in the methods that the 1:100 ratio is “by volume” rather than “by cell number”, which is appropriate, but elsewhere in the manuscript the implication is that cell numbers have been taken into account (e.g. the abstract: “at a low (1:100) donor-to-recipient ratio”). Since different strains have different OD-to-CFU relationships, this confounding factor must be explicitly addressed in order to make the claims about donor-to-recipient ratio valid.

As noted below, there is a complete lack of statistical analysis presented throughout the paper.
Validity of the findings: The major flaw of this study is the clear lack of statistical analysis. Given the nature of the data presented, this needs to be addressed prior to drawing conclusions.

Line 175-179, figure 1c: No statistical analysis is given to confirm the result here, though the data do seem to qualitatively support the claim.

Lines 193-202: Again, statistical analysis is required to confirm these conclusions. The results here (especially the red dots) are difficult to interpret. The claims made by the authors are not supported without thorough statistical analysis, taking into account multiple comparisons.

Lines 213-234: No statistical analysis is given to confirm these results, though the data do seem to qualitatively support the claims.

Lines 219-250: As above… These data are interesting but need statistical analysis to back them up.

Lines 263-4: The authors claim “pSubst by itself is unlikely to be able to enter, compete and replace pTarget that has already established in recipient cells”. However, this is not entirely clear; see below.

Line 278: The authors mention “not significantly different” but again do not present the results or type of statistical test used.

Lines 272-288: The authors try to address the question of whether a new plasmid can establish itself in a population that is already saturated with another plasmid from the same incompatibility group, but this is only tested in one direction with one pair of plasmids. The results are not broadly applicable. Given the tools on hand, the authors could have expanded this experiment to try a few different combinations before reaching conclusions here.

Lines 308-309: As above, the authors claim that “since pTarget and pSubst are from the same incompatibility group, pSubst cannot infect a cell that already has pTarget and vice versa”. To my understanding they haven’t tested it in both directions, so “and vice versa” cannot be claimed.

Figure 4C: I’m not sure what the authors mean by “…and plasmid replacement…” in the title for 4C. Is that evidenced by their experiment/data?

Lines 323-330: Again, no statistical analysis is presented.

Lines 331-332: The authors present a computer simulation in their supplementary material. It seems extensive – I see no reason why this could not be included in the main paper if the results are relevant.
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: A HIGHLY EFFECTIVE AND SELF-TRANSMISSIBLE CRISPR ANTIMICROBIAL FOR ELIMINATION OF TARGET PLASMIDS WITHOUT ANTIBIOTIC SELECTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: No comments.
Validity of the findings: No comment.
Additional comments: The manuscript by Wongpayak et al., studies dispersal of conjugative and mobilizable plasmids in E. coli hosts as well as the elimination of genetic target via CRISPR-Cas9 within recipient cells. To this reviewer, the manuscript appears to be of high quality. All the experiments are well-designed and -described. The study demonstrates that with specific plasmid combination a notable portion of the bacterial community can receive the plasmid and hence allow effective manipulation of the community even in the absence of selection for the desired plasmid.
However, conjugation experiments were carried out on nitrocellulose membranes where conjugation is very efficient. It would be nice to see what kind of recipient ratios would be achieved when conjugation is happening in liquid media and with/without shaking. Screening other conditions would also be valuable for the scientific community, like different nutrient ratios (e.g. high and low). These would help define what are the limitations of the observed number of recipients if there are any. Moreover, one practical limitations of the here-presented system is that one should know beforehand exactly the type of plasmid that needs to be replaced. In many instances, there are several plasmids present in e.g. ESBL-bacteria and as such targeting just one type of a plasmid may fail. The authors should discuss these topics in the manuscript. And overall, it should be mentioned that there is a need for in vivo and multi-species studies with these types of mobilizable CRISPR-plasmids in order to find the real limits and the potential of plasmid-based modification of heterogenous bacterial communities.  The language in the manuscript is overall good, but there are some small errors that should be fixed. With these changes, this reviewer would support the 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: A HIGHLY EFFECTIVE AND SELF-TRANSMISSIBLE CRISPR ANTIMICROBIAL FOR ELIMINATION OF TARGET PLASMIDS WITHOUT ANTIBIOTIC SELECTION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The general text has been improved and use of plasmid terminology throughout the manuscript has been made much clearer. I have no further concerns regarding the basic reporting.
Experimental design: I am pleased to say that the authors have addressed a major concern of mine: the OD-to-CFU relationship of the strains. This has now been appropriately defined and explained in the manuscript.
Validity of the findings: Generalisation of the system has been appropriately confirmed with an additional set of experiments. The authors’ use of a different plasmid replicon is particularly useful here, so is to be commended… However, I would disagree with their comment on supplementary lines 224-226 that “thinner” colony PCR bands imply lower target copy number. Band intensity from a colony PCR varies according to many factors and is not an appropriate way to measure plasmid copy number, hence no such conclusions can be drawn here. I suggest the authors simply remove this particular inference from the manuscript.

The authors have also added statistical analysis to the paper throughout, but there are some remaining issues:
1. The use of multiple t-tests to compare values within experiments is not ideal; an ANOVA with post-tests for multiple comparisons would be more appropriate, particularly in cases where a two-factor analysis is being performed.
2. There are some figure legends where the statistical indicators (*, **, etc) are not listed for each indicator that appears in the figure. For example, Figure 4 includes NS, ** and *** indicators, but only NS and ** are defined in the legend.
3. A full statistical methodology section could be added to the Materials & Methods.
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: IMPACT OF UMBILICAL CORD ARTERIAL PH, GESTATIONAL AGE, AND BIRTH WEIGHT ON NEURODEVELOPMENTAL OUTCOMES FOR PRETERM NEONATES
Review round: 1
Reviewer: 1

Output:
Basic reporting: Thank -you for asking me to review this interesting paper, exploring the link between umbilical artery pH and hypoxia by considering infant sucking skills.
Written style: Please have a thorough review of your written English. At times it is challenging to read. I can give a few examples which may help improve the writing, e.g. in the Abstract, line 9; “The initial assessment parameters such as the APGAR score and the umbilical artery pH ….”; in the Introduction, line 18, “Feeding problems are….” May be a better way to start your Introduction section.
References and literature review: I think that you need to revise some of the references used in your text to enable your paper to reflect fully the evidence base available to clinicians specialising in neonatal care.
-	You discuss parent absence or reduced access during COVID -19 – please use Fonte et al’s paper to support this statement, as you have no citation. Fonfe, A., Clements, D., & Mckechnie, L. (2021). Parental access to neonatal units: inconsistency during the COVID-19 pandemic. Infant, 17(2).
-	Please delete your sentence “The physical and emotional effects of separation should be investigated in further studies” in relation to your COVID statement as it has no bearing on your study, and you do not tie it to any aspect related to your study.
-	In relation to the development of sucking and swallowing, I would replace the Lau and the Reissland references you have and use the two Gewolb references here (these are the standard references in most neonatal papers in this area):
Gewolb, I. H., Vice, F. L., Schweitzer‐Kenney, E. L., Taciak, V. L., & Bosma, J. F. (2001). Developmental patterns of rhythmic suck and swallow in preterm infants. Developmental Medicine & Child Neurology, 43(1), 22-27.
Gewolb, I. H., & Vice, F. L. (2006). Maturational changes in the rhythms, patterning, and coordination of respiration and swallow during feeding in preterm and term infants. Developmental Medicine & Child Neurology, 48(7), 589-594.
-	Please study your literature review and mention that feeding readiness is an important part of infant feeding development and refer to White -Traut (2005) : White-Traut, R. C., Berbaum, M. L., Lessen, B., McFarlin, B., & Cardenas, L. (2005). Feeding readiness in preterm infants: the relationship between preterm behavioral state and feeding readiness behaviors and efficiency during transition from gavage to oral feeding. MCN: The American Journal of Maternal/Child Nursing, 30(1), 52-59.
-	Harding et al (2018) discuss non-nutritive sucking within the oral readiness paradigm – please cite: Harding, C., Cockerill, H., Cane, C., & Law, J. (2018). Using non-nutritive sucking to support feeding development for premature infants: A commentary on approaches and current practice. Journal of pediatric rehabilitation medicine, 11(3), 147-152.
-	Not all infants go home fully orally fed, and have a variety of presentations if there are early problems. Please cite: Harding, C., Frank, L., Botting, N., & Hilari, K. (2015). Assessment and management of infant feeding. Infant, 11(3), 85-89.
-	You mention positioning. This paper may be useful to cite: Clark, L., Kennedy, G., Pring, T., & Hird, M. (2007). Improving bottle feeding in preterm infants: Investigating the elevated side-lying position. Infant, 3(4), 154-158.
Experimental design: Method: Please state if the parent consent was written / signed. Please additionally state how long parents had written information about the project before agreeing to take part. Please can you present a clear rationale for using the NBAS to assess sucking reflexes? You discuss feeding problems, but you do not discuss anywhere the links between nutritive and non-nutritive sucking development (you can cite Harding et al, (2018) for this).
Data: Your correlations are not clear. In your Abstract, you report only the p value. I think it would be more useful for your readership to use the APA method or reporting correlations. I state this because you Abstract reporting is not clear – and the Spearman values are actually weak, 0.27 for one value, and moderate at .30 and .34 for the other two outcomes. Please re-consider how you will present your data.
Validity of the findings: Applicability: Please discuss how your study can have practical benefit and application for infants, clinicians and families in neonatal care. At present, its practical benefits are difficult to discern.
Additional comments: Please see my comments above. Although this is an interesting area, I feel that the paper needs further revisions and re-writing before it can be useful to the wider neonatal readership.


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: IMPACT OF UMBILICAL CORD ARTERIAL PH, GESTATIONAL AGE, AND BIRTH WEIGHT ON NEURODEVELOPMENTAL OUTCOMES FOR PRETERM NEONATES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The aims are reported to be identifying the neurodevelopmental factors associated with sucking. Neurodevelopmental factors, including sucking, were evaluated via the NBAS. The study’s aim was actually to identify how infant characteristics (gestational age at birth, birth weight, gestational age at assessment, and umbilical artery pH) were associated with neurodevelopmental outcomes measured by the NBAS, including sucking. The reporting and title need to better reflect this.

The introduction needs to provide background on all the neurodevelopmental outcomes that were assessed during the study, not just those that turned out to have a significant correlation with pH. The background information on sucking needs to focus more on feeding problems that occur in the neonatal unit – why some infants may have difficulty with sucking and feeding, how this is assessed on the NBAS, how it may present when attempting to feed, and why this is a clinically important problem.

The introduction is brief and needs to provide details of existing literature regarding correlations between infant characteristics and neurodevelopmental outcomes, including feeding.

The introduction includes several sections that are of little relevance to the study, or need to be more clearly linked with what the study aims to find out e.g. these findings are unlikely to help reduce length of stay and get infants home to their parents more quickly, and it is not explained how the study findings would help diagnose feeding problems to facilitate therapy. Additionally, I’m concerned about the suggestion that a chin tuck position may be ‘proper positioning’ – is there any evidence that this would be safe in neonates?

The discussion need to better discuss the findings, including those that were not statistically significant correlations, in relation to what is already known about factors associated with neurodevelopmental outcomes. Do these results agree with what previous studies have identified? Also, how could your findings impact on clinical practice? And what further research is needed to expand and further develop your findings?
Experimental design: As stated above, the stated research aims aren’t consistent with the study as it was carried out. Additionally, there is insufficient detail about the infants included in the study. Other than inclusion/exclusion criteria, how were the infants identified for study? First 100 to meet eligibility criteria? All eligible admissions between certain dates? The authors also need to give more details about the participants e.g. range of gestational ages, gestational age at assessment, proportion of the sample with common comorbidities e.g. intraventricular haemorrhage.
Validity of the findings: Raw data was provided and this shows many participants had missing data e.g. no pH data or incomplete NBAS data. Why was this data not collected and how was this accounted for in the statistical analysis? I would also like to see results for all the components of the NBAS, not just the results that had a statistically significant correlation.

Results need to include confidence intervals as well as, or instead of p-values, as it is not clear if the sample size (16 infants with an absent sucking reflex) is sufficient to reliably determine a correlation with other factors.
Additional comments: These findings are potentially interesting but more work is needed to develop this paper 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: IMPACT OF UMBILICAL CORD ARTERIAL PH, GESTATIONAL AGE, AND BIRTH WEIGHT ON NEURODEVELOPMENTAL OUTCOMES FOR PRETERM NEONATES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Much improved.
Experimental design: Much improved. However, with Spearman's correlation, please make the R you have small, as r, and please make sure p is in lower case and italicised.
Validity of the findings: Much improved.
Additional comments: This paper has been much improved by the changes.


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

Input:
Title: DETECTION OF SPREADER NODES IN HUMAN-SARS-COV PROTEIN-PROTEIN INTERACTION NETWORK
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written and easy to read. Background material is presented in a clear and concise way. Figures and tables are of high quality.
Experimental design: The research question is well defined. Methods are described in full detail.
Validity of the findings: The findings are valid, and can be easily replicated. However, see the general comments below.
Additional comments: The authors focus their study on the SARS-CoV protein-protein interaction network because of the high genetic similarity of SARS-CoV and SARS-CoV-2, but the protein-protein interaction network of SARS-CoV-2 has also been studied (10.1038/s41586-020-2286-9). The manuscript will be much more meaningful by performing the same analysis on the SARS-CoV-2 protein-protein interaction network as well. This would allow to draw further conclusions about the pattern of disease propagation from virus to human.


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: DETECTION OF SPREADER NODES IN HUMAN-SARS-COV PROTEIN-PROTEIN INTERACTION NETWORK
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is an interesting and important study that adds significantly to the field and will have a noticeable impact.

Although the manuscript is written in a professional English, in my view an excessive usage of "transmission of infection", "transmit the infection", "infected proteins", "susceptible proteins which are not yet infected but are at risk of getting infected",  "proteins that have recovered and again become susceptible: and other alike terms is misleading. Protein cannot be infected. A node in PPIN cannot transmit infection. Therefore, statement on lines 282-284 "the infection will penetrate further in human PPIN resulting in a significant fall in human immunity level followed by the severe acute respiratory syndrome" is misleading and confusing. Although it is clear what the authors want to say here, the used terminology is wrong, as in reality they are considering transmission of information, and not infection. Therefore, all related parts of the manuscript should be rewritten to make ideas less ambiguous.

Also, it is highly advisable to provide definitions of all the network-related terms (e.g., centrality, degree, node weight, neighborhood density, etc.) in a layman language. In fact, readers not familiar with graph theory would be completely lost.
Experimental design: Experimental design is appropriate.
Validity of the findings: Findings are interesting and important, but their description uses wrong terminology and therefore is very confusing.
Additional comments: The idea of introduction of the spreadability index for the analysis of the transmission of information within SARS-CoV and human PPINs and from SARS-CoV PPIN to human PPIN is very interesting and promising. Data generated as the result of the implementing of this measure are useful. However, the terminology used for the description of the work is misleading and confusing.