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

Input:
Title: DIVERSITY AND SPOILAGE POTENTIAL OF MICROBIAL COMMUNITIES ASSOCIATED WITH GRAPE SOUR ROT IN EASTERN COASTAL AREAS OF CHINA
Review round: 10
Reviewer: 1

Output:
Basic reporting: 1 BASIC REPORTING
Clear, unambiguous, professional English language used throughout.
The English language needs improvement. In particular substantial review for the style is necessary.
Intro & background to show context. Literature well referenced & relevant.
The introduction section has been improved. Please revise according to specific comments below.
Structure conforms to PeerJ Standards, discipline norm, or improved for clarity.
The structure conforms to PeerJ Standards.
Figures are relevant, high quality, well labelled & described.
Figures are relevant, of good quality, labelled and described as shown by figure captions and in the main text. Please revise according to specific comments below.
Raw data supplied.
Raw data are supplied in the supplementary files.
Experimental design: 2 EXPERIMENTAL DESIGN
Original primary research within Scope of the journal.
Research is in accordance with Scope of the journal.
Research question well defined, relevant & meaningful. It is stated how the research fills and identified knowledge gap.
Research objectives are well defined, relevant, and meaningful:
The workflow has been revised.
Rigorous investigation performed to a high technical & ethical standard.
Research activities are performed following high technical and ethical standard.
Methods described with sufficient detail & information to replicate.
The methods are described with sufficient information regarding procedures and materials used.
Validity of the findings: 3 VALIDITY OF THE FINDINGS
Impact and novelty not assessed. Negative/inconclusive results accepted. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
All underlying data have been provided; they are robust, statistically sound & controlled.
Data have been provided and they are relevant, statistically analysed and checked. Please revise according to specific comments below
Conclusions are well stated, linked to original research question & limited to supporting results.
Conclusions have been revised but still need minor corrections. See below.
Speculation is welcome, but should be identified as such.
-
Additional comments: Dear authors,
the manuscript has been carefully revised in its structure, changing the order of results presentation as correctly suggested by the Editor. However, this Reviewer still detected minor changes to be made throughout the manuscript. In particular, several errors highlighted by the Editor in the previous revision were not corrected. In addition, other errors and style mistakes need a substantial correction. For these reason I strongly suggest a "Final Minor Revision" prior to the publication in Peer J.

Please revise according to the following specific comments:
Specific comments
Line 44. Italicize “in vitro” and the microbial species (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis and so on). Carefully check throughout the manuscript. Italicize also phylum, class, microbial family and microbial genera!!
L48 Delete could. These species spoil grapes as revealed by the spoilage in vitro assay!!
Lines 48-51 Please revise in: This suggests that the microorganisms responsible for grape spoilage in eastern coastal areas of China are in accordance with those isolated in vineyards worldwide. For the first time, opportunistic pathogens were isolated from rotten berries.
L73-74 Please use et al. when the authors are more than two. Please check the references throughout the manuscript
L79 Add the sentence: This microbial consortium produces spoilage metabolites such as acetic acid and gluconic acid (Pinto et al., 2019).
Add this reference (Pinto L., Malfeito-Ferreira M., Quintieri L., Silva A. C.,  Baruzzi F. 2019. Growth and metabolite production of a grape sour rot yeast-bacterium consortium on different carbon sources. International journal of food microbiology, 296: 65-74. DOI: 10.1016/j.ijfoodmicro.2019.02.022) in the References
Line 70-71. Avoid passive voice revise to “Basidomycetes.. dominate intact grape”
L85 Replace with …than in asymptomatic ones.
L140 Mothur with capital letter. Please revise
L287-291 Please revise in: “We identified Firmicutes as the dominant phylum (60%), with nine Gram-positive bacteria species (i.e., Staphylococcus saprophyticus, Lactococcus garvieae, Lactobacillus plantarum, two Lysinibacillus species, and four Bacillus species). We also isolated six Gram-negative bacteria species assigned to the phylum Proteobacteria.”
L292 Remove ; and replace with whereas
L293 Remove that
L343-344 Replace sour rot with spoilage
L385 Replace “microbes” with “microorganisms” and “sour rotting of grapes in” with “spoilage is”
L430 Correct with “the biofilm formation…”
L439 ethanol to acetic acid (Pinto et al., 2019). Please add this reference already suggested for the inclusion in the Introduction section.
L454-455 Revise in: “The microbes associated with sour grape rot in eastern coastal China appear similar to those associated with this disease…”
L457 Delete can.
Table 1 Delete means
Table 2 Present all parameters as integers. Replace “OTUs diversity, number” with “Diversity indices of”
Fig 2  Legend. Insert space in “ongenus”
Figure 3 legend. Replace “lables” with “labels”
Figure 5 Revise in: The percentage of incidence of microorganism using merged (A) or separated (C) methods; McKinney index of microorganism using merged (B) or separated (D) methods. Different letters in each figure indicate significant difference between microorganisms (One-way ANOVA; α = 0.05)


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

Input:
Title: DIVERSITY AND SPOILAGE POTENTIAL OF MICROBIAL COMMUNITIES ASSOCIATED WITH GRAPE SOUR ROT IN EASTERN COASTAL AREAS OF CHINA
Review round: 10
Reviewer: 2

Output:
Basic reporting: Abstract: All scientific names but be italicized

Line 177-178: This scale does not establish the presence/absence of sour rot symptoms, but instead whether the berry was successfully colonized by the inoculated microorganism. “Disease spot” is not an accurate term in this context, as this test is not rating disease symptoms.

Line 245: While Figure 4A shows that the organisms have indeed colonized the berries, none of the berries show sour rot symptoms: lack of turgor in the berry, liquefaction of the berry pulp. All the berries appear intact, which is not consistent with sour rot. I recommend that the authors note this distinction – these organisms are associated with sour rot-affected grapes and not necessarily the causal organisms. If the authors want to see if these organisms can cause symptoms, they must include axenic Drosophila in the experiment, as fruit flies are causal organisms in this disease complex (Hall et al. 2018). What is the purpose of including the infection rates of these microorganisms if they are not causal? The authors may want to consider excluding these if they are not necessary, so as to make the paper clearer.

Citations: Formatting changes required throughout.

Tables 1, 2, 3  and 4 titles: Should be changed to ‘sour rot-affected grapes’

Table 3: Formatting needs to be corrected so words are not cut off on two lines

Figure 2: “on genus” and “on phylum” are two words each

Figures 3 and 4: All scientific names but be italicized
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: STATE-SPACE MODELING OF THE DYNAMICS OF TEMPORAL PLANT COVER USING VISUALLY DETERMINED CLASS DATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: It is an important subject. However, I have some reservations regarding the model and generally the English could be improved.

The formulas are not numbered so in the following line 113+ means the formula after 113.

Line 113+. I do not understand the time-series model. Why not an AR2 model (that should be discussed) and what happens if years are missing as is the case for the empirical data set.

Line 117+. The spatial variation among quadrats are here modelled by a random variable. But this variation is also modelled by delta. I suggest you save the random variable for among-plot variation and test if delta are adequate to model the within-plot variation. In the current model, the parameter delta cannot be interpreted.

Line 122+. Why not use a strong prior instead (as in line 117+), please explain.

Line 169. Only one plot is modelled. It would be more convincing if all plots were modelled (see also comment to line 117+).

Figure 4. Explain that class 0 and 1 was modelled as 1 class (if this is the case).

Figure 5. The mentioned red and black curves are missing.

Figure 6. I am not familiar with a “rootogram”, please explain


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: STATE-SPACE MODELING OF THE DYNAMICS OF TEMPORAL PLANT COVER USING VISUALLY DETERMINED CLASS DATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: please see my uploaded comments on the pdf of the article.
I feel sort of awkward basically saying "you should cite my work." But I hope providing those connections in the literature are helpful for all of us. My main confusion was around the highlighted section and the intepretation of Figure 2, but refer to my commented pdf.


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

Input:
Title: STATE-SPACE MODELING OF THE DYNAMICS OF TEMPORAL PLANT COVER USING VISUALLY DETERMINED CLASS DATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: na
Experimental design: na
Validity of the findings: na
Additional comments: I find that the author adequately has responded to 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: STATE-SPACE MODELING OF THE DYNAMICS OF TEMPORAL PLANT COVER USING VISUALLY DETERMINED CLASS DATA
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I appreciate the author's work to respond to my previous comments.
I found this work interesting and a contribution to the world of modeling plant cover data.
K.M. Irvine


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: PREVALENCE AND CORRELATES OF DEPRESSIVE SYMPTOMS AMONG CHINESE PATIENTS WITH CATARACTS TREATED IN TERTIARY GENERAL HOSPITALS
Review round: 1
Reviewer: 1

Output:
Basic reporting: None
Experimental design: none
Validity of the findings: none
Additional comments: see the attachment.


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: PREVALENCE AND CORRELATES OF DEPRESSIVE SYMPTOMS AMONG CHINESE PATIENTS WITH CATARACTS TREATED IN TERTIARY GENERAL HOSPITALS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The literature review is comprehensive
Experimental design: 1. The authors described that their sample of patients with cataract, but I think the representativeness of this sample is also limited because patients were from two hospitals only. Please consider to tone down their sentences or terms. The strength is consecutive sampling method used.
2. For administering the HADS scales, face-to-face interview, training of investigators and inter-rater reliability must be reported. Did the authors tested this before the formal survey?
3.To facilitate the policy-making of mental health services such as CLP, data on mental health services utilization are also necessary. It would be helpful if the authors provide such data.
Validity of the findings: Response rate of subjects is lacking in the results.
Additional comments: 1.If possible, the recognition and management of depression among patients with cataract in Chinese clinical practice is also useful. It would improve the quality of study much if the authors have investigated these.
2.The study procedures, completing self-administered scales via clinical interviews, would result in underestimation of the prevalence. Please discuss this possibility.


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: PREVALENCE AND CORRELATES OF DEPRESSIVE SYMPTOMS AMONG CHINESE PATIENTS WITH CATARACTS TREATED IN TERTIARY GENERAL HOSPITALS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The paper is written clearly and readable. The authors systematically summarized what has been known and unknown about depression in patients with cataract and also analyzed the limitations of existing literatures.
Experimental design: The study design is a hospital-based cross-sectional survey, determining the prevalence and correlates of depressive symptoms of Chinese patients with cataract. Given that studies in this area are limited, the current study fills some knowledge gaps.
Validity of the findings: The study design is appropariate and analytic approaches are correct. Findings are good and conclusions are made strictly.
Additional comments: I have the below comments for the authors.
1. One major limitation of previous studies is the limited sample representativeness as criticized by the authors. However, the present study is only a two hospital-based survey, I do not agree that the sample recruited by the authors is representative.
2. The sample size is 339.In general, considerations for sample size estimation should be provided for an epidemiological survey.
3. The term "depression" is unclear. In fact, the authors focused on depressive symptoms, not disorders. Please address this issue all throughout the paper.
4. The other question is no data on depressive disorders, such outcome measurement is more clinically relevant.
5. I speculate that there would be more clinical correlates associated with depressive symptoms such as length of illness, family support, functional impairments and chronic illnesses. However, it seems that the authors assessed a limited number of clinical characteristics of the patients.
6. HADS measure both depression and anxiety, but the authors focused on depression only. It would be helpful if results on anxiety are available.
7. For data analysis, moderate and good levels of family economic status were combined. Reason for this should be specified.
8. Treatment factors such as days before and after the operation and success in cataract operation are also potentially important for the emotional status of patients.


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: PREVALENCE AND CORRELATES OF DEPRESSIVE SYMPTOMS AMONG CHINESE PATIENTS WITH CATARACTS TREATED IN TERTIARY GENERAL HOSPITALS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no
Experimental design: no
Validity of the findings: no
Additional comments: i am satisfied with most of your revision. However, there are two minor suggestion for the revised manuscript.
1. Line 147. I suggest using "all, P<0.05" to replace "P≤0.047".
2. Table 2. OR is a abbreviation. Please add  a  footnote.


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: PREVALENCE AND CORRELATES OF DEPRESSIVE SYMPTOMS AMONG CHINESE PATIENTS WITH CATARACTS TREATED IN TERTIARY GENERAL HOSPITALS
Review round: 2
Reviewer: 2

Output:
Basic reporting: none
Experimental design: none
Validity of the findings: none
Additional comments: none


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

Input:
Title: PREVALENCE AND CORRELATES OF DEPRESSIVE SYMPTOMS AMONG CHINESE PATIENTS WITH CATARACTS TREATED IN TERTIARY GENERAL HOSPITALS
Review round: 2
Reviewer: 3

Output:
Basic reporting: No further comments
Experimental design: No further comments
Validity of the findings: No further comments. I am satisfied with the revisions.
Additional comments: No further comments.


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

Input:
Title: COMPREHENSIVE ASSESSMENT OF THE COUPLING COORDINATION DEGREE BETWEEN URBANIZATION AND ECOLOGICAL ENVIRONMENT IN THE SIBERIAN AND FAR EAST FEDERAL DISTRICTS, RUSSIA FROM 2005 TO 2017
Review round: 1
Reviewer: 1

Output:
Basic reporting: The relationship between urbanization and ecological environment is a problem worthy of study. This paper is well organized and provided sufficient analysis,but its novelty needs to be enhanced. And I feel that the literature review is not concise enough in the introduction part.
Experimental design: Methodology section needs to be strengthened. This study employed CCDM to evaluate the coupling coordination degree between urbanization and the ecological environment. I just wonder if the discussion about the methods is enough. It is better to add some contents of the methodologies usually used for this kind of study with the pro and cons. Besides, maybe I missed it, but how did you decide index themselves?
Validity of the findings: The conclusions and discussion part should be enriched and reorganized. It is better to give us more information about the comparison of your research with previous research. You need to compare your results in the context of literature research and discuss their implications.
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: COMPREHENSIVE ASSESSMENT OF THE COUPLING COORDINATION DEGREE BETWEEN URBANIZATION AND ECOLOGICAL ENVIRONMENT IN THE SIBERIAN AND FAR EAST FEDERAL DISTRICTS, RUSSIA FROM 2005 TO 2017
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The article is at a very high scientific level. The topic deals with important, practical issues. The theoretical background is well presented. The aim of the article was defined correctly. The research process has been deeply thought through and conducted without objections. Advanced statistics were also used. A reflexive summary was made. The scientific maturity of the authors is confirmed by the presented recommendations.


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: COMPREHENSIVE ASSESSMENT OF THE COUPLING COORDINATION DEGREE BETWEEN URBANIZATION AND ECOLOGICAL ENVIRONMENT IN THE SIBERIAN AND FAR EAST FEDERAL DISTRICTS, RUSSIA FROM 2005 TO 2017
Review round: 1
Reviewer: 3

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: This paper estimated the coupling coordination degree between urbanization and ecological environment in the Siberian and Far East Federal Districts, Russia. The research perspective and content of this study are innovative, and the conclusions are reliable. However, I still have some comments as follows:
1.     For the urbanization-ecological environment index system. In the urbanization index system, it includes three first grade indicators (demographic urbanization, economic urbanization, and social urbanization) and 11 basic indicators, while in general, urbanization should also include indicators of spatial urbanization, but why is it not reflected in the article. I suggested to increase indicators in this regard, or give reasons for why not. In addition, there are 11 basic indicators in urbanization index system, but only 6 basic indicators in ecological environment index system, which is unequal and has a big difference in quantity between them, this may lead to inaccuracies when calculate the coupling coordination degree between urbanization and ecological environment.
2.     For the results analysis. There are 5 basic indicators in social urbanization, 4 basic indicators in economic urbanization, but only 2 basic indicators in demographic urbanization. The index quantity was unequal among the 3 first grade indicators for urbanization, so that there is no doubt that social urbanization (44.29%) > economic urbanization (33.43%) > demographic urbanization (22.28%), thus this analysis was meaningless.
3.      For the discussion. The discussion in the present paper should be improved.


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

Input:
Title: COMPREHENSIVE ASSESSMENT OF THE COUPLING COORDINATION DEGREE BETWEEN URBANIZATION AND ECOLOGICAL ENVIRONMENT IN THE SIBERIAN AND FAR EAST FEDERAL DISTRICTS, RUSSIA FROM 2005 TO 2017
Review round: 1
Reviewer: 4

Output:
Basic reporting: Your introduction gives more research about the relationship between urbanizaion and enviornment, but introduction is not the list most of that research, you should summarize and extact the main thought and progress on the research, and give the gaps or problems of former research.
Experimental design: In your urbanizaiton-ecological environment index system, the basic indicator including total indicators and average indicators. I think some total indicators should change to average indicators, such as Gross regional product, number of high education institutions, number of sports facilities, and all the indicators of ecological environment subsystem.
Validity of the findings: After updating your indicator, you will get different findings. So the results and conclusion maybe need rewrite.
Additional comments: The structure, figures, tables are all good, and the raw data are valuable. Because your key indicators are inappropriate, the paper need rewrite and resubmit.


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: COMPREHENSIVE ASSESSMENT OF THE COUPLING COORDINATION DEGREE BETWEEN URBANIZATION AND ECOLOGICAL ENVIRONMENT IN THE SIBERIAN AND FAR EAST FEDERAL DISTRICTS, RUSSIA FROM 2005 TO 2017
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The revised manuscript has seriously solved my questions with the original manuscript. I think it has met
 the publication criteria of Peer J.


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: PHYSIOLOGICAL AND ANATOMICAL DIFFERENTIATION OF TWO SYMPATRIC WEED POPULATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The study deals with trait differences between two ecotypes of Capsella bursa-pastoris which are linked to gas exchange and photosynthesis. In short, both ecotypes were found to differ with respect to stomatal density and assimilation rates, particularly under high-light conditions. Although the contribution represents a quite short manuscript, the topic of physiology-related anatomical differences of different ecotypes should be of interest to many readers. However, the data analysis falls short of essential steps to evaluate gas exchange and assimilation parameters (currently, the manuscript looks more like a descriptive report). There are quite a few more things that can be done with the data, and which would make the contribution much more attractive.
From the available A/Ci curves, it should be possible to calculate key parameters, particularly Vcmax and gs against Ci (or Ca). Particularly, it would be relevant to determine the limitation of assimilation by stomatal conductance gs. It would also be possible to estimate gs max differences between both ecotypes on the basis of the microscope images (for example, using the equation of Parlange and Waggoner, 1970, Plant Physiology) and to compare the result with the measured gs. With respect to plant performance in the natural habitat: are there significant differences which can be derived from the lab results?
Furthermore, the Discussion section starts with discussing leaf type differences between C. bursa-pastoris ecotypes, on more than one page, until it is stated that “…we neglected the character leaf type in our experiment.” Why do the authors discuss leaf type when it was not considered here?
Some specific comments are listed below.

Specific comments
Line 81: “…indicating that overall evolutionary fitness remains unaffected…” Only the fitness-related factor “seed production” appears to be unaffected. Additionally, “evolutionary fitness” sounds awkward.
Line 145: “…a conductance of at least 0.2 was maintained…” Please provide units.
Lines 226 – 228: “The ecotypic adaptation of the leaf to various habitats and conditions at geographically and climatically different places of origin of many populations became obvious.“ What does this sentence mean?

Lines 242 – 244: “The physiological advantage is accompanied by higher stomata density on the upper and lower epidermis. It seems that the higher photosynthetic capacity is gained by a higher number of stomata per area. Physiological differences between high-light and low-light conditions might be the consequence of anatomical improvement,…” These assumptions may be supported by the data analysis suggested above.

Figure 4 and Table 1, and Supplement: “Stomata above” and “Stomata below”: Unusual description: should be substituted by adaxial/abaxial.


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: PHYSIOLOGICAL AND ANATOMICAL DIFFERENTIATION OF TWO SYMPATRIC WEED POPULATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: PEERJ 38123: Stable intraspecific sympatry between weed ecotypes in a single habitat

The objective of this work was studied the ecotypic differentiation of the rosette leaf using anatomical and physiological methods in C. bursa-pastoris (wild type) y C. apetala (Spe-mutant). At that point I recommended rejection due to the lack of sufficient depth and novelty in the manuscript, but I recommended resubmission with new data and/or rewritten. There are many aspects of the methodology that are difficult to interpret and thus need to be clarified. I include the most important doubts in that follows.
The major fails of the manuscript are in the next section.

Another minor comments
- The title is not very informative about the content of this work. I suggest rewrite
Line 93. Where the plant accumulate assimilates? In the same leaves or in storage organs as reserves?
line 94. The relationship between accumulation and yield need a citation.
What is plant habitus? Life form is a better term…. .
Line 152-155. All this paragraph is method… it did not report any result. How authors measured plant habitus?
Lines 170-174. All this paragraph is method….
Plant Material: For the analysis of both ecotypes, authors used a bulk seed of two populations?
the verb tenses of the results are incorrect
Line 181. What is “plants were grown in LL” LL never was defined.
Experimental design: Your introduction needs more detail, about the leaf trait that authors measured and why (justification of this work). It has a larger description of flower type and pollinators, fecundation, etc. only to support the idea that the population of both ecotypes C. bursa-pastoris and C. apetala have a lot of barriers limiting their crossing. I suggest reduce this information, because it is not relevant for the study of rosette leaves. However, nothing is explained about the importance of leaf traits for ecotypic differentiation, and specifically why the traits that authors choice (stomatal density and photosynthesis only).

The objective need to be better stablished, including some hypothesis about why authors expect differentiation in the rosette leaves between ecotypes. If populations are sympatric, and the leaf function is mainly (as described) photosynthesis, accumulation, and protection; Why authors expected that the rosette leaves differ? Also, in materials and methods, authors say that divided plants in two treatments: (i) high-light setting (600 μmol quanta m-2s-1); (ii) low-light setting (100 μmol quanta m-2s-1). Why? Which is the objective of the light treatment? In the result section authors report floral induction…. But neither in materials and methods nor in introduction mention this point.

Traits: Authors measured morphological and physiological traits such as: stomata density, photosynthesis rate and Ai vs Ci curves. I consider that there are many others leaf traits that provide important eco-physiological information like Specific leaf area, leaf thickness, leaf size, and are related to resource use strategy. To include some of these traits could greatly enhance the manuscript. I consider that there are not many traits to make a complete characterization of ecotypic leaf differentiation.
There is not a section of statistical analysis in materials and methods section. Why use a non-parametric analysis? The difference in stomatal density should be analyzed with a two-factor analysis: Light intensity and ecotype. I cannot understand the information showed in Table 1: it is incomplete? What is the number shown? What is compared? Differences between ecotypes or light intensities? Is there interaction?
Authors need to explain how to analyze the curve Ai vs ci. In the result sections describe a lot of parameters that is impossible to see in the figure.
Validity of the findings: I consider that the discussion section is not focused on the objective of the manuscript. It describes a lot of genes or loci responsible of the leaf type determination, while the objective of this work is a morphological and physiological characterization. If there are four leaf type possible… it would be described in the introduction. Which are these?
I can not to put in context the discussion about the differences in the responses of the ecotypes to the light environments because I do not understand the objective of this treatment. It is not clear along all 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: PHYSIOLOGICAL AND ANATOMICAL DIFFERENTIATION OF TWO SYMPATRIC WEED POPULATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript is now organized more clearly, and focuses on some well-defined aspects. Briefly, differences in assimilation and stomatal density of the two ecotypes are now addressed and reported, considering different light regimes. In this form, the manuscript is suitable for a Short Communication.
Experimental design: Information should be added how many leaves were used for the gas exchange measurements. Obviously, one individual was used for each type. These information should be clearly stated in the manuscript, because it is not obvious from Supplementary Table S2, which represents the output of the gas analyzer.

L. 142: In their response letter (but not in the text), authors explain that stomatal conductance is expressed as fraction of fully opened stomata (0.2 would then mean 20 %). However, there are still no absolute values provided. In Suppl. Fig. 1, stomatal conductance (as fraction) varies between 0.1 and 0.35 (roughly). It is totally unclear, what the reference for the the fraction values is. Usually, in gas exchange studies, total absolute values are provided.
Validity of the findings: No comment.
Additional comments: There are some comments left:
Abstract:
“Even under limiting CO2 concentrations….“ I would suggest: “Even under ambient and subambient CO2 concentrations….“
“Any disadvantage due to less…“ This and the following sentence are quite unclear. I recommend to overhaul this last part oft he abstract to provide a concise summary of the basic results.

L. 49: Maybe, “flower structure“ would be a better term?
Ls. 61-63: Which type was preferred by pollinators?


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: OPTIMIZING A RELIABLE EX VIVO HUMAN BLOOD MODEL TO ANALYZE EXPRESSION OF STAPHYLOCOCCUS EPIDERMIDIS GENES
Review round: 1
Reviewer: 1

Output:
Basic reporting: A good background is provided in this manuscript.
Hypotheses are clear and well explained. Results address the hypotheses and the article structure is well presented.
Literature references are comprehensive. One exception is on Line 138, where Turkey’s comparisons requires referencing.

The text needs some minor modifications particularly regarding English use:

Abstract

Consider replacing: ‘set-up conditions’ with ‘variables’.
In the second sentence limit the use of ‘however’ to once. (Lines 16-17)
Line 21: Plural of inoculum is inocula. Inoculums (used throughout text) is rarely used in English. Personally, I would consider replacing this with, ‘Higher bacterial concentrations produced a more significant loss of antimicrobial activity.’

Introduction

Line 32: Consider replacing originate with cause.
Line 33: Consider replacing urgent with important.
Line 34: Consider replacing endure with survive.
Line 37: Replace, ‘This model have’ with ‘This model has’
Line 40: Replace ‘faecallis’ with ‘faecalis’
Line 44-45: Consider replacing: ‘However, often, the implementation of these models lacks optimization’ with ‘However, the implementation of these models often lack optimization’
Line 52: Consider replacing: ‘Besides that’ with ‘Additionally’

Materials and Methods

Line 76-77: Consider replacing, ‘Negative control was accomplished’ with ‘Negative controls were achieved’.
Line 78-79: This sentence does not describe determination of bacterial concentration. Were the aliquots inoculated onto solid agar plates?  Was this performed using replicates?
Line 90: Separate overtime to over time.
Line 94: Consider replacing ‘during 10 minutes’ with ‘for 10 minutes’.
Line 103: Replace ‘mixed, on’ with ‘mixed in’.
Line 107: Exclude comma after rpm
Line 111: Consider replacing ‘experimental set-ups’ with ‘experimental variables’.
Line 134: Replace ‘Reactions efficiency’ with ‘reaction efficiencies’.
Line 138: ?two-away ANOVA or two way ANOVA
Line 153: Consider replacing, ‘Some bacterial death’ with a more concise description.
Line 160: Consider replacing ‘rest of’ with ‘remaining’.
Line 171: Consider replacing ‘inoculums’ with ‘concentrations’.
Line 174: Consider replacing ‘the is inherent to particular traits’ to ‘the inherent traits’.
Line 173-174: The author explains that the source of donor blood (gender and age) may contribute to variability of experimental results. Genders of the donors are revealed in Raw data for Figure 1 but not the age. I noted marked variation in total leukocyte counts in donor A compared to the donors J and N at T0 and 8 hours. Perhaps adding age range could add to the date set since age was initially presented as a variable by the author.
Line 184: Exclude comma after survival.
Line 186: Exclude ‘it’s’ at the end of the line.
Line 189-190: Consider replacing ’this percentage was slightly’ with ‘cell death rate was slightly’.
Line 197-198: Consider replacing ‘’this is an extensive period of incubation could yield’ with ‘ 12 to 24 hours is an extensive period of incubation which may yield’.
Line 202: Consider replacing ‘An easy…………the blood under gentle agitation’ with ‘simple way to ……the blood using gentle agitation’.
Line 205: Replace ‘leukocytes’ with ‘leukocyte’
Line 214: Consider rewording ‘very long periods’.
Line 215: Consider replacing ‘4h of interval’ with ‘an interval of 4h’.

Conclusion

Line 239: Replace ‘evasion from’ to ‘evasion of’.
Line 240-241: Please consider replacing ‘help to plan a better and more reliable model’ with ‘contribute to standardization of experimental conditions and produce a more reliable model’.
Line 241-242: Consider replacing ‘These findings are’ with ‘The findings from the study’
Figures 1, 2 and 3: Turkey’s multiple comparison test – Turkey has been spelled ‘Turkey’ and ‘Tukey’.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I commend the authors for their experimental work and manuscript.
Most suggestions are related to use of the English language and will ensure that an international audience can clearly understand the text.
I look forward to seeing the publication of this article.


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: OPTIMIZING A RELIABLE EX VIVO HUMAN BLOOD MODEL TO ANALYZE EXPRESSION OF STAPHYLOCOCCUS EPIDERMIDIS GENES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors clearly state the primary aim of the study, which is to identify the key parameters which could affect experimental outcomes using an ex vivo blood model for investigating s. epidermidis transcriptional responses. The authors rightly state that variation in experimental design between laboratories can result in varied results and understanding the parameters which have the greatest effect on experimental outcome could help guide future experiments and lead to standardised methods.
Although the manuscript is mostly well written, there are a number of grammatical errors and it would benefit from proof reading by a native speaker.
I feel the term “blood viability” needs to be clearly defined in the introduction as this term is ambiguous. Does it relate to the number of viable red blood cells, white blood cells, all cells, complement activity?
I also feel some of the claims made in abstract are too ambitious. For example “the volume of human blood could be reduced to as little as 0.18 ml without affecting the stability of gene transcription”. This sounds as if all genes within the genome were analysed. As only a small set of genes (three in total) were analysed, perhaps this could be rephrased to “the volume of human blood could be reduced to as little as 0.18 ml without affecting the stability of transcription of genes under investigation in the current study” or similar.
Similarly, the statement “Our data demonstrated that a loss of 2% of blood viability after 4h of collection resulted in a 5-fold loss of antimicrobial activity against S. epidermidis” It has not been confirmed that this loss of antimicrobial activity is directly related to the small reduction in leukocyte viability seen as the levels of other antimicrobial components of the blood were not measured during this time period. For example, a loss in complement activity may actually be responsible for, or contribute to, the reduction of antimicrobial activity.  Therefore, this should perhaps be rephrased as “Our data demonstrated that a loss of 2% of blood viability after 4h of collection correlates with a 5-fold loss of antimicrobial activity against S. epidermidis”
Experimental design: Please include the number of biological and technical replicates performed in the section relating to the influence of anticoagulants on bacterial growth.
Regarding the section on human blood collection, was the blood used immediately following collection for further experiments? If so, please state this. If not, please state how it was stored.
Experimental details are lacking in places. For example:
Lines 61-62, “The suspension was then washed once and resuspended in 0.9% NaCl in order to obtain an inoculum of 1 × 109 CFU/mL” how was this achieved? Was it adjusted to a specific optical density which correlated to a known cfu/ml? As this is a method development paper and a major parameter affecting experimental outcome was inoculum size, this step should be described in detail.
Lines 72-74, “TSB (Liofilchem Teramo, Italy) was added to the different blood collection tubes and were shaken for the same duration as the tubes containing the human blood”. How long was the duration? Please be specific.
Lines 78-79, “bacterial growth was determined by CFU quantification”. Which method was used? Spread plating, Miles and Misra?
Lines 103-104, “Whole blood was collected and an aliquot (0.9 mL) was immediately taken and mixed, on a 2 mL tube, with 105 CFU/mL of bacteria”. Do the authors mean that the final concentration of bacteria was 105 CFU/mL when mixed with the blood or was a volume of bacterial suspension already at 105 CFU/mL added to the blood?  If the latter, how much was added?
Validity of the findings: The authors aim to determine factors which influence experimental outcomes in an ex vivo blood model. One such parameter identified was the inoculum concentration. The authors hypothesise that at higher bacterial concentrations, bacterial survival and subsequent growth, is due to a corresponding loss of leukocyte viability, which presumably is not happening at lower bacterial concentrations. To prove this, the authors should show a reduction in leukocyte viability which directly correlates to bacterial inoculum size. The authors do show a reduction in leukocyte viability which correlates to time from blood collection, but this is different.
Furthermore, it is not made clear why the authors chose to measure leukocyte viability over other potentially important antimicrobial components of blood which are also known to degrade with time. Although leukocytes are an important antimicrobial component of the innate immune response, I feel the discussion does not acknowledge other relevant antimicrobial components of blood, such as complement. As there will be a limited amount of complement available in the blood samples for binding to bacteria, its antimicrobial capacity will be directly influenced by the concentration of bacteria present. In my opinion, this will much more likely have a greater effect on the variability of experimental outcomes with regards to transcription than leukocyte viability, which is unlikely to be altered by the presence of differing concentrations of S. epidermidis.
The authors aim to determine if the total volume of blood used in the model can alter gene transcription levels and therefore introduce variability within results. The authors conclude that “no significant differences were found in the expression of the selected genes using, in any of the different volumes of human blood tested. Noteworthy, a volume of blood as low as 0.18 ml per reaction can be used without impacting the transcription of the selected genes”. This is an important preliminary result and is useful to the field, but I feel it should be stressed that this is a small set of genes and that this may not hold true for all genes within the genome.
Lines 209-212, “As can be seen in Figure 2, the results showed that a higher antimicrobial activity was detected when blood was used immediately after collection, resulting in 97% of bacterial cell death. In contrast, when blood was used after 4h of its collection, only 84% of bacterial death was detected”. I’m assuming that “immediately after collection” relates to 0 hours on figure 2? However, there is no bar for bacterial death at 0 hours – Is the figure correct?
Line 231, “AMPS produced by the host”. Could you please define the acronym – I’m assuming antimicrobial peptides?
Figure S1 (A) which reports bacterial growth in the presence of different anticoagulants has significance values reported above specific time points but there is no figure legend to explain what these represent or what samples have been compared. Is this versus the TSB control?
Additional comments: Although I feel the manuscript does contain findings which may be useful to the field, especially those wishing to undertake transcriptional analyses in blood, I feel the manuscript is not acceptable in its current form. Too many statements are overly ambitious without discussing possible alternative reasons for the results achieved and experimental limitations are not fully acknowledged.


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: OPTIMIZING A RELIABLE EX VIVO HUMAN BLOOD MODEL TO ANALYZE EXPRESSION OF STAPHYLOCOCCUS EPIDERMIDIS GENES
Review round: 1
Reviewer: 3

Output:
Basic reporting: The authors investigate variations in the parameters of ex vivo models for Staphylococcus epidermidis (SE) blood infection, and report that different collection tubes, SE concentration, and blood processing time all have an impact. I commend the authors for highlighting the importance of optimisation, and agree that these factors are often not reported in the literature. I do however, have some major concerns regarding the manuscript, which are outlined below.

There are some grammatical errors throughout the manuscript, which should be corrected to improve clarity. For example, on lines 16/17 the word “however” is used twice, only the second is needed. Line 24, the phrase “ex vivo gene expression” is confusing. Line 37 should read “This model has”. Line 103 should read “in a 2 mL”. Line 173-174 “due to the is inherent” is confusing. Removing some of the commas in lines 103/104 would make the text flow better. Line 166 “lower stimuli” is confusing.
In addition, the text is ambiguous at times. For example, on line 43 it isn’t clear if “the transcriptional response” refers to the transcriptional response of human blood, or that of SE. Again, line 156 “regarding gene expression” should instead specifically state “expression of SE genes” to make it explicitly clear what is being measured. Similarly, line 167 “analysis of the transcriptional response” is ambiguous.

In Figure 1, there are 4 lines in the top right corner of the graph with stars indicating significance, but it isn’t clear what these comparisons are. This needs addressing.

In Figure 2, it isn’t clear from the legend which results relate to blood alone or blood plus SE. Further, it isn’t clear in the legend that results from two separate viability assays are presented; flow cytometry for blood, and CFU enumeration for bacteria.

In general, all figure legends should contain all necessary information to interpret the Figure. In Figure 3, the legend doesn’t provide sufficient detail; CFU? Length of incubation?
Experimental design: There are significant details missing in terms of the methodology. Specifically, more detail is required in how CFU was determined. The methods describe “CFU counting” but was this done by spotting serial dilutions of bacterial preparations onto plates followed by overnight incubation? Or counting under a microscope? Since much of the results and interpretation is based on assessment of bacterial viability, this needs to be described in sufficient detail.

In addition, the authors state that they used blood from five donors, but no demographic information is presented for these individuals. At a bare minimum, age and gender should be reported.

Regarding the flow cytometry analyses of leukocyte viability, some representative flow plots should be shown alongside a gating strategy including the exclusion of doublet cells, debris etc.

Regarding the primers used for detection of SE genes, were the PCR products sequenced to confirm that the correct product was being amplified by the designed primers?
Validity of the findings: The rationale for the results presented in Figure 2 isn’t clear from the text. Initially the authors state that this experiment was performed in light of the results in Figure 1; lines 184/185 “it was hypothesized the increase of bacteria survival, in the higher inoculum experiment, was related to the loss of viability of blood cells”. After reading this, I expected to see results relating the highest inoculum to blood cell viability. Instead, the authors performed this experiment using only 105 CFU/mL. Figure 1 clearly shows that at an inoculum of 105 CFU/mL, blood could control infection; only ~25% of bacteria were alive at 4 hours, and even less were alive by 8 hours. Essentially, the authors hypothesis was not tested by the experiment presented in Figure 2. The authors later describe the importance of time between blood collection and utilisation and in that regard, the experiment for which results are presented in Figure 2 are justified.

In addition, there seems to be a discrepancy in the results between Figure 1 and 2. In Figure 1, a 4-hour incubation with 105 CFU/mL resulted in ~25% bacterial survival, which is equivalent to ~75% death. However, in Figure 2, these same culture conditions (4-hour, 105 CFU/mL) resulted in close to 100% bacterial cell death across three independent experiments. Can the authors clarify this?

Finally, can the authors justify their choice in using the highest inoculum (108 CFU/mL) for the experiment presented in Figure 3? Since the data in Figure 1 shows that at this concentration, SE can happily survive in blood culture up to 8 hours, I would expect gene expression to be stable at this concentration, regardless of blood volume.
Additional comments: I would suggest changing the title slightly to “Optimizing a reliable ex vivo human blood model to analyse expression of Staphylococcus epidermidis genes”.

The authors conclude that blood has lost its antimicrobial properties following a period between collection and utilization. Can the authors validate this claim by measuring total protein or specific antimicrobial peptides in the blood serum following this period of time?


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: OPTIMIZING A RELIABLE EX VIVO HUMAN BLOOD MODEL TO ANALYZE EXPRESSION OF STAPHYLOCOCCUS EPIDERMIDIS GENES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I feel that the overall quality of the manuscript is much improved. The manuscript feels much more focused, is less confusing and the limitations of the study are clearly described.
Experimental design: Methods now contain all relevant details for reproducibility. The authors have also clearly justified and explained their selection of using leukocytes as an overall measure for the degradation of blood over time.
Validity of the findings: Figures are improved and easier to interpret. Limitations of findings have been discussed.The work provides an important contribution for those wishing to develop ex vivo blood models for gene analysis and highlights some of the important experimental factors which may impact the variability of such studies.
Additional comments: I commend the authors on a much improved manuscript


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

Input:
Title: IDENTIFICATION OF PROGNOSTIC RISK FACTORS FOR PANCREATIC CANCER USING BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this study, the authors identified DEGs in Pancreatic Cancer, and demonstrated that DEGs were mainly involved in cell migration, cell-cell adhesion and cell adhesion; the cellular components were enriched in extracellular exosome and cytoplasm; and the molecular functions were enriched in cadherin binding involved in cell-cell adhesion and protein homodimerization activity. Moreover, all hubgenes had higher levels in PAAD (Pancreatic adenocarcinoma) tumor tissues than that in normal samples, and the relationship between prognosis and prognosis was further analyzed. These results are consistent to previous study which showed stability of cell structure and cell adhesion is a major factor in the formation of pancreatic cancer. Examination design was a well-thought-out, and acquired results were consistent. The manuscript appears seems to be solid, but I found problems in Discussion.
Specific concern:
1. Discussion section should summarize the potential underlying mechanism and discuss the present results rather than giving a review of previous findings.
2. There are still many problems in the language of the article, which require further modification and improvement.


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 PROGNOSTIC RISK FACTORS FOR PANCREATIC CANCER USING BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I commend the authors for their extensive data set. In addition, the manuscript is clearly written in profession, unambiguous language. And your research question well defined, relevant and meaningful.
Experimental design: Methods described with sufficient detail and information to replicate. However, there are some weaknesses
Validity of the findings: 1.According to the discussion of your manuscript, TOP2A is more related to CDK1, but why CEP55 was chosen for further research?
2.Your statistical analysis needs be consummated. I suggest that you analyze the expression of hubgenes, such as CDK1, in pancreatic patients with or without lymphatic metastasis and add ROC to explain the prognosis and diagnostic value of the genes.
3.The relationship between CDK1and CEP55 with  the tumor grade is not right in the Oncomine。
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 PROGNOSTIC RISK FACTORS FOR PANCREATIC CANCER USING BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: - Resolution of figures needs to be improved. It is not easy to see clearly.
- There are minor grammatical errors & typos that can be improved in the revised version.
- To mention Gene Ontology, the authors should provide more relevant bioinformatics studies that worked on it, such as https://doi.org/10.1016/j.ab.2018.06.011, https://doi.org/10.1016/j.jmgm.2017.01.003, and https://doi.org/10.1016/j.ab.2019.03.017.
Experimental design: - The authors have to provide more information to show the literate reviews as well as how they fill an identified knowledge gap in this problem. Recently, this lacks much information in the current version.
- What is the idea of using different levels of p-value in their methods? I checked that sometimes the authors used p<0.05 as significant level, but sometimes is 1x10^6 or 0.01. I think it is not consistent and there must have some explanations on their choices. Without them, it is not easy to say that their results are significant enough.
- How to select a set of parameters in Cytoscape?
- Similarly, how did the authors choose the optimal cutoff criteria in transcription factor analysis?
Validity of the findings: - A big missing is that the authors indeed didn't link their found genes with pancreatic cancer. How do the functions of these genes play in pancreatic cancer? It is interesting and they need discussing more of their findings.
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 PROGNOSTIC RISK FACTORS FOR PANCREATIC CANCER USING BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this study, the authors found that 210 differentially expressed genes (DEGs) were identified, including 186 upregulated and 24 downregulated geneswas in pancreatic cancer. the DEGs and hub genes identified in this work can help uncover the molecular mechanisms underlying the tumorigenesis of pancreatic cancer and provide potential targets for the diagnosis and treatment of this disease. Examination design was a well-thought-out, and acquired results were consistent. The manuscript appears seems to be solid. However, there are some fatal problems.
Specific concern:
1.	There have been articles reporting similar research content by authors. (Lu W, et al. dentification of Key Genes and Pathways in Pancreatic Cancer Gene Expression Profile by Integrative Analysis; Zhou J, et al. Identification of novel genes associated with a poor prognosis in pancreatic ductal adenocarcinoma via a bioinformatics analysis). It greatly reduced the novelty of the work.
2.	Please inform the author of the specific information of the chip (chip type, source, etc.)
3.	It is disturbing that the authors concealed the fact that this is a re-analysis study. Why did the authors re-analyse data generated by others and then did not even mentioned the original study?
4.	This article only carries on the biological analysis, has not carried on the clinical sample and the basic experiment confirmation, the experimental result's authenticity and the reliability are doubtful.
5. In this paper, the authors should make clear which type of pancreatic cancer gene chip to study.
6. There are still many problems in the language of the article, which require further modification and improvement.


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 PROGNOSTIC RISK FACTORS FOR PANCREATIC CANCER USING BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 2

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


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

Input:
Title: IDENTIFICATION OF PROGNOSTIC RISK FACTORS FOR PANCREATIC CANCER USING BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 3

Output:
Basic reporting: Satisfactory
Experimental design: Experiments are well conducted.
Validity of the findings: Findings are valid as GEO2R software was used and its well know for finding DEG.
Additional comments: Authors have made substantial corrections to the ms.


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 PROGNOSTIC RISK FACTORS FOR PANCREATIC CANCER USING BIOINFORMATICS ANALYSIS
Review round: 3
Reviewer: 1

Output:
Basic reporting: The innovation of the article is general, the author's work is not bad, but there are still some problems in the article
Experimental design: good
Validity of the findings: goog
Additional comments: The innovation of the article is general, the author's work is not bad, but there are still some problems in the article
1. The author should collect some clinical samples to verify the result.
2. The language of the article needs to be further improved.
3. The discussion part of the article should include a comparison of the original chip data and discuss the results of your own and the results of other people's chip data.
4. Authors should also investigate the link between the prognosis of collected clinical samples and the results of online analysis.


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 PROGNOSTIC RISK FACTORS FOR PANCREATIC CANCER USING BIOINFORMATICS ANALYSIS
Review round: 4
Reviewer: 1

Output:
Basic reporting: good
Experimental design: good
Validity of the findings: good
Additional comments: The author's research is very good, the workload is very large, the experimental design is also very good, but there are still some problems:
1. In the method of the abstract, the author has written in the content of the result, which needs to be modified.
2. Why did the author choose CDK1 and CEP55 for follow-up research.
3. In Figure 8, WB results should be analyzed statistically, rather than simply presented.
4. The author collected fewer clinical samples, it would be best if they could be increased and supplemented.
5. In the discussion part, the author wrote more of his own research results. The discussion part should be the analysis and summary of own results and other people's research, rather than the presentation of the summary results.
6. The language of the article needs further improvement.


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: QUANTITATIVELY ASSESSING MEKOSUCHINE CROCODILE LOCOMOTION BY GEOMETRIC MORPHOMETRIC AND FINITE ELEMENT ANALYSIS OF THE FORELIMB
Review round: 1
Reviewer: 1

Output:
Basic reporting: Stein and others analyzed the mechanical properties of humeri in mekosuchine crocodylians that are endemic to the Eocene-Pleistocene of Australia. Mekosuchines are known to exhibit a set of bizarre craniomandibular and postcranial features, and arguably more terrestrial among Crocodylia. Therefore quantitative analysis of mekosuchine appendicular skeleton may give an insight into the osteological adaptation to more terrestrial lifestyle.
  References are meticulously cited, background is provided in the introduction, and detailed analysis protocol is given in the materials and methods and in the supplementary data.
  The largest concern is the small sample size of extant comparative materials. They only sampled 3 individuals from 2 species (C. porosus and C. johnstoni). There are more 'terrestrial' taxa among living crocodylians (e.g. Paleosuchus and Osteolaemus) that should be included. If mekosuchines are really unique in the limb morphology and mechanical properties cannot be tested here. However, I believe the data presented here may be useful in the future mekosuchine study. PeerJ seems to welcome row data and any scientifically sound analysis.
Experimental design: Experimental design is fine. Authors provides the background info for all the fossil materials. CT scan setting (voxel size, resolution etc.) is in the supplementary but may also be described in the main text.
Authors normalized the mechanical properties with the estimated body mass. However, allometric change in the limb bone shape (Dodson 1975; Meers 2002) still needs to be taken into account. The allometric growths of limb bones are also different interspecifically (Iijima and Kubo 2019). If allometric correction is difficult, authors may want to add caveats by citing above papers.
Validity of the findings: Many of their claims do not have strong support. For example,
1. Differences in the cross sectional shapes between extant crocs and mekosuchines are unclear. As I see Fig. 4, I cannot find any trends. In Fig. 5, Imax/Imin is highly variable among 3 extant individuals and among mekosuchines.
2. Similarly, there is no clear difference in the stress distribution patterns between extant crocs and mekosuchines (Fig. 6). Patterns in the Murgon specimen (Fig. 6I-L) look similar to those in extant crocs (Fig. 6A-H).
3. "Deviation of the mekosuchine specimens from rounded cross-sectional shape", and "apparent de-emphasis of torsional loading", which are repeatedly mentioned in the abstract and discussion (lines 515-518) do not have strong support. Comparisons with extant samples are not enough, and differences between extant crocs and mekosuchines are ambiguous.
These issues can be addressed by qualifying the statements throughout the abstract and the main text.
Additional comments: Materials & methods-Analysis of cross-sectional shape and biomechanical properties: Explanation of J (polar second moment of area) seems to be missing.
Lines 345-346 'Small values for Imax/Imin indicate bending strength along Imin and larger values indicate greater bending strength along Imax (Ruff, 1987)': Smaller Imax/Imin indicate similar Imax and Imin, and larger values indicate discrepancy in Imax and Imin?
Line 406: primary actors: primary protractors?
Lines 464-466: Please provide slope values in your study and Meer (2002) for comparison.
Lines 472-476: Is PC3 really related to cross-sectional flattness?
Line 496: It should be more informative if the difference of stress magnitude is mentioned as percentages.
Lines 551-562: Similarity of Riversleigh mekosuchines and extant crocs in the stress patterns might be due to small size in Riversleigh forms. Smaller individuals generally have very slender limb bones.
Lines 568-571: 'This result confirms that the morphologies of mekosuchine humeri generate a different loading regime than that which occurs in extant crocodylians': Replace confirm with 'may suggest' or sorts.


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: QUANTITATIVELY ASSESSING MEKOSUCHINE CROCODILE LOCOMOTION BY GEOMETRIC MORPHOMETRIC AND FINITE ELEMENT ANALYSIS OF THE FORELIMB
Review round: 1
Reviewer: 2

Output:
Basic reporting: In general the language is well presented, though I have several editorial suggestions (detailed in section 4). The Introduction provides useful background, and the delineation of sections follows standard presentation. The figures are generally executed well, though I do have suggestions about how to refer to them more to improve their effectiveness (detailed below). Some raw data (e.g. PC eigenvalues and vectors) are not clearly supplied at this point.
Experimental design: The research is original and within the scope of the journal. The research gap that this work addresses is noted clearly. Technical execution of the work is strong, with methods described in detail and following ethical standards.
Validity of the findings: I have a number of points to raise in the context of the findings, in order of importance:

(1)	L453-466. I am struggling with the regressions of cross-sectional shape reported here and illustrated in Fig. 3.  First, it is not clear whether the salt and freshwater crocodiles plotted in these figures are also included in the sample that is used to calculate the reported slopes. If these slopes are supposed to reflect mekosuchine traits, they really should not have those modern taxa included. Second, there are no confidence intervals reported for these slopes. This makes comparison to the slopes reported by Meers quite challenging.  The assessment provided, that they are typically similar, includes a span of differences (as best as I can determine) of from ~0.04 to well over 1.0. A direct notation of which numeric slope reported from Meers should be related to which slope from the present study would be very helpful – it is not exactly explicit as currently reported in the text, without referring out to the Meers paper, which preferably would not be necessary. I will add that it would be helpful to potentially compare the slopes reported to predictions for isometry or allometry. I also don’t recall seeing the mode of regression being reported (reduced major axis would be most appropriate). But overriding all of these points is that once restricted to a mekosuchine sample, the number of samples is very small, which will likely make confidence intervals larger than will be straightforward to compare to other patterns.  Overall, I would encourage the authors to rethink how this comparison is performed.

(2)	L468-481; 507-510. I also struggle with the presentation of the principle components analysis. This presentation is different than I am familiar with from other studies, as it appears to use the coordinates of each of the landmark points as an original variable, without correcting for size. There are no data reported that I can find on the eigenvalues/eigenvectors/loadings of the original variables on the new axes. Moreover, interpretation is quite challenging, as the mekosuchines appear to san nearly the full extent of morphospace. I do see the different shapes represented on the extremes of the PC axes, but with the mekosuchines spanning most of these dimensions it is difficult to resolve what can be inferred with confidence about implications for the functional abilities of the group. It is only in the Discussion that the point is made about the specimens plotting with respect to time and geography. However, the groups of two on each side of PC 1 are not distinct with regard to geography (Queensland specimens on each extreme) or time (Miocene specimens on each extreme). I think the presentation of this analysis also needs reconsideration.

(3)	L488-497. The FEA results are one of the strongest points of the paper, with the comparisons of the different replicated loading conditions providing interesting insights, such as that previous experimental findings of increasing stresses with upright posture may have been present in ancient crocodilians as well. (I will note here that, the point made in the Discussion L564-566, about two specimens showing a decrease in stress with upright posture, was not very evident in the presentation of  these data in the Results). This presentation of the results is very efficient, but I wonder if it might be over-distilled. Readers could probably use a bit more guidance as to what they should be gleaning distinctly from the four visually intense figures that are referenced in this paragraph.

(4)	L515-517. The idea that a shift to non-circular cross sections might reflect a shift away from torsional loading is reasonable – Blob 2001 (Evolution of hindlimb posture in non-mammalian therapsids: biomechanical tests of paleontological hypotheses. Paleobiology 27:14-38) makes the same inference for non-mammalian therapsids. However, I think the analyses that produced the shape assessment might be reconsidered in order to make the case for this argument in a more straightforward fashion.

(5)	L520-526. I would be very cautious about inferring any evolutionary trajectories based on the limited sample of specimens analyzed.

(6)	L594-608. Some of the speculations offered here are stimulating, but I think they may stretch a little too far. With only 4 specimens analyzed, for example, I have a hard time with the statement that “the somewhat discontinuous hydrological history and structuring of the Australian continent, that is more artesian and ephemeral than orogenically influenced (Habeck-Fardy & Nanson, 2014), was an important influence on mekosuchine evolution.”  In one sense, it probably was in a lot of ways. But to infer it specifically for humeral shape, I’m not sure there is enough evidence to really make such a statement.  I’d recommend re-looking at this whole section, this latter point in particular, with a finer comb to evaluate how far it is appropriate to propose some of the ideas presented.

(7)	L634-635.  Here again, this statement about the likelihood of facultative burrowing seems too strong.
Additional comments: L48. I think “constraint” is the word that should be used here, rather than “restraint”. But actually, I don’t think this broad statement is really needed for the abstract, which typically focuses on the study conducted. So, I’d remove the whole first sentence, and limit the generalization to ”Morphological shifts observed in the fossil record of a lineage might indicate concomitant shifts in ecology of that lineage.”

L70.  I’d recommend inserting “often” before “is reflected”, since there are many exceptions to such expectations.

L98. To clarify the reference in the sentence, I’d change “this” to “such terrestrial specialization”.

L100.  “verses” should be “versus”.

L103. “a held near” should be “are held nearly”.

L128-129.  For clarity, I would change “Variation in curvature may not necessarily relate to strain either; curvature has been shown to allow physical space for muscle belly packing” to “ Variation in curvature also might relate to factors other than strain, such as allowing physical space for muscle belly packing.”

L134.  Change “is” to “are”.

L137.  “short time span” – how short?  If referring to the whole duration of mekosuchines, isn’t it over several tens of millions of years?

L144.  In fact, torsion has also recently been reported as a primarly loading mode for the humerus of crocodilians: Blob et al 2014, Integr Comp Biol 54:1058–1071.

L149. I’d add a comma after “plane”; also, it might be helpful to add a citation of Reilly & Blob 2003 (J Exp Biol 206:4327-4340) to the Blob and Biewener 1999 citation, since it verified the finding of increases in loading with upright posture and explained its mechanism.

L152. Move “from extant crocodylian humeri” before “indicative” for clarity.

L155.  Add something like “with trophic habits” after “correlate”, to show what they correlate with.

L178.  I’d add “the loading consequences of “ before “cross-sectional shape variance”.

L185. Add a comma after ‘mitigation’ – but also specify ‘same imperatives of stress mitigation’ as what/who?

L189. Add a comma after mekosuchines.  Also, in this context of interpreting what deviations from rounded shape might imply for the presence or reduction of torsional loading, a useful reference for comparison would be Blob 2001 (noted above).

L229. Change “boarder” to “border”.

L268-272.  I am not following the text in this section. It is fine to acknowledge that phylogenetic relatedness was not considered in this study, but I am not sure how it can be justified by saying that not considering phylogeny prevents morphology of interest from being exluded.

L402, etc. Are there any experimental data, such as EMGs, that can provide a basis for these reconstructions of muscle activity, beyond the anatomical analysis from Meers 2003?

L414.  Hyphenate “pulley-like”.

L514.  “Considerable moment forces”.  This phrasing is confusing.  Forces are part of what determine moments. Is “forces and moments” what is meant? Also, things aren’t really ‘loaded under torsional stresses’ – the stresses result from experience a twisting load. Probably just ‘loaded under torsion’ is better.

L574.  To be most accurate, it would be best to add “as a result of bending” after “tension”. In addition, the rest of the text in this paragraph, indicating increases in tension relating to increases in compression, is a bit hard to follow and would benefit from some reworking.

L598. “represents” should be “represent”.

L622.  These behaviors might not be precluded due to the high safety factors of crocodilian forelimb bones, which could be referenced here (e.g. Blob et al. 2014).


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: QUANTITATIVELY ASSESSING MEKOSUCHINE CROCODILE LOCOMOTION BY GEOMETRIC MORPHOMETRIC AND FINITE ELEMENT ANALYSIS OF THE FORELIMB
Review round: 1
Reviewer: 3

Output:
Basic reporting: A1: The manuscript was generally well-written but there were certain sections that were over-generalized. For instance, line 70 includes “offer niche opportunities for those that adapt” but phenotypic plasticity could lead to morphologies that could also make use of those niche opportunities. Lines 143 – 144 suggest that the loading regime would be similar between the humerus and femur in the alligator yet Blob et al. 2014 (https://academic.oup.com/icb/article/54/6/1058/636968) found that the safety factors and yield strains are different. My guess is that the text was supposed to read that torsional loads would be important in the humerus since it is also important in the femur.

A2: Given how bone curvature plays such a substantial role in their study, it is surprising that it is not mentioned in the abstract. The effects of bone curvature on limb bone stresses is an important component to evaluating to the locomotor biomechanics of tetrapods and played a particularly valuable role in evaluating the morphological differences between their taxa, so it would be useful to incorporate some of that information in the abstract.

A3: The raw data do not seem to be shared, other than the data presented in Table 1 and the scan settings in the Supplementary Material.
Experimental design: B1: While the text is generally well-written, additional information about the geometric morphometrics would help clarify some details. For instance, the landmarks were described to have been obtained from the 3D models by extracting the Cartesian coordinates where 16 equidistant radii extended to the edges of the bone. Based on this description, these points seem to be more traditionally defined as semi-landmarks in the geometric morphometrics vernacular. To what extend were these landmarks homologous across the taxa? Addressing this information as well as identifying the program (and potentially functions) used to run these analyses would help clarify this section.
Validity of the findings: C1: The manuscript could be strengthened by addressing any validation models or sensitivity analyses on the finite element analyses (e.g., see Porro et al. 2013 and references therein: https://onlinelibrary.wiley.com/doi/full/10.1111/joa.12080). The material properties assigned to the FEMs were reported but those values appear to be based on mammals or sharks and most (if not all) on cranial material based on the references provided. Currey 1988 (https://www.sciencedirect.com/science/article/pii/0021929088900061) reports that the Young’s modulus is about 12 GPa in the alligator femur is about 6.65 GPa in the alligator cranium (see references in: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmor.10627), so choosing values that better matched the stylopods of crocodilians would seem to be more biologically relevant. Similarly, it is unclear whether FEA output generally remains robust despite modelling the lattices with properties of steel (perhaps a reference could be included to address this if that topic has already been discussed elsewhere). The Zapata et al. 2009 (“Material properties of mandibular cortical bone in the American alligator” paper in the Bone journal) could help support the value chosen for the Poisson ratio. Although validation models may not necessarily be part of this manuscript, it could be addressed by relating the results to published work on alligator stylopods (e.g., Blob et al. 2014 reports strain data for the alligator humerus during terrestrial locomotion: https://academic.oup.com/icb/article/54/6/1058/636968).The manuscript compares the outputs between the mekosuchine and extant crocodilian models, but it would also be useful to compare the output from the extant crocodilian FEMs with empirical data on crocodilians.

C2: On line 504, PC1 is suggested to illustrate “a radiation in mekosuchine locomotory habitus” but that is not clear from the plot given that the mekosuchines are spread throughout the morphospace. What seems clear is that only the Crocodylus occupy the lower left square and the Pleisocene mekosuchine occupies the top left corner of the PCA plots. What is reported in lines 508 – 510 sounds correct but it’s unclear how that necessarily suggests a radiation.

C3: Also, the differences in the extreme ends of PC2 and PC3 are fairly subtle based on the thin-plate splines provided, so it would be useful to report the variables that loaded strongly on these axes so it is clearer how the factors were interpreted.
Additional comments: The present manuscript integrates geometric morphometrics and finite element analysis to evaluate the locomotor capabilities of mekosuchine crocodylians compared to extant taxa, based on the functional morphology of the humerus. Specifically, morphometrics of the cross-sectional geometry and whole-bone finite element models are used to evaluate the loading regimes that could have been supported by mekosuchines. While the introduction sets the stage to evaluate how variation in bone morphology (especially curvature) could affect the moment arms and, thus, bone stresses associated with terrestrial locomotion, the current draft of the manuscript could be improved with further clarification (see sections above). Not only would additional justifying information help to strengthen some of the conclusions drawn from the data (i.e., be less speculative) but would also help highlight some of the important details that may be overlooked at the moment.

D1: Why study the forelimb when hind limbs tend to be primary propulsor in reptiles and have been the focus of most studies in crocodilian locomotion? There are some really valuable studies on different limb function but it wasn’t clear whether that was part of the motivation of this study.

D2: It is great that the authors have included overviews of the bone stress data across individual bones but the current presentation of the data may not emphasize the patterns enough. Perhaps changing the format such that the y-axis remains as the stress values but that the x-axis is the distance (or landmark) along the bone, with each taxon being plotted as a line graph rather than bar graphs. For instance, see some of the graphs in Doube et al. 2018 (https://royalsocietypublishing.org/doi/full/10.1098/rsos.180152)

D3: Figure 5C doesn’t seem necessary. If the point is to emphasize that there was variation in theta values, that could be expressed by providing the raw values in the main text.


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: QUANTITATIVELY ASSESSING MEKOSUCHINE CROCODILE LOCOMOTION BY GEOMETRIC MORPHOMETRIC AND FINITE ELEMENT ANALYSIS OF THE FORELIMB
Review round: 2
Reviewer: 1

Output:
Basic reporting: I have previously reviewed this manuscript. Authors addressed all the points raised by three reviewers and I am happy with the revised MS.
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: QUANTITATIVELY ASSESSING MEKOSUCHINE CROCODILE LOCOMOTION BY GEOMETRIC MORPHOMETRIC AND FINITE ELEMENT ANALYSIS OF THE FORELIMB
Review round: 2
Reviewer: 2

Output:
Basic reporting: The editing performed for this revision has done a good job of clarifying requested topics, and appropriately qualifying some of the proposed ideas. Additional references to figures are appreciated.
Experimental design: The additional descriptions added to the Methods are helpful and reinforce that the execution of the analyses was appropriate.
Validity of the findings: Adjustments have been made to several analyses (e.g. regressions and slope comparisons) that give appropriate confidence in the findings presented.
Additional comments: Overall the revisions have been quite thorough in addressing all the points raised in review. The authors have done a good job incorporating some additional context for many of the issues noted in the reviews. I really only found a few further typographical items to mention.

L89. Add a comma between “behaviours” and “and”.

L119.  Change “curvatures” to “curvature”.

L165.  I would use either “second moment of area” rather than “second moment area of inertia.”

L378. Use “nearly” in place of “near”.

L495.  “Extend” should be “extends”.


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: QUANTITATIVELY ASSESSING MEKOSUCHINE CROCODILE LOCOMOTION BY GEOMETRIC MORPHOMETRIC AND FINITE ELEMENT ANALYSIS OF THE FORELIMB
Review round: 2
Reviewer: 3

Output:
Basic reporting: The authors mention: “The raw data has been set to open viewing on Figshare prior to resubmission (DOI: 10.6084/m9.figshare.9820961).” The link does not seem to reference the correct data set on FigShare, though. Is this the correct link? https://figshare.com/articles/Stein_et_al_2020_Dataset/9820961.

Line 348: Holt and Trinkaus 2006 seems to be missing from the list of references.
Experimental design: The experimental design and research objectives are well described.
Validity of the findings: Line 480: how strong is this correlation? Provide the correlation coefficient to support this claim or change to “positively correlates”. Table 3 contains very useful information about the regressions, but mentioning a strong correlation implies that a correlation was calculated from a statistical standpoint.

Please report the PCA loadings in the Supplementary Information to make it more accessible, as the differences being described in the results are subtle across PC 2 and almost non-existent on PC 3. Making broad generalizations about the patterns across these axes is a bit spurious without the quantitative information to support these statements.
Additional comments: The revised manuscript is much improved and better highlights the impact that the results provide in interpreting the locomotor capabilities of mekosuchines while paying closer attention to which hypotheses could be tested with a larger and more comparative data set. I have some additional recommends to help strengthen the manuscript further but am pleased with the quality of the manuscript overall.


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 POTENTIAL ROLE FOR GALECTIN-3 INHIBITORS IN THE TREATMENT OF COVID-19
Review round: 1
Reviewer: 1

Output:
Basic reporting: English is great.
The authors report the possible use of galectin inhibitors for COVID 19 treatment. The rationale is based on structural similarity between the pikes and galectin 3.
The authors haven't addressed the work of David Platt, see section ''validity of findings'' , still, the information is important and the hypothesis is strong.
Experimental design: The authors should strengthen the hypothesis by referencing how does structural similarity between two proteins may lead to mechanisms that inhibitors will work, for example COVID spikes?
Validity of the findings: The authors must address this statement and include the results from David Platt in their discussion. :

 ''There is strong evidence that supports the possible use of a galectin inhibitor in COVID-19.  According to the Centers for Disease Control and Prevention, the elderly population who have underlying medical conditions, such as diabetes, hypertension, organ fibrosis, or cancer are at a higher risk of getting very sick from this illness.  What these people have in common is high lectin type galectin expression.  High galectin blood serum concentrations are all associated with these underlying medical conditions which is why clinicians are having such a hard time treating COVID-19 using traditional therapies.  Galectins have a tendency to degrade the immune system of people with underlying disease, which leaves them vulnerable against a cytokine storm.

Bioxytran’s new viral inhibitor is expected to restore the adaptive immune system to normal function, which should modulate any existing cytokine storm.  In addition, there is preclinical evidence that a galectin inhibitor can bind to the protein spikes of the coronavirus.  The company’s medical advisory board has theorized that binding to the virus could stop cell entry and assist in elimination of the virus which would then be attached to the drug and processed out by the liver.

Galectins are also at the center of a number of inflammatory cycles and thereby crucial in the pathogenesis of many chronic diseases such as organ fibrosis and psoriasis.  Targeting these inflammatory pathways with an inhibitor could have the potential to quiet the immunological response which ultimately leads to a healing or a reduction in the side effects in many of these potential disease indications.  Targeting galectins may have far reaching implications in many diseases thereby having platform technology potential.

“I have been researching galectins and complex carbohydrate modifications for over 35 years, and recent events necessitate an adjustment to our strategy,” said Dr. David Platt, CEO of Bioxytran Inc. “Galectins are part of COVID-19’s recognition system that facilitates viral entry.  A few preclinical studies of the coronavirus genus have demonstrated a common galectin fold on the spike protein that is universal to the coronavirus genus.  Galectin inhibitors are designed to interfere with this recognition process and prevent viral entry.  Galectins are also modulators of the immune response and can be upregulated or downregulated to generate a pro-inflammatory or anti-inflammatory response.  Our galectin inhibitor may be able to block viral entry and reduce the T-cell anergy.  Our rationale for a viral entry inhibitor is based on extensive scientific evidence.  We believe that our drug candidate can eliminate COVID-19.  It is an important distinction to make that the viral inhibitor is not an antibody.  Although it will be used as an antiretroviral, it should be recognized as an entry or fusion inhibitor that prevents the virus from entering the host cell.”

“The research that links COVID-19 to galectins is very attractive and an eye-opener to novel approaches to fight these deadly viruses,” said Juan Carlos Lopez-Talavera, MD, Ph.D., Consulting Medical Director for Bioxytran Inc.  “During the SARS and MERS outbreaks much research was conducted on the composition of the virus with the hope of understanding how the virus works.  Some of these studies openly concluded that galectins may represent a therapeutic target and should be investigated further.  These outbreaks eventually subsided, and along with them, the motivation to conduct further research and development.”

“Bioxytran is simply connecting the dots by testing its theories with existing galectin inhibitors.  The study titled Receptor Recognition Mechanism of Coronaviruses: a Decade of Structural Studies seems to implicate galectins in the pathogenesis of coronaviruses.  Hence, galectin may represent an optimal target to treat COVID-19.  Reduction of the viral load is a good treatment option, but may do nothing to address the cytokine storm which eventually results in Acute Respiratory Distress Syndrome (ARDS). Our galectin inhibitor can potentially reduce viral entry, help clearing the virus from the blood, and restore homeostasis to the immune system.”
Additional comments: no 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 POTENTIAL ROLE FOR GALECTIN-3 INHIBITORS IN THE TREATMENT OF COVID-19
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This manuscript proposed by the authors as a review of the literature in the context of covid-19 is very relevant, as it touches on the current serious problem of the whole world - how to stop the virus invasion in the human body, how to neutralize it, and how to strenghten human immune response. Aspect of structural similarities of the spike proteins of coronaviridae and the human Galectin-3, as well as issue of the search for Gal-3 inhibitors is very intriguing.