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: DOPAMINE AND EYE MOVEMENT CONTROL IN PARKINSON’S DISEASE: DEFICITS IN COROLLARY DISCHARGE SIGNALS?
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study examined the ability to monitor eye movements possibly through corollary discharge signals of patients with Parkinson’s disease. Patients and healthy control participants performed a double-saccade task in which subjects were required to saccade to two briefly presented target sequentially. In this task the second saccade should be made taking into account the information about the errors of the first saccade. The same task was also performed with visual guidance.
Two main results are described.
First, the patients had difficulties to perform the second saccade taking into account the error in the generation of the first saccade when the second saccade was performed towards the side that was dominant for the motor symptoms.  As the authors discussed the bias in the errors of the second saccade in the Parkinson’s patients were observed in both memory and visually guided movement ruling out that the initial hypothesis that the saccade errors depended only on a deficit of internal monitoring of eye movement. To account for the errors in both tasks the authors proposed a more complicated explanation that considered the possibility of an additional problem of precision of the bottom-up information.
Similarly, to previous studies it showed that a reduction in DAT binding was associate to more hypometric saccades, however it shows also a new result that the dopaminergic system can be important for eye monitoring because of the correlation between DAT binding and the amplitude of the saccade to the second target in the memory condition. However, spatial memory can also have a role for the longer duration of the stimulus presentation as discussed by the authors and the screen can be a reference frame to memorize the targets making harder to interpret the results.
Although the analyses are appropriate, the results are difficult to interpret for the similarity of the results in the visual and memory tasks. The title reflects the interpretation issue containing a question.
Experimental design: Although the analyses are appropriate, the results are difficult to interpret for the similarity of the results in the visual and memory tasks. The title reflects some of the interpretation problems being formulated as a question.
Validity of the findings: The interpretation of the findings should be explained better. The discussion should be improved because the interpretation of part of the results is unclear.
Line 558, “For instance, the patients may fail to assimilate visual information and information about the earlier saccade with their internal model of the world.” It is not clear this part. Does it mean that the bias in the angle of the saccade in the visually guided task (that is similar to the bias in the memory task) might be explained by a difficulty to assimilate visual information, while in the memory task the problem concerns eye movement monitoring? It is not clear to me.

Line 636, “Our results provide preliminary evidence that the patients may have impairments in incorporating information about previously made movements and incoming visual information into their current, internal model of the world.”  I see a problem with this statement related to my previous question. This interpretation is true only in the visually guided task but not in the memory task. Please explain better.

Minor comments
The part in the introduction on prefrontal cortex should be extended to include more references to previous studies that have shown monitoring signals about previous actions such as an inactivation study of Postle and Tsujimoto (2012). For a review, consider on the effect of previous movements see Genovesio and Ferraina 2014.
Other papers on the influence of previous actions that might be considered. For example, the paper in the rats’ striatum of Kim H, Lee D, and Jung MW (2013), Signals for previous goal choice persist in the dorsomedial, but not dorsolateral striatum of rats.
Parietal cortex might also important for monitoring previous movements, see the paper of  Genovesio, Brunamonti, Giusti, Ferraina (2007) on the influence of eye movement vectors and eye position.
I suggest changing the introduction by eliminating the subdivision in subparagraphs; it does not look to follow the journal style for the introduction.
Line 439, Use upper case
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: DOPAMINE AND EYE MOVEMENT CONTROL IN PARKINSON’S DISEASE: DEFICITS IN COROLLARY DISCHARGE SIGNALS?
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The Authors did a nice work in reviewing the manuscript. I find it significantly improved.
I have no further comments.


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

Input:
Title: DOPAMINE AND EYE MOVEMENT CONTROL IN PARKINSON’S DISEASE: DEFICITS IN COROLLARY DISCHARGE SIGNALS?
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors replied to all my comments, I have no more comments.
Experimental design: The authors replied to all my comments, I have no more comments.
Validity of the findings: The authors replied to all my comments, I have no more comments.
Additional comments: The authors replied to all my comments, I have no more 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: RIP-MD: A TOOL TO STUDY RESIDUE INTERACTION NETWORKS IN PROTEIN MOLECULAR DYNAMICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript describes an analysis tool for interaction network of protein static and dynamic structures. First part of the manuscript is more like a program documentation, which attempts to show some features of the script package based on MDAnalysis. After the program description, authors showed results of their RIN analysis for two case studies.
General comments are as follows:
(1)	It is recommended the authors find a native English speaker to proofread the manuscript. I believe some of their main findings is not recognized by the reviewer due to unclear English language used. Please don’t use ‘van der Waalss’
(2)	Most of the figures need improvement. For example, it took some time to find “i” and “e” in Figure 2 (According to figure caption, they stand for intra- and extracellular spaces). While Figure 5 is matured and sophisticated, Figure 4 is far less informative.
(3)	Notations are unclear and not systematic in the text.
Experimental design: To my opinion, the original aim of the manuscript was to provide an easy-to-use tool for advanced structural protein analysis and to demonstrate usefulness of the RIP-MD with two examples. Authors missed this aim, since it remained unclear what kind of extra chemical knowledge can be achieved by using RIP-MD which cannot be obtained by a few lines of scripting code. In the beginning of Section 4.2, authors stated that RIP analysis of vdW and Coulombic interactions are “disregarded” showing limitation of the current implementation, however there is nothing said about other limitations. RIP analysis neglects the protein interactions with the surrounding molecules (e.g. membrane molecules, water as well as ions), however these species play an essential role in the protein structure making difficult to draw a proper chemical conclusion about the system studied from RIP analysis. Although, RIP analysis would be an important part of a more general interaction analysis tool. Further, the estimation of the half-lifetime for interacting residues would be also very useful to identify the important interaction sites.
The chemistry part of the methodology can be found only in Supplementary Information and therefore Methods section became very technical and superficial. A short definition of the interaction used in the analysis should have been the part of the main text.
Selection of the two case studies is not obvious, explanation should have been given.
Validity of the findings: Besides issues discussed above, I think, the manuscript is lack of novelty in the present form. No benchmarking and comparison is made with the performance of other RIP codes. Authors missed also the opportunity to embed their analysis results into previous research findings to support the importance of the use of their RIP-MD code. If there is no such result for these two systems, other system should have been analyzed.
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: RIP-MD: A TOOL TO STUDY RESIDUE INTERACTION NETWORKS IN PROTEIN MOLECULAR DYNAMICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The methods are described properly and with sufficient details. Illustration of the method on a sample protein is very useful. English is, as far as I can judge, good. Literature is properly cited.
Experimental design: The methods described in the article are not completely new but they are placed into a nice web program and nice VMD plug in. It fits well the journal.
Validity of the findings: I tried to run the server and to install and run the VMD plug in (in the PDB mode only, not for trajectory) and everything was running smoothly. The only exception was that when I did some analysis (e.g. H-bonds only) and I decided to do another analysis (e.g. cation-pi) it seems that the program freezes (a hint for improvement). It works if used canonically.
Additional comments: I believe authors can fix or explain the above mentioned problem (freezing when redoing the 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: RIP-MD: A TOOL TO STUDY RESIDUE INTERACTION NETWORKS IN PROTEIN MOLECULAR DYNAMICS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article "RIP-MD: A tool to study residue interaction networks in protein molecular dynamics" by Contreras-Riquelme et al. describe software tool RIP-MD for analysis of residue interaction networks online and as a VMD plugin in molecular dynamics.

This software tool might be interesting, but this reviewer failed to install RIP-MD core program on his freshly installed Windows 10 computer and therefore was only able to analyze the data presented within the manuscript.

The article is written in well-readable English meeting professional standards.

Figures are appropriately labeled, but some minor adjustments will be mentioned in the latest section of the review. It would be also great to put into the SI and manual how to get visualizations using Cytoscape as the results are not provided from within VMD plugin (well at least according to manual).

The article is self-contained description of piece of software and its use.
Experimental design: Submission clearly define the research question, which is relevant and meaningful - to find interaction network between residues, but as stated in previous section, reviewer was unable to install the software in full to actually use the software in all possible described ways.

Selection of testing proteins and simulation protocol is appropriate; however selection of several cutoffs is beyond this reviewer comprehension as will be stated in the author comments section.
Validity of the findings: Data provided within the manuscript are hard to follow. It is true that the visualization of all interactions within a medium sized protein of around 500 residues is quite large given approximate average of 20 interactions of all types per residue and therefore a reviewer would expect a list of filters or any protocol for meaningful pruning of the data to obtain the better overview over the effect of simulation on e.g. the subset of specified residues. The only exception of coulomb and vdw interactions, which are pruned by thermal noise.

However, this note may be hindered by the fact of only visualization which was available to the reviewer – which was visualization of the webserver generated results within the Cytoscape 3.6 or only statically within VMD plugin.
Additional comments: Here I list all troubling points which I have identified thorough manuscript, SI and manual of the program:

1.	As stated above, this reviewer had access only to the freshly installed Windows 10 computer and as such he was unable to run other analysis than using webserver. While the installation of VMD plugin on Windows is well described, the installation of the core program is provided only for Linux using bash or apt-get installation scripts. Since the program is written in Python, it would be nice to provide installation instruction of core program on Windows (and possibly Mac) within manual.
2.	Manual is also lacking instructive example of the RIN analysis on static structure as well as MD trajectory using both Cytoscape and VMD plugin.
3.	Webserver is not providing any visualization of the results, nor at least the statistics, which is a bit pity.
4.	While I have submitted several jobs with my email address, I have never received email with confirmation that the job is done.
5.	RIN analysis does not consider HETATMs. This is unfortunate as the interactions of the ligands within binding pockets are of utmost importance in the drug design field.
6.	Description, how to obtain figures should be given within SI as it would be instructive for future users of the program
7.	Citations are a little bit tricky within the article. As an example, in sentence
„RIP-MD is available as a web server for static RIN derivation using PDB files [2], or as a Visual Molecular Dynamics (VMD) [19] plugin to obtain dynamic RINs derived from MD trajectories.“
reviewer expected that ref. [2] will be citation to web server and reference [19] will be citation to VMD plugin not to PDB database and VMD software themselves.
8.	Windows in Table 1 and Figures 3 and 4 should be described as open, closing and closed cavity
9.	It is not understandable, what are numbers in Table 1 before brackets.
10.	While quantification of the interactions like the ones in Tables can be usable, the analysis of protein structure from MD or from single structure are often more qualitative in the nature, e.g. interactions around ligand or any specified residue, identification of the most interacting residue or identification of the correlated motions. The manuscript unfortunately fail to provide such examples.
11.	The selection of the cut offs of individual parameters is not entirely understandable
a.	why is distance between Calphas 8A? That will give unnecesarily large numbers of interacting pairs
b.	HB parameters are ok (3A), but distance for salt bridge is unnecesarily large (6A) given the electrostatic screening by the water solvent.
12.	P7 – typo in COMbetan, please check typos within whole 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: RIP-MD: A TOOL TO STUDY RESIDUE INTERACTION NETWORKS IN PROTEIN MOLECULAR DYNAMICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: see report for the previous version
Experimental design: see report for the previous version
Validity of the findings: see report for the previous version
Additional comments: I am happy with the changes made by authors regarding my comment and also responses to other reviewers look reasonable.


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: RIP-MD: A TOOL TO STUDY RESIDUE INTERACTION NETWORKS IN PROTEIN MOLECULAR DYNAMICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Since this is a re-review, I think that the most useful format will be answering to remaining individual arguments in rebuttal letter:

> We also reviewed the English and made some minor changes to improve how the article reads.

Still needs work
Check of language and typos is highly recommended even in the newly added text (examples: cationπ without dash, maitaining, Figure vz figs., RIP-MP instead of RIP-MD, etc.)

> We also included a summary table describing all interactions calculated by RIP-MD but given the length of their complete description users/reader will still have to refer to the supplementary material.

Thanks for clarification in maintext

>> Citations are a little bit tricky within the article. As an example, in sentence
„RIP-MD is available as a web server for static RIN derivation using PDB files [2], or as a Visual Molecular Dynamics (VMD) [19] plugin to obtain dynamic RINs derived from MD trajectories.“
reviewer expected that ref. [2] will be citation to web server and reference [19] will be citation to VMD plugin not to PDB database and VMD software themselves.

> We improved this and several other minors issued in the text.

Improve them more - References are not properly formatted nor consistent to each other - e.g. ref. 3, 5, 6, 7, 8, 9, ...

>> It is not understandable, what are numbers in Table 1 before brackets.

> This is better explained now, as you will notice in the text.

Increase the size of font in Table 1
Experimental design: > First, RIP-MD only works in Unix systems, we know it can be made to work on Mac OS but it was designed and tested on Ubuntu and Debian OS. This incompatibility is caused by some of the libraries we employed to build it being only available for Unix systems (MDAnalysis). To overcome this incompatibility, we made available a virtual machine with RIP-MD pre-installed under an Ubuntu distribution, so it can be used under Windows and Mac OS with very little effort. One should keep in mind that VMD is licensed so we can not distribute it in the same virtual machine.

OK, but it should be explained on the webpage.

>> It would be also great to put into the SI and manual how to get visualizations using Cytoscape as the results are not provided from within VMD plugin (well at least according to manual).

> We now provide as supplementary material all scripts employed to generate the figures shown in the article as well as improved versions of the SI and manual file where readers can find a step by step guide to analyze RINs in Cytoscape.

I fail to see any scripts in SI.
Manual should be also added to SI
The description of the analysis in Cytoscape do not cover the visualization of the example result in Cytoscape window and what to see from the presented data -> e.g. which values are important for what.

>> Webserver is not providing any visualization of the results, nor at least the statistics, which is a bit pity.

>The web server is now providing a summary table showing the occurrence of each type of interaction in the query PDB file. For proper visualization of the resulting RIN user must employ Cytoscape or VMD (see user manual where a detailed explanation on how to do this is provided).

If the results of the analysis would be provided directly on web (e.g. listing of the most important contacts + some visualization of the contacts in the structure e.g. JSmol, LiteMol, NGLviewer) In that case, any user might consider to try the tool on static structure online first to see what can be learned from those results before pursuing the installation of software itself and third party software as well (especially for Cytoscape, whose use for analysis is not entirely easy for first time user - I frankly still do not know what I should be specifically doing after few hours spent on this review and typical user will not have such patience.)
Validity of the findings: > In second place and with respect to the benchmarking, we do not know about any other software that allows to create multigraphs from MD trajectories so we could not perform it. The only possibility is to compare it with the method presented on reference 33, which only considers Calpha contacts making us disregard this option, or to employ other software that generates RINs from static PDB structures, something that is exactly what RIP-MD aims to prevent.

Why haven’t you provided comparison at least for Calpha contacts then?
I have found multiple downloadable software that allows analysis of the contact maps on trajectories against which it would be interesting to run benchmarking of results on the RIP-MD -> MDcons, ConAn, PROTMAP2D, MD-TASK, MDAnalysis.org …

> What we did instead was to report the computational resources and times we employed to carry out the analysis described in the article in each of its steps.

Time is not that important as the benchmarking of the validity of the findings.

>> It remained unclear what kind of extra chemical knowledge can be achieved by using RIP-MD which cannot be obtained by a few lines of scripting code. In the beginning of Section 4.2, authors stated that RIP analysis of vdW and Coulombic interactions are “disregarded” showing limitation of the current implementation, however there is nothing said about other limitations. RIP analysis neglects the protein interactions with the surrounding molecules (e.g. membrane molecules, water as well as ions), however these species play an essential role in the protein structure making difficult to draw a proper chemical conclusion about the system studied from RIP analysis. Although, RIP analysis would be an important part of a more general interaction analysis tool. Further, the estimation of the half-lifetime for interacting residues would be also very useful to identify the important interaction sites.

> RIP-MD is meant to be an intuitive and easy-to-follow visualization tool for (pairwise) residue interactions, the latter is particularly relevant for MD in which the generated data is enormous. Consequently, we do not expect to produce new chemical data (the physico-chemical information is already present in the phase-space trajectories); however, due to the employment of networks, the users can take advantage of the mathematical formalism of network theory (i.e. by using Cytoscape) to further analyze their simulations. The main novelty of our tool is that it adds many more descriptors than contact maps and includes the capacity for analyzing MD trajectories, a sentence in the manuscript emphasizing the features of our tools was added in the main manuscript.

Yes, physico-chemical information is already present in the phase space trajectories, but RIP-MD fails to provide simple measures to mine this information for easy comprehension of the user of the software let alone further use in analysis and presentation of research findings towards (scientific) public.

Nothing is however still said about limitations of RIP analysis – that it neglects the protein interactions with the surrounding molecules (e.g. membrane molecules, water as well as ions), however these species play an essential role in the protein structure making difficult to draw a proper chemical conclusion about the system studied from RIP analysis.

>>Selection of the two case studies is not obvious, explanation should have been given.
Besides issues discussed above, I think, the manuscript is lack of novelty in the present form. No benchmarking and comparison is made with the performance of other RIP codes. Authors missed also the opportunity to embed their analysis results into previous research findings to support the importance of the use of their RIP-MD code. If there is no such result for these two systems, other system should have been analyzed.

> Regarding the two examples present in the main manuscript; i) The first example (Fig. 4) is meant to show how RIP-MD can visually discriminate among the different stages of a conformational change and how correlated interactions guide the process and are lost when the "closed" state is reached, which might be a common trend in process guided by non-polar interactions; this is indeed "new" chemical information that was not reported in Ref. 14. (the original studies in which for the first time the closing process was reported); ii) The second example is meant to emphasize how interactions in x-ray protein crystals are not necessarily the same. Moreover, the visualization power of RIP-MD is highlighted as a very complex system (12 monomers) is very easily visualized by our method. A sentence in the main manuscript was added, emphasizing the previous.

The explanation of the selection of given examples was added in sufficient detail, however the results of the analysis of the second system are not explained well.

Table 5 contains several weird results – last lines for Both combining Dynamic and Static results (or maybe I am reading wrongly its description) should have at least as contacts as the maximal value in the previous lines. This part requires further clarification.
Additional comments: >> Most of the figures need improvement. For example, it took some time to find “i” and “e” in Figure 2 (According to figure caption, they stand for intra- and extracellular spaces). While Figure 5 is matured and sophisticated, Figure 4 is far less informative.

> We also corrected all these, figure 2 has a larger font now to indicate the different cellular compartments and improved the detail of figure 4 by using color codes to differentiate between interactions and amino acids with and without interactions.

Please enlarge font in Figure 1 and Figure 5
Are all edges in the Figure 4 similarly distributed? Can you indicate where is residue 1, 100, 200, etc for clarification?
Table 3 is over the edge.

>> Description, how to obtain figures should be given within SI as it would be instructive for future users of the program

> We now provide as supplementary material all scripts employed to generate the figures shown in the article as well as an improved version of the SI where readers can find a step by step guide to analyze RINs in Cytoscape.

I have seen no scripts in Supplemental Informations.

>> While quantification of the interactions like the ones in Tables can be usable, the analysis of protein structure from MD or from single structure are often more qualitative in the nature, e.g. interactions around ligand or any specified residue, identification of the most interacting residue or identification of the correlated motions. The manuscript unfortunately fail to provide such examples.

> Further analysis as those commented by the reviewer can be easily carried out within Cytoscape, where by adding further information to the RINs (e.g. residue conservation) as node attributes will help in the processes. Proper instructions to perform such analysis are now provided in both the manual as a work example.

The explanation of usage of Cytoscape is still insufficient.


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: BACTERIAL COMMUNITIES IN THE DIGESTER BED AND LIQUID EFFLUENT OF A MICROFLUSH COMPOSTING TOILET SYSTEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: clear and unambiguous

professional structure, figs, tables, raw data shared
Experimental design: original primary research

rigorous investigation performed to high technical & ethical standards
Validity of the findings: Conclusions are well stated.
Data is robust
Additional comments: This is a solid research paper and the conclusions make sense.

I think the paper deserves publication at this level of detail.

Open question for me is the question of at what point the spore forming bacteria of the Clostridium XI which are potentially associated with disease and threats to public health, are they no longer detected.

The safety of the microflush composting system would be further verified if we knew the answer to this question. But it might require months or even a year or more of sampling. I would like to see that work done as a follow-on research paper.

However, this work is worthy of publication and is well done. It is original and important and worth publication


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

Input:
Title: BACTERIAL COMMUNITIES IN THE DIGESTER BED AND LIQUID EFFLUENT OF A MICROFLUSH COMPOSTING TOILET SYSTEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written with clear structure  and use of English language. The manuscript touches upon a lesser known and relevant aspect of such systems. The microbial community is both an indicator of the function of the system as well as its efficiency to remove pathogens. However several aspects in building a case for the study needs to be better emphasized.
(1)	Please update the statistics and reference for the line 44 to 49. It is usually better to use the JMP reports since these are the most up-to-date and is the source of all the information used across the UN publications. There is a 2017 progress report.
(2)	The system that is under study was designed for rural areas but no information was given as to why it focusses on rural areas. Is it because of the space requirement? Is because they are behind urban sanitation in using safely managed sanitation? Please provide a case on why it is necessary.
(3)	The paragraph starting at Line 77 seems to be pointing to studies done within the group on this particular system? This is not immediately clear. Please emphasize this other wise you need to update the literature as there are more recent studies on e.g. vermicomposting
(4)	There is no clear hypothesis and no mention of expected microbial community and their importance to the system or expected bacteria based on literature.
Experimental design: While much emphasis has been places on microbial community analysis which has been clearly described, less is given on the test system and parameters of interest. Thus, the study can be significantly improved if the following is addressed:
1.	As stated prior, there is no clear hypothesis, this can help to understand the methodology and findings e.g. why sample liquid for effluent treatment at day 15 and not earlier or later?
2.	This may also be clearer if a description or process diagram or even a picture is added to show the design of the ‘pilot scale’ system that is used to generate the results. It is unclear what are the operational parameters used to generate the final treated products and this may have influences on the microbial community.
3.	Please report the physico-chemical properties of each sample taken e.g. pH, temp, ammonia, VSS, conductivity etc.
Validity of the findings: The data are well reported. However the lack is description of the pilot set up and operation as well as the properties of the samples prevented the authors from identifying areas for further work as well as provide inferences. Some speculations were provided but no information was used to support the speculations for example, no information was provided on the microbial community that was in the conditioned system prior to this experiment. Further, as far as I can tell, the experiments were done only once without repetition.  If these were included, the study could potentially be improved. Specific comments includes:
1.	Please clearly name the samples take at day 0 for the ‘liquid’ portion or effluent and the sample taken at day 15 for the liquid treatment processes. It is a bit confusing  as to which samples you are talking about in 376-380 and 319-321.
2.	Line 404 change ‘the’ to ‘to’.
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: CONSERVATION IMPLICATIONS OF PRIMATE TRADE IN CHINA OVER 18 YEARS BASED ON WEB NEWS REPORTS OF CONFISCATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Study is generally well designed and the manuscript is nicely developed and structured. Overall, clear and unambiguous, professional English used throughout, but here are many problems with language throughout the manuscript, and I suggested below that it needs editing by a native English speaker. Manuscript is adequately supported by references, and sufficient field background/context is provided. Manuscript also has professional article structure, with adequate figs and tables, and raw data was provided for review (I am not sure if it is going to be published online in some data repository though). Manuscript is also self-contained with relevant results to hypotheses.
Experimental design: The study represents original primary research that fits Aims and Scope of the journal. Research question well defined, relevant and meaningful, and the authors stated how research fills an identified knowledge gap. Investigation seems to be performed to a high technical & ethical standard. However, methods are not described with sufficient detail and information, which does not allow for study replication or to judge the validity of the study. I have therefore suggested a major revision of the manuscript to address those issues.
Validity of the findings: Data in general appears to be robust, statistically sound and controlled. There is however insufficient information on the approach, so it was not possible to judge its validity fully. While general conclusions are adequately stated, there is certain level of over-interpretation of results, and conclusions drawn that were not supported by the study. I addressed this issue in my general comments below, and suggested a major revision of the manuscript.
Additional comments: In their manuscript titled "Public knowledge on primate trade in China over 18 years based on web news reports: Implications for urgent conservation actions of slow lorises", MS #30188, authors made an analysis of the online news articles dealing with national trade in primates in China, in order to assess the extent and impact of illegal trade, and related public awareness and knowledge. Study is novel and potentially highly relevant given the ongoing level of illegal wildlife trade worldwide, and especially given the lack of reliable information on primate trade on in China. Study is generally well designed and the manuscript is nicely developed and structured, and should be of interest for a wider readership.

There are however several issues that would have to be resolved before the manuscript can be considered as suitable for publishing. My main concerns are related to the Methods section, as the data collection and assessment approach were not described in sufficient detail, so it is not possible to evaluate validity of the study. I listed my main comments below. Manuscript should be also edited for language by a native English speaker.

Major comments:

1. The main focus of the paper seems unresolved, as the paper strays in different sections from addressing all primates to being focused on slow lorises. In Methods, web search terms represent all primates in China, not just slow lorises, and such focus is also confirmed in many sentences (e.g. Lines 121-122, "We focused on 27 indigenous primate species in China"), as well as in the statement about the study objective in Lines 84-91. As a reader I was confused by such shifting of focus from all primates to lorises and back, and the mention of slow lorises in the title, abstract and elsewhere in the text was misleading, as it does not seem supported by the rest of the manuscript. It might be better to make it clear in the paper, title and abstract that the focus is on all primates, but that the emphasis will be placed on lorises due to their prominence in illegal trade and their endangered status.
	This should be addressed also in the title - either to keep a broad focus and state just "Implications for urgent conservation", or to revise manuscript and clarify and justify the focus on slow lorises. Furthermore, I think that in the title it would be more appropriate to use "for slow lorises" or "on slow lorises" than "of slow lorises".

2. There seems to be also a mix-up in the study regarding the metric that was used, number of rescue reports. Authors mainly claim that rescue reports represent an indication (a proxy) of the level or intensity of primate/loris trade. However, elsewhere they seem to use the same metric as a proxy of public knowledge and awareness of primate rescues, or as it was even more broadly described, "to measure public awareness about primate conservation" (Line 123). What does the amount and content of online news on primate rescues really indicate, trends in primate rescuing or trends in the public awareness on rescuing activities? It appears as the authors couldn't decide about this either - for example, in Lines 125-126 they said that the statistical tests were applied to "examine variations over periods in rescuing frequency and the proportion of public knowledge towards those species".
	In my opinion it is a combination of both, frequency/amount of such news articles indicates both the presence of that activity (primate rescues) and public awareness and attention towards such activity - and, arguably they also represent interest of news agencies in such activities. This should be clarified in the text, perhaps also addressed as a methodological problem in Discussion, and use of the same metric for different interpretations should be avoided.

3. I would avoid equating number of news articles and public awareness on that topic (Line 123 and elsewhere), since the former does not have necessarily to result in the latter - presence of news articles (especially on Internet, since only a small portion of population has Internet access) does not have to result in or be proportional with public awareness.

4. It is left unclarified in the Methods whether the search was made by using some automatic method (such as the Google API is often used for Google search), or the terms were simply entered manually on the webpage of each search engine. If the latter was the case, authors should address in the Methods section the problem of personalized results provided by search engine algorithms and previous personal search history, as a potential source of bias in their results. Automatic search methods, such as the above mentioned Google API for Google search, have the advantage of providing depersonalized results (with no effects of personal search history, geographic location of the person doing the search, etc.) which prevents risk of this source of a bias and provides replicability of the study.

5. It is not clear from the Methods whether only simplified Chinese key terms, representing species names, were used to conduct web search, or some additional terms were used that represented rescue of confiscation activities. In order to allow replicability of the study, the exact search phrases entered in each search engine should be presented, either in the text or in a supplementary material.

6. Authors stated that they have selected news articles that were related to rescuing events. How was that done? This is one of critical steps in the methods, but it is not explained properly. Did the authors do this manually, by accessing and checking each news article separately? I don't expect that this was feasible, since it is mentioned in the text that there were millions of results obtained. Was there a second search step, used for filtering of results, prior to their manual analysis? If there was another search conducted within news articles obtained based on species names, exact search phrases and other relevant information should be provided. Authors mention filtering of results in Results section (Line 135, "we could filter 372 valid news reports based on the topics"), but leave it unexplained.

7. If authors had to deal with millions of news articles obtained through search engines, what was the stopping rule that was applied (i.e. criteria to decide at which point all relevant articles were identified, and further results are unlikely to be relevant)?

8. Authors used three search engines to obtain news articles. How were results from the three engines pooled together? This is left unexplained in the text.

9. I also have an issue with the "unknown" category used for different characteristics of news reports, and the way this is interpreted in the text, which sometimes seem to indicate that the author of the news article, general public or officers doing confiscation/rescuing were unable to determine the species, or its destination, etc. The way I understood it was that this category represents only situations where such information was missing from the news article, but that does not mean that the author of the article or persons involved in the described rescue event were not in possession of such information.
	For example, in Lines 179-181 it is stated that "individuals in 102 events (27.4%) could not be recognized by the reporters or the public when rescued". How was this determined, whether reporters or even the general public was unable to recognize the species? The only thing that can be confirmed by the news article was that the species name was not disclosed by the journalist. Or the authors used some additional information to determine this? This goes on further in Lines 181-186, and the authors seem to mix-up the fact that the species name was not reported in a news article with the one that the species was actually not recognized. This issue will have to be clarified.

10. Results seem also to be over-interpreted - in the Discussion, authors state for primates in China that "rescuing or confiscating news reports revealed that they were notably threatened by domestic trade" (196-197). How was this estimated, based on which information or baseline value is the observed number of online news on rescue events used to make judgment about illegal trade as representing a notable extinction threat? I would also expect that the level of illegal wildlife trade is certainly an important threat, but this cannot be claimed based on the results of the study alone. Similarly, they claim that results indicate the number of reported individuals might be "just the tip of iceberg" (Lines 198-199), or that it is a "rampant domestic trade" (Line 287) or "rampant illegal trade" (Line 307) - although this is likely, it cannot be concluded based on presented results.
There are other statements in the Discussion that do are not supported by the results, so they should not be presented in that way, for example in Lines 220-224: "Some stable supply-and-purchase partnerships, including wildlife brokers and their patrons, should be responsible for most of these underground transactions. We observed also the presence of three reports regarding Internet fraud about primate sales, suggesting that owning primate pets was still attractive and worth taking a risk for some citizens." I would suggest either rephrasing or deleting these sentences.

11. There are many problems with language throughout the manuscript. I listed many such instances below, but the list is far from complete. Manuscript should be carefully checked and edited by a native English speaker.

12. Figure 4 is confusing, I could not understand what is exactly shown there, or what is represented by "market" and "healthy"

Other comments:

13. Lines 35-36 - I suggest replacing "education concerning awareness initiatives to the public" with  "education to the public through awareness initiatives"

14. Line 40 - delete "in trade", since "trade is already mentioned in this sentence

15. Line 44 - replace "For many these species, they are" with "Many of these species are"

16. Line 45 - insert "national" before "pet trade"

17. Line 49 - replace "collapse for many species" with "collapse of many species"

18. Lines 53-54, "Primate trade is a growing concern for this group of long-lived slow-reproducing species" - I suggest rephrasing the sentence as "Wildlife trade is a growing concern for primates, a group of long-lived and slow-reproducing species"

19. Line 76 - replace "four" with "for"

20. Line 84 - delete "and" after the word "of"

21. Lines 85-86 - replace "examine trends which these data changed over time and varied between regions" with "examine trends over time and differences among regions"

22. Lines 89-91 - consider revising this sentence, to improve the language and clarity.

23. Line 94 and elsewhere throughout the text - "rescuing or confiscating news" is a bit confusing term (it suggests that news are rescuing and confiscating something), I would suggest replacing it throughout the text with "rescue or confiscation related news"

24. All species should be presented with both their scientific and vernacular name when they are mentioned in the text for the first time, and afterwards either scientific or vernacular names should be consistently used throughout the text. For example, in Methods (Lines 99-103) only Latin names are presented, while in the Discussion all species are referred to only by their vernacular name.

25. Line 127 - there is one equals sign out of place there (the second one)

26. Line 129 - variable pi for Shannon-Wiener Index is incorrectly defined here, it does not represent the proportion of S comprising the ith species, but the proportion of individuals belonging to ith species.

27. Line 135 - replace "We could filter" with "We filtered"

28. Lines 140-146 - this section is very confusing. I don't understand the meaning of rescue events being reported "in 10 years", "in seven years". Did the authors want to say that they were recorded only in that many of the total number of studied years? If that is so, it is not really informative and could be perhaps omitted - it would be more informative to discuss here about the number of news articles per species, instead of years.

29. Lines 145-146 - replace "to be mounting" with "to increase", and rephrase "appeared to be more fluctuated"

30. Line 151 - replace "during seventeen years" with "over the studied period". Also, use numbers if a number is larger than 10.

31. Line 155, "significantly high" - a value can not be significant by itself, only in comparison with another value, so either state just "high" or "significantly higher than" and compare it with another value.

32. Line 177, "Public recognition of species" - is it really a general"public", if the one making identification was an official person, or a journalist? I would suggest shortening the title to just "Species recognition".

33. Line 178 - replace "could be firstly recognized as" with "were reported as"

34. Line 181 - "there were no variations in recognitions on..." should be replaced with "the recognition of .... was consistent"

35. Line 185, "Only recognition of "species"" - I do not understand this, nor the use of quotation marks.

36. Line 191 - replace "occurred in species" with "were related to species"

37. Line 236 - replace "of smuggling" with "for smuggling"

38. Line 241 - delete "might"

39. Line 244 - delete "away"

40. Line 257 - delete the second comma, and replace "and were" with "and the two species were"

41. Line 266 - I would suggest inserting "might experience elevated mortality and" before the word "perish"

42. Line 269 - delete "oftentimes", and replace "was" with "is often"

43. Line 275-276 - I would suggest mentioning here also the problem of introduced specimens threatening local populations as disease vectors, and referring to some relevant references.

44. Line 281 - replace "Along" with "As"

45. Lines 287-288 - replace "emphasised" with "emphasize", "on some certain" with "of some", and "called" with "calls"

46. Line 300 - replace "their" with "them"; I am not sure if "Chinese people" is a proper term

47. Line 304 - delete "its"

48. Lines 305-306 - this sentence is unclear, there seems to be more Chinese terms than translations.

49. Line 322 - delete "Fundamentally,"

50. Lines 329-330 - replace "high ranked protecting category" with "high threat level" or "high threat category", and "less public knowledge" with either "low public awareness" or "poor public knowledge"

51. Line 330 - delete "extremely"

52. Line 334 - delete "certain"

53. Whole Conclusion section needs thorough language editing

54. Line 336 - replace " 'invisible' " with "unrecognized"

55. Line 337 - replace "involved" with "used"

56. Line 338, "making the topic regarding captive management less sufficient" - please rephrase

57. Line 338 - Start the sentence with "Nevertheless, we hope..."

58. Line 341 - replace "managements" with "management"

Figures and tables:

59. Figure 1 - units are missing in the figure legend (i.e. "number of species", "number of reports", etc.)

60. Figure 2 caption - replace "total" with the "the total number of", "in each" with "per each", "Databse" with "Database"

61. Figure 3 caption - replace "Annual change of" with "Annual trends in"

62. Figure 4 caption - delete ""Significant"

63. Table 1 caption - insert "studied" before the word "periods"

64. Table 2 - insert commas and spaces between terms in the third column

References:

65. Reference Reuter & Schaefer (2016), cited in Lines 44 and 52, is missing from the reference list.

66. Order of citations in the text where multiple references are listed should be checked and corrected throughout the text, they should be ordered first chronologically and then alphabetically (e.g. see Line 70)

67. Line 254 - one of the authors is cited here as Wuester, while in the reference list it is cited as Wüster

68. Line 281 - one of the authors is cited here as Wisweda, while in the reference list it is cited as Wiswedel

69. In Line 328, there is a reference Nekaris et al. (2014) which is missing from the reference list, while in the reference list there is a reference Nekaris (2014) (Line 424) which is not cited in the text. Should that be the same sentence

70. Reference Nekaris and Starr 2015 is listed twice in reference list, in Lines 426 and 431

71. References in the reference list should be reordered, so they are listed first alphabetically, then for the same first author to list first single-author publications, followed by two-authored and finally multiple-author papers, and then chronologically.

72. Some journals names are abbreviated (e.g. Line 354), some lack proper capitalization (e.g. Line 351)

73. Line 469  - "cites" should be capitalized


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: CONSERVATION IMPLICATIONS OF PRIMATE TRADE IN CHINA OVER 18 YEARS BASED ON WEB NEWS REPORTS OF CONFISCATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The MS is written well, although there are some minor grammar issues throughout that should be very easy to fix that would improve the clarity (e.g. line 41 'many these species' should be 'many of').

The referencing is done well but in places there are statements made where citations should be be added, or where referencing could be improved:
L47/48: provide reference that shows that IWT can remove countries' control of natural resources
L58, 66 and 120: correctly reference the UNEP WCMC Trade Database where figures from the trade data are used (in L58 this might be a reference to the following sentence's citation, if so, include it earlier too) - citation for Trade Database should be as suggested here: https://trade.cites.org/cites_trade_guidelines/en-CITES_Trade_Database_Guide.pdf
L80-81: I am not sure if media attention always promotes conservation, and this paper doesn't seem to say that directly. I would suggest finding another reference here.

Figures
Figure 2 is confusing - does it mean the % of total CITES trade reported? I also think the two panels are hard to compare because the species are in order of proportion, so the order is different for each panel. A different format might be more appropriate - maybe a stacked bar with both panels combined into it?

Figure 3: suggest changing the colours in C so they are different to B, to clearly show that it is different taxa and not still individuals and events, as reading quickly down the graphs makes it unclear.

Figure 4: I found this very confusing to read, and I wasn't sure why these two things were reported together, and I am not clear what the take away message is from this figure at all.
Experimental design: L96: Please give more details on your search protocol. For example, when did you carry out your search? Did you use all results or did you limit it in anyway? L104 What was your definition of a news article? Was it only formal news outlets, or informal blogs etc too? Also 104: how did you define rescue events? Did you use extra keywords for this, or did you sort the results by hand to judge which were rescue events?

L119: My main concern with the MS is that the methods around the CITES Trade Database analysis have not been described in any detail. In order for a reader to know what you have done, and for anybody to replicate it, the following information needs to be included when you describe your analysis: when did you download data?; which Terms, Units and Sources did you use in your analysis?; Did you look at importer or exporter reported data, or a combination of both? And if the latter, if exporter and importer reported data differed, which did you go with?; Did you omit re-exports from your analysis?; Did you look only at imports into China (I ask, because there are raw data labelled exports too - does this mean exporter reported data of exports to China from other countries?).
Validity of the findings: There are some conclusions that are not supported by the data collected, and more that need some strengthening.

L73/74 and L283: CITES does not cover national or illegal trade, and in fact this is clearly not its role. In particular, references to how CITES is not doing anything about national trade should be reworded, because that's right, it shouldn't be. It should pick up regional trade (apart from in the EU), although it will still only be records of legal trade. Your whole discussion section on how better data are needed to inform conservation is a good point, but it is undermined by the use of CITES as an example, as you have not focussed solely on seizures of primates as they enter the country (which would show a discrepancy with the CITES data). You also don't link your methods of monitoring seizures via news reports to this - are you suggesting that this is a way of collecting these data instead?

L200: This conclusion should be toned down - if it is not reported on internet news this does not mean that it has not been recorded in official data by the Chinese authorities - there are likely to be many seizures not reported in the news for several reasons. If you want to keep this point in then I would suggest a brief discussion of potential biases of news reports here unless there are official statistics available that can be cited.

L307-309: You measured seizures and confiscations, which surely is a sign of effective enforcement? Unless there is evidence that there are many more primates in trade that are not being seized, I don't think you can draw this conclusion from your findings. While I am sure massive IWT in primates is the case, you should strengthen this argument.

L315-317: Awareness raising is not the same as demand reduction, and simply raising awareness is not gong to automatically lead to behaviour change in consumers (e.g. see diagram here: Breaking the Brand (2016). https://breakingthebrand.org/how-much-is-spent-on-rhino-horn-demand-reduction-campaigns/?doing_wp_cron=1534087399.6144099235534667968750

L338: I think there are more limitations to your study apart from this one, and I think these should be discussed in more detail earlier in the MS. I have highlighted most of these already earlier in the review (biases of news reports, for example).
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: CONSERVATION IMPLICATIONS OF PRIMATE TRADE IN CHINA OVER 18 YEARS BASED ON WEB NEWS REPORTS OF CONFISCATIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is an interesting study about the temporal and spatial trends of primate trade in China over the last 18 years using news reports from the internet. The authors estimated national primate trade and public awareness towards primate rescue and confiscation by quantifying the number of native species uncovered in unique web news from 2000-2017. This is potentially an important study in the area of illegal wildlife trade and one that provides some evidence that an alternative estimate to the illegal trade might be obtained using the web. The writing is clear and there is sufficient context provided. Nevertheless, the authors will need to provide some clarifications to their existing methodology and I also provided some suggestions to improve the manuscript.
Experimental design: Some issues with the methods are listed below.

The source of the reports is not available anywhere. I thought that is critical and must be included in the supplementary materials. For instance, provide a link to each news report.

Line 82. The authors should describe how public knowledge is quantified by looking at the comments and data. The exact approach is unclear. This will affect the other data such as public recognition of the species.

Line 107. How did the authors evaluate the physical condition of rescued individuals? If the information is gleaned from the news, which is the authority (e.g., vet) that did it?

Line 126. Again, be clear on how public knowledge is measured.

Line 127. In this sentence, it is not clear what the diversity indices are used for.
Validity of the findings: The validity of the findings provided will depend on the methods used, which at this moment is quite unclear. But at this moment, the findings seem fine.

The data fills an important gap in the illegal wildlife trade in China. More data is coming out from the internet or online and this research is I believe one of the first ones to present information on the Chinese primate trade in the last decade .
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: CONSERVATION IMPLICATIONS OF PRIMATE TRADE IN CHINA OVER 18 YEARS BASED ON WEB NEWS REPORTS OF CONFISCATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: The text has been strengthened well and the clarification of the methodology has been really helpful. The reporting of the CITES Trade Database analysis that I particularly highlighted has also been improved, with only the following points of clarification:

L63 - you say 11,000 other individuals traded as body parts - unless you have applied some kind of conversion factor here to translate parts into whole organisms (as is done in Harfoot et al. 2018 Unveiling the patterns and trends in 40 years of global trade in CITES-listed wildlife. Biological Conservation) then you can't make the link between individual body parts and individual animals. I you have converted it then mention this. It is a minor point, but could confuse readers.

In addition, Table 1 suggests that some of the species are not listed in the CITES Appendices, but there is an Order listing for primates, and several Family listings so I am not sure if this is correct - species listings can be checked here (unless they are unlisted synonyms or new species): https://www.speciesplus.net/species
Validity of the findings: No comment
Additional comments: The text has been greatly improved since the first submission, and it is now much clearer. I am also impressed by the approach that the authors have taken to incorporating references where suggested, and I think this has strengthened their points. The figures look great, and I think that the new figure 1 is really useful for understanding the methodology. Finally, and most importantly, the conclusions are now much better linked to the findings.


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: DEVELOPMENT AND INTERNAL VALIDATION OF A NINE-LNCRNA PROGNOSTIC SIGNATURE FOR PREDICTION OF OVERALL SURVIVAL IN COLORECTAL CANCER PATIENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This study is objected to developed and validated a nine-lncRNA prognostic signature for individual mortality risk assessment in colorectal cancer patients. The article has a good design framework. However, many similar articles have carried out the same research, so it seems that the innovation is insufficient.

Major comments:
1. Most of all is that the subject of article is about colorectal cancer, but the authors only used data on colon cancer of TCGA except rectal cancer. Can colon cancer represent all colorectal cancer?
2. According to Figure 1, 424 patients were included in final statistics, how did the authors divided these samples in model cohort (n=424) and validated cohort (n=424) in Table 1 ?  The count here seems a bit contradictory.
3. There is limited overall survival (median 28.6 month follow up) and few events (108). For these analyses, it is very important to determine if these associations hold up in an additional cohort particularly one with longer follow up.

Minor comments:
Molecular mechanism of these nine-lncRNA prognostic signature could be discussed.


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

Input:
Title: DEVELOPMENT AND INTERNAL VALIDATION OF A NINE-LNCRNA PROGNOSTIC SIGNATURE FOR PREDICTION OF OVERALL SURVIVAL IN COLORECTAL CANCER PATIENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Very clear and professional english through out the paper, I think. I am just unsure of whether "Wholly gene expression" is the correct wording, or "Whole" "Total" "Complete" would be more correct.
Experimental design: The research question is clear, and the attempt of developing and validating a prognostic model for colorectal cancer survival through a lnc-RNA signature is conducted to a high technical standard, and both methods and raw data is shared and described clearly.
Validity of the findings: no comment.
Additional comments: Very nice manuscript, within aims and scope for the peer journal. The mehod for developing this prognostic tool os interesting, and well described. I think this manuscript could be of interest for readers of peer journal.


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: URBANIZATION, ENVIRONMENTAL STABILIZATION AND TEMPORAL PERSISTENCE OF BIRD SPECIES: A VIEW FROM LATIN AMERICA
Review round: 1
Reviewer: 1

Output:
Basic reporting: A few grammatical/English mistakes throughout, which need to be edited and corrected- for example L50, there are grammar mistakes. Otherwise yes, professional.

Background is fine. There is more literature that could be used, however this would moreso be for discussing and elaborating upon points. For example- you only gave a single sentence to nest boxes in urban areas. There is more literature that could be added here and discussed in much more detail- it depends on the depth you want to go. I think you've covered the basics of the temporal resource dynamics, but there are a few more papers dealing with avian homogenisation and urban adaptation/exploitation (recent ones on parrots in Australia, plus a few from South Africa (e.g. Hornbills) and South America) that could be worth adding into the discussion, if you think they add value.

Professional structure-yes

Self-contained- yes
Experimental design: Original Primary Research within Aims and Scope- yes

Research Question well defined, meaningful and fills gaps- Yes. It addresses some very interesting, relevant and applied aspects of urban ecology and diversity

Rigorous Investigation and Details Methods:
- One concern here is that you only used Google Scholar. Can you be sure that Google Scholar picked up all the relevant research that a search engine such as Web of Science would have picked up? Google Scholar is fine, however used in isolation, I'm just worried some key literature may have been missed?

-Additionally, I think that there also needs to be more detail in your methods. You said keywords used 'such as'. I think you should list all the keywords used to search. What criteria did you use for inclusion/exclusion?- only peer reviewed? English language? Published time period? And how many did you start with, exclude at each step and then end up with?
Validity of the findings: A good presentation of the current available research on temporal stability of resources and avian homogenisation, with well considered conclusions.
Additional comments: Some specific comments

L50- fix up grammar (and little things like this throughout)
LL64-65. Can you provide an example?
LL70-73: I don't quite understand this part about the from a human perspective?...
L91: can you give some examples (positive and negative)?
L112-113: is the association positive or negative?
L156-157: expand a little more- not only an important topic, but needs at least another sentence or two to explain the significance a little further
L224-226: Make it clear where you are talking about- really important as different for different countries etc
L228-295: There is also some parallel literature on nectarivorous lorikeets from Australia


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: URBANIZATION, ENVIRONMENTAL STABILIZATION AND TEMPORAL PERSISTENCE OF BIRD SPECIES: A VIEW FROM LATIN AMERICA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The task of the review work is to show the weaknesses and strengths of scientific cognition and to draw conclusions important for future research directions. The latter depend on a thorough analysis of problems, depending on precisely formulated questions.

In recent years there have been several works or books summarizing some aspects of bird ecology in urban areas (Marzluff 2001, Chace and Walsh 2006, Chamberlain 2009, Lepczyk et al. 2012), however, because new data is constantly being added, a look updating the knowledge of certain areas of issues and deriving new research questions is valuable. This is the intention of the author, who attempts to summarize the knowledge on the diversity of the urban bird communities structure in terms of the stability of urban environment resources in three time aspects - short-term changes (night compared to the day), seasonal and long-term (rows 68-70). Generally, the idea of the work is interesting and worth continuing, because the author intends to review the state of knowledge regarding the avifauna of cities of different continents, geographical regions, areas located at different latitudes, which could lead to valuable comparisons and generalizations.

In my opinion, the weakness of the research assumptions (rows 68-70 and 74-77) is the small precision of the questions (study aims). The intention contained in the title and being the formulated aims of the work is not exactly as precise as it is for me. There is no description what aspects of stability of the bird communities the author analyzes, or only species composition ?, or also the population size? or diversity? – after all, in relation to the questions asked, the content of the result chapters summarizing the data contained in the various works should be constructed. Chapter 4 (row 165) suggests that only the species composition, but in terms of diurnal variation (chapter 4.1), the author presents and analyzes data on various aspects of the birds activity (rows 167-173), not the diversity of the species composition of communities. It is difficult to explicitly agree with the validity of the concept of the author analyzing the changes of avifauna compositions (or homogeneity) between the night and day. Similarly, in the aspect of seasonal changes (chapter 4.2), it undertakes an analysis of comparing the species composition of urban and suburban areas (rows 186-187, Table 1B) – there is a lack of a clear division into various communities – breeding avifauna, post-breeding avifauna, and finally, in certain latitudes, avifauna of wintering period. Various ecological factors may affect the quantitative and qualitative structure of birds communities. In the aspect of indicating greater settling of species and the emergence of partial migration an unnecessary reference to Fig. 3 (rows 184-185), which presents several photographs of selected species. These species could only be mentioned in this paragraph. This figure does not bring any relevant information to work.

Ecological factors the author divided in few types: the role of lighting, food, temperature and urban space management (Figure 1). Presentation of the state of knowledge about these constituents of the urban environment is quite chaotic (chapters 3.1-3.3). Most researchers in the division of environmental factors pay attention to the coverage of vegetation, microclimate, the presence of additional food sources, changed predation pressure, environmental quality (pollution, also lighting as pollutions type). Personally, in such a division context, data should be analyzed, but even with such a division used by the author (fig. 1), the information in the chapters 3.1-3.3 is missing, which we know about the differentiation of these factors, and what the author describes as "resource stabilization". There is a lack of a similar method of analysis that the author adopted when trying to describe the diversity of species composition, presenting the data in Table 1.
Figure 1 showing the scheme of impact or linking various ecological factors and variability of the composition of birds communities is interesting, but should result from the analysis.
Experimental design: Another aspect is the completeness of the analyzed data – I am not sure if the method used (rows 78-86) ensured the proper selection of papers for analysis. It should be only a starting point, because it depends on the introduction of digital work and defining key words. After selecting the papers, the source publications could be reached on the basis of the literature cited. Personally, the analysis of comparisons of urban and suburban urban bird communities as well as the urbanization gradient lacks of references to a series of studies on the impact of ecological factors or urbanization gradient on the structure of avifauna (eg authors' teams such as Pennington', Blair', Emlen', Lepczyk' (North America), Jokimaki', Luniak', Tomiałojć', Witt' (Europe), in the context of additional food sources and their impact on wintering and breeding avifauna (eg Grubb' - North America, Brittingham', Cowie', Gaston', Fuller', Tryjanowski', Van Balen' - Europe), some works on long-term changes in avifauna of urban areas under the influence of environmental changes and progressive urbanization.
Validity of the findings: The work contains a new perspective on the research issues, potentially interesting.
The list of analyzed works in the context of the issues should be supplemented.

The conclusions should result from the analysis - this aspect depends on the additions and editing of the work.
Additional comments: A valuable analysis would be to focus not only on the analysis of species composition as such, but also to consider the impact of urban environment factors on the diversity of the ecological composition (food or nest guilds of birds communities).
The work in my opinion should have been published after a thorough rewording – precisely defined objectives allowing better definition of problems, a clear data presentation (similar as in Table 1), supplemented with a review of source publications, derivation of conclusions from analyzes.


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: URBANIZATION, ENVIRONMENTAL STABILIZATION AND TEMPORAL PERSISTENCE OF BIRD SPECIES: A VIEW FROM LATIN AMERICA
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I think that you are addressing very interesting and important topic with potentially important ecological consequences for birds. However, I think your manuscript does not follow the methodological assumptions most often used in case of reviews. First of all, it seems that your literature check has been performed without any clear methodology or you are just not providing info on that. You do not provide any details concerning the search (e.g. dates), and you just provide some examples of key words used in Google Scholar. This is not enough; you need to provide all the details concerning the search as well as present the results in detail: how many papers confirm a given process, etc. Did you summarize all the papers referring to your aims in the table 1? Anyway, this is not explained clearly in the ms. It is hard to believe that you found only 3 papers showing that artificial light affects nocturnal foraging in birds, as I found – during a very quick search – several others that are not included in your table (e.g. Byrkjedal, I., Lislevand, T. and Vogler, S. 2012. Do passerine birds utilise artificial light to prolong their diurnal activity during winter at northern latitudes? – Ornis Norvegica 35: 37–42. or Ockendon, N., Davis, S. E., Miyar, T. and Toms, M. P. 2009a. Urbanization and time of arrival of common birds at garden feeding stations. – Bird Study 56: 405–410 or Clewley, G. D., Plummer, K. E., Robinson, R. A., Simm, C. H. and Toms, M. P. 2015. The effect of artificial lighting on the arrival time of birds using garden feeding stations in winter: a missed opportunity? – Urban Ecosyst. doi: 10.1007%2Fs11252-015-0516-y). So why didn’t you include those papers as well? I suspect that your Google Scholar search is rather poor, perhaps because you included only 300 first papers (sorted by relevance or what?). I do not follow the logic behind the table 1 and papers selection you used – this should be described with much more details and in systematic manner. So this is my main comment to your study which I think should be addressed before the manuscript can be considered for publication. Below I also add some minor comments. But I still think your general idea was very interesting and thus I suggest improvement of the manuscript.

Introduction as a whole – to me more details are needed to put your study into context and justify better the need for the review. You need to present biological mechanisms potentially important for the temporal homogenization of the communities in response to stable resources. It would be also good to mention some local adaptations and provide some examples concerning birds foraging at night or wintering individuals in cities etc. As PeerJ is not an ornithological journal it would be also good to provide some justification why birds are good and important for such studies and how can we infer about other groups of species based on ornithological research.

28 – maybe add three „time” scales consider
42-44: I would delete these sentence, they do not add too much (further research are always needed etc.). Maybe just write directly which questions should be addressed in the future instead of writing that such questions are listed in the discussion.
51: double check but I would prefer ‘its’ instead of ‘his’
59-65: ok, but give examples and describe better the mechanisms behind the positive and negative response to resources stabilization. This issue is central for your study and justifies your work thus should be presented with more details.
76: I would delete the last aim, as this is only part of the interpretation so this is not a strictly scientific aim. Just write that you also give some recommendations for the future studies.
79: much more details concerning methodology is needed. Please provide dates when the search was conducted, write how did you analysed the results, how many articles in total did you consider, what was the distribution and range of publication year of these articles etc. Just saying that you searched google scholar is not enough – you need to provide detailed description of the methods used as your work could be potentially repeated by other researchers in the future.
91: don’t write about effects on humans – as far as I understand here you present your results so please focus on your result and skip other issues in this chapter.
126: well, not necessarily as you don’t have data on absolute amount of invertebrates, so this statement seems to be unjustified.
176: you write “most studies” and refer to table 1B but in the table all studies report negative effects so the question is: are all studies included in the table or is this just a subset of studies found during the search. This must be clarified.
191: did you mean Table 1C?
230-231: why do you think so? Could you provide more details or references supporting this statement?
241: if you consider invertebrates as a food for birds this chapter could be presented earlier, as a part of the chapter concerning habitat stability in cities. Now it is a bit strange to discuss stability of invertebrates and other taxa just after the discussion concerning birds.
250-256: I don’t understand why you provide data concerning mammals – it is rather hard to find a link between brown bears in garbage dump in Turkey to birds in cities. I would focus on the main aim of the study and delete all such inserts.

Figures – I don’t think your figures are useful. Fig 1 is very simple and shows only general conception of possible effects, with no clear link to your findings based on the literature review. In your analyses you don’t provide any clear justification nor evaluation of the effects presented on the figure so these are just your presumptions, not results supported by references. Fig 2 does not show any clear vegetation changes except some differences in colours of the photographs, which can also be driven by the weather conditions (the differences between two pictures taken in city are also visible). So this is not a proof for the stability-urbanization relationship. Fig3 – figure caption is unclear (what does “species that changed’ mean?), and showing example of species that were somehow related with urbanization does not bring too much to our understanding of the whole mechanism.

Table 1 is not very informative, and it is really hard to follow what you want to show here. Tables headings are lacking and it is hard to distinguish columns. Why horizontal line separates riparian sites from remaining part of the table? Not clear. Why study length is only given for the C section of the table – it seems that a substantial part of the data in the table 1 is missing? Why you present only a few papers out of 300 returns from your search? And many other similar questions.


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: JACLY: A JACOBIAN-BASED METHOD FOR THE INFERENCE OF METABOLIC INTERACTIONS FROM THE COVARIANCE OF STEADY-STATE METABOLOME DATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The ability to infer the Jacobian matrix for a system from metabolomics data is indeed a powerful approach, but the authors have failed to provide sufficient background on how the Jacobian matrix (J) for a system can be derived mathematically from a mechanistic description of the biological system. The mathematical derivation of J from the stoichiometric matrix (S) of the network and the gradient matrix (G) is given by $J = S \cdot G$ where G is a function of how the kinetics of the reaction are described (see DOI: 10.1038/msb.2008.8 or other articles by the same authors for a more complete description). The authors should provide background on this mechanistic approach for deriving J as a complementary approach to the data driven one discussed in this manuscript. Further, the authors could then discuss the obvious benefits of being able to infer J from data instead of deriving it mathematically from a mechanistic model.
Experimental design: (1) With such a plethora of metabolomics data available, the authors should use real data (i.e., experimental values instead of in silico data) to validate their model rather than using an unvalidated model (i.e., in silico data) to validate a model. I understand the need to use sufficiently large amounts of data (i.e., 1000 in silico data sets) to validate a data driven approach such as the one presented here, but the in silico data should complement validation with real data, not replace it.

The authors of the the E. coli model being used (DOI: 10.1002/bit.10288) provide measurements (Table VIII) that could be used to validate the model presented in this manuscript. The authors should then compare the J matrices obtained from network inference and from the measured data.

(2) To the point above regarding the mathematical derivation of J from the structure of a network and metabolomics measurements, the authors should compare their inferred J matrix to the J matrix obtained mathematically. In this context, it is important to recognize that J is not unique for a given system; rather, J depends on the mechanistic detail (i.e., rate laws) used to describe a system (e.g., mass action, Michaelis-Menten; see DOI: 10.1186/s12918-016-0283-2 or DOI: 10.1002/bit.20558 for a discussion). The simplest validation here would be to compare against a model that is based on mass action kinetics (e.g., DOI: 10.1371/journal.pone.0189880), although a more sophisticated model would provide the most accurate representation of network dynamics.

The authors of the E. coli model being used also provide the kinetic rate equations for their model (Table IV); the authors should therefore use this model to derive J and compare it with the J matrix obtained from their network inference method for validation.

(3) The models being used for E. coli and S. cerevisiae here are quite small (18 and 13 metabolites, respectively). Genome-scale metabolic models for these organisms exist with 1,192 metabolites (DOI: 10.1038/nbt.3956) and 2,220 metabolites (DOI: 10.1371/journal.pcbi.1004530), and recent advances in constraint-based modeling allow for network-level dynamics to be studying at the genome-scale (DOI: 10.1038/srep46249) which at least partially alleviate the need for kinetic models. There is still obviously a need for kinetic models of metabolism, but even these models have advanced well beyond the scale of the models used here that are 15+ years old (e.g., E. coli more with 93 metabolites from DOI: 10.1016/j.ymben.2014.05.014) and have even looked at the dynamic characteristics of the network using the Jacobian on the cell-scale (DOI: 10.1371/journal.pone.0189880). Solving these network inference problems are computationally intensive and NP-hard (as the authors note), but is it entirely intractable to apply this method to a model with 93 metabolites (DOI: 10.1016/j.ymben.2014.05.014)? It is unclear from the authors’ description approximately how long simulating a larger model would take (i.e., how does this method scale with respect to time?). In the first Results section, the authors note that it takes 6 minutes to run their software for E. coli, totaling 2 hours for a total of 20 runs; it would be good to provide sensitivity analysis to show the cutoff for when the network becomes so large such that using this method becomes intractable. Methods are available for reducing the size of genome-scale metabolic models (e.g., DOI: 10.1186/s12918-015-0191-x); the authors could use a method such as this to test their method on realistic models of varying size.
Validity of the findings: Overall, the validity of the findings are impossible to assess because of the points raised above regarding the experimental design.
Additional comments: n/a


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: JACLY: A JACOBIAN-BASED METHOD FOR THE INFERENCE OF METABOLIC INTERACTIONS FROM THE COVARIANCE OF STEADY-STATE METABOLOME DATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comments
Experimental design: no comment
Validity of the findings: no comment
Additional comments: General
An improved method is presented determining the Jacobian matrix (network) from in silico steady state data. The method is significantly faster and better than the previous one. As is mentioned in the paper but not in the abstract the method is only capable of inferring small networks. As input the method (solving the Lyaponov equation) needs a so-called fluctuation matrix. This matrix is approximated with a diagonal matrix containing the standard deviation of the individual metabolites obtained from replicate simulations. The methods and results are in general well described and seem scientifically sound.
The main aim of an inference method would be to use it on measured data. It is not clear to me how to get a fluctuation matrix in that case because the fluctuations would be dominated by measurement errors and not by the randomness of the system itself. I would like the authors to comment on how they expect their method to contribute to the knowledge on metabolic networks.
Detailed comments:
Line 60: Hidden in the data rather than hidden behind the data
Line 61:  of that information
139 the – sign on equation 3 has nothing to do with taking the log10 also without taking log10 of the error there has to be a minus sign because the error is to be minimized while the object function is to be maximized. Please rephrase. In my opinion not taking the log10 of the error would result in larger lambda but the same results.
Line 150 I would like more information how the SDE look. This is necessary to reproduce the results.
Line 228 I think there is no correct value for lambda. There is a range of lambda that gives sensible solutions.
Section starting at Line 250
I think for the simulations you can calculate the exact Jacobian as well as the covariance matrix with equation  1 you could calculate the true D of this system I would be interested how it looks like and how this compares to the approximation used here.

The matlab file for the analysis are provided. I would like some more comments without these the script is hard to understand. Only results from the SDE are provided not the files to do the SDE.


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: JACLY: A JACOBIAN-BASED METHOD FOR THE INFERENCE OF METABOLIC INTERACTIONS FROM THE COVARIANCE OF STEADY-STATE METABOLOME DATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed several of the major points and clarified the other aspects of the original manuscript which were unclear.

Although the authors have updated the text with additional background and references, the reference list at the end of the article does not reflect these changes; please update the references at the end of the study to reflect the in-text citations.

The manuscript should be edited for English and for readability (e.g., “SDE” is never defined).
Experimental design: The authors' point regarding the current technological limitations and availability of metabolomics data is well taken, however the discussion regarding this point in the text (final paragraph of Discussion) is still lacking. Ultimately, the authors have not provided sufficient information regarding the specifications of Jacly for its use by those studying these metabolic systems; if someone were interested in applying Jacly to study their system, the exact limitations on the size of the network and the required amount of data are unclear. Although the data may not currently exist, the authors should at minimum provide clear expectations for (1) the maximum size of the metabolic network and (2) the minimum number of biological replicates needed in order to apply Jacly to real data if/when it becomes available. Ideally, sensitivity analysis would show how Jacly performance scales with (1) network size and (2) number of replicates, as these pieces of information would be necessary for someone attempting to apply the results from this study to other research.
Validity of the findings: no comment
Additional comments: I would second the comment made by the other reviewer regarding the statement that the abstract should explicitly state that the method is only capable of inferring small networks; perhaps the authors could quantify "small-scale" by providing the size of the network (to my point above):

"...method to infer the metabolic interactions of small networks (<20 metabolites)..."


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: AN INTEGRATIVE TAXONOMIC APPROACH REVEALS OCTOPUS INSULARIS AS THE DOMINANT SPECIES IN THE VERACRUZ REEF SYSTEM (SOUTHWESTERN GULF OF MEXICO)
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a clear well-written paper that tackles an important subject and provides a definitive answer.  Most of the figures and tables are necessary although I would suggest figure 5 and figure 9 could be merged. The text size on figures 7 & 8 needs to be increased.  Although abbreviations are fine for localities in figures and tables, I think it would be helpful if VRS was written in full throughout the text.  Genbank accession numbers are reported for new sequences.
Some points of grammar:
Line 68: ‘lies’ not ‘lays’
Line 73: ‘to date’ not ‘up to date’
Line 90: “it is now known” not “now it is known”
Line 208: ‘data are’ not ‘data is’
Line 324: “in contrast’ not ‘On the other hand’.  In English, ‘on the other hand’ is very informal.
Line 324: “differentiating” not “differencing”
Line 331: “shared” not “share”
Line 378: delete “on the other hand” it is not necessary
Experimental design: This is original primary research which falls within the aims and scope of the journal.  The question is an important one concerning correct identification of a commercially fished species.  The paper uses standard techniques which are well executed and I find little to criticize within the methods.  They are well described and the data are clearly presented.
Authors should check that they are always citing the paper they intended and citing correctly.  For example, Line 209, I think the authors are referring to Allcock, Strugnell & Johnson, 2008.  Similarly Line 215.
Authors might also check  references in Table 4.  I think, for example, that Allcock et al. 2006 included O. vulgaris from France, not from Brazil.  Sequences from Cistopus indicus are available in both Gukiz et al. 2005 and Strugnell et al. 2014, and additional rhodopsin sequences may be found in Strugnell et al. 2014.
Validity of the findings: This is all well done and I find little to criticize.  Perhaps the authors could add a little more on the identification of O. insularis versus O. vulgaris based on the external skin sculpture.  Norman and Hochberg have often mentioned the classic "patch and groove" sculpture of Octopus s.s., so I think it would be helpful to include a more directly stated comparison of how O. insularis external colour/sculpture differens from "patch and groove"
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: AN INTEGRATIVE TAXONOMIC APPROACH REVEALS OCTOPUS INSULARIS AS THE DOMINANT SPECIES IN THE VERACRUZ REEF SYSTEM (SOUTHWESTERN GULF OF MEXICO)
Review round: 1
Reviewer: 2

Output:
Basic reporting: It is a well structured and integrative study dealing with a complex issue such as redefining a "plastic" octopod species originally identified as Octopus vulgaris.

The authors did a great morphological and genetic job to show that the species inhabiting the Veracruz reef system is O. insularis, rather than O. vulgaris.

I only have minor comments that are attached to the pdf.

1. I would like to see a PCO plot rather than MDS because it shows the true differences in mulditimensional space for the 10 traits measured in two axis that account for a certain % of total variance, rather than maximizing these differences in the first two axis which is the representation of MDS.

2. I would suggest to concatenate the sequences obtained to have a better phylogenetic resolution.
Experimental design: Good experimental design, enough samples analysed for the morphological and genetic analyses.

The authors need to clarify why the number of specimens analysed for genetics (n=24, line 224) are different than those specified on line 324 (n=19). Indeed, the number of sequences deposited on genbank N= 46 (MH550422-MH550467) is less than the number os genes analyzed (4) and the specimens indicated on line 324 (19x4=76).

Also, I missed a table showing the details of the sequences retrieved form Genbank (Acc number, location, species, authors...) so other authors can have a clear picture of the comparisons carried in this study.
Validity of the findings: Great job done by the authors, with important findings that will hopefully change management strategies off the coast of Mexico and Caribean Sea.

Conclusion is well stated and linked to the origial research question.
Additional comments: Overall, a good work with minor things to be changed. Great effort and a good morphological and genetic analysis.