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: THE EFFECT OF JOURNAL GUIDELINES ON THE REPORTING OF ANTIBODY VALIDATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The work is well presented, nad reported well according to the four criteria given
Experimental design: This is a critically important issue ... it is becoming increasingly apparent that using the wrong antibody, or the right antibody in the wrong way, or insufficient reporting of the antibodies used, is one of the major drivers certainly of difficulties in attempted replication and likely also of findings which do not replicate.

I have some experience of conducting a similar (but much more shallow) review of changes in reporting at Nature journals, so I understand at least some of the challenges.
1. We analysed over 800 manuscripts, with each manuscript assessed independently by two assessors, and differences resolved by a third. The reason we did this many was because our sample size calculations indicated that this large number would be required to detect a significant improvement in reporting. No power calculations are offered in the current manuscript, which is a weakness.
2. We are not told whether the approach, or the statistical analysis plan, were determined in advance. If this is not the case, it is possible that the approach taken might have changed - consciously or unconsciously - in response to emerging data. This is a weakness.
3. The disagreement between assessors - based on a small sample of the total - is substantial. Either the first assessor is close to perfect and so this doesn't matter, or the complexities of what is being assessed (and I agree it is complex indeed, and these papers can be surprisingly difficult to read) mean that one assessor is not enough. Our more recent evaluation of the MDAR framework where in-house editors tried to apply the tool (see https://osf.io/2k3va/) suggests that disagreement is the norm, and that two assessors (with reconciliation from a third) would give more reliable information.
4. The time periods over which change was sampled were substantial - in this quasi-experimental setting we rely a little on Bradford Hill criteria, of which timeliness is critical (the change in behaviour followed the intervention). With a stretched timeline, this is less convincing. An alternative might be to sample over time, with an interrupted time series analysis or even a quality improvement tool such as a control chart.
Validity of the findings: See my concerns above. I appreciate the provision of the underlying data, and the characterisation of this work as relatively early (more exploratory than hypothesis testing), but I do think this could very usefully form the basis for the design and pre-registration of an adequately powered study.
Additional comments: I think this is a very worthwhile endeavour. However, to provide sufficient motivation to overcome the inertia which resists change, I think we need more convincing evidence.


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: THE EFFECT OF JOURNAL GUIDELINES ON THE REPORTING OF ANTIBODY VALIDATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The manuscript is of good quality and interesting. Perhaps some condensation would make the article more readable. I do not agree with the notion that the guidelines of the journals "might have some limited influences". The general interpretation seems to be too negative compared to the results reported. From my point of view, the influence of the guidelines was surprisingly large. One has to consider that the sample size was relatively small and long term effects were not examined. The significant differences between the raters also show that the extraction ("coding") of the data from the written text is by far not trivial and unambiguous. This also can be suspected for any referees and the journal editors, who have to decide, whether the manuscript meets the validation guidelines or not. I would conclude from these results that the effect of explicit guidelines is significant and that some standardization is needed to facilitate the examination of the validation level and in the ideal case might make these data even machine-readable.


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: THE EFFECT OF JOURNAL GUIDELINES ON THE REPORTING OF ANTIBODY VALIDATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: no further comments
Experimental design: no further comments
Validity of the findings: no further comments
Additional comments: no further comments


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

Input:
Title: THE EFFECT OF JOURNAL GUIDELINES ON THE REPORTING OF ANTIBODY VALIDATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I think that the manuscript is fine now. I do not agree with all points with the authors, however, I respect their opinions. One major objection is left, however. In this article, the authors point out that mainly antibody identification is improved by the guidelines but not many experimental validation efforts. This might be correct. I disagree, however, that this needs to be a validation deficit. If an unequivocal identification of a previously validated antibody has been performed, this antibody can be accepted as validated in all future papers using exactly the same protocol for the same application. Some antibodies have been validated many times. In my opinion, such routine applications of antibodies or assays are quite frequent. I would not demand any further validation if there is not a specific reason for that. Therefore, you should introduce a third category, besides explicit and implicit validation, which might be termed traceable or previous validation. In this case, only an unequivocal identification (and perhaps citation of original work, where the validation can be found) would be required. If this is seen as a fully acceptable validation approach, your appraisal of antibody reporting guidelines would be more positive.


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: AIR TRANSPORTATION, POPULATION DENSITY AND TEMPERATURE PREDICT THE SPREAD OF COVID-19 IN BRAZIL
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an interesting article, testing various habitat-related traits of Brazilian cities, from population parameters to socio-environmentally driven effects, and verified the confounding of these, more classic epidemiological traits, with temperature. Air flight connections were also verified as source of invading infected people.
 They assumed the disease is new and make assumptions about its delay in spreading in hot temperatures. However, a few of the statements are contradictory to the fact that the virus biology and its fast population dynamic are poorly understood. For instance, they stated the effect of humidity and temperature, likewise lack of vitamin D (thus, few sun exposition), and even the fact that sun deactivates the virus, as important factors. All this may have some relevance to define or circumscribe what makes human habitats susceptible. However, I wish to see more on that concerning uncertainty and how this could be relevant at this moment or for this particular paper. Eventually, a few words on air pollution and sanitarian precarity as well.
An interesting point about this manuscript is that the hottest cities, thus the least vulnerable in Brazil (concerning only this factor), are also the poorest, and worse watched by sanitarian vigilance, about food, hygiene and pollution control in general. Hence, the advantage of having a hot climate, if it is not prohibitive to the disease, may be overcome by the vulnerability caused by these confounding habitat conditions. Authors stated this well by the end of the introduction, but did not rescued these aspects in their discussion, which may be of great interest for decision makers.
Experimental design: - As they modelled from the very first days, indeed they will have the chance to confirm the trends found with time, considering the speed of dissemination of the disease. Also, several non-capital (what were excluded here) are already contaminated, and could provide a further step in analysing the urban environmental parameters in stronger contrast, mostly due to population size variance in a same region. In this sense, the paper defines an excellent starting point for future monitoring.
- Said that, the chosen variables to be test are very good. An excellent choice and a great use of a good public database. Still, a have few questions:
- Why did they use cities as random factors as the independent fixed factors  had one measure per city? AS the dependent variable is case counts per time per city (also one measure per time per city), I see the city as the actual replicate level and counts along time as repeated measures. I just wish they would comment and justify the model choice in this concern, or try it in this way I am proposing, if they agree this is a better format. It sounds for me, in terms of structuring the d.f., won´t change mush, however, the most theoretically correct design should be chosen. Apart from this, the analytical design was competently built.
- Why did they not interact significant factors? I see risks of a few important confounding factors, some they pointed in the introduction, that must have been tackled by terms interactions. I will come back to this below.
Validity of the findings: - I have just one concern about their findings and, therefore, conclusions about temperature. The figure 1 shows clearly that the warmer capitals are those in the Amazon, West, and few in Northeast Brazil. Those are the cities with less flight numbers too. Also, they mentioned Ribeiro et al, in preprint, and those authors showed a likely 40 days delay between the South-East capitals getting highly infected and those here showed as the hottest ones. Should they not had interact these terms and tried to conclude whether a temperature effect is indeed happening, or if there is a dynamic itself hiding an unfortunate confounding? In the statement “Nevertheless, a change in 1 ºC predicted 162 a decrease in the number of confirmed cases by [exp(-0.25/3.11)-1 ]×100 = 7.9%, 163 independently of other factors (Table 1).”, they assumed to interpret the temperature independently of other factors, and I don´t see this way.

Still, the predictions made in comparison with extremely different cities for temperature (lines 198-203) is of great importance, but I just wish to see this adjusted to the time expected for the arrival of the COVID-19 in each one of them, that is dependent on flight numbers. A correction here may help authorities to plan even better priorities along time.
Additional comments: - I consider extremely important to fit this confounding or re-calculate whether an actual temperature effect is expected to happen, by correcting its relative importance in contrast with the other significant effects. If at least this is discussed more openly it would help better policy makers to act. My fear is the results as now presented, may pass the false idea that Amazon, for instance, is a less worrying region, and facts are showing otherwise already.


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: AIR TRANSPORTATION, POPULATION DENSITY AND TEMPERATURE PREDICT THE SPREAD OF COVID-19 IN BRAZIL
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, the basic reporting is ok, with a few editorial corrections noted on review.
Experimental design: As noted, most of the experimental design is ok, but with some concerns regarding testing results and selection of temperature data.
Validity of the findings: While the data is useful for the researchers working on viral disease outbreaks, my concern is that the conclusion that temperature correlated to infection may be skewed by accurate testing as well as overall temperature data.
Additional comments: I have outlines some concerns in the attached review and hope that the suggestions can contribute to an improved manuscript.  Specifically, I think that the results section should be expanded with more explanation of the dataset and implications for policy makers.


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: AIR TRANSPORTATION, POPULATION DENSITY AND TEMPERATURE PREDICT THE SPREAD OF COVID-19 IN BRAZIL
Review round: 1
Reviewer: 3

Output:
Basic reporting: Need to describe by more figure
Please use high resolution figures.
Very well written, need to give more attention in unambiguous text.
Explain more result section.
Experimental design: This is an interesting study and the authors have collected a unique dataset using cutting
edge methodology. The paper is generally well written and structured. However, in my opinion the paper has some shortcomings in regards to some data analyses and text, and I feel this unique dataset has not been utilised to its full extent
Validity of the findings: Result should be more elaborative.
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: AIR TRANSPORTATION, POPULATION DENSITY AND TEMPERATURE PREDICT THE SPREAD OF COVID-19 IN BRAZIL
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed my concerns in the revised manuscript.
Experimental design: The author's considered and implemented additional comparisons and included these data in the revision.
Validity of the findings: The authors explain the most significant results from the data and have greatly improved the discussion section.
Additional comments: The revised manuscript has addressed reviewer comments and I now recommend 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: AIR TRANSPORTATION, POPULATION DENSITY AND TEMPERATURE PREDICT THE SPREAD OF COVID-19 IN BRAZIL
Review round: 2
Reviewer: 2

Output:
Basic reporting: na
Experimental design: na
Validity of the findings: na
Additional comments: Acceptable


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: MONITORING OF UN SUSTAINABLE DEVELOPMENT GOAL SDG-9.1.1: STUDY OF ALGERIAN “BELT AND ROAD” EXPRESSWAYS CONSTRUCTED BY CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: I found the manuscript very unclear and ambiguous. The introduction didn't have enough and well-structured paragraphs, lack of consistency. I put all my comments in the PDF.
Figures and Tables were well illustrated, visible and clear. However, there are minor mistakes, please find my comments in the pdf attached.
English should be improved to ensure that an international audience can clearly understand your text. I provided some examples to improve, but it really needs to be fully revised by the authors.
I also found that the authors need to familiarise themselves with the following terms and their meanings: sustainable Development Goals, Targets, and Indicators. There was a lot of confusion in the text.
Many of the references need to be revised.
Experimental design: Even if the article fits within the aim and scope of the journal, unfortunately, the aim of this study, research questions were unclear and undefined.
A rigorous methodology was attempted, however, I found a major mistake in the NDBI calculation, therefore, major revisions need to be accomplished.
Validity of the findings: Please see my comments in the pdf attached. Thank you.
Additional comments: Please find attached the PDF where I left the comments. Please follow the suggestions. If you don't agree please state the reason. Best wishes, AA


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: MONITORING OF UN SUSTAINABLE DEVELOPMENT GOAL SDG-9.1.1: STUDY OF ALGERIAN “BELT AND ROAD” EXPRESSWAYS CONSTRUCTED BY CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript needs some further improved before to be accepted for publication. In general, there are still some occasional grammar errors through the manuscript especially the article ‘’the’’, ‘’a’’ and ‘’an’’ is missing in many places, please make a spellchecking in addition to these minor issues. The reviewer has listed some specific comments that might be helpful of the authors to enhance the quality of the manuscript further.
Experimental design: •	This section is also well written.
•	Please explain what was the data resolution used in this study (hourly, daily…) and why?
•	Please explain, why did the authors have chosen a case study from Algeria to compare with those from China?
•	Did the authors used the census data to validate the data retrieved from remote sensing, please explain?
•	What was the raster resolution used in this study?
Validity of the findings: Some sensitivity analysis is needed, perhaps using box plots.
The discussion should provide a summary of the main finding(s) of the manuscript in the context of the broader scientific literature, as well as addressing any limitations of the study or results that conflict with other published work.
Please include some quantitative findings in the conclusion section.
Additional comments: In general the manuscript is well written and deserve to be published in PeerJ 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: MONITORING OF UN SUSTAINABLE DEVELOPMENT GOAL SDG-9.1.1: STUDY OF ALGERIAN “BELT AND ROAD” EXPRESSWAYS CONSTRUCTED BY CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1) In Figure 3, the Landsat images for 2011, 2015 and 2019 are shown. But, in the raw data, the Landsat images for 2011, 2014 and 2019 are provided.

2) In Figure 5, the population is shown on the X-axis. The values shown on the X-axis are so close to each other as they are high numbers. The log of the values can be taken, to make the bar chart more readable.

3) In Figure 5, only 36 provinces are shown. As mentioned in Wikipedia,  https://en.wikipedia.org/wiki/Provinces_of_Algeria there are 48 provinces. Please mention if other provinces due to valid reasons.

4) Figure 5 can be enlarged to show the provinces mentioned in the lines between 224 and 231. For instance, the provinces Algiers and Oran are mentioned but those are not visible in the figure.

5) Across the articles, the Tipaza highway and Cherchell Ring Expressway are alternatively referenced. Please try to use the same name or mention the alias name in the article. Similarly, there is the usage of Bekaya highways and Bejaia Highways.

6) In Figure 1, the Tibza expressway is not highlighted in the picture.

7) Please maintain the same level of line spacing in Table 3.

8) In table 4, the header name has Muridale ring road, instead of the Cherchell Ring Expressway. Please mention the alias in the article if applicable.

9) In the Abstract section, the numbering as made (2), (3), (4) and (5). But the first number (1) is missing.

10) Across the article, the population values for each year are mentioned continuously which affects the readability.

For instance, in line 42, the population values are mentioned as 911,549, 127,471, 71,411, 30,583 and 41,657.

Instead, it can be mentioned as " HRSL population grid statistics indicate that the East-West expressway has 911,549, Bejaia Expressway has 127,471.......population count in 2015"

The values between lines 255 to 257 are very much clustered. Please consider placing them in a table or rewording them as mentioned above.

11) Please have similar wording for SDG9.1.1 as it is also represented as SDG-9.1.1, in lines 81, 87, 129 132 and 133.

12) There was no Literature Review explaining any previous researches performed in this area.
Experimental design: The article suits all of the criteria mentioned in this section.
Validity of the findings: In the conclusion section, between lines 414 and 416, the reason to select the respective methods, which is the accuracy from the RMSE value should be mentioned.
Additional comments: 1) This a great work in gathering data from different sources and performing spatial analysis.

2) Try to avoid the clustering of numbers and make the articles more readable. It would help to identify the statistical values quickly from the article.

3) It's a nice analysis done using ArcGIS which is a sophisticated tool.


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: MONITORING OF UN SUSTAINABLE DEVELOPMENT GOAL SDG-9.1.1: STUDY OF ALGERIAN “BELT AND ROAD” EXPRESSWAYS CONSTRUCTED BY CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Accept!
Experimental design: Accept!
Validity of the findings: Accept!
Additional comments: Accept!


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: MONITORING OF UN SUSTAINABLE DEVELOPMENT GOAL SDG-9.1.1: STUDY OF ALGERIAN “BELT AND ROAD” EXPRESSWAYS CONSTRUCTED BY CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article is revised well with all suggested changes. The figures, tables and the content are corrected as recommended.
Experimental design: The article suits all of the criteria mentioned in this section.
Validity of the findings: The recommended changes are updated as expected.
Additional comments: Thanks for updating the article based on the review 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: PROGNOSTIC VALUE OF KRAS MUTATION STATUS IN COLORECTAL CANCER PATIENTS: A POPULATION-BASED COMPETING RISK ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript was written well and English is good.
Experimental design: I would like to ask IRB approved at hospital for this clinical study
Validity of the findings: this study seems to use a more specific statistical method and nomogram was made.
Please explain this more easiler to readers.
Additional comments: this study was done whether K ras mutaiton can impact the prognosis of CRC using large patiens cohort ( SEERS data). author analyze prognostic factor including K ras mutation in CRC, In addition to that, they also want to develop nomogram to predict prognosis. But data itself showed too hetergenous and detailed information about chemotherapy regimen and radiotherapy in rectal cancer, as well known, there have been many prognositc factos TNM etc. but only K ras mutation was compared with other clinicopathologic factors, Author also indicated the limitation of this stduy it need a other genetic mutation such as BRAF and MSI  etc .  Regading nomogram and many figures did not geve us confidence,


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: PROGNOSTIC VALUE OF KRAS MUTATION STATUS IN COLORECTAL CANCER PATIENTS: A POPULATION-BASED COMPETING RISK ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Written in a language foreign to the authors
There are a good number of grammatical and linguistic errors.
The introduction and discussion do not provide sufficient information about the known status of KRAS mutation and prognosis form colorectal cancer
There is another paper by Charlton et al
J Natl Compr Canc Netw. 2017 Dec;15(12):1484-1493. doi: 10.6004/jnccn.2017.7011.
KRAS Testing, Tumor Location, and Survival in Patients With Stage IV Colorectal Cancer: SEER 2010-2013.
Charlton ME1, Kahl AR1, Greenbaum AA2, Karlitz JJ3, Lin C4, Lynch CF1, Chen VW5

This study has used the same data and included a similar number of patient and reported largely similar findings. The differences between the current study and the Charlton study should be clearly detailed.
Experimental design: This is a statistical study and it would be appropriate to get a statistics expert to review the statistical methods used.
Validity of the findings: If the statistical methods are appropriate the results appear valid and will be of some clinical value
Additional comments: There is some novel data about the effect of KRAS mutation status in Stage III cancer patients.
Written in a language foreign to the authors
There are a good number of grammatical and linguistic errors.
The introduction and discussion do not provide sufficient information about the known status of KRAS mutation and prognosis form colorectal cancer
Re the paper by Charlton et al
J Natl Compr Canc Netw. 2017 Dec;15(12):1484-1493. doi: 10.6004/jnccn.2017.7011.
KRAS Testing, Tumor Location, and Survival in Patients With Stage IV Colorectal Cancer: SEER 2010-2013.
Charlton ME1, Kahl AR1, Greenbaum AA2, Karlitz JJ3, Lin C4, Lynch CF1, Chen VW5

This study has used the same data and included a similar number of patient and reported largely similar findings. The similarities and differences between the current study and the Charlton study should be clearly detailed.


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: PROGNOSTIC VALUE OF KRAS MUTATION STATUS IN COLORECTAL CANCER PATIENTS: A POPULATION-BASED COMPETING RISK ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Much improved
There remain some grammatical errors that could be corrected by the editorial team
Experimental design: They have responded satisfactorily to the reviewers comments
Validity of the findings: Better presented
Additional comments: Minor grammatical errors remain


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: WOODLICE CHANGE THE HABITAT USE OF SPIDERS IN A DIFFERENT FOOD CHAIN
Review round: 1
Reviewer: 1

Output:
Basic reporting: Language is generally clear, but there are some vague statements that need to be clarified as mentioned below in the comments section. Also the MS could use a good read over and edit for typos. I started pointing them out but there are quite a few.

Backbone structure of the paper is good but it is strange that results from the data outlined in the results are presented in the introduction. I realize this it done to set up the 3 models created to explore the first results presented but it makes it quite confusing to follow. I think they can more broadly present implication of the question without stating the results in the introduction (i.e. we present follow-up models testing X). This problem is reflected to some degree in the structure of the abstract as well (see comments)

The three models are presented as alternatives but the third model really seems like a complementary rather than a competing model and their interpretation seems to support this viewpoint as well. Rewriting throughout to clarify the relationship between the models and explicitly state how they are being used would help immensely.

Good job on archived data and code! It would be nice if the Readme file in github did a better job of referencing which code and data files specific figures and analyses in the paper and the pipeline that generated them.
Experimental design: The hypothesis being tested in some instances is vague. For example, in the abstract, the methods section states that "hypotheses" are tested but only one is explicitly mentioned in the background section above (this may be due to a confusing writing style). Further, I found that the paper would benefit from more specificity about which hypothesis were being examined by each of the three models.

The statistical design is well communicated and rigorous- the experimental field design requires more explanation before publication (see comments). Additionally, I learned new and relevant information about the field set-up in the discussion (i.e. the instar of grasshopper observed was standardized) that needs to be presented in the methods instead.
Validity of the findings: There are some unsupported conclusions. For example, on line 431 they claim that they demonstrate feed-backs between plant and detrital food-webs. From the data here a uni-directional impact is shown ( woodlouse makes spider move= detrital --->plant) I don't see any effect back to the detrital system. On line 437 I am not sure that this paper shows that sit and wait predators have that much of a functional impact specifically. This paper demonstrates that the spiders move, but shows no impact on grasshopper predation rate and no data showing previously documented effects on soil N in the absence of effects on predation.
Additional comments: Guiliano et al leverage 4 years of data to pursue the mechanism behind a surprising result from a previous study. This work (by the last author) found that the presence of spider predators results in changes in soil nitrogen due to the impact of predator on grasshopper behavior. The presence of woodlouse individuals in experimental mesocosms disrupts this effect leading to higher predation rates of grasshoppers by spiders which is coupled with loss of impact of spiders on soil nitrogen. This impact on ecosystem processes is not examined in this paper. The paper takes this result as a jumping off point and considers why spider predation rates may go up in the presence of wood lice. The authors hypothesize that it may be due to either spiders moving higher in the canopy or grasshoppers moving lower resulting in more encounters. They gather behavioral observations from 1 day each (I think) of habitat domain from four summers (2013, 2015, 2017, 2018) where spiders, grasshoppers and woodlice were manipulated. They let the mesocosms rest for the summer and then recover the individuals at the end of the season. They find that spiders move up in the canopy when woodlouse are present rather than grasshoppers shifting down. However, they are not able to replicate across years the result of higher predation rates of grasshoppers by spiders in the presence of woodlouse. In 2018 they add a “warmed treatment” to test whether spiders moving up in response to woodlice is counterbalanced by warming that has been shown to move spiders downward. They demonstrate that this does occur. They then run three models to figure out what the best explanation for the spider movement is. One is a net energy model, one a combination of signal detection theory and habitat domain theory incorporating encounter rate based on observed domain overlap, and one is an individual-based model of spiders moving away from encountering a woodlouse. They find that the best model reflects that spiders move away from encounters with woodlice rather than move toward grasshoppers to maximize net energy gain. They do not uncover as far as I can tell the reason WHY the spiders move away because no cost is detected for interacting with the woodlouse.

In general, the study design seems appropriate along with the analytic approach which nicely deals with multiple sample years and unbalanced experiments across years. The models are certainly a value-add to the paper and there has clearly been much effort to parameterize them properly. However, I found the framing and layout of the paper fairly difficult to follow with a number of logical jumps that need to be clarified for the reader. In addition, there are quite a few details on the experimental approach that were missing and are necessary before the paper is suitable for publication. The authors do have their data and code available.

Section specific comments:

Title: I am hesitant say that the title is strictly true for the data presented in this paper. Certainly the paper this one is based on does that, but here what is being demonstrated is 1) an impact of the woodlouse presence on a spider which causes a domain shift. However, no impact is documented of an impact of this shift on either the detrital or plant food chain as there is no effect of this shift on grasshopper survival and no data on soil processes presented.

Abstract: In general, this needs to be proofed for wood choice and specificity. For example, in the background it is unclear whether the “new hypothesis” is being tested in this study or a previous one. In the abstract background it is assumed that the spider moves but the intro does a nice job of setting up the option of either the spider or the grasshopper moving which this paper does nicely test! I would again use that framing.

Ln 40: Is maximizing energy gain the same as shifting toward the grasshopper? what does this mean biologically?
Ln 42: the biotic factor of alternative prey comes out of nowhere in the abstract and it isn’t mentioned much in the rest of the paper.

Ln 54: Insert “consumer” in front of species
Ln 54: Plant and detrital-based food chains are referenced throughout but are not really defined. Since in some sense of the term detrital food chains are also “plant-based” what is the difference? Is it that detrital is microbial necromass- based? It it really living vs dead plant tissue based? Clarify this early

Ln 61- missing “a”

Ln64: how does this link break? a directional change would be useful.
Ln66: If the woodlouse is a common part of this system then presumably the original mesocosm studies that detected the impact of spiders on nitrogen also had “hidden” woodlouse treatments. Wouldn’t they have broken the link in those other experiments as well?

Ln 72- How does lower grasshopper survival relate to the soil N result?

Ln 80- this line seems to contradict the feeding trial data. reconcile?

Ln81- insert “in response to woodlice”

Ln 93- This assumes that the grasshopper doesn’t also move in response to warming

Ln 97- vague. explain what the concept means in practice

Ln 115- why is this behavior unexpected?

Ln 117- Outline the hypotheses tested by the 3 models in the intro and provide background

Ln 94- this is a convoluted way of saying “whether spiders or grasshoppers respond”

Experimental details missing:

When were the behavioral observations started each year?

How many days of observations were completed each year?

How many degrees did the warming treatments raise the temperature?

Adult or nymphal grasshoppers stocked? Which instar if the latter?

Were spider sizes similar and/or was sex a potential determinant of predation? Do only some sizes of spiders eat grasshoppers?

Other guilds of spiders are reported being in the experiment for controls and then the data is discarded (although it is in the supplement). A short statement of what it shows and why it isn’t considered further seems appropriate?

What are the field densities of each player? They are referenced in the discussion but methods seems more appropriate

Ln  169- do these reflect field densities or margin densities

Ln 204- Is the date of September the same for all years of the experiement?

Ln 273- But I thought the woodlice and grasshoppers/spiders come in contact with each other in the early morning on the ground?

Ln288- define signal detection theory before relaxing assumptions

Ln 333- what is being always attacked? woodlice, grasshoppers or both?

Ln 346- why would they move away if there is no cost to attack?

Ln 369- link to the analysis name in the code

Ln 371- is “inappropriate” the best word here?

Ln 410- in your model attack success is 25%- this doesn’t seem that low…

Ln 431- this feedback seems unidirectional to me

Ln 445- change “a bias” to biased.


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: WOODLICE CHANGE THE HABITAT USE OF SPIDERS IN A DIFFERENT FOOD CHAIN
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment; refer to general comments
Experimental design: no comment; refer to general comments
Validity of the findings: no comment; refer to general comments
Additional comments: This is an ambitious study that incorporates carefully designed cage experiments, sophisticated statistical modeling, and mathematical modeling of behavioral interactions to evaluate which of two basic explanations for a previously documented shift in foraging position of a generalist predator is most likely. The addition of the impact of global warming is somewhat of a stretch conceptually, but is so clearly presented that it should be retained. The manuscript is extremely well written and the supporting material is thorough.  These two points are critical strengths, because the major contribution of this study will not be its findings, but rather its broadly comprehensive research design.  Thus, readers who are intrigued by their synthetic approach, or have a more narrow interest, such as learning about Bayesian modeling, or the “novel” combination of the “habitat domain theory” and “signal detection theory,” will be able to consult the references and the on-line code and data files to explore the details for themselves.  Those who are skeptical of their approaches will also be able to make an in-depth evaluation.
	I am concerned about the degree to which these data may have been over-modelled, and the danger of generalizing from the results of modeling a highly simplified cage environment to being better able to “anticipate changes in ecosystem dynamics” (last sentence of abstract); however, these reservations reflect a personal philosophical point of view.  Readers will be able to evaluate for themselves the validity of the approach, and most importantly, should be able to re-construct all the details of the statistical and dynamic modeling is they should so desire.
	My only major suggestions are that (1) the authors spend considerably more time, in the final part of the Discussion, pointing out which specific behavioral interactions should be studied in more detail (such as the actual behavior of the predator when encountering the detritivore – just one example) as a means to demonstrate the strength, or weakness, of their models; and (2) defend, in the Discussion, the value of very simplified cage experiments as a means to estimate parameters needed for more complex, and hence realistic, dynamic models that may someday actually describe basic features of the dynamics of this old field ecosystem.  The manuscript is OK without these changes, but I feel that adding them will increase the readership considerably by convincing skeptics of the power of the research approach this manuscript espouses.

Some more-minor suggestions:
Lines
Title	Rather bland.  It doesn’t capture the breadth or major contributions of the research; in fact, this general conclusion is already known for this system.
49-50	Overly broad statement of how two chains can be linked; for example, consumers can be linked indirectly because their two food chains are joined by a shared top generalist predator, a linkage that is not a trait-mediated indirect interaction.
65	link BRINGS in the
80	does “carnivorous” = “predaceous” in this case, or are they scavengers?
114	“significant” is either too broad or it implies “statistical significance” – both usages should be avoided --- especially for Bayesians!
128-32	These facts suggest that your cages are not caricatures of the old field community, but instead, of the narrow ecotone between forest and field.
138 	THE spider . ..
159	specify basal and height dimensions
167	“communities” is a bit of a stretch:  six detritivores, two hoppers and a spider do not a community make; strike out “communities using” and go straight to “combinations”
172	Give actual range of field densities; “slightly” is too slippery.
177-8	Why not consider these data?  Do they not support the other conclusions?  Are they too few to make generalizations possible?  If the latter, they probably should not be included even in the supplemental material. If the latter is not true, they should be presented and discussed, since they describe the results of a type of “replicated” treatment.
194-5	These were cages placed on tables in the field – which is fine, but these cages do not incorporate the complexity of the old field community (even though sod was used), and thus should not be termed “mesocosms” in the Abstract or throughout the manuscript.  This term is unfortunately vague, but the suffix “cosm” implies a somewhat natural world, which this carefully contrived collection of a few individuals in a cage is not.  Again, a matter of opinion, but any usage that can reduce skepticism in the reader’s mind will increase the likelihood the reader will be open to what your study has to offer.
197-8	Excellent.
199-02	Give numbers in the Suppl. Materials
203-09	More details are needed here and throughout the Methods section: dates each year so that collecting period and elapsed time between events are clear: temperatures under the heat lamps, and plastic-wrapped cages, compared to controls; instars of hoppers added, and when they were added; differences between years in average temp and rainfall during the experiment.  Some of these points are brought up in the Discussion, but most of them should be in the Methods section.
216	clarify “began with the average height”, because this statement appears to be contradicted by the following phrase, which implies that the 30-minute observations were the raw data points, which is the case, correct?  This distinction is critical to understanding the basic structure of your mixed-model.
247-53	Lack of actual observations between woodlice and spiders is a major weakness of the experiment – interactions at dawn, dusk and during the night should have been made.  This absence of direct observational data does not invalidate your modeling approaches, but it would seem to weaken them considerably. This fact is the basis of my general recommendation that in the Discussion you address future empirical work that would strengthen confidence in your modeling results.
312-3	“does not cross zero” – please remove this (sole) reference to NHST!! Your data presentation is simple and elegant, with parameter estimates and 95% Credible Intervals – this approach is excellent, so don’t tarnish it with statements (implied just as bad as explicit) of “statistical significance.”
373	change ; to ,
388	arthropods; however, this
437-8	“sweeping” is a tad over the top.  In fact, the whole sentence 436-8 is overly broad, and it really does not encapsulate the major contributions of your research.
440	This line begins to better describe your major contributions – refer to my earlier general comments on how to strengthen the impact of your study.
446-8	Ditto, i.e. comments on line 440 apply here also.
Fig. 1C	I find these colors difficult to distinguish against the dark-gray background.


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: THE PREDICTION OF SWIM START PERFORMANCE BASED ON SQUAT JUMP FORCE-TIME CHARACTERISTICS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article in general is written well and is technically correct. I would suggest that you ensure that the references are in the format recommended by the journal. The year appears to be in the wrong position and places should have capital letters (e.g. Sydney). The mix of swimming starts, jumping techniques and gender appear to be appropriate in the reference section.

https://peerj.com/about/author-instructions/

The figures are relevant and appropriately labelled with all data supplied for review.
Experimental design: With the equipment that was used within the study I was looking for force information from the starting block, but it appears that the only comparisons made were between the squat jumps and times to 5m or 15m.

The logic behind the study was sound but it does feel like similar work has been conducted previously by other authors. Is there some way that you could add the block data to the regression analysis?

Information on each of the key variables would be useful for clarification purposes. Further notes are presented in the general comments section.
Validity of the findings: This research provides conclusions based on starts with larger subject numbers than previous research. I would question why the 15m value was not used for all strokes in order to add to the current research. Male/female differences have been reported previously but it is good that this research has validated the finding with a large group of elite swimmers.
Additional comments: Line 5 – close margins between success and what?
Line 9 – primary is used in two consecutive sentences
Line 15 – insert the word “and” before 34
Line 22 – Look to rephrase the sentence to something like “Faster times to 5 m and 15 m in males”
Line 27 – consider changing the start of the sentence to “Variables impacting time to 15 m”
Line 34 – you mention rate of force development – was this investigated? There are some results in your raw data table but I could not find any mention of it in the discussion.
Line 36 – check that you are using US spelling as required for this journal (individualized)
Line 48 – breaststrokers are legally allowed to perform one undulatory fly kick so you may wish to consider referring to multiple kicks in the other strokes
Line 58 – should you have the reference after Thing et al rather than at the end of the sentence?
Line 65 – US spelling for utilized
Line 67 – use correct reference (FINA)
Line 73 – was there any impact from changes to the angle of the block between the old and new design?
Line 82 – change “may” to “that”
Line 84 – what do you mean by ecological validity
Line 87 – are these subject numbers correct? I have not been able to access the article that you are referring to so am unclear of the 8 papers that were reviewed
Line 101 – were these sex-related differences surprising? Could you be stronger in your wording? What differences have been used to assess muscle fibre type within genders?
Line 118 – this sentence is repeated from the introduction/abstract
Line 124 – how do you define regularly?
Line 132 – where do you identify the variables used in the analysis? What is concentric impulse 2?
Line 150 – look to rephrase this sentence to something like “46 variables provided by ForceDecks were initially extracted for use in the analysis process”
Line 159 – why did you use different protocols for the different strokes? Previous research has identified similarities in the underwater phase for backstroke, freestyle and butterfly so it may have been possible to group the information or make note to the differences in the strokes for the sample that you used.
Line 194 – look to rephrase the sentence commencing with second order polynomial
Line 208 – make reference to other papers that have found that males were significantly heavier, taller and faster than females
Line 234 – have you described how concentric impulse is calculated? You should also be clear that this is during the squat jump rather than on the block.
Line 241 – for clarification the sample size is smaller for time to 15 m so why include table 3 in this section of the results?
Line 257 – can you be more specific than “around 230 N.s”?
Line 259 – change the word “outlined” to “presented”
Line 276 – why only “may”?
Line 278 – US spelling for maximize
Line 292 – if one of the aims of the study was to determine the level of prediction between the 5 m and 15 m start times, why did you only measure 15 m times in freestyle?
Line 310 – is the comment related to underwater phase valid for all strokes and distances?
Line 352 – time of force application is important but there is no reference to this time on the block
Line 360 – does this sentence have any relevance to concentric training?
Line 367 – US spelling for utilize


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: THE PREDICTION OF SWIM START PERFORMANCE BASED ON SQUAT JUMP FORCE-TIME CHARACTERISTICS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This article is generally well written. The language is clear and consice and the findings are clear to understand. I have made a few suggestions for improvement below.
Experimental design: It was not clear that the other strokes were excluded from 15 m analysis.

Was the different stroke data reported in te 5 m analysis? It was not in the discussion.

Why was 7.5 and 10 m time not considered as well?

Did you consider only using dive and glide trials?

Does the self-selected swuat jump depth affect overall jump height? please provide evidence to support this.

No limitations to the current study design were discussed?

Is there a limit on the number of tables and figures for this journal?

Provide some supporting evidence around the statistical analysis used.

Why did you not use a weight squat jump?

Was the time between jumps testing and swim start testing always consistent?

Were the trials suited ir unsuited?
Validity of the findings: The data analysis is strong and the findings of this study are novel. But I would have liked to see more data on the baseline strength of each of the athletes as I think the main differenes in Sex exist because females are in general weaker than males. Please dicuss this more...

Also discuss...if females are weaker could a tactic be to increase their strength first and then their start predictors would be similar to males?
Additional comments: First few lines in the abstract...this is fairly obvious. Please remove. Could maybe add something like "The start has been shown to contribute to XXX about of total race time" instead.

If word count permits, could add a bit more detail around the methodology in the methods secton of the abstract.

Line 53 - replace ref number 6 with a more relevant referene that utilises the kick start.

Line 86 - consider a new paragraph

Think about splitting the conclusion into major findings and practical applications.

Try to insert references at the end of the sentence to enhace flow of the manuscript.

Overall, I well written and constructed study. Great Work!


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: THE PREDICTION OF SWIM START PERFORMANCE BASED ON SQUAT JUMP FORCE-TIME CHARACTERISTICS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The information presented in the revised version of the article meets the PeerJ standard of reporting.

Changes were made to the referencing but there is one reference that uses capital letters for the title.
Experimental design: The research questions are well defined with the gap identified from the author's earlier article reviewing current literature.
Validity of the findings: No comment
Additional comments: The work that the author has done in reviewing the original paper is to be commended.


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: THE PREDICTION OF SWIM START PERFORMANCE BASED ON SQUAT JUMP FORCE-TIME CHARACTERISTICS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Thank you for addressing all of my previous comments. It is clear that the authors have thoroughly considered all feedback and made the changes needed.

The article is well written and will contribute to body of knowledge on swimming start performance.
Experimental design: The added detail in the methods sections has made the experimental design much clearer.

My main concern is that there is some research out there (Tor. 2014) that has explored the contribution of the free swimming phase to the Start performance. Given that all swimmers must resurface before 15 m there is some element of free swimming involved when assessing time to 15 m. The contribution of free swimming obviously changes with race distance and individual under water kick ability etc. I am wondering if the results would change if you looked at time to 10 m or time to 7.5 m in addition or instead?

Please address this either in your methods or discussion phase as I think this is quite important given there is a lot of things that can occur to affect over time performance.
Validity of the findings: The practical applications are not much clearer and the research questions/aims the authors have started are addressed well within the article.
Additional comments: Here are some typos that I picked up.
Table 2 - think about adding units.
Line 96 - change have to has
Line 110 - Remove therefore
Line 231 - check PeerJ formatting guidelines but I am unsure there is allowed to be a space between number and percent sign.
Line 253 - What is meant by "visual inspection"? Is this reliable and valid? Please provide more details.
Sentence starting on Line 370 - please reword its very repetitive.
Line 384 - The sentence starting on this line is very long. Please consider rewording.


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: STATUS OF CORAL REEFS IN ANTIGUA & BARBUDA: USING DATA TO INFORM MANAGEMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: Intro and Background – If the paper is going to reference the 2016 TNC report card for comparison with the AGRRA survey results, more information is needed about the surveys used for the report card.

Figures – A map of all MPAs and sites should be included.  I would recommend including the sites used to develop the TNC report card in the map as well.  Figure 3 should be split into two tables in order to avoid misinterpreting the columns.
Experimental design: This paper compares data across NDNP, Redonda, and NEMMA where the sample sizes are unequal, and the range of habitat types represented in the data is unknown.  There needs to be an explanation of how and why the site were chosen within each of these regions.  Can four sites accurately represent baseline data for an area as large as the proposed Redonda MPA?  If the representation of habitats determined by reef structure, depth, and distance from shore is not considered, the results may not be representative of the true population of the functional groups recorded.  Therefore, comparing across the MPA’s will provide skewed results.

If large scale reef habitat types are known such as barrier reefs, patch reefs, and fringing reefs, why were they not included as a variable in these results?  Much of the variability identified between sites within each region may be been a result of the varying habitat types.

As stated in the Basic Reporting section above, if results are going to be compared to those reported by TNC, there must be an explanation of how the spatial coverage and sample size of each survey effort differed and what makes them comparable.
If the spatial coverage of the three AGRRA surveys is only representative of a portion of the reefs surrounding Antigua and Barbuda, I would avoid extrapolating the information to make statements about the reef nation-wide.

The AGRRA benthos methods section needs better clarification and needs to identify which data were used in the analysis of the paper.  Furthermore, the analysis methods need to include how the data was compiled for each site to generate percentage values.
The methods section would benefit from some additional explanations of the data collected where the terms promotors and detractors are defined.
Validity of the findings: The paper should include a full disclosure of the sampling design and power analysis used to develop sample sizes within each region (MPA).

When sample sizes, habitat representation, and seasonality vary across datasets, I would advise using caution when comparing between them.  In addition, due to the variability among the datasets, I would also advise against making inferences or speculations about what might have caused those differences within the discussion of the paper.
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: STATUS OF CORAL REEFS IN ANTIGUA & BARBUDA: USING DATA TO INFORM MANAGEMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: The writing itself is OK but there were mistakes.  The first several figures are in fact tables.  In manuscript literature citations are unconventional but not a serious problem.
Experimental design: Problems are described in general comments to authors
Validity of the findings: Problems of the survey design are described in the general comments to the authors.
Additional comments: General Comments

This is a study of three coral reef systems on or near the island of Antigua (in the country of Antigua and Barbuda).  The authors used several established indicators of reef condition such as  live coral and crustose coralline algae  (CCA) as indicators of reefs in good condition (called reef "promotors") and macroalgae and thick sediment trapping algal turfs as indicators of reefs in poor condition (called reef "detractors") .

The results of this study showed considerable variability within sites but significant differences among regions.  For example, the NEMMA region had abundant coral and CCA (i.e., "promotors") but it also had abundant macroalgae detractors.  This is just one of several examples of the variable results from this study.  The authors clearly acknowledge these confusing patterns.

My primary concerns relate to the lack of stratification in the design of the study and the lack of a clear idea of how managers can reduce "detractors" and increase "promotors" of healthy reefs. I'll describe what I see as problems below but I want to stress up front that Antigua is an important island that had extensive coral reefs but most (all?) have declined over the past several decades.  So, studying the state of the island's management is extremely important.  However, I found this study frustratingly incomplete.  All problems can and should be fixed.

It would have been helpful to see detailed charts showing the location of each of the study reefs within the study regions.  Readers are left wondering were the reef surveys conducted on exposed or protected reefs?  Were fore reefs, back reefs or patch reefs studied?  None of those important variables were described in the manuscript.

Per region water depths were reported but they ranged remarkably from 1.5 m to 10.6 m.  Pooling data over such a great range in water depths is a problem especially since the average water depths among regions varied (i.e. NEMMA averaged 5.3 m, NDNP averaged 8.6 and Redonda averaged 9.0.   Most rate processes such as algal productivity and herbivory vary considerably over depth ranges that broad.  Importantly, both "benthic promoters" of coral cover and CCA abundance are depth sensitive.  Tropical CCA are usually most abundant in shallow water (Adey and Vassar 1975, Dean et al  2015 ). Fig. 8A shows the greatest CCA abundance at the shallowest (NEMMA) site.  Further, the relatively high coral cover at the NEMMA region was said to be the result of abundant Acropora prolifera which is a shallow water branching coral.  This leaves open the question of whether any differences in management or simply differences in water depths resulted in the regional differences illustrated in the table in Fig. 3.

Several important points were not clearly described.  For example, the North-East Marine Management Area (NEMMA) is said to be the largest managed marine area on the island of Antigua but there is no indication of what is "managed" and if enforcement and/or compliance exists in this area. Specifically, is this a no-take reserve?  Or are there some other restrictions on fishing or other activities?  These questions seem central to this paper.

I would have liked to see more data analyzed.  What coral species were present?  As mentioned above, it was revealed that one site included the branching coral Acropora prolifera.  That is important and interesting for two reasons.  First that is the genus that built most coral reefs in the Caribbean and that species is a hybrid of two other Acropora species that would have to be on the island but were not mentioned.  Other coral species are susceptible to bleaching or disease.  It would be good to document (perhaps in an appendix) all coral taxa.

While relatively few studies have been conducted on Antigua's coral reefs, beyond the AGRRA and TNC studies the recently published study in Science Advances (Steneck et al 2018) included several study sites in Antigua.  Those might provide additional context for this paper.

Finally, the composition style of the paper could be improved.  The first three figures are not figures at all but are tables.  Figure 4 is the first true figure.  Several words or phrases that are not proper nouns were capitalized.  "Macroalgae" was not written as a single word.  There were misspelled words such as "assess" (not spelled that way), references were cited in non-traditional ways.

Literature cited:

Adey, W.H. and Vassar, J.M., 1975. Colonization, succession and growth rates of tropical crustose coralline algae (Rhodophyta, Cryptonemiales). Phycologia, 14(2), pp.55-69.

Dean, A.J., Steneck, R.S., Tager, D. and Pandolfi, J.M., 2015. Distribution, abundance and diversity of crustose coralline algae on the Great Barrier Reef. Coral Reefs, 34(2), pp.581-594.

Specific Comments:

English composition and style:  Cite only author's last names.  The exception is if several authors have the same last name - in which case you include the authors first initial.

Only capitalize proper nouns (e.g., Line 81: "invasive alien species" should be all lowercase.  Line 146, 147 " crustose coralline algae" and "coral cover" etc. are  common names of organisms and thus are not proper nouns.  It is OK to capitalize acronyms.

Abstract becomes confusing towards the end when this study is compared to other studies.  It would be clearer if you state "our study" or  "we".  For example,  rather than "While the results of the surveys mirror..." It would be better to write: "While the results of our surveys mirror"..

Line 48:  MPA don't generally 'stem the decline' as much as they improve potential recovery after mortality.

Line 60:  Figure 1 is a Table.  In fact, Figs 1 - 3 are all Tables and should be presented as such.

Line 75: A map that includes all three study sites would be helpful for readers who do not know the area.

Line 128 (and throughout):  You used "quadrats" not "quadrants".

Results:

Starting with line 145: Comparing sites having different depths creates a problem.  Note that the data for all three study sites are different depths (see the Table mislabeled as Fig. 2).  NEMMA average depth is 5.4 m (+ 1.06 SE), Redonda sites average 9.05 m (+ 0.38 SE) and NDNP is 8.6 m     (+ 0.5 SE).  At the very least for NDNP, the 10 sites > 8m depth could be used to compare with Redonda.

Line 218:  The abundance of Acropora prolifera at one site illustrates why this study should be depth stratified.  Acropora species grow in greatest abundance in shallow zones where they occupy considerable substrate.  The authors describe this at one of the shallower site.  However, there is no support in the literature to suggest that outplanting this coral will restore reefs at the scale of the three study reefs in Antigua.

Line 226:  The word "macroalgae" is one word not two as in line 226 and not hyphenated e.g. in Fig. 8.

Line 239:  The discussion of reef fishes is interesting.  However, I didn't see anything describing the method of fishing on these reefs.  Where fish traps and spear fishing is most common, herbivorous fishes (especially parrotfishes) decline in abundance.  Where hook and line fishing predominates, carnivorous fishes decline.

Line 246:  Good point about the increased importance of large bodied parrotfishes.  Why wasn't this illustrated to see if that was a factor in this study.

Line 248:  High intersite variability is a problem for this study to make clear conclusions.  For that reason, stronger stratification of sites is warranted.  The remarkable depth range at the NEMMA sites (i.e. going from 1.5 to 10.6 meters) should have been controlled.  Perhaps use depth bins.  Also, if the sites varied by wave exposure, this would likely affect growth rates of algae and/or grazing rates by herbivores.

Line 257:  Why weren't live coral cover per species report?  The concern about diseases and bleaching can be better evaluated when species are reported.

Line 281:  Marine surveys around Redonda "have been fed directly onto the rationale for the creation of the Redonda Ecosystem Reserve management plan."  EXACTLY WHAT WAS USED FOR THAT RATIONALE?  That is the sort of information that should be evident in this paper but is not.


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: STATUS OF CORAL REEFS IN ANTIGUA & BARBUDA: USING DATA TO INFORM MANAGEMENT
Review round: 1
Reviewer: 3

Output:
Basic reporting: I did have a great interest in the research topic addressed in the ms and did enjoy reviewing the material.  The manuscript would benefit from some general reorganization and recrafting of the hypotheses before publication. I've provided several general recommendations for the authors to consider that would improve the overall layout and flow of the manuscript while also providing some specific, directed comments that should be included in a revised ms.

Musts in a revised ms.
1.  Figures - A map of the study area and study sites.  It's important to know the distance between some of the research areas, spatial distribution, and how the location of the sites may affect the results.  It would also be beneficial to identify the type of habitat surveyed for each survey site (e.g. patch reef, fringing, etc.)

2. Methods - Statistical interpretation of the data.  Several AGRRA techniques are mentioned in the methods (line intercept, quadrats, juvenile coral counts) yet only live coral cover is presented in the results and figures. First, was the only the line intercept data used?  Second, if so how was live coral cover calculated and summarized?  Were the points pooled for all transects or averaged across transects at each site?  How was the data treated for the management type analyses (pooled or averaged?).  Third, if data from some of these surveys were not used in the analyses then it can be omitted from the methods.  For example, I did not see any data presented on large and small coral juveniles (the authors call these recruits in the methods).

3. Introduction - I understand that this manuscript is presenting baseline data.  That is perfectly acceptable and provides a starting point for the study region.  The authors continually emphasize this point throughout the ms however they would be better served defining and interpreting the results in the context of the 3 management areas assessed.  From the descriptions offered in the Intro and Methods it seems that there is a wide disparity in the management actions between the 3 study areas (NEMMA, Redonda, & NDNP) yet the interpretation of the results and discussion never allude to how the differences in protection, access, or geography might correspond with the differences in coral cover, TAS, or MA cover.  Certainly some hypotheses could be generated that would state that live coral cover should correspond with increased protection or more restricted access.  These would be a priori assumptions based upon the literature.  Regardless of the paucity of long-term data for the study region the present day assessments provided by the authors could still be the result of the current management zone practices that are in place.  It doesn't have to be a temporal analysis.  The same point can also be made for the results of the fish surveys and integrated together does the highest herbivore fish biomass correlate with the highest coral cover.  These are all hypothesis that could addressed in a revised ms.
Experimental design: General considerations

As mentioned above the authors reiterate that this is a baseline study and that there is no long-term data from the study region. However, if they wanted to analyze the decline of corals across the 3 study areas AGRAA demographic surveys do estimate the amount of old mortality as part of the survey.  While the metric of live coral tells readers what is currently there the authors could summarize the frequency and the amount of "old mortality" on the corals surveyed to indicate what might have been lost in the 40 years of degradation in the study region.

Figures - The figures should be re-orientated.  It's not visually appealing to see the data typically placed on the Y axis to be on the X axis (e.g. fish biomass, coral cover).
Validity of the findings: With the exception of the mention A. prolifera at one of the sites there is little mention of the coral composition either at the management zone level or site level.   Are any of the differences across the 3 study areas tested due to coral community composition?  Or the habitat (reef types) assessed in each study region?  Differences across the 3 study zones might be explained by the presence, absence, or abundance of certain coral species.  Density or abundance data would help assist in understanding the difference across the 3 study zones (for example numerous small colonies vs. few large framework building colonies).
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: STATUS OF CORAL REEFS IN ANTIGUA & BARBUDA: USING DATA TO INFORM MANAGEMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: Overall, the context of the paper has greatly improved by providing greater detail in the methods and clarifying differences between the TNC and AGRRA datasets.  However, despite the improved context, I feel that the writing technique needs a great deal of editing.  Throughout the manuscript, there were an abundance of run-on sentences and back to back compound sentences with differing subjects.  In addition, I felt the discussion contained a lot of redundancy in stating what the data was useful for in regard to management actions. There might be some value in making your findings more concise.

A few other grammatical errors I found included improperly capitalizing words (coral reefs, seagrass beds, mangroves, etc.) and switching between past and present tenses.

Once the grammatical errors and writing format have been revisited, I feel that an additional review is needed to finalize the manuscript.  Again, I feel that the manuscript has greatly improved from the first version I reviewed and provides informative and important results that will ultimately evolve into a great publication.
Experimental design: My concerns with the experimental design were addressed in my prior review of the manuscript.
Validity of the findings: The manuscript does a great job at identifying the need for basic reef assessments and regular monitoring to establish baseline data and evaluate the status of marine resources to improve management decisions.  However, I would suggest adding in some additional detail to the future research recommendations included in the discussion.  Stated several times within the manuscript is the need for additional surveys and funding to support those efforts to best understand how to manage a reef system.  I feel that researchers may look to this publication for information on where to fill data gaps and what management applications these missing data may support.  This is certainly just a suggestion, but I feel that insightful recommendations may generate more interest towards these protected areas of Antiqua and Barbuda.
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: STATUS OF CORAL REEFS IN ANTIGUA & BARBUDA: USING DATA TO INFORM MANAGEMENT
Review round: 2
Reviewer: 2

Output:
Basic reporting: Good and improved
Experimental design: Major problem with stratification etc has been resolved.
Validity of the findings: Findings are valid
Additional comments: Good job with the revision


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: PROGNOSTIC SIGNIFICANCE OF PI3K/AKT/ MTOR SIGNALING PATHWAY MEMBERS IN CLEAR CELL RENAL CELL CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: K-M plotter and HPA prognostic analysis seems to do the same thing to the same TCGA dataset.
Validity of the findings: Please add the marker information, catalog number of the antibodies, secondary antibodies and the software/method to analysis the WB.
Additional comments: The manuscript entitled ‘Prognostic significance of PI3K/AKT/mTOR signaling pathway members in clear cell renal cell carcinoma’ describes the analysis of public TCGA ccRCC and GTEx normal tissue, including mRNA and protein expression to explore potential prognostic roles of PI3K/AKT/mTOR signaling pathway in ccRCC. They used GEPIA database to analyze mRNA expression level. Then they used a total of 3 databases to perform overall survival. The authors also experimentally demonstrated the expression of the highlighted potential markers using immunoblot. Though the conclusions seem to be valuable, I am not fully convinced by some details in the manuscript.

Major comment:
1.	My major concern about GEPIA analysis is the batch effect, even though the correction is considered in GEPIA server. The GEPIA analysis in this study combined normal samples (n = 100) from both TCGA and GTEx. There are 72 matched normal samples in TCGA-KIRC. TCGA tumor versus TCGA normal only analysis should also be performed to validate the results. TCGA matched tumor versus matched normal may also be more convincing.
2.	As mentioned in the “Experimental design”, both K-M plotter and HPA databases analysis generated the K-M plots. It seems that the authors replicated the analysis of the same dataset using two different databases. The difference would be number of patient samples involved in the analysis (n = 530 versus n = 528). Would you explain why both analyses are necessary?
3.	Take HPA analysis as an example, what would be the cut-off for survival analysis? Please provide the analysis details.
4.	In Figure 3-5, for each gene, patients were divided into two groups: high expression and low expression. Please list the exact patient number of high versus low for each gene.

Minor comment:
1.	In line 119, ‘P-value were displayed’, however, only ‘P>0.05 Figure 1’ was mentioned without the exact numbers of each group.
2.	In line 120, it mentioned that the unit of RNA-seq is TPM, which is correct. However, the unit in the figure is log2 normalized TPM. The unit should also be mention in the legend of Figure 1.
3.	In Figure 1 legend, you may need to mention that the figures were from GEPIA server.
4.	Please include molecular weight in Figure 2A (as shown in supplement materials).
5.	Clinicopathological parameters was mentioned and listed for public dataset. Would you provide the information of the three samples used in immunoblotting?


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: PROGNOSTIC SIGNIFICANCE OF PI3K/AKT/ MTOR SIGNALING PATHWAY MEMBERS IN CLEAR CELL RENAL CELL CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: 1. mRNA level of PTEN, PIK3CA, PIK3CB, PIK3CG, AKT3 and mTOR should be tested by qRT-PCR to validate the bioinformatic analysis;
2. Western blot should be optimized.
Validity of the findings: no comment
Additional comments: This manuscript by Fan et al. reported the analysis of the mRNA expression levels of multiple PI3K/AKT/mTOR signaling pathway components, including PTEN, PIK3CA, PIK3CB, PIK3CD, PIK3CG, AKT1, AKT2, AKT2 and mTOR, in ccRCC and normal tissues based on GEPIA database, and detected PI3K, AKT and mTOR protein expression by WB. The analysis of these nine members at mRNA levels and proteins levels in ccRCC patients was investigated based on K-M plotter, HPA and TCPA. In general, the manuscript is clearly presented and written, and contains appropriate introductory material, methods, bioinformatic analysis and reasonable. As noted above, the entire study sounds entirely plausible and provides useful information for further research in the future. However, there are several major concerns as described as follows. I would suggest the paper being accepted for publication if the authors can incorporate these comments in their revision.
There are several concerns proposed as follows:

Major concerns:
1.	There are a lot of analysis based on different databases with different outputs. For example, the GEPIA revealed no significantly different between ccRCC and normal tissues at the mRNA expression level. However, the analysis based on K-M plotter and HPA shows that PTEN, PIK3CA, PIK3CB, PIK3CG, AKT3 and mTOR were positively correlated with overall survival (OS), whereas PIK3CD mRNA expression was negatively correlated with OS. Please provided reasonable explanations of the completely different results. And I strongly suggest that you should check the mRNA level of PTEN, PIK3CA, PIK3CB, PIK3CG, AKT3 and mTOR by qRT-PCR to validate your analysis based on different database. Especially, PTEN should be tested.
2.	Validation of P13K, AKT and mTOR protein by WB. There are nine members were investigated in this study, why do you just check these three members? And in Figure 2, the N2 has problems compared with N1 and N3, the Actin level of N2 is lower than Actin level of N1 and N3, but the mTOR lever is much higher in N2. For the Akt, T1 and T3 shows larger bands (maybe phosphorylated), but T2 doesn’t have this feature. Could you explain it? For the Supplementary file 1, the label on each lane is confusing, you’d better load sample orderly. If you use two blots, each blot should use Actin as a control. The marker is missing in mTOR blot. It will be better you labeled the Molecular weight of each bands of the marker. For the control, the amount of Actin should be the quite similar in each sample. Antibody information should be labeled for each protein.
Minor concerns:
1.	In line 96, “(Han et al. 2017) discovered that numerous protein biomarkers” should be corrected as “Han et al (Han et al. 2017)discovered that numerous protein biomarkers”, the similar problems also happen in line 317, line 323 and line 334.
2.	In Table 2, the font of I, II, and III should change into Times New Romans.
3.	The Written Informed Consents in supplementary file 2 should be signed.


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: PROGNOSTIC SIGNIFICANCE OF PI3K/AKT/ MTOR SIGNALING PATHWAY MEMBERS IN CLEAR CELL RENAL CELL CARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The study presents a survival analysis of nine genes in renal cell carcinoma patients. Although, some of the genes were found to be correlated with the overall survival, the authors didn’t perform any additional analysis to explain why and in which cases this correlation might be significant. In addition, gene expression and protein level of the same factor was not significantly different between the tumor and normal tissue, which was not explained as well.

1. Despite being correlated with overall survival, the expression of the mRNA and level of the proteins of the markers were not different between cases and control conditions! Can this be explained? For example, the markers can be investigated on a granular level. There might be a pattern that is hidden in the full dataset. Gene expression and/or protein level could be different when stratified by clinical or demographic characteristics of the cases.
2. The section on “GEPIA database analysis” refers to the number and sources of the datasets and to the platform in which the data were processed. However, there is no mention on the origin of the data, the type of analysis performed or the criteria for significance.
3. The description of the databases and the platforms used in the study is confusing (Materials & Methods). GEPIA and KM plotter are not exactly database, but rather analysis platforms that rely on data generated from other projects, mainly TCGA. Please, consider describing the datasets separately from the type of analysis that was performed in each, then link them in a workflow/pipeline section.
4. It is not clear from the description of the workflow which datasets were used for testing/validation. Some of the analysis platforms rely on the same datasets, while presented as independent.
5. A univariate and multivariate analysis were not described in the methods section.


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

Input:
Title: PROGNOSTIC SIGNIFICANCE OF PI3K/AKT/ MTOR SIGNALING PATHWAY MEMBERS IN CLEAR CELL RENAL CELL CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have addressed my concerns in the revised version.
A minor comment: It would be better if F value could also be kept in Figure 3, because it is ANOVA 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: PROGNOSTIC SIGNIFICANCE OF PI3K/AKT/ MTOR SIGNALING PATHWAY MEMBERS IN CLEAR CELL RENAL CELL CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: This edition is much better. The authors corrected all of the proposed questions carefully and reasonably. It is awesome and suitable to be published.


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

Input:
Title: PROGNOSTIC SIGNIFICANCE OF PI3K/AKT/ MTOR SIGNALING PATHWAY MEMBERS IN CLEAR CELL RENAL CELL CARCINOMA
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors responded to some of the issues raised in the review. They revised parts of the text to detail their methodology and added two figures; one to outline the workflow of the study and another to show the expression of the nine genes in different stages of the disease. The revised manuscript fails to address two critical issues.
1. In the revised manuscript, the authors show a correlation between six of the nine genes of interest and the tumor stage. However, the small effect size, the lack of comparison to control patient samples, the protein level comparison and the absent difference in three of the nine genes make it difficult to accept the difference in expression as a possible explanation for the suggested correlation.
2. The added figure (Figure 1) outlines the workflow of the study. The figure, and the text, fail however to respond to a serious issue. Some of the tools/platforms on which the study were performed use similar sources of data while they were presented in the manuscript as independent, as in some serves as discovery and others as validation.


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: ANCIENT GENETIC DIVERGENCE IN BUMBLEBEE CATFISH OF THE GENUS PSEUDOPIMELODUS (PSEUDOPIMELODIDAE: SILURIFORMES) FROM NORTHWESTERN SOUTH AMERICA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is clear and unambiguous, with professional English used throughout. The literature references provide sufficient field background/context. The article has a professional structure and the raw data are shared.
Experimental design: The scope of the project is within Aims and Scope of the journal.
The research question well defined, relevant & meaningful. The manuscript states how the research fills an identified knowledge gap.
The research was performed with high technical & ethical standards.
The methods are described with sufficient detail & information to be replicated.
Validity of the findings: The data are robust, and the interpretation are statistically sound. The conclusion is well stated, linked to original research question & limited to supporting results.
Additional comments: An excellent study and worthy of publication in PeerJ.  One of the strengths of this study is the use of two fossils to time-calibrate the trees. A drawback is the use of only two genes to construct the molecular phylogeny. Many observers consider a two gene analysis to be deficient in 2018, but in this case the results from each gene are in strong agreement with one another, and make sense in light of the geological literature of the area under investigation.  The authors should be advised however that the days of publishing results from just two genes are coming to an end. However I would also like to see an analysis using both genes together, or least an explanation in the text as to why that was not done.

The figures are well-rendered and clear.  However it would help the reader if you could include in a figure or figure caption the river basins associated with each rag2 cluster and cox1 lineage.  Also, given the non-monophyly of P. bufonis and P. schulzti on the trees, it would be useful to know the location (and river basin) of the type locality of P. schulzti.

The 7.56 Mya date cited (L259) for the uplift of Western Cordillera is unsupported; this precise date is not present in Duque-Caro (1990) or Albert et al (2006), and as far as I know there are no precisely dated estimates for the onset of this uplift.  Kellogg and Vega (1995) refer to this uplift as occurring in the "Late Miocene to Pliocene".