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: HOW MANY FISH? COMPARISON OF TWO UNDERWATER VISUAL SAMPLING METHODS FOR MONITORING FISH COMMUNITIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript overall is clear. English is good in general, except for the first line of the abstract where “are preferred than” should be “are preferred over”.

L61: This statement refers to the present use of UVS, and yet it cites papers from the 90s. Consider citing more recent work, such as Caldwell et al. (PLoS ONE 2016) and/or others.

L89: “a” should be subscript in “Pa”

Introduction is well structured and provides good background information. However, I was surprised to see no reference to previous comparisons of line and strip transects, such as the (rather old but relevant) papers by Burnham and colleagues in 1984 and 1985 (J Wildlife Management).

One component of bias that is not mentioned is the fact that transects (strip or line) are not snapshots. The way we calculate densities for both methods assumes that no new fish entered the sampling area as we sampled, but that is not the case. It is not only about fish movement due to the observer, but also about fish movement per se. And the faster the fish move relative to the observer, the highest the potential overestimation this may cause. This was discussed by Lincoln Smith (MEPS 1988), and more recently observed in simulation approaches such as Ward-Paige et al (PLoS ONE 2010) or Pais and Cabral (Ecological Modelling 2017) (already cited, not shamelessly asking for citations here). This is relevant because you refer line transects take more time for the same distance, so I assume an average slower speed. This could, at least theoretically, lead to higher counts for mobile species.

Tables and figures:
Figures in general are quite heterogeneous. They seem to be formatted exactly as they are output by the different software packages. Consider matching figure styles where appropriate, at least for the same type of graph (e.g. histograms).

Please correct typos in species names (D. labrax on all tables, E. marginatus on t3).

Table 2: asterisks should be explained in the legend or as a footnote.

Table 3 is very similar to figure 5 and more difficult to interpret. Maybe just a figure 5 with 95% CI instead of standard errors could be a hybrid solution. If error bars are too big, then standard errors would suffice, and maybe table 3 could go as supplemental data.

Table 4 could also benefit from being represented as points and error bars, with zero as a vertical line separating species that are favoured by either line or strip transects. This would greatly improve interpretation and the values in table 4 could still be supplemental.

Figure 3, on the other hand, simply compares 2 values per species, so it could be easily interpreted on a table. Simply marking the highest value in bold on a table would help interpret the pattern.
Experimental design: Some aspects in the methods section should be clearly stated to help with replication:

- the average swim speed (or time taken) for each transect type is very important, since it is known to affect bias.

- The number of transects per station should be clear. This is important because between-transect variability can be quite large, and even two transects on the same site at different times can lead to very different density/richness estimates. If sampling effort is small, or very different sites are being pooled together, this should be discussed, and any possible implications on the interpretation of results.

The explanation for picking one of the two stations from each site should be on the methods (2.5) and not on the results (3.5), as it is not clear initially how and why this was done. You could still mention in the results that picking the other stations led to similar results. An alternative would be to aggregate both stations per site into a single point, so the choice of picking one could be addressed in the discussion.
Validity of the findings: Data analysis and results seem adequate, but see concerns with replicability and replication in point 2 above.

L299 onwards: Other authors (e.g. Sale and Sharp 1983) observed that wider transects lead to lower density estimates. This means that it is probably not just width that explains higher densities in line transects. I suspect it also has something to do with additional, non-counted fish being added to line transects to compensate for detectability, something that is not done in strip transects.

It would be useful to discuss what your findings mean to the viability of other proposed methods such as nested sampling (e.g. Prato et al. 2017 PLoS ONE, Minte-Vera et al. 2008 MEPS), or the application of (constant) correction factors per species to strip transects (e.g. Christensen and Winterbottom 1981, Ward-Paige et al. 2010, Pais and Cabral 2017, etc.)
Additional comments: The paper is well structured and approaches important research questions about the choice of UVS method, while providing important data on species behaviour and detectability for the study area. The authors address density estimates on a per-species basis, which I believe it is the correct approach, and they do not fall into the temptation of referring to higher estimates as better, as it has often been done in the literature. This is even specifically referred in the discussion, and gladly so.

The paper fits the scope of the journal and I believe it can be published if some concerns are addressed, particularly those related to reproducibility, presentation and discussion of results. I enjoyed reading the paper and most of my comments are suggestions that can hopefully help improve the 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: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 1
Reviewer: 1

Output:
Basic reporting: See below.
Experimental design: See below.
Validity of the findings: See below.
Additional comments: In the current study Rafferty et al. present an agent based model of VZV transmission with an aim to evaluate the incidence of shingles after implementation of VZV vaccination campaigns. They calibrate the model to observed data in Alberta and find a temporary increase in incidence in certain age groups. The manuscript is generally well written and the modeling seems sound – though some details need to be better explained and some of the presentations reworked.

Comments:

- The study is set in Alberta; the title needs to reflect this. Something like: “Evaluation of the effect of chickenpox vaccination on shingles epidemiology in Alberta, Canada using agent-based modeling”

- Lines 133-136: all of the reasons you list for using ABMs apply to compartmental/ODE models as well. Better justification for ABMS is needed.

- AnyLogic is not familiar to the modeling community. A better explanation of the software is needed. The authors should also consider making the source available for replicability’s sake.

- Lines 216-219: the authors need to be more specific on the contact parameterizing. Why were 1-9 year olds chosen? Why not 1-5 or each year specifically? They also need to present the actual rates, perhaps in a contact matrix.

- The authors should be more explicit in their policy recommendations. Do they think deploying a vaccination program is a good idea?

- Figure 4 is confusing. Why is positive cases averted and negative cases added? It makes more sense to have up be more cases and down be fewer cases.

Minor comments:

- Ref 14 is incomplete.


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: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 1
Reviewer: 2

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: •	Reference No. 7 incomplete, therefore difficult to find.
•	Reference 26, Idem. If the citation format from the journal does not allow to have access to the name of the chapter it will be difficult to check the reference source.
•	In figure 1 I would separate each part of the figure (A, B, C, D) in boxes, as it gets confusing to read/interpret them without the text.
•	I was not able to download the “Data reference 2” to better understand the scenarios or baseline scenario that were/was used.
•	Figure 3 is missing the legend to differentiate what red and blue mean.
•	Overall I think there is a problem with the treatment of “scenarios” information. Through my reading I had to keep going back and forth to learn the specific characteristics of each scenario. When I tried to understand the differences I referred myself to Table 2, however when explaining Table 3 in the results section (line 326), the authors talk about vaccination and non-vaccination scenarios, and at that point I felt that the reader is left out of the loop because from the list of ten scenarios presented in Table 2, there is not information about which ones are vaccination and non-vaccination scenarios. Hence, the specific details of each scenario should be stated.


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: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: As it stands, the method is not described with sufficient information to be reproducible by another investigator.
Validity of the findings: no comment
Additional comments: This an interesting and well written paper about VZV epidemiology that suffers from a lack of description of the model assumptions and behaviours. Some sections (introduction) are particularly clear, and even if I have tons of questions and that the model is not described enough, I am very confident that it could be turned into a useful paper. One of the study strength is also that it is based on reliable demographic and epidemic data, and represent realistic assumptions regarding population vaccination attitudes.

1.	The section describing the calibration and validation of the model was really unclear to me. The authors wrote that the model was calibrated to “the age-specific incidence of shingles and chickenpox prior to vaccination using a step-wise approach”, but the first step “calibrate our model output to age-specific incidence of chickenpox and shingles prior to vaccination”, which is the same quantity. Also, we don’t know how (method) this initial calibration was performed. I don’t understand how the chickenpox incidence can be fitted if only the shingles connection range is varied. Was there no uncertainty in the number of contacts and the risk of transmission on such a contact (mentioned line 186)?
Then, why was a second step needed? Is it because you wanted to inform the model calibration using another data, in the vaccine-era? You could have used this data in the first procedure and estimate your parameters / calibrate the model in one go. As it stands it looks like DoB and WoI have been estimated twice. Later in the manuscript, I found out that the particular parameter DoB wasn’t initially informed by data, as it was varying ~uniformly from 0.42 to 10 (steps of 1 between 2 and 10). Once again, it looks like it would have been simpler to vary this duration from 0.42 to 10 within a Latin Hypercube sample, and try to fit the model directly, just like you did with the other quantities.
It is interesting that the model could not fit the empirical age-specific shingles incidence rates when very short and very long duration of boosting were assumed. Perhaps a simpler calibration process could allow a proper estimation of realistic values of DoB and WoI.

2.	Line 214: the authors state that their model represent a low-density and a high density region. Adding this “dimension” into the analysis is extremely pertinent, but there is absolutely no other information or result that mention this model feature. For example, we have no idea what is the relative size of each region.
VZV hazard is one of the most remarkable marker of human connectivity. As an example, in 1928 Fales showed that children residing in rural Maryland were infected 2 years after those residing in urban Maryland (Fales WT (1928) The age distribution of whooping cough, measles, chicken pox, scarlet fever and diphtheria in various areas in the United States. Am J Hyg 8: 759–799). It has already been shown that ABM’s have the capacity to reproduce the current socio-spatial heterogeneity in VZV hazard (Silhol R, Boëlle P-Y (2011) Modelling the Effects of Population Structure on Childhood Disease: The Case of Varicella. PLoS Comput Biol 7(7)), so literature suggests that this model feature could give useful results.
The paper would really benefit from a better description of the differences between the two areas, and show results stratified by region density (e.g. mean age at varicella infection when the vaccination function is disabled, distribution of the number of boosts in each area). Did the authors assume that the chickenpox and shingles incidence in the pre-vaccine era were the same across all regions? Is there data that could support this assumption? This should be discussed.

3.	Line 212: Please include some references on the distance-based network. The reader needs to know what is this “proximity” and what the contact rates are. Would it be possible to describe and show the resulting intensity of contacts between the different age groups?
The authors say that “An agent’s chance of being infected with chickenpox was dependent on whether they came into contact with someone with infection and the risk of transmission on such a contact”, but we don’t know how these two quantities were parametrised and used by the model.

4.	According to CDC, the majority of breakthrough chickenpox cases are 1/3 as infectious as those of unvaccinated individuals (https://www.cdc.gov/chickenpox/hcp/clinical-overview.html). It would be useful to know what is currently assumed by the model, and how does it impact its predictions on shingles incidence.

5.	From the line 132 to 142, it seems like the authors make a series of statements that implicitly compare ABM’s and compartmental models. I would really suggest to be more precise and cautious when making these types of statements. For example “simulate the indirect effects of varicella vaccination, including the changing risk of disease over time, herd immunity and increasing age of infection”, can be done by an age-structured compartmental model. I would really suggest this section to be reviewed by someone with a strong background in both ABM and compartmental models.

6.	Line 165: It would be useful to know why was a burn-in period needed.

7.	The cumulative incidence (or seroprevalence) of VZV by age before vaccination is introduced is now very standard (see this recent paper: Marangi L, Mirinaviciute G, Flem E, Scalia Tomba G, Guzzetta G, Freiesleben de Blasio B, et al. (2017) The natural history of varicella zoster virus infection in Norway: Further insights on exogenous boosting and progressive immunity to herpes zoster. PLoS ONE 12(5): e0176845.), and can be easily outputted by the model. Please state why the model wasn’t fitted on this quantity (data gap in the pre-vaccine era?).

8.	Some model parameters are not described and sourced, such as the mortality rate, which could impact the results since ageing is linked with shingles incidence.

9.	From what I understood, at least runs 30 were performed for one single parameter set (scenario). The text could mention the fact that this high number of agents should almost remove any stochasticity (judging from your figures).

10.	Please define exogenous infection rate (line 255). Is it related to shingles only, as suggested by your introduction?

11.	It would be useful to give the reader more information about the distribution of the age at first shingles case. As the authors mention earlier, a vaccine against shingles is available and this distribution could inform the age at which individuals should get vaccinated.

12.	I also found that some terms could be used more consistently throughout the manuscript
Line 92, perhaps consider replacing “population” by “persons” ?
Line 118 and 264, replace “case” or “rate” by “incidence”
Line 315: “tried to fit model to empirical data”. Same with Figure 2

Table 1: some units are missing. For example, is the force of reactivation a yearly rate? How is the exogenous infection rate actually used in the model? We also don’t know what “preferential” and “normal” distance mean, how it is used etc… . It would have been useful to know which prior range was tested during the calibration process, as we currently only have the posterior values. What do “preferential” and “ordinary” contacts mean? I don’t think it is defined or mentioned anywhere.

Figure 2: Please state what the blue polygon represent (pointwise minimum and maximum values?).

Table 3: First column. Is the “cumulative incidence” the mean incidence of shingles per year calculated over the first 10 years following vaccination, averaged over the 30 or more runs?

Table 4 line 5: perhaps replace “was calculated” by “, calculated”

Supplemental figure 2 and 3: I think it would be clearer to say as a first sentence that what you showing are simulated and empirical age-specific shingles incidence rates. Once again, we also need to know if the blue polygons represent pointwise min/max or 95% uncertainty interval, or something else.

Also, there was a problem when I tried to download the file “Sums of residuals squared_VZV_ABM.csv”   ({"message": "Entity not found: file", "code": "EntityNotFound"})


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: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: I still disagree that the title accurately reflects what is presented in the manuscript. As the authors state in response to Reviewer 3’s point #2: “…our aim in including the low and high-density regions was not to compare the results in the two groups but to ensure an accurate representation of a typical public health region in Alberta (or in Canada or other comparable jurisdiction)…”. I still suggest changing the title to something like “Evaluation of the effect of chickenpox vaccination on shingles epidemiology in Canada using agent-based modeling”.
Additional comments: Rafferty et al. have revised their manuscripts answering my comments.


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

Input:
Title: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: The method and model behaviours are still not described with sufficient information to be reproducible by another investigator.
Validity of the findings: no comment
Additional comments: I think that the authors answered satisfactorily to some of my comments, and that the method is better described overall, but large parts of the revision are unsatisfactory as the model behaviours are not sufficiently described.

As raised previously by reviewer 1 and I, we need to know the total number of contacts (you can call it contact rate) that occur between the different age groups (perhaps over the first year or first month of the simulation).

I am a little bit confused by the way the probabilities of infection per contact were parametrised, and I think this needs clarification. An agent makes a certain number of contact every day and three parameters describe the probability of the three types of infections during a particular contact. The probability of “normal” chickenpox infection for such single contact is 0.78 (78%) in the model, whereas in the Ceyhan et al. (2009) study, which is cited as the parameter value source, 78% is a probability of infection (the SAR is a good proxy for it in this particular case) calculated over (roughly) 21 days of contacts with an infectious individual in the household. Please include one or two sentences in the method to explain how these probabilities were derived. It is quite important since these three values are fixed throughout the analysis, and as such, considered as “exactly known”, which is quite uncommon for transmission probabilities.

From what I understand, there is no input or output information which is stratified by “urbanicity”, except a number of contacts, but we still don’t know how this heterogeneity is parametrised. Basically, we don’t know how, in practice, these numbers of contacts differ between places. If “rural” individual have less agents within their connection range than “urban” ones, then I understand that the connection range can be assumed to be the same for urban or rural individuals, but another parameter has to vary. It seems to me that the table 1 doesn’t present such parameter.

I don’t understand why we can’t have a sense of the incidence of chickenpox or shingles in both rural and urban areas, as it is an important check of the contact and transmission assumptions, and provides useful information. I have to say that this omission really contrasts with the section that describes how detailed can be an information when provided by an ABM. As mentioned earlier, there seems to be no empirical input or fitting data describing rural/urban differences, so this population stratification should be justified, the differences between the settings (e.g. number of contacts per individual per week/months/year) should be clearly measured, and the differences in epidemic outcomes should be evaluated. If there are no differences in incidence or vaccination impact by urbanicity then one line in the discussion will be enough. it could be that urbanicity doesn’t influence the results, making them more robust to uncertainty in population demograpics and assumptions about the number of contacts, but the reviewers and readers need to be reassured that every possible model outcomes was calculated and checked against data or common sense (=the downside of complex models!).

The proportion of VZV-naïve individuals by age in the model (pre-vaccine era) should be at least be visualised as a model check, as it is related to the first stage of your fitting process, and it will impact your model results. There is good data on the population of Newfoundland (S Ratnam. Varicella susceptibility in a Canadian population. Can J Infect Dis 2000;11(5):249-253. ), and I think their proportions could be compared to your model outcomes, even if Alberta is more densely populated. Once again, I think that every model should be fully checked before being used for publication, especially if they are relevant to public health issues. If the model disagrees with the data, then this needs to be discussed.

I have been able to download and visualise the “contact frequency profile” under the form of a heatmap, but I don’t know how this matrix has been computed. The sum of each column is 1 which is a little bit confusing because the matrix is triangular. Please include more details about how this matrix was calculated.

Please mention at line 179 that one day is the model time step (if it’s the case).

Line 184-188, I think you are describing probabilities and not “infection rates”.

It I understood well, the model is first fitted on age-specific incidence of shingles and chickenpox prior to vaccination, but chickenpox incidence data is re-scaled by the model during the same step of the fitting process. I think this should at least be mentioned in the discussion.

Line 222, please explain what the “AnyLogic calibration experiment” is. Does it maximise the model likelihood? It is not a standard method.

Is there a reason why you don’t use the actual years throughout the paper and don’t assume a certain year for the start of vaccination (could be 2002)? It is not mandatory but I think showing results with the actual years would better illustrate your results (e.g. figure 3 with “2002” instead of “0”, etc…). Similarly, “2002-2012” would be more explicit that “T10” on your figure 4, and it seems to me that in your case, it would be fair to assume that vaccination started in 2002.

Figure 1, the four flowcharts are very nice but it looks like what is shown are not state names but state variables names as they were coded. Even if it’s not very nice (I am not asking this to be changed), the coded names are explicit enough, but could you mention somewhere what “PHN” is? The flowchart “A” could be a little less confusing if a little text at the right side of “shingleVacc” was added to state that vaccination against shingles was not modelled (already mentioned lines 142-145).

Please add a table showing which data that was used for calibration/fitting: outcomes (with age groups), years of data collection, source. At the moment this information, especially the years of data collection, are not provided.

Some figures have misplaced legends (hiding the data), such as Figure 2 (or Figure S4).

Figure 4: I think you should be consistent with age ranges and present values until 100 years old.

Table 1 should show the values of the (key) model parameters. Please replace “Range of values tested” by both prior and posterior parameter distributions so that we will know what was tested and how data informed the model.

Figure 2 and S2-4: Please specify which year (or when, e.g. “before chickenpox vaccination is introduced”) this has been calculated. I guess it is “time 0”, but it is not clear.


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: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1.	There are consistent estimates of the probabilities of chickenpox infection per contact or day, deriving from models using time-use data (Zagheni, Am J Epidemiol 2008, ~100 citations), social contact matrices (Ogunjimi, already in your list of references), Census data (Silhol, PloSCompBiol 2011) etc…. and they are ~5 times lower than the probability you assume to be exactly known in your analysis (16% vs 78%). You end-up having a secondary attack rate (in your model, calculated as the proportion of contacts that become infected by a single newly-infected index case over the course of the epidemic?) that is twice lower than your probability of infection per one contact/day, which is paradoxical. By the way, line 240 “We considered an attack rate in our model (41%)…” is unclear, as we don’t know if it is an assumption, a model outcome, and how it is calculated.
I think it is a strength for our field to have different models using different assumptions, “distance-based network” vs “network structured by household, communities etc…”, but your assumptions about the transmissibility of VZV need to be seriously discussed because they hardly make sense when compared to other estimates and common sense. I think most of the differences could be simply due to your network that is less “structured” than in other models (despite accurately representing age-mixing). In short, using an SAR (originally calculated within households over 2-3 weeks) as a fixed probability of infection per contact/day is clearly problematic here and should raise a lot of questions as transmission probabilities are the main driver of VZV incidence. A more appropriate way to handle the uncertainty in these probabilities of transmission per contact could be to acknowledge it and use a range based on published estimates, and fit these probabilities to the data you have.

more minor point:
2.	Looking at your Supplementary Figure 3A/D (by the way, the figure caption is missing). The chickenpox incidence levels are the same in urban/rural settings (looks like a saturation effect where a “low” density is dense enough to produce the same epidemic levels as a “high” density area), but the incidence curves are overlapping so much that it looks as if there was a lot of contacts between the two areas. What was your assumption about that? For example, what is the proportion of contacts of rural agents that belong to the urban area?
The shingles incidence looks slightly higher in rural settings is the absence of vaccination (could due to lower number of boosts?), but becomes lower when there is vaccination (I find difficult to interpret this!!). I think it would be interesting to mention these differences, as it seems that you would like different jurisdictions (more or less dense) to use your result when considering implementing chickenpox vaccine. It could also be considered as a sensitivity 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: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 4
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: 1) I am really sorry, as it could only me that has this problem, but I still don't understand how VZV spreads within the model, and the terms that you are using seems to misled me. It should be noted that you have made an effort to better explain it, and I think that in the example line 253 is particularly useful. As I said during the first review, the study and the results still make sense to me, but...

Here is more precisely what I don’t understand and why I think the model should be presented in a clearer way:
"78% (as shown in Table 1) is the probability of infection per contact (message) received by a susceptible agent." (from a normal chickenpox-infected agent, and 23% if the agent has breakthrough infection or shingles)
Then,
"An infected agent in the preferred age group (i.e. a child) may send 20 messages per day, each to a randomly connected agent. Considering that the mean number of connections per agent in this age group is 10.87, this gives us about 20 / 10.87 = 1.8 ≈ 1 to 2 messages per connection-day. "
So, from what I read, if one susceptible child and one infectious child are connected together, they usually have 1 or 2 contacts between them, and the probability of infection over one day is 78% if they had one contact during the day, and something like 95% if they had two contacts.
For most of the readers, the term “probability of infection on contact” will relate to the first principles of epidemic modelling, such as the R0 definition. I don’t know how this 78% probability should be named if the “true” probability of infection is actually derived from this original 78% probability, as well as from network characteristics at that time point. Since your ABM explicitly modelled the contacts between the susceptible child S and the infectious child I, and since you also know the probability of infection between S and I, how can other quantities come into play when deciding if S is going to be infected? Perhaps 78% is not a “probability of infection on contact”, but something else. Perhaps a diagram would help, I don't know...
And, as a result, in the table 1, surely this 78% probability can’t be fixed and at the same time “calibrated”. By the way, I don’t think that we know what the durations of the VZV infectious stages are.

2) It is something we might have debated quite a lot already (sorry!), but I still disagree with the authors about understanding the model behaviours when both population density and number of connections are decreased. Since at the same time you assume a similar number of contacts and a same transmission probability per contact within “rural” and “urban” areas, it seems to me that it would be important to understand why you obtain the same chickenpox epidemic before vaccination.

Romain


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: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 5
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Despite the fact that the model calibration is now better described, I am really sorry but I still consider that the model hasn’t been fully checked and should not be published as it is. My questions regarding its strange behaviours have not been answered despite a few iterations and it looks like my questions will remain unanswered, so I think the editor should do without me.

The fact that the chickenpox incidence rate (without vaccination) is the same when the parameter modelling the number of agents per distance is decreased by 33% should be explained, otherwise it will really look like you only partially understand what is happening in the model. By the way, I am not sure that including population density in the model design is really compatible with the pattern-oriented modeling approach since you don’t have any empirical patterns/data of VZV/HZ incidence by regions/density.

The duration of the chickenpox infectious period is still not reported.

Finally, if an index case sends 20 or 23 messages per day to 10 or 17 connections (let’s assume here that 5 of them are susceptible), and if the resulting varicella SAR is 40% in the model (which is totally fine), 2 out of these 5 susceptible individuals got infected during the two weeks of varicella infectious period (on average). Something like 300 or 350 messages would have been sent by the index case during the 2 weeks, and it seems unlikely that only 2 infections among 5 susceptible would have happened if the probability of infection for one single message is 78%, even if the pool of contacts comprises 20/30 individuals.

Romain


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: EVALUATION OF THE EFFECT OF CHICKENPOX VACCINATION ON SHINGLES EPIDEMIOLOGY USING AGENT-BASED MODELING
Review round: 5
Reviewer: 2

Output:
Basic reporting: This article is generally well written. It includes sufficient details for readers to understand the model and interpret the simulation results. The figures and tables are well designed and presented.
Experimental design: The study has a sound experimental design.
Validity of the findings: The authors provided sufficient details for others to replicate the model and results. Although the model includes several simplifying assumptions, which are necessary for any simulation models, the authors have sufficiently justified the use of these assumptions.
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: DISSEMINATION OF ANTIBIOTIC RESISTANCE GENES ASSOCIATED WITH THE SPOROBIOTA IN SEDIMENTS IMPACTED BY WASTEWATER
Review round: 1
Reviewer: 1

Output:
Basic reporting: As the study is of importance in various fields; this data would be of importance to the researchers working in similar lines. However, few more inputs are required.
1. It is necessary to correct the usage of the terms Sporobiota and Sporobiome through the text. Sporobiota - is the collection of sporeforming bacteria. Sporobiome - is the collection of genes of sporeforming bacteria.
For example: lines 53-53, states as "In terms of dissemination, the so-called
54 “sporobiome” is a portion of the bacterial community of great interest."

However it is should be: "In terms of dissemination, the so-called
54 “sporobiota” is a portion of the bacterial community of great interest."

The same issues should be resolved throughout the text.

2. Line 158-159, primer's sequeces shouldl be listed.

3. Line 213 "sporobiome DNA" - my suggestion is to take DNA off. For example no one use "microbiome DNA", as microbiome/sporobiome is  DNA totality.
Experimental design: The research desing match well with the goal, results and discussion. The report is clearly written, with a logical flow. Experimental design aims to answer the research questions.
Validity of the findings: The report is clearly written, with a logical flow. Authors describe an important data showing exploring new ways of antibiotic resistance spreading due to the presence of highly resistant spores. The work is of high importance as sporobiota and sporobiome represent a particular challenge for ARG spreading
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: DISSEMINATION OF ANTIBIOTIC RESISTANCE GENES ASSOCIATED WITH THE SPOROBIOTA IN SEDIMENTS IMPACTED BY WASTEWATER
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: The experimental design is sound, although it is a pity that they have not included more resistance genes in their analysis. However, I have several questions regarding the statistical methods (see comments below), which would need to be addressed or clarified before publication. Particularly I am worried that the correlations they report between resistance genes and taxa may not statistically hold.
Validity of the findings: The implications of the sporobiome in the dissemination of antibiotic resistance has barely been investigated before, making this an important inroad into an under-investigated topic. The study is very small in scope, covering only two antibiotic resistance genes. Overall the conclusions are supported by the data. That said, I feel that the authors could caution a little bit more on the generality of their findings, as they only investigate two antibiotic resistance genes and in some sentences suggest that what they see for those two would be valid for all or most resistance genes.
Additional comments: - It would have been interesting to see a comparison between the ARGs in the sporobiome and those in the full community. I don't think this is totally necessary for the study to be publishable, but since the authors seem to have those results already, I think a supplementary figure comparing the two would add some more value to this study at a very low time investment for the authors.

- Line 57-59: This is a very important point, and I am very happy that the authors point this out explicitly.

- Line 74-75: What would actually promote HGT in aquatic sediments? Sure it can happen, but this does not seem to be one of the most important environment for transmission of ARGs.

- Line 85: I suggest adding the word "potentially" after "thus".

- Line 102: What was the rationale for selecting those two specific genes (tetW and sul1)? There are a multitude of tet resistance genes, and sulfonamides are not that widely used in human medicine (in Europe), so I think this would need some further motivation.

- Line 111-112: I think "spatial distribution of ARG tet(W) and sul1" is strangely formulated. Please rephrase.

- Line 122: What type of cores?

- Line 145: Is this supposed to say "21.460 x g"?

- Line 146: I am not sure what "with 1 volume of 70% ethanol" means

- Line 196: Please specify which environmental parameters already here.

- Line 196-199: To me the use of Spearman correlation seems inappropriate as both those collections of numbers convey important abundance information, which I believe is important for the interpretation the authors make. Please motivate the use of Spearman correlation rather than Pearson correlation. Also, were the correlations corrected for multiple testing? There are a lot of tests being done here, so I think controlling the false discovery rate is important in this context!

- Line 199-201: What was the use of these density plots?

- Line 203 and 208: What standardization method was used?

- Line 222: Actually, the copies of ARG per g of sediment does not necessarily reflect the total ARG pool. With only two genes is very hard to estimate the total ARG abundance, and tetW and sul1 are not the most suitable genes for that either (I have data to back this statement up, but unfortunately it is still unpublished).

- Line 224-225: Note that the ARG frequency may also be biased due to differential ratios of bacteria in the samples, which should be pointed out.

- Line 232-233: Are the p values for correlations corrected for multiple testing? Otherwise, that should be done. Also, what correlation measure what used for this? Spearman?

- Line 236-237: This is unexpected to me, but interesting. My guess would have been that distance would explain a lot of the variation in ARG abundance and frequency.

- Line 238: Remove "a" before "different"

- Line 239: Change "pattern" for "patterns".

- Line 241: Remove "the" before "dilution"

- Line 246-248: Without further evidence for this, I think the tetW-metal connection is a rather far fetched speculation.

- Line 254-255: This seems like an important finding to me, that deserves more highlighting. At the same time, comparative data from the same sample in the total community composition would really be needed to draw firm conclusions (see earlier comments). Could that be included?

- Line 262: Add a comma after "community".

- Line 263: The question associated with the definition of "resilience to the extraction method" is what the degree of noise is, i.e. how many bacteria that persist the treatment for random reasons. Has that been assessed?

- Line 270-271: To say this more samples would be needed from an even more remote area of the bay to compare to, as even the distant samples look pretty much the same. I would refrain from drawing this conclusion from this data alone.

- Line 272-273: However, this could aslo be driven by similar selection conditions all across the lake. This could be an instance of species sorting driven communities OR dispersal driven. See the metacommunity work in e.g.:
Leibold MA, Holyoak M, Mouquet N et al. (2004) The metacommunity concept: a framework for multi-
scale community ecology. Ecology Letters, 7, 601-613.
Loreau,M. et al. (2001) Biodiversity and ecosystem functioning: current knowledge and future challenges. Science, 294, 804-808.
Bengtsson J. Applied (meta)community ecology: diversity and ecosystem services at the intersection of local and regional processes. In: Verhoef HA, Morin PJ (eds.). Community Ecology: Processes, Models, and Applications. Oxford: Oxford University Press, 2009, 115-30.

- Line 277-279: It could equally well be a pretty small fraction originating from the WWTP, because the variation between samples seems to be pretty small. This conclusion is overstated with the evidence presented.

- Line 281-283: With regards to Clostridia and Bacilli, I agree with the authors that the conclusion is supported.

- Line 287: Shouldn't this be the genera most associated with proximity to the WWTP rather than the most abundant? The most abundant ones were virtually the same regardless of distance to the WWTP.

- Line 290-292: I can't find this in any of the figures, where is this data shown?

- Line 293-294: The samples with high metal concentrations are also among the most nutrient rich samples. Couldn't that be an alternative/complementary explanation than metal exposure? This fits with the observation that WWTP-associated organisms are enriched in those samples as well.

- Line 314 (Table 2): Please provide p-values (corrected for multiple testing) for the correlations in table 2

- Line 323-324: Note that it is not known from these results if any of these genera are actual carriers of tetW, or if they just happen to correlate for other reasons. I would really refrain from this speculation.

- Line 338-339: Partially, confirmation of tetW presence in these genomes could be done by just searching a genome database for tetW. Therefore, if the authors really want to speculate about dissemination, such a search would really improve the support for their argument.

- Line 342-344: I actually think this is more surprising for sul1 than for tetW. Sul1 is (I think) more widespread among environmental bacteria.

- Line 350-352: This is true also for tetW, so the speculation above is... well, quite speculative.

- Line 370: Change "sporobiome community abundance tet(W) in greater amounts than sul1" into "sporobiome community abundance of tet(W) is greater than sul1".

- Line 371-373: This is the reason why it is a pity (and a big limitation) that only two resistance genes were studied!

- Line 382-383: Unclear if this decay appeared in this study or the cited one. Rephrase and clarify.

- Line 385: What is "TM"?

- Line 391-392: What is to be expected? Unclearly formulated.

- Line 393-407: I would like to know if these correlations are actually significant after correction for multiple testing (see earlier comments). Otherwise I would say that this statement is not supported by the results.

- Line 411-412: This part I agree on. What I am suspicious about is the specific species/genes correlations pointed out earlier.

- Line 413: This seems like it could be random effects. Please check the significances!

- Line 417-422: See previous comment.

- Line 435-436: This is an important point which could be stressed more.

- Line 439: Change "Comparison" to all lowercase.

- Line 439-440: "study on a sediment core taken away from the influence of a local contamination source" It is unclear what this part of the sentence means. Please rephrase.

- Line 443-446: This is a very good and important point and I would like to stress that this conclusion holds even if the correlations between taxa and resistance genes reported turn out to be non-significant.

- Figure 1: I think that this figure is somewhat non-essential and could potentially be moved to the supplement. I have no strong opinion on this, however.

- Figure 2: What is tested for in the global model? Relation between distance and abundance/frequency? Is this a linear model?

- Figure 4: It is impossible to distinguish genera with the same colors. Please use different symbols in addition to the colors to make this plot 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: DISSEMINATION OF ANTIBIOTIC RESISTANCE GENES ASSOCIATED WITH THE SPOROBIOTA IN SEDIMENTS IMPACTED BY WASTEWATER
Review round: 1
Reviewer: 3

Output:
Basic reporting: For the most part the paper is reported well. I have suggested a number of edits as there were sentences that were less transparent than I would have liked.

The literature cited is appropriate.

Data has been made available and the supplementary material is helpful.
Experimental design: The aims and objectives are clear. The authors do make an effort to contextualise their study in the literature. There could be more clarity in the methods when it comes to the associated data about the site. There is no mention of where this data comes from.
Validity of the findings: The findings can be more clearly stated at times and I have made suggestions below where that might be possible.
Additional comments: The following are specific comments on the manuscript:
Is the 'Sporobiome' a vector for ARG dispersal (as stated in line 30) or is it something that is drawn
upon by many vectors and disseminated? I think the latter.

I think the abstract should read (line 36), "...the dissemination of tetW and sul1, two common antibiotic
resistance genes." Or simply leave out the latter bit...it's not correct the way it's currently worded
as it's two genes in total, not two tet genes and sul.

Line 37. You cant have 'spatial distribution analysis of ARG in the sporobiome DNA', you can only have it across a landscape.  This section needs rewording.

It's not clear how important a 'sporobiome' could be for humans or the environment if by definition it is
not active. I imagine what the authors mean is that spores are a potentially important fraction of the
community that can have atypical dissemination characteristics which could allow for greater
dissemination of ARGs than would be predicted by metabolically active and growing cells.

Line 92. 'associated with'
Line 97-99. Surely ARGs and ARBs are everywhere in the lake. I challenge you to find a litre of water that does not contain an ARG/ARB.

Line 185, commas are more commonly found on the bottom not the top (i.e., 100,000 not 100'000)

Line 203. The parameters stated here are not mentioned earlier and so the abbreviations need to be explained.

Line 236. Clarify what is meant by 'R2-adj'

Line 258. Can you clarify what is meant by M4_med,

perhaps say what it means and then put this in ()

Lines 300-304. This needs to be reworded to clarify the point being made.

Lines 374. This sentence needs to be reworded, I'm not sure what it means.

Line 383. Can you restate this sentence--i'm not sure what is meant.

Line 385. What does 'TM' mean?

Line 391. I think you should extend your definition of where the sporobiome is metabolically inactive, as it seems that it should extend to the samples you acquired, which are not found in a wwtp.

Line 393. Is it appropriate to say that ARGs are accumulating in the sporobiome? Perhaps you can say
that there is selective loss of ARGs not in spores and a concommittant persistance of ARGs in spores.

Line 398. I don't thin the 'heat-resistance' of Firmicutes is relevant to this study.

Line 404. Should be 'pointed to'.

Line 439. lowercase 'comparison'.


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: DISSEMINATION OF ANTIBIOTIC RESISTANCE GENES ASSOCIATED WITH THE SPOROBIOTA IN SEDIMENTS IMPACTED BY WASTEWATER
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: The authors have addressed my comments satisfactorily. I am happy that the p-values seem to hold for multiple testing correction.
Validity of the findings: The conclusions are supported by the data, and in the revised manuscript the language is more well-balanced in terms of interpretations of the findings.
Additional comments: The authors have addressed almost all of my concerns very satisfactorily, either by reasonable explanations, straightening out misunderstandings or performing additional analyses. I still have two minor points that I think should be clarified.

1.	I think there was a misunderstanding about my comment on the biases of ARG frequency and abundance (line 244-251 in the revised manuscript). To be clear, what I meant is that I agree with the authors that total ARG abundance could be biased by the differential microbial load in sediments and the proportion of different bacterial groups. However, what I wanted the authors to acknowledge is that ARG frequency the number of copies of ARG per ng of extracted DNA) can ALSO be biased by differential abundance of different bacterial groups. Please add this note to avoid confusing other scientists designing similar studies.

2.	I don’t really but the authors’ explanation that “the fact that Tet(W) has several domains related to Elongation factor Tu and G (...) makes it difficult to verify the identity of the blast hits obtained.” First of all, the supplied BLAST searches makes it clear that they were carried out using very permissive identity cutoffs. I re-did the same searches and filtered the data for >90% sequence identity and e-value < 1e-170. This filters out most of the hits that would be ambiguous, particularly for sul1. In these searches I only found the Actinomycetaceae family from the sul1 correlations, and the Ruminococcus and Clostridium genera from the tet(W) correlations.
Given that the authors assume that their primers are specific enough to only detect sul1 and tet(W) (and not the elongation factor proteins), such stringent cutoffs would be reasonable. Note that these results indicate that using correlations between taxa and resistance genes is a flawed approach to finding carriers of resistance genes and at best provides some possible candidates. I personally do not think that there is any substantive support for the speculation about resistance gene carriers in the “Correlation tests between OTUs and ARG” paragraph (lines 329-374), and that it could be substantially shortened as it does not (again in my opinion) provide that much value to the study.


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: CRANIAL MORPHOLOGY OF SINOVENATOR CHANGII (THEROPODA: TROODONTIDAE) ON THE NEW MATERIAL FROM THE YIXIAN FORMATION OF WESTERN LIAONING, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, the manuscript is very well-written. So far as I know, all relevant references are cited. The most commendable, greatest aspect of this manuscript is excellence of figures, especially individually segmented bones based on CT data. These figures will be invaluable references for future researches on theropod morphology.
One aspect of writing that I noticed is that the authors' descriptions sometimes contain seemingly unnecessary statements. For example, lines 391-395 states "The frontal contacts the nasal anteriorly, the lacrimal anterolaterally, the postorbital posterolaterally, the parietal posteriorly, and the laterosphenoid posteroventrally." I believe this condition is universal in Dinosauria and thus such a description seems to be unnecessary. Of course, it is not an incorrect statement and, considering this is an electronic journal in which you do not worry about the page number of the article, leaving these statements as they are is also permissible.
Experimental design: The analysis including digital segmentation and phylogenetic analyses are appropriately done. This manuscript provide so much of detailed information of cranial morphology of troodontids, which tend to be under-represented in the fossil record.
Validity of the findings: This is a solid and substantial description of osteology of a previsouly poorly-known taxon.  So much new information is reported here. The conclusion is also well-supported by their observations.
Additional comments: I am really impressed by the quality of the manuscript, especially 3D-segmented images of bones and detailed description. I made some suggestions in writing, as well as a couple of questions, in the attached PDF. Because I am also a non-native English speaker, I do not claim all my suggestions would improve the quality of MS. However, I believe at least some of them are relevant. Anyway, I am very excited to read through MS, especially the description of the proatlas and atlas ribs!


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: CRANIAL MORPHOLOGY OF SINOVENATOR CHANGII (THEROPODA: TROODONTIDAE) ON THE NEW MATERIAL FROM THE YIXIAN FORMATION OF WESTERN LIAONING, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript by Yin and colleagues provides a detailed anatomical description of cranial material, which is referred to the genus Sinovenator, a troodontid from the Lower Cretaceous of China. The manuscript is well structured and illustrated with many figures, which help to understand the description. Apart from a couple of typos, the English is very well. The relevant literature is cited and the study is presented in a broader context.
Experimental design: It is absolutely necesarry that more information on the discovery of the fossil is provided (see my comment below).
Validity of the findings: As mentioned above, the manuscript containes a detailed anatomical description, which needs only minor improvement. Both text and figures allow to understand the anatomy of the fossil and all conclusions drawn from the description are sound. I am with the authors, that the new material resembles Sinovenator best. However, due to the fragmentary nature of both the holotype and the referred material, only one diagnostic character was identified that allows a classification as Sinovenator. On the other side, the new material shows also some differences to Sinovenator, which are listed in the text. It would be good, if these differences could discussed in more detail, because they are relevant for the final classification as Sinovenator or maybe cf. Sinovenator. Furthermore, could the authors list more differences to Sinusonasus? Why was the latter taxon not included in the phylogeny? As Sinusonasus has an interesting mix of characters it would be relevant to know, where it is placed within the tree, also relative to Sinovenator and the new fossil.
Additional comments: - P7L34f: “As a close relative ...” - In my opinion, this sentence can be deleted to avoid repetitions.

- P8L62: Can the authors provide more information on the discovery of the fossil. When and where was the fossil found? Was it found during an excavation of a Chinese research institute?

- P8L69: Change “uA” to “μA”

- P9L79,L81,L83: Please, provide the name of the institutes abbreaviated as IVPP and PMOL so that it is known where the specimens are housed.

- P10L98: What makes the skull so remarkable?

- P10L101: Please mention that the anterior margin of the AOF is not complete and that the shape of area is an interpretation.

- P10L107: Please add that the ascending process of the maxilla is only preserved as a small peace of bone on the right side of the skull.

- P10L109: The contact between the ascending process of the maxilla and the anterior contact of the lacrimal can be better seen in Fig. 4B, may add.

- P10L109: Please, add that only the ventral portion of the interfenestral bar is preserved.

- P10L111: Please, add that the ventral ramus of the maxilla = jugal process

- P11L124: Change to “develops”.

- P12L146: Please add that the anterior process of the lacrimal points anteroventral.

- P14L182: Change “and” to “but”.

- P15L207: Change “The suborbital process” to “It” to avoid repetitions (see sentence before).

-P17L243: Please add, that the QJ covers the ventral portion of the quadrate laterally. As written on can assume it covers the quadrate of the whole dorsoventral dimension.

- P17L252: Change “The quadrate head” of the second sentence to “It” to avoid repetitions (see sentence before).

- P20L321ff: The seperation of the anterior triangular depression and a posterior sub-triangular depression by a transferse ridge can be also found in the Schamhaupten specimen of Archaeopteryx, so may cite Rauhut et al. (2018).

- P24L396f: May add further comparsions with other Jehol troodontids, like Mei.

- P38L694: Change “proatlas” to “proatlases”.

- P46L861: Non-arctometatarsalian pes is the normal condition in theropods, not only dromaeosaurids.


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: CRANIAL MORPHOLOGY OF SINOVENATOR CHANGII (THEROPODA: TROODONTIDAE) ON THE NEW MATERIAL FROM THE YIXIAN FORMATION OF WESTERN LIAONING, CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Some of the strongest parts of the paper are the descriptions.  I strongly recommend addressing with figures the referral to Sinovenator as I could just as easily believe you have a new taxon based on what has been figured.  My photos of the type don’t include the surangular, so again I believe you are correct in your referral, I just cannot assess it for myself.  Great paper and very nice illustrations.  In conclusion, I recommend acceptance of the paper whether or not the concerns below are addressed.

Notes to the authors:

I enjoyed the paper, and I have just a few suggestions that I believe will make the paper stronger.

Again, just a little more on the referral would be nice.

General comments:

Abstract:
This is a good summary, I will have to take your word for the referral as the original description does not figure the surangular cross-section.

Introduction:
Lines 53-55: I will have to take your word for the referral as these features are not figured for the type.

Materials and Methods:
Line 64: replace miss with lack.
RESULTS

Locality, horizon, and AGE.
Line 85:  add age to heading.

Revised Diagnosis
Very nice.  Much better than what we have been going off of.

Description:
Line 98: The skull preserves a partial antorbital fenestra, large orbit and temporal fenestrae.
Line 191: Distally, this process is isolated from the quadrate shaft; likely due to taphonomic distortion.

Discussion:
Very nice work.  I like that you discuss whether or not it is Sinovenator but are conservative.  Every paper should be written in this way!

Figures
Overall the figures are exquisite.
Consider adding a cross-sectional image of the jugal and surangular

If you have any questions feel free to contact me at mloewen@nhmu.utah.edu.


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: GESTURE: AN ONLINE HAND-DRAWING TOOL FOR GENE EXPRESSION PATTERN SEARCH
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript describes a web tool called GEsture that allows users to find gene expression patterns in time series data by hand-drawing the desired pattern. I see a clear need for such a tool to help biologists mine gene expression data, Being able to search for genes that show a contrasting expression pattern, or a time delayed pattern is also very nice. I could not find other tools that offer similar functionality through a web interface.

I had some difficulty running the tool with other data than the example files. Every time the uploading seemed to work fine, but upon clustering using K-means I got an undescriptive message saying: “sorry,please try again!”. I found out I that had to remove the header lines (which is mentioned in the manual) and take care of missing values in the data. Since the tool is meant for biologists without a bioinformatics background, the file upload functionality should be made more robust and get more helpful error messages.

Figure 4 is not very informative, why is this depicted as a network?

The English still needs quite some work, and I noticed two quoted sentences from published papers, which is rather unusual. Please find below my line by line comments and language corrections/suggestions (not exhaustive):
line 28: unclear what is meant with: “conforming to users’ expectations”
line 45: “genes expressing similarly expression” -> genes showing similar expression
line 52: “a CLARITY algorithm” -> the CLARITY algorithm
lines 56/57: unclear: “some genes that are high expression while the other genes are low expression at the  same time”
line 57: Xia designed an eLSA package -> the eLSA package
line 59: “the clustering algorithm has” -> clustering algorithms have
lines 62-64:  incomplete sentence followed by a literal quote, I would suggest to remove the quote and rewrite the sentence.
line 64/65: to my knowledge, clustering algorithms in general do not discard clusters with a small number of genes, please include a reference if the authors disagree.
line 67: unclear: “However, it cannot always cluster a category that is expected. Because a time-delayed phenomenon often appears in gene expression, K-means clustering cannot recognize it and
mistakenly divides it into many categories instead of classifying only one category.”
line 73: program searched -> program searches
line 78: user-friendly interface -> a user-friendly interface
line 93: with mouse in the drawing board -> with the mouse on the drawing board
line 98: pattern -> patterns
line 98: negative regulated genes -> negatively regulated genes
line 99: be founded -> be found
line 110: by user -> by the user
lines 161-163: unclear, should be rewritten: “This example demonstrated that GEsture was more straightforward and efficient to identify genes that were expected.”
line 169-170: rewrite: “‘SBF and MBF are sequence-specific transcription factors that activate gene expression during the G1/S transition of the cell cycle in yeast’, as suggested by Iyer et al.(2001) says.”
line 171: “the similar regulatory mechanism” -> “a similar regulatory mechanism”
line 207: information was listed -> information is listed
line 209: we have found AT5G25830, AT5G15850, AT5G56860 are -> which are
line 213: still annotated as in the -> still shown as annotated in the
line 219: “the three example data sets are provided on the Gesture website”: I could only find two?
line 222: “Programming was written in” -> “The program was written in”
lines 225-231: unclear
Legend figure 1: “List the the main operation procedures of this tool. Rectangular boxes labelled same color” -> “Lists the main operation procedures of this tool. Rectangular boxes with the same color
Figure 5: “The result gene” ->  “The resulting gene”
Figure 7: Hand-drawing curve: hand-drawn curve. Not sure that “searched out.” is the proper expression here…
Table 1: the STE12p row should be 100% instead of 1.00%
Experimental design: Nothing is mentioned in the paper about any transformation of the data: should the uploaded data be log transformed (intensities/counts/FPKMs) or not? In figure 6 the data look log transformed, figure 7 the data seem normalised (and transformed), in figure 8 the data were  untransformed and not normalised. Since log transformation is non-linear, this will affect the expected expression patterns.
Validity of the findings: Example 1 shows that the tool works, but the authors do not make clear why the 11 found genes “were expected” (line 163).

For Example 2 the authors use the yeast transcription factors TEC1p and STE12p to show that GEsture is able to find co-regulated genes, by claiming that 73% of the found genes are regulated by these two TFs. I am not sure that I use the YEASTRACT tool correctly, but I find in total 4900+ genes potentially regulated by the mentioned TFs. Assuming a total number of genes for yeast of 6600, this comes down to 74% of all genes, a percentage very close to the 73% the authors find. I would like to see more details for this example, like how many genes in total did the authors find to be regulated by TEC1p and STE12p, and for instance an enrichment test (i.e. Fisher’s exact test).
Additional comments: Web tool error messages in the web interface are not always clear/descriptive: when trying to upload a file with another extension than .csv, there is a “File Upload Error”, without specifying what the error is.

The icons on the csv files for removing and uploading do not seem to work (chrome/firefox on Mac).

For the graphs showing the expression patterns, it would be nice to have an option to show normalised curves (z-scores) in case the data were not normalised


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: GESTURE: AN ONLINE HAND-DRAWING TOOL FOR GENE EXPRESSION PATTERN SEARCH
Review round: 2
Reviewer: 2

Output:
Basic reporting: The writing is clear and easy to understand. The related studies were also sufficiently discussed and referenced.  The figures and tables are also very appropriate and support authors' arguments.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors presented a web-server named GEsture, which can be used to query the expression
patterns from given input expression file.  The users can either hand-draw
the expression patterns or choose the patterns from clustering results to get
all genes associated with those patterns. This tool is very user-friendly and functionally versatile.
I have only a few relatively minor concerns/comments and I hope the authors find them useful when revising the manuscript.

1. Yes,  the clustering is very important to identify genes with similar expression.
In this work, the authors used K-means to cluster the genes based on the expression.
For the K-means, it is always a problem for users to specify K (# of clusters) for clustering.
It would be great if the GEsture can provide a suggestion of best K for clustering if users have no prior knowledge.  Although this is a very hard problem and no perfect solution, still there are some works can be done here. For this task, maybe the authors can use some clustering metrics such as Silhouette or BIC to determine the best K for given input expression file.

2. The hand-drawn pattern searching functions are very useful.
But it seems that the expression is restricted to the range [-4,5].
What if users want to explore the patterns with much higher expression (say 8).
It would be great if the users can customize the expression range.

3. similar to the shift pattern search.
It would be great if the users are allowed to customize the shift range for searching.

4. Figure 4, can't read the text inside the node.
Please make it larger or change the color to make it more contrast to the background

5. Figure 8, The left size text is not readable, please enlarge the text

6. In table 1, how did the ratio is calculated?
It seems that there is something wrong
STE12P, 5 only accounts for 1% while TEC1p 3 accounts for 60%.  shouldn't 1.00 here be 100%?


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: INCIDENCE OF ILL-HEALTH RELATED JOB LOSS AND RELATED SOCIAL AND OCCUPATIONAL FACTORS. THE “UNFIT FOR THE JOB” STUDY: A ONE-YEAR FOLLOW-UP STUDY OF 51,132 WORKERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: There are problems with syntax and terminology eg abstract, objective - medically unfit to (do) their jobs; abstract, methods - unfit workers rather than unfit patients; abstract, results - numbers as well as percentages; line 46 ...it is (an) important to ... ; line 47 - Most data about these (pathologies) - suggest - occupational diseases instead of pathologies; line 50 - (epidemiological) assessment by a specialist - I think you mean the gap between assessment by a specialist removed from the workplace and assessment by an occupational physician linked to the workplace; line 132 number unfit rather than number of unfitness; the term mental ill-health is preferable to psychopathology throughout the manuscript.

It is usual to start the discussion with the most important findings and then discuss them in a wider context. For example, there is no reference to a) the study by Whitaker and Aw in Occup Med 1995; 45: 75-80 of 9139 pre-placement assessments in the NHS in which 0.7% were found to be unfit for the job and 1.3% fit for restricted duties. Similarly most of those found to be unfit/restricted were because of obesity, MSk problems and mental ill health.  b) the study by Alavinia et al in Scand J Work Environ Health 2009; 35: 325-33 of factors in long-term sickness absence in which the highest attributable fraction was those >age 50.
Experimental design: Not collecting data on 'fitness for modified work or occupational reclassification' is a weakness of the study. This figure could be much higher than those found to be unfit for their job. It is not clear to me whether the 0.778% figure relates to unfitness for job or unfitness to work for that employer or unfitness to work at all. I suggest this is made clearer.

Under Methods please define how workers were defined as blue collar.

Also line 215 refers to the global 1-year incidence of unfitness as 7.78%. Yet the proportion found to be unfit to do their job was 0.778%. I do not understand the difference.

In lines 150, 151 and 167 there are references to the proportions ill health thought to be work related by occupational physicians. How was work-related defined? Numbers should be given as well as percentages. For example, attribution of mental illness to work is thought to involve the consideration of 18 factors (11 workplace stressors and 7 personal factors of vulnerability) - see Wong et al. Occup Med 2015; 65: 391-7. This paper should be referenced to illustrate the complexity of attribution.
Validity of the findings: Under statistical analysis line 131 please explain ORc and ORa and how the adjustments were made.
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: INCIDENCE OF ILL-HEALTH RELATED JOB LOSS AND RELATED SOCIAL AND OCCUPATIONAL FACTORS. THE “UNFIT FOR THE JOB” STUDY: A ONE-YEAR FOLLOW-UP STUDY OF 51,132 WORKERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: •	This article was concise with a well-articulated rationale. The introduction provides a nice background of context. The literature is well-referenced and relevant.
•	There are some potential English language concerns that limit clarity, e.g., “the outcome is job loss, which is an objective data…”(line 209); “this must not be considered as a limitation” (line 204); ‘the difficulties are:…’ (line 52; difficulties with what?); ‘ it is an important to set the priority actions concerning health and safety at work’ (line 46); ‘Seventeen Ops followed up employees of this employment area’ (line 108); ‘all occupation groups… were concerned’(line 171). I was also confused by the term ‘work related accountability.’ A thorough review for English language is recommended.
•	The tables are extremely difficult to interpret – the variable names run together and the variable headers do not align with the information (E.g., mean(sd)) above age distributions. It is unclear whether this was a technical issue with the upload; but, I was unable to evaluate the validity of the findings because of this issue.
Experimental design: •	Research design is well-defined and relevant – this manuscript addresses an important gap by examining incidence by time within a medical system vs. relying on workers’ compensation records.
•	The main concern is the potential of selection bias with this region of the country in France. Because of the Table issue above, the occupation and activity sector distribution of your study is hard to assess. Is the occupation/activity sector of your sample representative of France as a whole? Does the generalizability of your findings need to be qualified by your sample? (e.g., few cases in manufacturing, construction, and information and communication). Why were farming and public service employees excluded?
•	The abstract states that the design allowed ‘two data frames to be merged.’ But the Methods describe this as one case control study (line 107). Clarification the statement made in the abstract would be helpful.
•	I am concerned about the recommendation that no ethics approval is required because a similar, previous study did not require ethics approval. I recommend sending this data analysis to the institutional review board to provide a letter or assurance that review is not needed.

•	“The reader should be aware that this study design does not identify the work related diseases, neither can it provide a job loads attributable risk, but rather assesses the impact of diseases, work-related or not, on the capacity to maintain the current job.”
o	The authors make a very good point about the focus of this manuscript on job loss vs. overall work-related disease vs. work-related accountability (As primary). The scope is well-stated.
Validity of the findings: •	Please define “ORa” in the manuscript.
•	See point above related to the Tables – until these numbers can be interpreted, a statistical review is difficult.
•	The statement made on Line 252 about psychopathology being invisible and being ‘very difficult to determine occupational accountability’ – is probably correct but should be labelled as speculative.
•	The statement made on Line 247 about workplace rarely adapted for age is also probably correct.. but should also be labelled as speculative.
•	The statement made on Line 265 ‘ Traditionally, a high proportion of women work in activity sectors with high physical or psychological loads, such as health care, accommodation for seniors or social care’ requires a reference.
•	Overall, the conclusions are well-stated, linking to the original research question.
Additional comments: This large-scale study provides a significant contribution to the literature in that it provides information about health-related job loss, which has not yet been explored extensively previously.


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: INCIDENCE OF ILL-HEALTH RELATED JOB LOSS AND RELATED SOCIAL AND OCCUPATIONAL FACTORS. THE “UNFIT FOR THE JOB” STUDY: A ONE-YEAR FOLLOW-UP STUDY OF 51,132 WORKERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is better than the previous draft but there are still several problems with the English, grammer, syntax, typing and meaning. As there are so many of them I will just refer to the line numbers - Abstact: methods - South of France  ... analysed ... Results: occupation ... sector ... lines 61, 65, 70, 110, 139 - OP's ...the work ... 182, 190, 192 - compared with who?, 195-196, 198, 200, 217 & 221 - why is it ok to determine work-relatedness for MSk conditions and mental ill health, 231 - how can comparisons be made with other countries when we have different ways of collecting work-ralted ill health, 295, 297 - a link to how attribution was made by the French OPs needs to be made here, 299, 309, 311, 323, 334-336, 338 what is a common thesaurus, 338-342 what is meant by increasing quality and processing speed?

It is well structured with two good tables but poorly written. The main findings are well made in that older workers, blue collar workers and women are more likely to loose their jobs due to musculoskeletal disorders or mental ill health.Comparisons are made with another French study and with findings from the THOR surveillance scheme in the UK which is good.

There is no need to report unfitness for the job to two decimal places. 7.8% will do!

As the authors are suggesting more similar research with a larger population size, I should like to know how vague diagnoses like musculoskeletal disorders and mental ill-health will allow tageted preventative interventions. Surely diagnoses need to be more specific than this such as epicondylitis, tenosynovitis, mechanical back pain, anxiety, depression, PTSD, etc.
Experimental design: This is good. Multivariate analysis is appropriate.

Could the authors add how many cases were seen per day by each OP. I estimated 13. If this is the case it does not give much time for attribution to be determined, particularly when this can be complex such as for mental ill health. For example, do the OPs visit the workplace? How would a system specialist be able to evaluate the workplace factors? The large numbers of cases seen per day should be stated as a limitation with regards to attribution.
Validity of the findings: This research adds to the literature. I should like to know why it has taken 3 years to submit this work for publication.
Additional comments: The authors still need to do more proof reading. I was distracted from the main messages by the way the manuscript is written.


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

Input:
Title: INCIDENCE OF ILL-HEALTH RELATED JOB LOSS AND RELATED SOCIAL AND OCCUPATIONAL FACTORS. THE “UNFIT FOR THE JOB” STUDY: A ONE-YEAR FOLLOW-UP STUDY OF 51,132 WORKERS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The language flows better, but there is still some awkward language throughout. Also, please be sure to edit for detailed grammatical and punctuation issues. I see two periods after sentences, sentences beginning with lower case letters, etc.

Table 1 has improved but still needs a row label for the numbers included in the header (presumably these are overall sample?) Note that this is somewhat odd stylistically and these numbers in the header would be much better as a row at the bottom of the table --
 since technically we still don't know that N% represents each column. Also, the incidence % needs to be clarified so that the table can stand on it's own (Incidence of what?). Table notes would be helpful.

Similarly, Table 2 includes bolding -- the significance of which is unclear without specification. The OR definitions/ adjustments are helpful on the website. It is unclear whether these are actually table notes...

"primary prevention of workplace tasks is probably rare"... does not make sense

Still no references for statement in the original Line 265 (a high proportion of women work in activity sectors with high physical or psychological loads)
Experimental design: A major concern is the conduct of research and submission of the manuscript involving personal health information without prior Institutional Review Board approval. It is unfortunate that the authors did not wait to receive this approval (or an official determination that the project is exempt from review) prior to the conduct of the study.
Validity of the findings: Overall, the authors were largely responsive but there are a few instances in which they provide rebuttal responses that are not incorporated into the manuscript.

It is recommended that the authors include the following discussion in the manuscript:
-Discussion about the limits of generalization (geographic and specific sectors not represented)
-Implications for future research (related to the extrapolation of socioprofessional categories to France in general)
Additional comments: Please note that this review was provided in concert with Rebecca Wolf, JD, MPH, OTR/L.


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: INCIDENCE OF ILL-HEALTH RELATED JOB LOSS AND RELATED SOCIAL AND OCCUPATIONAL FACTORS. THE “UNFIT FOR THE JOB” STUDY: A ONE-YEAR FOLLOW-UP STUDY OF 51,132 WORKERS
Review round: 3
Reviewer: 1

Output:
Basic reporting: The paper is now much better written. In the section - What is new? the authors only refer to the use of mutivariate analysis. What are the new findings from this research?

Abstract - 7.8%, not 7.78%
L 63 psychiatrists
192-193 associated with rather than 'concerned by'
196 There were 153 declarations of unfitness caused by mental ill health - not ... were delivered
220 what is meant by - number of cases is underevaluated - do you mean in other surveillance schemes such as THOR?
245 subacromial impingement is not a good example here as sytematic reviews have shown this to be associated with heavy manual handling, lifting above shoulder height and throwing. Suggest mental ill health instead.
314 all workers are at risk - rather than - are concerned
Experimental design: no comment
Validity of the findings: It is still not clear to me how causality (work relatedness) for the reason for job loss was determined. I presume by the OP in the short time with the worker. How would having a larger sample size help? The large difference between causality as determined by the OP and by the insurance system is not addressed in the discussion. Why?
Additional comments: I am happy for all my comments to be shared with the authors.


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: INCIDENCE OF ILL-HEALTH RELATED JOB LOSS AND RELATED SOCIAL AND OCCUPATIONAL FACTORS. THE “UNFIT FOR THE JOB” STUDY: A ONE-YEAR FOLLOW-UP STUDY OF 51,132 WORKERS
Review round: 3
Reviewer: 2

Output:
Basic reporting: The authors have been largely responsive and addressed major concerns.
Experimental design: The authors have been largely responsive and addressed major concerns.
In the text, please state the name of the IRB that provided approval.
Validity of the findings: The authors have been largely responsive and addressed major concerns.
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: FLOATING NURSERIES? SCYPHOZOAN JELLYFISH, THEIR FOOD AND THEIR RICH SYMBIOTIC FAUNA IN A TROPICAL ESTUARY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Structure problems:
_ The Zoological nomenclature was not used appropriated! For example species usually is written in italic words! In the first moment that a species is informed, it is important to inform the investigator that described the species’ diagnoses;
_ Legends is not self-explanatory;
_ There is disorder in the manuscript topics, for example, line 114 to 116 is Result don’t Materials and Methods; line 211 is Discussion doesn’t Result; and all Discussion the authors mentioned again tables and figures that is usual in the topic Results!
_ Figures 3 and 4: it is very difficult to understand some pattern!
_ Table 3: There are several references, so it is usual to use in the Discussion don’t in the Results.
Experimental design: "Original primary research within Aims and Scope of the journal" - Yes;

Methods were not described with sufficient information. For example:
_ Materials and Methods
Lines 125 until 150 - need some references. The authors created all methodology!
Validity of the findings: Lines 131 until 136 – To inform that “were sent to taxonomic experts for identification” is not enough! The authors need to inform each expert and the bibliography used. If the authors were auxiliated by experts, why are taxa no identity such as the classification only “crustacean” or only “fish”. At some point is not possible to identify in others is possible to identify Brachyura larvae. In studies with “the gut contents” is normal to show figures of each prey item such as Gonçalves et al. (2016 – Symbiosis, vol. 69 (3): 193-198). The prey identifies here was not photographed, why?
Additional comments: Dear authors, I regret to inform you that I rejected your manuscript. I feel that the manuscript has merit, however, I identified several problems. However, I would like to offer and encourage the authors to see my comments and questions to a resubmission.


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: FLOATING NURSERIES? SCYPHOZOAN JELLYFISH, THEIR FOOD AND THEIR RICH SYMBIOTIC FAUNA IN A TROPICAL ESTUARY
Review round: 1
Reviewer: 2

Output:
Basic reporting: All my comments are summarized in one section below.
Experimental design: see below.
Validity of the findings: see below.
Additional comments: This manuscript is fairly interesting and well written, but I have major two issues with the write-up.

First, the diet study analyses counts of gut contents, including *numerical abundance* of diatoms and phytoplankton. This does not seem justifiable, and analyzing "prey items" by quantifying counts of phytoplankton and fish equally is not ecologically nor statistically valid, so the ANOVA results are suspect.

Second, the paper emphasizes "symbiosis" including in the title, subtitle, yet the data for the associations are a relatively minor part of the manuscript. For most biologists, the phrase "Scyphozoan symbionts" would suggest the endosymbiosis of Cassiopea or Linuche. Although its use is technically correct, I would prefer that the term "Symbiosis" be largely replaced by "association" in the title and body of manuscript.
On that subject, I would like to see the results for new associations *minus* H. zelotes. Using (Fish) fish (Fish + Other) does not allow examination of the patterns for (Other). In the plot of Body Size vs Symbiont community (Figure 4) the pattern is literally obscured by the H. zelotes points. These should be moved to a second panel, and the points made partially transparent so the overlap can be seen. In the table, the new results are buried with literature review. I would like to see those in a separate subsection.

In the plots for Figures 2 and 3, the selection of point shapes and colors is essentially random. There should be some reason to the assignment of these properties, and that assignment should be consistent between the two figures. For example, Month could be coded by shape (using the same shape between Season 1 and 2) and the season could be coded by color (all the same within each season). Or Month could be by color and season by shape. This would allow the reader to look for patterns and correspondences in what currently looks like a random scattergram.

Other minor comments:
13: what makes this a "basal trophic pathway"? Most medusae are high level predators, and not operating near the "base" of the food chain.

23: State of their symbionts: To me this means algal endosymbiosis, since it has not yet been defined and qualified. Please change to "associated" fauna.

26: algae are not a significant contributor to nutrition, so abundance is meaningless. How were diatom chains even enumerated?

29: Associated *with*  [not "to"] -- but yes, associated, is the preferred phrase here.

30: Thereby -> Therefore

34: occurrence [fix spelling]

37: consistent abundance of algae: not to be emphasized.

94: cannonball [spelling]

114: permit number instead of permission number?

115: Medusoid occurrence numbers should be in results, not methods

144: Abundance of each taxon: again, not meaningful

177: Two species of scyphozoan jellyfish [more than two jellyfish were found]

199: between month differences [not months]

265: remove "on average" - makes the phrasing confusing and not needed.

275: Were those years really "El Niño/La Niña?" — which one was it, since they alternate.


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: FLOATING NURSERIES? SCYPHOZOAN JELLYFISH, THEIR FOOD AND THEIR RICH SYMBIOTIC FAUNA IN A TROPICAL ESTUARY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is written clearly and generally with unambiguous text (a few minor changes suggested below for clarity). The tables and figures are appropriate and the raw data is supplied in a suitable format.
Experimental design: I found this to be interesting research and commend the authors on their data collection, I know first-hand how tricky collecting this information is.
Validity of the findings: This work fills an area of research where there is a paucity of information on and is often overlooked. The conclusions are clear and intelligible, as well as supporting the authors’ research question and are supported by the results.
Additional comments: Review of: Floating nurseries? Scyphozoan jellyfish, their food and their rich symbiotic fauna in a tropical estuary
Riascos et al.
I found this to be interesting research and commend the authors on their data collection, I know first-hand how tricky collecting this information is. The manuscript is written clearly and generally with unambiguous text (a few minor changes suggested below for clarity). The tables and figures are appropriate and the raw data is supplied in a suitable format.
This work fills an area of research where there is a paucity of information on and is often overlooked. The conclusions are clear and intelligible, as well as supporting the authors’ research question and are supported by the results.

Minor suggestions:
Line 104: Sampling: A map with the study area and its location in the region would be a useful addition.
Line 107: Change “one of the rainiest places in the western hemisphere” to “an area with one of the highest levels of precipitation in the western hemisphere”
Line 110: Is the tidal range always 4.1m? If this is an average please add ‘mean’ to the text.
Line 181: Change “body” to “bell diameter” for clarity as this is what you have measured, body is too ambiguous.
Line 210: change “below the bell´s host” to “below the host´s bell”.


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: FLOATING NURSERIES? SCYPHOZOAN JELLYFISH, THEIR FOOD AND THEIR RICH SYMBIOTIC FAUNA IN A TROPICAL ESTUARY
Review round: 2
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: Dear Authors,
I my opinion, now the manuscript has merit. I just want to suggest two corrections:
1.	Please, pattern species in italic words (see line 56);
2.	I suggest new nomenclatures in the table 1, because when the authors use “Arthropoda: Crustacea” include all others crustaceans, so my suggestions are:
“Arthropoda: Copepoda” to “Crustacea: Copepoda adult”
“Arthropoda: Crustacea” to “Crustacea: Unidentified”
“Arthropoda: Cirripedia larvae” to “Crustacea: Cirripedia larvae”
“Arthropoda: Brachiuran larvae” to "Crustacea: Brachyura larvae”
“Arthropoda: Amphipoda” to “Crustacea: Amphipoda adult”
 “Arthropoda: Decapoda” to “Crustacea: Anomura (Emerita sp) adult”


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: ALLOMETRIC SHELL GROWTH IN INFAUNAL BURROWING BIVALVES: EXAMPLES OF THE ARCHIHETERODONTS CLAIBORNICARDIA PALEOPATAGONICA (IHERING, 1903) AND CRASSATELLA KOKENI IHERING, 1899
Review round: 1
Reviewer: 1

Output:
Basic reporting: The ms is fairly well written, supported by literature references, well structured and with good illustrations.
Minor parts could be deleted/shortened.
The usage of "infaunal burrowing" is redundant, as explained in the notes.
Experimental design: Allometric growth is well known among bivalves, as discussed in the ms. However, the work offer a valuable contribution to shape analysis based on "longitudinal data". I don't think "longitudinal" is a good term, but the method is interesting and only scantly used in palaeontology.
Methods, from data acquisition to processing should be more clearly reported and/or explained, in particular:
1) Concerning the acquisition of growth-related shell outlines from a single valve, the only explanation is "digitized in different angles". It is very difficult to orientate valves in order to capture different growth stages (growth line). Are authors sure that outline acquisition was not biased by wrong orientation? Which method did they follow for handling and properly orienting valves?
2) Authors should give more information about the software used to digitize outlines. Further, more importantly, they should specify how many points were used, and how/where the starting point was selected. It is very difficult to find a starting point along a bivalve outline, particularly when the bivalve shape lacks any sharp/pointed traits which can offer a reliable starting point.
More unclear points about methods are remarked in the text.
Validity of the findings: Findings and implications are interesting, though not particularly new or useful, since the allometric growth is well known for bivalves.
Probably the most innovative contribution is the method ("longitudinal data") as reported above. For this reason, shape analysis methodology should be more carefully explained and illustrated.
Palaeoecological implications of allometry, though supported by data, are not a novelty.
Taxonomic implications are interesting, and could deserve to be more exhaustively discussed.
Additional comments: No additional comments