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

Input:
Title: THE SPLEEN BACTERIOME OF WILD RODENTS AND SHREWS FROM MARIGAT, BARINGO COUNTY, KENYA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Basic reporting in the article has been improved. However, there are still two areas that need more clarification:

1. How Shannon Diversity was calculated. Was this done by first aggregating relative read abundance (or even prevalence?) to species level (i.e gamma diversity), and then performing the calculation? Or by calculating individual-level SD and taking the mean/median?

2. The new statements attempting to clarify the meaning of the SD do the opposite (more below). The authors should either remove these or reformulate.

Finally, again, there are no attempts to make *statistical* hypotheses, even though the authors attempt to compare SD among species without using any estimates of error.
Experimental design: This is not relevant, as the authors have stated that they do not have a research question. However, given that they attempt to compare bacterial diversity among small mammal species, there clearly is an underlying interest in making statistical comparisons.
Methods appear reproducible.
Validity of the findings: Underlying data is provided, figures (mostly) accurately depict the data and findings (see comments attached).
Conclusions are somewhat overstated in that the authors seem to imply that by identifying small mammals with high spleen microbial diversity, they are also identifying species/individuals with high health risks to humans. This is not necessarily the case.
Additional comments: I appreciate the efforts that the authors have made to improve the text. There are several sections where additional text has provided more clarity, and the figures are much more readable and accessible.

Below are line-by-line comments:
All line number references are based on the line numbers in the tracked-changes document.

L19-20 Does higher bacterial diversity correlate with increased human health hazards? This seems like a bit of a stretch for this paper, as it is very difficult to make any statements about the pathogenicity of detected bacterial groups, nor their likelihood of transmission to humans.

L23-28 This section could be shortened substantially. Details about sequencing can be simply listed in the main text.

L29-30 If you intend to keep it as a single Shannon value for each species (i.e gamma diversity for each species, as opposed to a mean +/- SE on an individual level), then you could clarify that this is a species-level Shannon index, rather than an individual-level Shannon measure.

L30 Avoid using ‘individual animal species’. There are both individuals and different species, so statements like this are confusing.

L53-55 Clarify that this is across the whole species (gamma diversity), rather than an average across individuals, if this is the case. I’m still not sure what you calculated, because there are individual-level estimates shown in Figure 5, but the rebuttal comments seem to indicate that calculations were performed only at the species level. If this is the case, then there needs to be a statement about the fact that Shannon diversity is biased low at small sample sizes and if there was a correction for that (e.g. rarefaction, using a jack-knife estimate etc.). I also have some issues with this because the sample sizes are very different depending on the species. It’s hard to say much about species-level diversity patterns when there are only two samples (e.g. Rattus), and thus, Shannon Diversity for these low-sampled species is likely underestimated.

One alternative is to calculate mean individual-level Shannon diversity using relative read abundances as an abundance metric (it looks like this was done for Figure 5). Another is to report the mean number of bacterial groups per individual (richness). The total number of bacterial groups per species could be reported, but this also has issues with small sample sizes.

As shown in Figure 5, you clearly have a response metric (Shannon Diversity at the individual level) with several replicates per group, thus giving you the ability to estimate a mean (or median) and associated variation. This would then allow you to test the null statistical hypothesis that there is no difference in mean individual-level diversity among species (e.g. using a 1-way ANOVA).

L70-78 The additional text here greatly improves the study context and rationale.

L34-37 These sentences are not necessary.

L109-120 While this is a fair argument, I am not sure it is totally relevant to this study because the species investigated are not too difficult to distinguish from one another (at least for rodents). However, it seems that in this study, the researchers did not have access to the skins/preserved specimens, so perhaps a more relevant point is that NGS methods allow for more streamlined/accurate use of tissues of an unconfirmed host species.

L122-124 “Disease risk” is a strong term, as the pathogenicity of these bacterial groups is not being tested in this study. Simply stating that bacterial diversity, and in particular, diversity/presence of certain bacterial groups was investigated is sufficient.

L231-232 It is unclear how Shannon diversity was calculated at the species level. Was this simply based on the number of OTUs detected across all individuals of a given small mammal species?

L323-325 This statement is confusing and does not explain why significance can be drawn without estimates of variation/uncertainty.

L396-398 This statement is confusing as readers most likely know what Shannon Diversity is. Additionally, if a particular species had a microbiome twice as diverse as another, this would not necessarily indicate higher infectiousness.

L404 If these papers report the new method, then the statement ‘as we went to press’ does not make sense, as the papers were published in 2009 and 2016.

L415 A citation is needed for this statement.

L416 This statement seems a bit strong. I do not think that this study can definitively make a connection to human health hazards, which are complex and depend on many things (e.g. environmental transmission mechanisms, exposure routes, immunity, pathogenicity of investigated bacterial groups), but rather that it shows a method to determine microbial diversity in these animals, many of which may have been uncharacterized previously, and identifies species that are capable of carrying certain bacterial groups of potential human health interest.
The focus on Shannon Diversity does not relate directly to the article's attempt to connect the findings with potentially pathogenic bacterial groups.

There is potential to discuss the two species investigated here that are well-known for being involved in zoonotic infections (Rattus and Mastomys).

There is also more potential for more discussion as to why the spleen is investigated, and why this is useful for monitoring (as opposed to feces, for example, which represents material that enters the environment and is likely to serve as a source of exposure).

Figure 2:
I am assuming that these bar charts are the result of aggregating all reads within species (i.e. using the mean/sum)?

Figure 5:
This figure is very helpful; however, it is inaccurate to show small sample sizes using boxplots. The text states that there are only 2 samples for Rattus, yet a boxplot is shown. Additionally, the figure legend is confusing: does ‘alpha diversity measure’ refer to Shannon Diversity or some other alpha metric?


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

Input:
Title: THE SPLEEN BACTERIOME OF WILD RODENTS AND SHREWS FROM MARIGAT, BARINGO COUNTY, KENYA
Review round: 2
Reviewer: 2

Output:
Basic reporting: o	Suggested places to review the use of “clear, unambiguous, technically correct language”: Line 19: not clear how “systemic microbiome” might be defined; consider in particular the common definitions of “microbiome” as a collection of living microorganisms together with their host, and whether DNA sequences obtained from the spleen can be expected to represent such a community.

o	Line 323: Contrary to what is written, the study by Ge et al. (2018) reported Firmicutes as bacterial phylum that predominated the samples (>70%) whereas Proteobacteria were a more minor component (~23%). Please correct and clarify how this differs from the results reported in the present study.

o	Whereas the text emphasized comparisons of bacterial taxa at the phylum level, Figures 3 and 4 emphasized OTUs identified to genus. These genus-level comparisons appear more relevant (and interesting) to the research aims the authors posed. For example, whereas there are many Proteobacteria OTUs in the data, they are (by far) predominated by Bartonella. Bartonella is a known pathogen with a reasonably well understood natural history, as the authors review in the discussion (lines 334-346). The paper could be improved by emphasizing through the basic reporting these predominant features of the data at a finer grain, and better describing the known life histories of the taxa involved to underscore relevance to the main research question; the current emphasis on phylum-level comparisons and the large number of taxa with particularly low sequence relative read abundances can obscure these predominant data features and could introduce qualitative errors.

o	Throughout: minor typos and changes in tense or plurality should be checked. It may be possible to address these through copyediting.
Experimental design: o	Commendable steps: I appreciated the use of mitochondrial DNA barcoding methods to identify small mammals and evaluate results in a phylogenetic context; this is a strength of the paper.

o	Suggested review of whether the “research question is well defined”: Line 21: It would help to specify how monitoring DNA sequences in the spleens of small mammals could conceivably serve as an indicator for human health at this point in the abstract; there are many ways that human-rodent interactions involve health considerations, but evidence relevant to public health requires the ability to identify a pathogenic strain of bacteria (not necessarily possible using 16S markers) and a plausible transmission pathway (not to be taken for granted even in the presence pathogens). Could such a monitoring program be said to provide more direct information about the potential health status or rodents, with indirect implications for human health?

o	A description of the experimental controls would be helpful, including any sequencing results obtained from extraction blanks and PCR controls. Several the putatively pathogenic bacteria listed in this paper are common laboratory contaminants in microbiome studies (see, e.g., the report by Salter et al., 2014). Proteobacteria in particular are common laboratory contaminants, and when the template is based on a low biomass sample these contaminants can appear to be a relatively abundant constituent of the data. A comparison of the sample data with controls would help rule out laboratory contamination as a concern.
Validity of the findings: o	Line 44: it would help to clarify even in the abstract how potential pathogenic bacteria were identified from the strains, and issue a reminder that taxonomic classifications may provide an indication of *possibly* pathogenic bacteria without implying that these sequences definitively represent pathogenic organisms. Bradyrhizobium, for example, includes strains that have occasionally been associated with human disease, but also includes a large number of strains that primarily serve as nitrogen-fixing bacterial symbionts in legumes (and it has been cited as a common laboratory contaminant by Salter et al., 2014).

o	Lines 41-42: Is it concerning that Proteobacteria were identified as the most abundant phylum in the sample set, at nearly 65%? In published reports of small mammal spleen microbiomes, Firmicutes have been the most relatively abundant and Proteobacteria have accounted for a smaller fraction (e.g., Ge et al., 2018).

o	Line 52: “the study confirms the role of the spleen as a microbial filter”—the study did not report on the function of the spleen as a filter, but instead used prior knowledge that the spleen has this function to investigate the bacterial 16S rRNA sequences that were present in the tissue.
Additional comments: I was not assigned to review the original manuscript and this I evaluated the manuscript in light of the most recent version.

I was quite pleased to see the combination of host DNA barcoding and bacterial profiling in this paper. I was especially excited to learn more about the bacterial profiles obtained from spleens in wild small mammals, and appreciated the speculation about how these profiles might be connected to variation in local land uses (e.g., cattle ranching, farming, etc.).


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: SPECIES DIVERSITY AND COMMUNITY STRUCTURE OF CRUSTACEAN ZOOPLANKTON IN THE HIGHLAND SMALL WATERBODIES IN NORTHWEST YUNNAN, CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is very straightforward and clearly shows the high diversity of zooplankton in a set of small waterbodies in Southwest China. Apart from this important description, comparing the magnitude of zooplankton diversity with other much larger localities (but with similar or lower diversity!), authors also explored differences among seasons and the relationships between local species compositions and environmental variables with canonical correspondence analysis. I believe this last goal deserve a little more attention. The correlation between species composition and environmental variables assume that environment is filtering the species able to occur in a certain site. Authors selected a set of limnological variables as candidates of likely predictors of species abundance, which is fine. It seems most variables indicate a gradient of productivity. It is unclear how collinearity was treated, in the first place. Apart from that, I believe that authors could also include other candidate variables related to major waterbody features, maybe authors can dig a little further and get depth, area and margin perimeter of the waterbodies (maybe others). This other set of predictors relates to waterbody morphology, which can also be an explanation of species sorting among sites. Moreover, the chance of dispersal among sites can also explain species abundance differences, as described in metacommunity framework (see a review in Heino et al. 2015, Freshwater Biology). Then, dispersal routes among waterbodies can be represented by spatial variables generated using Principal Coordinate of Neighbour Matrices (PCNM) to generate spatial predictors. Therefore, you can use partial redundancy analyses (pRDA) instead of CCA to explore relationship between species abundance and predictors, using three predictor matrices (limnological, morphological and spatial variables). This analysis will explore the relative role of likely different mechanisms explaining species abundance variation. Also, to avoid overfitting and collinearity, you may use a forward selection in variables of matrices before pRDA. Given the seasonality observed in sampling sites, this analysis could be done for each season separately, which could be used to explore of relative roles of different mechanisms are seasonal. Finally, I would suggest you to avoid interpretations on causality, but focus on interpretations of which mechanisms correlates indicates. Apart from this general comment, I must congratulate authors for text fluency and clarity, and also for the amazing report. Considering this and the fact that I am not also a native speaker, I preferred not to indicate comments of the text to preserve author’s writing style.
Experimental design: Comments in topic 1.
Validity of the findings: Comments in topic 1.
Additional comments: Comments in topic 1.


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: SPECIES DIVERSITY AND COMMUNITY STRUCTURE OF CRUSTACEAN ZOOPLANKTON IN THE HIGHLAND SMALL WATERBODIES IN NORTHWEST YUNNAN, CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language is overall well-written, but the text would benefit with many (lacking) details provided in Introduction, Methods and Results as I exemplify below. Authors have a great amount of data that can be better explored and displayed in the text. Tables and figures might also be changed in order to better display the obtained results. I believe the field sampling and lab routine is correctly performed, but in the present form the results are under-evaluated. Many analyses on basic community ecology might be performed to better display the results and reach the goals of the study. As a consequence of such changes the Discussion will benefit.

In the Introduction, the text would benefit if small wetlands are contextualized in an ecological perspective, displaying their importance for aquatic organisms, their temporary nature (if this is the case in this study), isolation from other aquatic systems, lack of fish, threats and conservation value. In the current form the text shows explicitly the context of wetlands in China. Especially for microcrustaceans small wetlands are valuable because they usually lack fish and display high habitat heterogeneity mediated by aquatic macrophytes. The text would reach more general ecologists if such context is present in the text. In addition, the text states for spatiotemporal variations in crustaceans, but note that no spatial variables are included in the text (such as coordinates) (see lines 31, 70, 136). I suggest including spatial variables or removing spatial variables from the text. Finally, based on previous knowledge about wetlands and other aquatic systems in the region, can authors provide any hypothesis that was tested?
Experimental design: Lines 73 – 81 – there is some division of the landscape in west and east sides plus upstream and downstream subgroups, but note that this separation are not important for data analyses, results or discussion. Consider removing them.

In figure 1, consider showing the study site also in the context of China. I believe most readers are not aware of Yunnan location.

Please provide more details on the aquatic systems: do they have fish? How about aquatic macrophytes? Are they permanent or temporary? (I suppose some are temporary). What affects their hydroregime? (rains, hydroconnectivity to other systems, watertable changes). How often they connect to each other? What is their average depth or range? All these information may help understanding the patterns of crustacean communities. Note that this study observed high species richness when compared to others. Maybe the lack of fish predation may partially explain this pattern? See the paper from Scheffer et al. (2006) in Oikos. “Small habitat size and isolation can promote species richness: second‐order effects on biodiversity in shallow lakes and ponds.”
Line 93 – How 20L of water were collected? By buckets? In open water or macrophytes stands?

Statistical analysis lacks many tests displayed later in the results and may benefit also from commonly used methods in community ecology. Briefly, please indicate that Mann-whitney tests were used to compare species richness and abundance. Even better, consider using rarefaction curves or rarefied species richness to compare species richness between rainy and dry seasons. Community composition may be compared with PerManova and a non-metric multidimensional scaling will nicely display community variation. SIMPLER or Indval may be used to find species that are typical of rainy or dry seasons. Note that in the current form many results are descriptive.

Consider displaying exact p values instead of < 0.05 or > 0.05 (see lines 130 and 135, for example)
Validity of the findings: Please write the full genus name of each species when first mentioning them.

Consider using the above mentioned methods to compare community metrics: rarefaction curves, NMDS, PerManova, SIMPLER, IndVal.

In tables 1 and 2, what is meant by % of area? Is that % of lakes? Please clarify. In addition, consider separating species by cladocerans and copepods.

Figure 2A – The axis is a bit weird as it varies from 5 to 1 to 5. Please double check it.

Before CCA, can authors provide a brief description of limnological variables? Raw data is provided as supplemental material, but I believe the text will benefit with a table showing maximum, minimum and mean values for each season. For CCA, were limnological variables previously correlated between them to avoid covariation?

Discussion

The structure of Discussion might be changed if more analyses are provided in the manuscript. I suggest that each community parameter (species richness, abundance, composition) can be discussed taking into account the seasons (rainy and dry). The text might also benefit from some implication of the findings, provided in the conclusions. I provide below comments on specific topics.

Lines 165-167 – Use Permanova to state that communities differ. I believe the use of % of occurrence is not the most appropriate method.

Lines 180-182 – consider discussing the role of fish predation. See the paper from Scheffer et al. (2006) in Oikos mentioned above. Small habitat size and isolation can promote species richness: second‐order effects on biodiversity in shallow lakes and ponds.

Line 186 – I am not sure that in your study area nitrogen increased algae biomass, which in turn supported crustaceans. If that happened, why algae biomass did not differ between rainy and dry seasons? Please show chlorophyll a content results.

Line 203 – Dissolved oxygen values are very high. Please double check it.

With more analyses, specific to each community parameter, the Discussion can be rephrased. I suggest contrasting rainy and dry seasons whenever possible.
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: SPECIES DIVERSITY AND COMMUNITY STRUCTURE OF CRUSTACEAN ZOOPLANKTON IN THE HIGHLAND SMALL WATERBODIES IN NORTHWEST YUNNAN, CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: I appreciate the effort made in the current version of the ms as most of the previous suggestions were taken into account. The text is now easier to read and more straightforward in my view. However, I would suggest a few items to improve the final version:
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Species diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan, China
by Chen et al.

I appreciate the effort made in the current version of the ms as most of the previous suggestions were taken into account. The text is now easier to read and more straightforward in my view.

I would suggest a few items to improve the final version:

1) Is it possible to infer what caused the differences in crustaceans between the dry and rainy seasons? Maybe the ponds are more variable in terms of limnological variables in the dry season as they receive less water, allowing more species to colonize the water column?

2) Some results on RDA are displayed in the Discussion for the first time, which is not usual. See line 235 stating that "We identified the limnological variables could explain the most variation of crustacean zooplankton community in both the rainy (NO3N, DSi, Cond, DO) and dry (NO and WT) seasons. Consider displaying the information on RDA in the Results section.

3) Finally, I see many issues in English language, especially in the Discussion section. I suggest reviewing all the text. Some examples follow:

lines 80-83 - goal 3 - Something is missing in this sentence.
lines 114 - 115 - Something is missing in this sentence.
line 152 - to reduce the weight of the ABUNDANT species....
line 211 - complicated habitats? Do you mean heterogeneous habitat?


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: EXTENDING DENSITY SURFACE MODELS TO INCLUDE MULTIPLE AND DOUBLE-OBSERVER SURVEY DATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall the writing was of high quality (see Specific Comments for a few grammar errors and typos I caught), the introduction and literature cited were well referenced, and the figures were great.  I was able to access the data and code via David Miller's github site.  I suggest this material be archived to a publicly available repository after manuscript acceptance.
Experimental design: I found that the methods, data, and results to be reliable.
Validity of the findings: The statistical methods developed are sound and the text identifies how the research fills into existing knowledge gaps.    Code and data provide a useful template from which readers can replicate the author's results and exemplify how they can apply these methods to their own research.
Additional comments: Miller and colleagues describe a framework for modeling animal count data from multiple types of surveys, including strip transects, point transects, and various distance sampling setups.  Specifically, they describe how a common spatial model can be assumed for animal density, and how this can be integrated with different types of observation processes.  The framework uses a two-stage framework, whereby inference is first made about detection probability, and those results are incorporated as offsets into spatial models.  Importantly, uncertainty about detection probability is propagated into abundance estimates via a variance propagation method.  They show how this framework can be used by applying it to fin whale and fulmar data sets.

I thought the manuscript was well written and represented competent research.  In addition, the software extensions to the \texttt{dsm} R package should allow other researchers to apply these types of analyses to their own data sets.  I view the latter as the manuscript's primary strength.  I only have a few very minor comments, mostly on grammar, below.  However, the authors might want to reflect on whether the fulmar surfaces should be added together instead of averaged.

Note that I am going to attach a properly formatted review; however here is some raw .tex giving specific comments

\item Line 55, for a very recent example of combining various detection methods via integrated likelihood, see Conn et al. 2021 (https://doi.org/10.1371/journal.pone.0251130).  Just FYI, I'm not suggesting the authors need to cite this as it uses very similar ideas to the Sigourney paper.

\item Lines 58-62.  Various grammar fixes needed here

\item Line 81.  Is is worth saying that for line transects it is usually perpendicular distance from the transect line rather than distance when the sampler detects the animal?

\item Lines 150-151.  This looks like a subsection heading with a formatting issue?

\item Lines 159-160. Worth talking about this in discussion... e.g. future extensions to software that can partially accommodate detection heterogeneity via point independence

\item Lines 202-206.  It would be slightly clearer if things were given subscripts here, maybe with ``For each $b \in \{1,2,\cdots,B \}$:"  (not a big deal though)

\item Lines 216-217.  The bird example is an interesting one.  In this case, wouldn't you add the two (flying and non-flying) rather than take a mean?

\item Lines 237-246.  This seems to be the first time availability is mentioned in this paper.  Is there capacity in \texttt{dsm} to put in availability and it's associated variance?  If so, is it a new or existing feature?  It seems like it might be a useful topic to discuss earlier in the paper (e.g. combining platforms with and without availability issues)

\item Line 272.  Were there ``unknown species" recorded?

\item Lines 274-275. Grammar

\item Line 277.  A bit of a fourth-decimal-place question, but were $x$ and $y$ lat-long or in projected space?

\item Line 286.  Wow! I guess this gives the GAMs flexibility to capture extremely fine scale patterns if they exist, but it's quite a bit larger than default \texttt{mgcv} values.  Just curious if this is something the authors often do in DSMs?

\item Discussion.  Currently there's a paragraph about the fin whale example here but nothing about the fulmar example. Should lessons from the fulmar example be covered here to balance things out?


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: EXTENDING DENSITY SURFACE MODELS TO INCLUDE MULTIPLE AND DOUBLE-OBSERVER SURVEY DATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written and addresses a potentially very useful extension to current approaches to the estimation of spatial variation in abundance using distance sampling data. I have a few general comments listed below, but these are mostly minor.
The main area for improvement in my opinion, is to provide a bit more general framing of the new methodology in the Introduction and Discussion, to really drive home the usefulness of the approach. I think this is needed to provide a bit of a “hook” to sell the approach to users, and to perhaps to explain how the methodology fits into more general thinking about modelling spatial variation in abundance. Perhaps also framing the approach terms of a more general trend in ecological statistics to use multiple data types in a single model to achieve more than would be possible with each data type in isolation could be the way to approach this. To my mind, there are parallels here with methods such as Integrated Population Models, or with various kinds of Bayesian models that seamlessly integrate different kinds of data and sampling processes into a common framework to furnish strong ecological insights and maximise the efficiency with which all of the available data are used. I realise the approach in this manuscript it not the same as these methods (which are often Bayesian), but I strongly feel that they are scratching the same itch – combining disparate data that have something to say about an ecological question.
Experimental design: I have no criticism of the analytical approaches that are employed in the manuscript. The methodology is clearly presented and likely to be easily applicable to other comparable data sets. The fact that it has already been integrated into the dsm R package will make the approach widely known and easily accessible. Provision of code and data for the examples on the author’s github site will also facilitate adoption of the methods.
Validity of the findings: I have no criticism to make as to the validity of the findings. The work is technically sound and all underlying code and data have both been made available for scrutiny.
Additional comments: 1.	The examples in the paper are largely framed around marine surveys from ships and planes. I wonder if a more general explanation would help, including stressing how these methods could apply to a multitude of different species and ecosystems. I would well envisage these approaches being applied to estimation of spatial abundance models for animals and plants in other environments.
2.	I realise it is widely used in distance sampling literature, but I find the term “platform” a bit confusing. I always think of the “platform” as being the ship, aircraft etc on which the observers travel. This becomes confusing when for example there are multiple data types being collected from the same ship (as is the case for the fulmar example in the text, in which the multiple simultaneous survey types are referred to as “platforms”). I would prefer “survey type” or similar be used to refer to the different data types (CDS, MRDS, plot sampling) while the vehicles can be referred to as “platforms”.
3.	Line 61. “leading *to* a number of detection models”.
4.	Lines 57 – 72. These are certainly a good examples of situations where this methodology could be readily applied. Perhaps mention that this is a non-exhaustive list of possibilities?
5.	Lines 373-376. References to using an alternative approach here with mgcv and jagam will be a bit opaque to non-specialists. Can I suggest an explanation in more general terms of what is intended here would be worthwhile? I love the idea of making this process automatic (or nearly so).
6.	Figure 1 could do with a scale bar, and possibly an inset map to illustrate the location – I presume this is somewhere on the Atlantic coast of North America, but this isn’t clear from the figure.
7.	Table 1. It’s pretty obvious from these results which model fits best, however the caption says “fit diagnostics”, without actually providing any measure of fit for each model – it is left to the reader to decide which model fits best. Would some Chi-squared statistics in another row of the table make this clearer to the reader at a glance?
8.	Figure 3 – what are the units of density? Birds per square kilometer, or something else? Same applies to Figure 4 – no units provided.
9.	Figure S1 – the caption doesn’t say what the dashed lines are. Presumably these are the transects? Did data from the transects outside the study area also contribute to estimation of the detection processes? Also, the grey shadings used for the bathymetry contours are very difficult to distinguish. Would a different colour scheme, or means of mapping the bathymetry such as a coloured raster plot work better?
10.	Figure S3 – state units of density, as mentioned above.


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

Input:
Title: EXTENDING DENSITY SURFACE MODELS TO INCLUDE MULTIPLE AND DOUBLE-OBSERVER SURVEY DATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors have done a great job responding to my (minor) comments on the previous draft.


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: EXTENDING DENSITY SURFACE MODELS TO INCLUDE MULTIPLE AND DOUBLE-OBSERVER SURVEY DATA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been greatly improved by the revision. Thank you for so thoroughly addressing all of the comments raised by both reviewers. The responses to all of the comments are thoughtful and well integrated into the revised manuscript.
Experimental design: No further comments
Validity of the findings: No further comments
Additional comments: One very minor error is that there are duplicate references to Miller et al. 2019 in the reference list.


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: LEVEL OF ANXIETY AMONG HEALTHCARE PROVIDERS DURING COVID-19 PANDEMIC IN SAUDI ARABIA: CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Manuscript with a relevant theme in the current context.
Methods:
-The authors do not detail the data analysis process, such as the tests used.
More detail is needed on how data collection and recruitment was done.
-Was the questionnaire validated?
Results
- It is suggested to divide the characteristics of the results by the outcome and present relevant statistics.
-Present the study flowchart.
-Review the discussion and present strengths.
-The conclusion is beyond the objectives.
Experimental design: No comment.
Validity of the findings: Statistical analysis data do not support discussion.
Additional comments: Manuscript with a relevant theme in the current context.
Methods:
-The authors do not detail the data analysis process, such as the tests used.
More detail is needed on how data collection and recruitment was done.
-Was the questionnaire validated?
Results
- It is suggested to divide the characteristics of the results by the outcome and present relevant statistics.
-Present the study flowchart.
-Review the discussion and present strengths.
-The conclusion is beyond the objectives.


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: LEVEL OF ANXIETY AMONG HEALTHCARE PROVIDERS DURING COVID-19 PANDEMIC IN SAUDI ARABIA: CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: References are insufficient in introduction and methods.
Cite the following: Magnavita N, Chirico F, Garbarino S, Bragazzi NL, Santacroce E, Zaffina S. SARS/MERS/SARS-CoV-2 Outbreaks and Burnout Syndrome among Healthcare Workers. An umbrella Systematic Review. Int J Environ Res Public Health. 2021;18(8):4361. Doi: 10.3390/ijerph18084361.Chirico F, Magnavita N. The Crucial Role of Occupational Health Surveillance for Health-care Workers During the COVID-19 Pandemic. Workplace Health & Safety. 2021;69(1):5-6. doi:10.1177/2165079920950161. Chirico F, Ferrari G, Nucera G, Szarpak L, Crescenzo P, Ilesanmi O. Prevalence of anxiety, depression, burnout syndrome,and mental health disorders among healthcare
workers during the COVID-19 pandemic: A rapid umbrella review of systematic reviews. J Health Soc Sci. 2021;6(2).doi: 0.19204/2021/prvl7.Chirico F, Nucera G. Tribute to healthcare operators threatened by COVID-19 pandemic. J Health Soc Sci. 2020;5(2):165-168. 10.19204/2020/trbt1, Chirico F, Nucera G, Magnavita N. Protecting the mental health of healthcare workers during the COVID-19 emergency. BJ Psych International. 2020. 1-6.  Doi: 10.1192/bji.2020.39

English should be largely improved
Experimental design: Research question should be reformulated
The association between socio-demographic characteristics and levels of anxiety and depression should be defined in terms of predictors, by using ORs.
In methods the authors do not report important ethical aspects and do not describe how they use dependent variable.
I suggest  using multivariate regression logistics where dependent variable (yes/no) is anxiety or depression and individual and occupational predictors are independent variables
Validity of the findings: Conclusions are supported by results
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: LEVEL OF ANXIETY AMONG HEALTHCARE PROVIDERS DURING COVID-19 PANDEMIC IN SAUDI ARABIA: CROSS-SECTIONAL STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The changes were done.
Experimental design: The changes were done.
Validity of the findings: The manuscript improved.
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: LEVEL OF ANXIETY AMONG HEALTHCARE PROVIDERS DURING COVID-19 PANDEMIC IN SAUDI ARABIA: CROSS-SECTIONAL STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The reporting is clear and unambiguous. Literature references are sufficient.
Experimental design: Research is within aims and scope of the journal.
Research question is well defined, relevant and meaningful.
Methods are described sufficiently
Validity of the findings: All data look robust and conclusions are well stated
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: REVISITING FOOD-SOURCED VITAMINS FOR CONSUMER DIET AND HEALTH NEEDS: A PERSPECTIVE REVIEW, FROM VITAMIN CLASSIFICATION, METABOLIC FUNCTIONS, ABSORPTION, UTILIZATION, TO BALANCING NUTRITIONAL REQUIREMENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The "Survey Methodology" part seems vague, which need more details for the readers to fully understand how authors performed the survey. For examples, in line 159-160, "we applied discretion to strike a balance between the year of publication and the relevance of the information." Yet, it is not clear what is the specific strategy they use. What's the threshold for year of publication? How they determine the relevance? The authors should clarify this with details in the text.

Based on my understanding, the main research items, according to line 151 are vitamin absorption, transportation of vitamin, and cellular uptake of the vitamin. Yet, in my following reading of the paper, I got very limited new knowledge in these areas. Majority of the content goes to the detailed introduction of different vitamins which can be found in many popular science articels on the internet. I would suggest the authors focused more on the research findings in the specific research items they mentioned in the method.

As for the presentation of the data, I think there are too many figures, I would suggest the authors put the structures of different vitamins into one figure.
Validity of the findings: In line 589-592, the author claims "This paper provides insight for future reviews/studies, which should help to further establish the intricacies underpinning how fat- and water-soluble vitamins interact within the food component matrix, as influenced by its absorption, transport, and cellular uptake."  However, I don't see enough content to support their conclusion. In my opinion, the review provides very limited novel insights or raise any unresolved questions in the field. The authors should discuss more about the key questions that need to be addressed as well as gaps that need to be filled in the future.
Additional comments: Generally, the review provide very comprehensive introduction to the food-sourced vitamins in regarding to their classification, sources, functions,etc. However, the review seems unbalanced, which loses focus on its scientific domain. The authors should reshape their writings to make it more suitable for a scientific review rather than a popular science article.


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

Input:
Title: REVISITING FOOD-SOURCED VITAMINS FOR CONSUMER DIET AND HEALTH NEEDS: A PERSPECTIVE REVIEW, FROM VITAMIN CLASSIFICATION, METABOLIC FUNCTIONS, ABSORPTION, UTILIZATION, TO BALANCING NUTRITIONAL REQUIREMENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The review meets the criteria of reporting and within the scope of the PeerJ journal.
Experimental design: The review is self-contained and meets the criteria of the PeerJ Journal.
Validity of the findings: The question is well-defined with relevant discussion and meets the criteria of the PeerJ Journal.
Additional comments: This review by Chigozie E Ofoedu et al describes the classification, metabolic functions, absorption, transport, deficiencies, and toxicities of vitamins, an essential micronutrient of our body. The detailed and orderly presentation is impressive. The review is organized logically into critical subsections which are well developed and explanatory to the goals set out in the beginning of the article. I am recommending accepting this article with minor revision.

1)	The authors could consider compiling figures from 2 to 14 (structure of vitamins) to a single figure.

2)	The manuscript could use some editing, since some sentences are difficult to read.

a)	Line number 487-488 of the manuscript should be written as

“These vitamins, however, are coupled with blood lipid-rich chylomicrons that are largely synthesized in intestinal mucosal cells”

b)	Line number 512-513 of the manuscript should be written as

“Essentially, if the human body were to maintain an adequate vitamin status, there are a variety of vitamins that have to be supplied in different amounts”

c)	The full form of ATP (adenosine triphosphate) has been mentioned in line number 281, but the word ATP has appeared before this in line number 243.

d)	Use punctuation mark (.) in line number 383 after references [4,25].

e)	Line number 278-279 of the manuscript should be written as
“Also, niacin aids in nervous system function and digestion by participating in oxidation-reduction metabolic reactions, protects against neurological degeneration, and has lipid-lowering ability [4,11,28]”.

3)	The authors could elaborate more on these sentences of the manuscript:

a)	In Line number 122-123, what is “bloodstream-physiological activities”?

“Further, the water-soluble vitamins diffuse through the intestinal walls into the
bloodstream-physiological activities.”

b)  In line number 242-243, the sentence could be framed as
“In addition, as a key player in the synthesis of neurotransmitters, it is also required for RNA, DNA, and ATP synthesis [11].”


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: REVISITING FOOD-SOURCED VITAMINS FOR CONSUMER DIET AND HEALTH NEEDS: A PERSPECTIVE REVIEW, FROM VITAMIN CLASSIFICATION, METABOLIC FUNCTIONS, ABSORPTION, UTILIZATION, TO BALANCING NUTRITIONAL REQUIREMENTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comments
Experimental design: no comments
Validity of the findings: no comments
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: REVISITING FOOD-SOURCED VITAMINS FOR CONSUMER DIET AND HEALTH NEEDS: A PERSPECTIVE REVIEW, FROM VITAMIN CLASSIFICATION, METABOLIC FUNCTIONS, ABSORPTION, UTILIZATION, TO BALANCING NUTRITIONAL REQUIREMENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors made a great effort to reshape their writings and the revised manuscript improved by addressing reviewers' concerns. I have no further comments.


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

Input:
Title: REVISITING FOOD-SOURCED VITAMINS FOR CONSUMER DIET AND HEALTH NEEDS: A PERSPECTIVE REVIEW, FROM VITAMIN CLASSIFICATION, METABOLIC FUNCTIONS, ABSORPTION, UTILIZATION, TO BALANCING NUTRITIONAL REQUIREMENTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript meets the basic criteria of reporting.
Experimental design: The manuscript meets all the criteria set out by PeerJ.
Validity of the findings: Please see the General Comments section for details.
Additional comments: My all comments have been addressed by the authors and the manuscript can be accepted for publication.


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

Input:
Title: REVISITING FOOD-SOURCED VITAMINS FOR CONSUMER DIET AND HEALTH NEEDS: A PERSPECTIVE REVIEW, FROM VITAMIN CLASSIFICATION, METABOLIC FUNCTIONS, ABSORPTION, UTILIZATION, TO BALANCING NUTRITIONAL REQUIREMENTS
Review round: 2
Reviewer: 3

Output:
Basic reporting: none
Experimental design: none
Validity of the findings: none
Additional comments: Overall the revised manuscript was well prepared. The authors provided detailed descriptions and additional sections, which are interesting and significant. Now the manuscript is ready to be accepted, while still need minor revision before publication.

1, noticed an equal contributor were added as a cofirst author, but the names, labeling, the order, and footnote in the first page were confusing. There should be some mistakes.

2, The keywords (Line69): could be modified by being replaced with more appropriate words, removing “animal sources; plant sources” at least.

3, The subtitle in each section is not well organized. For example, in “Absorption of Vitamins” part, there is no “ a) ”.

4, Be careful with word typing, capital or lower case, and consistence, e.g. COVID-19 vs Covid-19.

5, I don’t think the references were well adjusted according to the journal standard, in both text and ref list. For example, the number of authors, name, journal abbreviation.

6, The figure 2 quality is not good. Those structure figs, some of them, should be well prepared. Screenshot even contains watermarks, are not acceptable.


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

Input:
Title: THE BIOMECHANICAL CHARACTERISTICS OF THE STRONGMAN ATLAS STONE LIFT
Review round: 1
Reviewer: 1

Output:
Basic reporting: I believe this study meets all the standards of Peer J reporting.
Experimental design: The experimental design meets all the standards of Peer J.
Validity of the findings: I have a few comments on the discussion.  I put my notes to the author in that section.  I do believe the validity of the findings meets all the standards of Peer J.
Additional comments: Great study on a topic that does not have much literature on it.  The authors did a nice job on recruiting a trained sample and used validated methods for the kinematic analysis.  I see the statistics were professionally done as well.

This paper is well written and is easy to understand.  I do not see any methodological flaws in the design or the data analysis.  I feel the discussion linking the exercises to the joint positions does a nice job on creating a bridge between which exercises someone should do to improve the phases of performance for the atlas stone lift.  Lastly, I agree with the analysis that different arm to lower body length ratios are why females had a greater degree of hip flexion at the second pull phase

I have two questions about a reference in the Introduction and a measurement in the Discussion.  In addition, I have a small suggestion for the authors in the Discussion.

Minor Change: Introduction, Line 138: Does the author mean to reference Lisman et al (2021) as opposed to Lindbeck and Kjellberg, 2001)?  Because in the previous sentence, they refer to the females have a more upright position in the OHS, which is what Lisman et al (2021) examined.  I don’t have the paper in front of me but based on the abstract, I don’t think Lindbeck examined OHS.

Minor change: Discussion, Line 389-409: This is just a suggestion.  For the first pull phase, the author makes a connection between the RDL as an exercise similar to the atlas stone lift due to similar hip position.  Yes, I agree.  My additional suggestion is the good morning exercise.  The hip position is similar (70-750) and activates comparable muscles.  I understand the loading is on the back for the GM and not below hips therefore, the RDL is much better. However, this can be a secondary option if the athlete can’t perform RDL due to injury.  For example, if the athlete had a hand injury.  I have put a reference below on GM hip position.

Schellenberg et al. Kinetic and kinematic differences between deadlifts and goodmornings.  BMC Sports Science, Medicine, and Rehabilitation 2013, 5:27 http://biomedcentral.com/2052-1847/5/27

Minor change: Discussion, Line 475-480: I agree with the author that the reason for greater hip flexion in the females at the beginning of the first pull phase is likely due to a greater arm-leg length ratio for males compared to females.  My question is, why didn’t they measure this?  They measured tibia length and femur length in Table 1, it seems to make sense to measure arm length as well, therefore you can see if this actually is the case.  As opposed to deducing from Keogh (2008) 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: THE BIOMECHANICAL CHARACTERISTICS OF THE STRONGMAN ATLAS STONE LIFT
Review round: 1
Reviewer: 2

Output:
Basic reporting: Line 204- When describing the heaviest stone lifted, consider using different terminology than “maximum mass stone”
Line 453- Replace “sees” with either “demonstrates” or “represents”.
Line 456- Replace the word “powerful” with a temporal descriptor since “power” was not measured in this study.
Line 458-  Qualitatively explain “pop”
Line 460- Qualitatively explain “grind”..
The authors of this studies provided the requisite amount of references to the background and context provided.
Lines 488-489- Consider citing a study which performed a similar task (e.g., deadlift or stoop lifting) and provided between sex-differences in lumbar spine net joint moments).

This article was structured well, all tables and figures were provided. Raw data was provided in the supplemental materials.

The relevant results of this study were consistent with the stated hypotheses.
Experimental design: This study was the first of its kind to explore the biomechanical characteristics of the Atlas stone lift and adhered to the Aims and Scope of the journal.

The research question was well defined, relevant and meaningful for individuals interested in learning the biomechanical characteristics and requisites of the Atlas stone lift.

This study provided all data collection methods and relevant information to the equipment used (e.g., sampling frequencies, equipment names, and model numbers). The authors also provided citations for the data collection methods demonstrating the validity of the methods and use in previous research.

For the most part, the methods were described with sufficient detail and information to replicate. However, the warmup protocols (lines 196-196) were ambiguous and not controlled. A brief general description of the warmups would allow future researchers to better replicate the data collection procedures.
Validity of the findings: The rationale and benefit to the literature was clearly stated. The authors provided future researchers with a method of assessing atlas stone lifting biomechanics and discussed the limitations of this study which provide future researchers with an opportunity to further contribute to the literature pertaining to this topic of the study.
All underlying data have been provided are robust and statistically sound. Due to the data analysis issues related to the variability in certain phases of the Atlas Stone lift, Absolute and Relative reliability (intra-class correlation (ICC) and coefficient of variations (CV) or standard error of measurement (SEM) should be provided to ensure that the phases analysis demonstrated sufficient reliability.
Conclusions were well stated and were link to the original research question and limited to the supported results.
Additional comments: Dear authors, thank you for providing me with the opportunity to review your manuscript which sought to explore Atlas stone lift kinematics and kinematic differences between males and females. The introduction provided a concise yet informative explanation about strongman biomechanics, the atlas stone lift, associations with similar resistance training exercises and the gap in the literature.


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: PREDICTORS OF PERIODONTAL AND CARIES RELATED PERINATAL ORAL HEALTHCARE, INVESTIGATION OF DENTISTS’ PRACTICES: A CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: A. English is globally acceptable but a deep revision performed by a native English speaker is strongly suggested.

B. Literature references are quite good even if I have to underline that in introduction (when dealing about periodontal disease and its association with Preterm LBW) no literature references to the crucial role of Oral Microbiota are given. I suggest you some references to be added in order to strengthen the global evidence emerging from the manuscript:
 1. Characterizing peri-implant and sub-gingival microbiota through culturomics. First isolation of some species in the oral cavity. A pilot study. Pathogens, 2020:9(5): 365;
 2. Oral microbiota: Discovering and facing the new associations with systemic diseases. Pathogens, 2020:9(4):313;
 3. Relationship between oral microbiota and periodontal disease: A systematic review. Eur Rev Med Pharmacol Sci, 2018:22(18): 5775-5788.
Experimental design: Some relevant issues to be highlighted in this section are:

A. Please report the study design in the title.

B. Association between oral diseases and Preterm LBW and ECC is to be better explained and commented in introduction.

C. The primary aim of the study has to be reported by conforming as much as possible to the PICO format.

D. In materials and methods section the eligibility criteria and methods of selection for study population are to be reported. Why questionnaires have been sent by mail? Why not through e-mail? This could have helped to reach a bigger number of potential respondents.

E. In discussion please report the external validity and generalizability of findings.
Validity of the findings: Some relevant issues to be highlighted in this section are:

A. For what emerges from results about included dentists it is evident that age interval is too short as well as mean experience. This evidence configures a selection bias that has to be disclosed in discussion. The result about Mean and SD of working hours per week is too high (more than 50 hours per week!), please double-check it.

B. Another element to be added when defining the profile of respondents is the geographic area of provenance (e.g. dentists from bigger cities and from rural areas) in order to compare answers from different locations.

C. In results please report also the other significative point emerging from Table 4. This element has also to be discussed in discussion stressing the fact that a potential explanation is that not all dentists are prone to go on with their scientific updating. This hypothesis could also be claimed for explaining the multiple elements about apparent ignorance of a part of respondents that emerge from the discussion.

D. Information about funding is missing, please report.
Additional comments: Dear authors,

 All the elements to be changed have been reported in the appropriate boxes.
My general suggestion is to have a first round of major revision in order to solve all highlighted problems.

Regards


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: PREDICTORS OF PERIODONTAL AND CARIES RELATED PERINATAL ORAL HEALTHCARE, INVESTIGATION OF DENTISTS’ PRACTICES: A CROSS-SECTIONAL STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: English language must be substantially improved for the publication.
Experimental design: Aim of the study
The aim of the study is very superficial and lacks details. Is impossible to understand the first and the secondary outcomes. Please consult STROBE for reporting.

Materials and methods:
Materials and methods are extremely hard to follow, the information is scattered lacks logical sequence or cohesion. Please add subsections (ex. Study design, Study population, Statistical analysis…..) and consult STROBE for reporting.
The statistical analysis section (within the material and method) lacks details. What is the dependent variable? What is the covariable? Did you use different models in the Binomial regression? How did you select the models? Have you made any adjustments? Please add more info.
Validity of the findings: Results
Some analyses in the statistical analysis are not reported in the results (Chi-square and Fisher’s exact test). Please add.
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: PREDICTORS OF PERIODONTAL AND CARIES RELATED PERINATAL ORAL HEALTHCARE, INVESTIGATION OF DENTISTS’ PRACTICES: A CROSS-SECTIONAL STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Required Reviews Completed


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: TOWARDS A PRAGMATIC USE OF STATISTICS IN ECOLOGY
Review round: 1
Reviewer: 1

Output:
Basic reporting: See my general comments
Experimental design: See my general comments
Validity of the findings: See my general comments
Additional comments: This is an interesting study and well-designed simulation work. I have just three comments

1) Given that this paper is for ecologists, the authors may have missed a couple of papers that dealt with Type M and S errors:

Lemoine, Nathan P., et al. "Underappreciated problems of low replication in ecological field studies." Ecology 97.10 (2016): 2554-2561.

Cleasby, Ian R., et al. "What is our power to detect device effects in animal tracking studies?." Methods in Ecology and Evolution (2021).

These publications should probably be acknowledged as they do deal with Type M and S errors.

2) I disagree with the use of "Effect size" in this paper. What the authors are calling 'effect size' is t values or z values (this use is unusual and even misleading). They are usually not considered so - see this Wiki page and references therein

https://en.wikipedia.org/wiki/Effect_size

I think they should use effect size such as Cohen's d (also known as standardized mean difference), which can be obtained for correlations via conversation.

3) Relating to my Point 2, I think the simulation should show the relationships among effect size, sample size and NHT (or IT). I think this will be much more meaningful than what is presented currently. Under their "effect size", the effect and sample sizes are confounded and I do not think it is very useful and not informative.


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: TOWARDS A PRAGMATIC USE OF STATISTICS IN ECOLOGY
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: The findings are interesting and well-supported.
Additional comments: The literature review should be significantly improved with summaries of recent studies (preferably after 2019)


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: TOWARDS A PRAGMATIC USE OF STATISTICS IN ECOLOGY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article is well written and clear. My one comment is that I suggest moving the last paragraph of the introduction, where you discuss some caveats of the work, to the discussion.
Experimental design: I found the topic and method of research to be very interesting. The debate between IT and NHST approaches has been an ongoing topic of discussion, and the author's simulations make an important contribution. Their R code all appears to be solid to me, and their general methods of comparing the two methods makes sense.

A potential aspect of the IT approach that I feel was somewhat missed out is that multimodel inference allows for quantification of measures of "variable importance" (often summarized as the sum of model weights for all models containing each variable) and model averaging of coefficients, which may have predictive benefits in some situations. I don't think these concepts need to necessarily be included in the simulations, however model averaging specifically might (I emphasize *might*) reduce the type-M error for the IT approach and might therefore bear mentioning at least.

I'd also be interested in how other information criteria perform. As the authors say, AIC doesn't assume that the true model is in the candidate set, which makes it vulnerable to overfitting in situations where the true model is one of the candidates. How might other criteria, like BIC, or truly Bayesian methods like WAIC, perform? Again, I don't think its necessary that these be included in the simulations themselves, as I think that the current design is quite elegant and well defined, but it would be good to mention them as possibilities.
Validity of the findings: The findings of this study are quite interesting, and I think will be useful for many researchers designing their statistical analysis. I think the fundamental point that we should focus more on designing experiments or observational protocols that allow us to easily detect and quantify "true" effect, rather than the relatively petty disagreement around IT vs NHST, is a very important one that I'm happy to see be made.

My one area of concern is in their discussion of p-values as a measure of evidence weight. While their simulations do show that, in these specific cases, there is a monotonic positive relationship between p-values and the weight of the null model, I'd emphasize, as the authors themselves state, that interpreting the p-values in this way is conceptually incorrect. While I understand their point, that previous studies that interpret p-values in this way are likely to have come to similar conclusions as they would have if they measured model weights, I worry that this could be read as encouraging future studies to use p-values in this way. If possible, I'd like the authors to clarify what their position is here, and potentially amend the text to more clearly indicate that while it can serve as a rough approximation, interpreting p-values as the likelihood of the null hypothesis is fundamentally incorrect.
Additional comments: This is an important and interesting simulation study, well conceived and reported. I look forward to hearing the authors responses to the few queries I've raised here.


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: TOWARDS A PRAGMATIC USE OF STATISTICS IN ECOLOGY
Review round: 2
Reviewer: 1

Output:
Basic reporting: I still think the use of Cohen's d or similar would be more in line with what I am used to and (probably more general and useful). However, I do see the authors' viewpoint as well. It is true many ecologists and evolutionary biologists are more familiar with t and z values rather than d. Given this, I have no further comments.

I believe the paper is clearly written with good simulation study (design) and it is great that all materials are open and accessible.
Experimental design: See above
Validity of the findings: See above
Additional comments: no comment


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

Input:
Title: EXPLORING PRIVATE LAND CONSERVATION NON-ADOPTERS’ ATTENDANCE AT OUTREACH EVENTS IN THE CHESAPEAKE BAY WATERSHED, USA
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. Your description of non-adopters as defined in the methods section is sufficient, but it will improve understanding of the introduction if you provide a short description of non-adopters in the introduction as well.

2. The section describing adoption of conservation practices in the study site in lines 118-129 could benefit from a discussion of conservation outreach/implementation initiatives in the area. Providing this general overview would also provide context for the conservation practices described in lines 185-202 that were classified for the analysis.

3. The labels on figures are difficult to read. I suggest flipping the graphs so that the bars are horizontal.
Experimental design: 1. The aim of the study could use clarification. Lines 98-100 state that the aim is to understand what characteristics are connected to adoption of conservation practices, but throughout the results, discussion, and conclusion the emphasis is on non-adoption. I suggest reframing the aim/introduction to reflect this.

2. Your definition of adopters and non-adopters required that both groups attended at least one outreach event, but you also interviewed respondents who did not attend outreach events and included these respondents in Figure 1 as adopters and non-adopters. Please clarify this discrepancy in the methods section.
Validity of the findings: 1. The manuscript could benefit from a deeper discussion of implications of investigating non-adoption for the implementation of conservation practices. In lines 506-511, you mention implications of the results for both conservation messaging research and outreach, but the following paragraphs mainly focus on research only. I suggest that the discussion also analyze implications of results for the implementation of conservation practices. That is, how do your specific results connect to the larger outcomes discussed in lines 45-54? How could conservation practitioners utilize the results of the study (e.g. features of outreach events that non-adopters attended) to improve the efficiency or effectiveness of conservation implementation of practices introduced in outreach events? Also, how do these results compare to outcomes of other types of conservation messaging research described in lines 71-82?

2. While the justification for considering conservation practices generally on lines 213-216 is sound, future analyses could benefit from examining associations between event characteristics and adoption for specific conservation practices. For example, was there a correlation between number or type of outreach events attended and adoption of specific conservation practices? I suggest you include these potential analyses in your discussion of future research.
Additional comments: This paper addresses the characteristics of conservation outreach events associated with non-adopter agricultural land operators. The article contributes to the literature on conservation messaging and implementation and can provide important insight to both researchers and conservation practitioners. Also, the manuscript is written in professional and concise language. However, it will benefit from a clearer description of its objective and justification, specifically in regard to the relevance of examining non-adopter event features to conservation adoption and implementation.


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: EXPLORING PRIVATE LAND CONSERVATION NON-ADOPTERS’ ATTENDANCE AT OUTREACH EVENTS IN THE CHESAPEAKE BAY WATERSHED, USA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Figure 3—Consider increasing the image quality here, it is difficult to read.

Lines 183-206: I might suggest creating a table out this information. I think it will improve readability---easier to scan this information in a table format than read the paragraph.

Lines 242-245: Could you provide a grounded example to illustrate this rule? I think a quick sentence or two would help to clarify this a bit.

Line 506: If the journal formatting will allow it, I would suggest breaking out your practical implications into a separate section, potentially with that title as a heading. These recommendations are important, and it would increase the readability for non-academic stakeholder if this section of the discussion was clearly demarcated in the article.
Experimental design: I’m not familiar with this approach to qualitative analysis and so I cannot offer an independent evaluation of the author’s use of QCA. That said, their explanation was clear and a reader like myself can certainly see the logic of their approach.
Validity of the findings: No comment
Additional comments: Interesting work and approaches! I found this easy to read and well prepared.


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: COVID-19 AND REGIONAL DIFFERENCES IN THE TIMELINESS OF HIP-FRACTURE SURGERY: AN INTERRUPTED TIME-SERIES ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is well written, interesting and accurate in how resulta are reported. To gain additional readability the paper can be shortened. It is not necessary to describe the two Italian Regions or the origin of the Italian health care system. Some information can be placed in a box but this is not full necessary. It means - you can omit all that info.
The discussion is also lengthy and can be downsized to 800 words. For instance the paragraph bw line 299 and 311 is a repetition of the results without much added value. It can be entirely removed.
Experimental design: The designa is appropriate. In this context there is no need to mention that an ITSA is "a quasi-experimental design that represents a robust alternative to randomized studies when the latter are not feasible". This is not the case in which an ITS is used as a substitute of an RCT.
Validity of the findings: Findings are valid. Confounders are well considered and the stat analysis is appropriate.
Additional comments: A minor suggestion: as identified by the authors the most relevant finding is the dynamic around the percentages of timely surgery for HF. Now this finding is preceded by few other findings that are relatively minor but get too much space.
Wouldn't be better to get this at the centre of the scene ?


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: COVID-19 AND REGIONAL DIFFERENCES IN THE TIMELINESS OF HIP-FRACTURE SURGERY: AN INTERRUPTED TIME-SERIES ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comments
Experimental design: The anlysis is well done.
Regarding the reduction in HP numbers, I can suppose two main causes: 1) lockdown and stay at home campaign hit older people that are more prone to be at home and then the risk of falls is reduced; 2) in the first wave SARS-CoV-2 infection was more frequent in older people and the number of died was higher in older people. Can you discriminate the dominant mechanisms? Other potential explanations?
Validity of the findings: Emilia-Romagna starts from a better performance as compared to Piedmont. It is plausible that before pandemic Emilia-Romagna is treating within 2 days more complex, older, more frial patients as compared to Piedmont. Then, this observation could explain the major drop in Emilia-Romagna as compared to Piedmont because it is more probable that during a pandemic scenario frail patients are at higher risk of under-treatment. Have you data to clarify this point? Do you have other explnations?
Additional comments: I read with great interest the manuscript
It is really important to analyse the performance of regional network during pandemic becasue we can obtain many information to further improve the helthcare
I believe that the Authors have to stress this important issue in their discussion. How can further improved the network?


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: COVID-19 AND REGIONAL DIFFERENCES IN THE TIMELINESS OF HIP-FRACTURE SURGERY: AN INTERRUPTED TIME-SERIES ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: All my issues have been addresed


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: GERMLINE MUTATION ANALYSES OF MALIGNANT GROUND GLASS OPACITY NODULES IN NON-SMOKING LUNG ADENOCARCINOMA PATIENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In their work, the researchers focused on a very specific patient sub-set of patients harboring malignant GGO and identified  specific germ-line mutations which might eventually be associated with cancer of risk development.

The manuscript is generally well written, with sufficient background and good use of references. The structure is professionally managed and Raw data are included.
Experimental design: The research question is well defined and of clinical relevance in terms of early diagnosis of lung cancer and differential diagnosis between benign and malignant GGO findings.

However, the patient sample is very limited in number and potentially biased by the fact that all the patients were non-smokers. The authors should state if these patients were identified at casual radiologic findings or as part of organized screening programs.

Furthermore, the timing of blood sample collection would be relevant. Was the blood collected before, during or after treatment? Was it repeated after treatment to make sure that these are germinal findings and not mutations in cfDNA related to the presence of neoplastic cells? If possible, a repeated blood collection after treatment might reinforce the concept that the findings are germinal and not caused by tumor shredding.

Since the patient number is limited, the authors should state the treatment which was received by the patients and more robust outcome data for these patients. This could be evaluated in order to define any possible mutation with prognostic significance within our limited population.

Another bias is represented by the lack of a control group including either healthy individuals or subjects with non-malignant GGO as comparison. This addition might reinforce the concept that the detected mutations are actually potential biomarkers of malignant pulmonary findings.
Validity of the findings: The findings of the manuscript are interesting and encourage additional studies designed to use circulating biomarkers for cancer screening. However, I have the following observations, which should be addressed either by further analyses (as suggested in study design) or at least by addressing all the issues in the discussion:

1) As previously stated, the results involve a small patient sub-group, even more selected by the non-smoker status, which is often associated with a different mutational landscape compared to smokers' lung cancer. Hence the findings cannot be generalized.

2) As a control group is not present, the direct association between the findings and tumor development can only be implied, but cannot be demonstrated at the current stage.

3) As never-smoker lung cancer is molecularly different from current smoker lung cancer, the analysis on tumor samples of a comprehensive mutational panel or at least the most relevant activating mutations (EGFR, ALK, ROS1, BRAF) should be performed, and these findings associations with blood samples should be stated.

4) Due to the current study limitations, the researchers should stress the concept that no conclusions for prompt use in clinical practice can be drawn, while the observations might encourage further studies, including prospective studies in screening populations.
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: GERMLINE MUTATION ANALYSES OF MALIGNANT GROUND GLASS OPACITY NODULES IN NON-SMOKING LUNG ADENOCARCINOMA PATIENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study examined germline variants of 13 patients who had GGO in their lungs and received pulmonary surgery.
The following points should be revised.

1. The authors should clarify why these 13 patients received  pulmonary surgery although their legions were small. Was the surgery done by physicians' decision or patients' strong will? The authors should show a consort diagram in which how the patients were properly selected.

2. A table or figure that explain how the detected variants were carried in each patient (mutually exclusive or overlapped in a subset of patients?).

3. The authors should show variant allele frequency for the detected variants in (non-cancerous) study population. Please explain "in-house database" in Table 1 in detail.

4. GGO (CT) and pathological images for all patients should be shown.
Experimental design: Method of patient selection is unclear since the authors do not show a consort diagram in which how the patients were properly selected.

Method of variants selection is unclear since the authors used an in-house database which are not explained in the text.
Validity of the findings: Authenticity of this study is lacked since the methods for patient and variant selection are unclear.
Overlap and/or mutually exclusiveness of detected variants are also unclear.
Additional comments: The authors should clarify the methods for patient and variant selection. Overlap and/or mutually exclusiveness of detected variants should be shown and discussed.


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

Input:
Title: GERMLINE MUTATION ANALYSES OF MALIGNANT GROUND GLASS OPACITY NODULES IN NON-SMOKING LUNG ADENOCARCINOMA PATIENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am generally satisfied with the revised version of the manuscript and the authors' answers to the referees. Globally, the quality of the manuscript is significantly improved compared to the initial version.
Experimental design: The authors improved the experimental design in a generally satisfactory way.

In lines 71-80 (study subjects), I suggest a global rephrasing, with particular reference to the sentence "When the GGO nodules increased in size or the nodule density increased or the solid components of pulmonary nodules increased, We recruited 13 patients were recruited who were histologically diagnosed and confirmed as having malignant  GGOs", as it is not really clear whether the patients underwent surgery or not after observation of size increase. Apart from this part, the other sections of the manuscript are generally fluent and clear.
Validity of the findings: The findings are generally valid, although the small patient sample limits the robustness of the information. As suggested, the authors stressed the limitations of the study in the discussion.

However, I would suggest to reinforce this concept also in the conclusion, eventually with a sentence immediately preceding line 207 (" Our observations encourage further studies").
Additional comments: I am generally satisfied with the revised version of the manuscript, I suggest only minor revisions based on what reported in the previous sections.


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: DONGSHA ATOLL IS AN IMPORTANT STEPPING-STONE THAT PROMOTES REGIONAL GENETIC CONNECTIVITY IN THE SOUTH CHINA SEA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea described by Liu et al. examined meta-population model of 9 marine species using mitoDNA and coalescent based simulation and found for species with relatively short larval duration (<40 days), stepping stone model is best supported and thus concluded Dongsha Atoll is an important place for regional connectivity. By applying coalescent based analysis, authors overcome the small number of samples per species and population that exist for traditional population based analysis. The manuscript is overall very well written and analyzed rigorously utilizing GEOME data set. The results obtained here are very important and useful for conservation of Dongsha Atoll and its surrounding region.
Adding some more information, I think the paper would be more understandable for non-specialist.

1) It was not clear for me, Dongsha Atoll is in particularly important stepping-stone for which 'regions' in the SCS (from where to where)?

2) What is the relative importance of Dongsha Atoll for sustaining SCS meta-populations? It also seems all the populations are important as they are connected by stepping-stone.

3) Fig2 and L121-L128 it seems only 3 models are tested not 5. Please explain in more detail. At least, it was not possible to identify 5 different models by looking at Fig.2.

4) Because this study focus only on mtDNA data set, please add some small notes that none of the target species suffer from ancient introgressive hybridization or sex biased dispersal etc.

5) for some species such as whorled nerite and the striated surgeonfish who had high proportion of private haplotypes, Dongsha Atoll is of importance for conservation of genetically unique population (evolutionary novelty) rather than just a stepping stone for conservation. It means the Atoll is isolated for relatively long time (evolutionary time scale rather than ecological time scale in terms of conservation).
Experimental design: Research question testing the hypothesis the Dongsha act as a stepping stone for regional connectivity is clearly stated.
Rigorous investigation performed to a high technical & ethical standard.

L106 please clarify what do you mean by " the surrounding area"
L140 please briefly describe why optimized on the m/u instead of Nem
Validity of the findings: Meaningful replications (3 independent runs for each coalescent analysis) using  9 species with different PLD were assessed.
The result and conclusion is robust and scientifically sound.
Conclusion are well stated but please more clarify the three points I wrote in the basic reports.
Limitation is it only based on mtDNA not multilocus genomic data.
Additional comments: The paper is of high scientific and conservation value.
Keep up a good work utilizing GEMOE data base.


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: DONGSHA ATOLL IS AN IMPORTANT STEPPING-STONE THAT PROMOTES REGIONAL GENETIC CONNECTIVITY IN THE SOUTH CHINA SEA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript is well-written and generally clear with a few small typos (see below). The final two paragraphs are duplicates and one needs to be deleted.
There are two major issues with the data presented:
1. I could not access the raw data/alignment files following the directions provided (and some probing). So I could not assess this part of the paper.
2. One of the supplemental files (Figure S2) I could not open despite trying multiple programs. Converting to a more common file type would be recommended. Again I could not assess this major part of the results.

Line 3 – semi colon between references
Line 17 - semi colon between references
Line 299- semi colon between references

Line 195 – This is the first time Okinoerabu is used in the text, and it does not match any of the locations in the map in Fig.1. I think it is somewhat intuitive that it is Okinawa, but consistency with the map or an explanation that it represents Okinawa would be helpful.

Figure S2 - The combined axes for all 9 species made this confusing to read and interpret, as the axes are not all equivalent. Separating them out would add clarity for the reader.
Experimental design: The research question is well-defined and clearly filling a knowledge gap, and I applaud the authors for taking such a broad taxonomic and geographic overview of this area.
The methods are generally sufficiently detailed and there is enough information to replicate, but there are a couple of issues.

Most importantly: Paragraph starting at Line 121 – It appears that the authors have reduced the number of population models they were including in their paper. The text says 5 but only lists 3, and later only shows 3. And the github repository link shows results for both 3 and 5 different model scenarios. Please correct the text to the 3 scenarios described. I think it would clarify things for the reader to use the same Panmixia/N-island/Stepping stone phrasing more clearly here in the methods, so that it matches the results.

Lines 89-91 – How was the alignment carried out, was it using the geneious alignment software or clustal/muscle plug in, and under what parameters? Please elaborate.
Validity of the findings: My main concern with this paper is whether or not their approach actually answers their question.

The science they did appears sound and interesting. However, the main premise of the paper centers on the significance of Dongsha atoll with respect to regional connectivity, but their migrate-n models do not place any special significance on Dongsha (as far as I can see). It appears from the linked github page that the authors originally ran some other scenarios which specifically highlighted the role of Donghsa atoll, but they are not included in this paper. Data that support the main finding that Dongsha atoll is key for connectivity for the stepping-stone model species are not shown. It appears from the diagrams in Fig 4 that Dongsha is not a key part of the stepping stone model for all of the “stepping stone” species, for example: Chaetodon auriga seems to show Palau as the key stepping stone location, and for Chaetodon striatus Dongsha is somewhat peripheral.

The authors could try some extra analyses removing Dongsha atoll as a location from the models and seeing if connectivity significantly declines or something to that effect. But at the moment the authors do not present clear evidence for the statement “Dongsha Atoll provides an important intergenerational stepping-stone for maintaining gene flow across the SCS” (line 263). They show evidence for a stepping stone model of connectivity but their current approach cannot distinguish the importance of Dongsha relative to the other sampling locations.

Line 262 – The means and standard deviations of PLD between the two sets of very wide, and overlap substantially. Are the values stastically different? Please state significance in the text.
Additional comments: No additional comments


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

Input:
Title: DONGSHA ATOLL IS AN IMPORTANT STEPPING-STONE THAT PROMOTES REGIONAL GENETIC CONNECTIVITY IN THE SOUTH CHINA SEA
Review round: 2
Reviewer: 1

Output:
Basic reporting: All previous comments have been addressed. With the exception of the file for S2. I don't have a mac or adobe illustrator, so opening an .esp file is challenging. I still believe a more common file type to me more appropriate such as .pdf, or .svg, or something that doesn't need proprietary software or a file converter. I still have not been able to assess this part of the results.

I think Figure 6 could benefit from having Dongsha atoll highlighted in some way, so the reader doesn't have to refer back to previous maps. I would also suggest adding a total number of reefs analyzed  to the figure (e.g. Dongsha rank = 10/112), so the reader understands the relative importance of 10th rank.
Experimental design: The authors gave the appropriate alignment program and settings in their response to authors but have not actually added it in the revised text, please do so.

The caption for Figure 4 still refers to 5 models. Please fix this.

All other comments were addressed well.
Validity of the findings: I commend the authors for their new analysis which does answer their research question about the importance of Dongsha atoll specifically. I think this highlights that Dongsha is one of the key connecting reefs in the area. It might be worth commenting on Zhongsha reef as this seems the most strikingly important reef from Figure 6. The authors comment on this in the results, but personal preference as to whether it deserves more discussion.
Additional comments: No additional comments


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

Input:
Title: INVESTIGATION OF INHIBITION EFFECT OF DAIDZEIN ON OSTEOSARCOMA CELLS BASED ON EXPERIMENTAL VALIDATION AND SYSTEMATIC PHARMACOLOGY ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Zhu and colleagues reported an interesting study on the cellular and molecular effects of treatment with daidzen, an isoflavonoid, in osteosarcoma models.
Experimental design: The experiments were conducted properly.
Validity of the findings: The results support the conclusion of the study.
Additional comments: Zhu and colleagues reported an interesting study on the cellular and molecular effects of treatment with daidzen, an isoflavonoid, in osteosarcoma models. The experiments were conducted properly and the results support the conclusion of the study. I highlight the findings of the systematic pharmacology analysis that allowed the identification of a potential mechanism of action that partially explains the observed results. The figures are adequate and the text is clear and well written. This reviewer suggests minor corrections to avoid misinterpretation by the readers.

1-) In the abstract (Line 19), the authors must include a sentence presenting the daidzen. Make it clear to readers to which class this compound belongs.

2-) In item 6 of the "Material & Methods" the "Tumor invasion assay" assay is actually a "Transwell migration assay", as there is no addition of extracellular matrix (e.g. matrigel) for the cells to invade.

3-) In item 7 of the “Material & Methods” the “Tumor migration assay”, the most appropriate term (to avoid conflict with item 6) would be “Wound assay”.

4-) After correcting items 6 and 7 of the “Material & Methods”, the terms migration and invasion need to be revised throughout the text (e.g. line 252).

5-) Describe the catalog number and the phosphorylation sites evaluated for each antibody described in item 11 of the “Material & Methods”.

6-) The authors use the units of the drug in "uM" and "umol/L". Although the terms are synonymous, the authors must be consistent throughout the text to avoid misinterpretation by the readers.

7-) Authors must include more details in all Figure legends. Readers need to be able to interpret the figures without having to read the entire text. For example, in Figure 1, include the description of the rationale for the study in the legend, the website links and the indication of the software. In all Figures, describe the statistical method and indicate p-values. In Figure 5D, what does the scale bar of the graph mean? Please carefully review all figure legends.