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: GENETIC DIVERSITY AND STRUCTURE OF THE CRITICALLY ENDANGERED ARTOCARPUS ANNULATUS, A CROP WILD RELATIVE OF JACKFRUIT (A. HETEROPHYLLUS)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article basically deals with the characterization of the diversity and genetic structure of populations of A. annulatus. This species occurs in a very particular, fragmented and threatened environment. In addition to describing the genetic diversity of the species, the authors make comparisons with closely related species and assess whether there is a difference in the diversity indexes when comparing different age groups. In general the article is well written but needs to improve in some points. The comments and suggestions are directly in the attached pdf, but I highlight some here:

Major points

- It is not clear how the data presented in Table 6 were obtained. I did not find in the cited literature whether the authors actually used the same loci and how the indexes presented in Table 6 were obtained. This should be better clarified throughout the text. See also comments made in the pdf file.

- In the discussion, indices calculated in the article by Miller and Gross (2011) were cited, see lines 294-297. I think it is difficult to make a comparative analysis, in terms of values, considering the results obtained in the present study. I suggest rethinking these sentences.

- The discussion item “Genetic structure within and across Artocarpus annulatus populations” should be completely revised, as the results obtained do not seem to coincide with the discussion on this topic. See comments in the pdf file.

- In the discussion, it is understood that the species under study is monoecious, but  this was not mentioned in the manuscript, although there are some suggestions. This should be better clarified and maybe discussed with more emphasis.

Minor points

- Check the correct way of writing all indexes. In heterozygosities, the H must be in italics, the F indices must also be in italics and the subscribed letters are capitalized. Also review K. See some indications in the text in pdf.

- The Figure 2 (map) should be improved. Is box C showing the geographical location of the sampled populations? This should be seen directly on the map.

- Please increase symbols and legends in figure 3 and improve resolution.

- In Table 2 what is N? and what is NA? This should be in the legend.

- In table 4, standardize: populations or pops?
Experimental design: The experimental design is adequate.
Validity of the findings: I think the results obtained are a good contribution to the study area and may help to outline conservation strategies for the species.
Additional comments: See more comments in the attached pdf.


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

Input:
Title: GENETIC DIVERSITY AND STRUCTURE OF THE CRITICALLY ENDANGERED ARTOCARPUS ANNULATUS, A CROP WILD RELATIVE OF JACKFRUIT (A. HETEROPHYLLUS)
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The reviewed article concerns genetic diversity of critically endangered species Artocarpus annulus as revealed by microsatellite markers. Authors used to microsatellite primers to asses of genetic variation of 5 populations of A. annulus and closely related species: cempedak and jackfruit. The study has some potential and valuable data but i I can't recommended the article for publication in present form. Below I presented my general suggestion, that could improve the scientific soundness of this study:

General comments:
Introduction:
The introduction requires corrections and supplementation of additional information. Details below.
1)	In the introduction, authors describe the karst ecosystem, the characteristic features of this habitat and  problems regarding the disappearance of this habitat. Of course this information are important and useful to understand the conservation of analysed population of A. annulus. However because the article is about genetic diversity, structure and conservation of  A. annulus the introduction should be more focused towards conservation genetics. I suggested shortening the paragraphs about the kars ecosystems and pay more attention to studied species. Example there is a lack of important information about study species (concerning biology and population resources), which are necessary in the discussion about genetic variation and strategies of conservation. This information would be help to understand justification for performed analyses. On the other hand,   description of  karst ecosystem too extensive for this purpose.
2) In the introduction, there is no scientific hypothesis, which should be assumed in this kind of study? Does authors suspect the genetic diversity as a bottleneck of population fitness?
3) It is also unclear how the genetic analysis of this species can impact management plans for in situ and ex situ conservation efforts …..(line 113-115). It should be explained.
Material and methods.

1)	Microsatellite methods.

In this research authors used microsatellite markers which were developed for A. altilis (Witherup et. al. 2013) and tested for closely related species like cempedak and jackfruit (Wang et. al. 2018).  Moreover for cempedak were observed more than two strong peaks and the rarest and weakest peaks were omitted. Additional peaks were also observed in this studies (lines 203-205 in manuscript). In addition, the starter MAA 178 amplified two readily distinguishable regions and authors was considered as two separate loci.  The author should better explain why this two peaks were treated as two separate loci. In my opinion such loci should be excluded from the analysis and SSR primer specific for  A. annulus should be developed, as it’s fast and cheap nowadays by using NGS sequencing.

2)	Results

Genetic diversity and genetic structure.

1.	I suggest to merge the tables 1 and 2.

2.	I suggest counting the allelic richness and adding this information to table. Allelic richness is a straightforward measure of genetic diversity, that is commonly used in studies based on molecular markers that aim at selecting populations for conservation. This is very informative parameter,  dependent on effective population size, a good indicator of past demographic changes that would have affected genes associated with adaptive traits as well as natural markers.

3. In the results, authors were repeated the information about results of Amova analysis. (line 250-252 and 257-259).

4. The Fig 3 is completely unreadable and should be corrected.
5. Structure analysis.  I suggest to present lnP(D)/K in a simple graph. This method does also show a “peak” at K=12 which might be also worth to be presented 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: GENETIC DIVERSITY AND STRUCTURE OF THE CRITICALLY ENDANGERED ARTOCARPUS ANNULATUS, A CROP WILD RELATIVE OF JACKFRUIT (A. HETEROPHYLLUS)
Review round: 2
Reviewer: 1

Output:
Basic reporting: -
Experimental design: I am impressed by the authors' effort to improve the manuscript. The manuscript has improved in both introduction and discussion. On the other hand, I believe that the number of markers used for this purpose is too limited.  Moreover, I have seen in Supplemental materials that SSR data have a large number of missing data.
This could affect the final result. I remain of the idea that authors should add more SSRs to improve the article. A sufficient number of markers would allow obtaining an excellent job.
Validity of the findings: -
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: GENETIC DIVERSITY AND STRUCTURE OF THE CRITICALLY ENDANGERED ARTOCARPUS ANNULATUS, A CROP WILD RELATIVE OF JACKFRUIT (A. HETEROPHYLLUS)
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The manuscript was carefully revised according to the reviewers' suggestions. I consider that all corrections and changes were made accordingly, making the article much stronger. Attached is the manuscript with minor corrections. After these corrections are made, I believe that it is ready 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: GENETIC DIVERSITY AND STRUCTURE OF THE CRITICALLY ENDANGERED ARTOCARPUS ANNULATUS, A CROP WILD RELATIVE OF JACKFRUIT (A. HETEROPHYLLUS)
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comments
Additional comments: Dear Authors, most of my comments have been included in this version of the manuscript. I have one more suggestion. Can the authors comment on the values of allelic richness in the Results and Discussion.


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

Input:
Title: IDENTIFICATION OF NUF2 AND FAM83D AS POTENTIAL BIOMARKERS IN TRIPLE-NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 1

Output:
Basic reporting: In the present article, entitled “Identification of NUF2 and FAM83D as novel biomarkers in triple-negative breast cancer”, authors have performed the computational and experimental analysis to identify the effective biomarkers to triple-negative breast cancer (TNBC) diagnosis and prognosis. It is good that after analyzing the GEO data sets, authors have experimented to validate the data analysis results.

However, some important points need to be clarified or fixed

1.	There are many vague sentences which should be edited, such as
a.	“GO enrichment  analysis contain 13 biological processes, 10 cellular components and 4 molecular functions”
b.	“...deal with various confusing biological issues”.

2.	Is there any novelty in the present work, which was not reported earlier?
Experimental design: 1. DEGs and survival analysis were done in different data sets. Will this create any technical error in the results? Authors should justify
2. Why was Recurrence-free survival (RFS) presented? Why not overall survival?
Validity of the findings: 1.	How are the GO and KEGG pathway analysis results linked to  TNBC development?
2.	PPI network was constructed from publicly available data, the network should be validated and should be compared with the random network model  [Molecular Genetics and Genomics volume 294, pages931–940(2019)].
3.	The authors should also calculate the expression correlation between hub genes. If there are higher correlation, then those hub genes are probably involved in similar biological function.
Additional comments: No additional comments


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

Input:
Title: IDENTIFICATION OF NUF2 AND FAM83D AS POTENTIAL BIOMARKERS IN TRIPLE-NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Zhai et al. submitted the manuscript” Identification of NUF2 and FAM83D as novel biomarkers in triple-negative breast cancer” they use multiple bioinformatics methods to identify two genes (NUF2 and FAM83D) as potential biomarkers for TNBC. Their correlation was validated by real-time PCR. Overall, the manuscript is generally well-written and clearly presented, figures are relevant, high quality. However, there are some typos and phrases that need rewriting. In addition, it will be more convincing if the authors present more experimental evidence to support the correlation between NUF2/FAM83D and TNBC. Here I have some minor comments and suggestions that may be helpful to improve the manuscript.
1.	There are some sentences that were grammatically incorrect.
Line 62 “Many genes have been found could be used as signatures for TN breast cancer diagnosis and prognosis”; Line150-151“The Venn diagrams showed that a total of 161 genes were co-expression”; Line 228-229 “Certainly, the specific molecular mechanisms by which NUF2 mediates TNBC carcinogenesis still need to be further study.”.
2.	Some other phrases, albeit grammatically correct, were scientifically confusing.
Line 67 “deal with various confusing biological issues”; Line 72-73 ” This  comprehensive  analysis may provide a meaningful contribution to the targeted treatment of triple negative breast cancer”; Line 151” clearly up-regulated”; Line 221-222 “However, the role of NUF2 in triple negative breast cancer has not been conducted”
3.	Line 155”161common” space should be place between “161” and “common”.  So does line 147 ” 259genes”
4.	Please define “BP” in line 158, and “CC” in line 160 and “MF” in line 161.
5.	There are two types of microarray in the three datasets, GSE65194 and GSE45827 are Affymetrix arrays while GSE38959 are Agilent array (line 76-84), please indicate more details about data normalization (Line 96).
6.	In section “DEGs in non-TNBC and TNBC samples”, Please submit the full list of differential expression genes (at least 161 common DEGs)  as supplemental files.
7.	The authors validated the correlation between NUF2/FAM83D and TNBC only by real-time PCR, however,  it still needs more evidence to make a conclusion that NUF2 and FAM83D are TNBC biomarkers. It will be very helpful if you can present histological evidence (you already have clinical samples, line 85) OR in vitro assay, for example, you may confirm the function of NUF2 and FAM83D on TNBC cell lines (if possible).


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

Input:
Title: IDENTIFICATION OF NUF2 AND FAM83D AS POTENTIAL BIOMARKERS IN TRIPLE-NEGATIVE BREAST CANCER
Review round: 1
Reviewer: 3

Output:
Basic reporting: Are NUF2 and FAM83D really a novel biomarker? Novel means that these genes have not identified as a biomarker yet but in previous studies eg. https://pubmed.ncbi.nlm.nih.gov/31140425/, https://www.spandidos-publications.com/ijmm/44/2/390, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823109/
, it has been shown that the prognostic significance of these genes. Suggest removing the word ‘novel’.

In the abstract, the author mentioned the need of identifying ‘effective biomarkers’ to diagnose or determine the prognosis of TNBC. However, this study merely reports the potential biomarkers. Further studies are needed to determine if the reported biomarkers are useful for diagnosis/prognosis. Consider revising some of the words/sentences in the manuscript as some might sound like an overstatement.
Experimental design: In line 88: the author mentioned ‘no important organ disease’. Please specify the example of organ diseases as the exclusion criteria.

Line 105-6: is the sentence a repetition? Shouldn’t it be ‘intermolecular interactions and intermolecular networks’?

Line 135-6: Why the need for the experiment to be repeated (independently) for more than 3 times? 14 pairs of TNBC samples were used, do you mean experimental replicates were done more than 3 times. If yes, why is this so because the replication level of your experiments will have an impact on the statistical tests.
Validity of the findings: Although the results from this study show no correlation between CENPH and TNBC, the author may discuss or elaborate more on the role of CENPH in other types of breast/other cancers.

The summary in line 244 is quite weak and inconclusive.

The language used in this manuscript needs to be improved; there are a few grammatical errors throughout the manuscript.

The manuscript lacks new information. My suggestion would be to further study the functional role of each potential gene identified in this study to reach a fair conclusion.
Additional comments: No additional comments


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

Input:
Title: IDENTIFICATION OF NUF2 AND FAM83D AS POTENTIAL BIOMARKERS IN TRIPLE-NEGATIVE BREAST CANCER
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have answered all comments
Experimental design: Authors have answered all comments
Validity of the findings: Authors have answered all comments
Additional comments: Authors have answered all comments


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

Input:
Title: IDENTIFICATION OF NUF2 AND FAM83D AS POTENTIAL BIOMARKERS IN TRIPLE-NEGATIVE BREAST CANCER
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Zhai et al. submitted the revised manuscript ”Identiﬁcation of NUF2 and FAM83D as Potential Biomarkers in Triple-negative Breast Cancer”, the revised manuscript has great improvement, in which the authors corrected the typos and rewrite some phrases, and provided more detailed data to support their conclusion. They addressed all my concerns. I would like to recommend the manuscript to “accept”.


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

Input:
Title: CONFIDENCE INTERVALS FOR THE COMMON COEFFICIENT OF VARIATION OF RAINFALL IN THAILAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: Comment to the Authors
Title: A common particulate matter dispersion in Thailand using confidence intervals for common coefficient of variation

This paper introduces the confidence intervals (CIs) for the common coefficient of variation (CV) of log-normal (LN) distributions based on four methods: the fiducial generalized method, the adjusted method of variance estimates recovery (adjusted MOVER), computational method, and Bayesian method. All CIs were conducted using simulations in terms of coverage probability (CP) and average length (AL). An example on PM2.5 from a part of Thailand is applied. I really appreciate the authors use the real data on air pollution (PM2.5) that are a current problem in many countries. The title of this paper is suggested to be “Confidence interval for the common coefficient of variation of PM2.5 in Thailand”. I still have the major comments as follows.
1.  The authors note in abstract that the common CV is usually used to COMPARE the dispersion of data from different populations. I do not understand. In fact, the common CV is a measurement that used to ESTIMATE the true parameter from k populations.  So, this estimator cannot use to compare the dispersion of many populations. Please make clear this point first.
Moreover, I suggest the authors point out the important issue in the manuscript that why it is of interest in the common CV, instead of compute the CV for each population. I say this because in applications the mean, variance, or CV of PM2.5 in the area is usually estimated. We can compare the values, i.e. CV, obtained from each area, which area has highest dispersion. If we compute the common CV for k areas (where each area may far away, as the provinces that used in this work), what can we interpret the result. This should clearly explain at the beginning section, and conclude when using the real data, not give only just the values.
2.   In the last paragraph of introduction section, the authors note that the CIs introduced in this manuscript allow heterogeneous LN distributions.  However, I think one method on page 7 is based on homogeneity case, where the ML estimator for \theta has been derived under \theta_i = \theta for i = 1,2,…,k. This is not the heterogeneity situation. Could the authors explain?  On the same page, please check the notation Y_i.
3.  The details in the top of page 4 are very common. They have been shown already in papers of Applied Mathematical Sciences, Vol. 7, 2013, no. 77, 3805-3810 and of Journal of Statistical Theory and Applications, Vol. 16, No. 3 (September 2017) 345-353. So, I recommend not to use the theorem, but leave them just information.
In this section, the common CV has been noted as \theta, computed based on the variance in population I, NOT from all available populations. If so it is not the population common CV. Moreover, I do not agree that Eq.7 (\hat{\theta}_i) is the estimator of the common CV for k populations, it is the same reason given before. Also, the formula in Eq.7 is different from the common CV (theta) used in R-code. It must be checked.
4.  Please define \bar{X}_i^* and S_i^*
5.  This paper lacks of prior knowledge, background, and well explain before derive and construct the CIs. I think it is very important and give a good motivation when we propose the new theory.  The authors should provide more details about Eqs.11, 12, and 15: its properties and the conditions of the fiducial generalized pivotal quantity. In a sentence, “…Equation (12) satisfies two conditions …” what is that two conditions? It is so important. For MOVER method, Eqs.17-22 are used for two populations, not for the general k sample cases where it is of interest in this paper. Furthermore, what is the idea to choose prior and posterior distributions in the Bayesian method?  Many equations in the statistical methodologies are obtained from previous papers without explication.
6.  Is \theta_{BS} in Eq.37 is the parameter of interest?
7.  How to set the simulation settings? What are the true common CV of LN distributions used in simulations? The situations considered in this work cover possible values of CV in LN? Moreover, the authors claim that the results obtained from the real data in Example 1 and Example 2 confirm simulation results. I recommend that we can say if those two works (in simulation and in illustrative method) have the same situation or related situation. See the sample sizes, standard deviations and common CVs given in Tables 1-2, compare to Tables 3-4. They seem to be different.  Also, I would like to see the true common CV, and please calculate the estimated common CV (point estimator) using simulations.
In many cases in simulations, the average CPs are 1. However, the coverage level of 95% is set. So that the value of simulated CP is too higher than the target value. Could more details be provided here and please the authors explain why the CI in such a case still performs well?
8.   The data used in application section are interesting. However, I am wondering why the authors use the data collected from the different time and why not use the data until 2020. Is there any limitation? Could the author explain? A little bit, please re-write the title of histograms and QQ plots. It should be “Histogram of PM2.5 in …… province”
I understand that the lowest AIC means the data fit for the LN distribution than the compared distributions. However, to make sure that the data follow the LN distribution, please use the hypothesis testing (goodness of fit test).
9.  I would like the authors check seriously your R-code (provided separately from the main manuscript) for the MOVER method. The simulation results from this approach presented in the main text are not correct, because R-code is not true. So that please carefully take a look at this point and all your R-codes, as well as conclusions.
10.  At the beginning of the last section, sample size is defined by n, not k.  In your conclusions, the number of case affects the coverage probability. So that I think to the sample case that is greater than 6. What happen with the performance of CIs when k > 6, as k = 10 15 and 20?
Experimental design: NA
Validity of the findings: NA
Additional comments: NA


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: CONFIDENCE INTERVALS FOR THE COMMON COEFFICIENT OF VARIATION OF RAINFALL IN THAILAND
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper makes an interesting contribution for confidence intervals for the common coefficient of variation for particulate matter as indicator of auir pollution in Thaiand.
Experimental design: data are routinley collected data.
Validity of the findings: in general, the findings are of interest and it is valuable to know what works and what not.
Additional comments: There are many detailed comments on the annotated manuscript.

The paper needs to be revsied. At the moment, the writing assumes that the reader knows already what this is about.


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: CONFIDENCE INTERVALS FOR THE COMMON COEFFICIENT OF VARIATION OF RAINFALL IN THAILAND
Review round: 1
Reviewer: 3

Output:
Basic reporting: Authors may be referring to smog instead of fog in lines 28-30

All the statements in lines 28-38 would benefit form a reference

Across the article, authors use the term dispersion in its statistical sense (i.e. the spread of the probability distribution, the relative standard deviation) such usage is confusing. Authors are encouraged to use a different syntax given that "dispersion" of particulate matter is a well described physical process -e.g
https://doi.org/10.1175/BAMS-D-14-00110.1 (see line 67 for a standalone example)

It is not clear if the authors are describing their work, or a pre-existing methodology in lines 65-66.

Authors may want to provide more relevant examples of using the log-normal distribution to model particulate matter rather than size of silver particles in a photographic emulsion...etc in lines 44-49. The same comment for examples of using the coefficient of variation in lines 57-64 where the authors cite usage examples in the fields of hematology and serology, finance, and medicine.

It is not evident why the authors go to length stating what studies report on confidence intervals of log-normal distributions (lines 50-56).
Experimental design: Authors state that the log-normal distribution is used to model right-skewed data (39-40) without stating (or citing) that PM2.5 measurements are right skewed.

In line 67, authors assume that measurements of PM2.5  are samples collected from independent log-normal populations with a common coefficient of variation with different variances. It is not clear how and why the authors make such assumptions, authors did not provide enough evidence to justify this assumption in subsequent statements.

The authors did not clearly state how their work fills a knowledge gap. There is no previous literature on applying their methodology to PM2.5 concentration measurements, authors propose "novel approaches for the confidence interval estimation of the common coefficient of variation of lognormal distributions" without considering the log-normality of PM2.5 concentration measurements in literature.
Validity of the findings: The dataset used is not referenced in time. It is simply a series of measurements (11 measurements in Sop Pat,16 measurements in Ban Dong, and 15 measurements in  Mae Mo, and around 25  measurements in each of Chiang Mai, Lampang, Chiang Rai, Nan, Lamphun, and Phrae). Any inference made on such small datasets without taking the temporal spread into account is doubtful.
Additional comments: This work is better placed in statistics. It uses PM2.5 measurements as a dataset like any other to infer on statistical application.
Given measurements of PM2.5, physical dispersion models are able to solve for spacio-temporal PM2.5 levels. This work, and in order to better describe (forcibly atemporal) PM2.5 measurements, presupposes as true, underlying assumptions that need validation. These assumptions are:
- PM2.5 measurements is a stochastic process that can be modeled as a log-normal distribution
- PM2.5 measurements across different areas are independent but have a common variance
- PM2.5 measurements made in different time periods in different geographical locations are comparable


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: CONFIDENCE INTERVALS FOR THE COMMON COEFFICIENT OF VARIATION OF RAINFALL IN THAILAND
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thank you so much for the response. I still have only a comment. Could the authors check your R-code (from supplemental material) in the following? I understand that qnorm() that the authors used gives the lower percentile.

#-------------------------------------------------------------------------------------------------------------------
# Compute CI based on MOVER
#-------------------------------------------------------------------------------------------------------------------
z <- qnorm(alpha/2) 				    		# compute z at alpha/2

Please check also your results from this.
Experimental design: no
Validity of the findings: no
Additional comments: no


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: CONFIDENCE INTERVALS FOR THE COMMON COEFFICIENT OF VARIATION OF RAINFALL IN THAILAND
Review round: 2
Reviewer: 2

Output:
Basic reporting: ok
Experimental design: na
Validity of the findings: ok
Additional comments: Thank you for doing such a very careful revision.


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

Input:
Title: CONFIDENCE INTERVALS FOR THE COMMON COEFFICIENT OF VARIATION OF RAINFALL IN THAILAND
Review round: 2
Reviewer: 3

Output:
Basic reporting: Statement "In meteorology, the coefficient of variation has been used to describe the dispersion of PM2.5"  lines 84-85 can benefit from a reference

The work might also benefit from some further english editing
Experimental design: Authors have added "For measurements of PM2.5, physical dispersion models are able to solve for spaciotemporal of PM2.5 levels if the following three assumptions are satisfied: (i) PM2.5 measurements is a stochastic process that can be modeled as a log-normal distribution (ii) PM2.5 measurements across different areas are independent but have a common variance and (iii)  PM2.5 measurements made in different time in different geographical locations are comparable." lines 90-95. Authors have misunderstood my comment.

My comment was: "This work, and in order to better describe (forcibly atemporal) PM2.5 measurements, presupposes as true, underlying assumptions that need validation. These assumptions are: i) PM2.5 measurements is a stochastic process that can be modeled as a log-normal distribution, ii) PM2.5 measurements across different areas are independent but have a common variance, and iii) PM2.5 measurements made in different time periods in different geographical locations are comparable"

This work will only be valid if the authors can prove these assumptions are correct. It is my belief, however, that these assumptions do not hold. I will expand on the assumptions here:
i) In order for the author's research to be valid, they should be able to prove that PM measurements is a stochastic process that can be modeled as a log-normal distribution. The authors cite Rumburg et al. (2001) as the sole example of using log-normal distribution to fit PM measurements. However, Rumburg et al. (2001) estimated the distribution parameters for a single location based on hundreds of measurements over the period of several years. In this work the authors use at most 25 measurements per location in 9 separate locations without regard to the dates in which the measurements were taken.

ii) The authors assume that PM2.5 measurements across different areas are independent but have a common variance, whereas they actually don't. Some PM sources are intermittent in nature and some are more constant. Therefore depending on what sources affect the particular location, the variances will be different.

ii) Ambient PM concentrations are affected by a multitude of well studied sources and sinks, and as such measurements made in different time in different geographical locations are not necessarily comparable. Again, in Rumburg et al. (2001), the only similar work the authors cited, one location is taken in consideration and the result are only assumed valid for that particular location. In this work, the authors present as comparable distributions fitted from different locations, taken at probably different times, and with a very small sample size.
Validity of the findings: The authors propose 4 approaches for the confidence interval estimation of the common coefficient of variation of log-normal distributions (FGCI, MOVER, computational, and Bayesian). Given that the authors were not able to ascertain the validity of necessary underlying assumptions, the validity and the value of applying these approaches to PM measurements is not clear.
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: Θ-SEIHRD MATHEMATICAL MODEL OF COVID19-STABILITY ANALYSIS USING FAST-SLOW DECOMPOSITION
Review round: 1
Reviewer: 1

Output:
Basic reporting: I write my comments as an attached file. Please see the attached file.
Experimental design: I write my comments as an attached file. Please see the attached file.
Validity of the findings: I write my comments as an attached file. Please see the attached file.
Additional comments: Review report paper number: Theta SEIHRD mathematical model of Covid19-stability analysis using fast-slow decomposition (#49600).

The paper is very interesting and important from a practical point of view, especially these days and periods.
The paper deal with the application of the singular perturbed vector filed (SPVF) to the theta SEIHRD mathematical model of Covid19. Stability Analysis using a method to decompose the mathematical model into fast-slow subsystems.
Before the publication/ accepted the paper needs a major revision.
The authors (3 authors) should address the following comments to the above paper:
-	  The abstract is very short and not include all the results presents in the paper. I think that the abstract should include all the main results of the paper.
-	What is the meaning of the result: "almost 96 percent"? The authors need to be correct!
-	I'm not sure that the title is adequate for the main content of the paper. They should be more specific.
-	The introduction is very clear but it seems that it divides into two parts that the connections between these two parts are missing. The first part deal with the review of the COVID-19 and the second part deal with the review of the SPVF. ILDM, CFD, QSSA, etc. which are a method applied to complex ODE and PDE systems. The authors need to connect between these two parts presents in the introduction.
-	In addition to the above comment, the introduction includes a subsection of stability analysis. Which also needs to be connected to the above two sections present in the introduction.
-	The initial conditions of the mathematical model should be present explicitly.
-	The authors present the parameters used in order to solve the mathematical model of COVID 19. But the initial conditions present as a segment and not as one point. So, I ask how the authors solve the model? The need to take one point at each segment of the initial conditions.
-	The functions present in equation 17 need an explanation in detail.
-	Line 132: " We apply the steps of the algorithm present at 1-8" where is the algorithm.
-	If the authors transfer the mathematical model using new coordinates so what are the SMALL parameters of the "new" mathematical model at the new coordinates?
-	What is the meaning of the vector present at equation 25?
-	The authors claim that the stability of the equilibrium point does not change with the linear transformation. This needs to be proved and present in the paper.
-	Line 184: " table ??. At table ??"
-	The discussion section needs to be extended.
-	The graph present at the paper needs to explain in detail as well as the tables present in the paper.
-	The list of references should revise according to the journal format.
-	The article should undergo English language editing. There are a few grammatical errors.


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: Θ-SEIHRD MATHEMATICAL MODEL OF COVID19-STABILITY ANALYSIS USING FAST-SLOW DECOMPOSITION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is important to predict the number of infected people by covid-19 using mathematical tools. The authors present the mathematical model called Theta SEIHRD model and analyzed the stability of the equilibrium point of the model after the application of the SPVF method.
Why do the authors need to transfer the mathematical model into new coordinates using the eigenvectors of the vector field of the model? They can't investigate the stability of the equilibrium points of the model directly?
The authors should present the graph of the original system as well as the graphs plots of the new model and compared the results.
Nomenclature needs to add the article with its relevant units.
The authors should explain every equation and its expressions and the connections of each dynamical variables of the model.
The abstract need to extend.
Why the authors present subsection of stability analysis at the introductions? This should be a part of the mathematical formulation section.
The algorithm of the SPVF maybe introduces in the article.
The methods ILDM, QSSA, and so on are not relevant for this article since they are asymptotical methods and the SPVF is an algebraic method to transfer the model and present a given mathematical model in new coordinates where at the new coordinates the model can be decomposed into the fast and slow subsystem.
What are the small parameters of the new model?
How the GAP of the eigenvalues indicated the fast and slow system?
The system written in equation (24) is not clear for the reader. Please clarify this system of ODE equations as well as the initial conditions.
The initial conditions of the model are given as a segment. How the initial condition of the model transfer under the eigenvector's transformation and present at the new coordinates?
Equation 29 not clear.
table ??. At table ?? not clear.
Why equation 30 as well as the other equation presents the relative error of the given governing equations.?
Experimental design: The authors didn’t use and prove any results in accordance to the lab. As I understand they are a theoretical researcher. But they can compare their results to experimental results present at the relevant literature.
Validity of the findings: The authors present and compare their results to the numbers that report by the authority of China. The results as present at the Tables the stability analysis of the equilibrium points of the considered model are relevant and they validate their results.
Additional comments: The article is important and can be published at the respectable journal PeerJ but need a major revision. Please take care of my comments very carefully and revise the article in accordance with the PeerJ journal format and criterions.
In addition, the paper needs professional English editing.


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: Θ-SEIHRD MATHEMATICAL MODEL OF COVID19-STABILITY ANALYSIS USING FAST-SLOW DECOMPOSITION
Review round: 1
Reviewer: 3

Output:
Basic reporting: Please see my comments at the file
Experimental design: I attached a file with comments
Validity of the findings: Please see my comments at the file
Additional comments: Please see my comments at the file


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: Θ-SEIHRD MATHEMATICAL MODEL OF COVID19-STABILITY ANALYSIS USING FAST-SLOW DECOMPOSITION
Review round: 2
Reviewer: 1

Output:
Basic reporting: Ok
Experimental design: Ok
Validity of the findings: The authors revised the paper
Additional comments: The authors revised the paper but there are still comment that should be addressed before publication:
1: The NOMENCLATURE is not complete
2: The graphs of the governing equation are missing
3: The plot graphs of the new model after that the authors applied the SPVF method are missing
4: The connections between the solution profiles of the model and the "new" model should be present in details at the paper
5: The paper needs English editing.
Good luck


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: Θ-SEIHRD MATHEMATICAL MODEL OF COVID19-STABILITY ANALYSIS USING FAST-SLOW DECOMPOSITION
Review round: 2
Reviewer: 2

Output:
Basic reporting: I write down my comments to the editor and the authors
Experimental design: I write down my comments to the editor and the authors
Validity of the findings: I write down my comments to the editor and the authors
Additional comments: The draft of the paper includes all my comments that I wrote previously. There is some issue that should be addressed before the publication of the draft paper:

1: The title should be more correctly specific to China's case. If the authors want to write some general cases they should be compared their results to other countries around the world. Then the paper will be more general.
2: The keywords are generally. They should be more specific to the paper.
3: Units are missing for the Nomenclature.
4: The authors need to explain from where did they get the functions present at Eq. [12]
5: The list of references should be revised according to the journal format.


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: Θ-SEIHRD MATHEMATICAL MODEL OF COVID19-STABILITY ANALYSIS USING FAST-SLOW DECOMPOSITION
Review round: 2
Reviewer: 3

Output:
Basic reporting: The authors have corrected the article taking into account my comments.
Experimental design: The authors have corrected the article taking into account my comments.
Validity of the findings: The authors have corrected the article taking into account my comments.
Additional comments: The authors have corrected the article taking into account my comments.


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

Input:
Title: DEVELOPMENT OF A CAMERA TRAP FOR PERCHING DRAGONFLIES: A NEW TOOL FOR FRESHWATER ENVIRONMENTAL ASSESSMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: It is my opinion that the manuscript conforms to the standards of reporting in the field.

As I have essentially no electronics expertise, I don’t feel especially qualified to comment on the description of the camera trap itself. However, for what it’s worth, I was able to follow along such that I feel I could replicate their set-up if I wanted to. Perhaps someone with more direct experience with camera traps will feel differently about this section.

The introduction and background provided nice context and cited appropriate literature. The raw data was supplied. I think the content of the figures is nice, though 8 seems kind of excessive for this manuscript and I wonder if there might be ways to combine them.

I have some structural comments that I think will improve the readability of the manuscript, which I elaborate on below, but in general I did not have huge complaints here.
Experimental design: This is original primary research within the scope of the journal.

The research question—can camera traps be used to monitor dragonfly assemblages—is meaningful and relevant. I might personally frame the “hypothesis” that they state on L92-97 differently to reflect the simplicity of this question a bit better, but otherwise I think the question is valid.

I do have some concerns about the rigor of some of the methods, which could simply result from a lack of detail in the methods. I do not think that any of these concerns invalidate the general utility of the camera-trapping method, but I think they may cause the authors to re-consider some of the stated benefits.

1)	In my experience doing behavioral surveys of percher dragonflies, it is not uncommon for an individual on a perch to take off and: 1) fight with a rival; 2) patrol its territory; and 3) mate with a female. After this, the dragonfly will often return to the same perch within its territory. Perhaps this is a reflection of the species I have personally studied, but my experience is that oftentimes a single individual will return to a perch within its territory well after 20 seconds has elapsed. As a result, I wonder what their metric of “perching events” is really conveying it seems to me that this could often be the same individual (L231-241). Similarly, if two individuals fight over a territory, and the previous territory-holder loses, then a new individual could plausibly take over the territory and land on the same perch before 20 or even 10 seconds has elapsed. This case wouldn’t register as a new perching event even though it is.

Although none of this will affect the ability of this method to be used for characterizing the presence/absence of a particular species in a particular location, I do wonder about some of the broader inferences the authors seek to make with this kind of method eventually (e.g. L222-226, L304-325). Of course, I feel that even just detecting presence/absence is still very useful and valuable, but certainly it’s also less useful than methods that could eventually be harnessed to provide some estimate of population size. If it is the case that the natural history of the focal species negates these concerns, the authors should state that while also keeping in mind how reliable this method may be for other perchers. One thing that might help is if the authors provide some more detailed information on how sensitive the results are to extending the interval time far beyond 20 seconds (L235-237).

2)	The authors take two critical steps to evaluate the robustness of the camera-trapping method, which I appreciated. First, to examine how many “false negatives” the authors were getting from this camera-trapping procedure, I believe (though am not certain) that the authors set up a video camera that continuously monitored the perch to assess how frequently individuals landed on the perch but were not detected by the trap (L216-220). Although I commend the authors for undertaking (what I imagine was) this hugely labor-intensive validation of their camera-trapping method, I felt this section needs considerably more detail. In part, the fact that it is lumped into a paragraph that included many other methods made it not immediately obvious that this was what the authors were describing. Second, the authors also collected census data at their sites to assess if the number of perching events was related to the number of individuals observed by an experienced observer (L222-226). The purpose of this method also wasn’t immediately obvious to me as I was reading it. Moreover, I could not replicate their methods here if I tried. I have a couple of suggestions for improving how these key elements are presented.

a.	First, under the subheading CASE STUDY, I would recommend that the authors create a new separate section for the video monitoring procedure and then another separate section for the census. This will help alert readers to the fact that these methods are being conducted, and I think will help the authors describe more clearly about what these methods are for.

b.	In the new sub-section for the video monitoring, I’d recommend that the authors begin by stating exactly what this method is for. Then describing the method in detail. Particularly, I would be keen to know more about how the videos were checked thoroughly and matched up to the camera-trapping pictures to get an estimate of false negatives. I would also move the statistical analyses that accompany this validation directly into this section. Here, the authors should provide a clear statement of what prediction is being tested, how it is being tested analytically, and what the readers should expected to see reported if the predictions are supported. Concurrently, I would also put the corresponding results for this into a sub-section in the results with a sub-heading that matches the one used here in the methods. In particular, I would personally be interested in an analysis that considers differences in false negatives among the sites, since it looks like only the pond site had many (Fig. 7).

c.	In the new sub-section for the census, I’d recommend that the authors start by providing an explicit rationale for why they did this, as well as what can and cannot be inferred from this method. Then I’d provide a more detailed methodological description of exactly how these 10 min surveys were conducted. For instance, how did the authors move around the site (or did they stand in a single location?). How did the authors ensure that individuals weren’t counted more than once? Was the order in which the sites visited randomized to ensure that site wasn’t confounded with time of day? Then, as with the other new subsection, I’d recommend moving the statistical analyses that accompany these methods into this new subsection. Here again, the authors should provide a clear statement of what prediction is being tested, how it is being tested analytically, and what the readers should expected to see reported if the predictions are supported. Lastly, I would make a corresponding sub-heading in the results to match this new sub-section in the methods.

3)	It’s not at all clear to me how the relationship between the detection frequency and observation was analyzed (L278), or what that relationship even is telling us really. I took it to mean the correlation coefficient between the number of perching events at a site and the cumulative frequency of observed dragonflies at that site. If so, n=3 for this analysis, which is not very large for evaluating one of the main stated goals of the paper (L105-107). At any rate, the authors need to clearly state what this test is, what it is for, and report the full statistical output (is this pearson’s or spearnman’s correlation? What is the test statistic with degrees of freedom and the p-value? Etc.).

I also wonder if this is really the best way to look at this relationship given that this small sample size will almost never show a “significant” relationship. I think that a large number of readers will be interested in whether or not camera-trapping could plausibly be used to estimate population size, so I think it would be helpful for the authors to explore the possible benefits and limits as fully as they can. Another way of looking at the data is that the authors have 6 censuses at each of their three sites. If we ignore the non-independence for the moment (we’ll come back to it), there could be 18 total datapoints rather than three. Koenig & Albano (1985, Am. Midl. Natl.) and Moore & Martin (2016, J. Evol. Biol.) found that the average duration over which individuals typically held reproductive territories was ~1.5-2.5 hours, so is there some way to evaluate detection frequencies from the camera-traps in the 1-3 hours around when each census was taken at each site? This would also allow the authors to have match the observations from the camera-trapping method to the in-person observations and perhaps get some estimate of real-time dragonfly activity. To control for the non-independence of site, the authors could consider analyzing this relationship using a mixed-effects model with site as a random effect.

4)	L212-215. Please provide more information about the field and pond sites. For example, how large are each of these sites? What vegetation is available for the dragonflies to perch on?

5)	L269-271. Is “false positives” a typo here? In the preceding paragraph, the authors say that there were no false positives, and here they say there were many. Since I can’t find the actual number of false negatives anywhere, I wonder if this is what the authors mean? If not, the authors should clarify what they are talking about here, and also directly report the number of false negatives that occurred in text somewhere. It is available in Fig 7, but I think it would be good to have it in text as well.
Validity of the findings: The analyses are mostly appropriate, though, as noted above, could use more description.

Other than the concerns I stated above, I thought the authors did a reasonable job interpreting their results. In future versions of this article, I’d like to see some discussion of how the concerns I raised above influence how the interpretation of data from this camera-trapping technique.

One additional thing I wonder about is that, given that the pictures from the camera-trap are predominantly capturing the ventral side of the dragonfly, what is the broader capacity of this method to discerning among different species (L263-266; figs 2b, 4d)? The authors say they are able to distinguish some species based on wing markings, which is great, but not other species without wing markings. I would like to see some more discussion about the implications of this method if it is difficult to distinguish between most anisopterans.
Additional comments: The submitted manuscript (“Development of a camera trap for perching dragonflies: a new tool for freshwater environmental assessment [#42325]) reports on a novel technique for detecting the presence or absence of perching dragonflies at an area.

I enjoyed reading and thinking about this mostly well-written manuscript. Although I think some revisions are necessary, I believe it could eventually be a nice addition to the literature. In the other sections, I provide my comments on the manuscript following the preferred format of the journal.


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

Input:
Title: DEVELOPMENT OF A CAMERA TRAP FOR PERCHING DRAGONFLIES: A NEW TOOL FOR FRESHWATER ENVIRONMENTAL ASSESSMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: This well-written and very interesting manuscript describes a novel apparatus and technique for documenting perching dragonflies. The authors correctly note that this type of technology is quite advanced already for larger animals, but existing methods can’t adequately document insects. I think their device will be extremely useful for dragonfly taxa that perch—in their study, they focus on Sympetrum, but there are many other perching dragonflies that could be detected with this approach. I think this manuscript will make a valuable contribution to the study of larger insects globally. Most of the figures are very useful to the manuscript, but below I provide some specific feedback for figures 6-8.
Experimental design: The authors are to be commended for explaining the technical set-up as simply as possible for a general audience. Although I have no technical expertise in the types of electronics used in the study, I was mostly able to follow their descriptions. In addition to designing, building, and testing the apparatus, the authors deploy the apparatus in three different settings and use a secondary time-lapse camera as well as expert observers (dragonfly ecologists) to test the sensitivity of the device (e.g. false positives and false negatives)—which is an excellent approach.
Validity of the findings: In general, the authors do a good job providing a proof-of-concept for the apparatus. However, I’m a little confused about the statistical approach of this manuscript. Why is the main question of statistical interest whether the “probability of dragonfly occurrence is equal between sites” (line 246)? The authors test their apparatus at three sites-- a pond, an open field, and a building rooftop—which are very dissimilar to one another and in what resources they could provide for dragonflies. What’s the ecological reasoning for assuming an equal distribution of dragonflies among these three sites? I would assume from the start that there should be an unequal distribution across these sites—because the rooftop would not have much to offer in terms of food or habitat. And why is that question of interest for the proof-of-concept for the apparatus? It seems like the real question here is if the efficiency or accuracy of the device differs in these three settings (e.g. number of false negatives relative to true positives; or the frequency of false positives compared to true positives) -- but it doesn’t seem like that’s what this manuscript’s statistics address. I would like to see some additional clarity and justification for the authors’ current approach if it is to remain, and would suggest they think deeply about what they’re asking and why—and perhaps adopt a different statistical approach based on that. Finally, it would be valuable to statistically compare the densities/frequencies of dragonfly sightings from the human observers to those of the apparatus— relative comparisons are made in the Discussion section, but this could be addressed quantitatively too.
Additional comments: Minor comments:
Line 161—“a continuous perching signal for Z seconds was required” – what do the authors mean here by ‘Z seconds’? It becomes apparent later in the paper, but should be explained better here.

Line 225—was the cumulative number of dragonflies observed really used as the “frequency of dragonflies observed”? It seems that this should be expressed as a unit of abundance over time, e.g. # of dragonflies observed per minute or per hour.

Line 254—“Add your materials and methods here.” ??

Figure 6 through 8-- formatting looks unprofessional (e.g. inconsistent fonts types and sizes)

Figure 8—make the y-axes the same, need more info in caption to make it standalone

Line 288—citations?

Line 297—why is a value of “a few tens of false positives” considered “very low”? Especially considering the relatively low number of true positives (e.g. only 50 true positives at the pond site)


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

Input:
Title: DEVELOPMENT OF A CAMERA TRAP FOR PERCHING DRAGONFLIES: A NEW TOOL FOR FRESHWATER ENVIRONMENTAL ASSESSMENT
Review round: 2
Reviewer: 1

Output:
Basic reporting: I continue to be pleased with the basic reporting of this manuscript and believe that it adheres to standards of this journal.
Experimental design: The authors have addressed all of my previous concerns for this section, and I believe the manuscript meets the standards of the journal.
Validity of the findings: The authors have addressed all of my previous concerns for this section as well, and I believe the manuscript meets the standards of the journal.
Additional comments: I commend the authors for their substantial revision of the manuscript, and I look forward to seeing this manuscript published soon. I have only a few (very minor) outstanding comments about wording that the authors might consider prior to publication.

L231-232. "For photos obtained within a few seconds, the first was removed from the analysis". I think a word must be missing here. This is for instances where there are multiple photos within a few seconds, correct?

L337-349. These two sections report on different components of the overall project, and I think it would be helpful if the first sentence of each section re-stated what the ensuing results are in reference to. For instance, L342 starts by immediately describing the number of true positives in the field study. However, the sentence that immediately preceded it (in the previous section) described the number of false positives. As I was reading this, I initially reacted by adding those numbers together in my head and thought that the number of false positives vastly exceeded the number of true positives. Having a sentence at the beginning of each section that just briefly restates what the goal of each section is will help readers remember that the results refer to totally different contexts.

L397-398. "The GLMM analysis showed that camera detection was related to the population density, as measured by the census data; however, the opposite was not true." To clarify the directional nature of these statistical relationships, I would recommend changing this sentence to "The GLMM analysis showed that camera detection predicted population density, as measured by the census data; however, the opposite was not true."


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

Input:
Title: DEVELOPMENT OF A CAMERA TRAP FOR PERCHING DRAGONFLIES: A NEW TOOL FOR FRESHWATER ENVIRONMENTAL ASSESSMENT
Review round: 2
Reviewer: 2

Output:
Basic reporting: This revised article represents a good improvement over the first iteration.
Experimental design: I appreciate the work that the authors have done to improve the clarity of the statistical approaches in this revision. I'm still a little uncertain as to why the goodness-of-fit tests are included to compared differences in detections among sites, since there is no reason to think that these three sites (field, pond, rooftop) would have similar numbers of dragonflies anyway, but that's okay. The authors clearly describe the patterns of false positives, and the relationship between the trained observer and the dragonfly camera (with the new models they added), so the important aspects are covered well. And the lack of false negatives in the entire study is very encouraging for the approach.
Validity of the findings: For the most part, the authors do a good job talking about the limitations of the study, and addressed well the concerns that both myself and the other reviewer had about the previous version of this manuscript. My final suggestions would be to:

(1) be careful when talking about the future uses of this approach. For example, in line 457, the word "perching" needs to be inserted before "insects". This approach is very promising and exciting, but it only applies to perching insects and not any others. This is highlighted by the fact that the rooftop site did indeed have dragonflies (I think 8 were observed in flight by the human observer), but none were detected by the camera because none perched. So be careful here and throughout to qualify the approaches use with "perching".

(2) highlight the issue with 'false positives' a bit more in the discussion when talking about limitations of this novel and exciting approach. The rate of false positives due to sun or clouds was pretty high at times, so it seems like a goal for follow up studies should be to reduce that rate of false positives before trying to use this approach widely.
Additional comments: I am excited to see this technology and approach develop further to enhance our understanding of perching dragonflies and other insects!


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: DIFFERENCES IN SMALL NONCODING RNAS PROFILE BETWEEN BULL X AND Y SPERM
Review round: 1
Reviewer: 1

Output:
Basic reporting: DNA data checks
Have you checked the authors data deposition statement?
Yes, the authors indicate the data deposition as accession codes PRJNA624261 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA624261/) in the GEO datasets in the topic “Preprocessing of small noncoding RNA data” of the revised manuscript.
Can you access the deposited data?
Yes, the above-mentioned data can be easily accessed via https://www.ncbi.nlm.nih.gov/bioproject/PRJNA624261/.
Has the data been deposited correctly?
Yes.
Is the deposition information noted in the manuscript?
Yes, as appears in line 152-155 of the revised manuscript.
1. BASIC REPORTING
1. From the original version of this manuscript, the authors received the comments on professional English language. In the current one, the usage of English language has greatly improved. The proof reading of the manuscript has been made to correct typographical and grammatical errors.
2. The authors indicated the data deposition as accession codes PRJNA624261 in the Sequence Read Archive (SRA). Those raw data are now available through the NCBI Gene Expression Omnibus.
3. Details of the piRNA cluster have been added to Introduction, Methods, and Discussion.
Experimental design: 1. The authors have consistently used the term “abundance” in place of “expression” to describe the presence of sperm-borne sncRNA in their data. Similarly, the use of “differential accumulation” instead of “differentially expressed” throughout the revised manuscript is corrected.
2.  To verify the enrichment level of X and Y bearing spermatozoa in the current study, the authors have added the statements in line 112-119 of the revised manuscript to show the detailed method of sort reanalysis and thus provided with reference. The use of aforementioned method is certainly recommended, and the study design allows it. The results of resorting procedure are quite acceptable, as shown in Table S1. Using this approach, the replication of information could be achieved by another researcher.
3. The RNA integrity number (RIN) of 2.4-2.6 (in the current study) is quite controversial whether they are already degraded or not. Most RNA-seq experiments rely on the RIN above 5 to be considered as high quality RNAs. From Georgiadis et al (2015), they considered that the mature sperm samples have RIN of 2.7 are poor quality for downstream application. It will be better if the authors could provide some pictures of FastQC for raw sequence data.
Ref: http://dx.doi.org/10.1016/j.juro.2014.07.107
Validity of the findings: 1. The real-time PCR experiments (qPCRs) to validate the findings of abundantly presence of miRNAs were conducted and the results are included in the revised version of the paper. The methods (Quantitative real-time PCR (qPCR) validation of the sequencing results) and results are shown in line 210-219 and line 343-348, respectively.
Additional comments: The typo errors of previous version of manuscript have already been solved. However, a few typo and punctuation errors, such as (HOSSAIN et al. 2001; Penfold et al. 1998) of line 50-51; using the sort reanalysis method(Welch & Johnson 1999). of line 111 are found in this version.


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: DIFFERENCES IN SMALL NONCODING RNAS PROFILE BETWEEN BULL X AND Y SPERM
Review round: 1
Reviewer: 2

Output:
Basic reporting: Zhou et al described the difference of sncRNA between X and Y sperms of the bull which may play an important role in the regulation of mature mRNA in fertilized oocytes and subsequent embryogenesis. The general content was well organized with professional English. The figure and table here were suitable and sufficient. I find some mistakes of citation in the text, for example, in line 50, (HOSSAIN et al. 2001) should be edited in the proper format. Please carefully check it throughout MS.
Experimental design: The detailed background and methodology gave were sufficient to understand the main objective. I have some suggestions as below;
(i) The information of bull used in this study should be given in necessary detailed such as age or breed because these factors may influence the DA.

(ii) The author employed NGS with the BGISEQ-500 platform for sequencing; however, the author should provide the reference of the platforms used. Also, RNA integrity must be fall in the high-quality criterion for doing NGS. The author should provide the information on RNA integrity obtained from this investigation in MS. Please specify where these data were detailed in Table S1?

(iii) the author did validation of sequencing result by qPCR for four miRNAs including bta-miR-204, bta-miR-3432a, bta-miR-652, and bta-miR-378. The author gave the information of primers for these miRNAs but I note the primers of each miRNA have only an oligonucleotide. Should they have forward and reverse sense? please verify them.
Validity of the findings: The finding of this study was well-written with a logic style. I have some suggestions a bit in the results section. I find the author provides few discussion points in the result context, for example, in line 270-271, “The RNA integrity number (RIN) was approximately 2.5, which was consistent with previous studies (Mao et al. 2014; Sendler et al. 2013).” and in line 286-288 “A considerable portion of the sperm small noncoding RNA could not be annotated in existing public databases, which was consistent with a previous study (Krawetz et al. 2011).”. These statements should be moved in the discussion parts.

Besides, the author found the difference in tsRNA between X and Y sperm, resulting in tRNA-Ser-AGA and tRNA-Ser-TGA. In the discussion, why this point has not been mentioned?
Additional comments: (i) The scientific name must be written in an italic style, please check in the supplemental table.
(ii) The abbreviation should be written with full name in the first place such as ICSI and MII in the discussion.


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: DIFFERENCES IN SMALL NONCODING RNAS PROFILE BETWEEN BULL X AND Y SPERM
Review round: 1
Reviewer: 3

Output:
Basic reporting: The role of sperm borne sncRNAs are more and more studied as key elements for embryo development, in many species. In bulls, more results have to be produced to paint a clear overview of the content/variation/involvement of these sncRNAs in different biological pathways.
Establishing a comparison of sncRNAs content of X and Y sperm cells, represent an interesting way to increase our knowledge around these elements. Some minor modifications have to be brought to your manuscripts, but to my point of view also some important lacks have to be filled in your study (as the used of adjusted or corrected p values instead p values). The number of significant miRNAs will change and potentially the interpretation of results.
Experimental design: Line 103 : The number/origin of sample are not clear. You talked about 3 bulls, but how many samples? 6 (X and Y fractions for each bulls) or 2 (X and Y fractions polled) ?

Line 124 : “In brief, the samples were thawed on ice and added to TRIzol…..”
Do you started from frozen semen? It was not mentioned on the previous paragraph (semen collection).

How many sperm cells have been used for the total RNA extraction?

According to several works published recently in bovine (example: Sellem et al., 2020), the lysis step of bull sperm cell is quite difficult, and Trizol alone is not enough to lyze properly the cell. Have you met some difficulties with your approach? Have you some pictures of the sperm cell after the treatment?

Line 162 : “…putative known mature miRNAs…”
You have to add the word “and” between putative and known

Line 183: “…By applying thresholds of a P-value < 0.05….”
: you have qualified miRNAs as “differentially expressed” based on the FC and the p-value. Due to the statistic hazards on important number of tests, you will be able to detect a false significant tests (p-value < 5%)…that why it’s important to use the adjusted p-values and not just the p-values. Please to re-analyse your data under this new approach.

Line 187: “Functional analysis of DA miRNAs”.
May I ask you to change the word “analysis” by “annotation”? The work done here was only in silico, while the expression “functional analysis” tent to thing about real lab work.
Validity of the findings: Line 227: “…indicating a lack of foreign RNA in sperm RNA samples…”
Indicating a lack of intact foreign RNA….

Lines 343 to 348: May I ask you to put this paragraph before the one about the identification of DA miRNA?

May I ask you to be less “positive” about the concordance of results between the two technologies? The results for the miR-204 and 652 are not so equal…and they represent the half of your tests.

Line 242: “…A considerable portion of the sperm small noncoding RNA could not be annotated in existing public databases, which was consistent with a previous study (Krawetz et al. 2011)…”
May I ask you more details? “A considerable portion” means how many in your case?
The Krawetz et al., work was published in 2011…The reference database (miRbase) has been updated. May I ask you to compare your results with another publication (example: Sellem et al., 2020)?

Lines 245 to 247: “…In total, 490 and 202 known Bos taurus miRNAs were detected by Unitas and Mirdeep2, respectively… »
It’s not clear….May I ask you to rephrase these 2 sentences?
Lines 247 to 259: Once again, the use of “p value” is not recommended due to the high number of tests…You need to use the “adjusted p value” (whatever the correction applied).

Lines 297 to 313: The number of targets could be very important per miRNA. Do you have applied of filter to choose the most relevant ones?

Discussion
Lines 353 to 357 : “…Previous studies have revealed that adjacent sperm cells can share gene products through intercellular bridges during spermatogenesis, suggesting that miRNA molecules may be shared between X and Y sperm cell during spermatogenesis (Fawcett et al. 1959), which may explain why a part (118) of non-DE small RNAs were identified between X and Y sperm…”
This supposition is too hazardous. Several other explanations could be involved...May I ask you to change your sentences or to bring more details?

Lines 368 to 383: New studies have been published between 2017 and 2020, and especially Sellem et al.,2020 in bull semen. May I ask you to compare also your results to theirs?

Line 413 to 450: We would expect more discussion about the differences between X and Y sperm cells. You have highlighted several interesting genes with your KEEG analysis. So please may I ask you to bring more information about their potential role in embryo development (in a X and Y context)?

Lines 451 to 467: The number of piRNAs identified in your studies is quite different from those obtained in another ones. May I ask you to add some comparisons with freshly published studies?

What about the tsRNAs?  May I ask you to add a paragraph in the discussion part?

Conclusions
You mainly discussed about miRNAs…It’s just a suggestion but maybe you should change the term “sncRNA” into “miRNAs”.
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: DIFFERENCES IN SMALL NONCODING RNAS PROFILE BETWEEN BULL X AND Y SPERM
Review round: 2
Reviewer: 1

Output:
Basic reporting: 1. The typographical and grammatical errors are carefully rechecked by the authors. No obvious errors are found in MS_R2.
Experimental design: 1. From last comments delivered to authors concerning the RNA quality, the plots of per base sequence quality of raw sequencing data by FastQC are given as Additional material 1 in the current revision. Entire raw sequence reads (n = 6) have Phred quality scores above 30 represent the estimated probability of very small error in base calling. Then, the results in this study are reliable. Detailed information on FastQC could be found in the topic “Preprocessing of small noncoding RNA data” in M&M and “Read counts of each RNA class” in the results. I believe that most of my concerns expressed in the previous review has been handled.
Validity of the findings: I have no additional 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: DIFFERENCES IN SMALL NONCODING RNAS PROFILE BETWEEN BULL X AND Y SPERM
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript meets the criteria to accept for publishing in PeerJ.


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: DIFFERENCES IN SMALL NONCODING RNAS PROFILE BETWEEN BULL X AND Y SPERM
Review round: 2
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
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: ENDOCRANIAL ANATOMY OF THE CERATOPSID DINOSAUR TRICERATOPS AND INTERPRETATIONS OF SENSORY AND MOTOR FUNCTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: See general author comments.
Experimental design: See general author comments.
Validity of the findings: See general author comments.
Additional comments: This manuscript presents new data on the cranial endocast for the horned dinosaur Triceratops, based on two previously undescribed specimens. The basic anatomical data are a worthy contribution to the literature, and the anatomical identifications seem accurate based on the provided information. The functional interpretations and numerical analysis need considerable revision, through a deeper engagement with the literature in this area as well as more cautious interpretation of the raw results. For instance, calculations of best hearing frequency for non-avian dinosaurs by necessity must be based upon equations that were often calculated for much smaller organisms. Thus, the size of something like Triceratops may be far outside the range of where estimates can be considered reliable. This is, in part, why the results presented here show negative frequencies for some estimates (e.g., Table 3), which is not physically possible. Similarly, allometric effects may make it hard to interpret things like canal proportions, especially when comparing animals of very disparate size. I suggest a deep revision of these parts of the paper in particular, either removing them altogether, or a major reworking to limit and update the assumptions underlying the various functional analyses. Specific comments in these areas are outlined below.

DETAILED COMMENTS
- I would suggest rewording the title to remove the colon, and make the title more direct -- e.g., something like "Endocranial anatomy of Triceratops (Ceratopsidae: Dinosauria) and interpretations of sensory and motor function" or "Endocranial anatomy of the ceratopsid dinosaur Triceratops and interpretations of sensory and motor function" (totally optional, of course!)
- line 78: Forster 1996 should be added here.
- line 87-105: Can you provide more information on the thresholding protocol used? I suspect a fair amount of manual segmentation was required, but it would be helpful to note this. Maybe provide an example slice to show the general character of the scans?
- line 88: Some additional basic information shold be provided. How were these identified as Triceratops (versus Torosaurus)? Do you have enough of the skull to infer species (T. horridus vs. T. prorsus). Do you know where in section the fossils were recovered? Are the braincases crushed or distorted? Can you provide some basic dimensions so that size can be compared with other braincases and perhaps more precisely infer skull size? Optionally, a photo of the braincase would be helpful.
- line 115: was area calculated from width and height of the occipital condyle? If so, these should be provided as measurements, to be more directly comparable with other specimens. (area is not a common metric outside of the Anderson 1999 paper)
- line 122 (and relevant places later in description): the linear measurements, not just ratios, should be provided. Ratios are very hard to interpret, especially when allometric effects might be a factor. Some other studies have found allometric patterns in semicircular canal proportions, so I would use ratios with caution for any inferences. Departures from allometric expectations are of interest. Furthermore, the "raw" measurements are more easily used by future researchers for comparison with other specimens.
- line 148-154: Can you provide volume of the endocast for FPDM-V-9677 w/o the olfactory bulb? I would make sure to provide all comparable measurements possible relative to, e.g., P. lakustai
- lines 170-197: It is important to note that the various nerve canals didn't *just* carry nerves, but also had vasculature and other tissues. I might suggest a brief statement in the text to clarify this point--I am find with using the anatomical shorthand for simplicity, but do think an acknowledgment that these are only approximate reconstructions based on the bony dimensions, not a true representation of the exact form/size of the neural tissue.
- lines 199-212: It would be helpful to add some discussion on similiarites/differences between the two specimens. Is there any evidence of asymmetry in the individuals? I would suggest adding views to Figure 3, to show the right side of FPDM-V-9775, as well as views of the canals in FPDM-V-9677
- lines 256-276: I would suggest augmenting this section to include other discussions of the functional morphology of semicircular canals. The Georgi et al. 2013 paper is one. Coutier et al. 2017 and Berlin et al. 2013 also provide an overview of the use of the lateral canal in inferring head posture, along with some appropriate cautions.
- lines 285-292: This seems like a pretty big stretch of the evidence.
- It's interesting to note that Figure 5 in this paper compares very favorably with the head orientation hypothesized by Ostrom & Wellnhofer (1986), as shown in their Figure 7. See also Tait & Brown 1928, which uses semicircular canal orientation and other lines of evidence to show a similar posture for Anchiceratops.
- What is the source of the skull in Figure 5? How was the braincase orientation within the skull determined?
- Figure 6 is plotting a ratio against a ratio...this isn't necessarily wrong, but I do wonder if it isn't obscuring some information or variation within the data. What does this plot mean biologically? At the appropriate part in the text (lines 257-273), you might add some explanation of what these values are indicating biologically.
- The 2017 paper by Bruce Erickson (History of the Ceratopsian DInosaur Triceratops in the Science Museum of Minnesota) illustrates a Triceratops endocast and should be cited / referenced. Available here: https://www.smm.org/sites/default/files/public/attachments/history-ceratopsian-triceratops.pdf
- Brown & Schlaikjer 1940 provide some of the best illustrations and such of the endocast for Protoceratops, and so this would be useful to reference here.
- Can you comment on differences between these endocasts and others described for Triceratops (e.g., USNM 5740)? On USNM 5740, it looks like the olfactory region is more angled relative to the rest of the endocast. Is this distortion? Individual variation? Morhardt and colleagues (2018) had an abstract on Triceratops endocranial anatomy; it might be cited here (although it is only an abstract, so data are limited).
- I would strongly suggest that the CT scan data should be deposited in an appropriate digital repository. I recognize that museum policies may vary in terms of how freely this should be done (and it thus may have to require permission from a collections manager prior to granting access for other workers), but I would strongly advise this to allow greater reproducibility of results. Particularly for small structures, a difference of pixel interpretation or thresholding may alter measurements between observers.
- Raw data underlying the charts as well as the ratios should be provided in a supplemental table.
- Table 3: The calculation of negative values does not make sense (as far as I know, Hertz can only be a positive value). This is the fault of the original equation, which was only developed with a set of organisms much, much smaller than many non-avian dinosaurs (including Triceratops). Thus, I think the dinosaurs are far outside the limit of where the equation can be considered reliable. I would suggest removing this section from the paper, or else choosing a different method. Gleich et al. 2005 provide another equation, although this too suffers from the limitations of being calculated from animals much smaller than Triceratops.
- The Zhang et al. 2019 paper on Auroraceratops endocasts should probably be incorporated into the paper.

CITATIONS
Berlin JC, Kirk EC, Rowe TB. 2013. Functional Implications of Ubiquitous Semicircular Canal Non-Orthogonality in Mammals. PloS One 8:e79585

Coutier, F., Hautier, L., Cornette, R., Amson, E. and Billet, G., 2017. Orientation of the lateral semicircular canal in Xenarthra and its links with head posture and phylogeny. Journal of Morphology, 278(5), pp.704-717.

Georgi JA, Sipla JS, Forster CA (2013) Turning Semicircular Canal Function on Its Head: Dinosaurs and a Novel Vestibular Analysis. PLoS ONE 8(3): e58517. https://doi.org/10.1371/journal.pone.0058517

Gleich O, Dooling RJ, Manley G. 2005. Audiogram, body mass, and basilar papilla length: correlations in birds and predictions for extinct archosaurs. Naturwissenschaften 92:595–598.

Mordhardt, AC., et al. 2018. STUDY OF ENDOCRANIAL ANATOMY AND ONTOGENY IN THE LATE CRETACEOUS NON-AVIAN DINOSAUR GENUS TRICERATOPS. Journal of Vertebrate Paleontology, Program and Abstracts, 2018, p. .186

Zhang, Qian-Nan, et al. "Endocranial morphology of Auroraceratops sp.(Dinosauria: Ceratopsia) from the Early Cretaceous of Gansu Province, China." Historical Biology (2019): 1-6.