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: THREE-DIMENSIONAL DATA-TRACKING SIMULATIONS OF SPRINTING USING A DIRECT COLLOCATION OPTIMAL CONTROL APPROACH
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This was a well-done revision.  The inclusion of muscles concurrent with the multibody dynamics and air drag are very nice additions to the model.  Two remaining concerns from this reviewer, the first minor and the second less minor:

(1) Line 353 states “The first set [of equality constraints] enforced that the pelvis residuals obtained from evaluating the skeletal dynamics equations were zero.”

If I understood correctly, this constraint refers to the first six of the 37 multibody dynamics equations, relating to the pelvis DoF where no generalized forces act.  I think it may be confusing to readers to describe this constraint separately from the other 31 multibody dynamics constraints, assuming I understood the method correctly and the “pelvis residuals” constraints are indeed these six multibody dynamics equations.  Rather than describing this constraint as what it results in (pelvis residual elimination), I suggest instead or also describing its form along with the other multibody dynamics constraints, and presenting the full set of constraints in equation form for clarity.  Van den Bogert et al. (2011) is a good example, or Ackermann & van den Bogert (2009) although the latter is an explicit formulation.  I may have missed it but I did not see it stated directly in the text that the full multibody dynamics were implemented as constraints.

(2) I apologize for the length of this second comment.  I tried to make it as short as possible but ended up needing a lot of text to make and support my point.

Even recognizing that the athlete studied here is elite (10.33 sec 100-m), the strength and power capabilities endowed to the model’s muscles through the maximum isometric force (Fo) and maximum fiber velocity (Vmax) parameters did not seem realistic.  I think these choices need greater justification and consideration than what was given beyond referencing the Lai and Dorn studies which used different methods (more on that below).

I will give an example demonstrating why I think the model’s muscle strength is not realistic, using the quadriceps muscles.  Handsfield et al. (2014, 2017) presents muscle volume data for the lower limb in a group of healthy young adult “controls” and in competitive sprinters similar in class to the athlete studied here (NCAA Division I).  Assuming a typical muscle density of 1056 kg/m^3, the unilateral quadriceps mass was 2.7% of the body mass for controls and 3.6% for sprinters.  Assuming a typical specific tension of 300,000 N/m^2, the quadriceps mass in Hamner’s model is 2.5% of the body mass, similar to Handsfield’s controls.  Tripling Hamner’s Fo’s by tripling muscle mass produces a quadriceps mass of 7.4% body mass.  Even though the Handsfield sprinters were likely all from the same college team and likely did not all have ~10.3-sec speed, it does not seem likely that the athlete here had double their quadriceps mass relative to body mass.  Tripling Hamner’s Fo’s while matching the 3.6% from Handsfield requires a specific tension of about 620,000 N/m^2.  This specific tension is not outside the realm of possibility and similar values have been used in other models (e.g. Rajagopal et al., 2016), but regardless of how the tripling of Fo is achieved, it produces a model with unbelievable strength.  The maximum isometric knee extension torque of Hamner’s model with tripled Fo’s is 718 Nm or about 10 Nm/kg.  Elite sprinters in dynamometry studies typically produce only about 200-300 Nm and it is rare to see any athlete produce a max isometric torque much above 400 Nm.  For example, even assuming a very long moment arm of 0.5 m, the youngest (age 43) elite masters Olympic weightlifters in Pearson et al. (2002) averaged 618 N x 0.5 m = 309 Nm of torque or 3.5 Nm/kg.  Even considering things like antagonism and lack of true maximal activation in human data, 700+ Nm is an unbelievable level of strength.

The assumed value of Vmax = 20 is also not realistic.  There are no studies on human muscle to my knowledge reporting Vmax much faster than 10-12.  Such an extreme value of Vmax should not be needed to simulate elite speeds.  Previous optimal control simulation studies (with much coarser controls) have reached world-class speeds with Vmax = 10-12, without super-human muscle strengths (Sellers & Manning, 2007; Miller et al., 2012).

The values used for Fo and Vmax were justified in the text as being consistent with previous modeling studies on fast running/sprinting (Lai and Dorn references).  Dorn indeed used triple the Hamner Fo’s and Vmax = 20, but Dorn was also solving an inverse dynamics problem, where the model is forced to produce joint moments computed from experimental GRF that result in the Hatze “Fundamental Problem” in my first review, leading to the need for things like reserve actuators and unrealistic muscle properties to compute muscle activations less than 1.0.  Lai was also solving an inverse dynamics problem and also used larger values of Fo and Vmax than Hamner but should not be cited to support the values used in the present study.  Lai did not use triple Hamner’s Fo values, and used Vmax = 15 not 20.  The issues in Lai and Dorn’s methods that required these things do not affect the present methods, the model can deviate from the measured joint moments a little and still track them reasonably well overall.  Relatedly, the need for reserve actuators and extreme muscle parameters in the standard OpenSim IK/RRA/CMC workflow typically appears in low-force situations when the muscle model is in unusual states, not in high-force situations which is where an optimal control simulation would likely benefit from these things.

I mention all of these things (again apologizing for the length of this comment/rant) not because I think the present work is heavily flawed (it’s great work), but because there seemed to be several elements in the present model that were included not for physiological reasons but for fear that the model will not track the data well: reserve actuators, unrealistic Fo’s, unrealistic Vmax.  These things should not be needed here for this model to produce quality tracking simulations.  If the authors have not already done so, I would encourage them to check if the model can track the data reasonably well with more reasonable values of Fmax (e.g. maybe 1.5-2.0 Hamner’s values, or the values from Rajagopal where max knee torque is a less extreme 470 Nm), Vmax = 12, and no reserve actuators, and if this is possible, replace the present results with those results.  If the model is not able to track the data well without 3xFo and Vmax = 20, this is concerning and the reason for this should be investigated, as these values will likely produce inhumanly fast sprinting speeds in predictive simulations.  It would be helpful to include some justification of the parameter values, e.g. in reference to the Handsfield et al. (2017) data, Vmax studies, and studies like Erskine et al. (2011) on specific tension increasing with strength training, rather than references to Lai and Dorn which are great studies are not very relevant for justifying parameter values when using direct collocation methods.


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: INTEGRATED ANALYSIS OF IMMUNE-RELATED LONG NONCODING RNAS AS DIAGNOSTIC BIOMARKERS IN PSORIASIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper, F Fan, Z Huang and Y Chen present data on the potential use of lncRNA as “biomarkers” for psoriasis manifestation. They make use of three publicly-available datasets of gene expression studies of lesional and non-lesional psoriatic patients, as well as healthy controls. Using various bioinformatic methods, they define a subset of 16 “immune-related lncRNAs”. Next, using LASSO logistic regression, they identified 10 of these as potentially diagnostic biomarkers for psoriasis. They validate their findings using independent datasets and find 8 lncRNAs with “excellent diagnostic efficacy”. Finally, they show that some of the identified lncRNAs correlate with either drug response or infiltration of specific immune cells. Studies aimed at elucidating the functional significance and disease-relevance of lncRNAs are highly needed, and bioinformatic analysis provide ample opportunities to do so. However, the manuscript, in its current form, provides too little details on how these analyses were performed, especially the rationale for choosing certain tools, thresholds and cutoffs. Also, as already mentioned by the authors, additional, experimental validation would strongly increase the impact of their findings.

Major issues with regard to basic reporting:

•	A few important examples of functional lncRNAs important for psoriasis (e.g. PRINS (doi: 10.1007/s00424-016-1803-z.)), as well as for the skin (e.g. TINCR (doi: 10.1038/nature11661.), ANCR (doi: 10.1101/gad.182121.111.) and PRANCR (doi: 10.1101/gr.251561.119.)) are described in literature. Some of these are even show to have important immune-related functions. However, the current introduction and discussion fail to put the findings on the important of lncRNAs in psoriasis in the broader context of known lncRNAs in either epidermal homeostasis or psoriasis.
•	The manuscript provides not enough details on the experimental design. Please find the specific concerns in under “2. Experimental Design”.
Experimental design: The research question in this paper; whether lncRNAs play a role in the manifestation of psoriasis, is an important research topic, as it provides important insights in the disease-relevance of lncRNAs. However, due to the lack of rationale and underlying judgements for using several thresholds, choice of bioinformatic methods and selection criteria, the Experimental design and methodological soundness are difficult to judge appropriately. PeerJ serves readers from a wide variety of disciplines, and this manuscript, in its current form, fails to clarify vital details, especially with regard to this broad readership.

Some major concerns with regard to Experimental Design:
•	The three data set used in this manuscript have some important differences. Different gene sets include Lesional and non-lesional samples from psoriatic patients, as well as normal skin samples. It is currently unclear what samples are compared to screen for DEGs. Also, all data use the Affymetrix Human Genome U133 Plus 2.0 Array. Are lncRNAs well-represented on this array? How many lncRNAs are present on this array? Is there a bias? Also, the authors state the perform “background correction and normalization”, but it is unclear what this normalization step entails? To what are the data normalized?
•	It is unclear how “immune-related lncRNAs” are defined. It seems that these lncRNAs are selected because of a ‘co-expression’ with previously known, differentially expressed, immune-related genes. The definition of “immune-related lncRNAs” is fundamental to the findings in this manuscript. What is the rationale for using co-expression as a parameter to score a lncRNA as immune-related? Also, why is the threshold for co-expression set at a coefficient as low as 0.4? I would favor additional parameters to score a lncRNA “immune-related”, such as their preferential expression in immune cells or skin, etcetera.
•	“Of the 16 immune-related lncRNAs, 10 were identified … using LASSO”. More details on LASSO and its application are required, such as: What is the response variable and the binary expression value? Although LASSO is an important logistic regression tool, more details are needed to fully understand its usefulness in this particular case.
•	How is drug response defined? Also, is using the general term “drug response” appropriate? Data are almost solely dependent on the use of the drug ‘Ustekinumab’, yet the manuscript provides no details on this drug.
•	How is infiltration of immune cells “estimated”?
Validity of the findings: The way data are depicted is currently of insufficient quality, which hampers a fair judgment of validity and robustness of the findings. Figures should be self-explanatory, with detailed legend and descriptions. Also, I feel that important data that is now presented as supplementary, should be implemented in the main figures to allow a valid, more easy-to-read manuscript. Lastly, the lack of experimental validation is a great limitation of the current study, that should be addressed, rather than only mentioning it.

Major issues with respect to Data Validity:
•	The identification of “immune-related lncRNAs” is interesting, and central in this manuscript. Yet, their identification is not displayed as a main figure. I would strongly recommend to provide a plot that indicates some kind or ranking score for these lncRNAs. In other words: how are the 16 immune-related lncRNAs (line 171) defined, and what sets them apart from other lncRNAs? This extends to the 10 lncRNAs identified as “biomarkers for psoriasis”.
•	Many figures are very difficult to interpret. This is partly due to visualization concerns (e.g. figures 2B, 3B, 4A, 7B), as well as a very low number of details provided in the figure legends.
•	Figures 3C and D provide “GO/KEGG analysis of immune related lncRNA target genes”. What is exactly the input of this? How could these “target genes” be reliably defined? In my opinion, the reasoning seems to go “in circles”. First “immune-related lncRNAs” are defined by their co-expression with immune-relates genes, and then target genes are defined by co-expression with this same set of lncRNA genes. One would expect very similar results during gene enrichment, as the definition of these lncRNAs was already dependent on the expression of a subset of these genes. Not surprisingly, the results in figures 2A and 3C are very similar. As such, this is questioning the validity of the Experimental Design used, and, as a consequence, the findings.
•	The authors recognize the limitation of experimental validation. However, I feel this limitation is too important to only mention. While I would strongly encourage the authors to select one or two lncRNAs for biological studies, I also think that additional bioinformatic approaches can be applied as experimental validation. This could include the use of GWAS data, which are readily available for psoriasis. Do any of the lncRNA identified as “biomarkers” in this study contain SNPs that are suggested to be associated with psoriasis by GWAS?
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: INTEGRATED ANALYSIS OF IMMUNE-RELATED LONG NONCODING RNAS AS DIAGNOSTIC BIOMARKERS IN PSORIASIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the abstract number of samples analyzed and validated is needed in the methods.
Results in the abstract do not report metrics of the machine learning classifier. This should be added. Especially needed are accuracy, sensitivity and specificity.

In the introduction,although the premise is built well, why these 3 GEO datasets and not other psoriasis gene expression datasets were used is not mentioned nor justified, this implies a bias is selecting favourable datasets.

The findings from the 3 geo datasets must also be summarized in the introduction to allow the reader to follow the results.
Experimental design: The materials and methods - GEO IDs are mislabelled, for instance
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13355 is Nair et al 2009 and not Correa da Rosa et al 2017/Suárez-Fariñas M et al 2012 which is https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30999.

Again referring to GEO30999 derived from Correa da Rosa et al 2017/Suárez-Fariñas M et al 2012 which is https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30999. This is a treatment response study, among the 85 samples which samples were used to validate the Lasso model? Before or post treatment this should be mentioned. I would suggest using a figure to convey the message about which cohorts were used as validation and training and number of samples in each of these cohorts.

More details on the normalization need to be mentioned , was it a zscore or a log normalization or quantile normalization ?

The total number of probes in the final analyses need to be also mentioned to understand the burden of multiple tests and its implications for P value adjustment.
Was eBayes moderation used when fitting the limma model? The top differentially expressed genes must be included as a supplementary table with columns indicating if they replicated across datasets.

If possible, meta analysis of all the baseline gene expression from the three datasets should be performed and presented as a supplementary table.
Which lasso model was used? How were they hyperparameters of the model selected? Was cross validation performed ? If so, how many folds ? How was the tuning parameter lambda selected? These should be mentioned in the methods.
Validity of the findings: Results line 154 to 159, the PCA and normalization methods are not informative in results and should be moved to methods. More description on the 394 DEGS would benefit this section, a table with top genes expressed would be appropriate. (see point 5 in experimental design section). These top DEGS should be described with regard to how many up and down regulated. Volcano plot should be labelled with top DEGS in both up and down directions.

Pathway analyses - its a good validation that IL-17 associated pathways show up. Can the authors do pathway analysis only on up-regulated and down-regulated separately this would be informative.

Its unclear if the lncRNAs are part of the 394 DEGS from point 1 above. Please make this clear in the results.

How many coefficients in total were non-zero in the lasso model? Were all the 394 DEGS used as input variables to train the lasso model? If not how many variables/probes did you include in the model? If only 11 lncRNAs were used in the lasso model it is not the best machine learning framework to use? As lasso is most suited for P > N problems.

I would suggest to perform cross-validation in the GEO dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13355 derived from Nair et al 2009 and present the metrics as a figure. Log Lambda vs no of variable in the model as cv.glmnet from R package glmnet outputs.

More metrics must be presented in the results Accuracy, PPV, NPV etc. A confusion matrix of the classifications in the model in particular must be presented to understand the performance of the lasso model.
The validation cohort derived from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30999 also has treated samples, were they excluded or only baseline samples used?

Can the authors speculate why although IL-17 associated pathways are upregulated but no TH17 cells were seen in immune cell infiltration analyses? These should be included in the discussion.

A genetic basis for the overexpression of lncRNAs could be helpful to understand these results. Are there any genetic associations already described for e.g in Nair et al 2009 or more recent psoriasis GWAS studies that regulate the expression of lncRNAs? If so these should be included in the discussion.

Discussion also must take into account these points and must be sharpened.
Additional comments: Fan et al conduct re-analysis of existing gene expression datasets derived from psoriasis samples and find differentially expressed gene sets with immune signatures. This effort involved 3 GEO datasets with primary analyses being done on 1 and the rest set aside as validation. They further train a lasso model on the 1 GEO dataset and find that lncRNAs are important coefficients in the model and predict moderately AUC ~0.7 the disease status and response to Etanercept in the validation datasets. The study adds to the body of biomarkers in psoriasis and its strength lies in validating the lncRNA based transcripts in independent datasets. I have few concerns as stated below which could substantially improve and streamline the main findings from the data.


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: INTEGRATED ANALYSIS OF IMMUNE-RELATED LONG NONCODING RNAS AS DIAGNOSTIC BIOMARKERS IN PSORIASIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The goal of the study by F Fan, Z Huang and Y Chen, to elucidate functional significance of lncRNAs, is an important issue. In general, however, the revised manuscript does not satisfyingly address the concerns raised by both me and the other reviewer. The revision has treated as if our concerns where “minor”, but they were major and need to be addressed thoroughly. Various suggestions are neglected and referred to as “future plans of the lab”, but some of these are required to increase the scientific soundness to a satisfying level. The main issue is that the authors should find additional ways to more convincingly demonstrate that the lncRNAs they identified are really immune/psoriasis-related.

Some important issues:
•	Both reviewers have postulated ideas to pursue this in the previous reviewing round and I recommend going back to the initial review and address various of these suggestions.
•	In the introduction, introduce the three GEO datasets used and provide a summary of the original findings in the papers that deposited these GEO datasets. Reduce the number of results from the own paper in the introduction. It would be good to include a Figure that clearly shows the GEO databases used and what information is retrieved for this study? This could be conceptual Figure 1A.
•	“Background correction and normalization were performed” (line 112). Although the authors explain it in the rebuttal, it is still not clear from the main text. Please specify.
•	Figure 2. Please make sure in the legend how DEIRGs are defined. Specify the meaning of BP, CC and MF. What does “GeneRatio” mean? Also, make sure that it is immediately clear what comparison is made: psoriasis vs normal skin, and which GSE is used? As all data in figure 2 is related to those of figure 1, I would suggest combining figures 1 and 2 into a new figure 1. Figure 2B is still difficult to interpret and inconsistent. If Log FC is plotted, then why does the legend state “fold change”? What do the numbers correspond to (KEGG pathway entries, I suppose)? What do the connected lines indicate? How does this data relate to those depicted in supplementary table1?
•	Table 3 is nice, but presents little extra information. How many lncRNAs were considered and what % is now considered “immune-related”? What are the exact correlation parameters of these “hits” and how do they relate to the ones that where non-hits?
•	Figure 3B: are these data now referring to all GSE datasets? Or still only GSE13355?
•	Figure 4A: it is unclear what is plotted in this figure. No legend, no explanation, no thresholds on inclusion. As stressed in my previous review, figures should be self-explanatory. Isn’t the main information in Table 4?
Experimental design: The lack of details, rationale and underlying judgements for using thresholds and selection criteria remains, and the methodological soundness is still difficult to judge.

Major concerns that remain:
•	I recommend going back to the initial review and address these suggestions.
•	“Background correction and normalization were performed” (line 112). Although the authors explain it in the rebuttal, it is still not clear from the main text. Please specify.
•	How many lncRNAs are on the Affymetrix Human Genome U133 Plus 2.0? How big is the subset of IR-lncRNAs found with respect to the total number of lncRNAs? In other words, how much detection bias is there? There are RNA-seq datasets that could be used for validation!
•	Figure 1 and Tables 1&2. This only shows GSE13355, but how replicate where these? How much of the top-10 did show up when considering the other two datasets? In other words: did the data replicate across datasets.
•	Line 180 “psoriasis was mainly involved in IL-17 signaling and proteasome pathway”. Please specify the parameters for highlighting these, so a reader can appreciate this, especially in light of sup. table 1.
•	“functional correlation analysis” (line 187). What does this mean? And what do the data in supplementary tables 2 and 3 present? This should all be imminently clear from the text.
•	“We used a LASSO-logitstic-Algorithm model, 10-fold cross-validation was used to identify the optimal lambda value." Where are these results of this lamda value identification?
Validity of the findings: More validation is needed, and referring to potential “Future studies” cannot be used as an argument in all cases.

•	I recommend going back to the initial review and address these suggestions.
•	Throughout the manuscript various thresholds have been used as cutoffs to include or exclude hits, but the rationale/discussion behind these is not always clear. For example, the correlation coefficient for including immune-related lncRNAs is set at 0.4. In the rebuttal, the authors state that: “We set threshold as 0.4 to screen the number of genes with appropriate data according to the actual situation, and set a higher or lower threshold, resulting in too many or too few genes.” However, a threshold set of 0.4 based on “too many or too few” genes is not very scientific. The point here is to have a threshold that actually includes lncRNAs that are immune-related. The authors need to provide better and more scientific arguments. This extends to the claim “exhibited excellent diagnostic efficacy (AUC>0.7)” (line 266-267).
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: INTEGRATED ANALYSIS OF IMMUNE-RELATED LONG NONCODING RNAS AS DIAGNOSTIC BIOMARKERS IN PSORIASIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Authors have been responsive to comments and significantly improved the manuscript, recommend 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: INTEGRATED ANALYSIS OF IMMUNE-RELATED LONG NONCODING RNAS AS DIAGNOSTIC BIOMARKERS IN PSORIASIS
Review round: 3
Reviewer: 1

Output:
Basic reporting: In comparison to the previous versions, the manuscript has improved significantly and the issue to elucidate novel functional lncRNAs is an important topic in modern science. However, various concerns need to be addressed before publication is fully acceptable:
•	As stated earlier, Table 3 should include statistical parameters, such as is done for Tables 1 and 2. Statistical parameters needs to be clear from the main documents and would not require to be looked up from the supplemental data.
•	In the rebuttal, the authors mention that 1,313 lncRNAs are present on the Affymetrix array, this also need to be included in the main text.
•	Include a better description (in methods) on how lncRNAs were defined, whether is was based on the gene description by Affymetrix, or what database (NCBI, ENCODE, …) to decide why a gene was considered a lncRNA.
•	Figure 3B is unclear and needs to be revised, please find another, better way to display these data.
•	Figure 4B does not add much to the figure and is hard to read. This could be moved to Supplemental data.
•	Figure 5A is hard to read and has no clear legend. Please revise.
•	Some sentences have language issues.
Experimental design: Please discuss the following concerns:
•	Include the choice of the different thresholds (0.4, 0.7 etc.) based on the literature references provided in the rebuttal in the main manuscript.
Validity of the findings: Although I still think further validation is needed, the following needs to be discusses and addressed minimally:
•	Because of the lack of validation, please tone down statements and decrease the use of wordings like “biomarkers” (without validation I would not refer to these as biomarkers) or “high diagnostic efficacy”. Such statements are only valid with more validation.
•	Discuss what a ratio of 16 out of 1313 lncRNAs (which is 1.2%) being psoriasis/immune-related makes sense in the context of the disease. Is this high of low and what would it mean?
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 VARIATION OF NIGERIAN CATTLE INFERRED FROM MATERNAL AND PATERNAL GENETIC MARKERS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This paper is relevant because it solves a gap of previous works in which samples from Nigerian cattle were scant.

However, I’ve found that the research presented has not been correctly discussed according to previous knowledge on this issue.

In my honest opinion, the subsection “demographic dynamic profiles” adds very little to the paper
Experimental design: Authors analyse a sample of Nigerian cattle using mitochondrial DNA and Y-Chromosome markers.

Authors used state-of-art methods and the information provided on sampling and results is good.
Validity of the findings: Results complements previous knowledge. However, they have not been discussed appropriately. Some issues are:

- Is lack of genetic structure in Nigerian cattle consistent with the whole African cattle scenario?

- Why didn’t you find taurine Y-Chromosomes in your samples?

- Do Nigerian cattle Y3 Chromosomes belong to the West African lineage or they result from a recent zebu introgression?
Additional comments: Manuscript peerj-50178 titled “Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers” by Mauki et al.

Authors analyse a sample of Nigerian cattle using mitochondrial DNA and Y-Chromosome markers.
The paper is relevant because it solves a gap of previous works in which samples from Nigerian cattle were scant. Authors used state-of-art methods and the information provided on sampling and results is good.

However, I’ve found that the research presented has not been correctly discussed according to previous knowledge on this issue.

1.- First of all, I was surprised when I found that the paper by Alvarez et al. (2017: Differences in genetic structure assessed using Y-chromosome and mitochondrial DNA markers do not shape the contributions to diversity in African sires. J. Anim. Breed. Genet. 134, 393-404) was not included in the list of L87-89 “To decipher the genetic diversity in Nigerian cattle, we employed the use of both mtDNA and Y-chromosomal markers, which have been widely used in assessing the diversity and genogeoraphic structure of many domestic animals”.

This paper is relevant when mtDNA and Y-Chromosome markers are used in African cattle. The well-known lack of genetic structure of African cattle at either the national or regional level occurs at the continental level as well. Differentiation between cattle groups is statistically significant for Y-chromosome markers only.

Actually, authors can use thoroughly the paper by Alvarez et al. (2017) for discussion.

2.- The paper by Alvarez et al. (2017) confirms the existence of a subfamily of taurine Y-Chromosomes in West African cattle previously reported by Pérez-Pardal et al. (2010: Y-specific microsatellites reveal an African subfamily in taurine (Bos taurus) cattle. Anim. Genet. 41, 232–241; not cited). You did not find taurine Y-Chromosomes in your samples (L275). The cause is not discussed sufficiently. May it be a simple consequence of sampling (northern Nigeria, basically)? or Can it be explained by a higher zebu introgression into Nigerian cattle (e.g. MacHugh et al., 1997 or Hanotte et al. (2000: Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub‐Saharan African cattle breeds. Mol. Ecol. 9, 387-396; not cited)?

3.- The notation of the different Y3 subfamilies identified is confusing (L282 and related pieces of text). Please use only one notation throughout the text, explaining why. I’d suggest to use the notation by Perez-Pardal et al. (2018; cited in the text) due to the following reasons: a) this paper confirms the suggestion by Perez-Pardal et al. (2010: Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites. Heredity 105, 511-519; not cited) that West African cattle have their own zebu Y-chromosome lineage; and b) this paper confirms that this African lineage, although putatively originated in India, is not present in Asia. Authors must clarify to which Y3 subfamily belong the Nigerian cattle Y-Chromosomes identified. Following Perez-Pardal et al. (2018), if belonging to subfamily Y3b they may be part of the West African “reservoir” while if belonging to subfamily Y3a they may result from a more recent zebu introgression. This will improve the Discussion section (e.g. L335-341 or L358-369).

Other concerns are the following:

i.- L236 and L322-323: don’t you think that the paper by Chen et al. (2010: Zebu cattle are an exclusive legacy of the South Asia Neolithic. Mol. Biol. Evol. 27, 1–6) would merit to be cited there?

ii.- I consider that the analyses under the title “demographic dynamic profiles” (L189, L197-205 and related pieces of text) add very little to the paper and could be removed from the text of the manuscript. However that’s an editorial decision.

iii.- I’m not a native speaker of English. The paper can be understood but I found some sentences difficult to follow (e.g. the first sentence in the Abstract section: L46-48). I would suggest to reconsider the English style of the manuscript, shortening the sentences as much as possible, and avoiding terms such as “indicine” (e.g. L343; please use “zebu”). Moreover, please use the revision of English to solve typos (e.g. L89: “genogeoraphic”).

In summary, I think that the discussion of the paper may be considerably improved including relevant previous reports on this issue. This will highlight the general interest of the research presented.


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 VARIATION OF NIGERIAN CATTLE INFERRED FROM MATERNAL AND PATERNAL GENETIC MARKERS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, the article is well-structured and the English used throughout the text is mostly objective and according scientific standards (see some suggestions for modifications on the annotated pdf file).

Figures and Tables are mostly relevant to the content of the article. Nonetheless, I suggest I suggest showing a network of Y-haplotypes instead of Table3 (which could be presented as supplementary material).

The introduction section is well-written and highlights the most relevant aspects related to genetic diversity and mtDNA analysis. However, in my opinion this section should also include information on mtDNA and Y-chromosomal variation found specifically in Africa (contrasting with other regions), e.g. frequency of T1 vs T3 matrilines and Y3 vs Y1/Y2 Y-lineages. The authors could also include some more recent papers regarding the genetic analysis of African cattle (this is also valid for the Discussion section, but see my specific comments in the appended pdf file).

Appropriate raw data for revision of this article was provided in the form of FASTA alignments for mtDNA and Y-chromosome sequences. But, accession numbers for public databases for the sequences derived from this study should also be provided in the respective Tables (S1, S2 and S4).

I should call attention to the fact that the ethical statement is written in Chinese language, I'm not sure if PEERJ demands for a translated copy.
Experimental design: The authors use mtDNA and Y-chromosome sequence variation to investigate the genetic composition of Nigerian local cattle. The design of the study was appropriate, as well as the methods used. The results presented here derive from original primary research that to the best of my knowledge has not been published elsewhere. The methods are well-described to allow for replication of the work done, but the cycle sequencing protocol and sequencing instrument should be mentioned (see annotated pdf file).

The statistical analyses were generally appropriate, but some aspects can be improved, in particular:
-Phylogenetic analysis of mtDNA sequences – to obtain a phylogenetic tree, the authors should use instead a method that allows for the appropriate evolutionary model to be defined as well as the corresponding parameters. This is recommended for mtDNA and should allow to recover the mtDNA phylogeny and separate major haplogroups. Regarding the mtDNA network no outgroup should be specified (see annotated pdf file).

-Population dynamics based on mtDNA sequences – I’m not exactly sure how mismatch distribution patterns can be interpreted here, perhaps a more suitable reviewer can comment on this specific analysis.

- Regarding Y-chromosomal variation, I suggest also obtaining a network of Y-haplotypes to depict genetic relationships, in particular between the Y3 haplotypes. The reduced-median algorithm may provide a better resolution and should be tested.
Validity of the findings: The findings are well-organized and presented in a logic way. There are a few things that need clarification. Regarding the mtDNA analysis, there are 2 sequences the authors classify within the T3-haplogroup. But, in my opinion, the position of these sequences in Figures 1b and S1 is not consistent with this classification. The authors should provide a justification for their decision to consider these sequences T3, while keeping in mind that other polymorphic positions may be needed to fully characterize some of the mtDNA haplogroups, namely Q and T2.

As for the Y-chromosome, the authors elaborate on possible aurochs contribution to Nigerian cattle patrilines. I find this highly speculative (there's no data for the Y-chromosome of African aurochs) and providing the polymorphisms determined for Nigeria42_Y3 are real (see my comments in the appended pdf file), most probably the reason why distinct haplotypes are found in local African cattle (often at low frequencies) is related with less intensive selection of these cattle where much of the original Y-chromosome diversity is maintained. Also, the use of artificial insemination, which is known to significantly reduce the Ne for the Y-chromosome, is probably less used in African countries in comparison to other regions such as Europe or North America. This should be discussed here.

The authors also make comparisons with the results of other studies on the Y-chromosome of African cattle, which is desirable. However, a note should be added regarding the fact that the markers used across these studies are different, including in some cases more variable Y-STRs were genotyped and used to estimate Y-diversity (for example data included in Table S9).

The discussion section can be further improved. It's a bit convoluted, where the authors use contradictory statements (see my comments in the appended pdf file). In its current form it is much more an extension of the results than a good interpretation of the cattle diversity found in Nigeria and the conservation impact of finding distinct lineages. In addition to the need for genomic studies to infer adaptive variation and demography, it also deserves a comment on the need to genotype other Y-markers to be able to detect additional genetic variation and make more reliable comparisons with other studies.
Additional comments: This study provides relevant information regarding the maternal and paternal genetic diversity found in Nigerian cattle. I made suggestions for modifications throughout the text in the annotated pdf file.

The results of this study need to be contextualized under the future perspective of analyzing other markers to characterize African cattle, e.g. autosomal whole-genome variation and other Y-chromosome markers.

Providing these minor modifications are done, it is my opinion that this study is suitable 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 VARIATION OF NIGERIAN CATTLE INFERRED FROM MATERNAL AND PATERNAL GENETIC MARKERS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This work reports an extended survey of mtDNA and Y-Chromosome markers in Nigerian cattle. It is an interesting study that certainly deserves publication but requires some revision and improvements before acceptance. Below, I outline my major concerns:
In the introductory section: some of the literature is outdated and does not report most of the recent findings regarding mtDNA and Y-chromosome patterns and origins in Africa and elsewhere. There are review articles and book chapters much more recent than some of those cited. For example, there is no reference on the most extensive work on mtDNA and Y-chromosome in African cattle (Hanotte et al 2002, Mol Ecol) and instead, it is mentioned a study on autosomal microsatellites made in the same individuals. Regarding the discussion, it is poor as there is a fair amount of literature regarding the origin and distribution of the African cattle and its archaeology, human genetics, and livestock genetics. The authors shall improve substantially this part of the MS and try to discuss their findings at the light of the recent human history in the region (Bantu expansion, European and Arab influence).
For example at L230, the authors mention that T3 haplotypes were also reported by previous works in other Northern Africa countries (although no reference is provided here), but did not venture in tracking the most probable origin of the T3 haplotypes they have found in Nigerian cattle. The available amount of data would permit the authors to go further and check whether it is related to commercial breeds such as Holstein-Friesian, Simmental, or other European breeds. Due to the tremendous lack of diversity, those cosmopolitan commercial breeds have very few mtDNA haplotypes that can be easily tracked.
Experimental design: The sample size is very different between samples and this can easily influence estimations of genetic diversity parameters.
A pitfall of this study regarding the experimental design is that although the authors mention that other studies were poor in terms of representation of Nigerian cattle, they do not consider this when they compare with the data they criticized to be poorly representative. For example, they compare the diversity between Mozambique and Nigerian Cattle (L248-252). Interestingly, they often get surprised with results that are no surprise:  like most of the differences that account for most of the diversity is intra-populational and that most of the genetic structure in terms of maternal lineages in cattle, is due to intercontinental differences.
Yet another issue, is the use of an outgroup in the network analysis. What is the propose of an outgroup in such an intra-specific network? its use is confusing.
Also confusing is the nomenclature of the Y-chrom. haplotypes. The authors mention several studies but they do not say what nomenclature they have followed. They shall be more precise regarding this.
Validity of the findings: The findings are valid and worthy of publication, but the interpretation of these findings can be considerably improved.
Additional comments: The authors must improve the introductory and discussion sections. The history of West Africa has been the subject of many studies in genetic and archaeology and this can and should be used to discuss their findings on Nigerian cattle.


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 VARIATION OF NIGERIAN CATTLE INFERRED FROM MATERNAL AND PATERNAL GENETIC MARKERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have addressed most my suggestions.
Therefore, I have no reason to delay acceptation for publication of this manuscript.
Experimental design: N/A
Validity of the findings: Their interest were previosuly assessed
Additional comments: This manuscript has been improved and I can recommend its acceptation for publication 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: IDENTIFICATION OF THE HUB GENES IN GASTRIC CANCER THROUGH WEIGHTED GENE CO-EXPRESSION NETWORK ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The use of English language is adequate
Well referenced
Article is well structured, all the used data is available with online or in supplementary material
Self contained
Experimental design: It is an elegant computational approach to a biological question, within the journal scope
Correctly defined research question and knowledge gap
General methods used are standard, and those are well described
Validity of the findings: I am missing further results to completely agree on validity of the findings.
Additional comments: Major:
data collection and preprocessing:  3 datasets with the larger sample sizes have been selected to “avoid batch effects”. However there exist computational approaches to overcome batch effects when working with datasets from different sources (Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods, Plos One 2011). Using such methods, you could have chosen many datasets for the training set and that would have greatly enforced this research.

Specify whether  the 3 selected datasets were normalized independently or not.

Module preservation:  you need to further interpret figures and results from this section.  It looks like bigger modules are more conserved, how do you explain that? In addition, how do you explain that modules preserved in GSE13911 are smaller that the same one’s identified in the training set? As those datasets were generated within the same platforms, detected genes should be the same.

Identification of clinically significant modules:  I am worried about the methodology used here. You do obtain a Pearson’s correlation between each ME and clinical traits. However pearson correlation is used to analize the relationship between two quantitative variables, but clinical traits (cancer/healthy) variable looks categorical. Please clarify that, perhaps providing additional scatter plots or so.

Validation of the hub genes:  figure 9 shows a great ROC curve using an independent gastric cancer dataset. However as you are addressing a gastric cancer specific hub genes signature, I am missing here a ROC curve obtained with a distinct type of cancer. In this way you could show that those hub genes are of great value for gastric cancer specifically. In the same sense, it might be interesting to show in fig 9  ROC curves obtained with another regression algorithm. Therefore, please add ROC curves to fig.9 to allow visual comparisons and strengthen your conclusions.

Minor:
L53 (gender ratio and age at diagnosis) : provide further details for readers

It would be great to further develop in introduction the use of regressions for such biological questions. In addition you don't specify in the intro that you are validating your model in an independent dataset at the end.

Justify the reasons why a simple glm regression algorithm was chosen instead of another available approach (neural nets, random forest etc) to validate you hub genes.


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 THE HUB GENES IN GASTRIC CANCER THROUGH WEIGHTED GENE CO-EXPRESSION NETWORK ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper describes a systematic strategy to discover putative biomarkers genes that can be used for the diagnosis of gastric cancer. This is an original paper focused on an important real problem. In addition, the manuscript is well written. So, it deserves to be published. However, several concerns must be corrected upon before Acceptance.

Title
I suggest eliminate the ¨validation¨ term from the title, because no experimental evidence is provided. Instead, the validation section corresponds to a statistical analysis used to test the reliability of the results, but it cannot be considered as a validation from the clinical or biological point of view.

Introduction
Line 141 change ¨types¨ by condition or a more appropriate term.

Material and methods
In this section must be defined the contrasting condition (e.g. type, stage).

Discussion
Lines 253-265 could be placed in the introduction. Instead, a brief paragraph to remember the subject of this study can be provided.
Experimental design: Results
-	The Supplementary Figure 1 is not self-explained. This Figure must indicate the meaning of the color bar below the dendogram. Please, add a figure description.

-	In the introduction, the authors mentioned that ¨There are two types of gastric cancer, diffuse and intestinal types…¨. However, they don´t indicate what kind of cancer type are the samples derived from. All the dataset employed come from the same cancer type?. Please specify.

-	Please clarify why you don´t remove any sample from your dataset. What was your decision rule?.

-	In Figure 2. Please enlarge the A and B images to clearly shown the plotted values. In Figure 2D, the R and slope values, must be plotted in the Figure, not in the title.

-	In Figure 4A, please explicitly indicate the meaning of the scale in the heatmap (p-value). In Figure 4B, please explicitly provide the meaning of y axis (z-score), and indicate the meaning of error bar. What does mean the p-value of the title in Figure 4B?, please insert it in the image.

-	Please provide a clear description for Supplementary Figure 2. Please, edit the image, indicating the cor and p value in the image, not in the title.

-	In Figure 6, please enlarge the axis title of the image, because it is difficult to read. How the adjusted p value was estimated? I suggest just plot the meaningful enriched GO terms. Please provide a description for the threshold value.

-	In the Supplementary table 2, I suggest remove all non-significative GO terms. In the description of Figure 7, please replace ¨in this¨ by in each. I suggest manually curate your annotation, since terms as ¨biosynthesis of antibiotics, not make me sense at all. Please edit the key to homogenize the format. In Figure A, count is above p-value and in B is upside down.

-	Why did you plot the adjusted-p value for GO-enrichment analysis but the p-value for the KEGG analysis?

-	In the Figure 9, I suggest to make a heatmap showing the expression profile of ¨hub genes¨, because the genes showed here are only a preliminary list of candidate genes that meet just one of the criteria taken into account and not correspond to the genes keep in the final list. Instead, this figure can be added as a Supplementary figure. If you decide maintain this figure, please indicate the meaning of the key scale and re-organize the clades in order to group the tissue condition to enhance the visibility of the clades in the x-axis. Another more simplistic option is provide a supplementary table with the FC of each gene and its associated FDR or adjusted p-value.
Validity of the findings: no comment
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 THE HUB GENES IN GASTRIC CANCER THROUGH WEIGHTED GENE CO-EXPRESSION NETWORK ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK
Additional comments: Identification of clinically significant modules: I still worried about the way you correlate a continuous variable and a categorical dichotomous variable. Because correlation talks about how much linear dependency is there between these two variables - if one variable increases whether another one increase or decrease- , your analysis is incorrect from a conceptual point of view. Furthermore, Spearson coefficient is used to correlate continous and a categorical which is ordinal/ranked, and so it is possible to obtain a linear relationship. Figure 5 A is definitely not a correlation matrix. And the pvalues obtained are ridiculously low, which is a bad sign. Please delete this correlation analysis and figure 5A from the manuscript.
In contrast, Figure 5B and its methodology are apropiate (since here you use a non-linear regression, which is oposite with your correlation analysis). Pvalues obtained in fig. 5B look more apropiate, and, in fact, they differ from figure 5A (black module pvalue is lower here than the blue module one, in contrast with figure 5A where it is not).
-
"l261: Using the screening criteria of |GS| > 0.75 and |MM |> 0.8, 148 genes were identified"
I dont understand your GS criteria; in fig 5B, maximum GS is close to 0.5

ROC curve figure will be much more informative if you integrate S fig3 curves, so visual comparison is straightforward. In addition, why didnt you perform cross-validation in the ANN regression to overcome overfitting 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: IDENTIFICATION OF THE HUB GENES IN GASTRIC CANCER THROUGH WEIGHTED GENE CO-EXPRESSION NETWORK ANALYSIS
Review round: 3
Reviewer: 1

Output:
Basic reporting: All the potential improvements have been fully adressed
Experimental design: All the potential improvements have been fully adressed
Validity of the findings: All the potential improvements have been fully adressed
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: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE OFP GENE FAMILY IN CHINESE CABBAGE (BRASSICA RAPA L. SSP. PEKINENSIS)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is not well written. The authors organized the paper so wordy and unclear. Extensive editing of English language is required. Besides,  the introduction failed to provide sufficient background and include all relevant references.
Experimental design: No comment.
Validity of the findings: The conclusions are not supported by the results.  The authors found that the expression levels of six OFP genes are higher in the Brassica rapa hybrid than in the parents. So, they summarized that the altered expression contributes to the heterosis. It's so weak. The changed expression of the genes in question may also contribute to hybrid weakness.
Additional comments: In this manuscript, the authors described the chromosal distribution of OFPs and their gene structure. They found all BraOFP genes owned light responsive-related and phytohormone-related cis-acting elements. Moreover, six OFP genes expressed at higher level in the hybrid than in its parents. It is likely that the findings in this paper may attract the interest of some readers in this field. However, I have some suggestions.
Major points:
1. The data don't support their conclusion that the altered expression contributes to the heterosis.
2. The manuscript is unreadable. Extensive editing of English language is required to make the manuscript clear.
3. The introduction failed to provide sufficient background.
Minor points:
1. Re-write the title.
2. Line 19: Define abbreviations and acronyms the first time they are used.
3. Line 20-23: The sentence is too long and unclear.
4. Line 34-73: So many unnecessary details.
5. Line 74-86: The research advances about OFPs evolution in related species?
6. Line 103-106: Move these sentences to "OFP gene expression analysis".
7. Line 176: rename? What's the original names?
8. Line 194: semblable --> similar
9. Line 199: Wordy.
10. Line 270 and 294: Additionally --> In addition
11. Line 270-272: All the subcellular locations were predicted. Besides, this sentence is too long and unclear.
12. Line 278-280: Wordy.


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: GENOME-WIDE IDENTIFICATION AND CHARACTERIZATION OF THE OFP GENE FAMILY IN CHINESE CABBAGE (BRASSICA RAPA L. SSP. PEKINENSIS)
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language is not great, with some unusual choice of wording and with a few typographical errors. For example, the term 'owned' was used in a very odd way perhaps 20 times in the manuscript. Possible the authors already had some general proof reading but not by a scientific proof-reader. I suggest they obtain some help from a scientific proof-reader service.

Literature was adequately cited mostly with two problems:
1) Some of the software used did not have any citation information (e.g. MEGA7) and similarly for some equipment (e.g. Qubit 2.0)
2) The authors wandered into discussion in the Results section and cited too much literature, which was more appropriate to the Discussion section.

The structure, figures and tables were good. My only criticism is that figures and tables did not provide footnotes or titles that explained abbreviations or specific terms. This prevented the tables and figures from being able to stand alone from the main text.
Experimental design: The process of identifying OFP genes was rigorous and useful. I am not aware of a similar analysis of this kind previously made in Brassica rapa.

I was not as happy about the way the RNAseq analysis was performed. Many genes are under diurnal control and so it is important to sample tissues at the same time for the parents and hybrid.

Equally importantly, it is unclear exactly what plants were sampled, only that there were 27 in total and 3 had biological replicates. This has to be clarified.

No measurements of biomass / other plant yield parameters were made and so no inferences can possibly made about heterosis. It is unacceptable that the term heterosis appears in the title, and I think it is doubtful that it can even be included in the abstract, only the Discussion.
Validity of the findings: The gene copy descriptions are valid and useful. Most relevant underlying data were provided. FPKM values in each plant should be provided along with standard errors or other statistical measure of variation.  It is unknown if the gene expression study had adequate controls as it was unclear about the nature of the replication. The discussion of heterosis is baseless without measurement of phenotype (e.g. biomass).
Additional comments: Give meaning of OFP in the abstract.
L65 Remove 'of cotton' (redundant)
L80 Replace 'fractionized' with 'fractionated'
L81 Restructure sentence as B. rapa has long season types (e.g. turnip) and a similar degree of morphological diversity as B. oleracea
L124 Rephrase this confusing sentence
L199-200 Note repeat information is provided in L204-205
L214 Replace ‘purifying’ with ‘purifying selection’
L222-223 This kind of statement belongs in the Discussion, not the Results.
L247 ‘which may also mean the functional diversgence of BraOFP7 gene’ is speculation, which does not belong in Results, which is for stating facts and observations. The same is true for the following complicated sentence (L248-252).
L252: The authors should spell out the evidence that indicates that introns were gained rather than lost in Brassica evolution.
L260 Explain the term ‘pI’
L281-282 Replace ‘it may become’ with ‘it is’
L303: It is unclear to me from your results that AT/Br pairs show a 1:1 relationship. As you covered previously, there is evidence for triplication followed by gene loss. Modify this statement.
L335-341: These references belong either in the Introduction or Discussion (or both), NOT in the Results.
L371 Cite your Figures or Tables in the Discussion section to support your arguments.
L417 Replace ‘transposable’ with ‘transposable element’ or ‘transposon’.
L468 This is complete speculation with no evidence provided to validate this discussion item. Phenotype information must be added or this aspect of the paper removed except for a sentence or two at the very most.


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: PHOTOSYNTHETIC RESPONSES OF HALIMEDA SCABRA (CHLOROPHYTA, BRYOPSIDALES) TO INTERACTIVE EFFECTS OF TEMPERATURE, PH, AND NUTRIENTS AND ITS CARBON PATHWAYS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This ms reports on the results of a physiological investigation on the interactive effects of temperature, pH and nutrients on photosynthetic characteristics in the tropical calcareous green algae Halimeda scabra. The paper is general well written, logically-structured and well referenced.  The introduction provides abundant background information on previous related studies and on the importance of Halimeda to tropical and subtropical reef systems.  The introduction also does a good job of setting up the rationale for conducting this particular study and why they examined the 3 abiotic variables of temperature, pH and nutrients.  The additional work investigating carbon acquisition mechanisms was also well presented and added to the discussion on possible mechanism responsible for the Pgross responses.  The figures and tables are clear and well described.
Experimental design: The authors use a clear 3-way factorial design, which they specifically describe in Table S1. The only major question I have about their methods involves their stated measurement of respiration in the light.  How was this done? Since other photosynthetic and respiration measurements were accomplished by measuring oxygen fluxes, the authors need to specify how they could measure respiration in the light, which is not possible with oxygen flux.  The authors also need to refer to their nutrient treatments based on relative concentrations (low, medium and high), not on ratios, which are constant at 10:1.
Validity of the findings: The statistical analyses of the experimental data were straightforward, clearly presented and appropriate to the authors’ objectives. Table S2 clearly shows which main effects and treatment combinations were significantly different from one another.  The authors do need to include more text in the results and discussion regarding the lack of a significant pH effect as this is a novel finding. Also, the control (no added nutrients), @low pH and high temperatures had the 2nd highest Pgross, which the authors do not discuss, although they do point this out in the results. This warrants some discussion. In Fig. 1 it appears that at low pH, an increase in nutrients reduces Pgross across temperatures while at high pH, nutrients increase Pgross.  These patterns need to be more fully discussed and possible explanations for the patterns need to be included.
The treatment of the carbon acquisition stable isotope and CA inhibitor data in the results and discussion is clear and well presented.
Additional comments: This paper presents valuable new data on the ecophysiology of an important macro-algae species.  With sufficient revision, addressing the comments above and those included in the annotated pdf, this paper should be suitable for publication.  Primarily, the similarity in Pgross responses between the control, low pH treatment plants and the high nutrient, high pH treatment plants with increasing temperatures needs to be acknowledged 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: PHOTOSYNTHETIC RESPONSES OF HALIMEDA SCABRA (CHLOROPHYTA, BRYOPSIDALES) TO INTERACTIVE EFFECTS OF TEMPERATURE, PH, AND NUTRIENTS AND ITS CARBON PATHWAYS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written and easy to follow. The ms provide general information about the topic covered. It is believed to be current and accurate, I would suggest to add some important references in the topic of carbon concentrating mechanisms in algae.

*Raven, J. A. 1997. Inorganic carbon acquisition by marine autotrophs. Adv. Bot. Res. 27:85–209.
*Beardall, J., Beer, S. & Raven, J. A. 1998. Biodiversity of marine plants in an era of climate change: some predictions based on physiological performance. Bot. Mar. 41:113–23.
*Fernandez, PA 2014. Bicarbonate uptake via an anion exchange protein is the main mechanism of inorganic carbon acquisition by the giant kelp Macrocystis pyrifera (Laminariales, Phaeophyceae) under variable pH. J Phycol. 50(6):998-1008.
*Beer, S. 1994. Mechanisms of inorganic carbon acquisition in marine macroalgae (with special reference to the Chlorophyta). Progr. Phycol. Res. 10:179–207.
Experimental design: Research questions are very well defined. However, I have some questions about the experiment design:

On line 121: The authors mentioned that n was = 8 bottles (I assumed this is one bottle per light treatment plus a blank). What about replication? how many replicates per treatment combination?  You have 3 pHs x 3 Temp x 4 Nutrients ratio x  ? replicates. They did not mention replication number per treatment combination. With a minimum of three replicate per treatment I got a total of bottles of 108. So, I would like to know how the authors carried out the photosynthetic measurements (e.g., all samples were carried out at the same time/day/hours?).

On line 124: The authors mentioned that the temperature was maintained constant, but they do not mention at what temperature. Were all experimental treatment combinations (pH, nutrients ratio and temperature)  carried out at the same time? they do not mention how the experiments were perform. This information is very relevant to interpret the results.

On line 139: Which is the reference for the seawater pH manipulation?
On line 170: How the seawater was sterilised (filter, autoclaved)?
O line 175: Why the authors used a different control temperature in this experiments (24°C vs 28°C)?
On line 182: Light saturation of 278 umol, How was this intensity estimated?

Results:

Figure 1: why the authors used a line graph instead of e.g.,  bar graphs ? were the experiments continuous over time? Did they used the same piece of tissue across the experimental temperatures? Also, why the graphs are separated by pH? were the experimental treatments carried out at different times? I would suggest to modify this figure and include the n replication in the legend.

Discussion:

On line 303: a CCM such us?
Validity of the findings: The results are novel and interesting for the specie, and conclusions are well stated according to the results.However, my main concern is about the replication and how the experiments where carried out. The authors will need to clarify this in the ms, previous acceptance of the ms.
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: PHOTOSYNTHETIC RESPONSES OF HALIMEDA SCABRA (CHLOROPHYTA, BRYOPSIDALES) TO INTERACTIVE EFFECTS OF TEMPERATURE, PH, AND NUTRIENTS AND ITS CARBON PATHWAYS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript "Photosynthetic responses of Halimeda scabra (Chlorophyta,
Bryopsidales) to interactive effects of temperature, pH, and nutrients and its carbon pathways"，in the study, it was divided into two parts, first part, it is about the effect of environmental factors on photosynthstic response of Halimeda scabra, second part, it is about the carbon pathways. Here are some major questions in the study, 1）please clarify the relationship between these two parts, the temperature is about 24℃ in field, and highest temperature in this sampling site is around 30℃, Why did you set highest temperature as 33℃, did you consider the temperature condition in future? Why all assays conducted at 28℃ in second part, did the condition (temperature and light saturation) from the first part experiment results? 2) which treatment is the basic control treatment in the experimental design，main effects and and interactive two of them on photosynthetsis, similar positive effect also caused by the interactive effect between high temperature and low pH. Why all didn’t be discussed?
I believe that study includes some meaningful results on the effects of photosynthesis for Halimeda scabra and its carbon pathways. So, I suggest that the authors revise the manuscript carefully and resubmit to PeerJ.
Here are some specific comments. Hopefully, it will help you to improve ms.

Specific comments:
English: proofread is needed.
Abstract:
P5 L19, 25: define Pgross and CCM for the first time in abstract
Introduction:
P7 L90：which kind of temperature (high or low) had positive synergistic effect in reference?
P7 L102: “nutrient ratios” change into “nutrient levels”
P8 L136-145：the content of experimental design move to line 115
P8 L136: How about the concentration of HCl and NaOH?
P8 L136: the ratio of nutrient is same in the experimental design, all “Nutrient ratio” suggest to change into “nutrient levels”
P9 L175: Why did you conducted carbonic anhydrase inhibition assays at 28 ℃，not the current cultivation temperature of 24℃?
P9 L182: In this experiment, there is no contents showed that the light saturation is 278 μmol photons m-2 s-1, how can you get it.
P10 L211: “p=0.0000” change into “p<0.001”
P10 L212-214: the result is too simple, is there major effect or interactive effects between two of them on photosynthetic? Show no details, and clarify the topic of sentence.
P10 L218-223: here described the effect of nutrients and pH effects on Pgross, the title is only show the temperature effects, it would be better clarify the background of  nutrient and pH ?
Figure legends：
P 20 L582：Please add the number of duplicate samples，“n=？”
P23 Figure 3：Complete the figure notes
P26 Tables：“Effect of temperature on P gross (Q 10 ) in three nutrient concentrations (Two Way-ANOVA)” change into “Effect of temperature on P gross (Q 10 ) in three nutrient concentrations and three pH levels (Two Way-ANOVA).”


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: A SET OF RT-PCR ASSAYS FOR DETECTION OF ALL KNOWN AVIAN PARAMYXOVIRUSES AND APPLICATION IN SURVEILLANCE OF AVIAN PARAMYXOVIRUSES IN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is written in clear, unambiguous language. Sufficient background and context is provided. The structure of the article is professional.
Experimental design: The research question is well defined. Ethical standards are met (including the use of animals). The methods are described in sufficient detail.
Validity of the findings: It would be beneficial to provide all of the surveillance data as opposed to only the positive. The negatives are likely informative as well.

I do have a concern about the specificity of the developed assays described in the manuscript. How can the authors establish the specificity of these assays? It does not seem like the authors have described this.
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: A SET OF RT-PCR ASSAYS FOR DETECTION OF ALL KNOWN AVIAN PARAMYXOVIRUSES AND APPLICATION IN SURVEILLANCE OF AVIAN PARAMYXOVIRUSES IN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript had generally good writing and presentation of background.

1. The Introduction should explain class I and class II NDVs. No mention of these two classes are made until Line 211 of the Results.

2. Line 195: To clarify, when you say “poultry”, which animals do you mean? Only chickens? Or chickens, ducks, and geese, but not pigeons? Perhaps cite Table 3 here. Also clarify what species are in poultry farms and markets.

3. Figure 2: What does the scale 0.05 mean?

4. Figure 2 caption: The sample labels appear to indicate species/location/___/year – I don’t know what the third item is. For example, “2126” in “Duck/Guizhou/2126/2018”.

5. Line 264: I’m not sure what you mean by “the surveillance of APMVs hitchhiked the surveillance for AIVs and NDVs”. Do you mean the APMV assay was done as a supplement on samples which were collected primarily for AIV and NDV detection?

6. Line 248: I suggest “dsRNA” instead of “RNA”.

8. Line 155: consider adding, “…using the hemoagglutination assay in order to test for the presence of virus” (or another appropriate explanation).

9. Perhaps mention in abstract that L gene is RNA polymerase

Some other small language corrections:
Line 37: I suggest saying "this RT-PCR assay" instead of "this assay".
Line 134: space in "assayin"
Line 203: "positives" -> "positive"
Line 241: I suggest "had been established" instead of "were established"
Line 251: “recognition” -> “knowledge”
6. Line 253: space in "NDVscould"
Experimental design: I thought the methods and question of the study were explained well.

1. Line 189: When you say “failed in sequencing”, do you mean that these positives were found to not actually be NDV? Or was there a technical failure during sequencing?

2. Line 193: “…our RT-PCR assays were significantly higher than…” What does this mean? Maybe the accuracy or sensitivity was significantly higher?
Validity of the findings: The conclusions seemed to match the data. The data files looked fine to me.
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: A SET OF RT-PCR ASSAYS FOR DETECTION OF ALL KNOWN AVIAN PARAMYXOVIRUSES AND APPLICATION IN SURVEILLANCE OF AVIAN PARAMYXOVIRUSES IN CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: I'm satisfied with the changes the authors have made following my earlier suggestions.
Experimental design: I'm satisfied with the changes the authors have made following my earlier suggestions.

Small correction: line 102 , "more stable"
Validity of the findings: I'm satisfied with the changes the authors have made following my earlier suggestions.
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: COVID-19: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is clearly written, with a good structure, figure tables and raw data shared.
The literature reference and the background/context is rather poor as far as the epidemic problem is concerned. It is acceptable, on the other hand, the literature on statistics and regression w.r.t. the problem at hand.
Experimental design: In my opinion the data set at hand is so poor that the use of data-driven models is not suitable. Few data points are available and their uncertainty is unclear. Moreover the use of the relation (1), with constants fixed as in Pueyo (2020), is crucial. How the results would change if these constants would be wrong? What is the validity of relation (1)? Pueyo (2020) is a blog, it is not a paper published on a peer reviewed journal, hence the present approach is based on a relation which is not supported by a scientific publication.

My personal feeling that any useful way to use these data should be model based, possibly using other assumptions suggested by epidemiologists. The tools used in the paper, both the bootstrap strategy and the algorithm to make associations based on similarity, are correct and sound; however I doubt that the results on this data set can be trustable, because few points are available.
Validity of the findings: I think that this paper fails to provide useful results for the estimation of the number of infected persons, because the data set is poor and because use of the equation (1) is problematic. I would not recommend any data driven method on this data set.
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: COVID-19: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see General comments for the author
Experimental design: Please see General comments for the author
Validity of the findings: Please see General comments for the author
Additional comments: The topic of interest in this article is timely and extremely important. In this sense, the article has the potential to answer one of the most important questions on the infection rate in the population. Please see my comments below.

Major:
1. In the abstract, it's mentioned that "The result obtained show that, while official data at March the 12th report 12.839 cases in Italy, the number of people infected with the CoViD–19 could be as high as 105.789." Please make the distinction between the number of reported infected people and the prevalence of the disease in the population. Here 12.839 is just the reported number and it's not claimed to be the estimate of the number of infected people in the population. So, please rephrase this sentence.

2. Please review the English language of the manuscript. There are some misuses of certain words.

3. Line 211-213, obviously the data published by the governments do not constitute statistical estimates of different rates in the population. They are just descriptive numbers. Thus, it is not fair to claim that "how the data collected by the Italian Authorities on the positive cases severely underestimate the current situation by a factor of about 8." This needs to be rephrased.

4. Line 28, "incorrect" is unsuitable to use with confidence interval since there is no correct confidence interval. Please consider that a confidence interval is an interval estimator.

5. The description of the proposed method in Section 2 is somewhat vague. Please rewrite this section to give a clear description of your method.

6. The validity of the ARMA assumption on the distance needs to be demonstrated. It is a quite strong assumption to expect to hold with a short time series data.

7. There is no reference given to Figure 1. Line 193, would be Figure 1-5 instead of Figure 2-5.

8. Please use a meaningful visualisation for the results presented in Table 2 and remove Table 2 from the manuscript.

9. Please include the file COVID_13_3_2020A.txt in your submission. Results are not reproducible without this file.

Minor:
1. You can consider using { } for your set definitions in Section 3.

2. you do not need to indent on line 68.


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: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 1
Reviewer: 3

Output:
Basic reporting: The overall paper is very well written. Quality of presentation, figures and tables, references cited are all satisfactory.

Minor comments:
line 24: mayor -> major

Why are the summations of Eqn 6,7 going upto 6?

line 196-197: denominator of C_T or w_T?
Experimental design: The fundamental components of the model is based on (Pueyo 2020). However this work itself is not peer-reviewed and not credible to this reviewer.

For example, in Eqn 1, proper estimates of \delta and \tau are challenging to get; why only consider average values when these terms may have large variance? The validity of Eqn 1 needs to be established properly as it forms the basis for the model proposed here.
Validity of the findings: The model depends on the currently recorded infected and death counts and does not consider the population density into account. This is somewhat captured in the average doubling time which in itself is not a good metric.

Since the model lacks credibility, all the corresponding conclusions are speculative at best. A proper validation of the model is required.

I would suggest the authors to execute a simple SIR or SEIR model using (i) the tested infected cases and (ii) the model estimates. It is expected that as time passes the model predictions come closer to the tested positives, considering the testing rates are increasing over time.
Additional comments: This paper tries to investigate a very important problem of estimated the actual numbers of infected people considering the tested positives in a region. However, the model needs rigorous validation exercises before it can be published. At its current state, the model is very speculative and makes some simplifying assumptions.


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: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 1
Reviewer: 4

Output:
Basic reporting: This is an interesting paper with specific and important objectives.

 Minor Comments

1.	Clear, unambiguous, professional English language used throughout. However, there are many stylistic issues, as noted below. The numbers in the last two lines of the abstract seem like decimals. Please change 12.839 to 12,839 and 105.789 to 105,789.

2.	Please choose more specific keywords. The current keywords such as “number of Italian people infected” or “model uncertainty” are vague.

3.	Line 9: do not use the word “diffusion” as it refers to randomness of disease spread. We don’t have any evidence supporting the randomness of COVID-19 spread.
4.	Lines 17,18: It is claimed that “people are tested for CoViD-19 on the 18 condition that some symptoms related to the virus are present.” Given the rapid changes in the policy and procedures related to COVID-19, can the author confirm that this is still the case.

5.	Line 69: change the word being with “where”
6.	Line 40: section 2 is not really the “proposed method” but an overview of the proposed method. Please

7.	Lines 75 and 76: Please include index “T” for C and M

8.	Line 84: the subscript should be capital T not small t

9.	Please include the related references for the first two paragraphs of the introduction. Your statements must be evidenced by reliable scientific publications and data sources.

10.	Equation 5, please change the notation of square root to the exponent of 1/2

11.	Lines 209 and 190: please include the links as references.

12.	Page 11, Table 1 should be centered.
Experimental design: N/A
Validity of the findings: Major comments

1.	The resampling method mentioned in section 4 are very standard and the author prefers, they can mentioned them in an appendix. Similarly, the max entropy method can be mentioned in an appendix

2.	Section 3: please include a map indicating the regions containing at least one death, and regions without any death.

3.	Is equation (5) always convergent? If yes, please mention it. If no, then state the condition under which the series is convergent.

4.	Lines 98, 99: Note that ARMA models work on the assumption of stationarity (i.e. they must have a constant variance and mean). You need to check if this assumption holds with your data. Specifically, check for stationarity before fitting an ARMA model---plot the data, inspect the sample ACF and PACF, pretest for unit root (ADF or other tests), difference if necessary, etc.

5.	The last row of Table 2 does not seem correct. Are the numbers on the third and fourth columns decimals or commas? Similarly, the population column has decimals instead of commas. The last column should be all decimals. Please correct them all.

6.	Lines 192-197: Figures 2-5 deserve a better explanation and justification. For instance, what is the justification for the huge spike in Figure 5?

7.	The distance function in equation 3 is not clear to me. Are we measure the distance from the center of a region without any death to the center of the region with death? Or we a measure the center of a region without any death to the closest death that occurred. If it is the first case, then you need to indicate it below equation 3. If it is the second case, then the data description in section 3 did not really mention the details of the data.
Additional comments: In conclusion: There are a few weaknesses in the statistical analysis (as I have noted above) which should be improved upon before Acceptance.


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: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The is no problem with reporting.
Experimental design: The research question is clear.
Validity of the findings: No problem identified on 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: COVID-19: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Presentation, language and references are fine.
Experimental design: Methods appear to be fine. However they are still speculative (See below).

Figs 1-5 are not that meaningful at all. They do not help with model validation in any way and simply show some numerical trends. These figures can very well be removed.
Validity of the findings: In the first round I asked for the following:

I would suggest the authors to execute a simple SIR or SEIR model using (i) the tested infected cases and (ii) the model estimates. It is expected that as time passes the model predictions come closer to the tested positives, considering the testing rates are increasing over time.

This comment was not addressed. The true infected as inferred by the model when incorporated in a SEIR/SIR model might be able to show the peak infections (timing and amplitude) which can serve as a model validation. It is expected that the reported infected counts will not be able to match the infection peak. This is specially meaningful in Italy where the curve has flattened already. I would recommend the authors to show a simple SIR model projection considering their estimated infected counts that should correlate with the observed peak infections in Italy.
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: COVID-19: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 3
Reviewer: 1

Output:
Basic reporting: Still, I find the statistical approach, and the handling of uncertainties, quite obscure for the general readership and I have doubts that precise inferences can be done out of these data. I see that the author has made some improvements in the new version but in my opinion the manuscript is not publishable yet.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Although the authors improved the paper, the revised version still fails to convince that the data analysis performed here, on these very limited data, would be interesting from the epidemiology's point of view.


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: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 3
Reviewer: 2

Output:
Basic reporting: All good with reporting.
Experimental design: Suitable
Validity of the findings: Validated appropriately.
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: COVID-19: AN AUTOMATIC, SEMIPARAMETRIC ESTIMATION METHOD FOR THE POPULATION INFECTED IN ITALY
Review round: 3
Reviewer: 3

Output:
Basic reporting: The presentation of the paper is fine.
Experimental design: The methods are rigorous.
Validity of the findings: The findings appear valid. The paper now includes a validation section which can provide some confidence to the results reported here.
Additional comments: My comments have been satisfactorily addressed.


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: MANIRAPTORAN PELVIC MUSCULATURE HIGHLIGHTS EVOLUTIONARY PATTERNS IN THEROPOD LOCOMOTION ON THE LINE TO BIRDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an exceptionally well written analysis and discussion of the evolution of the pelvic and hindlimb muscles in maniraptoran theropods. I have no major issues with this manuscript, and just a few definitional and organizational suggestions/ questions (below).

Page 6, Line 19: “controlled” is an unusual word choice. Influenced perhaps? Skeletal development is also influenced by genomic and other factors that are not direct musculoskeletal forces.

Page 10, Line 108: “leg” - do you mean thigh? Or the entire hindlimb? I would pick a more specific term – in a lot of anatomical literature the leg is the tib/fib, and thigh is the femoral region.

Results – it would be helpful to add subheadings for each taxonomic group (prior to inferred myology)

Table 5 – perhaps add to the caption that function is derived from previous studies and indicate that these were “averaged” for each muscle across the extant taxa. Were there any differences between sprawling animals and erect bipeds for muscle function in the extant literature? How do the numbers along the top correspond to the taxa in Table 1? This was not immediately obvious to me and could perhaps be clarified in the caption.

Figure 4: A, C, and D – is it possible to get clearer high resolution images of these panels? They are out of focus and very difficult to see.

Figure 6: just curious why this isn’t in color when PeerJ doesn’t charge for color? The Hutchinson etc papers usually use additional color labelling to demonstrate homologous origins/insertions across the various taxa. That would enhance the image.

Figure 7: The font size on this one is VERY tiny and hard to read. If it is at all possible to increase the font size for the key on the right side of the graph/chart and the genera along the top, that would be very helpful. Font size in Fig. 10 is also very very small and should be a little bit bigger so that the figure is readable without zooming in.

With PeerJ being an online journal, some of the supplemental figures could be added to the text. These data are valuable for comparison, and SI images often get lost (or forgotten) after a manuscript is published.
Experimental design: No comment beyond what is stated under Basic Reporting
Validity of the findings: No comment beyond what is stated under Basic Reporting
Additional comments: No additional comments