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 EXPRESSION ANALYSIS OF THE TREHALOSE-6-PHOSPHATE SYNTHASE (TPS) GENE FAMILY IN CUCUMBER (CUCUMIS SATIVUS L.)
Review round: 2
Reviewer: 1

Output:
Basic reporting: I consider that the authors answered the observations and comments made.  The information they added helped to complement the conclusions presented in this new version manuscript.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: No comment.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE TREHALOSE-6-PHOSPHATE SYNTHASE (TPS) GENE FAMILY IN CUCUMBER (CUCUMIS SATIVUS L.)
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The author has revised the manuscript as required. it can be acceptable 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: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF THE TREHALOSE-6-PHOSPHATE SYNTHASE (TPS) GENE FAMILY IN CUCUMBER (CUCUMIS SATIVUS L.)
Review round: 2
Reviewer: 3

Output:
Basic reporting: The paper is much improved in revision
Experimental design: Fine
Validity of the findings: Ok
Additional comments: The paper is much improved after revision


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

Input:
Title: PHYLOPRIMER: A TAXON-SPECIFIC OLIGONUCLEOTIDE DESIGN PLATFORM
Review round: 1
Reviewer: 1

Output:
Basic reporting: This article introduces a web-based tool for the design of taxon-specific primers and probes for microbial genes, and demonstrates its use by designing and evaluating primers for the genus level and species level detection of Streptococcus in several commercially available mock community DNA preparations.
The writing is excellent and I have only a few suggested changes:
1. Section 2, Implementation - the URL is needlessly given twice.
2. Line 213 - I noticed disagreement in verb tense. Check throughout to make sure tenses used are consistent.
3. Line 265 - Revise to "This is achieved by assigning..."
4. Line 357 - Change "nt" to nucleotide.
5. Line 364 - "The databases are not interchangeable." I doubt this is really what is meant. Maybe a better wording is, "The databases cannot be substituted."
Experimental design: The truly experimental part of this paper is the evaluation of the primers generated by the program. The methods are clearly presented and the results support the conclusions in the discussion section.

Currently section 2. Implementation stands by itself and is not part of the more traditional outline of Introduction, Materials & Methods, Results, Discussion. Because it goes into such detail about the design and workings of the program that it reads something like a methods section, and I wonder if it might  better be a part of Materials and Methods.
Validity of the findings: No comment.
Additional comments: No comment.


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

Input:
Title: PHYLOPRIMER: A TAXON-SPECIFIC OLIGONUCLEOTIDE DESIGN PLATFORM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript entitled “PhyloPrimer: a taxon-specific oligonucleotide design platform” submitted by Varliero et al. contains the description of interesting and useful bioinformatics tool for designing PCR primers for close-related bacterial species. However, I have some questions and technical recommendations to authors for enhancing their web tool. So, the main list of questions and recommendations using the numeration of strings are the following:
1.	String 39: the word “species- specific primers” should be without space after the hyphen, like “species-specific”;
2.	String 45: perhaps, should be noted that not only DNA, but also RNA can be used as the template for subsequent amplification (RT-PCR). The authors also can clarify that for PCR diagnostics of bacterial pathogens the most primers detect conservative regions of housekeeping genes;
3.	Strings from 87 to 101: the authors reviewed only well-known and popular web tools for primer design, but little information about tools for the primer dimer prediction (e.g. PrimerROC by Johnson et al., 2019 that can accessed at www.primer-dimer.com). The authors also should to cite some tools for PCR primer design like MPrimer (Shen et al., 2010), PrimerDesign-M (Yoon and Leitner, 2015), MRPrimerW (Kim et al., 2016), MRPrimerV (Kim et al., 2016), Oli2go (Hendling et al., 2018), and Uniqprimer (Karim et al., 2019). The pipeline of these tools very similar to PhyloPrimer at several stages (e.g. database screening, primer dimer check and scoring of final oligos). Please, briefly review these tools with similar workflow in the Introduction and make a comparison table of functions and useful options for these tools in the Conclusions;
4.	Strings from 109 to 111. Moreover, there are some tools for isothermal amplification methods (e.g. LAMP), which are also suggests annealing sites for oligos of 20 nucleotides. Therefore, these tools also can be used for PCR primer design. These tools include PrimerExplorer (Tomita et al., 2008; http://primerexplorer.jp/e) for primer design and MorphoCatcher (Shirshikov et al., 2019; http://morphocatcher.ru) for taxon-specific target screening using similar approach described for PhyloPrimer. I very surprised that authors use the same target DNA screening approach with alignment of orthologous genes and masking taxon-specific nucleotide positions without reference to the MorphoCatcher pipeline. The difference is that PhyloPrimer allows to automatize some steps of searching the orthologous sequences, making an alignment, but these points should be reviewed in your manuscript;
5.	String 145. The web address can be shown with http:// or https:// protocol. After the web link the space was incorrectly used;
6.	String 148. The time range can be shown as “40–50 minutes” and “5–10 minutes” (where “–“ is N-dash);
7.	String 151. The web links are without type of protocols;
8.	String 152. The web link is without type of protocol;
9.	Strings from 194 to 198. This part of the PhyloPrimer pipeline is identical with the MorphoCatcher pipeline. Please, clarify the difference of your approach;
10.	Strings from 203 to 204. Please, clarify how your pipeline can increase the level of taxon specificity using the certain nucleotide sequence. Some housekeeping genes as single sequence are rarely can be used for taxonomy of bacterial strains. In my opinion, the database should be validated by modern taxonomy and systematics, but if the approach uses the GenBank annotation only you should verify all orthologous sequences manually. Thus, automatization of this step should be verified by user or using different overall genome relatedness indexes (e.g. ANI, dDDH, or MLSA). The same question is to the “2.5. Databases” part of the manuscript;
11.	Strings from 406 to 407. Please, provide the original non-cropped images of your gels to verify the absence of primer dimers at weights lower than 100 kb;
12.	String 428. The “non-specific band” which was assigned to S. mitis or S. pneumoniae should be sequenced using Sanger method. If the sequence flanked by PCR primers for these two bacterial species are identical, the identity should be shown in text or additional figure.
Experimental design: Thus, I have several additional recommendations for enhancing the manuscript and this investigation. The authors should to provide these additional experimental data to clarify practical application of the PhyloPrimer tool:
1.	The gels after conventional PCR are good for demonstration size of the amplicons, but if the authors claim that the PhyloPrimer tool can be used for design primers and probes for qPCR (strings 48 and 53) I highly recommend to perform additional qPCR experiments with EvaGreen intercalation dye and melting curve analysis. The melting curve analysis can verify that each DNA band on gels is a single PCR product, because sometimes one DNA band contains two different sequences with the same length. Moreover, the melting curve analysis will be useful for evaluation of primer specificity during amplification;
2.	If differentiation of S. mitis and S. pneumoniae is difficult with the rpoB sequence, maybe the authors try to perform design primers to target another housekeeping gene? It is interesting to perform design of primers for the same PCR conditions (e.g. annealing temperature and magnesium ions) to claim the application of the PhyloPrimer tool for designing primers for multiplex PCR;
3.	It is highly important for phylogenetic analysis to use input sequences from validated database, but not from GenBank annotations. Modern phylogenomics reveals new species and genera each year from the deposited genomes and often some different species have very similar sequences of housekeeping genes. I recommend to use some mathematical approach for preliminary analysis of your databases, for example ANI (Goris et al., 2007) and core-genome MLSA (Neumann et al., 2019). Such approach enhance the accuracy of your primer design between target and non-target taxons.
Validity of the findings: I think that the PhyloPrimer tool will be useful tool for many researchers in molecular diagnostics. However, the manuscript can be enhanced with additional experimental data of primer specificity using the melting curve analysis. Computational or manual validation of the database used for creation of target and non-target groups is also very important for taxon-specific primer design.
Additional comments: Therefore, I think that after major revision of the manuscript this research work can be published in the PeerJ journal. I hope that authors can finish these additional investigations soon.

Best regards and stay healthy,
Your anonymous reviewer


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: PHYLOPRIMER: A TAXON-SPECIFIC OLIGONUCLEOTIDE DESIGN PLATFORM
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have adequately answered my previous comments for this section.
Experimental design: The authors have adequately answered my previous comments for this section.
Validity of the findings: No comment.
Additional comments: No comment.


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

Input:
Title: PHYLOPRIMER: A TAXON-SPECIFIC OLIGONUCLEOTIDE DESIGN PLATFORM
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: So, the authors made a user-friendly web-based tool for primer design. I only want to note that the References contain some incorrect formatting of Latin names for microorganisms, names of genes, incorrect symbols (e.g. "-" instead of M-dash), cutted titles of articles, and in some cases incorrect format of author's name. I agree that this tool will be helpful for many researchers, therefore the article can be accepted.


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: EVIDENCE OF INTEGUMENTARY SCALE DIVERSITY IN THE LATE JURASSIC SAUROPOD DIPLODOCUS SP. FROM THE MOTHER’S DAY QUARRY, MONTANA
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This was simple and concise reporting, and I am glad to see a student conducting and publishing their very own research. Tess should be very proud of her accomplishment. Documenting scale morphotypes in these small-statured diplodocids will be an important contribution towards further documenting and better understanding dinosaurian integument.


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: EVIDENCE OF INTEGUMENTARY SCALE DIVERSITY IN THE LATE JURASSIC SAUROPOD DIPLODOCUS SP. FROM THE MOTHER’S DAY QUARRY, MONTANA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The science here is good and the authors clearly made an effort to address the (apparently minimal) changes requested in prior review. I have mostly just a few comments related to readability of the text (see general comments, below). If I have one nitpicky issue, though, it would be the quarry map. I’m not sure it’s quite as good as it could be (maybe it is, I’m not party to all the info) – it just seems like a rather large area of uncertainty. It might also be useful to zoom in on the region of interest if possible – you can still have the whole map in the corner with a box indicating the zoomed in area, but I’m actually curious as to what variety of things are already mapped from the region of interest. I think the other figures are good, particularly given the difficulties of photographing things in the field and photographing things with relatively low relief. The one exception might be figure 9, in that it would be more helpful to know what part of the croc hindlimb we’re looking at – is that the trunk/limb transition that has the narrow, arching rows of scales? Is it the inside of the knee?
Experimental design: no comment
Validity of the findings: My one comment on the science is that while I think it’s probable that the rib and the skin are not associated, is it also not plausible that the carbonized skin simply eroded away, was removed accidentally in the excavation, or was not preserved from the surface of the rib? Are we looking at the internal or external surface of the rib?
Additional comments: Line comments:
Line 59 – I guess I would just make the note here that this is a “proposed” reason (perhaps “interpretation” is a better word)– I don’t know that it’s ever going to be possible to definitively prove it, even if the reasoning is pretty solid.
Lines 81-83 – unless this is a journal specific thing (I don’t think it is), I would just include the figure permissions in the caption for the map. I would also omit the second sentence as it is already assumed.
Line 87 – I’d make a figure reference here, at least to figure 2.
Line 90-92 – Again, I’d just omit this as it largely repeats the first sentence in the paragraph.
Line 109-110 – This repeats line 87.
General comment on the text in this section – I’d caution against using generic terms like “side” because it is not immediately clear which sides you mean – superficial/deep, anterior/posterior, etc. Please use specific terminology if possible.
Line 135 – “fetal”, perhaps
Line 140 – I’m not sure “diverge” is the right term here – perhaps “transition”?


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: EVIDENCE OF INTEGUMENTARY SCALE DIVERSITY IN THE LATE JURASSIC SAUROPOD DIPLODOCUS SP. FROM THE MOTHER’S DAY QUARRY, MONTANA
Review round: 2
Reviewer: 3

Output:
Basic reporting: All comments on manuscript. Some spelling and awkward wording issues.
Experimental design: All comments on manuscript.
Validity of the findings: Might be helpful to describe scale/tubercule types under headings and up front before describing the distribution of them on the skin patches.

Also, more direct comparison of the new types with previously described sauropod and more specifically diplodocid types would be preferred.

Other comments on manuscript.
Additional comments: All covered above or on the ms.


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: EVIDENCE OF INTEGUMENTARY SCALE DIVERSITY IN THE LATE JURASSIC SAUROPOD DIPLODOCUS SP. FROM THE MOTHER’S DAY QUARRY, MONTANA
Review round: 2
Reviewer: 4

Output:
Basic reporting: See general comments.
Experimental design: See general comments.
Validity of the findings: See general comments.
Additional comments: Many thanks for the opportunity to review this manuscript. Unfortunately at this time I cannot recommend it for publication, for several reasons:
• I  do not think it’s acceptable to publish on a specimen that is still in the ground when there are plans to excavate it in the future (vs. a scenario where the specimen cannot physically be excavated at all).
• The hypothesis that these skin impressions belong to a juvenile Diplodocus is not adequately supported yet, and alternative hypotheses are not investigated and rejected.
• In general, the manuscript needs to cite the dinosaur integument literature more extensively throughout.

I realize that the Covid-19 pandemic likely plays a role in my main concern about the specimen remaining unexcavated, which is really unfortunate. I know that this was raised by the editor prior to sending this to me to review, but I don’t find the current stated plan to excavate at an unidentified point in the future sufficient. If latex moulds of the specimen had been collected (e.g. as for the Dragon’s Tomb Saurolophus skeletons that remain partly in situ), or photogrammetric models collected, I might feel differently, but right now all we’re working with are field photos of partially exposed material. What if you can’t return to the site before the specimens degrade? I think this manuscript just needs to wait until the skin is physically collected and in a repository.

Despite this, I’ve taken a pass through the manuscript and have offered some suggestions for improvement for moving forward with the manuscript eventually. My other critique regards the identification of these skin impressions as belonging to Diplodocus – that seems reasonable at first glance given the predominance of Diplodocus in the quarry, but alternate identifications should be considered and you should attempt to reject alternate hypotheses. You should also consider whether or not the skin impressions could represent a region of an adult sauropod’s body in more detail, as identifying these as infant sauropod skin impressions is also a fairly bold claim that needs to be backed up with more evidence than is currently presented. I think your discussion of scale size is compelling and it would be good to see this expanded on by perhaps building a table of measurements of scale sizes in other dinosaurs with known skin impressions, either through a literature review or museum trips.

The reference list is currently very short and limited and I would strongly encourage the authors to dive into the literature on dinosaur skin impressions in much greater detail, including more references to scaly integument records outside of Sauropoda. The preserved integument is also variously referred to as a mould and as carbonous, which I think means carbonized or carbonaceous. This seems somewhat contradictory, as what I think we’re looking at is either a natural cast of the skin or the fossilized skin itself. This also warrants further discussion or investigation. In general, the manuscript could also use a bit more polishing, as there are several sentences that are either extremely vague, require citations, or have awkward phrasing.

I wish the authors luck in getting these specimens out of the ground in the near future (with hopefully few delays because of the pandemic!), and revising the current version of the manuscript.


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

Input:
Title: DNA-BASED DIVERSITY ASSESSMENT REVEALS A NEW CORAL BARNACLE, CANTELLIUS ALVEOPORAE SP. NOV. (BALANOMORPHA: PYRGOMATIDAE) EXCLUSIVELY ASSOCIATED WITH THE HIGH LATITUDE CORAL ALVEOPORA JAPONICA IN THE WATERS OF SOUTHERN KOREA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript has a clear goal: the description of a new species. The authors do so by combining morphological and genetic data, and compare their specimens with the type specimens of a closely allied species.

Per the "best practices" of peerJ, consider mentioning the name of new species in the title

The abstract needs to be improved grammatically, e.g. the first two sentences of the abstract are difficult to comprehend. Some of the sentences could be split into several shorter sentences as well. The discussion needs to be checked carefully for grammatical mistakes. Some examples are in lines 380, 396, 405.

The references are sufficient, the article structure is professional.

Table 1 is too large and hard to read, at least in its current form. Maybe move to the supplement, or try to turn it into a graph, e.g. heat map?

Figures are mostly well-constructed. I have a few minor issues, which I describe in the following:

Figure 1: species names and labels in general are pretty small and hard to read. Please enlarge them. Also, the colors are difficult against the map background. Maybe add a white background and use black and red font?

Figure 2: the abbreviations “RT” and “AP" in E and F need to be explained in the caption

Figure 5: It is not clear why some specimens are summarised (+ 2 sequences etc). Could this be handled differently? It looks confusing. I suggest you either write down all specimen names, or omit most of them?  If you omit most of them, you could label the “GenBank” tips with the species names you use on the side, and write down all of those specimens in the supplementary table. And only use individual labels for the specimens you sequenced yourself. This is not a “you have to do it this way” suggestion, but I do suggest you make this interesting figure clearer. The side labels are also not very clear. Could this become a table maybe? Or could you omit the countries of collection, as you have this info in figure 9?

Figure 8: under A, you write “Creusia spinuloda var. 1 sensu Darwin…”. It should be “Creusia spinulosa var. 1 sensu Darwin…”
Experimental design: Experimental design is mostly adequate. I only have one issue concerning the origin of the sequence data:

Lines 158-170: Do I understand correctly that the sequences were generated in Chan et al. 2018? If so, you should remove this section and refer to Chan et al. 2018 for the origin of the sequence data.
Validity of the findings: Overall, the link between sequences and morphology needs to be clarified. I think the authors had access to several of the specimens from which they used the GenBank sequence data. This is important to know because it increases my confidence in a correct morphological species identification. In general, this is a big issue when using GenBank data.

In addition, I have a few specific issues:
Lines 206-211: I think the parentheses are misplaced. As is, the sentences are partial. But they are all part of the bottles’ label? Instead of repeating the full label, consider introducing an abbreviation in the M&M section for each of the five bottles, such as “(hereafter referred to as the “Amboina” sample)” or similar.
Line 229: remove “and used”. Add a sentence detailing the percentage of missing data per marker.
Lines 239-244: I think this refers to the sequences of your new species.
Line 256: should it be: “with high sequence divergence”? Otherwise please rephrase, this sentence and the following seem to contradict each other.
Lines 259-261: How confident are you that the GenBank sequences were correctly identified?
Additional comments: My general comments concern mostly grammatical suggestions for the introduction.

In several instances, you write “the GenBank”. I would omit “the”.

Lines 57-58: what do you mean by lifestyle modes?
Line 99: replace “barnacle species did not match all available GenBank sequences” with “barnacle species did not match any available GenBank sequence”
Line 115: replace “euspinulosum’ from GenBank sequences “ with “euspinulosum’ entries from GenBank sequences “
Lines 117-118: Replace “As part of study, a mini-review on global distribution of Cantellius species was presented and discussed in aspects of management and conservation of the species diversity. “ with “As part of the study, a mini-review on global distribution of Cantellius species is presented and discussed with regard to management and conservation of the species diversity. “


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: DNA-BASED DIVERSITY ASSESSMENT REVEALS A NEW CORAL BARNACLE, CANTELLIUS ALVEOPORAE SP. NOV. (BALANOMORPHA: PYRGOMATIDAE) EXCLUSIVELY ASSOCIATED WITH THE HIGH LATITUDE CORAL ALVEOPORA JAPONICA IN THE WATERS OF SOUTHERN KOREA
Review round: 1
Reviewer: 2

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: Review
Hyun Kyong Kim et al. DNA-based diversity assessment reveals a new coral barnacle
(Balanomorpha: Pyrgomatidae) exclusively associated with the high latitude coral Alveopora japonica in the waters of southern Korea

One of the achievements of the present study is the retrieval of more than century old original material (Mortensen’s Pacific Expedition 1914–16), used by Broch for the description of C. euspinulosum, and comparing these to the new material using SEM techniques (figs. 3-4). These data are compared to the original graphic material (fig 8). The added to their data the description of the arthropodal characters which are missing in many if not most of the coral barnacles.
The general concept is that Cantellius is a generalist coral barnacle and there is no host specificity. It is the late W.A. Newman who proposed that host specificity is common within the coral inhabiting barnacles. (Hoekia in Hydnophora, Hiroa in Astreopra  and more). This concept was followed by other students of Cirripedia.
The authors used molecular techniques to support their hypothesis that Cantellius  from Alveopora is a monophyletic clade that currently is known from a single host species.  The molecular analyses justify that conclusion.

My conclusion is that the paper should be accepted with mini-minor revision.

In the legend to fig 5 the author should indicate that the phylogenetic tree is based on concatenated segment of 12S and COI.
I suggest that the authors will present the pairwise distances of the two molecular markers between the new species and the sequences from other barnacles morphologicaly  identified as C. euspinulosum. In addition they will indicate, in the text, what is the range of pairwise distances within C.  alveoporae specimens
Using the Zoobank data presented in the MS I could not find the new species. I am not familiar with this tool and it is possible that the data are released only after the paper is published.


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

Input:
Title: IDENTIFICATION OF QTL FOR BARLEY GRAIN SIZE
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript entitled “Identification of QTL for barley grain size” by Wang et al is focused on dissecting the genetic constitution of grain size in barley. Some interesting results have been obtained, which are valuable for understanding the genetics of grain traits in barley. However, the manuscript has some problems and needs correction before publishing. The author’s argument should be expressed in clear and readable English. There should be no errors of grammar. I have found numerous errors. Therefore, many improvements have to be made before this manuscript could be published in PeerJ.

1. Line 121, “The QTL analyses were based on BLUP from different sites/years”, it reads awkward. Please consider changing it” to “The QTL analyses were based on BLUP data of grain size from different years and sites”.

2. Line 157, Authors mentioned that MET-BLUP data were used in this study. However, they did not perform any methods of data analysis for MET-BLUP in the manuscript. The statistical analysis in Materials and Methods need to be described with more details about MET-BLUP.

3. Line 159, “Naso Nijo contributed longer grain alleles for QGl.NaTx-1H and QGl.NaTx-3H while TX9425 contributed longer grain alleles for QGl.NaTx-2H and QGl.NaTx-5H”, please rewrite this sentence.

4. Line 170, “QGw.NaTx-1H explained 9.5% of the phenotypic variance, with 4170979D1 being the closest marker and Naso Nijo contributing wider grain allele”, please rewrite this sentence.

5. Line 194, the subtitle “Comparison of seed size among different pairs of near isogenic lines differing in malt extract” is too long, please rewrite it.

6. Line 201, “Ten rice genes were identified in determining rice grain sizes (Table S1)” should be changed to “Ten genes determining rice grain size and their orthologs in barley were collected in Table S1”.

7. Line 205, “No rice homolog genes were identified on 2H and 3H QTL. However, genes within these QTL potentially involving phytohormones biosynthesis, cell elongations were also listed as potential candidate genes”, please rewrite this sentence to describe the results of QTL analysis more clear.

8. Line 237-241, “QTL alleles that made seeds larger or rounder also tended to improve malt quality but QTL alleles that increased the variability of the grain size were associated with poor malt quality (Ayoub et al., 2002). In this study, the QTL on 2H for GL is located at a similar position to that for malt extract (Wang et al., 2015). QTL analysis for GL using malt extract as a covariate showed a close linkage between these two genes instead of a pleiotropic effect”. The statement is ambiguous, please rewrite it.

9. Line 244, “Based on the cloned grain size genes in rice, we found three barley ortholog genes to rice within the identified QTL region in this study”, please rewrite this sentence.

10. Line 271, “Based on above knowledge”, please rewrite it.

11. Line 276-278, Several major QTL for grain size were identified. The major one on 2H is linked to the QTL for malt extract but controlled by different genes. The other one on 3H is in a similar position to a dwarf gene, uzu, but not due to a pleiotropic effect of uzu. The statement is ambiguous, please summarize the results in this study more clear and more readable.

12. The specific name of near isogenic lines should be added and showed in Figure 2 and the authors should provide a detailed description in this paper.

13. The word “QTL” should be instead of “QTLs” in many places in the manuscript.


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

Input:
Title: IDENTIFICATION OF QTL FOR BARLEY GRAIN SIZE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Basic report
1. Professional English. The draft has some issues for text improvement, such as the use of unabbreviated terms right after the abbreviation (line 27 for GW), requirements for rephrasing for some long sentences that are poorly structured, misspelling on Table 3. Sentences in lines 181-183, 222-224, 234-236, 237-239 are unclear and should be rephrased. Also, line 201 is written poorly and looks like plagiarism. I should also mention that English is not my primary language, so I can’t help improve the ms.
2. Introduction and References. It would be more informative to introduce QTL for GL or GW obtained via GWAS, if available.
3. Structure. The structure of the manuscript (ms) is good enough.
4. Figures. Figures of the ms are appropriately provided and given in good quality. Tables 1 and 2 have some abbreviations that should be unabbreviated in notes under Tables.
5. Row data. I didn't find the results of QTL mapping from three different sites and studied years.
Table 2 suggests that location and Year are significantly important for the variance of studied traits. Therefore, it would be informative to learn if those identified QTL were stable in different locations and years or not. Some incomplete information is given in the Results section with reference to Table 3. However, Table 3 has no QTL mapping data based on environment studies.
In the Abstract, the authors stated that grain size might vary in different environments. However, in the Results section, no sufficient data were provided to confirm this claim.
Experimental design: Experimental design
1.	Scope of the research.
A.	The authors provided results of QTL mapping for key grain parameters, such as grain length and grain width. I wonder why they didn’t include grain weight, which is another important yield-related trait? This way, they may connect selected morphological traits with the yield.
B.	It would nice to see if those identified QTL for GL and GW were stable in studied sites and years?

2.	Questions and hypothesis. As mentioned above, the authors stated that grain size might vary in different environments. However, in the Results section, no sufficient data were provided to confirm this claim. This is related both to morphological analysis of traits and QTL mapping.
3.	High technical and ethical standards. I think there no problems here, except the unfortunate sentence in Line 201.
4.	Detailed and informative Methods. Materials and Methods were described sufficiently.
Validity of the findings: The validity of the findings
1.	Report on the identification of two novel QTL for grain size is sufficient for the Results' novelty.
2.	Provided data were sufficiently robust. However, more statistical analyses, such as a correlation and genotype-environment interaction patterns, might be applied to describe the variation of two traits in studied environments.
3.	Speculations. In the Abstract, the authors speculated that grain size might be affected by environmental factors. However, no QTL mapping results for GL and GW supported this statement.
4.	Sentences in the Conclusions section should be rephrased.
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 QTL FOR BARLEY GRAIN SIZE
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well written and structured as a standard manuscript on QTL mapping in barley and identification of candidate genes behind QTLs. However, there are some small words missing or incorrect use of English, so proofing of English grammar is recommended.
The introduction give sufficient details and reference for this study, with links to similar studies in rice. This manuscript is a continuation of work carried out by the authors over the last 10 years and could be regarded incremental.
Legends to figure 1 and 2 needs a lot of elaboration, many information is missing, otherwise the figure can not be understood. Statistics in figure 2 is missing. Which isogenic lines were used?
Experimental design: The preparation of the barley DH crossing population was published by the authors some years ago, together with the field trials. It still fulfil general requirements for number of environments, years and replicates, and the grains harvested at that time has been published.
Research question is well define, but narrow and too little for a full publication, short communication seems more appropriate.
Validity of the findings: The findings are interesting, in particular taken together with already published grain and malt quality on the same material.
What would be an interesting addition is to demonstrate the use of identified markers in breeding program.
Or validation of identified candidate genes under the QTLs.
There is no information on nitrogen fertilization of the field trials, as this will effect the protein content and may change the balance between hordein (storage proteins) and albumin. It should be easy to determined total-N on grains and calculate protein-%, do GWAS  etc.
Additional comments: see above


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

Input:
Title: IDENTIFICATION OF QTL FOR BARLEY GRAIN SIZE
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In my opinion, the revised version of the manuscript 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: IDENTIFICATION OF QTL FOR BARLEY GRAIN SIZE
Review round: 2
Reviewer: 2

Output:
Basic reporting: ok, see previous review
Experimental design: ok, see previous review
Validity of the findings: ok, see previous review
Additional comments: I still recommend that grain protein-% and TGW is included in the study.


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

Input:
Title: EVALUATION OF CIRCULATING TUMOR CELLS AS A PROGNOSTIC BIOMARKER FOR EARLY RECURRENCE IN STAGE II–III BREAST CANCER PATIENTS USING CYTOSORTER® SYSTEM: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The method used in the study is remarkably efficient comparing to the other systems, but there is a very little information about it in the study itself, but also generally in the literature. It should be better described (and probably deserves some comparative study with, for example, CellSearch system?).
Validity of the findings: 1. The group of 36 patients in the study is very heterogeneous in almost every parameter. This is not optimal for the analysis of such a small group of patients. Some correlations may not manifest themselves, because the numbers in the analyzed subgroups are too small to find significance. It makes the study less reliable.
The description of the multivariate analysis is somehow cryptic and it is not clear how many parameters were included (“all univariate significant factors”, which means two? That’s hardly multivariate). On the other hand, fourteen is too many. This needs clarification.

2. It is not clear how the authors came up with the cutoff value of 4? Was the receiver operating characteristics performed?
Additional comments: In the manuscript entitled „Evaluation of circulating tumor cells as a prognostic biomarker for early recurrence in stage II-III breast cancer patients using CytoSorter® system” the authors address a very important issue of finding new ways to stratify patients with early breast cancer to assess the probability of metastasis, which is crucial for choosing the treatment options. The authors use a very efficient new method and their results imply that the pre-operative CTC count may be useful in the identification of BC patients with a higher risk for early recurrence. While the whole manuscript is well written and compelling, there are some issues that need to be addressed (details in sections: experimental design, validity of the findings).

Minor comments:
1. The caption of the Figure 1 is slightly incorrect, since the figure presents not only Kaplan-Meier curves but also (representative?) images of the identified CTCs.
2. The description of patients clinicopathological characteristics is in Table 1 not Table 2 (verse 172).
3. The citation of Bidard et al. (ref 17) to show that CytoSorter has a higher CTC detection rate than CellSearch is not correct since it does not mention CytoSorter and even general statements about microfluidics are not that categorical.


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

Input:
Title: EVALUATION OF CIRCULATING TUMOR CELLS AS A PROGNOSTIC BIOMARKER FOR EARLY RECURRENCE IN STAGE II–III BREAST CANCER PATIENTS USING CYTOSORTER® SYSTEM: A RETROSPECTIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: English used throughout the paper is sometimes incorrect, as well as there are some sentences difficult to understand and spelling mistakes.ex: lines 54, 75-77,82,116...

Some concepts should need more details, such as "triple negative" to make it comprehensive to the readers.

In some sentences references are needed. ex: line 68, 236, 238

The statement in line 78-79 should be revised.
Experimental design: Some of the parameters for the selected patients included in the study present bias: T and N stage, Hormone status, different treatments and CTCs. It would be better to compensate the groups.

The number of patients incuded in the study is very small. The cut-off value (4) should be validated in a larger number of patients.
Validity of the findings: In the results section "correlation of patients characteristics with recurrence and distance recurrence", some information regarding the clinicopathological characteristics is detailed (line 159-165). This information would fit better in the materials and methods section, in order to not confuse the readers with too much number information.

The cut-off value set up has a specificity of 55,6%, which means that almost half of the patients would be diagnosed as a positive being negative for the recurrence. This misclassification could generate over treatment of the patients among others.

In the conclusions the authors don't mention the disadvantages of using an EpCAM enriching device. Moreover, since the technology used to detect CTCs is quite similar to the already method aproved by the FDA (CellSeacrch), it would be interesting to make a point (less confusing than lines 217-221) of the potential advantages of CytoSorter over CellSearch.
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: EVALUATION OF CIRCULATING TUMOR CELLS AS A PROGNOSTIC BIOMARKER FOR EARLY RECURRENCE IN STAGE II–III BREAST CANCER PATIENTS USING CYTOSORTER® SYSTEM: A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: I have no further comments.
Experimental design: My comments have been addressed. I have no further comments.
Validity of the findings: My comments have been addressed. I have no further comments.
Additional comments: I have no further comments.


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

Input:
Title: EVALUATION OF CIRCULATING TUMOR CELLS AS A PROGNOSTIC BIOMARKER FOR EARLY RECURRENCE IN STAGE II–III BREAST CANCER PATIENTS USING CYTOSORTER® SYSTEM: A RETROSPECTIVE STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Dear Authors,
Thanks for the clarification and for introducing changes in the manuscript. I would recommend the new version of the manuscript to be published. However due to the impact that CTC can have in clinics it would be interesting to validate these results in a large number of patients, as well as in a more homogeneous samples.
Sincerely,


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

Input:
Title: HOW THE FEAR OF COVID-19 CHANGED THE WAY WE LOOK AT HUMAN FACES
Review round: 1
Reviewer: 1

Output:
Basic reporting: please see below
Experimental design: please see below
Validity of the findings: please see below
Additional comments: This is a nice study showing how covid-related information can shape the exploration of face stimuli. Briefly, participants made more fixations towards the eye region of faces described as belonging to covid-free individuals. Some comments are following.

1)  As far as I have known, ”eye contact effect” is an expression introduced by Senju et al (Senju & Johnson, 2009) to describe a wide set of neuro-cognitive consequences of making eye contact with another person (hence, it is not only restricted to attentional mechanisms). Other research groups, such as that of Hietanen, provided further insights and proposed the “watching eyes effect” (Conty, George, & Hietanen, 2016). You could therefore provide a short overview of the many meanings related to the “eye contact effects” by referring to these two works since they are relevant for your own study.

2) Eye-gaze stimuli are powerful stimuli that can deeply shape visual attention. Other than attentional capture and holding, they can also elicit spatial orienting, as recently summarized by a recent review paper, which could be briefly mentioned to provide a broader and more complete overview of this topic  (Dalmaso, Castelli, & Galfano, 2020)

3) Lines 111-114: I wouldn’t say your task doesn’t involve conscious control, especially because you focused on fixations, which can be modulated by participants' will. Please clarify this paragraph.

4) Looking at figure 1, one face was Asian, so I’m wondering how many other non-Caucasian faces were used (assuming that your participants were all caucasian). It’s well established that race can impact face processing and face scanning. I’m thinking, for instance, about a seminal work by Blais and colleagues you might cite (Blais, Jack, Scheepers, Fiset, & Caldara, 2008). Hence, I’m wondering why you decided to include faces belonging to different ethnic groups. More details about participants’ ethnicity could be also provided (if possible).

5) I’m not an expert on eye-tracking methodology, but just wondering whether some works tested the reliability of the data you’ve collected in such a way. Referring to some methodological papers could support your approach more strongly.

6) Data analysed split into two different time windows (500 ms and 5000 ms) could sound rather post-hoc, at least to me (you only cited one of your own work, Fedrico & Bradimonte 2019, to support this approach), despite the very same results emerged in both windows. So, I guess you might be able to provide more theoretical motivations for that.

7) Did you check whether participants contracted the virus? (or even if they were positive at the time of the experiment). This should be definitely clarified.

8) Figure 3: figures showing “example” participants should be always avoided, at least to me. You should show mean data from the whole sample, otherwise please remove the pic.

References
Blais, C., Jack, R. E., Scheepers, C., Fiset, D., & Caldara, R. (2008). Culture shapes how we look at faces. PLoS ONE, 3(8). https://doi.org/10.1371/journal.pone.0003022

Conty, L., George, N., & Hietanen, J. K. (2016). Watching Eyes effects: When others meet the self. Consciousness and Cognition, 45, 184–197. https://doi.org/10.1016/j.concog.2016.08.016

Dalmaso, M., Castelli, L., & Galfano, G. (2020). Social modulators of gaze-mediated orienting of attention: A review. Psychonomic Bulletin & Review, 27(5), 833–855. https://doi.org/10.3758/s13423-020-01730-x

Senju, A., & Johnson, M. H. (2009). The eye contact effect: mechanisms and development. Trends in Cognitive Sciences, 13(3), 127–134. https://doi.org/10.1016/j.tics.2008.11.009


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

Input:
Title: HOW THE FEAR OF COVID-19 CHANGED THE WAY WE LOOK AT HUMAN FACES
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the submitted manuscript, the authors compared gaze exploration behavior of faces that were previously labelled as: COVID-19 Free, Sick with COVID-19 and Recovered from COVID-19. The authors analyzed the eye movement data in two regions of interest, eyes and mouth, and reported that participants fixations were longer when looking at COVID-19 Free faces compared to the other two categories. This was true both for the first 500 ms of visual exploration as well as for the full exploration time of 5000 ms. Moreover, in the full exploration time window, participants fixated more the mouth region of Sick with COVID-19 and Recovered from COVID-19 faces, compared to COVID-19 Free faces. The authors suggest that the exploration behavior is indicative of a threatening perception of the COVID-19 faces (i.e. less time spent looking at the eyes) with more attention deployed on the possible vehicle of transmission (i.e. more time spent looking at the mouth in COVID-19 and Recovered from COVID-19 faces).

Overall, I think that the paper is very well written. The introduction and the discussion are exhaustive and well referenced, the method and result sections are very clear and easy to follow. The authors also provide all the raw data collected for the study.
Experimental design: The research question and the hypotheses are clearly stated at the end of the introduction section. I find the methods used in the present paper quite innovative. First the use of machine learning algorithms to create the stimuli and avoiding possible confounds related to facial features. Then, the use of an online platform allowing to reliably record eye movement patterns that, despite the spatio-temporal resolution constrains of the webcam, represent a very informative marker of people behavior. In general the method section is complete and properly described.

2.1 I have one question that I would like the authors to comment. The authors conclude that the avoidance behavior expressed with shorter fixation time on the Sick with COVID-19 faces reveal avoidance for a threatening stimulus. Do the authors expect to see a similar pattern of results if also another disease was used as immunological status? I think this would have been a good control to understand the impact of being in the middle of a pandemic on the perception of different diseases.

2.2. In the example of the stimuli used, the faces represent relatively young individuals. We know that COVID -19 affects especially the older portion of the population. From which age range were the faces generated for the study? Do the authors expect to see an effect of “age”, considering that the severity of the disease is directly linked with this factor?
Validity of the findings: 3.1 The difference in mean fixation between the different conditions is very small, about 25 ms in the first 500 ms interval and about 200 ms in the 5000 ms interval. From an eye movement perspective, 25 ms is about the time of saccade and I am a bit skeptical that it is enough to gather relevant information about the stimulus to support a difference between the two conditions. The 200 ms difference is a more reasonable duration, basically the mean duration of a fixation when looking at a stimulus. How do the authors interpret the magnitude of the effect they report? Are 25 ms really enough to acquire information and to lead to the avoidance of the stimulus? Moreover, the temporal resolution of the webcams used for the experiment is of 20Hz, that is 50 ms. This gives only 10 samples in the 500 ms time interval. This methodological aspects reduces my confidence in the 25 ms difference reported by the authors.
Additional comments: Minor comments.

In general, I would suggest to change the measure to "dwell time" rather than fixation time. Fixation duration usually refers to the duration of the single fixation, that I think you can not derive from your recording system.

For the plot, I would suggest to maybe use bars rather than lines, since “eyes” and “mouth” are two categorical factors and there’s no need to link them with a line. Also, it is not reported what the error bars represent in the plot.

Line 78 and elsewhere: The “JOHNSON” reference is formatted in capital.
Line 179: This reference seems to have the wrong formatting: “P Slovic, 198”
The numbering of the figures is weird. Figure 5 seems to be presented before Figure 2 and 3.


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

Input:
Title: HOW THE FEAR OF COVID-19 CHANGED THE WAY WE LOOK AT HUMAN FACES
Review round: 1
Reviewer: 3

Output:
Basic reporting: Line 48-50 it is not the depigmentation to be crucial but the relative contrast between sclera and iris (see Perea-Garcia et al, 2019: https://www.pnas.org/content/116/39/19248). Hence other primates are able to follow the gaze of a cospecific.
Experimental design: Line 304: The scree test could be unrelieble. Please use Horn’s parallel analysis, "the method of consensus in the literature on empirical methods for deciding how many components/factors to retain" (Dinno, 2009).
Validity of the findings: From the results it is not clear the role of the mouth as a possible threat. This is demonstrated by the fact that there is a significant correlation between severity and fixations of the mouth in the recovered-from-COVID-19 face condition but not in covid-19 face condition, it is puzzling this absence of a significant correlation.
A possible solution, in my opinion, is to add open mouth faces in the experimental design. Following authors' hypothesis an open mouth, representing a more dangerous threat, should collect more fixations then a closed mouth. This latter condition could solve what I think is the major weak point of this work.
Additional comments: I found the paper very interesting but affected by a major weakness. In order to make the conclusion more sound I think authors must improve their experimental design as suggested in section 3.


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

Input:
Title: HOW THE FEAR OF COVID-19 CHANGED THE WAY WE LOOK AT HUMAN FACES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I'm happy with the revised version of the manuscript.
Experimental design: I'm happy with the revised version of the manuscript.
Validity of the findings: I'm happy with the revised version of the manuscript.
Additional comments: I'm happy with the revised version of the manuscript.


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

Input:
Title: HOW THE FEAR OF COVID-19 CHANGED THE WAY WE LOOK AT HUMAN FACES
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors responded to all my questions. The corrections provided by the authors improved the readability and the clarity of the manuscript.


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

Input:
Title: HOW THE FEAR OF COVID-19 CHANGED THE WAY WE LOOK AT HUMAN FACES
Review round: 2
Reviewer: 3

Output:
Basic reporting: The paper has been improved as suggested
Experimental design: Is acceptable given the the measure put in place to prevent the spread of the virus.
Validity of the findings: The authors improved their conclusions
Additional comments: I appreciated the work done by the authors to improve the paper. I understand their problems in managing a further control condition (I.e an open mouth or a much more simpler case consisting of a mouth covered by a protective mask). Given the resolution of the webcam the authors used (20hz), a problem also raised by another reviewer,  I suggest the authors to stress this limitation in all the captions in which ms are reported, in fact the resolution is not 1ms but rather 50ms! Furthermore, the second part of the title of the paper can be misleading, clearly it is not covid19 per se that changes the way we look but instead the risk to acquire the infection.


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

Input:
Title: HOW THE FEAR OF COVID-19 CHANGED THE WAY WE LOOK AT HUMAN FACES
Review round: 3
Reviewer: 1

Output:
Basic reporting: The paper has been improved as suggested.
Experimental design: The paper has been improved as suggested.
Validity of the findings: The paper has been improved as suggested.
Additional comments: The paper has been improved as suggested.


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

Input:
Title: THE ROLE OF ORTHOGRAPHIC NEIGHBOURHOOD EFFECTS IN LATERALIZED LEXICAL DECISION: A REPLICATION STUDY AND META-ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a very interesting manuscript on hemispheric differences in the size/direction of neighborhood effects during word identification. It contains two interesting studies, the first study (empirical) was conducted to solve some previous discrepancies in the literature, and the second is a systematic review that offers both the whole idea and also some guidelines for future research. The manuscript was also very well written and elegantly analyzed.

The literature background is excellent. However, when indicating the reviews of neighborhood effects, the range of the cited reviews was from 1992 to 2001 (i.e., 20 years ago!). This offers the reader that the field is not (highly) active any more. Perhaps citing a more recent review of neighborhood reviews would be a good idea. There is a relatively recent review in 2015 on “Neighborhood effects in visual-word recognition and reading” published as a review chapter in The Oxford Handbook on Reading edited the Pollatsek and Treiman (doi:10.1093/oxfordhb/9780199324576.013.7)
Experimental design: The experiment (Experiment 1) has been competently conducted. The potential limitations (e.g., due to the online testing) have been cited and discussed. The systematic review has been competently conducted.
Validity of the findings: The findings have important implications for reading researchers.
Additional comments: I believe the the authors need to add an Introductory paragraph in the Introduction that engages the readers of the paper to eagerly continue reading it. It goes straight to what an orthographic neighbor is. This may work for the "word nerd" community, but not outside. The authors should be able to handle this issue easily.

Also, at the end of the manuscript, the authors need to offer the broader implications of their findings.


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

Input:
Title: THE ROLE OF ORTHOGRAPHIC NEIGHBOURHOOD EFFECTS IN LATERALIZED LEXICAL DECISION: A REPLICATION STUDY AND META-ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a bold trial to run visual field studies via online platform. The writing style is clear and professional, and the authors managed well the tricky work of merging empirical and review writing.

The introduction and discussion should pay some attention to the fact that the original Perea et al study from 2008 was conducted in Spanish, a language with much shallower orthography than English therefore the N effects might differ due to different information loaded at the beginning and ends of words.
Experimental design: It is encouraging to see that the visual field by N effects was replicated, even though it was not possible to control the actual distance, refresh rates, keyboards differences etc when subjects conducted the study at their homes. Most subjects were excluded due to lower handedness score rather than technical issues resulting from home-based sessions. Since the replication differs on crucial aspects from the original (different language), I wonder whether applying a strict handedness criteria is really justified? I think it is important to analyze all subjects to further validate the possibility of remote lab testing without direct control of actual visual fields, different hardware etc.
Validity of the findings: The replication supports the validity of remote lab tests.

The meta-analysis is good, the small number of studies is not surprising and represents well the research in this field.
Additional comments: Parker et al. did a great job and it is clear that on top of performing good science, they are interested and invest a lot in meta-science and the tools that enable transparent and honest science. I enjoyed very much seeing how our old ideas were tested and receiving new and brilliant interpretation. I wish that Carol Whitney could have seen this! She would love it. Alas Carol sadly died in 2019 after a brief illness.


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 A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study was carried out with detailed bioinformatics approach. Reasonable references were used to cover all the background about the research. The figures and tables are clear to understand the goal of the study. Also the results are focused.
Few points would be important to add,
1. Are the normal tissues collected from the adjacent part from of HCC patients?
2. It would be important to know if HCC patients had any other health conditions.
Experimental design: Experimental designs are hypothesis directed and answered most of the necessary questions. Also, the experimental approaches are reasonable and precise. The methods are explained in full details.
Validity of the findings: The findings are interesting and this study has provided sufficient data to strengthen their hypothesis.
Additional comments: Very detailed approach.


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 A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The writing is well organized and professional
Experimental design: The details of the analysis is well described
Validity of the findings: The methods are well described and that support their findings of the targets at the RNA level. However, a few more additional experiments will enhance the quality of the paper.
Additional comments: This article aims to identify markers for overall survival in HCC. Overall the methods are well detailed and the analysis well presented. The authors have identified some of the shortcomings such as validation of protein. Some of my comments are as follows

1.	Line 178 - 5 genes were altered in 93 (25%) of 372 samples. This appears to be a small percentage and sample size to be a marker without any protein verification. Any verification at the protein level is important and will increase the impact of the paper,
2.	Discussion lines 199 to 220 – For most targets, the authors have mentioned how they might have an important role but does not describe the role in details. Kindly elaborate the discussion further.


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 A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a well-written manuscript that identified a prognostic model with 5 genes by transcriptomic analysis on hepatocellular carcinoma databases. This 5 gene-based risk model was further validated by TCGA-LIUC and GSE14550 databases.
Experimental design: Some comments:
1. In the introduction, the authors need to introduce the current gap of the prognosis model for liver cancers and how this study can fill the gap.
2. Figure 1, I would suggest the authors to include a supplementary table listing the 15% upregulated genes in the tumor tissues. This would help increase the impact by allowing further exploration of the signatures by readers.
3. Are these 5 genes relevant to the clinical-pathological characteristics of the disease such as TNM stage, pathological type. etc?
Validity of the findings: The results have some promise but given the contradictory nature can you back it up with some experimentation to validate the finding?
Additional comments: No.


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

Input:
Title: IDENTIFICATION OF A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 4

Output:
Basic reporting: There are several grammatical mistakes at different places in the manuscript. For example in the methods part of the highlight section in the beginning there is a sentence that ends abruptly (" Then, gene set enrichment analysis (GSEA) was used to identify. "). There are several such mistakes and the authors should carefully review and correct these grammatical errors.

The literature review provided by the authors is very brief and almost irrelevant. Readers and reviewers would definitely gain from knowing other research efforts to identify prognostic gene expression based biomarkers in HCC or even other types of cancers.
Experimental design: The experiment design and the analysis performed by the authors was thorough. However, it would be beneficial if they compared their work and results with other efforts to identify gene-expression based biomarkers.
Validity of the findings: The authors showed convincingly that their 5-gene signature was sufficiently predictive of OS and PFS.
Additional comments: The analysis was straightforward and easy to follow. The authors clearly show the prognostic power of the 5-gene expression based signature in HCC. Some literature review and relevant to the point motivation for the study will help readers appreciate the work.


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

Input:
Title: IDENTIFICATION OF A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 5

Output:
Basic reporting: Manuscript details
Journal: Peerj
Manuscript ID: Peerj - 55265
Type of manuscript: Article
Title: Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
In this manuscript entitled “Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma”. There is some useful information, however, the further modification is required, and I have provided several advices shown below.
1.	This article uses a lot of data analysis, but the main reason for selecting these dataset is not very clear. I hope the author can discuss it in detail.
2.	The data has been analyzed in many aspects. Due to the wide range of genetic influences, it is recommended to use genetically modified mice for further research.
3.	The authors only discussed the mortality of genes. I suggested that related drug development strategies should also be discussed together
To sum up, the manuscript should be minor revision.
Experimental design: Reasonable experiment design
Validity of the findings: Manuscript details
Journal: Peerj
Manuscript ID: Peerj - 55265
Type of manuscript: Article
Title: Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
In this manuscript entitled “Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma”. There is some useful information, however, the further modification is required, and I have provided several advices shown below.
1.	This article uses a lot of data analysis, but the main reason for selecting these dataset is not very clear. I hope the author can discuss it in detail.
2.	The data has been analyzed in many aspects. Due to the wide range of genetic influences, it is recommended to use genetically modified mice for further research.
3.	The authors only discussed the mortality of genes. I suggested that related drug development strategies should also be discussed together
To sum up, the manuscript should be minor revision.
Additional comments: Manuscript details
Journal: Peerj
Manuscript ID: Peerj - 55265
Type of manuscript: Article
Title: Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
In this manuscript entitled “Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma”. There is some useful information, however, the further modification is required, and I have provided several advices shown below.
1.	This article uses a lot of data analysis, but the main reason for selecting these dataset is not very clear. I hope the author can discuss it in detail.
2.	The data has been analyzed in many aspects. Due to the wide range of genetic influences, it is recommended to use genetically modified mice for further research.
3.	The authors only discussed the mortality of genes. I suggested that related drug development strategies should also be discussed together
To sum up, the manuscript should be minor revision.


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

Input:
Title: IDENTIFICATION OF A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Grammar need to corrected in line 35. "up-regulation" should be "up-regulated".
Experimental design: No comment
Validity of the findings: No comment
Additional comments: Very detailed and covered all the queries.


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 A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: All the comments were properly addressed.
Experimental design: N/A
Validity of the findings: N/A
Additional comments: Thank you for properly addressing the 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 A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 3

Output:
Basic reporting: The revision looks good.
Experimental design: The revision looks good.
Validity of the findings: The revision looks good.
Additional comments: The revision looks good.


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 A FIVE-GENE SIGNATURE IN ASSOCIATION WITH OVERALL SURVIVAL FOR HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 4

Output:
Basic reporting: The manuscript is suitable to be published.
Experimental design: The manuscript is suitable to be published.
Validity of the findings: The manuscript is suitable to be published.
Additional comments: The manuscript is suitable to be published.


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

Input:
Title: STABLE ISOTOPE COMPOSITIONS OF PRECIPITATION OVER CENTRAL ASIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors present the analysis of stable isotope data in precipitation over central Asia. They used both δ2H and δ18O for construction of meteoric water line, although on couple of sites in the manuscript they explicitly stated they used only δ18O. I suppose the data refer to monthly precipitation samples, since some data were taken from GNIP database. For relation with various climatological and geographical parameters they used only δ18O values, which is understandable. However, since they have both δ2H and δ18O values, I suggest to discuss also deuterium excess that can also help in studying air mass circulation, altitude effect, seasonal changes, etc. Finally, they develop a model, although it is not an ab initio model, but rather an empirical relation between several parameters, to predict/calculate the δ18O in precipitation at Urumqi station. I miss some more detailed discussion on comparison between the measured and calculated values, why there are some large deviations, etc., and on a possible application for paleoclimatology, which was mentioned in the very first sentence of Introduction (although the sentence is rather disordered).
The presented results are interesting for the air mass circulation and isotopes-in-precipitation studies on regional scale, but can be important also for other regions. It shows the importance of GNIP database and other local/regional databases for general knowledge on air mass circulation. This is especially important if we think about the recent climate changes that can already be observed in both different seasonal distribution of precipitation and in changes in their isotopic composition. Therefore, the study may be accepted from the topical point of view, however, the manuscript itself contains various deficiencies that should and must be improved before final accepting for publication. I will list my observations and suggestion below separately as General and Specific comments.

I did not notice the raw data:
Experimental design: 1.	I found the title, the abstract and the content of the whole paper rather confusion. The title implies the analysis of stable isotopes (usually it includes δ2H and δ18O values) in precipitation, the abstract talks in the beginning of δ18O only (as well as the first line of Introduction), but the a few lines later the meteoric water line is established, and for MWL one needs δ2H data also! Similarly, the first section in Results and discussion is about MWL. The authors should better explain which data they used.
2.	The discussion on various dependences of stable isotope composition could be restricted to discussion on δ18O data, because δ2H is well correlated with δ18O through MWL, as the authors also showed. When they produced MWLs by using δ2H data, it could be informative to use also deuterium excess data.
3.	Various statistical methods are used in the manuscript, but some essential data are missing in most of the results, such as uncertainties, number of data, R values, p values for significance of correlations. In addition, care should be taken on the number of significant digits. For example, uncertainties in slope and intercept of the MWL line (line 21 in abstract) are given with 4 decimal digits and without uncertainties. From my experience, if uncertainties were correctly taken into account, no more than 2 decimal places should be presented.
4.	Please use δ2H instead of D.
5.	Central Asia is a wide region, and it would be nice to have the countries in the region by their names, add some political map with countries and the main cities in addition to the map of sampling locations (Figure 1), or at list the names of the main cities on map in Figure 1.
6.	I am not a native English speaker, however, I have a long experience with scientific paper written in English. I would suggest language check/proof reading.
7.	Line 35 – Could you please explain more about what do you mean by paleoclimatological applications? I have not seen any comment further on.
8.	I suggest numbering of all equations.
Validity of the findings: The presented results sound scientifically justified, but some more detailed discussion is missing (see suggestions)
Additional comments: Figures should be improved. Figure 8 is not mentioned in text.
See the specific comments in the attached file.


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

Input:
Title: STABLE ISOTOPE COMPOSITIONS OF PRECIPITATION OVER CENTRAL ASIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1.It is suggested to polish the use of grammar and sentences
Experimental design: The paper has a clear structure and correct logic, which is of great significance to the study of precipitation δ18O and water vapor transport in central Asia, even in arid inland regions
Validity of the findings: no comment
Additional comments: 1.The research methods and materials section of this paper mainly introduces the sources of data. It is suggested to supplement some detailed introduction of research methods；
2.How accurate is the linear relationship model between precipitation and geographical factors constructed in this paper；
3.It is suggested to add discussion section and make comparative analysis with other relevant studies to explain the consistency and difference; It is better to explain the principle and significance of the conclusion of this study


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

Input:
Title: STABLE ISOTOPE COMPOSITIONS OF PRECIPITATION OVER CENTRAL ASIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Basically, the revised version is much better than the original submission.
References are OK, but should be listed alphabetically.
Minor comments on figures, otherwise OK
Experimental design: no comment
Validity of the findings: only some minor comments given in the annotated pdf file in attachment
Additional comments: The authors took comments of the reviewers into account and the revised version looks better. However, there are some minor comments (for consistency, figure improvements - see the attached file) that should be answered and resolved. For example, you use R, R-squared and CC for correlation coefficient, and I have not seen any explanation what the three different symbols are used.
D has not been replaced with 2H at all places.
Not all references in the text are in italic blue font.
References in the list should be sorted alphabetically
Lettering in Figure 3 should be larger


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: MITOGENOMICS OF FIVE OLIDIANA LEAFHOPPERS (HEMIPTERA: CICADELLIDAE: COELIDIINAE) AND THEIR PHYLOGENETIC IMPLICATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study described the mitochondrial genomes of 5 species of the leafhopper genus Olidiana. It continues a series of recent papers that sequenced leafhopper mtgenomes, provided a standard set of genome composition statistics and comparisons to other leafhopper mtgenomes, and combined the data with those generated by previous analyses to produce a phylogenetic estimate of Cicadellidae. Given the recent flood of new mtgenomes for leafhoppers, the results of this study are only marginally novel because previous studies have included representatives of the subfamily Coelidiinae, including Olidiana species, and there does not appear to be anything particularly new or unusual about the newly described genomes.  The phylogenetic results are somewhat different from those of similar recent studies and this may be a result of adding data for additional species of Coelidiinae but the authors do not attempt to account for the differences between their results and those of other recent mitogenome-based phylogenies of Cicadellidae. The following issues need to be addressed:

1.	In the introduction it is stated that Olidiana is the largest group of Coelidiinae. This is not true. Thagria has many more species. Also, Olidiana species have not been reported “worldwide”; they occur only in the Oriental region.
2.	The Results section includes many details on various characteristics of the sequenced mitogenomes but the authors should add some comments to the Discussion explaining whether they found these genomes to include any unusual features compared to known genomes for other Coelidiinae and for Cicadellidae in genera. For example, were there any gene rearrangements?
3.	The caption for Figure 5 should explain what the numbers on branches of the tree represent. Also, the second node from the base of the Coelidiinae clade has no support values indicated. Does this mean that this node received <50% support?
4.	The whole manuscript needs to be edited to improve the English.
Experimental design: no comment
Validity of the findings: The findings appear to be reported in adequate detail but a more concise statement explaining whether these new genomes contain any unusual features not observed previously in cicadellid genomes needs to be added.
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: MITOGENOMICS OF FIVE OLIDIANA LEAFHOPPERS (HEMIPTERA: CICADELLIDAE: COELIDIINAE) AND THEIR PHYLOGENETIC IMPLICATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language should be improved. It should be checked by a native English speaker.
Background of the manuscript is a bit hazy, and a number of what appear to be relevant papers were not referenced in the manuscript. The authors should rework the paper and include a broader literature review.
Experimental design: There are few distinct research questions asked or answered.
Validity of the findings: There is no particular novelty in the manuscript. It just reports the new mitogenomes of five Olidiana species with the basic stats.
Additional comments: The MS presents the mitochondrial genomes of five leafhoppers of the genus Olidiana from the subfamily Coelidiinae assembled using the NGS method. The methodology is basically good, but considering that both the subfamily Coelidiinae and the family Cicadellidae are very large and diverse groups the comparative mitogenomic analyses and phylogenetic analysis are relatively weak (see the Results and Discussion part of the manuscript), so in its current form the paper is not suitable for publication in this journal.


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

Input:
Title: MITOGENOMICS OF FIVE OLIDIANA LEAFHOPPERS (HEMIPTERA: CICADELLIDAE: COELIDIINAE) AND THEIR PHYLOGENETIC IMPLICATIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Wang et al sequenced five Olidiana mitogenoes and constructed phylogenetic relationship among subfamilies within Cicadellidae. Overall the manuscript was enriched with figures and tables, and the results could be useful in further Cicadellidae studies.
1. Many redundant informtion for genome assembly, annotation and analyses. Authors should reorganize the structures and delete repeated sentences.
2. I am not sure that the software Mega could be used for sequence concatenation.
3. More detailed information needs to be provided, such as bootstrap, how to determine the chain convergence.
4. Authors should provide detailed comparative mitogenomic analyses between the five Olidiana species, and discussed with other Coelidiinae species of previous studies. However, authors only provided some simple descriptions for these mitogenomes. More discussion is needed.
5. How many topologies were obtained based on five datasets and two methods? How many topologies among subfamilies? Provide topology test results.
6. English language should be improved.


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: MITOGENOMICS OF FIVE OLIDIANA LEAFHOPPERS (HEMIPTERA: CICADELLIDAE: COELIDIINAE) AND THEIR PHYLOGENETIC IMPLICATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This version of the manuscript has been improved substantially but there are still some problems with the English. The authors should consult a colleague who is a native English speaker to fix several problems with the narrative.
Experimental design: Good.
Validity of the findings: As pointed out in a previous review, there have been several mtgenome-based phylogenies of leafhoppers published recently. The main novelty of this paper is its inclusion of multiple species of one genus, which allowed the authors to test the monophyly of the genus. The finding that Olidiana is probably paraphyletic is significant.
Additional comments: Another recent paper (Tang et al. 2020, Insects) added the first representatives of Hylicinae, showing that this group is closely related to Coelidiinae and Iassinae. The authors may want to add the data for Hylicinae to their dataset and re-do their analysis. Also, it may be a good idea to compare the phylogenetic results with those of Dietrich et al. (2017, Insect Systematics and Diversity) based on anchored-hybrid enrichment data. The latter analysis recovered Coelidiinae (excluding Equeefini) as a monophyletic group and also resolved relationships among tribes with strong support but the relationship of Coelidiinae to other leafhopper subfamilies was poorly resolved.


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: MITOGENOMICS OF FIVE OLIDIANA LEAFHOPPERS (HEMIPTERA: CICADELLIDAE: COELIDIINAE) AND THEIR PHYLOGENETIC IMPLICATIONS
Review round: 3
Reviewer: 1

Output:
Basic reporting: This is the third version of the manuscript I have seen. The authors have substantially addressed my previous concerns so I think this version is acceptable for publication.
Experimental design: n/a
Validity of the findings: n/a
Additional comments: n/a


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: DYSREGULATION OF MIR-381-3P AND MIR-23B-3P IN SKELETAL MUSCLE COULD BE A POSSIBLE ESTIMATOR OF EARLY POST-MORTEM INTERVAL IN RATS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The authors described an interesting work about the correlation of the early PMI in an animal model with the gene expression dysregulation of three miRNAs, miR-381-3p, miR-23b-3p, miR-144-3p. Interestingly, they also evaluated morphological changes of the bodies and correlate those macroscopic characteristics with the molecular information. All sections of the article are well described and the literature citations are appropriate. Even if the results certainly need to be more in-depth and the number of subjects tested should be increased to confirm the association found, this work is a good step forward in understanding the molecular mechanisms at the transcriptional level of the cells that happen in the early stages following death.


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: DYSREGULATION OF MIR-381-3P AND MIR-23B-3P IN SKELETAL MUSCLE COULD BE A POSSIBLE ESTIMATOR OF EARLY POST-MORTEM INTERVAL IN RATS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Martínez-Rivera et al. performed an interesting study on the expression of miRNAs and morphological patterns at post-mortem in rats.
However, the article needs some improvement before being considered for publication.

The introduction needs more detail; for example, other works involving miRNA expression in the post-mortem should be more explored. It is also not clear the choice of the miRNAs analyzed, and references to them were not mentioned.

The article structure should also be revised. For example, in the materials and methods, the morphological analyzes performed are not described. While that the method of euthanasia of animals is described in lines 130 and 132.

Figure 1 should be improved. The letters are too small.

The abbreviation IPM must be written in full the first time it is cited.

The link "https://github.com/nshuerta-203ForenseUNAM/Dysregulation_miRNA" does not work.
Experimental design: -As previously mentioned, the description of the morphological analyzes and how the descriptive statistics were performed in the study were loss.
-How primers were designed, and their sequences must also be incorporated into the manuscript.
-In the methodology, the authors describe that they used several tools to find the target genes of the analyzed miRNAs (e.g. DIANA, PITA, PICTAR) and selected the target genes that were present in at least three databases (lines 174-184), and identified biological pathways by using GSEA (lines 185-186). However, in lines 271-273, the authors affirmed: "Using the bioinformatic tool WebGestalt (see material and methods), we identified the target genes of miR-381-3p and miR-23b-3p". Please check this out.
-An important point is the concept of fold-change. FC is a measure describing how much a quantity changes between an original and subsequent measurement (e.g., the difference between 0h vs. 3h, or 0h vs. 6h post-mortem). However, the authors provide fold-change values (text and figure 2) for each time-point. Please, give us more information about it. Wouldn't the authors be referring to the mean miRNA expression in each group?
-How was performed the multiple correspondence analysis? Please, provide more details.
-The spearman correlations were not described in the methodology
-The authors performed a mixed effect model, using FC values. What would be the purpose of this analysis? Please insert in the text. In addition, review the use of FC (?) in these analyzes.
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: DYSREGULATION OF MIR-381-3P AND MIR-23B-3P IN SKELETAL MUSCLE COULD BE A POSSIBLE ESTIMATOR OF EARLY POST-MORTEM INTERVAL IN RATS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This article is interesting, however many questions must be considered.
The 3 microRNA are related with controlling which genes? Apoptotic,  necrotic? Because if they are not related, what the fundamental use of this Marker.
Also there are mistakes in expressão the results: I suppose that when they are writing ion expression of gene of miR.... they are expresssing the Gene that this miR regulate?. I did undestand that this is a misexpression. So the entire text must be reviewed. Also misinterpretation in the result I Don't think when increasing or decresing expression of miR is considered downregulation, or upregulation, because miRNA by itself is not regulated. Maybe there is a decrease in formation because the cells are in process of death.
the increase or decrease of miR expression is compared with fresh cell?
I understand that is was used a control miR? I think this strategy is not correct, or was not well written.
Experimental design: It is not clear how value was used to calculated delta delta ct?? The time 0? or internas controls? this data is very important.
In the tissue obtained was added any RNAse inhibitor? It is not mencioned.
Also the term gene expression of miR is not correct.
Validity of the findings: There is no validation. just a experimental Study in 25 mice
Additional comments: There is a lot of misexpression of Basic knowledge in molecular Biology terms
The design must have a more clear expression that can be Made using a workflow .
the methodology in real time must be more clear in the calculation of data
the conclusion is not representative as mentioned


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: DYSREGULATION OF MIR-381-3P AND MIR-23B-3P IN SKELETAL MUSCLE COULD BE A POSSIBLE ESTIMATOR OF EARLY POST-MORTEM INTERVAL IN RATS
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am satisfied wich how the authors have addressed of my comments. Therefore, I recommend publishing the article "Dysregulation of miR-381-3p and miR-23b-3p in skeletal muscle could be a possible estimator of early post-mortem interval in rats" in PeerJ . I would just like to suggest final revision of the English and text format (e.g. check italic form of genes).
Experimental design: no comment
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: TRANSCRIPTOMICS ANALYSIS REVEALS THE EFFECT OF BROUSSONETIA PAPYRIFERA L. FERMENTED FEED ON MEAT QUALITY TRAITS IN FATTENING LAMB
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this paper, the author investigated the effect of adding B. papyrifera fermented feed to the sheep meat quality. The fatty acid content and muscle fiber morphology of the longissimus dorsal transcriptome have been also characterized. The author concluded that the muscle fiber became smaller, tender, and more polyunsaturated fatty acids when added 18% of B. papyrifera in the feed.

Questions:
•	[line 110] About the description of GC method for fatty acid analysis, it would be helpful to mention which GC detector was used in the experiment.
•	In the figure 1, the annotations inside Fig1 are too small and vague. Please re-make the Fig1.
•	In the figure 2, note that (B) is the heat map and (C) is the column diagram, please make some changes based on your figure. Besides, please also put (B) after (A).
•	In the figure 4, the words below the x-axis are too small for readers.
•	The Figure 1, 3, 4 and 5 will become very vague after zoom-in. It would be very helpful to improve the resolution of these figures. It will help readers to look into more detailed information.