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 EFFECT OF SOCIAL INFORMATION FROM LIVE DEMONSTRATORS COMPARED TO VIDEO PLAYBACK ON BLUE TIT FORAGING DECISIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Video playback provides a powerful experimental approach to manipulate social information in many learning paradigms. As this paper shows, this method is especially relevant when the responses to video stimuli by observers are compared with live presentations, using the same demonstrators. Overall, the paper is well organized and clearly written, using professional language. Figure 1 is excellent; Figure 2 needs some changes to improve clarity (see my comments below and annotations on the pdf). Thanks are due to the authors for providing their raw data. Below, I suggest several references not taken into account by the authors in their introduction.
87-89: Ware et al. (2015) address all these issues and innovate in presenting a double teleprompter technique to simulate live social interaction in pigeons. Importantly, they demonstrate that image presentation rate (frames/s) can be critical in determining a social response behavior. In birds, a 60 Hz refresh rate (at the very least) should be used for editing the video clip. Some exceptional avian displays may require an even higher refresh rate to be perceived as smooth and “natural” by observers. These aspects are not considered in the introduction and methods section.
 83: Carouso-Peck and Goldstein (2019) brilliantly show that song copying by young male zebra finches improves significantly when social reinforcement – a video playback of a female exhibiting fluff-up behavior – is presented contingently with the auditory stimulus. A 60 Hz refresh rate was used appropriately for editing the video stimulus.
89-91: Thin film transistor liquid crystal display (TFT-LCD) monitors are flickerless and became available on the market in the early-90s (see Kuo 2013). Ikebuchi & Okanoya (1999) first demonstrated the superiority of the TFT-LCD monitor over the CRT monitor in triggering male courtship song, both in zebra finches and Bengalese finches. Importantly, the same female birds were presented live for comparison with video playback.
References:
Carouso-Peck, S. & Goldstein M.H. 2019. Female social feedback reveals non-imitative mechanisms of vocal learning in zebra finches. Curr. Biol. 29: 1-6.
Ikebuchi, M. & Okanoya, K. 1999. Male zebra finches and Bengalese finches emit directed songs to the video images of conspecific females projected onto a TFT display. Zool. Sci. 16: 63–70 (1999).
Kuo, Y. 2013. Thin film transistor technology - past, present, and future. The Electrochemical Society Interface, Spring issue: 55-61.
Ware, E, Saunders, D.R. & Troje, N.F. 2015. The influence of motion quality on responses towards video playback stimuli. Biol. Open, 4: 803-811.
Figures:
Fig. 2a: percentage values have been calculated separately for each condition (control, video and live). Results for each condition are compared to the expected probability (dotted line). This is fine except that the y-axis title should explicitly say: percentage of tested individuals ("per condition").
Fig. 2b plots the “percentage of tested individuals” that matched or did not match the demonstrator’s choice. In this case, the true percentage values are 15+20+35+30 = 100%.
Please, note that this information has been added on the Figures only to illustrate my point (see pdf).
Experimental design: Only one demonstrator (#134) was filmed retrieving food from a well, which was marked with a cross in one case or with a square in another case. Why not using the same design for all five demonstrators?
193: the sentence should read: …whereas the well covered with plain white was always empty.
203: Following up the point made by Ware et al. (2015), which recording mode was used when filming the demonstrators: progressive or interlaced? And what was the refresh rate (frames/s)?
207: How many control videos were edited?
255: the size of the demonstrator on the screen was smaller (70%) than the size of the live bird. Please, remove “slightly”.
289: Negative binomial are used for count data. Time to event measurements always have positive values and are truncated, which is not the case for a normal or binomial distribution. For latency data, Jahn-Eimermacher et al. (2011) recommend Cox regression analysis.
Jahn-Eimermachera, A.,  I. Lasarzikb & J. Raber (2011) Statistical analysis of latency outcomes in behavioral experiments. Behav Brain Res. 221: 271-275.
Validity of the findings: Overall, it is clear that symbols acted as distracting stimuli for the blue tits. The presentation of symbols also increased the variation among presentations instead of reducing it, which contradicts a good point made by the authors in the introduction (l. 79). As the authors report (l. 313), Cox regression analysis shows that birds started the task faster after seeing the video. In addition, it shows a shorter latency for the right-side of the tray.
coxph(formula = Surv(lat) ~ choiceloc + info, data = d)
 n= 39, number of events= 39
 (1 observation deleted due to missingness)
                             coef     exp(coef) se(coef)   z     Pr(>|z|)
choicelocmiddle 0.2592    1.2959   0.4820 0.538  0.59079
choicelocright    0.9020     2.4646   0.4321 2.088  0.03683 *
infovideo            1.1575     3.1821   0.4072 2.843  0.00447 **

Likelihood ratio test= 9.26  on 3 df,   p=0.02607
Wald test                 = 8.78  on 3 df,   p=0.03235
Score (logrank) test = 9.01  on 3 df,   p=0.02913

Looking at socially-educated birds only:
(1)	Eight birds out of eight (100%) failed to “match” their choice using information associated with two of the five demonstrators (#71 and #105). Not surprisingly, both demonstrators were filmed retrieving food from a well marked with a cross (non-preferred symbol).
(2)	By contrast, 5/8 birds (62.5%) did “match” their choice using information associated with two other demonstrators (#92 and #99). Not surprisingly, both demonstrators were filmed retrieving food from a well marked with a square (preferred symbol).
(3)	Finally, 2/4 birds (50%) successfully matched their choice based on social information acquired from one demonstrator (#134), which was filmed retrieving food from a well marked with a square (preferred symbol). The two other birds failed to match their choice when the same demonstrator was shown retrieving food from a well marked with a cross (non-preferred symbol).
These results can be tabulated as follows:
demonstrator	71-105-134	92-99-134
symbol	           cross	          square	    total
match	              0	              7              7
no match	    10                      3            13
total	            10               	    10	    20

Fisher exact test: P = 0.002

Importantly, the seven birds that did match a demonstrator’s choice acquired information - social and/or symbolic - roughly equally from live (3/7; 42.9%) and video (4/7; 57.1%) demonstrators  (Fisher exact test: P = 0.562). A Cox regression analysis shows that the latency was significantly shorter for birds that did match their foraging location on the demonstrator's choice, irrespective of social context (live: 60.7 s vs.979.6 s; video: 95.8 s vs. 521.7 s).
coxph(formula = Surv(lat) ~ match, data = data)
  n= 20, number of events= 20
                  coef   exp(coef) se(coef)  z      Pr(>|z|)
matchyes 1.058     2.879    0.539 1.962   0.0498 *
Additional comments: Owing to the presence of a confounding variable (symbol preference), the study fails to reach its goal in clearly demonstrating whether or not blue tits use “social” information provided by video recordings vs. live demonstrators. The authors acknowledge their inconclusive results on several occasions in their discussion (highlighted text on lines 330, 340, 366, 404).
The use of symbols during training obviously distracted the birds from acquiring social information based on foraging location by demonstrators. Similarly, the use of symbols at testing distracted the birds from making a choice purely based on social information acquired during training.
I understand the effort put in those experiments and that the perspective of trapping another group of unmarked blue tits will be time consuming. Unfortunately, if we are to make progress in understanding how birds use social information from video vs. live demonstrators, I can only recommend testing another group of blue tits in the absence of distracting symbols.
The strong preference of blue tits for square symbols, which is not seen in great tits, is really interesting and begs for an explanation. Are the brains of blue tits and great tits wired differently? What would be the ecological significance for blue tits of having visual neurons selective for square outlines? These issues are of course outside the scope 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: THE EFFECT OF SOCIAL INFORMATION FROM LIVE DEMONSTRATORS COMPARED TO VIDEO PLAYBACK ON BLUE TIT FORAGING DECISIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: In this revised version of the manuscript, the authors have adequately addressed all the points raised in the reviewers' reports.
Experimental design: See above.
Validity of the findings: See above.
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: THE EFFECT OF SOCIAL INFORMATION FROM LIVE DEMONSTRATORS COMPARED TO VIDEO PLAYBACK ON BLUE TIT FORAGING DECISIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: The authors have responded to all my previous concerns. The new title of the paper is consistent with the  revised version. It is fully adequate and I am glad the authors took this initiative. The revised analysis of the data demonstrates that, to some degree, social information acquired from live and video presentations does affect the foraging decisions of blue tits. Both figures are now excellent. The video is superb and very helpful. The experiments were conducted with great care and the paper will make a useful contribution to this exciting field of research. A few minor changes may improve the text before publication:

l. 57 … and even insects… even is not necessary.

l. 90  Here, I feel that my early work with zebra finches - using a CRT video monitor - should be cited: Adret 1997 Discrimination of video images by zebra finches (Taeniopygia guttata): Direct evidence from song performance. J. Comp. Psychol. 111: 115-125.

l. 223  the number of demonstrations for each symbol was balanced…

l. 232  see an examplar video clip…

l. 294  influenced the birds’ latency

l. 295 we also recorded the elapsed time (s)

l. 380 did not infuence the birds’ choices

l. 399 than birds that chose the left side of tray

l. 401: but this effect was marginal (effect of symbol (square): coefficient = 0.918 ± 0.526, Z = 1.745, p = 0.08)

l. 427: they responded similarly to video and live presentations.

l. 436: … juvenile females being more likely to learn from

l. 444 …suggesting that acquired social information did influence their behaviour. (as emphasized on l. 464).

l. 470: …were also found to prefer squares in another experiment

l. 472: A conspicuous square symbol…


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 COMPLETE CHLOROPLAST GENOME OF DENDROBIUM NOBILE, AN ENDANGERED MEDICINAL ORCHID FROM NORTH-EAST INDIA AND ITS COMPARISON WITH RELATED DENDROBIUM SPECIES
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a typical paper of NGS where chloroplast genome of Dendrobium nobile has been sequenced using standard procedure. Authors compare this genome with related chloroplast genomes of Dendrobium species.
Experimental design: Fresh leaves of D. nobile were collected from plants growing in greenhouse of National Research Centre for Orchids, Sikkim, India. Sequenced using Illumina HiSeq 2500-PE150. Standard procedure was used for checking quality of raw data and for assembling of genome. Genome annotation and codon usage was computed using existing tools that include similarity tools like BLAST.
Validity of the findings: Newly sequenced genome was map on related genomes using reference genomes. Different phylogentic trees constructec to show closeness with other related genomes.
Additional comments: Overlall it is important study for researchers working on Dendrobium species. Authors had implement all standard tools to provide comprehensive annotation of newly sequenced genome.


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 COMPLETE CHLOROPLAST GENOME OF DENDROBIUM NOBILE, AN ENDANGERED MEDICINAL ORCHID FROM NORTH-EAST INDIA AND ITS COMPARISON WITH RELATED DENDROBIUM SPECIES
Review round: 1
Reviewer: 2

Output:
Basic reporting: I strongly recommended that the manuscript should be thoroughly checked for language and grammar.
Experimental design: 1. The authors should make sure which DNA were they extract, chloroplast DNA or genomic DNA? If the authors use genomic DNA for the sequencing and assemble analysis, “plastid genome (plastome)” may be more suitable to instead of “chloroplast genome”. If the authors use chloroplast DNA for the analysis, they should add the chloroplast extract method in the “Materials and Methods part”.
2. The comparison studies of Dendrobium plastome, i.e., plastomic structure variation, mutational biases, hotspots and polymorphic SSRs selection, phylogeny, have been investigated already; however, none of these references was listed in this study. This manuscript was focus on the comparison analysis of chloroplast genomes of Dendrobium species; the authors should compare their results with those studies, and discuss their difference, find some new insights.
3. RNA editing sites are important for the function of chloroplast proteins, however, only predicted them is meaningless. Those predicted RNA editing sites should be verified by RT-PCR.
Validity of the findings: 4. There are two questions in the phylogenetic analysis.
a. The genus of Goodyera belongs to the subfamily of Orchidoideae, while the genus of Dendrobium belongs to the subfamily of Epidendroideae. Why the authors choose the plastomes of Goodyera spp. as outgroups? Why not choose the plastomes in the subfamily of Epidendroideae?
b. There are many complex in the genus of Dendrobium, for example, D. officinale complex and D. moniliforme complex. Only choose one plastome for each species can not reflect their relationships, the author should increase their taxon sampling. Moreover, the authors should use the correct species name. For example, D. candidum and D. officinale.
Additional comments: The manuscript entitled “The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from Northeast India and its comparison with related chloroplast genomes of Dendrobium species” reported the chloroplast genome of Dendrobium nobile and compared it with other genomes of related Dendrobium species. Though their data may provide some insights into the understanding of the evolution patter of Dendrobium chloroplast genome, the present manuscript is not logically assembled, which simply shows the data without comprehensive analysis.


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

Input:
Title: THE COMPLETE CHLOROPLAST GENOME OF DENDROBIUM NOBILE, AN ENDANGERED MEDICINAL ORCHID FROM NORTH-EAST INDIA AND ITS COMPARISON WITH RELATED DENDROBIUM SPECIES
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a generally well-written paper although some sentences could still be improved. For instance, the title states: "The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from Northeast India and its comparison with related chloroplast genomes of Dendrobium species". Here, the repetition of chloroplast genomes (x2 in the same sentence) is redundant. These typos occur often in the paper but can easily be fixed.

The aims of the paper are clear but the Introduction (as well as the Discussion) sometimes fails to contextualize the results for a wider audience. For instance, several important references are missing to understand the evolution of orchids, and the influence of polyploidy on their diversification:
https://onlinelibrary.wiley.com/doi/abs/10.1111/cla.12153
https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.12854
https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-14-20
https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/ajb2.1178

Also: I think the largest orchid genus is Epidendrum (not Dendrobium). Please clarify that.
Experimental design: Research questions are well defined, relevant and meaningful to understand the evolution of Dendrobium. Methods are generally described with sufficient detail except in:

1) Please clarify if some of the analyzed species are polyploid and how you have addressed this in the analysis.
2) A comparison of homologous genes were performed with other chloroplast genomes. Which ones?
3) The gene map on Figure 1 is hard to follow. For instance, the coding genes are not annotated on the gene map of Dendrobium nobile. Why is that?
Validity of the findings: Data is statistically sound and relevant for the genus, and probably also for orchids in general if the authors place the results in a wider context.
Additional comments: I think this is a fine study case that can potentially enlarge our knowledge concerning the evolution of an important genus of orchids: Dendrobium. Conclusions are well stated, linked to original research question and limited to supporting results. They can however be improved if authors backup their conclusions with other studies that have been published in the same subject.

Please clarify how this study contributes to the conservation of Dendrobium nobile. This seems an important question and it is mentioned in the title and in the Introduction but findings are quite unspecific, eg., it is hard to see how this data can contribute to the conservation of this species in its current stage.

In any case, I think these are all minor details that the authors can fix quite easily. So, I hope to see this manuscript published very soon.
Congratulations to the authors.


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

Input:
Title: THE COMPLETE CHLOROPLAST GENOME OF DENDROBIUM NOBILE, AN ENDANGERED MEDICINAL ORCHID FROM NORTH-EAST INDIA AND ITS COMPARISON WITH RELATED DENDROBIUM SPECIES
Review round: 1
Reviewer: 4

Output:
Basic reporting: The manuscript is well organized and written. The Introduction gives a comprehensive background to the study. The language used in the manuscript is clear and professional, however I have some minor comments:
1. line 36: Does the wording: “The present-day Dendrobium is the largest genus” means it is the largest genus among the tribe Dendrobieae or is Dendrobium just more species-rich than it was before? Please refine the statement.
2. lines 70-73: The sentence is long and a little bit confusing. Please, check if the wording “one such endangered orchid... that demands...” is grammatically correct. You could also replace the whole sentence with two shorter ones.
3. Check the text for double spaces and double dots (eg.: line 175, 178, 183).
4. Line 196: “ Synteny comparison...” - shouldn’t it be “Synthetic comparison”?
5. Line 247: “do no” replace with “do not”.
6. line 170: The gene rps12 is absent in the Figure 1.
7. Figure 1.: Lack of rps12 gene. LSC and “source Dendrobium nobile” signatures are hardly readable due to arrows crossing the signatures. If there are no gene names given in the figure, I would recommend deleting fragments of it eg.: ycf2 g... (in the green circle).
8. Figure 2., Figure 5: The are no italics in the caption (Dendrobium, Goodyera).
9. Table 1.: Please, explain in the table caption (or in the main text in the Results), what “count” and “percantage” is. For now, it is too laconic.
Experimental design: Materials and Methods is written flawlessly. It is clear, understandable and comprehensive and the methods used in the study are appropriate for the issue.
Validity of the findings: In the chapter Results and Discussion the results are well presented, however there should be more references to similar studies in a discussion part.
1. Line 194: “...quite similar to other orchid cp genomes.” - reference needed.
2. Line 202: “IR regions are generally considered to be highly conserved regions in the chloroplast genome.” – reference needed.
3. The whole discussion, especially in the part “Comparison with other chloroplast genomes with the genus Dendrobium” needs to be discussed with the results from other studies on different genera. What about the structural variation detected in the LSC/IR/SSC boundaries? Was it observed in other genera among Orchidaceae?
Additional comments: The manuscript entitled „The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from Northeast India and its comparison with related chloroplast genomes of Dendrobium species” is an effect of solid and well-planned study, taking an important and timely issue. Identification of endangered species using molecular markers is nowadays important and necessary skill. Therefore, studies broadening our knowledge on DNA sequence variability between closely related species are always welcome.


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 COMPLETE CHLOROPLAST GENOME OF DENDROBIUM NOBILE, AN ENDANGERED MEDICINAL ORCHID FROM NORTH-EAST INDIA AND ITS COMPARISON WITH RELATED DENDROBIUM SPECIES
Review round: 1
Reviewer: 5

Output:
Basic reporting: The whole logical structure was confused and unclear. The authors stated that they have analyzed the 33 newly sequenced chloroplast genomes retrieved from NCBI Refseq database was compared with that of the first complete chloroplast genome of D. nobile. However, actually, only one newly sequenced chloroplast genome was obtained in the material and methods. In the phylogenetic construction analysis, they have included D. nobile cp genomes from India and China along with 32 other Dendrobium cp genomes. How many species was actually included in the current analysis? Some results and discussion were wrong.

The abstract part must be re-written, the mean of whole abstract part was unclear and unlogical, the important results and conclusions were not summarized, the authors must to re-edit it.

The summary of introduction part was not complete, and some important literatures were not cited, the authors must re-edit their manuscript.

The many parts of the results and discussion were only the results, there are no any discussion to the many results. The authors should propose the important questions in their manuscript, rather than introduce the simple results.

Many sentences were wrong and errors, the authors must re-organize it. E.g.,
The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is the largest genus comprising about 800-1500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 newly sequenced chloroplast genomes retrieved from NCBI Refseq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150).
Experimental design: unclear
Validity of the findings: inaccurate
Additional comments: The whole logical structure was confused and unclear. The authors stated that they have analyzed the 33 newly sequenced chloroplast genomes retrieved from NCBI Refseq database was compared with that of the first complete chloroplast genome of D. nobile. However, actually, only one newly sequenced chloroplast genome was obtained in the material and methods. In the phylogenetic construction analysis, they have included D. nobile cp genomes from India and China along with 32 other Dendrobium cp genomes. How many species was actually included in the current analysis? Some results and discussion were wrong.

The abstract part must be re-written, the mean of whole abstract part was unclear and unlogical, the important results and conclusions were not summarized, the authors must to re-edit it.

The summary of introduction part was not complete, and some important literatures were not cited, the authors must re-edit their manuscript.

The many parts of the results and discussion were only the results, there are no any discussion to the many results. The authors should propose the important questions in their manuscript, rather than introduce the simple results.

Many sentences were wrong and errors, the authors must re-organize it. E.g.,
The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is the largest genus comprising about 800-1500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 newly sequenced chloroplast genomes retrieved from NCBI Refseq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150).


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 COMPLETE CHLOROPLAST GENOME OF DENDROBIUM NOBILE, AN ENDANGERED MEDICINAL ORCHID FROM NORTH-EAST INDIA AND ITS COMPARISON WITH RELATED DENDROBIUM SPECIES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is not logically assembled, especially for the “Result” and “Discussion” parts.
Experimental design: The author did not well resolve the questions we raised, i.e., verified the RNA editing sites, increase the taxon sampling. These are so important questions for this manuscript which need to improved.
Validity of the findings: Only report one chloroplast genome is not enough to publish a scientific paper, they need to do more comprehensive analyses with other published chloroplast genomes. However, they failed to do so. Moreover, they ignored the questions that we have raised.
Additional comments: Through the authors have made effort to improve their manuscript, the present manuscript is not logically assembled. For example, only two section “Genome organization and features”, “Simple sequence repeat identification” were in the Result part, however, other results were written in the Discussion part. The authors need to reorganize their Result and Discussion parts. Also, in the Instruction part, the authors should focus on introducing the significance of “why they need to sequence and analysis the cp genome of Dendrobium nobile” rather than review the progress of molecular marker studies of orchid and Dendrobium species.


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 COMPLETE CHLOROPLAST GENOME OF DENDROBIUM NOBILE, AN ENDANGERED MEDICINAL ORCHID FROM NORTH-EAST INDIA AND ITS COMPARISON WITH RELATED DENDROBIUM SPECIES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript is well organized and written. The changes made by the Authors significantly improved the quality of the manuscript.
Experimental design: The article meets standards of the journal,
Validity of the findings: no comment
Additional comments: I consider the article a valuable contribution to the area of plant genomics as well as for research considering Dendrobium species. 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: THE COMPLETE CHLOROPLAST GENOME OF DENDROBIUM NOBILE, AN ENDANGERED MEDICINAL ORCHID FROM NORTH-EAST INDIA AND ITS COMPARISON WITH RELATED DENDROBIUM SPECIES
Review round: 3
Reviewer: 1

Output:
Basic reporting: The article should include sufficient introduction and background to demonstrate how the work fits into the broader field of knowledge. Relevant prior literature should be appropriately referenced.
Experimental design: Original primary research within Aims and Scope of the journal.
Validity of the findings: Conclusions are well stated,Speculation is welcome
Additional comments: After the revision, the manuscript was great improved and can be accept in current form.


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: OFF-LINE AND ON-LINE OPTICAL MONITORING OF MICROALGAL GROWTH
Review round: 1
Reviewer: 1

Output:
Basic reporting: First, I would like to commend the authors for their work. It is a very interesting and useful research. Second, I appreciate for the raw data set available. In my opinion the article is good, but it needs an improvement on English language to ensure that it follows the professional clearly written form. Some verb tenses should be fixed to the past, which I think is the right way to describe a research done. There are also some extra commas. I suggest that you have a native English spoken colleague reviewing your manuscript.

I liked the organization of the manuscript, the objective is clear, the methods explained and discussed later. Conclusion is also understandable.
Experimental design: The experimental design it not well explained. The experimental design, the main hypothesis, treatments and how the data were going to be analyzed are not described.

I suggest a better explanation about the statistics analysis.
Validity of the findings: I consider the results valid although the statistic design is not well explained.
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: OFF-LINE AND ON-LINE OPTICAL MONITORING OF MICROALGAL GROWTH
Review round: 1
Reviewer: 2

Output:
Basic reporting: “Off-line and on-line optical monitoring of microalgal growth,” by Lazcano-Hernandez et al., describes the implementation of three optical approaches for assessing microalgal cultures based upon (1) the chlorophyll fluorescence ratio F685/F740, (2) the color of a culture backlit by a fluorescent lamp, and (3) the penetration depth of a superluminescent diode.  In motivating this work, the authors state that “real time non-invasive methodologies are still needed to monitor the growth conditions of the microalgae culture.”  As reviewed by Havlik et al. (“Monitoring of microalgal processes,” Adv. Biochem. Eng. Biotechnol. 153, 89-142, 2016), there have been several such methods pursued over the past decade, and I would recommend that the paper reference this relevant prior work.
Experimental design: As the authors state, the trends they observe in the chlorophyll fluorescence ratio F685/F740 of Chlamydomonas reinhardtii have been previously reported for plants.  Also, the relationship reported between luminosity and cell concentration should be expected to be dependent upon the spectral content of the backlighting (e.g., fluorescence lamps vs. LEDs).  To allow for reproduction by others, the spectral content of the fluorescence lamps should be reported.  Finally, I would recommend that the authors include the results of Experiments 4-5 in Fig. 8, as graphically depicting these results may motivate others to hypothesize reasons for the lack of agreement with Experiments 1-3.
Validity of the findings: The authors have demonstrated algal biomass assessment by measuring the attenuation of light.  This is somewhat routine practice by the phycology community in the measurement of OD 750 (see, e.g., the discussion by Griffiths et al., “Interference by pigment in the estimation of micoalgal biomass concentration by optical density,” J. Microbiol. Meth. 85, 119-123, 2011).  Lazcano-Hernandez et al. demonstrate methods for assessing light attenuation without needing to extract a sample.  A challenge, left unaddressed by the authors, is that the observed light attenuation remains dependent upon the measurement geometry, which would likely be different for every photobioreactor geometry.  And because the optical methods described depend upon the culture’s absorption, each new organism would require a new assessment as well.

Related to the topic of culture absorption, the authors should wonder why the slopes in Fig. 9 are all near unity.  The optical density of the culture is being measured at 640 nm, while the luminescent diode exhibits peak emission at 440 nm.  Chlamydomonas reinhardtii exhibits 2-3 times more absorption at 440 nm than at 640 nm (see de Mooij et al., “Impact of light color on photobioreactor productivity,” Algal Res. 15, 32-42, 2016), so one would expect the lines in Fig. 9 to display slopes significantly greater than unity.

In the Conclusions, the authors claim that their on-line techniques could be extended to remote sensing applications.  Without additional caveats, this should be clarified as speculation.  Remote sensing systems typically co-locate the transmitter and receiver, which would not allow for the off-axis lighting and backlighting geometries implemented by the authors in this work.
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: TRANSPRISE: A NOVEL MACHINE LEARNING APPROACH FOR EUKARYOTIC PROMOTER PREDICTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors of this well-written, easy-to-read, clearly illustrated, and unambiguously understandable manuscript are proposing their new machine learning Web-service TransPrize for recognizing transcription start sites (TSS) upon a whole genome DNA sequences via demonstrating its workability on the example of the RNAseq-data on the rice genome (except chromosome 2 as a control dataset) in comparison with the well-known Web-service TSSPlant.  Since the prediction accuracy expressed within a number of statistics , which was achieved by the authors seems to be significantly than those of the commonly accepted tools under comparison, it would be interesting for many readers of PeerJ, I hope. In my opinion, both main sections - Background and References, - are sufficiently brief and adequate to the current state of this field of intense research without minor details. As I understood from the manuscript, the only public data were studied here.
Experimental design: Since the results of the calculations were reproduced by the authors on 10 variants of independent data, as well as the contextual patterns, which they identified, are cjrresponding the most frequent regulatory signals known, such as INR-element, TATA-box, and several  transcription factor binding sites, then the originality of these results and their reliability are beyond doubt. In my opinion, the description of all the technical details seems to be sufficient to replicate them.
Validity of the findings: Since the authors present the results of their Web service TransPrize on the only example of the rice chromosome-2, then, in my opinion, their manuscript could look much more better and mature, if all the phrases presenting here about an applicability of this tool to analyze any other eukaryotic species and their viruses would have been mitigated to subjunctive assumptions.
Additional comments: As one minor comment, the statistical characteristics of the predictions made using TransPrize, which are shown in Table 1, do not coincide with those in both main text and  caption for Figure 3 so that this mismatch should be either corrected or discussed.

Taking the all above mentioned, I am recommending this manuscript for publication as soon as the above mismatch will have been eliminated.


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: TRANSPRISE: A NOVEL MACHINE LEARNING APPROACH FOR EUKARYOTIC PROMOTER PREDICTION
Review round: 1
Reviewer: 2

Output:
Basic reporting: Prediction of transcription start sites (TSS) is considered a difficult problem, because of lack of conserved elements around TSS and also possibility of multiple alternative positions  per single gene. Recent progress in PacBio’s  Isoseq technology for sequencing of full-length transcripts partially alleviated the need for computational predictions, as TSS could be found by direct mapping of full-length transcripts to the genome. Nonetheless, prediction of TSS based on sequence alone, as attempted by authors, presents some interest, e.g. for genomes without full-length transcriptome data.
However current manuscript needs some major revisions. Below are some suggestions:
1. Abstract should include some information about accuracy of method
2. Deep convnets usually have a lot of parameters, it is not clear from the text if enough number of sequences were used for training of parameters,  fewer  data may lead to overfitting
3. As it is a  2-stage algorithm it would be  helpful to provide some probability/score measure about reliability of ‘promoter’ prediction after 1st stage.
4. Authors report average error shift  for exact TSS prediction at about  ~48nt in 512nt length window. It is not clear how good it is relative  to  e.g,  random predictions.
5.Comparison with TSSPlant  was performed on chr.1 and 2 of O.sativa, the species where algorithm was trained, even if earlier authors indicate that chr2 was used for validation.  If this method intents to be not species-specific, it is better to test in another species, preferably where full-length transcriptome data available.

Some minor problems:
1.it is difficult to read manuscript in PFD format, as some figures have nonstandard sizes
2. line 94: ‘did use unreliable homology arguments..’  - not clear what means by that phrase.
3.line: 194:  ‘4 kernel sizes’ but at line 197: ‘There were one kernel size and ReLU in both situations’
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: TRANSPRISE: A NOVEL MACHINE LEARNING APPROACH FOR EUKARYOTIC PROMOTER PREDICTION
Review round: 2
Reviewer: 1

Output:
Basic reporting: Since the authors successfully satisfied all my comments in the revised manuscript, I recommend accepting it for publication.
Experimental design: Since the authors successfully satisfied all my comments in the revised manuscript, I recommend accepting it for publication.
Validity of the findings: Since the authors successfully satisfied all my comments in the revised manuscript, I recommend accepting it for publication.
Additional comments: Since the authors successfully satisfied all my comments in the revised manuscript, I recommend accepting it 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: TRANSPRISE: A NOVEL MACHINE LEARNING APPROACH FOR EUKARYOTIC PROMOTER PREDICTION
Review round: 2
Reviewer: 2

Output:
Basic reporting: Some minor points in text to change:

line 138:  2 times 'deep learning'
line 186: 512nt
Fig1. Meaning of abbreviations BN and MP in figure (batch normalizations and max.pooling)
Fig3 ROC curve for the training (and testing)  datasets
Fig4. should mention that data for humans and distance is 47.99 (not 47.68 - typo)
Experimental design: Methods described with sufficient detail and software is available
Validity of the findings: Results are valid
Additional comments: Authors revised the paper, according to reviewers suggestions, and I think in current form it is publishable in the journal.


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

Input:
Title: A BIOMECHANICAL ANALYSIS OF THE STAND-UP PADDLE BOARD STROKE: A COMPARATIVE STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is clear, very well written and relevant from the scientific point of view. It describes and compares the SUP technique, through articular angles, between experienced and inexperienced practitioners.
The references are adequate, but as it's a new issue to be investigated, there are really few references to be used. Table 1 is correct, but Figure 1 could be improved regarding its relation to the angular data found.
Experimental design: The experimental design is correct and it fits to the journal scope. Objectives are well defined. Methods were very well described and the study follows a high technical and ethical standard.
Validity of the findings: Data found are of relative importance, more related to the novelty of the study performed with SUP. Findings are robust, but effects size calculations are necessary to improve the discussion.
Additional comments: Congratulations on the work done and presented. However, in order to increase the quality of the study and better understand the results, I suggest some modifications:
In the abstract:
linha 27, você não pode "usar" seres humanos, eles eram "participantes".
linha 34: use a diferença "estatística" em vez de "significante". Eu sugiro que você faça essa mudança em todo o papel.
Introduction
line 48: are you sure that SUP is "easy to learn"? Maybe it's a very strong assertive.
Data analysis
line 146. Effects size of the groups is required, please see: J Exp Psychol Gen. 2012 Feb;141(1):2-18. doi: 10.1037/a0024338. Effect size estimates: current use, calculations, and interpretation. These results shoul be in Table 1.
Discussion
Line 177: "This is the first known study to examine the stroke kinematics of SUP."...Please be carefull, it's just to your knowledge.
Figure 1Although the Figure is very didactic, its design seems to indicate that the experienced ones have greater trunk flexion, which was not found.


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

Input:
Title: A BIOMECHANICAL ANALYSIS OF THE STAND-UP PADDLE BOARD STROKE: A COMPARATIVE STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well written in a good scientific english.
The references are appropriated
I suggest to add a figure with the angular diagram of each analyses angle.
Please add the hypotheses.
Experimental design: The article has a clear aim.
The research question is simple and descriptive, but it is useful for coaches and others.
All the experiments were performed to a good technical standard.
The methods section is well written, but some correction are necessary.
Validity of the findings: This paper is a descriptive study.
The statistics is good
Some sentence in the discussion and conclusion should be reformulated to avoid possible  misunderstandings.
Additional comments: COMMENTS TO THE AUTHORS

Dear authors, first of all, I would like to apologize for the time delay. I had some healthy problem during the last weeks and I did not have the possibility to work.

This manuscript describes a study undertaken to determine the kinematic differences between experienced and inexperienced stand-up paddle boarding participants. The authors use a 3D kinematical analysis to investigate the paddle technique on a specific ergometer. Results show that, inexperienced participants have larger shoulder ROM and a reduction in hip ROM compared with the experienced participants.
The manuscript is written well, but as you will see below, I have some methodological concerns.

MAJOR CONCERNS:

INTRODUCTION
The introduction is well written, but it is necessary to rearranged in order to improve the legibility.
In my opinion a simple structure could be useful:
-	What is stan-up paddle boarding?
-	Which are the positive benefits?
-	Describe the biomechanics of SUP and the positive or negative alteration.
-	Aims and hypothesis

As an example, in the first paragraph you defined the SUP and introduced the concept of SUP as positive “tool” to increase the heath of the participants.
However, at the beginning of the second paragraph, there is another description of the SUP.

Hence, in my opinion, could be useful to move the second paragraph on the first one.

Moreover, in the third paragraph (from line 75 to 89) you introduced your aim in the line 82, and reformulate the purposes in the line 86. Please, provide a clear statement of your aims at the end on the introduction.
Furthermore, please provide also your hypothesis.

METHODS
The methods section is well written and clear. No major concerns will be provide, but I have several minor comments (see below).

RESULTS
The results are well written and clear; however, I suggest to create an angular diagram to improve the clarity of the manuscript (see Nardello et al. 2019; Sports Biomechanics).

DISCUSSION
The discussion in well written, as the previously section. However, I suggest to highlight your speculation or consideration, as such.
As an example, Line 196: “The reduced hip motion, combined…”. The higher force generated by the biceps is a speculation, because you did not have the EMG or other kind of force measurements. Hence, please, reformulated all these kind of sentences.

SPECIFIC COMMENTS
INTRODUCTION:
Line 50: please add some healthy benefit of the SUP.
Line 82-84: “The purpose of these…”. You don’t have the possibility to state this, because you don’t have an injury or performance variable (e.g. velocity, power, mechanical stress…).

METHODS
Line 113: Provide some addition details regard the full Plug-In gait model, such as: the total number of markers and the number of body segments.

Line 116: Please provide the calibration parameters, such as the residuals. Are you sure that 100 Hz are sufficient to perform a good kinematic analysis? Do you have some references?

Line 127: “This was considered to be a…”. Did you have a measure of internal work, such as RPE or other kind of variables? I think that 20W are sufficient for the inexperience subjects and too easy for the experienced one.

Line 135: If you used the Plug-in gate, there is the possibility to obtain the joint angle from the Nexus software. Why did you choose to use a Matlab program?

Line 135: “The beginning and the end of each stroke…”. Did you use a threshold to identify this specific time instant or you visually defined this point?

Line 142: “The time series data were filtered…”. I suppose that you used a low-pass Butterworth filter, right? Please state which kind of filter did you use.
Moreover, if you use a 4th order Butterworth filter with a cut-off frequency of 20 Hz, how did you chose this frequency and order? I think that this filter is to strength, normally, a 2th order is sufficient.

FIGURE
Please provide an angular diagram of the analysed angle.


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

Input:
Title: A BIOMECHANICAL ANALYSIS OF THE STAND-UP PADDLE BOARD STROKE: A COMPARATIVE STUDY
Review round: 1
Reviewer: 3

Output:
Basic reporting: I´m not native speaker, but seems that  the language is clear, intelligible and professional.
The article/references shows sufficient introduction and background.
The structure of the article shows acceptable format of ‘standard sections’
Raw data have been made available in accordance with data sharing policy.
Figures and tables
Fig 1 needs to be improved, better described and labelled, better resolution, also illustrating the range of motion (ROM) and peak joint angles.
Table 1 needs to be improved, showing also effect size and 95% CI.
Experimental design: The research was conducted rigorously and to a high technical standard and in conformity with the prevailing ethical standards in the field. It is an original primary research within aims and scope of the journal. Research question well defined, relevant & meaningful. The aim of this study was to compare the differences in SUP paddle stroke kinematics between experienced and inexperienced participants. The authors highlight that “findings may assist in identifying optimal stroke mechanics in order to minimize injury occurrence and improve overall performance.” However, confronting the inexperienced vs experienced rowing technique does not give us any assurance that performing the experienced technique will lower the incidence of injuries. What are the main characteristics in the paddling technique of injured subjects, whether in the shoulder, elbow or hip?
Line 127 (“This was considered to be a moderate paddle intensity based on previous studies (Schram et al. 2016c”): Heavy, severe and extreme intensities were not evaluated, why? Not relevant? Not especific? Is technique not different?
Since methods should be described with sufficient information to be reproducible by another investigator:
-	Sample: could you show arm span, number of training sessions per week? Any dryland training sessions per week? Any physiological information (e.g. VO2)? Also, please clarify how many experienced and inexperienced male and female subjects; number of training sessions and dryland training per week…
-	Please, show effect size as well as 95% CI for all comparisons;
-	I strongly recommend one or two figures ilustrating the set-up (cameras and KayakPro SUPErgo)   and study design. I´m sure you can use power point to make very nice figures;
Validity of the findings: 'no comment'
Additional comments: The authors deserve to be congratulated for the effort of this work, which contributes to reduce the distance in science and practice. Works like this are very welcome, both in health and sports science. However, work is still needed to achieve the quality required for publication. Raw data can be opened, and is well described. I´m not native speaker, but seems that the language is clear, intelligible and professional.

Few comments
Line 42 (“These variations in strategy were…”): change “strategy” by “technique”.
Line 75 (“Currently, only anecdotal information”): Avoid jargon.


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 KEY GENES AND LONG NON-CODING RNA ASSOCIATED CERNA NETWORKS IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1-Figure legends could be more improved and have more information.
2- Legend of figure 10 could be more summarized and well provided (same information can be mentioned one time, for example it can be explaineed that these information are similar for these genes).
Experimental design: no comment
Validity of the findings: In conclusion the limitations of study may be explained, for example, small samples size.
Additional comments: 1- In line 124, what is ad before DEGs?

2-In result section:  " DElncRNAs and DEGs identification" should be improved and explain more details.

3-In result section: in "Construction of the lncRNA-associated ceRNA network", the 126 mRNAs can be listed in a supplementary files with informations.

4- In lines 176, 185, and 188  for  BP, CC, MF abbreviations, their full names should be described for the first time.

5- In line 210, it could mentioned, for example, poor prognosis with worse survival time.

6- In the section of "Validation of the expression of hub genes and DElncRNAs", it was mentioned that hepatic expressions of the hub genes were visualized by immunohistochemistry on The Human Protein Atlas..... While information about 10 genes were not mentioned in text, they can be seen in figure 10.

7-In section of "Validation of the expression of hub genes and DElncRNAs", it is suggested to summarize information about TPM of normal vs tumor samples (from this webserver) for the validated genes in a table or in figures 8 and 9 to see the significant  value of differential mRNA expression between these two groups.
8- Regarding Figure 8 and 9, it was better to mention the p value given by UALCAN web server (for most genes p value are approximately < 1E-12)

9-In the section of "Reconstruction of the lncRNA-associated ceRNA network", it was better to summarize all information in a table.

10- In section of "Co-expression analysis of lncRNAs and hub genes from ceRNA network", it is suggested to mention the correlation, for example, as weak, middle, strong, and very strong.

11-Line 262, it can be explained while the differential expression of SNHG3 was not so high ( If authors consider TPM), it showed poorer prognosis and the worst survival time. Therefore, authours may conclude other information for this.

12- In line 295, the hsa-miR-23b-3 should be miR-216b-5p as seen in figure 11?


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

Input:
Title: IDENTIFICATION OF KEY GENES AND LONG NON-CODING RNA ASSOCIATED CERNA NETWORKS IN HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: Simple Bioinformatic analysis.
Validity of the findings: More literature validation is needed.
Additional comments: In this paper, DEGs and DElncRNA were extracted using a set of expression profile data; miRcode was used to predict miRNAs; after functional enrichment of genes, several Hub genes were extracted using protein interaction (PPI) network data; GEPIA was used for survival analysis; finally, UALCAN was used for prognosis worthy of verification.

Major issues:
1.Too many predictors may lead to skewed results, therefore, more references should be provided for validation.
2.One set of data is not enough to justify the results.
3.The competing endogenous between DEGs and DElncRNAs should be briefly described.
4.Hub genes should be associated with HCC in other literature, the relationship should be added in the Results part.
5.A protein interaction network (STRING) is incomplete.
6.The English issues must be revised carefully.

Minor issues:
1.lncRNA-miRNA-mRNA network have little to do with this article.
2.The description at lines 85-87 is confusing.
3.At line 99-101, the phrase “not only ...but also..” lacks “not only”.
4.The line 42 in Abstract is wrong in English.
5.The line 84 is wrong in English.


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 KEY GENES AND LONG NON-CODING RNA ASSOCIATED CERNA NETWORKS IN HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: English language should be improved. There are some mistakes.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1- Lines 171-174: the analytical results conducted by the limma package, a total of 1673 mRNAs (Fig. 1A) and 11 lncRNAs (Fig. 1B) were differentially expressed (|logFC)| ≥1.0 and adjusted P less than 0.05) and they were defined as DEGs and DElncRNAs respectfully. Of these, 768 mRNAs and 12  lncRNAs were over-expressed.
How can we see 12 lncRNAs out of 11 lncRNAs? These are needed to be corrected.

2-Lines 215-218:Hub genes with red nodes (MCM4, ZWINT, MCM7, and KPNA2) had the strongest connections with others, while those with orange (CKS2, HMGB2) and yellow nodes (EZH2, H2AFX) had moderate and weak connections, respectively (Fig. 4B).
Other genes with orange color were not included in this part.
3-Line 260:  (R=0.7) was mentioned in this line and next line.
4- Line 329 and 331: Consistent with our finding was repeated.
5- Line 348: predicted word was repeated.


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: NEW INFORMATION ON THE EARLY PERMIAN LANTHANOSUCHOID FEESERPETON OKLAHOMENSIS BASED ON COMPUTED TOMOGRAPHY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Acceptable.
Experimental design: Acceptable.
Validity of the findings: Mostly acceptable. Anatomical description should be augmented (see Comments for the author).
Additional comments: All in all, this is a good descriptive and phylogenetic update, using CT data to glean information from physically inaccessible regions of a type skull, and it will be a very useful and well cited contribution to the paleontology of early reptiles. With some corrections and additions to the description, this submission will make a useful and well cited publication in PeerJ.

What is missing: the CT images are fine but a few elements received little or no attention. For instance, the dorsal surface of the parabasisphenoid is finally revealed but there is no description of major landmarks such as the dorsum sellae, cristae trabeculares, etc. Surprisingly, the parasphenoidal teeth seen in figure 1 of MacDougall and Reisz (2012) are not shown/segmented out at all.

Finally, and most interestingly, the authors use the term ‘sauropsid’ for parareptiles, diapsids, et al. throughout their work, and the term ‘reptile’ appears only in the bibliographic entries (and, outside of the bibliography, the name ‘Reptilia’ appears only as a key word). This is in contrast to MacDougall et al. (2018), who preferentially used the term ‘reptile’ and eschewed the term ‘sauropsid’ for members of this synapsid sister group. Therefore, I find the present authors extensive use of ‘sauropsid’ a little odd, for the following reasons.

Although the authors do not state which concept (phylogenetic definition) of Sauropsida that they use, I surmise that they are using the Laurin and Reisz (1995) definition (‘Sauropsida is the last common ancestor of mesosaurs, testudines, and diapsids’) because they do not include Archaeothyris, Archaeovenator and Mycterosaurus (i.e. the three varanopid taxa) as sauropsids in ‘their’ sauropsid clade. However, Gauthier (1994) had previously defined Sauropsida as “reptiles plus all other amniotes more closely related to them than they are to mammals” (inasmuch Gauthier espoused a crown-group concept/definition for Reptilia). Gauthier’s definition tried to encapsulate Huxley’s concept for Sauropsida but Laurin and Reisz (1995), by including mesosaurs in their definition of Sauropsida simply made a hash of things, especially in light of the ongoing phylogenetic lability of turtles (and current Phylocode recommendations). I think the authors need to explain why they are using a phylogenetic definition for Sauropsida which does not have priority (otherwise they are simply cherry picking clade names here). Oh, and please clarify what a reptile is in their study.

More detailed comments/corrections:

165–169: if these two rows are (or are not) the palatine portion of the pterygo-palatine tooth cluster, this should be stated clearly.

178–180: I am not entirely convinced that a suborbital foramen is absent. The authors note that the ‘intersection of the pterygoid, palatine, and ectopterygoid is unbroken’, yet the pterygoid does not contribute to the suborbital foramen, which in early reptiles is usually formed by the palatine and the ectopterygoid (e.g. Coletta) or the palatine and the jugal (in most captorhinids, in which the ectopterygoid is fused to the jugal). In Coletta, the suborbital foramen is tiny, and as there is not a good fit between the palatines and the ectopterygoids in the Feeserpeton scan I am not sure there is compelling evidence to state that the suborbital foramen is genuinely absent.

183: each gnathostome has a single mandible (divisible into two mandibular rami); also, description of the mandible should follow that of the skull (palate, braincase, etc.).

184–222: the splenial morphology is not mentioned at all here. Is there evidence for a foramen intermandibularis oralis? Do the splenial, the prearticular, and the angular for a foramen intermandibularis caudalis, as they do in Delorhynchus cifellii and other early reptiles?

189: use ‘lateral’ rather than ‘labial’ for describing this surface of the prearticular (a ‘post-dentary’ bone)

191: clumsy use of the word ‘however’ here

207: ‘The coronoid’ . . . ‘extends from its posterior articulation with the surangular to the middle of the dentary’. Please specify as far anteriorly as to which dentary tooth position.

232: is this a left or a right lateral view of the sphenethmoid in figure 5?

237–251: any evidence as to whether the epipterygoid contributed to the basicranial recess (basipterygoid joint), as in Captorhinus, or not, as in Mesosaurus?

313: typo in ‘synsapids’

Gauthier, J. A. 1994. The diversification of the amniotes. Pages 129–159
in Major Features of Vertebrate Evolution (D. R. Prothero and R. M.
Schoch, eds.). Paleontological Society, Knoxville.


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: NEW INFORMATION ON THE EARLY PERMIAN LANTHANOSUCHOID FEESERPETON OKLAHOMENSIS BASED ON COMPUTED TOMOGRAPHY
Review round: 1
Reviewer: 2

Output:
Basic reporting: There are problems both with the figures (the 3D reconstructions need to be smoothed out) and with the phylogenetic analysis (no multi-state characters were ordered, apparently, despite the fact that many are cline characters). See my comments in the section “General comments for the author ».
Experimental design: There are problems with the phylogenetic analysis: no multi-state characters were ordered, apparently, despite the fact that many are cline characters. See my comments in the section “General comments for the author ».
Validity of the findings: The problems of state ordering suggest that one of the main findings of the phylogenetic analysis is invalid; the results obtained by Laurin & Piñeiro (2018), which were ignored in the draft, do not support them. I suspect that this is partly because the authors don't like to publish a poorly-resolved consensus tree (I found that ordering the relevant characters, in this particular case, causes a loss of resolution). But certainly, this is preferable to publishing a better-resolved but erroneous tree or over-estimating support for their preferred hypothesis.See my comments in the section “General comments for the author ».
Additional comments: This draft redescribes an Early Permian parareptile through CT-scan data. It brings additional anatomical information compared to the original description and attempts at clarifying its phylogenetic position. It falls within the scope of PeerJ and in my opinion, should be published pending moderate revisions, which I summarise below. I have annotated the pdf file, so please ensure that the authors receive this attachment.

The description needs to be improved through an additional image processing step. The last step of the 3D image processing, the smoothing, was clearly not done, or not properly. This results in suboptimal images in which some texture appears, which looks like dermal sculpturing, but this is most likely purely artifactual. This is especially obvious in the lower jaws, with Macdougall & Reisz 2012 shows to have a fairly smooth ventral surface, wheras Figure 3 of the ms gives the impression of concentric grooved texture, like wood would have if differentially eroded. But this effect is visible on all anatomical figures. This should be corrected. For examples of how much better such images can look after smoothing, see, for instance Laloy et al. 2013 (though there is no need to cite the paper; I am just giving an example of what this should look like). And note that this last image processing step would actually highlight the true dermal sculpturing that is present on most elements, which is currently hidden by the false, artifactual texturing.

The phylogenetic part of the paper suffers from the omission of consideration of any of the detailed comments that Laurin & Piñeiro (2018) made on the matrix of MacDougall et al. (2018) that forms the basis of the analysis presented in the draft (the authors only modified the scores of a few cells of Feeserpeton). Most importantly, Laurin & Piñeiro (2018) pointed out that several characters should be ordered because they form morphoclines. Was this done here? This should be specified (it is not in the supplements either). This is mathematically obvious (though ignored by many systematists) and has been empirically demonstrated through simulations (Rineau et al., 2015, 2018). Both supplements and the paper itself suggest that all characters were left unordered, which is simply wrong (and not a matter of opinion, contrary to what many practicing systematists seem to believe). Yet, Laurin & Piñeiro (2018) demonstrated that ordering the characters reduced resolution, so the sister-group relationship between Lanthanosuchoidea and the large clade that includes Bolosauria, Procolophonoidea, Pareiasauridae, Nycteroleteridae, Nyctiphruretidae, and Microleter may not be supported by the data, if properly analyzed. That relationship was not supported by the strict consensus of the same data (except for the few changes in scores to Feeserpeton made in this draft) by the analysis made by Laurin & Piñeiro (2018), though it was weakly supported in the majority-rule consensus. If the authors carry out another analysis as I urge them to, I suggest that they also include the bootstrap percentages below 50% of the nodes that are in the tree; this is useful information.

On a more fundamental level, I find particularly troublesome to deliberately ignore colleague's comments because dialogue between scientists and the improvement in methods and accuracy of our data is at the core of the scientific procedure and a major (possibly most important) contributor to scientific progress. To deliberately ignore such comments is negligent at best, and dishonest at worst. I urge the authors to consider this carefully. The authors know about Laurin & Piñeiro (2018); Reisz (one of the co-authors) is the Chief Editor of the journal section in which it was published and we exchanged some e-mail messages about it before and during the review process.

Finally, note that I don't want to hide behind reviewer anonymity, which I consider a form of dishonesty and a hinderance to scientific dialogue. If the authors wish to discuss any of these issues (and the other, more minor issues raised in my annotations to both documents), they should feel free to contact me.

Best wishes,

Michel Laurin

References

Laloy F, Rage J-C, Evans SE, Boistel R, Lenoir N, and Laurin M. 2013. A re-interpretation of the Eocene anuran Thaumastosaurus based on microCT examination of a ‘mummified’ specimen. PLoS ONE 8:1–11. 10.1371/journal.pone.0074874
Laurin M, and Piñeiro G. 2018. Response: Commentary: A Reassessment of the Taxonomic Position of Mesosaurs, and a Surprising Phylogeny of Early Amniotes. Frontiers in Earth Science 6:220. 10.3389/feart.2018.00220
Macdougall MJ, and Reisz R. 2012. A new parareptile (Parareptilia, Lanthanosuchoidea) from the Early Permian of Oklahoma. J Vertebr Paleontol 32:1018–1026.
MacDougall MJ, Modesto SP, Brocklehurst N, Verrière A, Reisz RR, and Fröbisch J. 2018. Response: A Reassessment of the Taxonomic Position of Mesosaurs, and a Surprising Phylogeny of Early Amniotes. Frontiers in Earth Science 6:99. 10.3389/feart.2018.00099
Rineau V, Grand A, Zaragüeta R, and Laurin M. 2015. Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes. Contributions to Zoology 84:129-148.
Rineau V, Zaragüeta I Bagils R, and Laurin M. 2018. Impact of errors on cladistic inference: simulation-based comparison between parsimony and three-taxon analysis. Contributions to Zoology 87:25-40.


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: NEW INFORMATION ON THE EARLY PERMIAN LANTHANOSUCHOID FEESERPETON OKLAHOMENSIS BASED ON COMPUTED TOMOGRAPHY
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comments
Validity of the findings: no comments
Additional comments: The manuscript is very clean, I try to look for errors or contradictions but only found some typos and minor omissions (see attached) that do not affect any the validity of 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: NEW INFORMATION ON THE EARLY PERMIAN LANTHANOSUCHOID FEESERPETON OKLAHOMENSIS BASED ON COMPUTED TOMOGRAPHY
Review round: 2
Reviewer: 1

Output:
Basic reporting: Good overall; some minor typos and a couple of minor omissions in references section (see ‘General comments for the author’).
Experimental design: no comment
Validity of the findings: no comment
Additional comments: As I communicated in my first review, this submission is a good, CT-based description of an early reptile and a re-analysis of its phylogenetic position, and it will be a very useful and well cited contribution to the paleontology of early amniotes.

I have a few comments and corrections:

line 79: the ‘d’ in ‘Macdougall’ should be capitalized; see also lines 193 and 484

line 82: I think ‘Middle’ should not be capitalized (it should be ‘middle Permian’); see also line 86

line 209: end of sentence should read ‘.. (Figs. 3, 4).’

line 225: typo in ‘intermanibularis’

line 310: I think the first comma should be a semi-colon

line 336: typo in ‘charcters’

line 339: typo in ‘pareisaurs’

line 368: this structure is more of a ‘coronoid eminence’ than a ‘coronoid process’

line 376: change ‘does not’ to ‘do not’ (or to: ‘the presence of multiple coronoids does not’)

line 428: add journal name, volume/issue, and page numbers

line 488: typo in ‘Unniversity’

line 508: typo in ‘Tazania’

line 515: the Zaher et al. paper was published in volume 5, pages 111-138

line 546: semi-colon should follow ‘supraoccipital’


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: NEW INFORMATION ON THE EARLY PERMIAN LANTHANOSUCHOID FEESERPETON OKLAHOMENSIS BASED ON COMPUTED TOMOGRAPHY
Review round: 2
Reviewer: 2

Output:
Basic reporting: Now fine. But see my general comments to the authors.
Experimental design: Now fine.
Validity of the findings: Fine.
Additional comments: The revised draft has been sufficiently improved that I can recommend acceptance. The figures have been much improved by smoothing. From the rebuttal letter and the draft, I think that the authors are still a bit confused about ordering of multi-state characters because they state (in the letter) that do not wish to assume direction of evolution, but this is assumed only if you polarize a priori ; ordering assumes no direction . They also state (in the draft) that they “ did not want to make a priori assumptions regarding character evolution”, but assuming that any state can be transformed into any other is often a highly unrealistic assumption, which they apparently don't hesitate in making. However, given that they performed a second analysis with ordering,  the basic information is provided (in the supplements), so points of view don't matter much. I only lament this misleading sentence (“we did not want to make a priori assumptions regarding character evolution”) because it amounts to saying that it is the most reasonable hypothesis to assume that a species could evolve from the size of a mouse directly to that of an elephant (without intermediate evolutionary steps) as easily as from the size of a mouse to that of a rat, but few proponents of fully unordered states realize this, and this paper conveys this misconception. However, it is so frequent in the literature, that this is like a drop in the ocean... Let it be.

In the page proofs (if the paper is accepted now, as I suggest), the authors might want to clarify, at the beginning of the phylogenetic analysis section (starting at line 127), that they performed two analyses because this is unannounced till line 148. Also, in the legend of figure 8, they should indicate that this is the result of the first phylogenetic analysis (all states unordered). As it stands, readers will have to look at the supplement to understand what Figure 8 represents because its legend indicates « from the phylogenetic analysis ». But there are two such analyses, so the legend is ambiguous. It is interesting to see that with ordered states, the resolution actually improved, contrary to their earlier matrix ; of course, ordering states has an unpredictable effect on resolution, compared to not ordering them (it can either increase or decrease it).

Best wishes,
Michel Laurin


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

Input:
Title: A GENOMIC-CLINICAL NOMOGRAM PREDICTING RECURRENCE-FREE SURVIVAL FOR PATIENTS DIAGNOSED WITH HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors have elaborated the ways to explore the recurrence related genes (RRGs) and establish a genomic-clinical nomogram for predicting the postoperative recurrence of hepatocellular carcinoma. The study is well-designed, and the authors have performed the necessary controls and tests to validate their models. The manuscript is well-written with overall proper use of language and grammar and generally complies with PeerJ standards. Introduction is adequate with necessary background information needed to understand the gravity of the question being asked. The necessary raw data has been provided. The data provided corroborates the conclusions made by the authors.
Experimental design: The research though not entirely novel is critical in terms of outcome and effect on the patient diagnosis. The questions being asked about the lack of robust prediction tools for HCC recurrence up to 3 years post-operation and the nomogram constructed based on the genomic and clinical analyses is critical. All the methods have been described adequately. The checks and balances performed to validate the findings and the models are rigorous. The authors, however, should consider elaborating the significance of the tests performed i.e. the C-index, ROC and decision curve analyses (DCA).
Validity of the findings: As mentioned, the data presented supports the conclusions made by the authors. The authors have shown that the tests performed by the authors to check the performance of the nomogram, substantiate their model. However, the reviewer suggests that the authors should present a comparison of their nomogram with already established nomograms for HCC or even other cancers to further bolster their model. Other than this minor suggestion, the manuscript, overall, is suited for publication in PeerJ.
Additional comments: No additional comments


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

Input:
Title: A GENOMIC-CLINICAL NOMOGRAM PREDICTING RECURRENCE-FREE SURVIVAL FOR PATIENTS DIAGNOSED WITH HEPATOCELLULAR CARCINOMA
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this work, the authors used bioinformatics tools to analyze the gene expression profiles from GEO and TCGA databases and identified three potential candidate recurrence-related genes in hepatocellular carcinoma.

Overall, the manuscript is well-written and is self-contained except at few places as elaborated in general comments.
Experimental design: The aim of the study is well-defined and the methods used are appropriate.
Validity of the findings: Conclusions are well stated. Overall results presented in the manuscript support conclusion except at places elaborated in general comments.
Additional comments: 1)	On lines 158-161, it is not clear how lasso regression was used resulting in identification of 8 DEGs from 79 candidate DEGs from univariate analysis. Authors should describe this in more detail. Also, on line 161, “Consequently, 8 DEGs were screened (Fig. 3)”, figure 3 is wrongly referenced here as there is no information about 8 DEGs in this figure. Authors should mention what these eight DEGs are.
2)	In the methods section, I would recommend removing the “Statistical analysis” sub-section and move the necessary information (i.e. the packages used and the criteria for different analysis) under corresponding sub-sections. For example, lines 124-127 describing information related to DEGs identification should be moved under the heading “Exploration of differentially expressed genes (DEGs) and bioinformatics analysis”.
3)	Figures are wrongly referenced at several places in the manuscript. To mention a few: on line 173, “group in the discovery and validation sets, respectively (Fig. S3)”, the referenced figure should be Fig. S4. On line 174, “…..high-risk group among all of the 3 datasets (Fig. 5A-C). ”, the referenced figure should be Fig. 4A-C.


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

Input:
Title: A GENOMIC-CLINICAL NOMOGRAM PREDICTING RECURRENCE-FREE SURVIVAL FOR PATIENTS DIAGNOSED WITH HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have satisfactorily addressed the suggestions raised by this reviewer in their rebuttal and recommends that the manuscript be accepted for publication.
Experimental design: The issues stated with respect to experimental design have been addressed in the rebuttal
Validity of the findings: The issues stated previously have been addressed in the rebuttal
Additional comments: No additional comments


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

Input:
Title: A GENOMIC-CLINICAL NOMOGRAM PREDICTING RECURRENCE-FREE SURVIVAL FOR PATIENTS DIAGNOSED WITH HEPATOCELLULAR CARCINOMA
Review round: 2
Reviewer: 2

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: Authors have addressed all my concerns and the manuscript is now 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: APPENDICULAR ANATOMY OF THE ARTIOPOD EMERALDELLA BRUTONI FROM THE MIDDLE CAMBRIAN (DRUMIAN) OF WESTERN UTAH
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment (it's fine).
Experimental design: No comment (all fine).
Validity of the findings: No comment (in General Comments below I suggest a few details in the reconstruction that could be changed).
Additional comments: This is a useful update on a rare arthropod from the celebrated Wheeler Formation that was previously known from its holotype only.  The description is very sound, and the interpretation of caudal flaps as exopod derivatives is of general interest to workers on Palaeozoic arthropods.  I offer a few suggestions for the revision, and send along a handful of corrections, as follow

In Figure 4 (the reconstruction), I suggest showing a tripartite morphology of the exopod flaps, based on Stein and Selden’s interpretation of E. brocki, rather than non-articulated flaps. The tripartite morphology is included in the generic diagnosis in the paper, so the authors evidently infer that it applied to E. brutoni as well.

In the same figure (Figure 4), what is the evidence for the terminal claw on the endopods being simple?  Bruton and Whittington (1983) presented compelling evidence for a complex claw in E. brocki, so given that the figures herein don’t obviously contradict that, one would be surprised were the claw in such a similar species to be so different.

In the abstract, indicate that the discovery of eyes in new for the genus.

Typos and such minutae:

Line 60: Perhaps use “J.K. Rigby” rather than “J. Rigby”, as he went by “Keith”.

Line 93: “at odds”, rather than “at odd”.

Line 107: “Drum Mountains”, rather than “Drums Mountains”.

Lines 134 and 135: parentheses are used for the authorships of Artiopoda and Vicissicaudata but not for Euarthropoda. This can’t be because the ranks have changed, as parentheses are used for taxon names only for Linnean binomials.

Line 178: “Lower” doesn’t make sense in the context of “Head shield slightly lower than long”.  I am not sure what dimension “lower” refers to.

Lines 186 and 266: the relevant detail of the tailspine is in Fig. 2D (not 3D as cited).

Line 335: the caudal flaps are show in Fig. 2C (not 3C as cited).  Please check the whole paper in case Figures 2 and 3 were reversed at some point and this wasn’t updated.

Line 364: The Aglaspis paper was Briggs et al., 1979 (not Briggs & Fortey, 1979 as cited).

Line 380: “The remarkable Miaolingian” sounds better than “the Miaolingian remarkable”.

Line 411: capitals for “Evolutionary Biology”.

Line 434: In this paper (as usual), it is “Donoghue, P.C.J.” rather than “Donoghue, P.C.”.

Line 478: “Quarterly”, rather than “Quaterly”.

Lines 481 and 500 (respectively): capital for “Communications” and “Reports”.

Figure captions: “tp” is kind of odd for “tailspine”. It implies the word breaks down to “tails pine” rather than “tail spine”.


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: APPENDICULAR ANATOMY OF THE ARTIOPOD EMERALDELLA BRUTONI FROM THE MIDDLE CAMBRIAN (DRUMIAN) OF WESTERN UTAH
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript submitted by Lerosey-Aubril and Ortega-Hernandez describes a new specimen of the taxon Emeraldella brutoni from the middle Cambrian Wheeler Formation of the USA, and discusses the importance of the new anatomical data in particular with regards to the trunk appendages. This is a well-written paper on an interesting fossil, and the introduction and background information provided are excellent for framing the importance of the study. The structure conforms well to PeerJ standards and is perfectly adapted for the discipline. The English is excellent throughout, with only a few minor suggestions listed in “General comments”. I commend the authors on this excellent manuscript and thorough description of the fossil. The figures are highly relevant and important, and they contain high quality photographs and an informative reconstruction of the fossil. The only relatively major suggestion for improvement is the addition of drawings of the fossil specimens, which are essential for adequately showing the details of the more complicated structures in the specimens (point 1 below). Otherwise my suggestions are relatively minor, but would help streamline and clarify certain parts of the study.

1. The manuscript contains beautiful photographs of the fossils, taken under all appropriate conditions for this type of material (dry and wet, incident and cross-polarised lighting). However, the lack of associated drawings of the specimens make it difficult to follow the descriptive text in some places. This is particularly true for the described details of: (1) the insertion of the antennae on lines 192-194; (2) the first post-antennae appendages on lines 194-197; (3) the second post-antennal appendage, in particular the slender proximal part. Please add drawings of the whole specimens with labelled features, and/or a closeup of the head region of Figure 3A.

2. In general, the written descriptive text needs to form a better link to the figures. The call-outs in the text never refer to labels in the figures, but they absolutely should. Every time a structure is mentioned or described, please as specific call-outs to, for example, “an in Fig. 1A”. Also, some of the figure call-outs don’t make sense for the text (for example line 209 where Figure 2D is a photo of an antennae but the text is describing something else). It is also clear that often the authors call-out to Figure 2 when they mean Figure 3, and vice versa (for example lines 189, 192, 197, 199, 203, 207, 211… and probably more) so please check all figure references again.

3. The manuscript contains an extremely complete and well-delivered systematic paleontology section, that conforms to typical format/structure for palaeontological taxonomy. There are only a couple small additions that would make their systematic section even clearer. This consists of (1) Adding the holotype number and museum where it is deposited somewhere around lines 169-170; (2) Adding the specimen number of the new specimen and its museum of deposition to the same section; (3) Adding a description of the second and third post-antennal cephalic limbs to the Emeraldella diagnosis somewhere around lines 147-148, or a statement that they are like the trunk appendages; (4) The Description section (lines 175-212) is written often in a style more similar to shortened diagnostic text, often achieved by removing small words such as “the”, “a”, “is”, etc, rather than fully-formed sentences. This makes it difficult to read at times, and could benefit from being written in a more fluid style with those smaller linking words being used to make full sentences. This is particularly evident near the start of the section, with the first paragraph (starting line 175) being written almost entirely in clipped sentences, but with more normal writing style creeping in more and more by the end of the section (lines 203 to 212 for example).  (5) Minor spelling and grammatical errors listed in the “General comments".

4. The second (and to some degree third) post-antennal cephalic appendages look very different in the part (Figure 3A) than in the counterpart (Figure 2A, B). Is this just an artifact of preservation, and/or of the photographic settings used? This aspect could be cleared up if drawings of the specimens are included.
Experimental design: 1. The experimental design is excellent and completely follows the appropriate approach of describing fossil material. The research question is very well defined and creatively written in the Introduction, effectively illustrating the gap in knowledge in this animal and emphasizing the importance of this single beautiful specimen. The rigorous investigation was performed to a high technical standard, although the inclusion of drawings of the fossil specimens would be highly appreciated (see my point 1 in “basic reporting”).

2. The only improvement in experimental design is quite minor. The figure captions talk about “composite images” in Figure 2A and 2B. What does this mean? Are they vertically stacked in order to get everything in focus? Are they serial horizontal images that have been stitched together? Please describe in the methods more clearly and specifically in what way the “digital images were processed” in Photoshop (line 128) and how this related to the composite images of Figure 2A and 2B.
Validity of the findings: The manuscript delivers a clear and coherent description of the significance and evolutionary implications of this new fossil specimen. The authors state clearly where they have more or less confidence in their conclusions and interpretations, which is excellent. The conclusions are exceptionally well stated and link nicely back to the introduction and context of the study. I have six points to mention here in regards to the interpretation of the fossil itself, of which only the first is rather important.

1. The eye: The authors describe a dark ovoid patch of carbonaceous material as a lateral eye (lines 188-191). I don’t think the evidence is currently very convincing about this structure actually being an eye. My doubt is because of the later description of similar dark colored carbonaceous material running along the body, described on lines 207 to 212, and suggested to be some sort of internal structure (gut, circulatory system, decay fluids, etc.). Certainly if you look only at the counterpart (UMNH.IP.6162b) in Figure 2, then you only see the dark material in the body trunk region, BUT critically there is no eye preserved in this counterpart. The “eye” is only seen in the part, UMNH.IP.6162a, and in the image of the whole part specimen (Figure 1A), the black patch called the eye lines up very well with the rest of the black material that passes along the entire length of the animal. Could the “eye” actually just be a continuation of this black material, whatever it is, into the head? Indeed, the outline of the eye is irregular and there is an extension of material in the top right of Figure 3B that doesn’t look like a typical eye structure. So the eye has the same preservation style as the rest of the black material, it is positioned perfectly in line with the other black material, the shape and outline are irregular, and eyes have never been seen in any other specimen of this genus. To me, this means that the “eye” structure is probably not an eye. The supposed “ommatidia” (line 191) would indeed give strong evidence for it being an eye, but they are not adequately shown in the photograph in figure 3B, where similar closely-packed round structures of the same size can also be seen in the orange material comprising the top left of that photo… so perhaps they are not ommatidia, but some sort of underlying structure in the sediment (sediment grains or surficial texture). Given the lack of an associated drawing of any of the specimens, and in particular the head of the part (see my earlier point), the eye is not convincing and should be re-assessed.

2. Lines 78-81: This is a nice analysis of the number of taxa known from 3 or fewer specimens, but the reporting is awkwardly phrased and needs rewording. By saying 20 taxa are known from only one specimen, and then 29 taxa are known from fewer than 3, it sounds as though you are talking about at least 49 taxa (but the total is given as 45). I suggest rephrasing for clarity to “…20 of the 45 soft-bodied species it contains (44.4%) are described in the scientific literature based on a single fossil, and an additional 9 species (another 20%) are known from only two or three specimens.” Note the use of exact percentages as well here.

3. The endites of the endopods of the first post-antennal appendages are referred to as “paired” in the caption to figure 3C, but they are not described as paired in the text (lines 194-197). Please describe why you think they are paired and include a drawing of the specimen that shows this. It is not at all clear from the photograph in figure 3C that it is paired.

5. For the exopod description, it is a bit unclear what constitutes the limits of the “slender proximal part” (line 199), versus the “paddle-shaped distal lobe fringed with robust setae” (line 199), in terms of exactly where the authors would draw the lines between these regions, and if there is an articulation between them. Also, it is unclear where they attached to the body, or how far up onto the body they extend. Again, drawings of the specimen would resolve this uncertainty. If I understand correctly, there is a prominent kink, or change in direction between the narrow proximal region and the distal lobe with setae, but this kink or elbow is not mentioned in the descriptive text. Please add it.

6. When talking about the anterior sclerite, which the authors suggest is not actually present in Emeraldella, there is mention of a single specimen for each species showing putatively this structure (line 240). In the text this is only examined in detail for E. brocki. For the pre-hypostomal sclerite of the holotype of E. brutoni described by Stein et la. 2011 and shown in their figure 2.1 and 2.2, how do the authors interpret this structure?
Additional comments: Minor suggestions for improvements to the language follow:

Line 26: By saying that the “type material” of E. brutoni consists of a single specimen, it leaves the reader wondering if there are other specimens published, which were not considered as type specimens. Maybe rephrase to something like “However, E. brutoni was described from a single specimen preserved in dorsal view…”

Line 30: Remove “main” from before “body”, because otherwise it sounds like you are referring to the trunk, rather than the whole body.

Line 39: Correct “improvise” to “improves”.

Line 48: Correct to “…opening of the first quarry…”

Line 64: Remove “Already then,” and start sentence “Most of the remarkable fossils…”

Line 77: Change to “…in the area are still officially known only from a…” (add only)

Line 93: What do you mean when you say that the deep-water deposits are “at odd” with the other sedimentation? They are highly contrasted? They are enigmatic in some way? Be more specific here (or at least use the correct term, which should be “at odds”).

Line 112: correct to “…Wheeler Formation is twice as thick…”

Line 151: correct to “…endopod podomeres vary strongly along body.”

Lines 179: replace “slopes” with “sloped”

Line 241: Correct to “…specimens of E. brocki that are exposed…”

Lines 240-241: The correct figure reference in Stein et al. 2011 for images of the pre-hypostomal sclerite are Figure 2.1 and 2.2.

Line 271: The use of “Moreover…” at the start of the sentence here makes it sounds like you are continuing a point about the antennae, when actually you are starting to describe a new difference. Rephrase for clarity.

Line 306: The use of “…shed light on this question” is a bit vague here, especially as you use it right after describing a single long held interpretation, rather than a question or conflict. Rephrase to be more specific.

Line 328: Start this paragraph with something like “In this evolutionary scenario, Emeraldella shows the most ancestral condition of all known vicissicaudates with regard to…”

Line 369: Remove “cruelly” as it is not necessary to say (even if it is true)

Line 395: Here you start a sentence with “A similar feature…” but it is unclear to which feature you are referring.