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: EXOGENOUS APPLICATION OF NITRIC OXIDE DONORS REGULATES SHORT-TERM FLOODING STRESS IN SOYBEAN
Review round: 1
Reviewer: 3

Output:
Basic reporting: This paper needs careful editing throughout.
I think there is quite a lot of background about NO and flooding missing. It is not quite the virgin territory that the authors suggest. See Dordas et al., 2003 for example. I think it is fair to say here that hypoxic stress is relevant and therefore there is a significant body of literature which could be included that involves NO (eg Wany 2017) although I realise they are not writting a review article here.
The article is structured appropriately and is self-contained with relevant data.
Experimental design: Although the experimental design is generally overall okay I struggled with the methods section which I think needs far more information in places and some information removed. How to make standard solutions can be taken out but  I didn't understand the method on ROS generation, for example. This of course then impinges on the interpretation of the data. Literature citations need to be added to some of the methods too. Centrifugation should not be quoted as RPM but as xg. Then the section on SNO is primarily on protein quatification which could be a separate section and the SNO section done properly. Overall, the methods all need careful re-writing for clarity.
Can the authors say why NO was not measured, as this would have added to the robustness of the data?
No SNP and CySNO depleted controls were used and these ought to be done. SNP has by-products which are bio-active, such as cyanide (Bethke's work). Therefore controls are important. No NO scavengers were used either.
There are no ethical considerations needed.
Validity of the findings: The presentation and description of the data is fine. The data has statistical analysis and it is clear to see the data. However, please revisit figure legends and make it clear what panels A,B,C etc are. It is not always stated and one has to read the text section to find out or guess.
The conclusions are quite long and rambling and tend to repeat the results. In places key issues are skimmed over so the whole section could be re-visited and written in a tighter manner.
Additional comments: This is an interesting study but methods need to be clearer, and the background and discussion more focused and inclusive of flooding/hypoxia/NO literature.
Lastly, i would be good to know why the plant varieties were chosen, whether the authors expected the differences and discuss why they might be different, as the differences are both significant and interesting.


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: EXOGENOUS APPLICATION OF NITRIC OXIDE DONORS REGULATES SHORT-TERM FLOODING STRESS IN SOYBEAN
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am very happy to see that basic reporting has improved significantly in response to the reviewer comments, although I still find that English grammar and sentence structure should be addressed more seriously. Especially of the newly written parts.

- Right now, the statistical lettering in the figures is not clear to me. What do the minor and capitol letter represent, and do there represent statistically different groups? This should be clearly explained in ever single figure legend.

- i still think that raw data should include more than the processed values. For instance, of the qPCR, also the raw CTs of the genes of interest and the housekeeping genes.
Experimental design: The authors attempted to address my concerns in their rebuttal, but did not incorporate their responses in their manuscript. I find that they also did not address the technical issues raised by reviewer #3, in the manuscript. In other words, Non stressed NO controls are still not included, or a verification to detect whether NO application was successful. They claim that NO application could be verified by their SNO measurements, but these actually show that NO leads to lower SNO in one of the 2 cultivars, while one would expect higher SNO content if NO application was succesful. If the authors do not want to re-do experiments or include additional, but essential controls, they should discuss the limitations of SNP treatments somewhere (methods or discussion). For instance, indicate that SNP treated results could be attributed to cyanide, and not NO (Wodala et al., 2010).

To be specific this has to be explained in the manuscript to allow for reproducibility and validity:

- In my opinion, the potential flaws of using SNP as an NO donor should be addressed either in the methods but preferably the discussion. As the researcher can not rule out that the observed effects are not caused by actual NO effects, but other bio-active compounds released by SNP.

- Please clearly state which materials were harvested (whole shoot tissues, only leaf tissues?/etc). This is essential for reproducibility.

- Explain why no non-waterlogging SNP controls were included. If the SNP and CysNO treatments were succesful, would you not expect SNO content to go up in all of these treatments?

- The authors claim in the text (line 321) to have measured SNO in the roots as well, although I do not see these data anywhere. If they have this data, this would be very valuable to share as well, as these are the only tissues suffering from hypoxia.
Validity of the findings: See experimental design section. The data might be robust but have to be clearly placed into the context of the limitations of  using SNP (cyanide in the water) as an NO donor and the lack of non-waterlogged NO treated controls.
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: EXOGENOUS APPLICATION OF NITRIC OXIDE DONORS REGULATES SHORT-TERM FLOODING STRESS IN SOYBEAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: see below
Experimental design: see below, this is flawed as the paper stands.
Validity of the findings: see below, again flawed as paper stands.
Additional comments: The authors have considered the comments of the referees and the manuscript is better but I do have a major issue with it still. The paper, and I quote that: "we observed that exo-NO application reduces..."
BUT I don't agree. It may be the case but the experimental design and analysis does not support this. In the rebuttal they say:  "our sole focus was to understand the effect of most common exo NO source (SNP & CySNO) ..." which is true. This paper reports on the effects of SNP and CySNO, but it cannot claim to report the effects of NO. There are simply not enough controls carried out. I suggested measuring NO and yes, they are adding NO donors but it would be nice to know that NO was increased. There are no scavengers or depleted controls used. So, I would be happy if the paper is re-titled and re-written to be clear that the effects seen are after treatment of SNP and CySNO, but not NO. Yes, this would limit the impact of the paper, but as it stands I think it would be misleading to continue to claim that the effects were from NO.


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

Input:
Title: PLASTOME OF MYCOHETEROTROPHIC BURMANNIA ITOANA MAK. (BURMANNIACEAE) EXHIBITS EXTENSIVE DEGRADATION AND DISTINCT REARRANGEMENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please have a fluent English user examine the phrasing of the manuscript closely. The phrasing is could be misconstrued as speculative, e.g. "One nature of plastome is that its genes could be transferred or pruned." or "B. itoana plastome is not just downsizing..." or confusing "pseudogenized petG is retained"

Please review for misspellings e.g. "nonbioenirgitic", Burmannia is misspelled as "Burmania" twice, once in the abstract, once in line 41.

Line 50: Please either include all species representatives, or none. This is misleading.

Abstract: Inversion 2 (with accD) is touted as a result of a heterotrophic shift, which would be a very interesting result. This is nearly completely dropped in the discussion section, outside of lines 193 - 195.

Line 200: "Interestingly, the six rearrangements (Inv3/Inv4/Ins1/Ins2/Ins3/ins4) occur in IRs-SSC, IRs, IRs and IRs of B. itoana plastome, respectively" - I don't understand this sentence. Why are "IRs" repeated three times?
Experimental design: Line 54: I am not clear whether the DNA extracted was from the same specimen(s?) as those vouchered. It would also be useful if a better description could be given of the field site.

Line 61: please provide the sequences of these primers.
Validity of the findings: Line 80: Please specify your criteria for determining function vs. pseudogene
Additional comments: Lines 146 - 156: The identity of tRNA genes retained is interesting, and should be expanded.


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: PLASTOME OF MYCOHETEROTROPHIC BURMANNIA ITOANA MAK. (BURMANNIACEAE) EXHIBITS EXTENSIVE DEGRADATION AND DISTINCT REARRANGEMENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This article meets all the basic standards of PeerJ.
Experimental design: The experiment of this study was well designed and the methods used are valid, described with sufficient details.
Validity of the findings: The analyses of this study are sound, and the results are informative. The sequencing of a plastome of heterotrophs in Burmanniaceae and comparative genomic analyses will fill the gap of knowedge about plastome evolution in this family.
Additional comments: The paper is publishable in PeerJ and I only have some minor comments:
1) The title is a bit long.
2) In line 81-82, how did you indentify these genes as pseudogenes? Could you provide some evidence such as frame-shift, stop codon mutations?
3) I suggest authors to consider to add a piturece of B. itoana into the figure, showing the heterotrophic lifestyle of this plant.


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: PLASTOME OF MYCOHETEROTROPHIC BURMANNIA ITOANA MAK. (BURMANNIACEAE) EXHIBITS EXTENSIVE DEGRADATION AND DISTINCT REARRANGEMENTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is quite concise and straightforward and I had no problem following its main message. I should note however that it could be greatly improved by the proofreading by the native speaker. Also, there are multiple typos, including in the plant names (e.g. Burmania instead of Burmannia).
Figures and tables are OK, with exception of Additional file 1 (see below).
Experimental design: The topic is interesting, the research question is well-defined and the results are valuable for the scientific community. The methods are adequate and desribed in sufficient details. However, as soon as one of the main findings of the manuscript is the observation of rearrangments in B. itoana plastome I suggest to perform more thorough analysis of the rearrangements, including the search for the repeats that could have trigger the rearrangements (see e.g.  Weng et al. - 10.1093/molbev/mst257 and other studies of Geraniaceae plastomes which are highly rearranged and repeat-rich).
Validity of the findings: The data are robust, genome assembly is reliable. However, the annotation provided in the Additional file 1 is questionable - it looks like an uncorrected draft, with some notes on the results of the blast search  and strange ORFs such as
gene            complement(<319..>458)
                     /gene="atpI"
                     /note="blatX_hit atpI_Tacca_chantrieri_Copy.gb / position
                     619 - 728 / coverage 14.78% / match 11.16%"

ORF             complement(611..1291)
                     /Genetic_code="Standard"
                     /Reading_frame=3

which do not go to the final annotation (as far as I can see from the Fig. 1). As soon as you submitted the annotated genome to NCBI I would suggest you to replace Additional file 1 by the GenBank flatfile.

Also, I have concerns about the introduction and discussion which are somewhat shallow. Several statements in the introduction and discussion are arguable.
e.g. lanes 36-37: "ndh genes become dispensable once plants have the ability of obtaining nutrients using heterotrophic way" - ndh genes are lacking or pseudogenized in many autotrophic plants (e.g. Peredo et al. 2013 10.1371/journal.pone.0068591). Knockout experiments on model plants also showed that they are dispensable under certain environmental conditions (10.1093/emboj/17.4.868).
lanes 198-200: "It was hypothesized that MORFFO (mobile open reading frames) elements are regularly associated with inversions and changes to the inverted repeats". First, the term MORFFO stands for "Mobile Open Reading Frames in Fern Organelles" and is thus by definition can be applied only to ferns. Second, and more important - MORFFO are unusual ORF, that do not have close similarity to typical plastid genes. As far as see from the results that you present (Fig. 1, in particular), there are no such elements in the B. itoana genome.
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: COGNITIVE PERFORMANCE IN DISTINCT GROUPS OF CHILDREN UNDERGOING EPILEPSY SURGERY—A SINGLE-CENTRE EXPERIENCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1.1	Style, grammar and vocabulary are generally adequate, but there are some places where the manuscript would benefit from language editing (e.g., line 118: ‘In addition to that,…’;  line 190: ‘cognitive performance of studied patients’; lines 311-312: ‘with [a] very broad span of cognitive performance, in the later period we observed [a] decline in the straightforward cases (such as hippocampal and [an] increase in timely referral of complex cases’.
1.2	The introduction does provide an overview of the field. However, although this is fairly comprehensive, it is not very to-the-point. It currently reads more like a listing of different results, rather than a brief, topical review of the literature in the field. I would suggest condensing the current approximately one thousand words to something on the order of 500-700 words, or else fully restructuring the introduction to clarify what is the relevance of the information provided and how each of these data points contributes to an overall picture that informs the present study. It is important to note however, that the references provided are representative of the literature in this field.
1.3	References for the assessment instruments used (e.g., WAIS, WISC) should be included.
1.4	The formal structure of the manuscript is correct. However, the structure of the content can (and should) be improved in many places (see 1.2 above).
1.5	The quality of the figures is acceptable – I particularly like the visualization of the confidence intervals in Figure 1. Figure 2 needs clearer labeling but is otherwise ok.
1.6	The tables should be restructured to provide the information in a more condensed form (see also 1.7 and 4.1).
1.7	The proportion information in the tables (second column) should be integrated in a separate table reporting patient demographics and epilepsy variables, i.e., a condensed version of the current Supplementary Table 1. If this creates problems in terms of journal limits on the number of tables then the current Table 4 can be moved to the Supplementary information.
1.8	In line 242 as well as in many tables, p-values and other non-integer numbers are incorrectly reported with commas as decimal separator, rather than periods. At the very least this should be made consistent (because periods are used elsewhere).
1.9	Where results from statistical tests are reported they should always include the essential information that allows reproduction and interpretation. In particular, F-tests require reporting of the degrees of freedom and some measure of effect size, preferably partial eta-squared but in my opinion standard errors or confidence intervals of the effect are acceptable here since they have the advantage of being directly interpretable in terms of the dependent variable.
1.10	The raw data are available at the time of this review (though see 3.5). However, in their declarations the authors appear to suggest that only summary data will be made available.
Experimental design: 2.1	The manuscript reports on a retrospective study of pre- and post-surgical IQ in a fairly large single-center cohort of children undergoing resective brain surgery for treatment of intractable epilepsy. The study therefore clearly falls well within the aims and scope of PeerJ.
2.2	The research questions (lines 159-167) are somewhat poorly defined. In particular, the relation between question i) and questions ii)/iii) is unclear. Are these questions simply combined because they happen to be answerable with the present data? Or is there some particular idea behind this combination which I have been unable to identify? In addition, it is not entirely clear to me precisely what is the intended difference between question ii) and question iii), especially in the way they are addressed in the manuscript: the ‘groups’ mentioned in question iii) are effectively just splits based on variables such as those used in question ii).
2.3	Perhaps more importantly, these questions do not fully match the knowledge gaps identified in the previous paragraph (lines 156-158), which refer to aetiology and the identification of adequate controls. Although the question of suitable controls to assess the effect of epilepsy surgery is an important one, it is not addressed by this study. Aetiology is addressed in questions ii) and iii) but only as part of a larger set of variables. To address these issues, I would suggest a slight change by focusing on three interrelated questions: i) are there changes in cognitive outcome over time? Ii) are there changes in patient characteristics over time? Iii) are the results of these analyses related, e.g., is an (hypothetical) increase in patients with very severe forms of epilepsy responsible for an (equally hypothetical) deterioration in cognitive outcome? This requires two additional analyses: a) an analysis of patient characteristics over time, and b) a multiple regression analysis that includes date of surgery as well as variables previously identified as related to cognitive outcome.
2.4	The data collected for this retrospective study are remarkably complete. Nevertheless, as in any study of this kind, there are missing data and this should be addressed, or at the very least acknowledged (cf. the STROBE guidelines mentioned earlier).
2.5	The authors provide evidence of the ethical evaluation and approval of the study they report on, albeit post-hoc. In my personal opinion, there are no ethical objections against a study of this kind, or if there are, they are vastly outweighed by the benefits. In my view, the study also does not conflict with the Declaration of Helsinki in its most recent form, as accepted by the 64th assembly of the World Medical Association (https://www.wma.net/policies-post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-human-subjects/). However, the most literal interpretation of the PeerJ article requirements for human subjects research (https://peerj.com/about/policies-and-procedures/#human-subjects-research) does not allow this kind of study, since this text does not – at least explicitly – allow for any exceptions to the requirement for informed consent, not even for retrospective analysis of anonymized data as done here. Although the author declarations refer to a “patients' consent form used in clinical practice“, I cannot find this among the files.
2.6	For some patients, IQs in the 20s or 30s are reported. The range of modern, standardized intelligence tests typically does not normally extend much below 50. While there are commonly used techniques to calculate IQ scores for children who score below the lower end of an IQ scale, this needs to be clarified in the text, both to ensure reproducibility and also because such techniques do affect (lower) the reliability of the resulting IQ scores.
2.7	It is very difficult (even with the data in hand) to determine exactly how many patients are included in each analysis. To comply with the STROBE guidelines (https://www.strobe-statement.org/index.php?id=strobe-home), this should be made clear for each analysis. For example, whereas the header for Table 1 states that these are results for the whole dataset, the analysis presumably only included the 191 patients for whom pre-surgical IQ was available. Put differently, the sample size of 203 patients reported in line 234 includes some patients who did not meet the inclusion criteria reported in lines 173-176.
2.8	I also find it difficult to determine how many and exactly which analyses were performed. While I feel that correction for multiple comparisons is not appropriate in this case, since control of Type I error would come at the cost of inflated Type II error, it is essential that the reader is able to determine the structure of the analyses and their exact number.
Validity of the findings: 3.1	While I can generally confirm the results from the data provided, I am having trouble obtaining identical (or even similar) values for estimates. The meaning of the columns Median_difference, CI_low, and CI_high in Table 1 is also unclear, and the values listed there seem implausible (e.g. 9 values are listed with two zeros as the first two decimals).
3.2	The statistical analysis does not indeed suggest considerable improvements in IQ after surgery as the text suggests (line 299-300). The authors seem to refer to the regression equation corresponding to the top left panel of Figure 1. However, this equation suggests an increase of 9.1 points only for a hypothetical patient with a pre-surgical IQ equal to 0. For more realistic pre-surgical values, the predicted gain would be considerably smaller (and decrease with increasing pre-surgical IQ: pre 50 -> post 0.93 * 50 + 9.11 = 55.6, gain = 5.6; pre 100 -> post 0.93 * 100 + 9.1 = 102.1, gain = 2.1; pre 130 -> post 0.93 * 130 + 9.1 = 130.0, gain = 0.0).
3.3	Although the argument has been made that the effects of repeated measurement that are present in healthy adults are strongly reduced or even absent in children with epilepsy (Westerveld et al. 2000), this issue should definitely be addressed in the discussion, especially since other studies do suggest that practice effects cannot be ignored (Sherman et al. 2003).
3.4	The discussion repeatedly touches upon the pathogenesis of cognitive impairment (line 348; line 369; line 381). It seems to me that this, while not irrelevant, is beyond the proper scope of the manuscript, which provides no meaningful data on the pathogenesis of cognitive impairment beyond associations with particular etiologies.
3.5	The raw data are provided. However, to encourage their use, many small issues should be fixed:
-	Column BN (“slopacienta“)  repeats column A (patient_id). Please delete.
-	Column K (seizure frequency): ‘Lesst_than_monthly’ should be ‘Less_than_monthly’.
-	A few headers have spelling errors (e.g., AZ, BB, BD – ‘parcial’ should be ‘partial’). Please check and correct.
-	The seizure classes listed in column N (1-4) appear to correspond to the seizure classes in columns AZ, BB, BC, and BD, respectively. The meaning of column N is unclear and duplicates the information in the other four columns. I would suggest deleting column N.
-	Column Z is designated ‘MRS_finding’ but appears to specify only whether MRS was performed. I would suggest changing the header to simply ‘MRS’.
-	Column AK: ‘Lesionektomy’ should be ‘Lesionectomy’.
-	Column AO: the header ‘AWAKE’ in full caps suggests that this is an abbreviation, while it in fact appears to reflect simply whether awake surgery was performed.
-	Column AS: some of the histopathological findings have not been (correctly) translated, e.g., ‘Jizva’ and ‘Encefalitida’. In addition, the header should read ‘histopathology’ rather than ‘histopatology’.
-	Column AU: I would suggest applying the widely used Engel classification for seizure outcome (Engel et al. 1993), and coding this column accordingly. In addition, the ‘greater-than-or-equal-to’ symbol does not translate very well across computer platforms, so even if the current categories are maintained I would suggest changing the exact wording (e.g., ‘reductionover90pct’, since the percent sign suffers from the same problem though to a lesser degree).
-	As far as I can tell the columns AT, BE-BI, BK, and BL all contain essentially the same information. I would suggest keeping only column AT.
-	Similarly, column BM (‘epoch’) follows from column AH (although the exact cutoff, i.e., December 31st, 2010 vs January 1st, 2011 should be clarified in the manuscript itself).
-	To reduce the file size (in terms of viewing, not so much in terms of disk space), I would also suggest removing columns BP and BQ since they duplicate the information in column AI.
-	Why is the ‘surgery_extent’ (column AL) for some patients with the surgery type (column AK) ‘Hemisferectomy’ not ‘Hemisferectomy’ but rather ‘Focal resection’, ‘Multilobar resection’ or ‘Unilobar resection’?
-	In column AK I would replace the label ‘Individual_resection’ with the more commonly used ‘Tailored_resection’, which also used in the text of the manuscript.
Additional comments: 4.1	Given the use of multiple regression for the multivariate analysis, I would suggest framing the univariate analyses in terms of regression as well. While F-tests would still be required to assess the overall significance of effects that involve factors with more than two levels, for all other results a uniform method of reporting can then be used. Using the example of Table 1, each continuous variable or 2-level factor then only needs one line. For the univariate analyses, this line should report the variable, the intercept and its standard error, and the p-value (of the intercept). For the multivariate analyses, the global intercept should be reported on a separate line. The result could look something like this:
Determinants of pre-surgical IQ/DQ in whole dataset
 	Univariable regression	Multivariable regression
Variable	Intercept (SE)	Beta (SE) / F	p-value	Beta (SE) / F	p-value
Intercept	-	-	-	89.55 (10.14)	<0.001
Abnormal neurological finding1	86.83 (1.55)	-18.46 (2.91)	<0.001	 -10.95 (3.47)	 0.002
Epileptic syndrome2	64.08 (5.36)	F2,188 = 6.83	0.001	F2,175 = 2.26	0.108
TLE		20.95 (5.73)	< 0.001	9.53 (6.11)	0.120
XTLE		16.69 (5.73)	0.004	11.90 (5.70)	0.038
1 reference level: no abnormal neurological finding; 2 reference level: hemispheric epileptic
syndrome.
4.2	Custom checks:
Have you checked the authors ethical approval statement? Yes
Does the study meet our article requirements? Yes, but see 2.5
Has identifiable info been removed from all files? Yes
Were the experiments necessary and ethical? Yes
4.3	Raw data check – see 1.10 and 3.5
4.4	Image check – OK


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: COGNITIVE PERFORMANCE IN DISTINCT GROUPS OF CHILDREN UNDERGOING EPILEPSY SURGERY—A SINGLE-CENTRE EXPERIENCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: This study is welcome and the authors have clearly a very good understanding of the field and of the issues. The sample size is large.  I have a couple of small suggestions which the authors might like to consider when thinking about the study.

1. In the introduction the authors talk about seziure freedom in the context of epilepsy surgery outcome. I think while seizure freedom is a worthy goal signifcant seziure reduction (or disease improvement) is also worthy and this could be mentioned as for some patients seziure freedom may be difficult but seizure reduction is still a welcome result
2. The authors should mention as a limitation that different tests were used i.e. differnt versions of Wechsler and Bayley. I know this cannot be helped but it still makes comaprisons less valid due to use of IQ and DQ which are different concepts. There is also a risk of practice effects with only a 12 month period between restesting.
3. the authors might like to explain a little more why 2011 was chosen as the dividing line for the two time periods.
4. Lower IQ improves more-  this might be discussed a little more - perhaps there is more room for improvement in low IQ etc.
5. In the results section i might be nice to state the direction of findings in some instances where it was not stated e.g there was a signifcant difference on post hoc analysis - group 1 was signifcantly better than group 2 etc.
6. In discussion perhaps discuss findings in comparison to styudies which ahve not found a signifcant improvment in cognitive scores e.g. VIGGEDAL, Gerd, et al. Intelligence two years after epilepsy surgery in children. Epilepsy & Behavior, 2013, 29.3: 565-570.

Minor points
please use . and not , when referring to decimal points

Recent - remove this as 2013 may not be recent for some people

In the first paragaph the term 'to rid' is used - please use a better term if possible


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

Input:
Title: COGNITIVE PERFORMANCE IN DISTINCT GROUPS OF CHILDREN UNDERGOING EPILEPSY SURGERY—A SINGLE-CENTRE EXPERIENCE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors are to be commended for their substantial revision of the original manuscript. They have clearly put great effort into improving the manuscript, and they have sufficiently addressed the vast majority of the issues that I have previously raised. However, I believe there remain a few issues that merit further attention.

In my comments below, the numbering refers to my review of the first version of the manuscript, e.g., 1.6.1 is a comment regarding the issues discussed in point 1.6 of the previous review. Any comments that raise new issues are numbered in continuation of the previous numbering, e.g., 4.5.

1.6.1	The tables have much improved and are now easier to understand. However, I still feel that many tables contain too much empty space. For example, in the first part of Table 2 (Determinants of pre-surgical IQ/DQ), 49 of 88 cells (i.e., more than half) are empty. In this particular case:
- the second row can simply be deleted
- row 5 (epileptic syndrome), columns 2-4 should contain an estimate of effect size
- rows 8-9 (no/yes) can be deleted
- rows 12-last, columns 2-5 need to contain useful information or be deleted
I do not mean to imply that there should be no empty cells in the tables, but in their current form they take up more space than can be justified from their contents. Instead, some cells should probably be removed, and some cells need to be filled with information useful to the interested reader.
In addition, there are a number of inconsistencies to be addressed. To take the same example (Table 2):
- infantile spasms, status epilepticus and abnormal neurological finding are all factors with two levels, but only abnormal neurological finding gets three rows specifying the levels (two of which are almost empty – see above).
- epileptic syndrome, histopathology and FCD class are all factors with more than two levels, but only for FCD class are the levels specified in the table. If the reason for this is to clarify the precise classification used (e.g. FCD1/FCD2/FCD3 vs FCD1/FCD2A/FCD2B/FCD3A/FCD3B/unspecified MCD), then this should be done either in the table legend, or in the text of the manuscript. In the latter case the different classifications should be designated with labels which are then used throughout text and tables.
While I have here specified the problems specifically for one part of Table 2, these problems also apply to the rest of Table 2 and to the supplementary tables.

1.8.1	Commas still occur in lines 64 and 250. Additionally, in line 251 a period is missing (‘p=062’ [sic]), and in both line 250 and 251 there are commas missing between the reported numbers (‘F=0.48 p=0.49’ should be ‘F=0.48, p=0.49’).

1.9.1	The reporting of F-values still lacks indication of the degrees of freedom as well as effect sizes. The Publication Manual of the American Psychological Association (6th edition) gives the following example (p. 117):
‘For immediate recognition, the omnibus test of the main effect of sentence format was statistically significant, F(2, 177) = 6.30, p  = .002, est ω2 = .07. The one-degree of freedom contrast of primary interest (the main difference between Conditions 1 and 2) was also statistically significant at the specified .05 level, t(177) = 3.51, p < .001, d = 0.65, 95% CI [0.35, 0.95].’
For many other results, only p¬-values are reported. I believe most of the corresponding information is reported in the revised (supplementary) tables, but if so it would be helpful to point out exactly where the information can be found. Where this is not the case (e.g., line 238 and probably other instances), the information should be reported in the text.
Experimental design: 2.2.1	The rephrased research questions are a great improvement over the original version, and also correspond much better to the revised introduction. However, I think some further rephrasing may make it easier for the reader to grasp exactly what are the differences between the three questions. One source of confusion is the fact that the term ‘change’ [in cognitive performance] is used in two different meanings: individual change (post-surgical minus pre-surgical IQ) and historical changes (differences between the early and late period of the epilepsy surgery program). I would suggest something along these lines:
“In this study we aimed first to test whether there were differences in cognitive performance (pre-surgical IQ, post-surgical IQ, or change from pre-surgical to post-surgical IQ) between the early and late period of the paediatric epilepsy surgery program in our tertiary clinic. Next, we assessed whether there were differences in cognitive performance between the early and the late period for specific underlying aetiologies and epilepsy syndromes. Finally, we aimed to identify variables affecting cognitive performance in the entire cohort.”

2.9	I have belatedly realized that the authors reported using ‘generalized multiple regression’ (line 222). If this is correct, then the assumed distribution and the link function applied need to be specified (and some justification for these choices would be desirable). If, on the other hand, they used multiple regression based on a general (rather than a generalized) linear model, i.e., ordinary multiple regression, then this description should be corrected.
Validity of the findings: 3.1.1	I have now realized that the reason that these values occur is because it is indeed the median that is being reported, and not, as I erroneously supposed when reading the first version, the mean. However, that raises the question why the median rather than the mean is reported: the authors use statistical inference techniques which rely on assumptions of normal distribution (and equal variances), but report the observed differences in terms that appear to suggest these assumptions are not met. Can the authors explain this choice?
On the other hand, Table 4 now reports post-hoc tests and reports a median difference which I suspect is instead a mean or estimated difference. In that case the column label should be corrected.

3.1.2	I have also realized that this is probably the reason why the authors don’t provide similar results for factors with more than two levels (e.g., FCD class in Table 2), since such a median difference (and Hodges-Lehmann confidence interval) cannot be provided for specific levels of the factor. However, I would still advocate for one of three options:
a) Reporting the results from the regression, including effects of specific levels through either treatment or sum contrasts (the contrasts used should of course be specified to allow interpretation – I think treatment contrasts are probably preferable because the interpretation is somewhat more straightforward). This is what I suggested in my previous review.
b) Reporting the pairwise median difference and its Hodges-Lehmann confidence interval in a manner similar to the treatment or sum contrasts mentioned in option 1. That is, for treatment contrasts one level (e.g., FCD1) would be set as the reference level, and the table would report the median difference between this level and each of the other levels. To approximate sum contrasts, one would report the median difference between each specific level and all other levels combined (e.g., FCD1 vs all others).
c) Reporting the median and its Hodges-Lehmann confidence interval for each level of the factor. This is conceptually different from the previous suggestions in that it does not provide an estimate of the difference in the technical sense (since the median difference does not necessarily equal the difference of the medians), but it does provide the reader with some feel for the pattern of factor level results.

3.3.1 	However, I believe this [the issue of repeated measurement previously raised as point 3.3] is also relevant to the discussion regarding the greater IQ/DQ gain in children > 6 years (lines 318-322).

3.5.1
-	A few headers have spelling errors (e.g., AZ, BB, BD – ‘parcial’ should be ‘partial’). Please check and correct.
->	The header for column BA should be ‘seizure_class_partial_complex’ rather than the current ‘seizure_class_partial_komplex’
-	Column AU: I would suggest applying the widely used Engel classification for seizure outcome (Engel et al. 1993), and coding this column accordingly. In addition, the ‘greater-than-or-equal-to’ symbol does not translate very well across computer platforms, so even if the current categories are maintained I would suggest changing the exact wording (e.g., ‘reductionover90pct’, since the percent sign suffers from the same problem though to a lesser degree).
->     However, this classification should then also be used for the analyses (and reported in text and tables, e.g., Supplementary Table 3, lines 115-119).
Additional comments: 4.5	The discussion has improved and is acceptable in its current form, but in my opinion it does not do justice to the rest of the paper. I would therefore highly recommend that the authors take another look at the discussion and attempt to condense it. There are many possible ways to do this and what follows are therefore really just suggestions.
For example, the structure of the discussion could be made to follow the structure of the analyses: overall comparison between the two periods, then the same comparison for subgroups (mainly for FCD, and then factors predicting cognitive performance in the sample as a whole. As another example, the first three paragraphs (lines 296-322) could be combined into a single paragraph discussing the interrelationships between age at surgery, pre-surgical IQ and IQ change after surgery. As a final example, some of the text is still phrased in ways that suggest that the issues discussed are addressed in the current study (e.g., lines 325-342) when in fact they are emphatically not analyzed here.
Again, I do not think that these changes are imperative for the manuscript to merit publication, but I do think that they would benefit the quality of the paper and – therefore – the reader.
4.6	Something appears to have gone wrong with the formatting of the references to the Wechler tests (lines 620-623) – please correct. I would also suggest providing the version information (1st edition / new revised edition) in English. Unless the journal policy on such matters prescribes differently, I would also suggest adding an English translation to publications not in English.
4.7	The reference for the Stanford-Binet scale (lines 608-609) provides a street address for the publisher. This is unusual, and also appears to be unnecessary.
4.8	There are (still) many minor formatting glitches. For example: in line 443 the text reads: ‘on-going(Boshuisen et al. 2015a).’ The correct spelling would be ‘ongoing’ (no hyphen), and a space is required between ‘ongoing’ and parentheses following it. I assume such issues will be addressed during copy editing, but they ought to be fixed before publication.
4.9	‘epileptic sydrome’ [sic] appears twice in Table 2.


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: COGNITIVE PERFORMANCE IN DISTINCT GROUPS OF CHILDREN UNDERGOING EPILEPSY SURGERY—A SINGLE-CENTRE EXPERIENCE
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors deserve commendation for their persistence and hard work in revising the manuscript. The manuscript is now very nearly acceptable for publication. I have just a few small points that I do feel have to be addressed:
1.1	The authors still report that they performed **generalized** regression (line 225, line 281, the legend to Table 4, and Table 4 headers). **Generalized** regression implies that the distribution of either the dependent variables or the unobserved errors is assumed not to follow the normal distribution. If it is really true that they used a **generalized** regression analysis (and **not** a regular multiple regression based on the **general** linear model) then they do need to report details of this statistical model, including the distribution they used and the link function (quasi-normal with an identity link function?). However, the only thing in their results that I can see may suggest the use of a generalized regression is the dispersion estimate reported in Table 4. If this is not what they did then they should remove the word ‘generalized’ everywhere.
1.2	I appreciate the inclusion of the mean differences in Table 2. However, the authors should report a maximum of two decimals for these number (one decimal would be preferable, i.e., 9.0 or 9.03 instead of 9.03473). The authors should also clarify the meaning of the bracketed numbers in the columns ‘median difference’ and ‘mean difference’ – I think these are 95% confidence intervals? This should be explicit in the table itself, or in the table legend. In addition, the legend to Table 2 lists many abbreviations which are not used in the table.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: COGNITIVE PERFORMANCE IN DISTINCT GROUPS OF CHILDREN UNDERGOING EPILEPSY SURGERY—A SINGLE-CENTRE EXPERIENCE
Review round: 4
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I would recommend doing one more thorough spell check during the proofing stage to ensure that any errors that may have slipped in during the revisions (e.g., line 226 'modelby' instead of 'model by') are corrected.


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: ENDEMISM AND DIVERSITY OF SMALL MAMMALS ALONG TWO NEIGHBORING BORNEAN MOUNTAINS
Review round: 1
Reviewer: 1

Output:
Basic reporting: All points are integrated into one document; see General comments for the author
Experimental design: All points are integrated into one document; see General comments for the author
Validity of the findings: All points are integrated into one document; see General comments for the author
Additional comments: The manuscript “Small mammal diversity along two neighboring Bornean mountains”, by Melissa T. R. Hawkins and coauthors aims to describe distribution patterns of small mammals along elevation gradients on two mountains in the Kinabalu National Park. They perform a more intensive sampling than a previous work in order to evaluate if they would still detect a Mid-domain effect. The manuscript is well written in terms of English language, they follow adequate ethical and sampling protocols, perform a well designed sampling work and methods are described with enough detail to replicate.

Main comments
However, I am concerned with different aspects of the research that I explain as follows:

Introduction: the authors start the introduction describing what they did “We surveyed the diversity of the non-volant small mammals along the elevational gradients of
two neighboring mountains on the island … “ and what had already been done “Previous surveys of elevational transects have measured diversity”, with a rather brief comment on the Mid-Domain Effect (lines 31-51). Hence, it lacks a sound description of the theoretical background that is needed to put the study into context and present clear scientific questions.

As a result, I consider the authors work with a research question that falls very short of the potential of their data; namely their objectives [(1) to better characterize the diversity of the small mammal community along elevational gradients in Kinabalu National Park, (2) to evaluate whether the MDE previously described is robust to incomplete sampling of the low-elevations, (3) to determine if the same pattern of diversity across the altitudinal transect is the same on the two mountains], do not pose a novel, significant research question. As stated, they do perform a better description of the small mammal diversity, based on a more adequate sampling, of a elevational pattern that was already known.
Also, they do not justify why to compare the two mountains, what is the scientific question behind it. As a consequence, the information and data they obtain do not allow for a strict and thorough discussion of the evolutionary and historical factors that could have driven small mammal diversity with elevation in this context (their objective 4).

It is important to highlight that for the very basic question of the Mid-domain effect (MDE), one needs to determine if the data being analyzed (in this case, diversity along the elevation gradient) is autocorrelated. Autocorrelation is commonly present in this kind of data, thus analyses need to be done taking that into consideration. There is plenty of literature about Mantel tests, autocorrelation, variograms, etc., but see the published work of Christy MaCain for specific examples regarding MDE, Pierre Legendre for autocorrelation. Indeed, results can be completely different once the correction for autocorrelation has been performed.

I recommend that the authors think of more complex and novel questions that they can evaluate with the ample information they have gathered. Published literature about species richness, beta diversity and the sort, for diverse gradients including elevational, latitudinal, etc. are abundant. I am sure the authors can perform a more novel and gap filling 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: ENDEMISM AND DIVERSITY OF SMALL MAMMALS ALONG TWO NEIGHBORING BORNEAN MOUNTAINS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is poorly written. I believe the authors must rewrite the entire manuscript.
Experimental design: I found the general idea of looking for diversity patterns interesting.
Validity of the findings: The manuscript is really hard to follow due to the poorly written style of the authors.
Additional comments: The authors presented an observational study aimed to look at patterns of small mammals diversity along two elevational gradients in Borneo. I think that the general topic addressed in this manuscript is interesting, the methods used are straightforward and the amount of work in the field is to say at least impressive. A major but maybe fixable shortcoming of this manuscript is the writing style. I just listed the major issues that I see in each section of the manuscript.
(1) The Abstract is hard to follow. I read the first sentence several times and I still do not understand what the authors tried to say.
(2) The Introduction’s first sentence is what the authors actually did in the field. The authors should begin the introduction with a very general overview of the topic. Then, you can narrow the topic until you reach the aim of the study and the hypotheses tested.
(3) Methods: the Study site section is way too long with too much detail. Field survey, did the authors conduct the surveys in two consecutive field season in both mountains, or they only conducted two field seasons in Mt. Tambuyukon? Why the surveys were conducting in different time of the year? What is the rationality behind this change?
(4) Results: Line 161 – “The trap success calculations were done excluding pitfall traps and arboreal traps (due to inconsistent placement of traps).” This problem only happened in Mt. Tambuyukon? I do not understand what happen with the pitafall traps and arboreal traps.
The results are hard to understand because of these distracting issues.
Except for the Diversity subheading the whole Results section must be rewritten. I strongly believe that the natural history is really important, and looks like the authors know a lot about it, but it is hard to pick the main results among all the details presented by the authors. Additionally, there are too many tables and figures.
(5) The Discussion section presents the same problems that the rest of the manuscript, except for the subheading Conclusions. The first paragraph of the section should be a brief summary of the most important results.

If the authors are willing to re-write the entire manuscript, the study would be suitable for publication in PeerJ. However, a thorough revision of the manuscript should be conducted once the writing problems are fixed. I am sorry I cannot be more positive, especially because both the interest and importance of this work are clear, but I hope these comments can help 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: ENDEMISM AND DIVERSITY OF SMALL MAMMALS ALONG TWO NEIGHBORING BORNEAN MOUNTAINS
Review round: 2
Reviewer: 1

Output:
Basic reporting: All points are integrated into one document; see General comments for the author
Experimental design: All points are integrated into one document; see General comments for the author
Validity of the findings: All points are integrated into one document; see General comments for the author
Additional comments: I consider the authors made significant improvements following the reviewers and editor suggestions and considerations, rendering a manuscript with the potential to be published in PeerJ.
However, there are still some important problems that need to be addressed and corrected.

General comments:

The writing of ideas still needs to be clearer, direct, avoiding loose, out-of context phrases
Avoid de use of “very”, it is subjective and non-scientific (lines 36, 42, and all throughout the manuscript).

Specific comments:

Abstract and Introduction
Line 33 : delete second hypothesis

Lines 35-37 The entire phrase “These data enable … patterns” is confusing; what is meant by long elevational gradients? similar mountains –are very similar? What selective drivers in the environment determine what patterns? Speculative and unclear

Lines 43-46: this phrase is out of context here .. eliminate and concentrate on the biodiversity patterns background.

Lines 71-75 : another confusing phrase with several unconnected ideas ¿The other side? A simpler writing is: “Knowledge about tropical biodiversity is still incomplete”. … ¿More boots on the ground … in (on) the news … totally out of context.

Lines 97-102: the manuscript still lacks a clearer objective and specific predictions. Namely, what of the different “standing” hypotheses were considered? what underplaying assumptions, some, all? What would the authors expect to find given the nature of the mountains, and the hypotheses and assumptions? You have these in the discussion (lines 310-314)

Methods
The problem with autocorrelation has not been solved.
First, why estimating a Mantel test between elevation and similarity? the mid-domain effect refers to species richness (or Beta diversity) within a mountain, and then comparison between mountains can be done.
A Mantel is only a part of the needed analyses. The authors indicate in their answer that “However, our overall goal is to look at the curve of diversity with elevation, autocorrelations effects included. We are not testing the mechanisms causing the diversity pattern. Therefore, in our particular case, as we are considering only one variable, elevation, as our only explanatory variable for diversity, we think our approach is correct”
Autocorrelations effects included does not make sense. You do need to correct for autocorrelation,
It does not matter that only elevation is being considered, you are testing for a Mid-Domain effect hence the relationship has to be corrected for autocorrelation (see Mena & Vázquez-Domínguez. 2005 Global Ecology and Biogeography, 14(6): 539-547, for a detailed explanation)

Discussion
I urge the authors to work some more on the discussion, making an effort to summarize ideas, shortening and eliminating repetitive or speculative statements (in particular Pattern predictability and Conservation implications). This will strengthen the work and make it more succinct and fluent.

Lines 327-329 : see precisely Mena & Vázquez-Domínguez 2005.


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: ENDEMISM AND DIVERSITY OF SMALL MAMMALS ALONG TWO NEIGHBORING BORNEAN MOUNTAINS
Review round: 3
Reviewer: 1

Output:
Basic reporting: See the "General comment for the author" below
Experimental design: See the "General comment for the author" below
Validity of the findings: See the "General comment for the author" below
Additional comments: The authors took into consideration all of my (and other reviewers) comments and fully transformed the manuscript; they incorporated the new analyses required, rewrote some of the Introduction to incorporate the new objectives/questions, and also the Discussion, which changed accordingly with their new results.
Hence, I have no further comments and consider the manuscript is now appropriate for publication in PeerJ.


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

Input:
Title: ENDEMISM AND DIVERSITY OF SMALL MAMMALS ALONG TWO NEIGHBORING BORNEAN MOUNTAINS
Review round: 3
Reviewer: 2

Output:
Basic reporting: This manuscript represents an impressive body of work on Borneo's small, non-volant mammals. In the current state, however, major changes need to be made. First, the English reads quite strangely, especially in the introduction. I have made a few specific comments regarding this in my line-by-line comments. As a whole the manuscript needs language attention. A second issue is the discrepancy between hypotheses and statistical methods. In the introduction the only hypothesis that was stated was that mountain endemics shape diversity, versus the null that species are distributed everywhere. The authors appear to be testing hypotheses about the mid-domain effect, and should clearly state so in the introduction.
Experimental design: In the current state the research question is not well defined. A more comprehensive set of hypotheses need to be outlined.
The statistical methods were sound, though a few more details need to be provided.
Validity of the findings: The statistical methods appear to be solid, though I have a few comments in the line-by-line. The most challenging finding in the manuscript is the species-level identifications made using live-captured animals and a field guide with hand-drawn illustrations. Though I am not an expert on some of these species, I know, according to many experts, that many of these murine rodent and crocidurine shrew species can be incredibly hard to identify based on external characters alone. Many researchers would argue that DNA and/or cranial characters are critical in identifying these species. This is speculation, and I do not mean to diminish the authors expertise, however I find the consistent and accurate identification of 5 Maxomys species, a few of which are very poorly know, a bit suspect.

As pointed out in the conclusions, their survey results—which found no support for the MDE—differed from past survey results that found support for the MDE. This is to be expected. A single survey can never capture the full community of a place as diverse and challenging as Kinabalu. It may make more sense to combine modern and historic survey efforts to test these large-scale hypotheses.
Additional comments: The effort put into collecting these data is very impressive! The manuscript tests some interesting hypotheses about patterns of species richness along elevational gradients, but the hypotheses and framework remain unclear. I recommend working on simple statements of predictions in the introduction, and focusing on how these relate to the methods and results in those respective sections.


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

Input:
Title: IDENTIFICATION OF CRUCIAL GENES IN ABDOMINAL AORTIC ANEURYSM BY WGCNA
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this paper, the authors first detected differentially expressed genes between AAA samples and controls. Then they used WGCNA to construct co-expression networks to identify key modules and hub genes. The following lists my major concerns.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: 1.	The figures in this manuscript are not clear, especially for Figures 3, 4, 5, and 6. The characters are not clear to read. Can you draw them with higher quality?
2.	In line 119, the authors used 0.8 as fold change threshold. Why did you use 0.8 (2^0.8~=1.7)? Does this cutoff influence your analysis?
3.	In figure 3D and 3D, you used WGCNA to identify modules. Can you annotate the clusters with functional terms? Your figures could not deliver enough information.
4.	Similar to above question, in figure 6, you only show the down- and up-regulated genes. What are related functions of these genes?
5.	From line 176, the authors introduce the method to compare the AAA and control co-expression networks. Basically, the two networks are different in nodes and edges. Do you have computational method systematically compare them? In your result, the pathways like inflammation is appeared in both networks, although, it is scattered in one module. How can you tell they are different on network level?
6.	There are some GWAS studies reported some significantly AAA associated SNPs and genes from genomic data. Can you have a comparison between your differentially expressed gene list with them? Can your co-expression network explained the disease mechanism from genetic variations?


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 CRUCIAL GENES IN ABDOMINAL AORTIC ANEURYSM BY WGCNA
Review round: 1
Reviewer: 2

Output:
Basic reporting: 'no comment'
Experimental design: 'no comment'
Validity of the findings: 'no comment'
Additional comments: The authors analyze three gene expression datasets on both normal and AAA conditions. Network analysis is the best way to identify crucial genes in disease. Overall, the workflow for the whole study is reasonable, with some important caveats outlined below. As a whole, the manuscript would be more compelling if it combine the network analysis with GWAS study.

1, There are several GWAS studies on AAA. Following papers found some risk genes for this disease. I think it will be great to combine the current network analysis with GWAS study.
Jones, Gregory T., et al. "Meta-analysis of genome-wide association studies for abdominal aortic aneurysm identifies four new disease-specific risk loci."  Circulation research 120.2 (2017): 341-353.
Li, Jingjing, et al. "Decoding the genomics of abdominal aortic aneurysm."  Cell 174.6 (2018): 1361-1372.

2, I guess the variation between AAA and normal groups are big compared to the within group variation. Authors should show the variation of samples by Principal component analysis (PCA) based on 1) whole gene list and 2) differential gene list. If the variation between two groups are big, it is good to merge all the samples together and do network analysis. Only using the samples from normal condition and constructing network would loss too much information.  Modules on this network (from all samples) have different expression pattern, some of the modules would have high expression on AAA condition while some have high expression on normal conditions.

3, Please improve the quality of figures and enlarge the font size. It is hard to see the text on figures after zoom in 500%. Fig.2A, Fig.3A, Fig. 4A, Fig. 6A. In Fig.6, don’t use the color of red.

4, In the section “Mining crucial genes mediated in AAA”, please give detail of the ROC analysis. What is the features, what is the ground truth,…

5, please improve the language and writing.
i.e. “One hundred and two nodes and three hundred and three edges” > “102 nodes and 303 egdes”


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 CRUCIAL GENES IN ABDOMINAL AORTIC ANEURYSM BY WGCNA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Null
Experimental design: Null
Validity of the findings: Null
Additional comments: Thanks for the authors' response. I have the following concerns.

1.	About the quality of figures, I checked the original PNG files. Although the resolution is enough for clear visualization after zooming out, the character size is still not large enough when printing these figures on an A4 size paper. So I strongly suggest to improve the visualizing effect of all figures when reaching to the final publishing round.

2.	Figures 3F,G and 4F,G show the clustering modules by WGCNA, but the figures are not informative. I think labeling the exact functional terms you listed in Table S2-3 aside the modules will directly convey the information and improve the figures. Figure 3 and 4 are similar and redundant, it’s not clear enough for readers to tell the similarity and difference between normal and AAA. What do you want to deliver? Do you have better way to directly show? Otherwise you can put some of the figure to supplementary files.

3.	For last question 5, i.e. “Do you have computational method systematically compare them? In your result, the pathways like inflammation is appeared in both networks, although, it is scattered in one module. How can you tell they are different on network level? “. I could not understand your computation method. You mentioned “Related genes=Number of genes associated with targeted pathways in KEEG pathways with top 10 count number, All genes=Number of all genes in KEGG pathways with top 10 count number) ”. What does this mean? Can you explain it clearly and detially?

4.	About the GWAS study, you mentioned only two genes have some consistent evidence. What about the others? Does this mean there is still a big gap between the genetic variations and co-expression network? Do you have any comment on it?


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 CRUCIAL GENES IN ABDOMINAL AORTIC ANEURYSM BY WGCNA
Review round: 2
Reviewer: 2

Output:
Basic reporting: none
Experimental design: none
Validity of the findings: none
Additional comments: The authors’ response solved most of my concerns. But I still have some suggestions:
1, About the combination with GWAS study, I think the authors should go deeper. Those GWAS study provide some significant SNPs, which can be assigned to the genes by distance, enhancer-gene network (by PECA, http://web.stanford.edu/~zduren/PECA/), or eQTL (by GTEx, https://gtexportal.org/home/). Some interesting questions are:
1) Are those GWAS genes are significantly overlapped with the DEGs?
1)  Are those GWAS gene close to the DEGs in co-expression network?
PECA paper: Duren, Zhana, et al. "Modeling gene regulation from paired expression and chromatin accessibility data." Proceedings of the National Academy of Sciences 114.25 (2017): E4914-E4923.
eQTL paper: Brown, Andrew Anand, et al. "Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues." Nature genetics 49.12 (2017): 1747.

2, About the variation between AAA and normal, I think the PCA plots in response letter are informative. Because the variation between AAA and normal is small, so you need to 1) collect multiple gene expression data to differential analysis, 2) use network analysis to de-noise. I suggest authors put those figures to the article and show the variation first. It is a good motivation for collecting multiple datasets and network analysis.

3, I download the raw figures and find the quality is good. But I think authors need to enlarge the font size to make those easier to read. For example, the text in the Figure3 A are too small to read (please print it on an A4 size paper and try to read it). In Figure 3A, it is good to show the samples’ conditions (AAA or normal) and source study (GSE7084, GSE47472 and GSE57691) by different colors or markers.


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 CRUCIAL GENES IN ABDOMINAL AORTIC ANEURYSM BY WGCNA
Review round: 3
Reviewer: 1

Output:
Basic reporting: Null
Experimental design: Null
Validity of the findings: Null
Additional comments: Thanks for the authors'  detailed response. I have no further question or comment.


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

Input:
Title: IDENTIFICATION OF CRUCIAL GENES IN ABDOMINAL AORTIC ANEURYSM BY WGCNA
Review round: 3
Reviewer: 2

Output:
Basic reporting: None
Experimental design: None
Validity of the findings: None
Additional comments: The authors have addressed my comments.


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

Input:
Title: COMPLETE MITOCHONDRIAL GENOME SEQUENCE OF LABRIOCIMBEX SINICUS, A NEW GENUS AND NEW SPECIES OF CIMBICIDAE (HYMENOPTERA) FROM CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: Review of Yan et al. (PeerJ#34672)
The submitted paper provides description of a new genus and species of a sawfly of the family Cimbicidae. In addition, the complete mitochondrial genome of the species is reported. The information presented is new and interesting and should be published. The descriptions of the new taxa and mitogenome are adequate; the morphological illustrations should be improved. Furthermore, the taxonomic and phylogenetic context of the new taxon is not properly established and discussed and needs to be improved.
Some more specific points:
-	The authors are careful to point out (l. 119-122) that the electronic version of the paper, when published, constitutes the valid publication of the scientific name Labriocimbex sinica. This seems a bit superfluous, unless you realize that the name has appeared in print before: Labriocimbex in Li & Wu (2010) and Labriocimbex sinicus [sic!] Vilhelmsen (2019). In the case of the genus name, Labriocimbex, this means that it has been a nomen nudum for almost a decade. The two earlier mentions of the names (there might be more that I am not aware of) were not accompanied by a proper description, so they are not available in the sense of the ICZN code. While the authors are thus correct in asserting that their current submission will validate the names, they need to address explicitly the situation with the previous nomina nuda status; future readers might come across these previous publications and wonder if the current publication has priority, so it is better to explain the situation in full.
-	As indicated above, the proper full name of the new taxon is Labriocimbex sinicus as genus names ending in –cimbex are regarded as masculine in grammatical gender and sinicus/a is an adjective, it needs to follow the gender of the genus name (see Article 31.2 of the ICZN code).
-	The illustrations need to be improved. At least in the version I received for review, Figs 1 & 2 are of low resolution and with much highlight (e.g., Fig. 2A). The authors do not mention any attempts to disperse the light during photography; this can be simply done by placing a cylinder/cone of semitransparent paper or plastic around the specimen, and between it and the source(s) of light. I have a set of images of male and female of Labriocimbex which almost matches that of the authors, but of much better quality; one is published in Vilhelmsen (2019; fig. 3B).
-	In addition to describing Labriocimbex sinicus as the type species of the genus, the authors transfer Trichiosoma zaraeoides Malaise, 1939 to the new genus as Labriocimbex zaraeoides (Malaise, 1939) comb. nov. (l. 340). No mention is made of what material they examined of this taxon (did they examine the holotype?), in contrast to the detailed information provided for the material of Labriocimbex sinicus. Also, they should provide illustrations of Labriocimbex zaraeoides so the reader can see simliarites in differences between the two taxa; there is no real justification provided for the comb. nov., it is just ‘similar to L. sinica’ (l. 343) and then some differences are mentioned.
-	The authors state (l. 241) that ‘the new genus is similar to Pseudoclavellaria … and Trichiosoma’. There is no explicit statement at what characters indicate the similarity, but some differences are listed. Later, it is stated that Labriocimbex belongs to Trichiosomini (ls 518-19), and it is included in the key for this tribe (ls 250-266). There is no justification provided for this placement or the monophyly of Trichiosomini in the paper. Only three genera of Cimbicidae are sampled, two from Trichiosomini and one from Corynidinae (obs: not Coryninae!). Since no Cimbicinae outside Trichiosomini are included, the monophyly of the latter tribe is not tested. No explicit autapomorphies for the tribe is mentioned either. This contrasts with the results of Vilhelmsen (2019), which did not retrieve Trichiosomini, despite a much larger taxon sample (i.e., 100 cimbicid terminals, with all genera of Cimbicinae represented). The main reason for the authors to uphold Trichiosomini seems to be the unpublished thesis quoted as Deng (2000). Since this is apparently in Chinese and not published, it should not be included in the References; references are publications that can be checked by readers (this is why papers include a reference list!), this is evidently not the case for Deng (2000). If the authors want to cite information from this thesis, they should explain more about the taxon and character sampling of this paper, and discuss its results in comparison with those of Vilhelmsen (2019).
-	The choice of taxa for the phylogenetic analyses of mitogenomes is not properly introduced until the beginning of the Discussion (ls. 494-509); this paragraph should be placed in the Materials & Methods section. Furthermore, there should be more justification for the choice of taxa included. Specifically, why so many Cephidae and why so few Apocrita? Both are essentially outgroups when trying to place the new taxon, which undoubtedly belongs in the Tenthredinoidea. The inclusion of 13 species of Cephidae is overkill as these have already been analyzed in the Korkmaz et al. (2018) which showed Cephidae to be monophyletic. 3-4 representatives from Cephidae should be more than enough for the present paper, as long as both Cephini and Hartigiini are represented. I suspect the rationale is to include all ‘symphytan’ mitogenomes published; however, the ‘Symphyta’ – Apocrita subdivision is completely arbitrary as the former ‘suborder’ is paraphyletic. The only consistent way of sampling mitogenomes would be to include all those produced for Hymenoptera, but this would be beyond scope of the paper.
-	The discussion of the phylogenetic results (l. 510-521) is very cursorial and glosses over the substantial differences between the topologies of the other papers cited (in particular with that of Peters et al. (2017) and the rest), and between these and the current submission. For instance, all the papers cited (except for Vilhelmsen 2015, which did not include any carnivores) retrieved carnivorous Hymenoptera (Orussidae + Apocrita) in contrast with the present submission which has Siricidae sister to Apocrita, or even inside Apocrita. This is a highly unusual (and dubious) result and should be mentioned. In general, the language treatment of relationships in the paper is vague and imprecise, e.g., ‘grade basal to’ (l. 93), ‘connecting link’ (l. 524), ‘similar to’ (recurrent phrase). When you have a tree and want to discuss relationships, talk explicitly about sister groups. Why else produce a tree?
Additional comments are in the annotated pdf.
Best regards
Lars Vilhelmsen


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: COMPLETE MITOCHONDRIAL GENOME SEQUENCE OF LABRIOCIMBEX SINICUS, A NEW GENUS AND NEW SPECIES OF CIMBICIDAE (HYMENOPTERA) FROM CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript describes a new species from a new genus from Cimbicidae and reports its mitochondrial genome, presents comparative analyses of this mitogenome with the other known symphytan in particular cimbicid mitogenomes and a phylogenetic analysis of Symphyta based on the mitogenome sequences. The manuscript is clearly written.
Experimental design: There seems to be no methodological problem.
Validity of the findings: There are important results for the field and the findings are well constructed by authors. The findings have been discussed and supported by relevant literature sufficiently.
Additional comments: Here, the manuscript presents the characterisation of the mitochondrial genome of L.sinica for the first time. Then the authors aimed to comparison of various genomic features against other reported cimbicid species. The most interesting evidence is the presence of rearrangements in tRNA genes. The manuscript presents a newly constructed phylogenetic tree using available symphytan mitochondrial genome to validate the phylogenetic position of the species (L.sinica). Some minor changes or comments are listed below:
•	Line 187: It would be better if the authors prefer presenting a supplementary table explaining the best partitioning schemes and associated models.
•	Line 380: When looking Table 4, Leu, Ile, Phe, and Ser seem to be most frequently used amino acids rather than indicated by the authors.
•	Lines 386-388: I found two codons as absent and nine codons as used once. In my opinion, two times or four times used codons are also acceptable as rare. The related part should be revised.
•	Line 518-519: The authors have stated that Labriocimbex belongs to the tribe of Trichiosomini as well as Trichiosoma. However, it could not be suggested when looking through the trees. In the trees, there are only three cimbicid species from three genera representing two subfamilies. Therefore, without expanding the sampling belong to same genus as well as same tribus, we could not decide that this new genus belongs to the tribe of Trichiosomini.
•	Line 538-545: It would be better if the authors rewrite the phylogeny related part of the conclusions section.
•	The remaining minor corrections are shown on the manuscript.
In my opinion, the manuscript could be published in the journal PeerJ after major revision.


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

Input:
Title: COMPLETE MITOCHONDRIAL GENOME SEQUENCE OF LABRIOCIMBEX SINICUS, A NEW GENUS AND NEW SPECIES OF CIMBICIDAE (HYMENOPTERA) FROM CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: See General comments
Experimental design: See General comments
Validity of the findings: See General comments
Additional comments: This is the second version I see of this paper. There has been substantial improvements to some parts of the paper. The illustrations are now improved and illustrations of Labriocimbex zaraeoides are included, strengthening the case for its inclusion in the genus. The nomina nuda issues are addressed explicitly; however, the authors briefly discuss ‘differences’ between the specimen that was previously labelled Labriocimbex pilosus and L. sinicus, although they apparently do not want to recognize the former as a separate species; this could actually be construed as an argument for recognizing it as a separate species. It would be safer to state that the morphology of this species falls within the known variation of L. sinicus and leave it at that.
The authors have added a key to Holarctic genera of Cimbicidae. This is fine in principle; however, they include at least three genera that have previously been synonymized with other genera (i.e., Orientabia and Zaraea with Abia and Palaeocimbex with Cimbex). Furthermore, the results of the phylogenetic analyses of Vilhelmsen (2019) which included species in the synonymized genera did not support the recognition of these genera. No justification for the recognition of these genera are provide by the authors; it would be better to leave them out.
The phylogenetic part of the paper is still quite weak. While the phylogenetic analyses are performed saisfactorily, mistakes in both interpreting the results and correctly discuss them abound (see annotations in paper). It is stated (ls 616-617): ‘We demonstrated that mitochondrial genome sequences can be used to solve phylogenetic relationships at different taxonomic levels within Symphyta’. This is far from the case; the taxon sampling is much too poor to provide any confidence in results below the superfamily level, especially in comparison with other recent, much more comprehensive analyses (e.g., Malm & Nyman 2015). The poor taxon sampling might explain some bizarre results obtained (Megalodontes sister to Xiphydria; Tremex inside or sister to Apocrita). In their response to reviewer’s comments, the authors state that the sister of Apocrita is not within the scope of the paper; this is fair enough, but they still need to acknowledge the shortcomings of their analyses, which are substantial. ‘Strong nodal support’ is not in itself a guarantee that a clade in a phylogeny will be robust to further testing – especially not in a dataset like this where you have a comparatively large amount of data (mitogenomes) but a fairly small taxon sample. Unless there is strong character conflict, you are bound to get high support for most nodes, also for relationships that will disappear as soon as more taxa are included.


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: COMPLETE MITOCHONDRIAL GENOME SEQUENCE OF LABRIOCIMBEX SINICUS, A NEW GENUS AND NEW SPECIES OF CIMBICIDAE (HYMENOPTERA) FROM CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am happy to see the revised version of the manuscript about the mitogenome features and taxonomic position of Labriocimbex sinicus. I I feel that the text improved but I have highlighted some modifications on the manuscript attached.
Experimental design: no comment
Validity of the findings: I have question regarding the presentation of the phylogenetic figures (Figures 12 and 13) and explanation of the recovered relationship within the text. I think the authors should reepresent the phylogentic relationship on a single figure, because two approaches give a similar topology.  The authors also suggest that “The recovered trees supported a relationship consisting of Xyelidae + (Tenthredinoidea + ((Megalodontesidae + Pamphiliidae) + (Xiphydriidae + (Cephidae + (Orussidae + (Apocrita + Siricidae)))))) in the Hymenoptera” in lines 577-579, but when checking the trees, a different relationship was found in the trees: Xyelidae + (Tenthredinoidea + (Pamphiliidae + ((Megalodontesidae + Xiphydriidae) + (Cephidae + (Orussidae + (Siricidae + Apocrita)))))) in Hymenoptera.
Additional comments: no comment


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

Input:
Title: COMPLETE MITOCHONDRIAL GENOME SEQUENCE OF LABRIOCIMBEX SINICUS, A NEW GENUS AND NEW SPECIES OF CIMBICIDAE (HYMENOPTERA) FROM CHINA
Review round: 3
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: do
Validity of the findings: do
Additional comments: This is the third version of this paper I have seen. I have not gone through the text in detail again and will just comment on the main new addition to the paper, the CO1 dataset and analysis.
The authors want to make a case that the genera Orientabia, Zaraea and Palaeocimbex that have been previously synonymized with Abia and Cimbex, respectively, should be recognized as valid. To this end, they present a COI data set for 52 cimbicid terminals and two Arge spp. as outgroup. The sequences are primarily obtained from Genbank and the cimbicid sample contains a number of duplicates at the species level and many taxa unidentified to species. Palaeocimbex is apparently not included in the sample and the authors do not discuss it, but retain it in the genus key without further justification.

In the case of Abia, Orientabia and Zaraea, all are apparently included in the taxon sample, but in low numbers (three named species for Abia and Zaraea each and one Orientabia [seems to be missing in Table 2], as well as two Zaraea sp. which come out together in Fig. 13 and might be the same species). This is not an impressive taxon sample for Abiinae that comprises 60+ described species and barely allows for confirming the monophyly of Abia and Zaraea, while Orientabia is not tested. Curiously, only one taxon (Trichiosoma sorbi) from Liston et al. (2014) have been included despite this paper providing sequences for a number of additional taxa not in the present sample. This goes in particular for Abiinae; crucially Liston et al. included Abia sericea (Linné, 1767) and Abia fasciata (Linné, 1758), the type species of Abia and Zaraea, respectively. The type species of Orientabia, Abia egregia, is also not included. Without the inclusion of the type species, how can the authors be sure that they have correctly delimited these genera? Liston et al. (2014; fig. 1A) in their COI tree retrieved A. fasciata and A. sericea as closely related; their taxon sample for COI was similar in size (six species) to that of the current submission, but with little taxon overlap (Abia candens only).

The authors conclude (ls 691-692): ‘The clade of Orientabia, Zaraea and Abia, are recovered as monophyletic with high support for the both trees’. Assuming this means that they consider to have tested and confirmed the monophyly of all three genera, this is clearly not the case for Orientabia, which is only represented by one terminal; furthermore, having a one-gene data set with poor taxon sampling for the two other genera is hardly strong evidence either. Additionally, the results obtained do not seem to conform to that of Liston et al (2014) for Abiinae or for Abiinae and Cimbicinae when compared with Vilhelmsen (2019); this is not discussed at all, the authors are content to focus on their own data set as has been the case with previous versions of the submission. Similarly, it is stated (ls 636-638): ‘We found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters’. This glosses over considerable differences with results for Cimbicinae in Vilhelmsen (2019), e.g., the position of Praia and Cimbex.

Finally, the authors assert (ls 653-654) that ‘the three genera [i.e, Orientabia, Zaraea and Abia] can also be distinguished morphologically’. This is not surprising given that this was why they were defined in the first place, but that is hardly the point. Rather, the question is whether the character combinations used to define the different genera are delimiting natural (i.e., monophyletic) groups or are just random combinations; if the latter is the case, this can result in a proliferation of genera that are not of any use to anyone beside those who take pleasure in defining them. The conclusions of the authors in this regard runs contrary to the taxonomic treatments of, e.g. Taeger (1998) and Hara & Shinohara (2017; they synonymized Orientabia, why is this paper not cited?), as well as the phylogenetic treatments of Liston et al. (2014) and Vilhelmsen (2019), who all argued for placing all the Abiinae species they examined in Abia. The comparatively weak evidence presented in the current submission does not outweigh this.


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: COMPLETE MITOCHONDRIAL GENOME SEQUENCE OF LABRIOCIMBEX SINICUS, A NEW GENUS AND NEW SPECIES OF CIMBICIDAE (HYMENOPTERA) FROM CHINA
Review round: 3
Reviewer: 2

Output:
Basic reporting: I am happy to see the revised version of the manuscript about the mitogenome features and taxonomic position of Labriocimbex sinicus. I feel that the text improved but I have highlighted some minor linguistic comments or modifications on the manuscript attached. Also, the writing and presentation of the newly added part on the phylogenetic relationship of Cimbicidae using the COI barcode region need to rewritten to increase the clarity and flow of the manuscript.
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: COMPLETE MITOCHONDRIAL GENOME SEQUENCE OF LABRIOCIMBEX SINICUS, A NEW GENUS AND NEW SPECIES OF CIMBICIDAE (HYMENOPTERA) FROM CHINA
Review round: 4
Reviewer: 1

Output:
Basic reporting: see below
Experimental design: see below
Validity of the findings: see below
Additional comments: I think the current version is better than the previous one in the sense that the parts considering the generic classification of Abiinae has been remove and the key adjusted (you might want to call it 'Key to extant Holarctic genera of Cimbicinae' as it only properly deals with this subfamily); the genus names are still retained in Fig. 13 though, with no justification for using Orientabia and Zaraea. Also, you should be aware that Orientabia magna Takeuchi, 1939 is now considered a junior synonym of Abia relativa Rohwer, 1910; see Hara & Shinohara (2017).
The taxon sample for the mitogenomic analyses are still highly inadequate (especially with regard to Apocrita) and some of the results are weird: Siricidae as sister to Apocrita, Megalodontesidae as sister to Xiphydriidae; the latter is completely ignored, and neither is likely to hold up to further scrutiny.
The text should be checked for the use of 'nomina nuda'; this is plural, the singular form is 'nomen nudum'; you cannot say 'nomina nudum' (l. 279), and the plural should only be used when you discuss two or more names (l. 443, but not l. 99)


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: COMPLETE MITOCHONDRIAL GENOME SEQUENCE OF LABRIOCIMBEX SINICUS, A NEW GENUS AND NEW SPECIES OF CIMBICIDAE (HYMENOPTERA) FROM CHINA
Review round: 4
Reviewer: 2

Output:
Basic reporting: I am happy to see fourth round of the manuscript about the mitogenome features and taxonomic position of Labriocimbex sinicus. I feel that the text mostly improved by the authors. In my suggestion, the manuscript is now accepted in PeerJ.
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: SOCIAL MOTOR PRIMING: WHEN OFFLINE INTERFERENCE FACILITATES MOTOR EXECUTION
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a reasonably executed paper. However, the theoretical motivation is unclear. Specifically, is it joint action, or social context? The authors mention both but it’s not clear if they intend the terms to be interchangeable. If not, these are two separate mechanisms, and their influence and interaction needs to be clarified.
Experimental design: I think my main issue is that I am not convinced this is actually a social/ interactive  context. Participants were watching the model on the video and making same / different actions, as in previous literature.  They were not 'sharing' objects, however. Moreover, according to the stated methods, participants were never given any instruction that might bias them towards feeling an association (identification with) the model . Also, as far as I can tell participants also were not led to believe that the mug was ‘theirs’ in any way, so did they really believe they were engaging in a social event with the model?
If social context is not at play here, then I’m unsure how the findings advance on Newman- Norlund et al, and on Ocampo et al.

I would recommend another experiment, in which participants were given actual 'social' instruction
Validity of the findings: The section labelled ‘Visuomotor Interference’ is, I think, over-interpreted. It is difficult to conclude this for comparisons with Baseline, unless the participants perform the action in the presence of some other salient non-movement stimulus, yielding no interference. That is, it could just be the significantly 'large' amount of info that is causing disruption. Eg, a  still image of the model + mug, that has been scrambled
Additional comments: Minor points:
-the paper would benefit from a good editing pass, from a native English speaker. Sentences such as line 47-49: “Visuomotor priming, in particular, regards the facilitation to perform an action congruent with the observed one versus the difficulty to execute the same action during the observation of a different one” and line 72-74 “On the other hand, evidence that online interference occurs when an given action has to be performed, but a concurrently observed movement elicits a complementary different grasp has  been provided using a reach-to-grasp task.” are hard to follow.
-not clear how the idea of a continuum of interference was deduced - is it the magnitude of kinematic differences? I think the authors simply mean it can arise due to different mechanisms
-other relevant social context literature should be included: S. Sparks, T. Douglas & A. Kritikos, QJEP, 2016; Leighton, J. Bird, G., Orsini, C., & Heyes, C. (2010). Journal of Experimental Social Psychology,