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: ISOLATION AND IDENTIFICATION OF L-ASPARAGINASE-PRODUCING ENDOPHYTIC FUNGI FROM THE ASTERACEAE FAMILY PLANT SPECIES OF IRAN
Review round: 2
Reviewer: 2

Output:
Basic reporting: This manuscript describes isolation, identification and quantification of L-asparaginase activity of the endophytic fungi isolated from seven Iranian medicinal plants. The topic is generally interesting. The methods used seem appropriate and the research ended with novel conclusion. However, the manuscript needs revision for better clarity, pointing out the novelty and coherence.
Experimental design: The experimental design seems okay but this section needs enough technical details for reproduction by the other researchers.
Validity of the findings: The findings seem valid. However, the description of novelty and perspection in the discussion section is inadequate with relevant recent literature.
Additional comments: This manuscript needs major revision including editing by a native English speaker before considering for publication. Scientific names in the Tables should be critically checked and must follow the standard style (first appearance full name and then abbreviated form for the generic part). I made some comments and also edited in the manuscript.


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

Input:
Title: ISOLATION AND IDENTIFICATION OF L-ASPARAGINASE-PRODUCING ENDOPHYTIC FUNGI FROM THE ASTERACEAE FAMILY PLANT SPECIES OF IRAN
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors substantially improved their manuscript although a slight grammatical errors are still remained which I think would be removed during editorial work.
Experimental design: Seems sound.
Validity of the findings: Yes, the data seem original and valid.
Additional comments: Total number of references are too high. Please delete some references that are less relevant to the article.


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: AN ANALYSIS OF ABNORMALITIES IN THE B CELL RECEPTOR REPERTOIRE IN PATIENTS WITH SYSTEMIC SCLEROSIS USING HIGH-THROUGHPUT SEQUENCING
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript, Shi et al analyze the B cell receptor repertoire in SSc patients using high-throughput sequencing. The manuscript is well-written and easy to read, here are some comments to strengthen the manuscript.

- refer to Control as 'Control' and not Con, as that is not obvious to the reader.
- Figure 1 legend needs to be edited- currently includes random characters.
- Figure 2 legend needs to elaborate to make it clear to the reader.
- Introduction, line 40- 'SSc patients'
- In figure 1, statistical test comparing SSc-Males to controls and Non-ILD to ILD are missing. If the tests are not significant, it must be indicated in the figure.
- Is the Wilcoxon test one-sided or two-sided?
- In each figure legend, please clearly indicate what statistical test was used.
Experimental design: - The authors need to frame their research questions in context of previously published work by de Bourcy et al, 2019, Science Immunology. Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis. This important work relevant to this manuscript has not been discussed.
- One additional method of stratification to include is based on expression of other SSc-specific autoantibodies, if the authors have access to the data.
Validity of the findings: - Can the authors compare their findings to previously published work by de Bourcy et al?
- Why is it that patients with mild disease display more BCR diversity compared to with severe disease? Also, why is the BCR more diverse in SSc-Males compared to SSc-Females- is this difference statistically significant?
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: AN ANALYSIS OF ABNORMALITIES IN THE B CELL RECEPTOR REPERTOIRE IN PATIENTS WITH SYSTEMIC SCLEROSIS USING HIGH-THROUGHPUT SEQUENCING
Review round: 1
Reviewer: 2

Output:
Basic reporting: I have only few comments
1-	Concerning the form manuscript should be improved by correcting typographical error.
For example :
- line 41 the reference is incomplete: the year is missing
-line 82 Ficoll and not Ficol
- line 129 P=0.039 and not P 0.039
2-	All the figures quality must be improved:
-	Figure 1: number of patients and the statistic test are not indicated
-	figure 2: the legend must be develop to explain how to understand the result
-	Figure 3 C: almost unreadible
Experimental design: The analysis of the similarity should be more detailled in the text as well as in the figure legend
Validity of the findings: There is few results concerning B cells repertoire in systemic sclerosis and the development of new technologies using high-throughput sequencing gives the opportunity to investigate the question.
1-	My major comment concerning the paper is relative to the small number of patient included in the study that may not be enough to support the conclusions. There are only 8 patients and 4 controls which are not totally paired on sex and age. Moreover, the 8 patients are divided in subgroup of 4. I have strong doubts about the robustness of the results. Differences are observed between male and female in patient groups but there is only female in the controls!
2-	All the statistics are done using Wilcoxon test, that should be justified by the authors since patients are not paired.
3-	It has been shown in systemic sclerosis, an inbalance in naive/switched and unswitched memory B cells that can explained the B cell repertoire abnormality observed by the authors. I understand that it could be difficult to sort these population in the patients nevertheless the authors should discuss this point (Simon et al, Clin Exp Rheumatol. 2016)
Additional comments: In the manuscipt untitled “An analysis of abnormalities in the B cell receptor repertoire
in patients with systemic sclerosis using high-throughput sequencing” Xiaodong Shi & al analysed the B cell repertoire by high throughput technology. The analysis of the BCR immune repertoires of patients with SSc using new technology  has important application value for classification of the patients and treatment efficacy evaluation. Nevertheless, as it was already specify the weakness of this work is the low number of patients and controls


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: AN ANALYSIS OF ABNORMALITIES IN THE B CELL RECEPTOR REPERTOIRE IN PATIENTS WITH SYSTEMIC SCLEROSIS USING HIGH-THROUGHPUT SEQUENCING
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript by Shy et al has been improved as previously required but there is still few tipographical or spelling errors to correct
ex: in the discussion "imbalance" and not "inbalance"
There is an error concerning a reference the discussion that need to be corrected:
"As shown in the study by Brezinschek et al. (Forestier et al. 2018)",
Experimental design: No comment
Validity of the findings: Some points has been clarify compared to the first version of the paper (especially the statistics).
Concerning the small number of patients and the difference observed between male and female patients the autours have relativized their result and underlined that this is a pilot study .
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: STRUCTURE AND PIGMENT MAKE THE EYED ELATER’S EYESPOTS BLACK
Review round: 1
Reviewer: 1

Output:
Basic reporting: The information reported here is interesting, valuable, and relevant to the literature on beetle structural colors. I was surprised this had not been published on before, and am glad Alaus is receiving the attention it deserves.

The only unprofessional English usage is a sprinkling of arbitrarily capitalized common names, which I have highlighted in the attached Word file.
Experimental design: The experimental design here is more than adequate to demonstrate that the "super-black" of the eyespots arises from a structural mechanism.  There are a few small observations that could be added (SEM investigation of the interior structure of the scales; spectrometer measurements from additional directions relative to the beetle's longitudinal body axis) but these are by no means essential.

This research fills knowledge gaps around "super-black" structures in Coleoptera AND surrounding eyespots in Coleoptera, which have received little or no synthetic attention in the literature (to my knowledge, there are a few instances documented from tiger beetles).
Validity of the findings: These findings are valid and appear robust and reproducible. Statistics are not a concern here. Conclusions and discussion are well-linked to previous research.
Additional comments: Please see attached Word file for additional notes and markup.
Overall, this is a fascinating paper and will be a valuable contribution to the literature on beetle structural colors.

If it's possible to break open some of the scales (I suggest macerating them a bit with a pin or razor blade against a glass slide) and SEM their interior or cross-section, this may also shed light on how the contrasting light/dark of the eyeliner/eyespots is achieved. However, this manuscript is interesting enough on its own and I don't think it requires additional experimentation (and much setal morphology is already revealed through the combination of external SEM and transmission light microscopy).


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: STRUCTURE AND PIGMENT MAKE THE EYED ELATER’S EYESPOTS BLACK
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors reported the natural “super black” structures in the false eyespots of the eyed elater. In fact, a few cases on natural “super black” have already been reported involving butterfly wings, bird feathers, moths, etc. The structure investigation on the black eyespots of Alaus oculatus is interesting, which enriches the structure database of natural “super black”. However, based on my careful assessment on the overall work, the manuscript at current stage is not suitable for publication in PeerJ before the authors can well handle the following issues:
Experimental design: 1. The author demonstrated the intuitional observation results of the “super black” false eyespots of Alaus oculatus including digital photographs and SEM images. Apparently, these data are necessary but not enough to form a relatively complete research article. The underlying optical mechanism of the “super black” in this case should be discussed thoroughly and a set of schematic diagrams could be very helpful to make it clear for a wide audience.
2. To help distinguish the difference as compared to other natural “super black” structures, the feature structure details of the eyespot setae should be highlighted in Figure 2.
3. For reflectance spectra in Figure 5, to exclude the impact of melanin to the “super black”, a comparison group of samples should be included. One group is the original sample without post-treatment and another group should be the treated sample with thin metal coatings.
4. Optical modeling of the “super black” structures should be built up and corresponding optical simulation involving the structure models and incident light using FDTD or other recognized methods should be provided to improve the reliability of the conclusion.
Validity of the findings: No comment.
Additional comments: 1. “Super black” should be clearly defined in this manuscript and point out the difference between “super black” and ordinary black.
2. The authors claimed the structure similarity of natural “super black” between Alaus oculatus and other animals based on their shape, orientation, and general photonic properties. However, as I known, their feature structures responsible for “super black” are quite different. Thus, the structure differences of these typical biological prototypes of “super black” should be compared in details.
3. Other small issues were also highlighted as notes in .pdf version of the manuscript, please double check.


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: STRUCTURE AND PIGMENT MAKE THE EYED ELATER’S EYESPOTS BLACK
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article is well-written, and most of the appropriate literature references are included. I suggested some additional papers to include. The figures look nice and professional. I think a comparison SEM between black and white setae is needed since that seems to the be the main point of the paper, and higher magnification images are needed as well.
Experimental design: The research question is well-defined, but the data shown in the paper do not clearly answer the hypothesis that the eyespots are structural black.
Validity of the findings: Since only low magnification SEMs are provided, and there is not a comparison SEM of the white setae, it's currently impossible to fully assess the validity of the findings. A previous reviewer suggested that these authors sputter coat the sample to show if it's structural black, but this sputter coat experiment is not enough to confirm structural black. Suggestions follow in the detailed pdf attachment about how the authors may confirm structural black.
Additional comments: See attached pdf for these same comments but perhaps formatted better:

The manuscript “Super black eyespots of the eyed elater” describes how the “super black” false eyespots on the surface of a click beetle may be as black as they are due to structural absorption of light as well as pigmentary absorption. While this manuscript is well-written and gives sufficient background and context with references to other optical structures found in the “super black” literature, there are several major issues that need to be addressed before it would be suitable for publication. Most importantly, the authors claim to test if structural absorption provides the super black appearance, but the data shown here (1) do not support that the false eyespots are even a “super black” structure to begin with given that they only absorb 96.1% of incident light, which is more equivalent to black construction paper than a “super black” material or animal (black butterflies absorb 99.95% of light) and (2) do not support that the “perpendicularly aligned protuberances,” or setae, are the reason that the false eyespots are black. The experiment to sputter coat the eyespot with platinum-palladium was interesting but this still doesn’t confirm that the black is structural. Sputter coating doesn’t always penetrate deep in between microstructures like we would hope and it looks like the pigment at the bottom of the setae simply isn’t covered up. The authors may try bleaching the spot to confirm. There is also an issue of relating morphological structures that are on size scales that differ by orders of magnitude. For example, the nanoprotuberances on the eyes of moths and the polydisperse honeycomb structure acting as an aggregation of resonant absorbers that are found on many black butterflies are not on the same size scale as the setae the authors describe here on the black eyespots of their beetles. The authors do not do any optical modeling, and while I agree that an optical model is not necessary for publication of their manuscript, working through some of the optics and relating the morphological structure to the reflectance measurements might help the authors understand why their setae is not equivalent to other super black nanostructures that have been previously described in the literature. I suggest the authors reframe the point they are trying to make in the study since the spots aren’t even “super black.” However, it is interesting to use SEM to characterize the cuticular surface of the click beetle, as the authors begin to do in this study, but the measurement needs to be a direct SEM comparison between the black spots and the surrounding white. The authors provide a light micrograph of the white setae, but never even provide an equivalent SEM of the white part. If the authors have these data that support that the white setae are structurally different in the nanoscale than the black setae, they need to add a figure or show that additional data somewhere in the paper.

Technical details and line edits:

Introduction
Line 57 – reference 11. Corneal nipple arrays function quite differently than other structural black examples and wouldn’t actually be classified as a “super black” structure just an antireflective structure.

Line 64 – antireflective coatings are everywhere, not just use in the military. Example: eyeglasses, window panes, etc. Also, this is a different concept than super black

Line 97 – by depositing the sputter coating on the surface, you did not unequivocally confirm that you had covered up the pigment. If you zoom in enough on the SEM, you should be able to see if the sputter coating actually reached and covered the base of each of the setae. If you can’t zoom in/magnify to that level, you are probably getting charging of the surface and thus you didn’t actually coat it like you thought you did.

Line 98 – you say you compared microstructures from the black spots with areas elsewhere on the cuticle, but you never show direct SEM comparisons here. I only see the figure that shows the difference at the light micrograph level.

Materials and Methods
Line 125 – how do you confirm that the sputter coating was 40nm (20 nm + 20nm)? If it’s like most sputter coaters, you enter this thickness, or you sputter for a certain amount of time previously known to achieve that thickness. However, if you magnify to the point where you see structures at the size scale of 1 – 10nm, you could actually see the sputtering on the surface – did you do this then to confirm it actually covered the setae all the way to the base? The SEMs provided in Figure 2 are not very magnified at all (highest magnification has a scale  bar of 0.01mm so it’s impossible to tell).

Line 132 – for most “super black” materials, a white reflectance standard (whether Spectralon or other known calibration) is usually too bright and then results in nothing but noise when measuring reflectance of the “super black” material. However, the beetle false eye spots aren’t even that black, so you may not need to use a black spectralon standard for your reflectance measurements. Still, I’d try it with a different standard to see if that affects your reflectance measurements.

.
Results
Line 168 – why don’t you show any SEMs for the white setae? Figure 2A shows a transmitted light photograph, but we need to see a direct comparison SEM. It looks like the white setae are longer and that is why they are lying down, but even from the text, it’s unclear what is happening at the nanoscale with both the white and black setae.

Figure 3 and Figure 4 – again, the previous reviewers had a good suggestion to look to see if sputter coating would cover up the black pigment. But it looks like the black setae are very dense and it’s very difficult to sputter all the way to the base of dense structures. The supplemental video and the photographs at 30 degress and 45 degrees show the tips look coated, but it’s impossible from just the data shown to confirm it coated to the base. Try bleaching the pigment away.

Discussion:
Line 222 – The sputter coating was a good idea to start with, but this alone doesn’t confirm that it’s structural black just because it still looked black looking directly down onto the spot.

Line 224 – The large setae are “erect, black with longitudinal grooves, and evenly spaced” (quoted from line 170), but this is not “equivalent in shape, orientation, and general photonic properties of other super black structures.” You have not magnified the setae enough in any of the provided SEMs to show the nanostructure arrangement at all. If you have these data, please add them to the manuscript.

Line 230 – the nipple arrays of moth eyes are not at all similar to the SEMs you show in figure 2 in either scale or order. They are perpendicularly aligned, but lots of structures in biology are that have no optical function. This is where some discussion of the optics behind what makes structural black would be useful. You don’t need to make your own optical model for this paper, but you need to recognize the difference in scattering that would occur between a 20nm structure and a 2000nm structure.

Line 235 – is the 0.5% a typo? The blackest of which are made from a forest of carbon nanotubes are capable of reflecting as little as 0.035% of incident light (Theocharous, E., Chunnilall, C.J., Mole, R., Gibbs, D., Fox, N., Shang, N., Howlett, G., Jensen, B., Taylor, R., Reveles, J.R., Harris, O.B. 2014. The partial space qualification of a vertically aligned carbon nanotube coating on aluminium substrates for EO applications. Opt.s Exp. 22 7290-7307). And animals have evolved micro- or nanostructures that reflect as little as 0.05% of visible light. So I don’t think your citation of the birds of paradise at 0.5% is correct. Black things can reflect 3-11% but they don’t often fall in the “super black” category.

References
Also check out the following:
1.	Han, Z., Li, B., Mu, Z., Yang, M., Niu, S., Zhang, J., Ren, L. An ingenious super light trapping surface templated from butterfly wing scales. Nano. Res. Lett. 10, 344-351(2015).
2.	Siddique, R.H., Donie, Y.J., Gomard, G., Yalamanchili, S., Merdzhanova, T., Lemmer, U., Hölscher, H. Bioinspired phase-separated disordered nanostructures for thin photovoltaic absorbers. Sci. Adv. 3, 1700232-1-1700232-11 (2017).
3.	Theocharous, E., Chunnilall, C.J., Mole, R., Gibbs, D., Fox, N., Shang, N., Howlett, G., Jensen, B., Taylor, R., Reveles, J.R., Harris, O.B. 2014. The partial space qualification of a vertically aligned carbon nanotube coating on aluminium substrates for EO applications. Opt.s Exp. 22 7290-7307


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: STRUCTURE AND PIGMENT MAKE THE EYED ELATER’S EYESPOTS BLACK
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors addressed my previous concerns with lit references.
Experimental design: Authors addressed my previous concerns with defining the research question.
Validity of the findings: Authors addressed my previous concerns with the conclusions.
Additional comments: The authors have done a good job of addressing my previous comments, but there are a few minor issues to still be addressed prior to publication, mainly having to do with Figure 2 needing further clarification. Please see below for line edits.

Abstract, line 22: edit the sentence to say something like -
'Here we describe the false eyes of the eyed elater click beetle, which, while not classified as "super black," still attains near complete absorption of light partly due to an array of vertically aligned microtubules.'
Somewhere it needs to be clear that it's not super black, but you're going to talk about how it is black due to structure as well.

Figure 2: needs more clarification
B - I would suggest getting rid of the entire panel B. It seems to show the same thing as one of the eyeliner setae in panel A, so it is just confusing to have a different picture of it in a separate panel.

F, G, H - it is not clear exactly what is being shown here. I think you are trying to show the vertical eyespot setae next to the decumbent eyeliner setae, but I can't tell where the transition happens in panel F. Please add arrows to clarify this, or find some other way to indicate which is eyeliner and which is eyespot.

Can you add a photo of the beetle (or section of the beetle) and then add a dashed rectangle showing the region of interest and relate that to where F, G, and H are on the beetle? That would be good to do for all panels. You use the rectangle section idea effectively when going from panel I to panel J. I think you need to go back one more step and show where everything is on the beetle. Having a bunch of SEMs all arranged like that makes it hard to understand, even when you're carefully reading the caption. It wasn't immediately clear to me that you addressed my previous concern about not having the eyeliner setae SEMs.


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: DECLINES IN SKELETAL MUSCLE QUALITY VS. SIZE FOLLOWING TWO WEEKS OF KNEE JOINT IMMOBILIZATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No Comment
Validity of the findings: No comment
Additional comments: Muscle quality was examined by isolating the rectus femoris and vastus lateralis to intentionally cause atrophy within the muscle and examine the cross sectional area and echo intensity within the brace. The study was completed in college-aged females because they are more prone to ACL and MCL tears throughout sports. It was found that a decline in muscle size was lesser in magnitude than that observed for muscle quality. I appreciate the detail of methods as they could easily be replicated.
1. The introduction provides a concise overview of the muscular changes to immobilization, the use of muscle quality, and the purpose of this study, however, it does not provide a real justification of why understanding these morphologies are important or useful. For example, if echo intensity is reported in arbitrary units, to what extent are the values important to a practitioner, unless it is purely within that independent clinic (and not compared between independent cohorts or clinicians that may use different settings to record the data.) Can the authors please elaborate on the significance of this type of measurement and perhaps how it can be generalizable to all?
2.  It is my understanding that altering the depth of the signal with ultrasound will then alter the gray scale of the image. The authors report a scan depth of 4-7 cm, individualized for each participant. If the scan depth were to remain constant (6 cm-for example) and then normalized for subcutaneous fat, then the results will be more consistent when evaluating echo intensity.
3. Was menstrual phase recorded? The hormonal shifts estrogen during the follicular (higher) and luteal (lower) phases may alter the muscle-sparing response that naturally occurs in women.
Enns DL, and Tiidus PM. The influence of estrogen on skeletal muscle. Sports Medicine. 2010.
Wikström-Frisén L, Boraxbekk CJ, Henriksson-Larsén K. Effects on power, strength and lean body mass of menstrual/oral contraceptive cycle based resistance training. Journal of Sports Medicine and Physical Fitness. 2015.
4.The RF and the VL (although different in size) are both biarticular muscles. Would the flexed leg at 90 degrees and perhaps participants flexing at the hip impact the use of these muscles? RF would potentially be stimulated nearly as much with the anterior aspect of the thigh and proximity to the psoas muscles. This could be a potential reason for lack of noticeable change in the RF.
5. The tables and charts are redundant with the text. I think the table can be translated onto the line charts and then be eliminated. Also, the mean lines of the charts should indicate standard error bars/margins.


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: DECLINES IN SKELETAL MUSCLE QUALITY VS. SIZE FOLLOWING TWO WEEKS OF KNEE JOINT IMMOBILIZATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: All basic information meets PeerJ standards
Experimental design: The experimental design is fully adequate to answer the research question. Attrition rate and exclusion in results is clearly explained. Methods are meticulous and clear.
Validity of the findings: It appears that decline in echo intensity is a individual basis.Thee participants showed a decline but majority did not show a change in EI greater then the MD. Previous studies showed that unweighted legs showed increase in adopisity. Do to the nature and difference in immobilization strategies. Both are logical ways to unload the limb but may have many different neural components. Brace and position may actually influence more neural activity. Authors need to explain more why 90 degrees was chosen and possibly the influence this has with a elongated MTU.
Additional comments: Over all finding that immobilization has a greater affect on quality then size does contribute to the literature. Need to clear up the discussion as to differences observed and fi duration of 2 weeks is long enough to see adipose changes. Further explanation on why 90 degrees was chosen needs to be addressed.


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

Input:
Title: DECLINES IN SKELETAL MUSCLE QUALITY VS. SIZE FOLLOWING TWO WEEKS OF KNEE JOINT IMMOBILIZATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: Regarding the five PeerJ points, i.e., language, context and references, structure, figures, and raw data, the current manuscript meets all. I just have some minor suggestions in their context further presented in general comments of this review.
Experimental design: Among the four PeerJ points about experimental design, the current manuscript presented an original line of investigation and a well-defined research question. In addition, human research ethical was respected. Regarding the methods, further suggestions were provided in general comments of this review.
Validity of the findings: PeerJ listed four points for the validity of findings. The interpretations of findings and some decisions will be critically appraised in general comments of this review. In short, there is some comments and suggestions on results and some speculations, but all aiming to help reach a better level of publication.
Additional comments: Please, find in the attachment my general 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: DECLINES IN SKELETAL MUSCLE QUALITY VS. SIZE FOLLOWING TWO WEEKS OF KNEE JOINT IMMOBILIZATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I commend the authors for their revisions. The manuscript clarity and translation to broad impacts in support of future research with use of ultrasound imaging. I have one remaining concern/comment.
-Although the authors provide support for the correction of RF values, the general change between the RF and VL should mirror one-another. I feel the corrected and UNCORRECTED RF values should be represented in the manuscript so a more direct comparison of the two muscles can be drawn.
-Additionally, I'm curious how many participant's image depth deviated from 4cm? If they were removed fron analyses, would anything change? Thank you for providing the raw data in the response to reviewers.


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: DECLINES IN SKELETAL MUSCLE QUALITY VS. SIZE FOLLOWING TWO WEEKS OF KNEE JOINT IMMOBILIZATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: Meets basic Reporting
Experimental design: Questions regarding methods have been addressed with the changes.
Validity of the findings: Authors address the validity concerns of exceeding MD values and have clarified reliability statistics. With a novel approach and slightly different immobility set up as with all human research is not going to be perfect. The finding do start to shed light on the risks and physiological costs of immobilization.
Additional comments: Authors have rewritten the discussion to clarify the duration of disuse and possible implications.


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: DECLINES IN SKELETAL MUSCLE QUALITY VS. SIZE FOLLOWING TWO WEEKS OF KNEE JOINT IMMOBILIZATION
Review round: 2
Reviewer: 3

Output:
Basic reporting: Meets all basic reporting.
Experimental design: Meets all experimental design criteria.
Validity of the findings: Meets all validity of the findings.
Additional comments: General comments
	The manuscript “Declines in skeletal muscle quality vs. size following two weeks of knee joint immobilization” was improved after the last revision round. The authors should be commended for their efforts. All my comments were properly answered, and I just have a few minor suggestions that may help to improve Methods section:
1) Sample size – I agree to the authors regarding the incapability to estimate effect size for muscle echo due to the lack of previous data. Considering the aforementioned, it would be great for future studies if the authors provided the power reached with their sample size.
2) Ultrasonography Measurements and Analysis – Great. The authors have interesting data about the variability of muscle EI across different depths. To ensure readers the full information, I would like to suggest the authors to state briefly the results of this subsample, describing the coefficient of variation, and standard error mean. In addition, it would really great if the authors also indicate how many participants the depth had to be changed. It is really great that you have such important information for future trials and investigations.
I do not have any more comments/suggestions, and I would like to suggest the acceptance of this manuscript with the consideration of previous suggestions. Congratulations to the authors.


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

Input:
Title: DECLINES IN SKELETAL MUSCLE QUALITY VS. SIZE FOLLOWING TWO WEEKS OF KNEE JOINT IMMOBILIZATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: No Comment
Experimental design: No Comment
Validity of the findings: No Comment
Additional comments: Thank you for taking the time to make the suggested edits. Well done and congratulations.


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: INVESTIGATING LOS ANGELES’ URBAN ROADWAY NETWORK FROM A BIOLOGICALLY-FORMED PERSPECTIVE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The quality of English language used throughout is of a generally high standard, although a proof read to pick up on minor typographical errors is necessary (especially on in-text citations).

A good sample of the literature is referenced, but as there are an enormous number of papers on the topic of slime mould navigation, the reviewer recommends a few more are referenced for completeness. Specifically, the authors will be interested in the following articles, which examine slime mould navigation across 3d-printed surfaces.
A. Adamatzky et al. (2014) Slime mould analogue models of space exploration and planet colonisation. JBIS, 67, pp.290-304
T. Dillon et al. (2019) Interspecies Urban Planning, Reimaging City Infrastructures with Slime Mould. In Adamatzky (ed.) Slime mould in Arts and Architecture. pp171-187. River Publishers.

The second reference, ln 204-205, is to an arXiv preprint. Please update to the final publication: https://doi.org/10.1142/8482

Figures are generally good, although the image quality seems rather low: possibly the review copy is compressed, however. It would also be beneficial to include a figure showing the authors' slime mould incubator.

The reviewer considers that the research question could have been made clearer in the introduction, although the concluding statements do make the purpose and outcome of this research explicit.
Experimental design: The experiments presented appear to have been soundly designed and conducted with suitable rigour. Please see the final comment in the previous section regarding clarifying the research question in the introduction.

A few details of the methods section should be amended for clarity, please see the following comments.
1- "Makerbot 3D printer" ln 112, please state the model
2- "sterilized" ln 121, sanitized would be a more appropriate description of the UV irradiation technique used
3- "2% agar" ln 122, the reviewer assumes that this was non-nutritive (AKA "water") agar and that it had been autoclaved?
4- "Purchased" ln 127, please state the supplier and, if available, the strain of P. polycephalum
5- "four additional sterile oat flakes", ln 131, the network density will be directly proportional to the number of food sources. Why were these four oat locations chosen? Do they correspond to population centres?
6- Following from point #5, the network characteristics will also be time dependent. Why was 72 hours chosen as the end-point of the experiment?
7- The dimensions of the printed topographic map and hence the scale reduction don't appear to be given.
Validity of the findings: The number of replicate experiments were suitable to make statistically-significant conclusions and the conclusions follow on from the results in a logical manner.

The following points should be addressed for clarity:
1- "average" ln 154, the standard deviation should be given too (the reviewer notes that the range is visible in fig 3)
2- "high level of networks similarity" ln 176, How was this assessed? If only qualitatively, this is fine, but needs to be stated. Also, typo: networks >> network
Additional comments: This was an interesting paper that develops the concept of transport network bioevaluation, whose novelty lies in comparing P. polycephalum navigation to extant road systems on 3D printed cityscapes with a z-topography. The reviewer recommends that the manuscript is suitable for publication if the points above and below are addressed.

General comments:
1- "single-celled" ln 59, P. polycephalum is not single-celled, but acellular, please correct.
2- "plasmodium tubes consist of actin-myosin fibres" ln 64, the wording here is somewhat misleading as the intra-tube structure of Physarum is complex, recommend rewording to better represent that tubes contain actin and myosin as the components to achieve locomotion and shuttle streaming (with a relevant citation).
3- Sentence starting ln 73, It should be made explicit here that some other studies (including 2 cited by the authors) have utilised 3d printed maps with z-topography, before proceeding to explain where the gap in knowledge is and how this paper addresses it.
4- Ln 86-97, The justification for using LA as a map doesn't seem to flow well. This paragraph appears to initially state that traffic in LA is bad, before stating it's highly ranked for automobile accessibility?


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: INVESTIGATING LOS ANGELES’ URBAN ROADWAY NETWORK FROM A BIOLOGICALLY-FORMED PERSPECTIVE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Ti: Investigating Los Angeles' urban roadway network from biologically-formed perspective

This is an interesting report. In a broad sense, it attempts to further our understanding of how to incorporate biologically inspired systems in engineered systems such as the road system. In summary, it grows a network-forming slime mold into a 3D replica (2.4X) baited using oat flakes to recreate the human-engineered web of urban highways of Los Angeles, CA in the USA. They find a consistently shorted length of the network formed by the organism.

As I see it, while the work has enormous potential to develop interesting research, authors need to go a bit beyond the report presented here. The explicit development of a set of more ambitious research questions and hypotheses may help to frame the ms beyond a simple report of facts partially shown elsewhere presented here. Either in terms of energetics, by comparing energy costs in terms of the evolutionary adaptations or in terms of providing a more detailed description of the how these ~60 or so km less built by slime molds could really inform better planning for LA.
Experimental design: The experimental design is clear albeit extremely simple. I would have liked to see a more ambitious setup to deepen on the questions proposed.
Validity of the findings: While I find this piece of research very compelling I would have liked to see a deeper discussion, not only regarding the differences that may explain the difference between the empirical distribution of the road vs. slime mode network, but I also miss a more profound discussion on the experimental setup and the factors that may obscure this particular comparison and how it may contribute to use this type of approach for solving real-world problems. Particularly in the planning of urban systems and mobility. I truly believe that this type of contribution is a good first start, but we really need to make a large effort to convey this to a broader audience so that this kind of research may have a real impact on urban planners.
Additional comments: Ti: Investigating Los Angeles' urban roadway network from biologically-formed perspective

This is an interesting report. In a broad sense, it attempts to further our understanding of how to incorporate biologically inspired systems in engineered systems such as the road system. In summary, it grows a network-forming slime mold into a 3D replica (2.4X) baited using oat flakes to recreate the human-engineered web of urban highways of Los Angeles, CA in the USA. They find a consistently shorted length of the network formed by the organism.

As I see it, while the work has enormous potential to develop interesting research, authors need to go a bit beyond the report presented here. The explicit development of a set of more ambitious research questions and hypotheses may help to frame the ms beyond a simple report of facts partially shown elsewhere presented here. Either in terms of energetics, by comparing energy costs in terms of the evolutionary adaptations or in terms of providing a more detailed description of the how these ~60 or so km less built by slime molds could really inform better planning for LA.

While I find this piece of research very compelling I would have liked to see a deeper discussion, not only regarding the differences that may explain the difference between the empirical distribution of the road vs. slime mode network, but I also miss a more profound discussion on the experimental setup and the factors that may obscure this particular comparison and how it may contribute to use this type of approach for solving real-world problems. Particularly in the planning of urban systems and mobility. I truly believe that this type of contribution is a good first start, but we really need to make a large effort to convey this to a broader audience so that this kind of research may have a real impact on urban planners.


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: INVESTIGATING LOS ANGELES’ URBAN ROADWAY NETWORK FROM A BIOLOGICALLY-FORMED PERSPECTIVE
Review round: 2
Reviewer: 1

Output:
Basic reporting: All comments addressed.
Experimental design: All comments addressed.
Validity of the findings: All comments addressed.
Additional comments: The reviewer is satisfied that all points highlighted have been satisfactorily addressed and hence recommends publication of the manuscript in its current state.


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: INVESTIGATING LOS ANGELES’ URBAN ROADWAY NETWORK FROM A BIOLOGICALLY-FORMED PERSPECTIVE
Review round: 2
Reviewer: 2

Output:
Basic reporting: I still find this research effort a very compelling and interesting addition to the literature. Authors have made an effort to improve the manuscript by including a new paragraph in the Discussion. However, the link between the results and the potential usage of the evidence gathered here is still dim to my understanding. I would like to see a deeper exploration of the specific reasons as to why slime mold outlines a smaller path-length in this particular landscape compared to the way LA has been built over time. There are evidently inherent restrictions in which the road network has been built that may be modeled using a preferential attachment approach but not discussed here. How do their experiments relate to such facts? Do they? Additionally, some other social restrictions may be in play here. They may point towards the role of redundancy in path elections in urban planning as opposed to other biological processes in the taxis of slime mold exploration. Adding this bit will certainly provide a stronger link between this interesting experiment and urban planning.
Experimental design: I have no issues with this section
Validity of the findings: The experiment presented here is very interesting and results potentially revealing. However, the link between the mere facts and the objective of making a parallel between how LA has been constructed and how slime mold explores the landscape can, to my understanding, be iimproved.
Additional comments: I recommend to further expand the discussion on the potential causes that may explain the differences revealed by the experiment.


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

Input:
Title: THE COMPLETE CHLOROPLAST GENOME OF MICROCYCAS CALOCOMA (MIQ.) A. DC. (ZAMIACEAE, CYCADALES) AND EVOLUTION IN CYCADALES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors provide a valuable contribution by presenting the full chloroplast genome of Microcycas, the only genus that had not previously had a full genome sequenced.
Experimental design: no comment
Validity of the findings: The authors should strengthen their discussion of the results of the phylogeny presented.

The authors repeatedly mention the Cycadales as being divided into three families and present a proposal to classify the order within two families. However, several previously published phylogenies previously supported a division of the Cycadales into two families, and based on the examination of these phylogenies, Christenhusz et al. (2011) already published a formal classification including only the two families Zamiaceae and Cycadaceae. See: http://dx.doi.org/10.11646/phytotaxa.19.1.3 . The authors should therefore not propose this classification, but rather should just state that their topology supports this classification.

No molecular phylogeny supports Stangeria and Bowenia as belonging in the same clade. See 10 examples in figure 2 in Salas-Leiva et al. (2013): https://doi.org/10.1093/aob/mct192 . As with the example above, the authors should mention their results are consistent with all other molecular phylogenies and de-emphasize this finding in the abstract.

The authors should revise the number of extant cycads reported to 355, following The World List of Cycads, a list of accepted cycad names used as a taxonomic reference by the IUCN, CITES, etc...This reference should also be cited in the manuscript. See: https://cycadlist.org/

The authors claim that 40% of species have the possibility of becoming extinct, but this is true of all species, and so the sentence should be clarified. The authors should instead mention the percentage of all cycad species considered threatened by the IUCN Red List of Threatened Species.

The authors attribute the decline of Microcycas calocoma as being due to uneven sex ratios, but this is inconsistent with the following reasons provided by the IUCN Redlist entry for the species: "The plants are affected by habitat destruction (moderate) and over collecting of plants from the wild. Reproductive failure (pollinator extinction) is a concern, although this still needs to be verified." I am not aware of any published research discussing sex ratios in the wild for this species, so the authors should support their assertion with a reference citation or utilize other published data regarding threats to the species, such as the aforementioned IUCN Red List Entry.
Additional comments: The chloroplast genome of Microcycas will be a great resource for future researchers, and the results regarding the genome are well presented. The paper could be greatly improved by improving the interpretation and discussion of the phylogenetic results, as suggested above.


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

Input:
Title: THE COMPLETE CHLOROPLAST GENOME OF MICROCYCAS CALOCOMA (MIQ.) A. DC. (ZAMIACEAE, CYCADALES) AND EVOLUTION IN CYCADALES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The ideas are well structured, the objective is simple and clear, the English language is good (but there very few little details to solve).

The methods are clear, but few aspects should be better explained ("detailed in "General comments for the author").

Figures 3 and 4 can be summarized in one single figure.

Figure 2 should be better explained in the text (details in "General comments for the author")

The Tables are appropriate in number and information.
Experimental design: The objective is clear: all cycad genera have at least one cpDNA genome reference, except Microcyas. This study aims to fill that knowledge gap.

I think the research is simple but straightforward, making a simple description of the structure and composition of the genome and making phylogenetic comparisons with the other cycad genera.

The technical work is well explained, except for few aspects that are detailed below. Also, the authors will need to be requested to submit the accession number of the genome if the manuscript is accepted.
Validity of the findings: The results are clear and highly descriptive. However, the phylogenetic analyses are especially interesting. The authors apparently confused Stangeria with Bowenia in some part of the discussion (detail below), but I understand that it can be easily corrected.

I think the authors could have been more opened for speculation or more liberal for hypotheses proposal. The results are descriptive, but yet, there is no much discussion about the meaningful of the results. One thing that can improve the quality of this paper is to propose an explanation about the controversial position of Bowenia and Stangeria. Also, it would be nice to appeal better for the distinction of two families in the Cycadales, as many phylogenetic studies don't support the "three families organization". For the experts in cycad phylogenetics, it is clear that Stangeriaceae should not be recognized as a family.
Additional comments: In order of appearance, here are some points that should be considered to improve the quality of the manuscript:

Line 13: Missing comma in:  Cycadales – an order of seed plants in subtropical and tropical region[,] comprises...
Line 15: Missing comma in:… ten genera except Microcycas[,] making it an ideal plant group...

Line 34: Please verify “_” in “Wu & Chaw, 201_5"

Lines 80-82: “This ensues because females are more delicate and suffer high mortality rates as they require and expend more resources to reproduce and are more susceptible to die in stressful  environments (Field et al., 2013)”
Is this true for cycads in particular? I think it is a possible explanation, but maybe it is too liberal to confirm that this is the cause. Please rephrase to say that “it might be a reason”.

Line 106-107: “Can you please explain why did you choose Bowenia serrulata as a reference genome?

Line 110-111: “Can you please explain how local assembly was done to fill the gaps? Did you use any software? Which one?

Line 138: How many MCMC and burnin did you use in Bayesian inference method for phylogenetic tree construction?

Line 145: Why did Shuffle-LAGAN was used as parameter prior to run the analysis? Also, please change “to running” to “to run”.

Line 179: Cycas debaoensis and C. taitungensis should be in italics.

Line 191: "Sequence variation in cycads” is preferable

Line 192: add space in C. debaoensis

Line 191-199. I am confused with the explanation of Figure 2. The text mentions that purple color indicates conserved sites, and white color indicates sites with indistinct alignment (thus more variable sites). But Figure 2 suggest that purple color indicate protein-coding regions and pink are non-coding regions. I think there is no coherent description between figure and text. Can you please better describe the results shown in Fig. 2?

Lines 206-210. The position of Stangeria is deliberately ommited in this parragraph. But I think it is very interesting and should be explained. The position of Stangeria is not consistent with the concept of the “Neotropical clade”, but this opens a new opportunity to research about the relationship between Stangeria and the neotropical cycads. Please discuss this too.

Sentence 241-242: “The non-functional gene, tufA, was inherited from the charophyte lineage of green algae that once coded for a functional protein elongation factor.”. Please add citation here.

Line 244: Arabidopsis in italics.

Sentence 257-261: This is incorrect. Please check the figures 3 and4 in detail. Actually, Stangeria is joining the Neotropical group, and Bowenia is joining the Encephalartoid group. Please verify whether this confusion affects your ideas for discussion in lines 262-265.
Line 267-274. In addition, the PHYP gene tree produced in Nagalingum et al 2011 shows the same topology as the whole cpDNA tree. I think it is a worthy mention.

Lines 275-288. Can you propose any hypothesis to explain the position of Stangeria as member of the Neotropical group and Bowenia as member of the Encephalartoid group, based in morphological characters? Other previous studies have failed to successfully explain this, and I think this result is a convincing way to finally solve this problem.

In figure 2: Please indicate the extension of LSC, SSC, IRa IRb.

Figures 3 and 4. Topologies and branch lengths are similar. Can you show both results in a single figure? For example, please show only the ML tree, but annotate bootstraps of ML above branches and posterior probability below branches.


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

Input:
Title: THE COMPLETE CHLOROPLAST GENOME OF MICROCYCAS CALOCOMA (MIQ.) A. DC. (ZAMIACEAE, CYCADALES) AND EVOLUTION IN CYCADALES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Greatly improved manuscript, all my comments are in the attached reviewed pdf
Experimental design: Greatly improved manuscript, all my comments are in the attached reviewed pdf
Validity of the findings: Greatly improved manuscript, all my comments are in the attached reviewed pdf
Additional comments: Greatly improved manuscript, all my comments are in the attached reviewed pdf


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

Input:
Title: THE COMPLETE CHLOROPLAST GENOME OF MICROCYCAS CALOCOMA (MIQ.) A. DC. (ZAMIACEAE, CYCADALES) AND EVOLUTION IN CYCADALES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have satisfactorily responded to the reviewers' comments.

As I requested, authors have provided a discussion about the reasons supporting the two-family separation within Cycadales, making emphasis on clarifying the position of the genus Bowenia. Literature is appropiate,

Figures look better, but please be sure to use high-resolution figures for publication (resolution is low in the attached PDF).

GenBank accession is provided.
Experimental design: Methods are well explained, except for one thing:

Authors should provide detailed information about the dataset construction for phylogenetic analyses. Please provide detail instructions to allow for reproducibility. In particular. Please check my questions in "General comments for the author".
Validity of the findings: No comment.
Additional comments: The revision is satisfactory, and I think that the inclusion of the new paragraph in the discussion is good.

In abstract, the first sentence say that "Cycadales is an extant group of seed plants in subtropical and tropical region comprising two families and ten genera". This should mention that they comprise putatively three families and ten genera, since the number of families is something that is discussed a priori based in the results of this research. The same in line 120.

Line 121: "Calonge" should be "Calonje"

About the dataset used for phylogenetic analyses, can you please tell the length of the 81 concatenated genes? Were intergenetic regions excluded? Also, This dataset included all genes from LSC, SSC and IRs? Can you mention it, please?

Lines 426: . "Geographical patterns and distribution of cycads coincide with our phylogenetic analyses using cp genomes but with few exceptions”: Can you please briefly describe the exceptions?

I made a mistake in my previous revision:
I mentioned that the topology of the whole cpDNA tree is similar to that of the PHYP gene shown in Nagalingum et al (2011). This is incorrect. I meant that is similar to the "matK and rbCL" tree shown by Nagalingum et al (2011). Please eliminate the sentence in lines 455-456: (“In addition, the PHYP gene tree produced in Nagalingum et al. (2011) shows the same topology as the whole cpDNA tree”).


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: RISK-SENSITIVE FORAGING DOES NOT EXPLAIN CONDITION-DEPENDENT CHOICES IN SETTLING REEF FISH LARVAE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Introduction: I would like to know more about these groups of bluehead wrasse. What is the range of ages of fish in groups? Are the groups exclusively new recruits of the same cohort, more or less, or is there within-group variation in age/cohort? Has there been any documentation of aggression within groups, or descriptions of how groups interact with solitary wrasse? Also, do these solitary wrasse remain solitary their whole lives? If not, at what age do they typically join groups, and could this delay in joining a group tell us something about the putative mechanisms underlying their decision(s)?

Methods: Did you use a particular package in R to create your linear models?

Results: Same as my first question for the Introduction, what is the range of ages of fish in groups? Also, while the number of individuals in a group is visible in the Figures, consider reporting this range in the text.

L72: Change “encouter” to “encounter”
L208-210: Remove “Because” to make this a more coherent sentence.
L332: Change “post-poc” to “post-hoc”
L369: Change “study” to “studies”
Figure 2 is missing an x-axis label.
Experimental design: Methods: How do you know that all fish were collected after they had been active and feeding for at least one hour? Why did you choose to model site and month as fixed effects instead of random effects in a mixed effects model?
Validity of the findings: Discussion: I wonder if the “choice” of smaller fish to join or not join groups is an actual choice by the individual. For instance, do they try to join a group but find it too energetically costly to “keep up”? Are they rejected by groups, as you briefly mention in the Stamps hypothesis on Line 347? Is there any evidence of these kinds of behaviors given your close observations of these fish? There has also been a lot of recent attention paid to animal personalities. Thus, I wonder if the fish that remain solitary are more timid while the fish that join groups are more bold. There are many possible behavioral, physiological, and genetic reasons why you would observe the demographic patterns that you do. You can’t investigate or discuss all of them but consider acknowledging more of them.
Additional comments: I found this study very interesting, well-done, and well-written. I appreciate the power analysis, which improves the interpretation of the results within the context of the study, especially because the study focuses on patterns of variation. I also applaud the authors for pursuing publication of these analyses despite there being negative/inconclusive results. It is an important contribution to their field, nonetheless. In my opinion the manuscript requires only minor revisions.

One additional comment about the authors’ descriptions of animal behavior…

L64-66: “the bird will choose the higher-variance option (even if the mean payoff is insufficient for its needs) in order to have a chance at a life-saving high payoff”
L83-87: “For example, larval barnacles use chemical cues from intertidal organisms that share a similar range of environmental tolerances to select appropriate locations for settlement in the intertidal (Raimondi 1988). Larval coral reef fish also respond to chemical cues to identify higher-quality habitats (Dixson 2011, Dixson et al. 2014) and some species also avoid locations that are already occupied by competitors or older conspecifics in order to avoid competition”

…As a general rule of thumb when one describes animal behavior, one should be careful with the use of the word “to” (or “in order to”). “…in order to have a chance at a life-saving high payoff…” ascribes intent to the animal’s actions. We cannot know the reason why an animal behaves in the way it does, but we can describe what it does without assuming reason/intent. The same can be said for “…to select appropriate locations…”, “…to identify higher-quality habitats…”, and “…in order to avoid competition” in the second excerpt. Luckily, you can either remove these statements of intent, or simply re-word them to be less presumptuous. For example, the first excerpt could become, “the bird will choose the higher-variance option (even if the mean payoff is insufficient for its needs), thus improving its chance at a life-saving high payoff”


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: RISK-SENSITIVE FORAGING DOES NOT EXPLAIN CONDITION-DEPENDENT CHOICES IN SETTLING REEF FISH LARVAE
Review round: 1
Reviewer: 2

Output:
Basic reporting: I found this article to be well written and contained clear and relevant figures.
Experimental design: Overall, the research fits the aims and scope of the journal and has been conducted to a high standard.

1.I'm not convinced that the plankton sampling was conducted in a manner that is applicable to the experimental design. The authors state that they conducted planton towes over a 30m area for each transect. However, the authors state that these fish stay very close to shelter during the first few days. Sampling plankton in the manner done here will not capture if there was any spatial variation in planton supply between groups.

2. From your introduction you state that these fish spend there first 3 or so days in the sediment while they metamorphose. Can please clarrify if day zero collections (line 132) are fish that have settled to the reef that day or if they are fish that have emerged from the sediment that day. Given the experimental design I'm assuming that you mean day zero means emergency from the sedimental.
Validity of the findings: I'm not convinced that the statistical analysis actually address the stated questions. The experiment was designed to test for differences between solitary and grouped in the mean, max. and SD within groups for gut content and growth rates. This would suggest the analysis should directly contrast grouped vs solitary individuals. However, the authors have used group size as the independent variable and importantly exclude solitary individuals from the analysis (line 234). As such I fail to see how you can draw conclusions based about the decisions of individuals to join groups or not. Additionally, in the figures the authors include the data for the solitary fish. I'm not sure why these were included in the figures if they were not included in the analysis.
Additional comments: In this study the authors state that they aimed to examine whether the decision to join groups or remain solitary could be explained by risk sensitive foraging, where smaller fish would remain solitary and endure higher risk in order to potential gain access better foraging resources. To address this, they tested whether solitary fish and fish in groups differed in their mean, variance or maximal growth rates and food consumption. They found there was no effect of group size on growth rate or any difference between solitary and grouped fishes. My main concern is that as I read the results the authors have not actually tested for the effects of solitary vs grouped fish (more details above). Furthermore, I would suggest that the authors should be cautious in suggesting that the experimental design tested group joining decisions of individuals. Such results could also result from selective predation or from group members rejecting individuals from joining groups (see Coker et al. 2013 MEPS). Overall, I think this paper is of interest but needs either re-analysis of the data or clarification of the current analysis. I have added several minor comments below.

line 177: Please a reference to support that these fish feed continuously throughout the day. I would expect that they do feed continuously but that their feeding rate will vary during the day in line with predations risk (see risk allocation hypothesis and Catano et al. 2017, Oecologia; Feeney et al. 2012 coral reefs). It might be worth adding time of day of collection to your analysis.

Line 61-66: I think this section could with some editing. It currently reads as though the budget rule is specific to birds and thus leaves me wondering why you are discussing it in the context of fish. It would be good to talk about how it relates to all animals and add some additional refs.

Line 233: Can you please provide the statistical analysis for the age distribution of solitary vs grouped fish please. A figure might also be useful.

Line 235: Can you please explain why you only analysed 49 groups when you said you measured 97 groups (line 229)?

Discussion: As an alternative explanation to your results I would look into some of the work done of social groups, as studies have shown that fish tend to associate with similar sized fish in schools (e.g. Hore et al. 2004 Behavioural ecology). It seems to me that larger fish are more likely to encounter groups of similar sized fish than small as the groups are likely to have been feeding on the reef for a day or two and hence be larger than most settling fish. I would think you should be able to test for this with your data set by looking at the variance in size with and between groups.


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

Input:
Title: A NOVEL COMPUTATIONAL APPROACH TO THE SILENCING OF SUGARCANE BACILLIFORM GUADELOUPE A VIRUS DETERMINES POTENTIAL HOST-DERIVED MICRORNAS IN SUGARCANE (SACCHARUM OFFICINARUM L.)
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors have characterized the S.officinarum miRNAs that potentially target SBCGAV virus. They reported miR396 as a candidate miRNA to base the generation of amiRNA to combat SBCGAV. The background of the manuscript is poor and showed complete unfamiliarity of miRNAs features. The figures were also very poor and lacking information. The whole manuscript needs a great language improvement. The analysis performed do not support the results and conclusion. The authors based their research in a computational prediction of candidate miRNAs targets. However, the pairing between miRNAs:SBCGAV ORF was very bad. There is no evidence in the literature of plant canonical miRNA targeting of virus ORFs. Besides, they propose that S.officinarum resistance to SBCGAV is determined by miRNAs expression. While resistance is a very complex feature that are based in many different genes. The supplementary data was not cited in the manuscript. The authors must follow the structure of the journal PeerJ. The manuscript is lacking in many aspects and in this format is not suitable for publication.
Experimental design: The research question was weak. The applied methods were not robust to the study proposal.
Validity of the findings: The data was inconclusive. The conclusions presented are very questionable, since they do not showed a correlation between S.officinarum resistance to SCBGAV virus and expression of endogenous miRNAs. The study is very weak on the proposal of application of amiRNA to combat SCBGAV virus.
Additional comments: No additional comments


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

Input:
Title: A NOVEL COMPUTATIONAL APPROACH TO THE SILENCING OF SUGARCANE BACILLIFORM GUADELOUPE A VIRUS DETERMINES POTENTIAL HOST-DERIVED MICRORNAS IN SUGARCANE (SACCHARUM OFFICINARUM L.)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Language is ok only minor errors of not using articles a many places "a" and "the", not considering the plurality of the matter under discussion and a few others
e.g.and not limited to
line 102 permitted inside "the" seed region, line 108 ->"a threshold"
line 123    was ->were
line 138 binding -> bindings
false positive -> false-positive

similar studies have been published using multiple tools to find a best fit miRNA for a target in plant and virus interaction, authors should discuss how this study have a novel approach and how it differs from the other studies published on the same pattern in its novelty.

Tables are less organized (acceptable with few a changes) to show the characteristics of a single locus in the same row of an excel entry. it will be much easier for readers to verify the claims which have been made in this study. Figure quality should be increase greatly. Text shown in figures are almost unreadable specially fig 1 and 2. However, figures are showing correct positions of target sites and other energy related parameters.
Experimental design: Authors aimed to predict microRNA/s which could be used for a resistant GMO against this virus. Overall approach is very good that the authors tried to cover all the aspects of attachment parameters with its target computationally.
Objective is well defined.
Validity of the findings: Authors have concluded the study that 3 out of four tools used have predicted that miR396 is the best candidate miRNA to be considered for making a GMO against this virus. Data provided is correct and all tools have predicted the potential for this possible attachment.
However, in conclusion section author have made a claim to have shortlisted more than one miRNAs which is not correct.
Authors should amend the conclusion section with respect to the findings of the study.
Additional comments: 1. work using the same strategy has been published so it should not be titled as "novel approach".
2. graphs should be included in main file for an easy understanding and it will help the readers.


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

Input:
Title: THE INFLUENCE OF ECOLOGICAL INFRASTRUCTURES ADJACENT TO CROPS ON THEIR CARABID ASSEMBLAGES IN INTENSIVE AGROECOSYSTEMS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors investigated the effects of different types of green infrastructure on carabid beetle assemblages within the infrastructure and in adjacent cereal fields. The study addresses a timely topic – many publications at the moment focus on the use of semi-natural habitats and landscape elements to facilitate ecosystem functioning. The manuscript is to the point and well written but language could profit from a thorough revision and maybe the involvement of a native speaker.
Experimental design: In general the experimental design is sound and the experiment seems to have been conducted well. However, some specific parts need more clarification (as listed below) and using only 3 real replicates per treatment could be a problem for the transferability of the results. In my comments below I try to point out how this problem could be dealt with. The statistical analysis is performed in a modern, valid way however, model result tables should be included in the main text.
Validity of the findings: The findings are interesting and appealing for the scientific peer group. However, statistics need to be revisited in order to proof that the results are sound (see major comments below). The discussion is sound but could profit from a clearer focussing on the main hypothesis and from inclusion of some newer and on the topic literature (as stated below). The conclusion is based on the results and ends in broad but precise management applications which are good but maybe at the current state not completely supported by the data.
Additional comments: Major Comments

(01) Using functional traits is timely and can bear a lot of information about the ecological importance of species distribution data (i.e. when approximating ecosystem functions). However, I am missing some very important traits which could very easily be included – specifically the community weighted mean body size (as body size is a direct proxy for food intake rates and has been shown to be a very important predictor for predation rates (Rusch et al. 2015)).
I aslo think that other traits are a bit overstressed (e.g. the four size classes) and some could be left out – especially Figure 3 would benefit greatly if not 12 separate graphs were shown but maybe only the most important ones which depict significant differences. The remaining results could be shown in a table (as more or less already done in Annex 3).
Also, the authors do not state clearly which traits were assigned to which species (size, size class, diet, wingshape …). This could be easily added in the species list (Annex 2) and is very important for replicability of the results as occasionally the same species have been assigned different traits by different authors in the past.
(02) It is unclear to me on which level the authors analysed data. The study was performed on 3 sites with 4 treatments each and 2 transects per treatment at each site. So did the authors use 3 replicates (sites) per treatment (as could be deduced from the R script)? This is a fairly low number – it could easily be increased by treating the two transects per treatment / site as replicates and accounting for pseudoreplication by using a nested random term with transect nested within treatment / site combination. The authors should clarify how they performed their analyses and calculate the alternative proposed by me as I suspect these models to have more statistical power.
(03) The authors performed GLMMs – but the current state of the manuscript does not show the results (L 163ff). Please add a table with the results of all GLMMs (fixed effect results for each of the response varibales) – similar to Annex 3 but before the Tuckey post-hoc tests were performed. Also, please include degrees of freedom (numerator, denominator).
(04) Although the authors performed a substantial literature search, some very recent and essential papers dealing with very similar or exactly the same topics are still missing (e.g. Boetzl et al. (2018), Fusser et al. (2018), Van Vooren et al. (2018)). I suggest including some of this newer publications – this could especially be interesting for the discussion.
(05) Although the results for both hypotheses are shown, the whole manuscript and especially the discussion could benefit from a stronger focus on the discussion of the a priori hypotheses.

Minor Comments
Throughout the manuscript: Please always use ‘assemblages’ instead of ‘communities’ as the term community refers to groups with different taxonomic levels (e.g. animal community in a pond) and not only a single taxonomic group (such as carabid beetles).
L 54:	Replace ‘occaisioning’ with ‘causing’
L 55:	‘levels’
L 64ff:	Very long and complicated sentence – please restructure and simplify (maybe through devision into two separate sentences).
L 70:	‘preserve biodiversity locally in the fields’
L 71f:	Does this statement really need 4 references?
L 73f:	I suggest restructuring this sentence to: ‘In the European Union, perennial elements as well as a variety of annual flower strips can be established under the framework of AES’
L 77:	‘the edge-effect’ is a bit unspecific – I guess the authors mean a positive response of carabid beetles to crop edges. However, there are edge-effects of different nature – e.g. also an edge-effect on weeds which are increased by edge proximity. I suggest to clarify this.
L 82: 	skip ‘spatial’
L 82ff:	This sentence is unclear to me – please restructure to make the message clearer
L 86:	‘undergone radical landscape simplification or being historically intensive’
L 88:	change to ‘safeguard’ – I am not sure whether the word the authors mean by ‘implementation / safeguard’ is not just ‘establishment’
L 90: 	In my opinion, 3 references would be enough to make a point – maybe use: (see e.g. …..)
L 93:	‘to have different carabid beetle assemblages.’
L 95: 	‘traits within the’
L 100f: 	This sentence is lacking a main part (is rather a sub sentence of the previous one)
L 102: 		I do not understand what the authors mean by this sentence – please clarify.
L 114: 	Change to ‘In ArcMap …’
L 131f: 	‘they consisted of a mixture of grass species’
L 134f: 	‘were sampled.’
L 136: 	‘on which pitfall traps were placed’
L 140: 	Metal grids: Mesh size? It might influence the data a lot as very large species get filtered out – people later using the data might want to know.
L 145: 	Which weeks? E.g. always the first week? Or was the time interval between trapping intervals uneven?
L 151: 	How was data standardized? Please explain.
L 152: 	‘square root’
L 163: 	Which command? – It DOES make a difference sometimes …. from the R script I know that it is glmer.nb – please state it in the manuscript. (By the way: ‘Infrastructure + Parcelle+ Infrastructure*Parcelle‘ is exactly the same as ‘Infrastructure*Parcelle ‘ as the interaction also includes the fixed effects – if one wants to address only the interaction it is ‘Infrastructure:Parcelle’ – but this does not make any difference in this case).
L 175: 	RStudio is just a graphical interface – the authors used R which should be cited as stated when typing in ‘citation()’
L 195: This sentence is a bit clumsy – I would suggest combining the hint to the table with some information and just referring to the table in the end of the sentence.
L 202: 	I would suspect this is because of the use of metal grids ….
L 219: 	When referring to non predatory carabids, please use granivorous or spermophagous instead of herbivorous as they are not typical herbivores (not chewing on leaves for example)
L 224: 	replace ‘on the all’ with ‘overall’
L 228: 	replace ‘sheltered’ with ‘hosted’
L 230: 	‘Regarding functional traits, …’
L 231: 	‘predatory’
L 232:	 replace ‘last’ with ‘latter’
L 238: 	‘to abundance’ and replace ‘engage’ with ‘cause’
L 242: 	replace ‘seed-eaters’ with ‘granivorous’
L 244: 	Please rephrase this sentence – it reads quite clumsy.
L 279:	‘benefitting omnivorous and …’ and ‘groups’
L 280:	‘species which are more sensitive to …’
L 281: 	‘offered to carabids a habitat analogous to crops i.e. …’
L 286:	replace ‘modified as well’ with ‘also modified’
L 290:	When talking about genera, the ‘sp.’ is not needed
L 291: 	replace ‘What is more’ with ‘Moreover’
L 292:	‘hibernate’
L 294:	‘reproduces’
L 303:	‘in the crops’?
L 306:	replace ‘seed-eaters’ with ‘granivorous’
L 307:	replace ‘adapting’ with ‘enriching’ and ‘could provide’
L 311: 	‘due to species specific habitat preferences’

Reference list:	70 references is a bit long for a quite short manuscript – as mentioned before there is some potential of shortening in different parts of the manuscript.
Figure 2 and 3:	The placing of the letters (e.g. (a)) is a bit unusual – I would recommend the conventional upper left corner in both figures.
Annex 2: 	Change ‘Badister bipustulatus’ to ‘Badister bullatus’ as it is the correct name (following the databases carabidae.org or carabidfauna.org).

References

Boetzl, F.A., Krimmer, E., Krauss, J. & Steffan‐Dewenter, I. (2018) Agri‐environmental schemes promote ground‐dwelling predators in adjacent oilseed rape fields: Diversity, species traits and distance‐decay functions. Journal of Applied Ecology.
Fusser, M.S., Holland, J.M., Jeanneret, P., Pfister, S.C., Entling, M.H. & Schirmel, J. (2018) Interactive effects of local and landscape factors on farmland carabids. Agricultural and Forest Entomology, 20, 549-557.
Rusch, A., Birkhofer, K., Bommarco, R., Smith, H.G. & Ekbom, B. (2015) Predator body sizes and habitat preferences predict predation rates in an agroecosystem. Basic and Applied Ecology, 16, 250-259.
Van Vooren, L., Reubens, B., Ampoorter, E., Broekx, S., Pardon, P., Van Waes, C. & Verheyen, K. (2018) Monitoring the Impact of Hedgerows and Grass Strips on the Performance of Multiple Ecosystem Service Indicators. Environmental Management.


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

Input:
Title: THE INFLUENCE OF ECOLOGICAL INFRASTRUCTURES ADJACENT TO CROPS ON THEIR CARABID ASSEMBLAGES IN INTENSIVE AGROECOSYSTEMS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The focus of the article is interesting, especially considering the important role played by ecological infrastructures in maintaining functionally important groups of arthropods in agroecosystems. Nevertheless, there are certain issues that must be redefined and deeply improved.
First of all, I really suggest giving the manuscript to a scientific English native speaker since, as it is written now, there are many things really difficult to understand.
There are some sections that need to be restructured, like the methods, in which the statistical analysis is not clearly separated and needs to be on the whole more specific. Also the results section needs more clarity and precision.
Figure captions have to better describe the figure contents. For example, in Fig. 3 it must to be specified if boxplots are representing the estimated mean and error obtained from the GLMM.
Tables in the supplementary material do not include titles, descriptions or footnotes.
Experimental design: Sampling design is at odds with the goals of the study. It is not possible to test for differences in carabid community composition among hedges, grassy strips and flower strips since flower strips sampled are not independent infrastructures but are always associated to a hedge or a grassy strip.
The methods need to be better explained. There is a lack of information on the location of the sampled elements and consistency of their surroundings. Is the climate similar among sites? Are all the sampled elements within a site located at the same altitude? Are the elements straight? What other elements are surrounding them? Are sampled elements flat or are in slopes? What is the orientation of the elements? Is the sun exposure of the different sampled elements comparable? Are the elements straight? What is the mean length of the sampled infrastructures (mean ± SD)? All of these aspects can influence the potential results and the reader needs to know if their effects have been controlled.
Validity of the findings: Principal Coordinate Analysis is employed to test for differences in community composition between the three ecological infrastructure types, but as I mentioned above, it is not possible to evaluate if flower strips differ from the rest of typologies in their carabid composition because they are always combined with a perennial infrastructure, and do not constitute an independent type of element.
Is GLMM fitted using data collected from both the infrastructure and the crop field? I ask this because it is not possible to compare H, G, H+F and G+F combinations if you consider the whole collected data, since sampling effort differs between H/G and H+F/G+F. If you have worked only with data from crop field, you must clarify it in the text because is a crucial consideration. Additionally, there is a strong case for adding a table summarizing results obtained from applying the GLMM in the text.
Additional comments: Keywords are not provided in the manuscript.
One of the aims in this study is to compare carabid communities in different ecological infrastructure types to evaluate the potential of these elements for biodiversity conservation, so the value of carabids as a proxy of overall biodiversity should be explained in the Introduction section (L. 52: indicator of what?). Additionally, the importance of semi-natural elements or ecological infrastructures for carabid conservation should be better justified in this section.


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

Input:
Title: THE INFLUENCE OF ECOLOGICAL INFRASTRUCTURES ADJACENT TO CROPS ON THEIR CARABID ASSEMBLAGES IN INTENSIVE AGROECOSYSTEMS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Pecheur et al. studied the influence of sown annual wildflower strips on carabid beetles using pitfall traps. Thereby, AES were sown next to crop fields and adjacent hedges or grassy strips to test which combination is most beneficial for carabid communities (species richness, dispersion metrics, diet, size, wing morphology). Crops and semi-natural habitats differ in their carabid communities but both are dominated by predatory generalists. Nevertheless, hedges were poor in activity-density and changes in crop communities were mainly driven by the presence of annual flower strips. They emphasize the importance of local heterogeneity of crop edges and the low impact of hedges in poor landscapes in agroecosystems.

The manuscript is easy understandable and well written. The typical structure is given and the introduction highlights the current state of knowledge of AESs in agroecosystems. Used literature is relevant and well referenced with one exception (see general comments under line 158). Figures, raw data, and appendixes are relevant, but some details must be corrected.
Experimental design: At first, the primary research is within the scope of the journal. Methods are well described with sufficient details. Data and statistics are robust and well analyzed. However, the main limitation is the missing novelty of the study. At first, the introduction is well written and the research question is well defined. But, the second aim of the study is to discuss examples to promote ecosystem services by carabids for weed seed or pest control without testing the real potential for it (here depending on species richness and traits). Furthermore, they provide a landscape analyses based on different land use categories (crops, meadows, forests, percentage of AESs and semi-natural elements, etc.) but neither in the results nor in the discussion, they focused on that point. This however, the establishment of AESs or hedges in agroecosystems, highly depends on the surrounding landscape as they mentioned only in the conclusion at the end. Here, the authors have the data to check which impacts have different land use categories on carabid communities and in which landscapes new introduced AESs or hedges are most beneficial or not. The authors should reconsider and concrete the main aims of the study throughout the manuscript to identify the knowledge gap which is closed by their study.
Validity of the findings: see experimental design
Additional comments: Line 128: Did you measured environmental parameters of flower and grassy strips like vegetation height, coverage, soil parameter? Throughout Europe there are probably thousand kinds of AES for different taxa or aims. The audience should have a better idea how they look like here. It is an important point which you already discuss later.
Line 132:	please provide also some examples for grass species of the seed mix (see comment above)
Line 145:	Only one week per month can be critical. Please discuss the impact of weather (one week rain), if there was any!?
Line 158:	traits were taken from Scottish carabids (Ribera 1999) and a dissertation (Dufrene 1992); better use Homburg et al. 2013: Carabids.org – a dynamic online database of ground beetle species traits (Coleoptera, Carabidae). Insect Conservation and Diversity 7. 195-205
Line 180:	please provide p-values within the results and running text
Line 238:	“to low”, remove one “o”
Line 251-253:	Indeed, agrobiont carabids use open-ground sites during summer, but in autumn they search for overwintering sites; here hedges can fill an outstanding habitat in agroecosystems
Line 270:	“Ranjha & Irmler”, switch “j & h”
Line 281-282: That is not true. The implementation and characteristics of AESs depend on so many parameters (weather, soil, land owner, seed mix, etc.). For example, in Germany there are AESs, which are completely different to crops: high and very dense vegetation etc. Please concrete that statement. See also comment under Line 128.
Line 290:	“sp.” not italic
Line 399:	“Pterostichus melanarius” in italic
Line 431-432: abbreviations of first names in capital letters: e.g. Holzschuh, A.
Line 528-529: species names in italic
Figure 1:	change grey scale of grassy strip and annual flower strip, currently no difference visible
Figure 1:	for an international audience, the map should provide an overview, where the study sites are located within Europe
Figure 3:	add spaces between numbers and units in y-axis
Annex 1:	change “combinaison”
Annex 1:	categories (gardens, meadows, forests, etc.) have to be defined; Are forests comprise hedges or shrubs? AES? ELs?
Annex 2:	change abbreviations of Ani bin and Asa fla
Annex 2:	change Notiophilus biguttatus
Annex 2:	add missing brackets for all species if necessary, e.g. Agonum muelleri (Herbst, 1784)
Annex 3:	change abundance
Data PeerJ: change abundance
Data PeerJ: switch “,” into “.”


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

Input:
Title: THE INFLUENCE OF ECOLOGICAL INFRASTRUCTURES ADJACENT TO CROPS ON THEIR CARABID ASSEMBLAGES IN INTENSIVE AGROECOSYSTEMS
Review round: 2
Reviewer: 1

Output:
Basic reporting: No additional comments.
Experimental design: No additional comments.
Validity of the findings: With the revisions being incorporated, the analyses shown in the manuscript are conclusive and sound. No additional comments.
Additional comments: With the changes made, I beleive this manuscript improved greatly and I especially enjoyed Figure 1 (although I did not request it). With the recalculated analyses and all the essential parameters shown, I think the results are conclusive and transparent.
While this manuscrip is well written and ready for publication in the current form, I have two very quick revisions and an annotations which still need to be taken care of:

Minor comments:

L 93: "within the"
L 156: R version?
L191: A more up to date (and better) version for obtaining p-values (and also numerator and denominator Df estimated by bootstrapping methods) for mermod objects would be the Package 'lmerTest' (Kusnetzova et al. 2017)
For the problems of using 'Anova' from the 'car' package for obteining p-values from glmer, see also:
https://bbolker.github.io/mixedmodels-misc/glmmFAQ.html#what-are-the-p-values-listed-by-summaryglmerfit-etc.-are-they-reliable
('Testing hypotheses' section)
However, as p-Values usually do not differ essentially (other than degrees of freedom!) I would not insist on a re-analysis of the models. The authors stated how their models were analyzed and with the additional data provided, everybody can perform alternative, more up to date analyses if required.


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

Input:
Title: THE INFLUENCE OF ECOLOGICAL INFRASTRUCTURES ADJACENT TO CROPS ON THEIR CARABID ASSEMBLAGES IN INTENSIVE AGROECOSYSTEMS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The ms is in general well written and adds an interesting perspective regarding local scale studies on agricultural landscapes focusing on carabids, an indicator group responding both at the species and functional trait level to disturbances and supporting pest control and weed seed consumption services. Structure and literature seems sufficient as well as context. Yet, I missed support and references for a third hypothesis on your work: that competing interactions could also be occurring (lines 295-317). Author's could explore this explanations as well on discussion.
Experimental design: I was a bit confused on statistical analysis regarding the need for the use of PCoA and GLMM with the same data and purposes. Author's could elect one approach or strengthen (theoretically) the need to use the multiple statistical methodologies in the same work.
Validity of the findings: no comment
Additional comments: No additional comments