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: LYOPHILIZED CELL-FREE SUPERNATANTS OF LACTOBACILLUS ISOLATES EXHIBITED ANTIBIOFILM, ANTIOXIDANT, AND REDUCES NITRIC OXIDE ACTIVITY IN LIPOPOLYSACCHARIDE-STIMULATED RAW 264.7 CELLS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript was rectified following the Reviewer's comments and suggestions.
Experimental design: The manuscript was rectified following the Reviewer's comments and suggestions.
Validity of the findings: The manuscript was rectified following the Reviewer's comments and suggestions.
Additional comments: 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: LYOPHILIZED CELL-FREE SUPERNATANTS OF LACTOBACILLUS ISOLATES EXHIBITED ANTIBIOFILM, ANTIOXIDANT, AND REDUCES NITRIC OXIDE ACTIVITY IN LIPOPOLYSACCHARIDE-STIMULATED RAW 264.7 CELLS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The paper is clear.
Experimental design: The design is enough.
Validity of the findings: The statistics are correct.
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: EFFECTS OF NITROGEN TOPDRESSING AND PACLOBUTRAZOL AT DIFFERENT STAGES ON SPIKE DIFFERENTIATION AND YIELD OF WINTER WHEAT
Review round: 1
Reviewer: 1

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK

Regulation of nitrogen topdressing and paclobutrazol
Additional comments: (1)  Primary research should be hypothesis driven. Any hypothesis, which authors had at the beginning of the study, has, unfortunately, not been outlined by the authors, for example at the end of the “Introduction”. This should also include outlining in the “Discussion” if authors actually found support for their original hypothesis after carrying out their research work.
(2) The objectives of this study were to investigate Regulation of nitrogen topdressing and paclobutrazol in winter wheat  varieties . It would be useful for the reader to outline what particular research question(s) authors have asked to address the set objective.
(3) In the final “Conclusions” authors should briefly summarize the new results obtained by carrying out the research. In addition, authors should outline how their study has advanced our current knowledge on the importance of nitrogen topdressing and paclobutrazol in winter wheat  varieties, and to understand how the regulation effect of the nitrogen topdressing and paclobutrazol in winter wheat  varieties
(4) A final statement is also required on how the study has finally contributed to food security..


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: EFFECTS OF NITROGEN TOPDRESSING AND PACLOBUTRAZOL AT DIFFERENT STAGES ON SPIKE DIFFERENTIATION AND YIELD OF WINTER WHEAT
Review round: 1
Reviewer: 2

Output:
Basic reporting: This work presents interesting results on the regulation of nitrogen topdressing and paclobutrazol
at different stages on spike differentiation of winter wheat. In the present study, nitrogen topdressing and paclobutrazol significantly alleviated the yield in winter wheat by regulating the hormonal balance. Also explained well the hormonal regulation and expression TACKX2.2 gene and their role in reproductive organs development and differentiation.

However, there are few limitations.

There is a lot of grammar and English issues.  The authors did not maintain the control plants (without nitrogen topdressing and paclobutrazol) to compare the absolute effect of the treatments on growth and yield. Material and methods need to provide more details especially, RNA extraction and gene expression analysis part. The paper is written very descriptively, especially the hormonal results part, with many explanations that make the manuscript difficult for non-specialists to understand. It needs a lot of improvement; simplify the writing style and it needs to be crisp. Besides, there are many uniformity issues in the references.
Experimental design: The experimental design is good but the authors did not maintain the control plants (without nitrogen topdressing and paclobutrazol) to compare the absolute effect of the treatments on growth and yield. Material and methods need to provide more details especially, RNA extraction and gene expression analysis part.
Validity of the findings: Introduction: Well written, but, in the introduction part, the study is missing the rationale, how this study differs from the previous studies (Wu et al. 2014, Nouriyani et al. 2012a and b), and the significance of proposed objectives.
Materials and methods need more details in few places.

Results: Well written except phytohormone content part. The authors need to rewrite that part.
Discussion:  Well discussed the obtained results. However, it needs some improvement.
Conclusion: Well written
Additional comments: This work presents interesting results on regulation of nitrogen topdressing and paclobutrazol
at different stages on spike differentiation of winter wheat. In the present study, nitrogen topdressing and paclobutrazol significantly alleviated the yield in winter wheat by regulating the hormonal balance. Also explained well the hormonal regulation and expression TACKX2.2 gene and their role in reproductive organs development and differentiation.

However, there are few limitations.

There is a lot of grammar and English issues.  The authors did not maintain the control plants (without nitrogen topdressing and paclobutrazol) to compare the absolute effect of the treatments on growth and yield. Material and methods need to provide more details especially, RNA extraction and gene expression analysis part. The paper is written very descriptively, especially the hormonal results part, with many explanations that makes the manuscript difficult for non-specialists to understand. It needs a lot of improvement; simplify the writing style and it needs to be crisp. Besides, there are many uniformity issues in the references.

Title: Maybe it needs to change. Title should be focused to the yield related.

Abstract: Good,
Line 17-18: Better to mention the percentage change in the brackets between, how significant the TPJ is compared to other treatments (TJ, TS and TPS).
Line 20: Correct the enzyme name... change it to cytokinin oxidase/dehydrogenase.

Introduction:

Well written, but, in the introduction part, the study is missing the rationale, how this study differs from the previous studies (Wu et al. 2014, Nouriyani et al. 2012a and b), and the significance of proposed objectives.
Line
Line 72: Correct the enzyme name... change it to cytokinin oxidase/dehydrogenase.
Line 82:  Change improving productivity to improving the productivity.

Materials and methods:

Need more details in few places.
Line 88: Add the geographical coordinates for the field.
Line 93: Add the information. Where is it located?
Line 98: Add the information. From which company (like sigma) was this product brought? and the place details.
Line 99-100: Not clear rewrite the sentence by mentioning the doses correctly.
Line 101: Change the 270◊104 to 270×104
Line 113: What method was used for RNA extraction? Add the reference. If the kit method was used, add the product details (company, city and country).
Line 115:  Add the information cDNA kit product details (company, city and country).
Line 116-117: Provide the primer source reference. If authors designed? add the which software used for the primer designing?
Line 118: Provide the reference gene sequence.
Line 119: How did the relative gene expression was calculated (2–∆∆Ct)? Provide the reference.
Also, provide the qPCR conditions (Program details).
Line 120-122: Cite the reference/ kit product details for the ELISA method.
Line 135: Would be.. will used to indicate the future so change the sentence.  If not, the third 500-kernel sample was/were weighed. Correct it.
Results:
Well written except phytohormone content part. Authors need to rewrite that part.
Line 159: Change the sentence to.. Whether spraying paclobutrazol or not,
Line 167: Was that 1.81-3.81%? Correct it.
Line 187-189: Not clear what authors need to say here. Rewrite.
Line 196-197: This sentence is not clear. Talking about which hormone is increasing?
The differences between two paclobutrazol treatments were increasingly smaller during the panicle differentiation.
Line 208: Change flowers to flowering.
Line 215-226:  Correct the gene name from TACKX2.2 to TaCKX2.2
Line 229 and 231: No need to write the day after each number. Change to.. 0,6, and .12 days after flowering.

Figure 1: Better to change the line format between TS, TPS and TJ, and TPJ to avoid confusion (like how they did for the figure 3 solid and dotted lines).

Discussion:

Well discussed the obtained results. However, it needs some improvement.
Need the explanation for the relationship between the plant height and yield. As the plant height was high on TS and TPS compared to TJ and TPJ, explain how plant height could impact the hormonal content, reproductive organ development, and yield using the previous literature?
Line 243-244: Authors did not measure any parameters related to photosynthesis or NUE, then, how can they say that nitrogen topdressing combined with paclobutrazol at the jointing stage promoted more photosynthate accumulation in grain and improved nitrogen use efficiency? Need an explanation.
Line 260: duo (or due) ..correct the spelling.
Line 262: Give the space.. in reproductive
Line 266: Using could be and obviously in the same sentence does not sound good. Rewrite the sentence.

Line 288 and 297: Correct the enzyme name... change it to cytokinin oxidase/dehydrogenase
Line 289: Italicize the author name.
Line 296: Change the suggested to suggesting.
Line 301 and 302: Line 215-226:  Correct the gene name from TACKX2.2 to TaCKX2.2

Conclusion:
Well written
Delete this part… In this paper, it could be concluded that and replace it with … In conclusion,

Check the attached PDF for more corrections


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: EFFECTS OF NITROGEN TOPDRESSING AND PACLOBUTRAZOL AT DIFFERENT STAGES ON SPIKE DIFFERENTIATION AND YIELD OF WINTER WHEAT
Review round: 2
Reviewer: 1

Output:
Basic reporting: ok
Experimental design: ok
Validity of the findings: ok
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: DOES LONG-TERM FIRE SUPPRESSION IMPACT LEAF LITTER BREAKDOWN AND AQUATIC INVERTEBRATE COLONIZATION IN PINE FLATWOODS WETLANDS?
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is well written with a few places with excessive wordiness. The literature cited has some problems.

Lines 183-189: This is a lot of text to simply state that one litter bag was removed due to concerns about leaf mass loss probably caused by externalities.  Condense.

Lines 433-435, 468, 505, 513: Please ensure literature cited is properly formatted.
Experimental design: This manuscript has many positive aspects and provides more evidence for the importance of fire in southeastern USA wetlands. The design appears to be appropriate and with clarification, the analysis is adequate.  Most conclusions are well supported.

This manuscript has weaknesses in undescribed variability within the fire-maintained category, connections to salamanders, identification of insects to order, and the lack of reporting any measures of statistical variability.  Fire prescriptions and applications can vary intentionally (e.g., different regimes for different outcomes) and circumstantially (e.g., poor weather). Thus, there could be more variability within this category than between fire-maintained and fire-suppressed. To the best of their ability, the authors need to describe the fire prescription (frequency at least) and actual application. Although all fire is occurring on one installation by one agency, one cannot assume that the actual fire-maintenance is the same across study sites.  If the study is to be connected to salamanders, more information is needed to explain how these data inform salamander conservation. At a minimum, the authors need to provide more information on prey items and foraging by the salamanders to make the connection. As the authors acknowledge, identification to order limits the study. Interestingly, the community results were among the strongest. Potentially, identification to family or genus would have enhanced these results further.

Methods:
Lines 141-142: You need to provide more details on fire-maintained. Were all of these fires at similar times of year? Did they occur at similar frequencies?  There could be a lot of variability in the application of prescribed fire. It is understandable that local conditions and weather can make each fire different, however,  if the prescription is similar, this is sufficient as variability within the category would be due to local conditions. If the prescriptions varied, the variability within fire maintained may be too great to be a meaningful category.

Lines 164-165: There are multiple formulae and methods in the literature for estimating k. Indicate here the method that you used. Did you use the LMM for this as well? The manuscript reads as if estimation of k was one step and the LMM was another step, however, it also could be interpreted to be the same. If these were the same, why is k depicted as a nonlinear relationship in Figure 1?  The estimation method for k needs to be provided to resolve this issue.  If the estimation of k was separate from the LMM, why not estimate k with litter type and habitat type variables in one analysis?  Generalized linear models and nonlinear models allow for exponential decay estimation with other variables included.

Line 167: Order is a very coarse measure. This is a real limitation in the manuscript.

Lines 190-202: Although the LMM is a very useful and powerful analysis, the LMM does have a number of important assumptions. Please describe how these assumptions (e.g., linearity, normality of residuals, appropriate estimation of the G matrix) were evaluated and whether alternatives, such as generalized linear mixed models were evaluated. Given experience, these data were likely better analyzed with a generalized linear mixed model or generalized hierarchical mode. Abundance data very rarely meet the assumptions of LMM. Moreover, k is a rate with the same concerns. Abundances and rates are often better modeled by Poisson and negative binomial models with the generalized linear model framework.  Abundances and k  may have met LMM assumptions here, but it is the authors responsibility to establish this.

Lines 203-213: This is a well described and very appropriate analysis.  Like you did in lines 210-211, you should describe how you evaluated the appropriate use of LMM in Lines 190-202.

Lines 236-243: First, mention the use of a priori contrasts in the Methods. The first mention of a priori contrasts should not be the Results. Second, again, standard errors or 95% confidence intervals are needed. 4.3 sounds impressively less than 8.7, but 4.3±2.0SE is not really different than 8.7±3.0SE.
Validity of the findings: Throughout the manuscript, measures of statistical variability are not reported. Comparing means without standard errors or 95% confidence intervals is not reporting all relevant information and not giving context. A mean of 10 seems larger than a mean of 5, except that a mean of 10 with a 95% confidence interval of 0-20 may not be meaningfully different than a mean of 5 with a 95% confidence interval of 0-15. These measures matter and must be reported for the reader to fully interpret your data, interpretations, and conclusions.

Abstract: Please add standard errors or 95% confidence intervals to K, invertebrates per pack, and invertebrates per gram. Explain how community composition differed. This is more important than methods details.

Results:
Lines 218-225: First, please present the results in the same order as the methods. Therefore, present the estimates for k first.  Second, please add parameter estimates (betas) and their standard errors or 95% confidence intervals. These greatly aid in understanding the relative contribution of each variable. Consider standardized effect sizes to assist interpretation. Third, add standard errors or confidence intervals to k.

Lines 226-230: Standard errors or 95% confidence intervals are more helpful than ranges.

Lines 230-236: Similar to previous comment, parameter estimates and standard errors are very helpful.

Lines 236-243: First, mention the use of a priori contrasts in the Methods. The first mention of a priori contrasts should not be the Results. Second, again, standard errors or 95% confidence intervals are needed. 4.3 sounds impressively less than 8.7, but 4.3±2.0SE is not really different than 8.7±3.0SE.

Lines 256: Present standard error or 95% confidence intervals for this mean.

Discussion:
Lines 296-297: The variability among wetlands would be easier to understand for the reader, if confidence intervals were provided for k in the text and in Figure 1.

Lines 305-307: These data are not presented in a comparable manner. If you are going to make the point that canopy cover is important, the relevant canopy cover and invertebrate data need to be presented together in text or table.

Lines 326-337: Comparing invertebrate samples between an active and passive sampler is very difficult.  This is why comprehensive invertebrate studies include multiple sampling devices. There is nothing wrong with using one method, especially if the method is the best option for the research question. Waterfowl researchers often only sample surface or open water invertebrates, because these are the relevant organisms. Here, you sampled using leaf packs, which is where salamanders presumably forage, although this could be clarified in the manuscript.  If indeed the leaf packs, represent where the salamanders forage and allowed for concurrent estimation of leaf decay, you can state this and shorten this paragraph to: 1) we found this; 2) Chandler et al. (2015) found that; 3) we used different methods relevant to our question; and 4) continue with your conclusion.

Lines 338-342: There are two ideas in this paragraph that are not well connected.  First, an argument is made that salamander larvae need herbaceous cover and the Results do report very little herbaceous cover in fire suppressed wetlands. Second, prey requirements are discussed, presumably in relation to herbaceous cover differences (if so, make this clearer).  Isopods are leaf litter associates but Cladocera are not.  Therefore, it is not clear where in the wetland that the salamanders forage.  Here and in the Introduction, you need to describe where in the wetland salamanders forage, as this matters to your sampling method and to your interpretation of comparisons across treatments, and what are the top forage items, as this puts context to whether Isopods matter. If salamanders are not foraging in leaf litter, you really need to drop the connection to salamanders in this study.

Also, considering the previous comment on Lines 326-337, did you really adequately sample Cladocera?
Additional comments: Introduction:
Lines 61-62: Wildlife should be extensive, but is suppressed. Therefore, pervasive is not the right way to word it.
Lines 68-71: Except where actively managed by fire. It is important to note this.
Somewhere in the Introduction, you need to connect the salamanders to these wetlands and invertebrates to better support your later analyses and discussion.


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: DOES LONG-TERM FIRE SUPPRESSION IMPACT LEAF LITTER BREAKDOWN AND AQUATIC INVERTEBRATE COLONIZATION IN PINE FLATWOODS WETLANDS?
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well written and professional english used throughout.

A few additional recent citations were provided but the background/context is very good.

Article structure is fine and raw data are provided.

The results directly address study objectives.
Experimental design: This manuscript fits well within the aims and scope of PeerJ

The authors have identified and interesting and important research area/knowledge gap.

Technical implementation of the study is well explained and subscribes to accepted standards.

A few suggestions were made on the manuscript to improve details, but generally methods were adequate to allow replication
Validity of the findings: There was not a large effect of treatment (fire versus fire suppression) as the authors expected. However, this is interesting because it suggests that there is a great deal that we still don't understand about isolated wetland foodwebs in longleaf forest. I have challenged the authors to think a bit more about their results and what they mean in the context of how we manage wetlands in fire-maintained forests.

I have requested a bit more detail on data analysis, but the overall approach is statistically sound,

The discussion is a bit long in places, but I have provided a suggestion or two for condensation.

None of these comments undermine the value of this research and its presentation for publication.  Standards for the journal appear to have been met.
Additional comments: I made some comments about clarifying the name of the wetlands studied in this manuscript. I believe that these suggestions will help readers visualize the study system. The authors and editors are free to reject these suggestions.

The authors are measuring leaf breakdown or leaf processing, which is not the same as leaf decomposition. I recommend adopting the breakdown/processing terminology through out the manuscript.

I made suggestions on the text of the manuscript and it is provided. I hope the authors find my suggestions constructive as that is how I intend them. I feed privileged to read a preview version of this study.


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

Input:
Title: DOES LONG-TERM FIRE SUPPRESSION IMPACT LEAF LITTER BREAKDOWN AND AQUATIC INVERTEBRATE COLONIZATION IN PINE FLATWOODS WETLANDS?
Review round: 2
Reviewer: 1

Output:
Basic reporting: This revision is greatly improved.
Experimental design: Clarifications in this revision enhanced the manuscript.
Validity of the findings: Revisions were successful in conveying the validity of findings.
Additional comments: The authors did a very good job of revising and clarifying this 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: DOES LONG-TERM FIRE SUPPRESSION IMPACT LEAF LITTER BREAKDOWN AND AQUATIC INVERTEBRATE COLONIZATION IN PINE FLATWOODS WETLANDS?
Review round: 2
Reviewer: 2

Output:
Basic reporting: The article is well written and professional english used throughout.

The background/context is very good.

Article structure is fine and raw data are provided.

The results directly address study objectives.
Experimental design: This manuscript fits well within the aims and scope of PeerJ

The authors have identified and interesting and important research area/knowledge gap.

Technical implementation of the study is well explained and subscribes to accepted standards.
Validity of the findings: The findings are consistent with the study design and data presented. I see no issues with validity
Additional comments: I previously reviewed this manuscript. The authors have done an excellent job of addressing my questions and concerns. I believe that review cycles should have an end, so I do not have additional comments on this 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: WHOLE-LIMB SCALING OF MUSCLE MASS AND FORCE-GENERATING CAPACITY IN AMNIOTES
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The statistical analyses presented here on the primary and secondary anatomical data are well thought out valid. However, I do believe that some clarification is required in regards to the anatomical data itself, both those collected for this study and those obtained from previous work. And while I don’t believe any assumptions made regarding the use of these data would have had any major bearing on the study results, I feel that the manuscript will benefit from these additional clarifications.

These include:

Primary anatomical data
- Of course, measuring a certain amount of fascicles in order to generate a mean value and represent a muscle fibre length is standard practise in many muscle architecture studies. However, as these were fresh specimens, was any consideration paid to the fact that once the muscles were removed from limb, their fibres may no longer be at an “anatomically reasonable” or functional relevant length? This is usually mitigated in some studies by formalin-fixing the limb with joint angles locked at certain positions, which limits the changes in fibre lengths when muscles are removed, although this potentially introduces other uncertainties due to muscle shrinkage. I’m aware that in the Discussion you mention the potential “noise” in this dataset due to the different methods used, among other things, but I do think that this potential limitation of the primary data you present here is worthy of specific mention, particularly if it is to be used in future studies.
- I also think it would be beneficial to report your primary anatomical data in the supplemental data as means ± standard deviations, as this would give an indication of the variation of fibre lengths, pennation angles and PCSAs within the species you investigated.

Bipeds
-Is there a specific justification for grouping humans with birds as “bipeds”, beyond their shared gaits? One would assume that as their limb postures are very different, their muscle properties, particularly in the proximal limb, would be similarly disparate. I’m not necessarily arguing that you remove humans completely, however I feel that a short sentence justifying this grouping could be beneficial, as it could explain your wide CIs
Validity of the findings: no comment
Additional comments: The manuscript is nicely written with a clear introduction to the problem of a lack of knowledge of how muscle force generating properties scale across species, which introduces issues when attempting to predict these factors in extinct species. The interpretations of the results are clear and effectively related to many uncertainties which persist regarding muscle architecture and function (i.e. fascicle packing, tendon energy storage). I have no major comments beyond some additional clarifications of certain aspects of the anaomical data.


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

Input:
Title: WHOLE-LIMB SCALING OF MUSCLE MASS AND FORCE-GENERATING CAPACITY IN AMNIOTES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment here
Experimental design: no comment here, more detail on the methods are needed as described in section 4
Validity of the findings: no comment, but further justification behind some findings could improve the manuscript, see section 4
Additional comments: The authors sought to review recent work on the scaling of the fore and hindlimb musculoskeletal system as well as add their own data from tegus and opossums to determine if there are general patterns to how muscle strength varied against predictions with body size in amniotes generally. This paper is overall a great contribution to the literature and I am glad to see this sort of comparative analysis being conducted.

Although the overall approach is sound, the authors should be careful to identify the assumptions in their analyses and the true meaning of the shorthand they employ. For example, the authors make frequent references to ‘strength’, by which they mean either physiological cross-sectional area (PCSA), or PCSA normalized to body weight. Although it is unwieldy, a more accurate term for this value would be anatomical force-generating capacity, or something similar?. Similarly, it is not necessary to refer to muscle mass as ‘size’, because mass is more precise (cannot be confused with volume) and is already simple enough to be easily understood by readers.

Second, the authors present here many valuable analyses but need to do a better job – both textually and graphically – at pointing the reader to the most salient findings. The high number of tables and graphs will serve as excellent reference material but should be presented in a way that better indicates what the most important findings are. Figures 3-5 especially are somewhat redundant. I think it would be best for the authors to determine which of the 3 figures sends the most important message and put the other two figures in the supplemental material.

Finally, the authors state that they are curious about “Are there different strategies for packing PCSA into a given volume of limb muscle, or do the differences observed between individual muscles and between species ‘cancel out’ at the level of the whole limb?” This is a good question, but their general conclusion on line 624 could use more support. Could the authors show how this trade off plays out within each limb segment, or does it only remain universal at the level of the whole limb? The general conclusion made in this section is a bold and important claim and should be properly justified.

Abstract

Methods

It is not fully clear here how averages were calculated. Were averages calculated for each muscle and then each species? Were raw values averaged and then exponents calculated? This information may seem pedantic but will be vital for replication studies. What about when multiple individuals were included for each species? How were the individuals treated differently? Also, were the original values back-calculated to raw if the cited publication presented mass-scaled values? Looking at the spreadsheet, it seems that the largest individual from literature sources was this. This choice should be explained and justified. It seems to me that this choice would a) increase the chance of erroneous measurements being included instead of being averaged out from multiple individuals, b) this could set up a false equivalence because, by aiming for the largest individual of each study, it may compare some large individuals with some smaller individuals from studies which do not feature large adults. In this case, it would probably be more advisable to average all individuals from a species to give each species an equal influence. Whatever course is taken, the methods must be completely clear to the reader because they will influence the results.

Also, please explicitly justify each of your isometric exponents through dimensional analysis.

line 177 – ignoring pes and manual muscle contributions would have a differential effect on plantigrade vs digitigrade species – you should acknowledge the impact of this in the discussion

line 290 – Great idea, but other differences between the groups should be mentioned (lighter skeletons in birds, weight of feathers in birds).

line 295 – the use of mean size-normalized isometric strength is a good idea but needs more defence/qualification. How would the meaning of this value change with differences in body posture and among muscles with different functional roles? I realize the muscles are being averaged, but this glosses over some important functional considerations.

line 298 – PCSA is actually a pretty good measure of area. Did you mean force here?

line 348 –  Is isometry meant here to mean no change in pennation angle with muscle size? If so, why not measure that, or at least mention the similarity here.

Results

403 – re-define CFL here

410 – listing the non-mathematical version of each section heading also, e.g.  “Total Muscle Mass vs. Body Mass” will substantially increase the impact of the study to non-specialists.

416 – what is meant by Cs ?

419 – starting with “reptiles have a lower…” is this for the phylogenetically-corrected analysis or not?

512 – Call these Quadruped Amniote regressions?

Discussion

lines 546 – can the CIs be included here as +/- values? This will help the readers to decide how much weight to put into your findings

lines 560 – can an estimate be made of how the weight of the tail affects these results? It would be very interesting if reptiles actually had less muscle mass than mammals in the limbs adjusted for tail weight, and by how much!

lines 564 – spell out body weight

619 – In this section especially it becomes unclear how results were calculated. Are these arguments being made for limb segments or for the limb as a whole, or for both limbs?

624 – That the relationship between PCSA and muscle mass does not vary between groups is an exciting finding. Could it mean that the statement on line 616 – that there are genuine physical differences in size or strength between each group – has more to do with how body mass is measured in birds or reptiles or mammals? Is it reasonable to say that reptiles are weaker than mammals because more muscle mass is put in the tail? For this reason I think the authors should 1) abandon the use of “strength” and “Size” as shorthand for their actual variables measured (PCSA, for example) and 2) further clarify and discuss how the study design affected the findings.

624 – This claim might be better supported by making comparisons of individual limb segments here in addition to whole-limb strength.

627 – it should be emphasized here that you are calculating relative biomass. Other factors that may influence

678 – If you are not sure what would be the most appropriate scaling base measurement, why not suggest that authors always report the raw data as well as the mass-scaled version?

There should be a table of the muscles included and classified as to whether they are proximal or distal that also defines the species codes in the supplemental excel file.

Figures / Tables
Figure 2 – For ease of comparison, please place the whole, proximal, distal labels on the left margin. Please edit the axis legends to be more readable such as log 10 Muscle Mass (kg) to facilitate quick comparison between different figures for the reader. Can the intercepts of the lines of isometry be moved to overlap with the plotted data? They would be much more useful this way! Can the same axis range be used for all plots? This will help in quick visual comparison of different slopes, which is the main point of these figures anyway. Can the font sizes of the slopes in the figure legends be increased and number of observations be listed as (n) ?

Figure 3 – Same comments as in Figure 2.

Table 8 – Can the slopes be listed before (to the left of) the intercept? They are more important and should be easier to read. Can the slopes of isometry also be listed here for easy comparison?


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: WHOLE-LIMB SCALING OF MUSCLE MASS AND FORCE-GENERATING CAPACITY IN AMNIOTES
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No comment


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

Input:
Title: WHOLE-LIMB SCALING OF MUSCLE MASS AND FORCE-GENERATING CAPACITY IN AMNIOTES
Review round: 2
Reviewer: 2

Output:
Basic reporting: All correct.
Experimental design: All good here, my comments have been addressed.
Validity of the findings: All good here, my comments have been addressed.
Additional comments: Thanks to the authors for addressing my concerns and questions. They may wish to cite a new paper (not my own) ond different methods used to calculate PCSA in their relevant section ~ line 220.

Martin ML, Travouillon KJ, Fleming PA, Warburton NM. 2020 Review of the methods used for calculating physiological cross-sectional area (PCSA) for ecological questions. J. Morphol. 281, 778–789. (doi:10.1002/jmor.21139)


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: HELICOBACTER PYLORI VIRULENCE FACTORS: RELATIONSHIP BETWEEN GENETIC VARIABILITY AND PHYLOGEOGRAPHIC ORIGIN
Review round: 1
Reviewer: 1

Output:
Basic reporting: •	Comment 1: Plasticity region is flexible genes. Four genes of plasticity region could not determine that whole region.
•	Comment 2: Lines 255-260, please include the analysis and p value.
•	Comment 3: From copy number matrix, does it keep groups without cagPAI genes? Because this groups look like more defined due to cagPAI genes existence not other genes.
Experimental design: •	Comment 4: I am not sure that positional analysis and rearrangements of adhesin can correlate virulence of H. pylori. Because adhesin or OMPs activity is under functional condition and some of them have on or off type (Y.Yamaoka et al., Gut, 2006). What was your hypothesis before your analysis for this part?
•	Comment 5: Please write about possibility of monophyletic group A (EAsian population) can be ancestral strains.  Also, at lines 286-288, if there was no relationship between phylogeographic and 66 rearrangements, previous sentence (lines 281-282) was no meaning.
•	Comment 6: Please mention about study limitation and further direction in the discussion.
Validity of the findings: •	Comment 7: Please correct all H. pilory to H. pylori
•	Comment 8: Please describe the cut-offs of identity and coverage percentages using VFs detection in method section.
•	Comment 9: Conclusion should be clear and summarized the key supporting ideas with less hypothetical.
Additional comments: The manuscript named “Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic” tried to identify correlations between virulence factors, its copy numbers and phylogeographic origin.

Generally, the research question is good, and explanation of result were not insufficient. There are several points that may help the paper become more impactful as shown in each 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: HELICOBACTER PYLORI VIRULENCE FACTORS: RELATIONSHIP BETWEEN GENETIC VARIABILITY AND PHYLOGEOGRAPHIC ORIGIN
Review round: 1
Reviewer: 2

Output:
Basic reporting: Dear Editor
The review of the manuscript with title: Helicobacter pylori virulence factors: relationship
between genetic variability and phylogeographic origin has been finished and i think in addition of the virulence factors if authors wrote about the antibiotic resistance genes it could be very interesting and informative.
Experimental design: About the design of the study its very good.
Validity of the findings: The finding is very interesting, but about the validity as authors indicated this study is based on bioinformatic and may be in practice the data have some controversy and need to done in practice.
Additional comments: As i wrote in above, if the authors mention the antibiotic resistance genes, i think the study could be very interesting and informative.
Best Regards


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: HELICOBACTER PYLORI VIRULENCE FACTORS: RELATIONSHIP BETWEEN GENETIC VARIABILITY AND PHYLOGEOGRAPHIC ORIGIN
Review round: 1
Reviewer: 3

Output:
Basic reporting: This bioinformatic study has analyzed 135 strains of H. pylori genome to determine genome variation and its relation to VF with respect to their geographic distribution. In general, the manuscript is written in clear English but same sentences are unnecessarily long and flue that require revision. Sufficient amount of data have been gathered and evaluated in an appropriate tools and methods. All findings has been appropriately presented in general and discussed in the light of sufficient and related literature.  Overall, this study has been achieved successfully to reach its aims. In my opinion, finding of this study enhance our understanding of H. pylori genome and its association to their pathogenicity.
Besides, some comments, suggestions and corrections has been done on the attached manuscript that required to be fulfilled.
Experimental design: Genomes were analyzed by appropriate bioinformatic tools and methods.  This is an original bioinformatic research within the scope of the PeerJ journal. The question is well defined in the introduction section, clearly proves the gaps in our knowledge and clarify the importance of the study.
Sufficient amount of data were analyzed with well defined advanced bioinformatic tools and well evaluated in accordance with the aim of the study.
On the other hand, some comments and corrections need to be made on the attached manuscript.
Validity of the findings: No doubt that Findings of this study would enhance our knowledge on the genome variation and its relation to the pathogenicity of H. pylori. It is clear that data are robust but there are some ambiguities related to the genomes stored in the Genbank that is taken into consideration and well discussed in the discussion. Conclusion are made reasonably but require some amendments as stated on the attachment.
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: HELICOBACTER PYLORI VIRULENCE FACTORS: RELATIONSHIP BETWEEN GENETIC VARIABILITY AND PHYLOGEOGRAPHIC ORIGIN
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised version is well-written.
Experimental design: The revised version is well-written.
Validity of the findings: The revised version is well-written.
Additional comments: none


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: HELICOBACTER PYLORI VIRULENCE FACTORS: RELATIONSHIP BETWEEN GENETIC VARIABILITY AND PHYLOGEOGRAPHIC ORIGIN
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has generally been revised and corrected based on my comments. (1) On the other hand, there are some typos like lewis (line 113), citotoxins (line  263). (2) The citation of references in the text and the style of the text in the references were not written according to PeerJ's instructions. Please correct all references throughout the text. (3) I would recommend having the English checked by a native speaker. (4) Some corrections have not been made in the so-called revised PDF copy.
Experimental design: Done
Validity of the findings: Done
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: SYSTEMATIC REVIEW AND META-ANALYSIS ON THE EFFECT OF CONTINUOUS SUBJECTIVE TINNITUS ON ATTENTION AND HABITUATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: -	Overall, the manuscript is well-structured and reads fluently, although some minor grammatical errors and inconsistencies (especially noticeable to me in the discussion section) might be resolved by an additional read-through.
-	The introduction provides a very nice overview of the context in which the results of this systematic review should be interpreted. However, I feel that the paragraph on attention (starting at line 60) might benefit from a bit more detail, and some of the information regarding attention provided in the Discussion section (starting at line 361) might be better moved up to the Introduction. Additionally, I would like you to go slightly more in depth about why the MMN and P300 can be used as electrophysiological measures of attention, and what exactly the difference between both measures is. There should at least be an explanation of why a smaller P300 amplitude might be viewed as a deficit in attention to facilitate interpretation of the results.
-	I agree with the comments of the editor that the exact contribution of this systematic review, in light of previously published reports, should be stated. Specifically, systematic reviews regarding the impact of tinnitus on cognitive performance (Clarke et al., Trends in Hearing, 2020) and late auditory evoked potentials (Cardon et al., Plos One, 2020) have been published recently. Both of these reviews reported results that are very comparable to the results of the current manuscript. This does not necessarily make the results of this review any less relevant, as the combination of behavioral and electrophysiological indices is an aspect that was not addressed by these earlier publications, but those existing reviews should at least be addressed and referred to in this manuscript.
-	I did not find any figure legends (neither in the manuscript itself nor in the additional figure files). Is this correct? Additionally, please improve the resolution of Figure 1.
-	No raw data are supplied. I agree with the authors that the original published articles function as the raw data. Nevertheless, it would be beneficial to provide access to the completed data extraction form, in which the authors have summarized all included papers, should anyone wish to check the validity of the meta-analysis results.
-	A minor issue: I think the number of included records mentioned in the abstract should not include the duplicates, i.e. should be changed from 2271 to 1293.
Experimental design: -	The research question is clear to me, although it could be stated more explicitly. In particular, it might be compelling to state how the present research benefits the existing literature, especially regarding two recently published systematic reviews in the field (see also my above comment in the Basic reporting section).
-	My main concerns lie with the methodology of the meta-analyses. Almost no information is provided in the Methodology section. I understand from the Results section that you performed two random-effects meta-analyses; this should also be stated in the Methodology section (together with a rationale, cf. heterogeneity of the included papers). Did you conduct any post hoc analyses in order to explore possible outliers or influential studies? Were there any investigations into possible publication / reporting bias, explored via funnel plots and/or Egger’s regression tests? Ideally, a separate paragraph regarding data analysis addressing all of these questions would be added to the Methodology section.
-	It seems like there is a very large number of papers rejected due to high risk of bias. Would it be possible to add more details about this rejection procedure to the manuscript? In particular, I would appreciate answers to the following questions: how many papers were rejected based on each of the stated categories of bias? How did you assess the risk of bias, e.g. were these decisions based on quantifiable criteria? If possible, I would suggest to add a table regarding risk of bias assessment to the manuscript.
-	Differences between tinnitus groups and control groups, especially regarding age and hearing levels, could have a serious impact on the outcomes of the meta-analyses (both for behavioral and electrophysiological paradigms). Would it be possible to account for possible differences in the meta-analysis? Have you, for instance, considered conducting subgroup analyses to parse out possible effects of differences in age and/or hearing level on the overall results?
Validity of the findings: -	As no raw data (in the form of the filled-out data extraction form) are supplied, it is not possible to check the validity of the meta-analysis results. From figure 3, it seems that the Hong 2016 study might be considered an outlier. Did you check for outliers or influential studies in your analyses? Could you check whether the overall effect would still be significant if this study is removed from the dataset?
-	The discussion accurately states the relevant conclusions and provides a very good overview of any deficits in the current literature, such as the question whether there exists a (linear?) relationship between attentional deficits and tinnitus severity, and the lack of studies investigating behavioral and electrophysiological indices in the same sample.
-	I do not quite understand the comments made in the paragraph ‘Generalizability of results’ (line 355-358). Are the systematic review and, especially, the meta-analyses presented in this paper not specifically performed to address this very issue? Can you add a comment on this question to this paragraph?
Additional comments: This review aimed to summarize all relevant literature on the roles of attention and habituation in tinnitus. Within the framework of a systematic review, the authors provide an overview of the existing literature on tinnitus and attention, and seek to confirm that attention is affected in individuals with tinnitus by performing two separate meta-analyses. Unfortunately, the literature on habituation and tinnitus proved too heterogeneous to arrive at any definitive conclusions.
The authors provide a satisfying overview of the current literature and accurately pinpoint the deficits in the field. To thoroughly underpin the conclusions provided in this paper, some important methodological concerns regarding the conduction of the meta-analyses and the assessment of risk of bias should 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: SYSTEMATIC REVIEW AND META-ANALYSIS ON THE EFFECT OF CONTINUOUS SUBJECTIVE TINNITUS ON ATTENTION AND HABITUATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: See general comments
Experimental design: See general comments
Validity of the findings: See general comments
Additional comments: The current review presents a narrative as well as quantitative synthesis of studies focusing on the attention mechanism of tinnitus. This is much-needed work. However, there are some major limitations of the review in terms of how it is conducted as well as reported some of which are outlined below:

1) The method section does not provide all details including the method used for meta-analysis. This limits the reproducibility of this work. Authors should consider using a standardized reporting format.
2) There are many issues in the way inclusion/exclusion criteria have been applied in relation to registered protocol. For example, the preregistered protocol does not discuss excluding studies based on the risk of bias, although almost all studies on habituation have been excluded. Authors have used CASP rating although they had planned to use a different scale.
3) The results section is superficial with the limited synthesis of findings. The authors fail to consider study design when synthesizing the results and have treated all studies as same. Despite conducting the risk of bias using CASP, the details of ratings have not been provided.

In my opinion, the review is not ready for publication in the current form. I would have liked to have provided a more in-depth review if it was a matter of writing. However, it appears that much work is needed to redo some elements of the review in line with the pre-registered protocol. It is at least required to discuss some reasons for deviations from the protocol. Again, I do not believe that the authors could justify their choices for deviating from the protocol in all instances.


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: SYSTEMATIC REVIEW AND META-ANALYSIS ON THE EFFECT OF CONTINUOUS SUBJECTIVE TINNITUS ON ATTENTION AND HABITUATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript uses mostly clear and unambiguous language. The title could be improved. Some terminology needs to be more clearly defined.

The introduction could be improved as outlined under General comments for the authors.

I think it would be easier for the reader if the manuscript used different levels of headings so that Method, Results and Discussion were more clearly defined. Some of the tables could be improved as outlined under General comments for the authors.

Tables 3 and 4. I am missing the actual results from these studies. It is not possible to follow how differences in outcome measures may have influenced the meta-analysis.
Experimental design: The manuscript lacks a clearly stated aim. I would have expected an aim that clearly indicates the effect studied an in what population. I would appreciate if the aim was stated according to PICO.

The rationale for the study could be improved as outlined under General comments for the authors.

Some additional information is needed in the method as outlined under General comments for the authors.
Validity of the findings: According to the authors this is the first systematic review and meta-analysis on the effect of tinnitus on attention and habituation. However, the rationale for the present study could be more clearly stated. A better argument is needed as to why this review is “essential”.

I am missing the actual results from these studies. It is not possible to follow how differences in outcome measures may have influenced the meta-analysis.

One of the conclusions (in abstract and L450-455) from this study is that single case studies are important to be able to study interaction between attention and habituation. It is unclear from the argument put forward how this will be possible, why this conclusion is drawn and based on which results reported in the present study. It would be easy to argue – based on the findings in the manuscript - that the effect of tinnitus on attention is more adequately studied using larger, closely matched cohorts.
Additional comments: This manuscript is reports on a systematic review and meta-analysis of studies that examine the effect of tinnitus on attention and habituation. Overall, the text is easy to follow but several clarifications are needed. Also, there are several problems with the current version. I refer to line (L) below.

Major issues:
The title is not very clear. I cannot deduce what effect is studied. This needs to be more clearly stated.

I think it would be easier for the reader if the manuscript used different levels of headings so that Method, Results and Discussion were more clearly defined.

The manuscript lacks a clearly stated aim. I would have expected an aim that clearly indicates the effect studied an in what population. I would appreciate if the aim was stated according to PICO.

One of the conclusions (in abstract and L450-455) from this study is that single case studies are important to be able to study interaction between attention and habituation. It is unclear from the argument put forward how this will be possible, why this conclusion is drawn and based on which results reported in the present study. It would be easy to argue – based on the findings in the manuscript - that the effect of tinnitus on attention is more adequately studied using larger, closely matched cohorts.

L58-59 and elsewhere. It is stated that “A contributing factor to tinnitus disorder may be the attention focused on tinnitus…”. I agree but this needs to be more clearly explained. I assume that the authors mean that a portion of available cognitive resources are required to suppress tinnitus leaving less resources to perform the task at hand. This needs more explanation since it is stated in the discussion (L299-300) that “The prevailing notion is that increased attention towards tinnitus prevents individuals from habituating to it.”. This is not clearly stated in the introduction.

L83-95. I believe that habituation needs fuller explanation. Habituation to external sound sources may be different from habituation to tinnitus. The latter may be influenced by many different factors. “sensory gating” needs to be defined. The link between habituation and electrophysiological measures needs to be more clearly explained and a rationale why the latter is a reasonable measure of habituation is needed.

L97-105. The rationale for the present study could be more clearly stated. A better argument is needed as to why this review is “essential”. The aim stated here is imprecise.

L153-160. It is unclear how the assessment of bias was converted in to different levels of risks. How was this rating made?

L163-176. More information on the meta-analysis made is needed. The information provided here and in the results is not sufficient to be able to replicate the study. A rationale is also needed for the parameters collected in the data extraction. It would be easier for the reader if the main outcome measures were defined here as well and not only in the results.

L199-239. Tinnitus characteristics, hearing acuity and psychological and psychiatric factors a mentioned here. However, the introduction provides little information or rationale why these factors are important. I think it would be valuable for the reader to have some information about these factors in the introduction since they are an important part of the discussion.

In the discussion, I am missing a discussion on the fact the level of task demands may influence the relation between tinnitus and attention (c.f., Lavie, 2005). Increasing task demands may reduce the influence tinnitus have on performance since more resources are required to be able to solve the task while decreased task demands may increase the influence of tinnitus on attention.

In the discussion, I am missing a brief discussion on the pros and cons with the own study design and how the study was conducted.

Minor issues:
L43. Check tempus.
L49-51. This is probably the most dominating cause but subjective tinnitus may have different causes.
L70 and elsewhere. I think it would be more appropriate to not abbreviate “don’t” but to write “do not”.
L84. “model” should probably read “models”.
L166. It is unclear what “residual inhibition information” means. Please clarify.
L318. The confounder hearing needs to be explained earlier in the manuscript. Why is it a major confounder?
L327-329. It is unclear why the assessment of tinnitus characteristics is important. Please clarify.
L333-335. I am missing reference to the studies by Frans Lin and colleagues.
Table 1. The order of the studies is unclear. Check that the studies are accurately referenced. E.g., Weachter et al. should probably read Waechter and Brännström.
Table 2. It is unclear how PTA and HFHL are defined.
Tables 3 and 4. I am missing the actual results from these studies. It is not possible to follow how differences in outcome measures may have influenced the meta-analysis.
Figure 1. It is unclear what “Abstracts identified from 0.5 databases” means. Please clarify.


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: SYSTEMATIC REVIEW AND META-ANALYSIS ON THE EFFECT OF CONTINUOUS SUBJECTIVE TINNITUS ON ATTENTION AND HABITUATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: I thank the authors for making these adjustments to the manuscript. For me, the introduction now contains the necessary information to interpret the results of the paper. I would still suggest to add figure legends, especially for the forest plots, e.g. to specify whether mean differences or standardized mean differences were used.
Experimental design: Many thanks for providing the data extraction form. However, after reading through this document carefully, it is still not possible for me to check the results of the meta-analysis, as it is not clear which data were extracted from the original papers. The data extraction form contains a lot of data that are not very relevant for the paper, but does not (unless I have missed it) contain a tab with the raw data that were used as input for the meta-analysis. I would urge the authors to provide these data and streamline the data extraction form. In its current form, I do not see how the provided data extraction form enables the reproducibility of the reported results.

The methodology concerning the conduction of the meta-analysis has been sufficiently expanded in the manuscript.

The authors have also provided the risk of bias analysis forms. However, only decisions from reviewer 1 and 2 are available. They state that twenty-six papers have been rejected due to high risk of bias. However, a remaining point of concern for me is that according to the ROB analysis table, a large number of these papers has been rejected NOT based on bias, but based on their relevance to the aim of the review or used methodology (reasons that are given in the column ‘Reason for rejection’). These are papers that, in fact, should have been rejected BEFORE risk of bias assessment (i.e. after full-text screening). I would like to ask the authors to alter their results section accordingly and update the PRISMA flowchart to reflect these alterations.
Validity of the findings: No further comments.
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: SYSTEMATIC REVIEW AND META-ANALYSIS ON THE EFFECT OF CONTINUOUS SUBJECTIVE TINNITUS ON ATTENTION AND HABITUATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: Please refer to “Additional comments” below.
Experimental design: Please refer to “Additional comments” below.
Validity of the findings: Please refer to “Additional comments” below.
Additional comments: This revised version of the manuscript is improved over the previous. Most of the previous concerns have been addressed adequately by the authors. I refer to line (L) below.

Two versions of the abstract are provided. One in the system and one in the actual text.

L75 and elsewhere. I still think it would be more appropriate to not abbreviate “don’t” and write “do not”.

L79-101. I still believe that habituation needs fuller explanation. Habituation to external sound sources may be different from habituation to tinnitus. The latter may be influenced by many different factors. “sensory gating” still needs to be defined. The link between habituation and electrophysiological measures needs to be more clearly explained and a rationale why the latter is a reasonable measure of habituation is needed.

L85. Consider removing “&” before “habituation”.

L103-110. I think that the argument that the review is essential is still not a strong argument since no actual new reasoning has been added.

L110-113. I still think that the aim could be more clearly stated. It is still unclear what the study population is. I assume adults.

L283. Can a paradigm where the deviant stimulus occurs equal amount of times as the standard be considered to be an oddball-paradigm? Could it be an explanation as to why the largest range is seen for that study (see Figure 5)?

L301. Add period at the end of the sentence.

L403-404. The last sentence seems to contradict what is stated on L375-380.

L424-426. Please clarify what “A meta-analysis performed” refers to. Present study or a previous?

L448-450. I am still not convinced that single case studies will provide much information.

L474. The abbreviation CNV is only mentioned in one of the tables prior to this occurrence. It would be easier for the reader to write out it here.

Tables 1-4. It is unclear what order the articles in the tables are presented. Please use alphabetical order or similar.

Table 1. B, U, L and R need explanation. From a perceptual perspective one decimal is sufficient for assessments of loudness.

Table 2. From a perceptual perspective one decimal is sufficient for PTA results. I assume that PTA here stands for pure tone audiogram and not pure tone average. HFAHL needs definition (calculated from what frequencies?). Should it be “slopping” hearing loss and not “sloping”?


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: MONITORING NEWT COMMUNITIES IN URBAN AREA USING EDNA METABARCODING
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is interesting and globally well-written. Especially, this survey method is very useful since the habitat fragmentation occurs in a context of global rapid urbanization.
Experimental design: This is a relevant manuscript that perfectly fits the aims and scope of "PeerJ".
Validity of the findings: no comment
Additional comments: 1.The Materials and Methods section should include a description of the study area.
2.The figures in the article are not clear. I recommend using vector graphics.


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: MONITORING NEWT COMMUNITIES IN URBAN AREA USING EDNA METABARCODING
Review round: 1
Reviewer: 2

Output:
Basic reporting: Unfortunately, the manuscript requires significant edits to make it suitable for publication. I can appreciate that English may not be the authors first language, and where possible, I have tried to help resolve grammatical issues. My main concerns involve the structure of the manuscript, the lack of clarity in several areas, the failure to include key figures (such as a map of the study region), and the failure to incorporate all citations in the reference list.    I have made several comments in the document with respect to this. With respect to the map, I realise one is provided in Fig 3, but it reflects the results of the eDNA work.  A lot of my uncertainty in the design may have been alleviated by a clearer figure to better orient me to the general region.

In particular, I would like to emphasize that it was unclear what was done for this study and what had been done in previously published works. Was the barcoding work specific to this study? No sample collection was made explicit; only GenBank numbers. The main sampling seems to have been for the primer design (which was still vague) and the eDNA work.

Within your introduction, the specific aims and hypothesis of your study were not stated. Nor was any substantial mention given to your study region and why it was chosen or appropriate. It would seem that one species of subspecies could be invasive in certain ponds; however, the importance of detecting invasives and that this was possibly a key aim of this study was never mentioned. Because of this the introduction seemed broken up and ill-structured.

There were also instances where content presented in one section would be more suited in another. For example, parts of the results should be in the methods, parts of the methods in the introduction, etc.

I also encourage you to better integrate your figures into your statements. In many instances it reads as though the figure caption is simply pasted into the results, for example. Try to make your narrative flow, and cite your tables and figures where appropriate to help enhance your point.
Experimental design: Overall, I understand the general eDNA approach used by the authors and I perceived their aims to assess the effectiveness of the eDNA approach compared to demographic surveys, and to assess the distribution of 5 newt species in the Geneva canton, including assessing the extend of some invasive species. Unfortunately, these were not explicitly stated. As such, I may have misinterpreted things.

The first components of their methods was not provided in sufficient detail. I was confused as to whether the reference library (DNA barcoding) was performed by them or if this was previously published. GenBank numbers were provided for 4 sequences, but the authors report generating 16 sequences. Also, the development of the primers was not provided in adequate detail. Perhaps a more comprehensive account of this could be provided in Supplementary material if it would not fit within the world limit.
Validity of the findings: The validity of the findings are weakened by the fact that in some instances, the methods applied were not consistent. Also, key aspects of the discussion may be better suited as the background in the introduction.

With that said, I do believe there may be valid findings here. The paper simply needs to define clearer objectives and remain focused to these.
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: MONITORING NEWT COMMUNITIES IN URBAN AREA USING EDNA METABARCODING
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This was an interesting manuscript to review. The manuscript is well-organized and describes an excellent application for eDNA metabarcoding to detect and quantify newt assemblages in urban aquatic habitats. I have some minor questions and comments, but these should be considered as food for thought and not essential revisions. My only substantive comment is that I would encourage the authors to have a colleague whose first language is English to go through the manuscript to improve the grammar and wording, as this will improve the manuscript’s reader uptake and impact.

The organization and content of the manuscript are sound, and describe a novel and well-executed study. My only substantive suggestions are to include more information on what negative controls were included in the eDNA sampling and processing steps (e.g. field negative controls, likewise filtering, extraction, and amplification negative controls) and to improve the wording to make the manuscript easier to read (see minor comments below).

If the authors wanted to take their results further, it would be interesting to quantify alpha and beta diversity within and among the sampled waterbodies, particularly since these are primarily urban and near-urban habitats. This is just a suggestion, however, as it was not a stated objective of the manuscript.

Minor comments:
l. 32 – change “Since few years” to “In recent years”
l. 33 – change “became” to “has become”
l. 34 – I’d suggest changing “with focus on the detection of great crested newt using qPCR assays” to “a focus on detecting individual species of interest rather than newt assemblages or species richness”
l. 41 – change “the species” to “a species”
l. 42-43 – please reword this sentence to improve clarity
l. 45 and throughout the manuscript– change “Geneva area” to “the Geneva area”
l. 48 – change “newts diversity in urban area at larger scale” to “newt diversity in urban areas at larger scales”
l. 57 – remove “factors” (redundant wording)
l. 63 – add “IUCN” before “red list” for clarity
l. 87 – change “On the opposite,” to “Alternatively,”
l. 91-92 – reword the first part of this sentence to read “Recently, analysis of environmental DNA (eDNA) has been formally recognized as an efficient method…”
l. 97-98 – reword the first part of this sentence to read “In the case of newts, eDNA studies have largely focused…”
l. 103 – reword the end of this sentence to read “…newt species has not been tested”
l. 106 – change “use” to “used”
l. 108 – remove “it was” and “the”
l. 117 – change “later” to “latter”
l. 119 – change “therefore are considered as hybrids” to “are therefore considered as potential hybrids”
l. 120 – remove “and have been”
l. 125 and elsewhere – the 16S rRNA mitochondrial region is not a gene; better to refer to it as a region
l. 145-146 – change “the primers pair” to “the primer pairs”; also change “the five different newts DNA extracted from tissues samples” to “tissue-extracted DNA from the five newt species”
l. 146-150 – please include references to support these statements
l. 157 – change “campaign was performed” to “was carried out”, “was conducted”, or something similar; also change “the beginning of newts” to “the beginning of the newt”
l. 159 – add a space between Table and S1
l. 161 – change “25 of ponds” to “25 of the sampled ponds”
l. 162 – add “a” before “Nalgene”
l. 165 – remove “step”
IMPORTANT: please include information on what negative controls were included in the eDNA sampling and processing steps (e.g. field negative controls, likewise filtering, extraction, and amplification negative controls)
l. 166 – add “the” before “dark”; also replace “on” with “through”
l. 171 – change “extract” to “extracted”
l. 174 – change “Water eDNA samples were then amplified” to “Extracted eDNA was amplified”
l. 177-178 – were index tags included in the initial PCR reaction, or added in a secondary PCR reaction? Please clarify this
l. 179 – please provide more information on the negative control; presumably this was an amplification negative control?
l. 192 – data not available to check
l. 194 – change “chimera” to “chimeric”
l. 221 – add “the” before “GenBank database”
l. 228 – if using formal names, this should be “the Order Anura”
l. 234 – change “newts metabarcodes” to “newt metabarcode sequences”
l. 240 – remove “the”
l. 241 – remove “of”
l. 247 – change “newts species” to “newt species”
l. 249 – remove “the” after “Remarkably”
l. 251 – remove “the” before “site GCO”
l. 252 – change “later” to “latter”
l. 253 – change “capable to hybridize in Geneva area” to “hybridizing in the Geneva area”
l. 253 – change “at Fig. 3” to “in Fig. 3”
l. 268 – change “In the case of 25 sites” to “At 25 sites”
l. 270 – add “the” before “25 sites”
l. 274 – add “sites” after “42”
l. 275 – remove “the” at the end of the line
l. 280 – change “the species” to “a species”
l. 284 – include this information in the Methods, since it has a large effect on what’s filtered out before being considered data
l. 285 – add brackets around “I. alpestris”
l. 288 – remove the comma after “9 sites”
l. 292 – clarify whether the result shown in light green should or should not be included (ie decision criteria – this should be stated in the methods)
l. 296 – add “physically” before “observed there”
l. 304 – similar comment on inclusion criteria for observations shown in light blue
l. 309 – who is the “pers. comm.” From (name and affiliation)?
l. 331 – change “newts” to “newt”
l. 348 – add a comma after “Italy”
l. 361 – change “the amazing result” to “an encouraging result”. Saying the result is “amazing” would contradict the authors’ arguments for using eDNA in the Introduction, as well as the growing literature that documents the effectiveness of eDNA detection
Figure 2 – change “newts’ ” in the figure caption to “newt”
Figure 3 – please state what the enclosed areas of the figure show


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: QUADRICEPS FEMORIS CROSS-SECTIONAL AREA AND SPECIFIC LEG STRENGTH: RELATIONSHIP BETWEEN DIFFERENT MUSCLES AND SQUAT VARIATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Throughout the manuscript, please change “gender” to “sex” when referring to biological sex differences.

Beginning of line 31 appears to be an extra space or underline
Line 79 compare should be “compared”
Line 151 accessed is misspelled
Line 171 measurement should be “measurements”
Line 205-206 “model with VM” should be changed to “the VM model”
Line 232 “in squat” should be “in the squat”
Liner 247 and earlier when you use the word “dimensions” it is unclear what you mean, please revise.
Experimental design: Line 83-84 “The sample included 16 randomly selected university students (9 males and 7 females)“ please provide more details about how they were randomly selected and the method of randomisation. Surely they volunteered versus being  “selected”, per se. So, for example, was the study advertised to all departments at the entire university?
Line 94 “a two-familiarisation sessions” should just be “two familiarisation sessions” without a or a hyphen
Line 93-94 If I understand correctly, the order of the tests was fixed, and not randomised, if that’s the case please add as a limitation in the discussion that the fixed order of the strength testing could have introduced systematic error into the findings, such that fatigue from the first test session could have influenced strength in the second session.
Line 94-95 You mention there were two familiarisation sessions, but don’t describe them, please provide details of these sessions.
Line 103 Please clarify Figure 1. In the methods you state the participants were tested once on the deep squat and once on the parallel squat; however, Figure 1 shows a re-test of the two squats. Did all participants do both squat variations twice? If so, which test was used for correlational analyses with CSA? How far apart were retesting sessions?
Line 129 you state dominant leg skeletal muscle mass was measured, please describe the procedure for determining the dominant leg.
Validity of the findings: Line 191-196 you state a higher correlation was observed, but only report the p value but not the r values. Change the wording to indicate Table 3 shows the strength of the correlations and report p values for each finding. For example “Both deep squat (p = 014) and the parallel squat (p = 0.004) 1RM were significantly related to QF CSA, but the correlation was stronger for the parallel squat (see Table 3). Or similar.
Line 239-241 your statement that squatting to a 90 degree depth in the squat is optimal for quadriceps training is not supported but the references immediately preceding it. Bloomquist observed superior hypertrophy with deeper squats and Kubo observed no significant differences between groups. Please update your statement to reflect the data you cited or provide sufficient evidence that deeper squats are inferior for QF hypertrophy. Note that it is also a stretch to state that training studies are in line with your results as you performed a cross sectional, correlational analysis. Just because there were slight differences in 1RM to different depths with different QF muscles does not necessarily mean that those squats would result in differential hypertrophy in heads of the QF.

Limitations section: in addition to the non-randomised order of testing, please add to your limitations that this a cross sectional analysis, and that correlations should be further explored with longitudinal training studies to better explore how specific hypertrophy of QF regions is impacted by variations in squat depth.
Additional comments: Overall this is a solid study; however, it needs revisions to the methods primarily from the viewpoint of making sure that the reader would have sufficient information to replicate the study.

Secondly, some of the conclusions need to be made sufficiently conservative based on the nature of this analysis, and the extant research.

Finally, the limitations of this research need to be more clearly stated.


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: QUADRICEPS FEMORIS CROSS-SECTIONAL AREA AND SPECIFIC LEG STRENGTH: RELATIONSHIP BETWEEN DIFFERENT MUSCLES AND SQUAT VARIATIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: This is a well-written manuscript with a very interesting methodological approach, population, and outcomes. The study determined the relationship between the cross-sectional area of the quadriceps femoris and strength performance in the deep and parallel barbell squat. The results indicate that there is a significant correlation between the CSA of QF and 1RM strength in both squat variations, but a stronger association was found with PS. Squat performance is largely dependent on the CSA of all three vastii muscles, with VM dimensions playing a significant role in the manifestation of strength in both squat variations. The contribution of VL CSA appears to be more pronounced in the parallel compared to the deep squat. I would like to praise the authors for the research topic and experimental design. All sections are well-described. I hope my comments will help the manuscript quality to be published in this Journal. I strongly recommend the authors to emphasize the novelties of the present study. Similar studies are found in literature. Moreover, the practical applications of the results are superficially explored. Moreover, it seems that the external load was evaluated also using Bioimpedance measures. This procedure is often poorly reproducible, I recommend to add reliability data in results section.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: Page 6, Lines 21-22: “while the performance in the deep squat requires an additional engagement of the hip and back extensor muscle groups.” How could the authors confirm it based on the results?
Page 7, Line 53: “EMG estimates of the deep muscles”. Please check the gramma agreement here.
Page 9, Lines 83-84: The participants had no experience on strength training exercises and 1RM tests. I suppose this issue could be an issue (specially related do deep squat), although two familiarization sessions were performed. What do the authors think about that?
Page 10, Line 131: Different nutritional aspects as well as pre-test habits could play different roles in Bioelectrical Impedance. Could the authors better explain the pre-test recommendation as well as show the reliability of this measure?


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: QUADRICEPS FEMORIS CROSS-SECTIONAL AREA AND SPECIFIC LEG STRENGTH: RELATIONSHIP BETWEEN DIFFERENT MUSCLES AND SQUAT VARIATIONS
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors effectively addressed all my comments in this section; however, there are a few minor English language errors that need to be corrected in the revisions, listed below.

"“Which leg would you use to shoot the ball?“ (van Melick et al., 2017) and that variable was used for further analyze (lines 140-142)."

The wording should be further "analysis" vs analyze.

"Previous training studies with deep and half squats, showed that performing deep squats (ROM 0º-140º) influence higher relative increase in squat 1RM and significantly affect the volume of adductor and gluteus maximus muscles, in compare to half squats (Kubo et al., 2019). However, the level of quadriceps hypertrophy was similar in both groups. On the other hand, Bloomquist et al. (2013) demonstrated greater QF hypertrophy after full ROM squats (0º - 120º) compared to partial (0º- 60º). These partial disagreements could be explained by different squats ROM prescription, which might affect the level of stimulus on different leg muscle groups (lines 245-249)."

In the first sentence, "increase" should be "increases" and "compare" should be "comparison".

"The second limitation refers to strength testing protocol, as the order of the tests was fixed, which could have resulted that increased fatigue from the first test session influenced strength in the second session. Therefore, we strongly encourage that future studies apply randomized strength testing design. Also, it should be noted that this is a cross sectional research, based on correlation analysis, and longitudinal training studies are required to better explore how specific hypertrophy of QF regions is affected by squat depth variations (lines 294-299)."

In the first sentence "the" should be placed before "strength testing", "that" should be changed to "in", and "influenced" should be changed to "influencing". In the second sentence "a" should be placed after "apply". In the third sentence "a" should be removed prior to "cross".
Experimental design: The authors effectively addressed all my comments in this section
Validity of the findings: The authors effectively addressed all my comments in this section
Additional comments: Thank you for revisions.


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: QUADRICEPS FEMORIS CROSS-SECTIONAL AREA AND SPECIFIC LEG STRENGTH: RELATIONSHIP BETWEEN DIFFERENT MUSCLES AND SQUAT VARIATIONS
Review round: 3
Reviewer: 2

Output:
Basic reporting: The sections were improved after the first revision. I have no additional comments.
Experimental design: The sections were improved after the first revision. I have no additional comments.
Validity of the findings: The sections were improved after the first revision. I have no additional comments.
Additional comments: The sections were improved after the first revision. I have no additional comments.