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 ECOMORPHOLOGY OF THE SHELL OF EXTANT TURTLES AND ITS APPLICATIONS FOR FOSSIL TURTLES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study investigated the relationship between shell morphology and ecology in turtles in order to evaluate if the turtle shell can be used to reliably infer the paleoecology of extinct taxa. A 3D geometric morphometric approach was used to quantify the shape of the shells in a broad sample of extant species (N=69) that represent all major turtle clades and three fossil turtles. Based on their results, the authors conclude that there is “much overlap between habitat groups”, but they detected “significant differences” between the extremes (highly specialized terrestrial and aquatic turtles). Indeed, the secondary analysis using fewer ecological categories revealed similar results with a lower misclassification rate.

Basic reporting
In my opinion, the introduction is globally sound. The material and methods section provides all necessary information on collected data and used analytical methods (but refer to specific comments below). The results are presented in a clear manner, making it easy to follow the descriptions. The discussion section could benefit by including some additional, relevant references (refer to specific comments below).

The figures are straightforward. Nevertheless, I would like to mention that some colleagues prefer to use color-blind-friendly colors (or, alternatively, to use different symbols in addition to color) to make their graphs accessible to everyone. The tables are informative. The data sampling appears reasonable. The supplementary material is ok, but I recommend to think about providing the raw data of the (semi-)landmark coordinates placed on each specimen as well as the R code. For instance, refer to other works published in PeerJ:
- Ascarrunz et al. 2019 PeerJ Supplementary material “raw landmark data in tps format”, doi: 10.7717/peerj.7476/supp-7 and “R scripts”, doi: 10.7717/peerj.7476/supp-8
- Mallet et al. 2019 PeerJ Supplementary material “raw data tps file”, doi: 10.7717/peerj.7647/supp-9 and “R code used for the analysis”, doi: 10.7717/peerj.7647/supp-10
Experimental design: The present study is within the scope of the journal. The methods are sound. The authors explain that they investigate the relation between shell shape and ecology, but I miss some specific hypotheses; in particular, because there are previous studies that examined this relation as well (as correctly mentioned by the authors).
Validity of the findings: The results appear valid and meaningful. We lack the raw data to be able to replicate the analyses, but the intermediate data (results from PCA etc.) are provided in the supplementary material. The paper discusses the limits of the present study. The work could benefit by including some important references (refer to specific comments below).
Additional comments: Specific comments (alternatively refer to attached document)

Overall, this is a very interesting and comprehensive work! I enjoyed reading the manuscript. I do have some suggestions and comments that should be addressed before acceptance.

Abstract

[30 ff] “Principal component analysis (PCA) highlights much overlap between habitat groups. Phylogenetic flexible discriminant analysis (pFDA), on the other hand, suggests differences, but only between highly specialized terrestrial turtles, highly specialized aquatic turtles, […].”
In my opinion, the differences between the extremes are also evident in the PCA. Thus, I would not state “on the other hand”. I would recommend to just leave the “on the other hand” out.

Introduction

[56] “The resulting bones of the carapace of a typical turtle are called […].”
Not sure if it is very informative to name the individual bones (at least in its current form) without giving any further information, such as a figure or some other detail, to explain why this is important for the present study.

[78] “Given that correlations appear to exist between shell shape and ecology […].”
Here or maybe at the end of the introduction, I would have expected some precise hypotheses (based on functional assumptions for example). What exactly do you expect from your study?

[123 ff] “The correlations observed among extant turtles are then applied to the Triassic turtles […].”
It’s a bit misleading that the Late Jurassic Plesiochelys bigleri is not mentioned here.

Material and Methods

[190] […] inguinal buttress (landmarks 6 and 7) […] (Fig. 1)
I am wondering if landmarks 6 and 7 (visible in Fig. 1E) should be shown in Fig. 1C as well? Furthermore, I have the impression that landmark 1 is not positioned exactly in Fig. 1A. Do you mind checking this?
[193] […] twelve semi-landmark curves […] (curves C1 and C2) […]
I suggest to name the curves in figure 1 (as it is done in figure 2). It would then be easier to follow the description in the text.

[193] […] twelve semi-landmark curves […] (curves C1 and C2) […]; Fig. 3, Tab. 1
The reader can imagine that the ecological category numbers (“Ecol 0-4” in table 1 and “Cat0-4” in Table 3) correspond to the webbing types (A-E) displayed in figure 3, but it would be useful to indicate the numbers in figure 3 as well to avoid any misunderstandings. Furthermore, I would avoid writing “Cat” in table 3 because you do not use “Cat” in table 1. It’s unnecessary and may confuse some readers.

[235 ff] […] The PCA was computed using the function PlotTangentSpace in the software package Geomorph […] and the R software and language […]”
Please consider revising the sentence. Geomorph is a package in R.

Results
[275] […] For SET1 (Fig. 6A) […]
Fossils are indicated as diamonds in the legend of figure 6, but shown as stars in some PCA graphs. Please correct that.

[278] […] (negative PCs) […]
Since you’re describing PC1 here, I suggest to write “negative PC1 scores” instead in order to be precise. Dito for the other PCA descriptions (SET1-4).

[279] […] categorized by the presence of flippers (4) are scattered […]
I suppose you mean “category 4”. I strongly recommend to make this homogenous throughout the whole (!) manuscript (including the tables and images). Refer also to my previous comment on line 193, Fig. 3 and Table 1.

[331] This is perhaps a result of the tear-drop-shaped shells of these taxa.
In my opinion, this sentence should not be part of the results section, but of the discussion section.

Discussion

[408 ff] “Discussion”
The authors should have a look at the following references. In my opinion, they are important to be considered in the present work:

Rivera (2008) Ecomorphological variation in shell shape of the freshwater turtle Pseudemys concinna inhabiting different aquatic flow regimes. Integrative and Comparative Biology. doi:10.1093/icb/icn088
>> (…) the carapace and plastron show significant morphological differences between habitats characterized by slow-flowing (i.e., lentic) and fast-flowing (i.e., lotic) water. (…) Of the two shell components (carapace and plastron), the carapace shows greater divergence between habitats (…)
Stayton (2011) Biomechanics on the half shell: functional performance influences patterns of morphological variation in the emydid turtle carapace. Zoology. doi: 10.1016/j.zool.2011.03.002

>> Aquatic turtle shells differ in shape from terrestrial turtle shells and are characterized by lower frontal areas and presumably lower drag. Terrestrial turtle shells are stronger than those of aquatic turtles; many-to-one mapping of morphology to function does not entirely mitigate a functional trade-off between mechanical strength and hydrodynamic performance. (…) Given that the shells of terrestrial turtles perform fewer functions than those of aquatic turtles (terrestrial shells are not under selective pressure to improve hydrodynamic performance) (…)

[422] […] possible to recognized two […]
Typo: “recognize” (without the “d”)

[492 f] […] of the same primary dataset of shell (SET1) of extant and fossil turtles.
Do you mean “dataset of shell morphology” or maybe “shells”?


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 ECOMORPHOLOGY OF THE SHELL OF EXTANT TURTLES AND ITS APPLICATIONS FOR FOSSIL TURTLES
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a new paper using 3D data to estimate the relationship between turtle shell shape and ecology. It is applied to fossils. The dataset is new and the shape variation analyzed is original. I was overall interested and curious by the results obtained. Gross methodology is fine but analyses can be refined in details.  In view of the obtained results the discussion and result section sound.
The paper can be slightly restructured, methods should be clarified or corrected, and depending on results and discussion reworked.
Experimental design: Methods should be reworked see general comments.
Validity of the findings: See general comment (make sure to use jacknife for estimating whether your categories are well discriminated)
Additional comments: This paper is an original study but I suggest several modifications to improve it.

1. Problems regarding R and geomorph, phrasing 'morphometrics'
- geomorph package is badly spelled: geomorph not Geomorph

- I hope that you are not using an R version as old as 2013 since several things were improved since and especially because geomorph packages has seen important changes including sliding semi landmark procedures, please update your reference.

- proCD.lm does not exist in geomorph (it is badly spelled, and it is deprecated in current versions); please update.

l. 236: The PCA was computed using the function PlotTangentSpace in the software package Geomorph (Adams & Otarola-Castillo, 2013) and the R software and language (R Core Team, 2013). -> rephrase the end :
 PlotTangentSpace of the geomorph package (Adams & Otarola-Castillo, 2013) in R (R Core Team, 20??)
-> rephrase also the begining: PlotTangentSpace do not only present pca of superimposed coordinates but also project observation onto the tangent shape space by performing an orthogonal projection (look at the package online help).

2. Potential issues regarding morphometric procedures and statistical analyses

2.1.Allometries :
I suggest testing allometry by directly applying the multivariate test rather than by looking at relationship between prediction and actual data. It is much easier. geomorph can do it or you can also simply do it by looking at Claude, 2008 (Morphometrics volume) or 2013 (Hystrix volume). It is actually what you do.
Indeed l.271: anova permutation -> should be in methods: it is actually how you tested the multvariate regression (see remark above).
In doing so, you can also represent the allometric component (shape variation between large and small individuals). I, however, guess that it is likely biased: the largest species is Dermochelys but for that species you have been using a very small and juvenile individual.
l.272-273: Note that correcting for allometries is not obligatory, it depends on the scope of the study: some studies might be interested in shape differences, including those due to allometries !!!.

2.2.Superimposition procedure:
As you are sliding 3D semi landmarks, it is important to say whether you slided them in minimizing the procrustes distance or the bending energy. Both methods can yield rather different results, especially when there is a lot of sliders (it is the case here).

2.3. Ecological categorization:
Ecological categories are rather important in numbers by comparison to previous studies, note that, however that the classification is sometimes complicated and still uncertain: For emydines, the cut between 1 and 2 is sometime difficult: see for instance Emys that I could have classified as more webbed than Glyptemys.

l.380: I suggest modifying the title of that section and reorganizing your text. It is confusing as it refer to methods and results. I suggest to reorganize the text in agreement. You should also re run the LDA analyses with these new grouping. Say in your methods that you tried two different categorisations, explain them here, and then present the results for LDA and pFDA.

2.4: ecological categories and discrimnant analysies
As far as I know, discriminant analysis do not recognize the gradient between all the categories but consider them as independent. In that case, increasing categories could be related to a loss of discrimination between groups. This may explain why discrimination is not so strong in the present analysis.
you simplified your categories in 3 rather than 5 but did you find a similar result in  binarizing your factor ?

2.5. Important errors regarding PCA
l.234 : "variables that contain a true biological meaning by using orthogonal transformation (Karamizadeh et al., 2013)" -> please remove that, PC axes are no biological axes: they are purely mathematical axes of maxima of variance covariance (they strictly depend on statistical sampling not on biology). PCA is just a rotation of the data; it is a way to represent multivariate ordination (no more), look at older publication if you have doubts: Reyment, Joliffe....Etc.
l. 275: Principle -> OHHHHH NO!

2.6. LDA and PCA
l. 239: which distinguishes morphological differences between groups (McLachlan, 2004). LDA uses a similar approach compared to PCA but identifies the axes that maximize the separation between multiple classes
-> update reference regarding lda (you can use a reference closer to the original, or some more general textbook, lda is a technique much older than the 21 century).
LDA is not similar to PCA. It looks at axes that maximize intergroup variation and minimize intragroup variation. It is therefore not working on the Variance covariance matrix of the data but on something else (for fast explanation, regarding morphometrics you can return to Claude 2013 or 2008).

2.7. The Brocken Stick method is not from Jackson 1993. Please cite the original citation.
There is no obligation to select only the first PCs axes for the LDA. But you have indeed to remove shape variables because the number of variables in your data set is much larger than the number of observation and categories. Keep in mind that the more you reduce your data set, the more you lose information. However the more variables you keep, the more your result will be sample dependent.
Note that you have several categories but your Brocken still model sometime reduce the shape space to about the same number of dimensions the number of categories, it is therefore not surprising to have a discrimination that is soso, what if you include axes up to 90% or 95 % of total variance ?

2.8. Confusion table and predictive power:
Confusion tables are interesting but more easy to interpret after a one leave out cross validation for avoiding to be sample dependent. You have to estimate it with the argument CV=TRUE when you use lda function. It is not said whether you have been using this in the text.

Discussion part about 2D and 3D data, ok only if your confusion table are based using jacknifing methods (one leave out cross validation). If not, it is just normal to see a better score of 3D because there is an inflation of data by comparison to observation in that case.

3. Data availability and publishing 3D models
It would be good to publish the 3D models and eventually landmark data sets as this represented some important work, you can think about Morphomuseum journal for it (it is free access, and free of charge for authors).

4. How to be sure about the problem of fossil deformation ? How did you manage for that ?

5. discriminant analysis, pca and related shape variation

Note that FDA cannot be easily interpreted in terms of morphology: it does not work on a linear combination of original variables. It is therefore hard to identify features that discriminate groups and to depict discrimant axes in terms of shape differences (landmark data are indeed all inter-dependent). By contrast LDA allows you to draw shape differences along axes. Claude 2008, 2013 explain how to do it in R and released several examples with scripts. It seems that you do this at least for your PCAs, but it is not explained how you computed extreme shape on axes (maybe based on these publications ??). I suggest to do that also for LDA.

6. pFDA, comparative method and position of fossils in the tree:
It is certainly not a good idea to use an ultrametric tree especially if you are using a method that is based on GLS regression such as pFDA, your fossil should be set in time in the tree. This is especially important because some of your fossil are close to the root of the tree. you can not consider that Proganochelys evolved independtly from the root for more than 200 My. This is not realistic. This should be corrected.

7. Interpretation of variation along PCs
l. 277: size of the plastron -> relative size of the plastron (GPA scale everything to unit centroid size, you can not have size differences at this step). Note that this relationship between carapace doming and plastron size is an bias of the method (it scales everything to unit centroid size).
l.283: avoid speaking about clustering when you are just looking at the first PCA plan (less than 42% of total variance): we have absolutely no idea of what is happening on other axes. If you want to know how data are clustered you must use clustering methods.

8. Identifying shape parameters that discriminate among groups:
For the LDA at least you can represent shape variation along axes as for the PCA, see Claude 2008, 2013 again for scripts in R. This can help you to further discuss about the morphological features that discriminate among groups. (See however my remark about binarization because LDA or FDA do not see the categories 1 -> 5 as a continuum). This is particularly important because in the last chapter of the study you speak about things that allows to differentiate groups, but nowhere you characterize these morphological differences.

9. Other
l.276: here and elsewhere in the text at several places: check the punctuation: "explains, 28.5%" -> explains 28.5%

In the discussion, you should also speak about the prediction of the LDA and not restrict it to the pFDA. It is maybe not as advanced as pFDA but it is interesting as well.

Julien CLAUDE, Institut des Sciences de l'Evolution de Montpellier, FRANCE


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 ECOMORPHOLOGY OF THE SHELL OF EXTANT TURTLES AND ITS APPLICATIONS FOR FOSSIL TURTLES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have carefully revised their original manuscript, taking into account all questions and remarks. In my opinion, the revised version of the manuscript is ready for publication after the following minor issues are addressed:

[46] “an armored body plans”
Delete the “s”.

Figure 1
The figure is improved by the labeling of the anatomical parts, but there is no explanation of the abbreviations. Please consider adding this information in the figure caption.

In general, check for typos and try to write terms always in the same manner (e.g., “linear discriminant analysis” vs. “Linear Discriminant Analysis” etc.).
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: No additional comments


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

Input:
Title: THE ECOMORPHOLOGY OF THE SHELL OF EXTANT TURTLES AND ITS APPLICATIONS FOR FOSSIL TURTLES
Review round: 2
Reviewer: 2

Output:
Basic reporting: The ms was well improved since the last version. I have just three minor remarks. See general comments.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: l. 235: add position as gpa also remove translation

l. 238: there is no need for transforming size by its log. Allometry is the relationship between shape and size, not between shape and log size. We are not working on linear measurements (where which require the allometric equation with logs) here but on shape data (defined by landmarks).

l. 280: should precise the nature of the allometry -> interspecific allometric signal


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: VISCOELASTIC CHARACTERISTICS OF THE CANINE CRANIAL CRUCIATE LIGAMENT COMPLEX AT SLOW STRAIN RATES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is written with clear and unambiguous, professional English and technically correct text, conforming to professional standards of courtesy and expression.
The authors include sufficient introduction and background providing Relevant literature references that fit into the broader field of knowledge.
Professional article structure is used in this article. All figures are relevant to the content of article and have sufficient resolution with appropriate descriptions and labels. The article is self-contained with relevant results to hypotheses but
Self-contained with relevant results to hypotheses.
One important raw data should be added. As dissipated energy or hysteresis is an important finding in this research work, therefore it will be useful if the authors can provide the detailed calculation of dissipated energy in Materials & Method (Data analysis) for future readers to clearly understand your work.
Experimental design: The article is original primary research within Aims and Scope of the journal.
Research question is well defined which is relevant & meaningful. It is stated how research fills an identified knowledge gap. By using slow strain rates, the authors investigate quite valuable results that can fill the knowledge gap and discrepancies which have been recently occurred in this research field.
The investigations in this article have been conducted rigorously and performed to a high technical standard. The prevailing ethical standards in the filed such as a full ethical permission from the Veterinary Research Ethics Committee ((VREC65), Institute of Veterinary Science, University of Liverpool).
Methods in terns of Cranial cruciate ligament storage and preparation, Cranial cruciate ligament length, Cranial cruciate ligament cross-sectional area and mechanical testing are well described with sufficient information to be reproducible by another investigator except Data analysis. The detailed calculation and analysis of hysteresis or dissipated energy should be added as also mentioned in 1 Basic reporting.
Validity of the findings: The article contains findings that should have high impact and novelty in the relevant research field. The authors clearly described all meaningful replication encouraged where relational & benefit to literature is clearly stated. The authors provide the useful raw data in supplemental materials, including P-values obtained from Bonferroni post-hoc statistical analysis on ligament lengths at different planes, appropriate figure of specimen (The cranial cruciate ligament (CCL) from a right canine stifle joint) showing the different plane views, the middle cross-sectional area (CSA) of the cranial cruciate ligament (CCL) estimated by firstly creating an alginate paste and  the stress-strain characteristics of individual canine cranial cruciate ligaments (CCL) during the ascending (Asc) and descending (Desc) tests at strain rate of 0.1, 1 and 10 %/min. However, the author missed to provide the metadata of dissipated energy or hysteresis of each stress-strain curve as this is important in the current research work and this data should add value to the literature.
Conclusions are appropriately stated, connected to the original research question investigated and limited to supporting results. Claims of a causative relationship is supported by a well-controlled experimental intervention.
Additional comments: This manuscript contains original results of strain rate dependence on the mechanical properties of the canine cranial cruciate ligament complex at slow strain rates (0.1, 1, 10 %/min). The authors claimed that the findings in this study are the first to report the slow strain rate dependency of the canine cruciate ligament across three orders of magnitude with ascending and descending test arrangements. The authors aware of their small number of specimens which have only 6 pairs stifle joints from skeletally mature Staffordshire bull terriers, however, their findings are quite valuable to future readers in this related field. For examples, the statistically significant effects of strain rate were observed on the dissipated energy and the recovery of ligament lengths of the testing protocols, this preliminary result may be useful for further studies, such as investigations on the viscoelastic behaviour of the canine CCLs when loaded with different orders of strain rates or investigations of microstructural organisation of the ligaments during mechanical tests in larger number of specimens etc. This quantification is important when comparing the mechanical characteristics of the CCL and when developing synthetic, auto and allo-grafts to be used in future therapies for ligament replacement. In order to improve the manuscript before publishing I have some additional comments for the authors to consider as in following points.
1. As the toe region of stress-strain curve is important in this work. It should be useful if the authors can provide an example of a stress-strain curve of typical viscoelastic material or if possible the chosen CCL specimen that can illustrate three major regions of the stress strain curve: 1) the toe or toe-in region, 2) the linear region and 3) the yield and failure region to help readers better understand your focus point.
2. From the result of Cranial cruciate ligament length, in paragraph; “The ANOVA test showed statistically significant results in measuring CCL length in different plane views. The analysis showed that length measurements recorded at different planes were statistically different except for comparisons between medial and lateral planes (Supplementary Material (Table 1)).”, please explain in more detail why the difference in the CCL lengths in medial and lateral planes is smaller than other planes.
3. From these sentences “Prior to testing, the samples were thawed at room temperature and two 1.1 mm arthrodesis wires (Veterinary Instrumentation, Sheffield, UK) were drilled through the tibial and femoral bone ends (Fig. 1). These pins were placed to provide extra grip as well as to replicate the ligament’s slight proximal-to-distal outward spiral when secured using custom built steel clamps (Arnoczky, 1983; Arnoczky and Marshall, 1977)“ in Materials and Method (Cranial cruciate ligament storage and preparation), it is quite difficult to follow why these two pins can provide extra grip as shown in Fig. 1. I suggest that the schematic diagram showing the way these pins placed should be useful for clearly understand this point.
4. From Fig. S3 to S5,  the stress-strain characteristics of individual canine cranial cruciate ligaments (CCL) during the ascending (Asc) and descending (Desc) tests at 0.1 to 10%/min strain rates, respectively, the label in all graphs of ligament specimens No. 6 should be CCL6_Desc instead of S6_Desc.


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: VISCOELASTIC CHARACTERISTICS OF THE CANINE CRANIAL CRUCIATE LIGAMENT COMPLEX AT SLOW STRAIN RATES
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. In the introduction part from line 62 to line 64: "Similarly, ligaments inherit non-linear viscoelastic characteristics exhibiting both elastic and viscous behaviour, hence they are history- and time-dependent". Nonlinear viscoelasticity is complicated, The viscoelastic specimen can also show elastic & viscous behavior in its linear viscoelastic regime. More clarification is needed here.
Experimental design: 1. How do the authors ensure each tested sample has the similar dimension between different specimens?

2. Is the increase in strain a step change or a continuous change? If the increase is a step increase, what is the interval between each step? Because difference in these intervals will allow different time for the sample to relax and lead to differences in test results.
Validity of the findings: 1. How did the authors account for the change of cross-sectional area during the measurement to calculate stress? Or the authors are using engineering stress rather than true stress.

2. In Figure 3, the authors show the nonlinear stress-strain relation. Could the authors fit these nonlinear functions or plot the data in semi-log scale to see if the curves have any similarities in stress-strain behavior?

3. Following the above question, it would also be helpful to show the unloading part of the stress-strain curve to demonstrate the viscoelastic behavior.

4. Another more direct and quantitative way to measure viscoelasticity is to conduct a stress relaxation or creep measurement instead of just measuring the stress-strain curve with only changes in strain rate.

5. Most energy dissipation in Figure 5 takes place after the first precondition cycle and plateaus towards the 20th cycle with few changes. Could the authors elaborate more on this behavior?
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: VISCOELASTIC CHARACTERISTICS OF THE CANINE CRANIAL CRUCIATE LIGAMENT COMPLEX AT SLOW STRAIN RATES
Review round: 2
Reviewer: 1

Output:
Basic reporting: -
Experimental design: -
Validity of the findings: -
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: VISCOELASTIC CHARACTERISTICS OF THE CANINE CRANIAL CRUCIATE LIGAMENT COMPLEX AT SLOW STRAIN RATES
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: All my comments are addressed in the revised 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: THE AICHI BIODIVERSITY TARGETS: ACHIEVEMENTS FOR MARINE CONSERVATION AND PRIORITIES BEYOND 2020
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper reads well with ample references.
There are no figures and two tables. One table restates the well known Aichi Targets. The second lists some well-known impacts on major marine habitats/biomes.
Experimental design: The methods appear to be a literature review by authors who attended a conference workshop.
The length of the references is nearly double that of the main text.
Validity of the findings: The study is a broad sweep of threats to marine biota and biological habitats. This reiterates the well-known threats which led to the Aichi Targets.

The review is not particularly critical and shows no novel insights. For example, (1) several studies have criticised the use of % MPA coverage as a statistic of ocean protection and the high values are accepted uncritically here - these grossly exaggerate protection because most MPA do not even aim to fully protect biodiversity Lines 162-4). To say that MCI 2008 'argue' that the true figure is less is misleading. They simply use the % that aims to be fully protected (within which enforcement may vary).
(2) The section on connectivity perpetuates old arguments from its fans which overlook the real nature of marine connectivity, stepping stone effects and that it is implicitly included in conservation designs that are representative (see recent reviews in TREE).
(3) line 245 cites a website for "50% of the worlds coral reefs have died" which is clearly untrue. Most reefs are already comprised of dead coral, and mortality caries greatly between species due to heatwaves, and recolonisation occurs from deep-water and other refugia.
(4) the section on monitoring makes no mention of marine-GEO, Reef Life Survey, CPR, MBON, BioTime and other resources.
(5) line 362 - cold-water coral reefs are hardly a recent discovery. The species were described in the 19th century and they were being mapped in the 1990s.

Thus the breadth of this review lacks depth and any new advances. Thus the paper does not "Does the Conclusion identify unresolved questions / gaps / future directions?" because all the issues are very well known already.
Additional comments: I emphatise with the work that went into this review and efforts of many authors. However, I feel it has sacrificed depth and critical assessment of the literature in favour of breadth, and on a very well-known topic.


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 AICHI BIODIVERSITY TARGETS: ACHIEVEMENTS FOR MARINE CONSERVATION AND PRIORITIES BEYOND 2020
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a great paper. The authors make use of recent literature and a workshop to identify key areas for progress against Aichi targets and the post 2020 review.
Experimental design: No comment
Validity of the findings: I have one main overarching comment for the paper which the authors may choose to consider. The central premise of the conclusion is that:
•	We need improved sharing of data, information and experiences
•	We need better data and understanding of marine ecosystems
•	We need more data
•	We should include the knowledge and views of the public
•	Better communication
I would argue that whilst these are adequate suggestions they are not novel and it is here that the paper looses its imperative. They are very focused on an ecology-centric view that ‘if we have more/better data and we tell people the facts – they will make better decisions’. This viewpoint has only taken us so far and is now failing. Some suggestions:
We need a ‘systems response’ across agencies to the sharing of data, information and experiences – towards a common goal
We need to identify the indicators that link ecological to social and economic systems
We need standardised, scalable data. Not Data rich – information Poor (DRIP) data. We have lots of data! Not all of it is usable – targeted- relevant.
We need to communicate in a relevant way. Information does not =behaviour change. What do we need to communicate?
Much of the literature for this can be found in the outputs for the Defra Marine Pioneer and the Natural Capital Committee outputs. Also see
Johnson, D.E., Rees, S.E., Diz, D., Jones,P.J.S., Roberts, C., Barrio Froján, C. 2018. Securing effective and equitable coverage of Marine Protected Areas: an overview of global efforts by the Convention on Biological Diversity and analysis of national efforts on behalf of the United Kingdom" Accepted Aquatic Conservation: Marine and Freshwater Ecosystems.
Diz, D., Johnson, D., Ridell, M., Rees, S., Battle, J., Gjerde, K., Hennige,S., Roberts, M. 2018. Mainstreaming Marine Biodiversity into the SDGs: The Role of Other Effective Area-Based Conservation Measures (SDG 14.5). Marine Policy Special Issue SDG Synergies for Sustainable Fisheries and Poverty Alleviation. Volume 93 251-261.
Rees, S.E., Foster, N.L., Langmead, O., Griffiths, C., Fletcher, S., Pittman, S., Johnson, D. Attrill, M.J. 2018. Bridging the divide: A framework for social-ecological coherence in Marine Protected Area network design. Aquatic Conservation: Marine and Freshwater Ecosystems. 28(3): 754-763.
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: THE AICHI BIODIVERSITY TARGETS: ACHIEVEMENTS FOR MARINE CONSERVATION AND PRIORITIES BEYOND 2020
Review round: 1
Reviewer: 3

Output:
Basic reporting: This article is a nice review of some of the Aichi targets including 6, 11, 15, and 19 and it is worth publishing after a very major revision by the authors. The Abstract lacks information about how this study was designed, and why? adding that this paper was part of the mentoring program in WCMB is recommended also.
The Introduction is not will-written and the structure of the most sentences do not make sense. It also lacks the knowledge gap part, and what this review brings to science and helps to achieve the targets in a longer time.
The article has to go through a very careful English-proofread, at the moment, sentences are very long, and many sentences do not make sense and are confusing.
The authours did a good job for the literature review, but there are some areas such as deep-sea biodiversity that still many citations are missing. Regarding the Perspectives, authours have some perspectives that they have never reviewed in the review part. So, I recommend either removing those perspectives from the list or adequately review them in the review part. For example, climate change effects on marine biodiversity, deep sea, citizen science, and so on.
There are some general comments for the authors, but also the Reference list needs to be revise as many citations do not follow the same citation style.
Experimental design: This does not apply here as this is a review paper.
Validity of the findings: This does not apply here as this is a review paper.
Additional comments: Abstract
It worth mentioning that this paper is part of the WCMB mentoring program
Introduction
In general, the Introduction is very poorly written, both in English and contents. The authors should design their Introduction. In my opinion, a clear statement of why this review has been done, what is the knowledge gap, is missing. However, they briefly mentioned some background information.
Line 43. Add “WCMB” after World Conference on Marine Biodiversity
Line 44 - 45. This paper is a part of the mentoring program held in the World Conference on Marine Biodiversity 2018 (WCMB) in Montreal, Canada which aimed at connecting early-career scientists and senior scientists from across the globe”.
Line 45 to 50- needs revisions, the sentence is very long and unclear, hard to understand.
Line 52, add a comma after “.. November 2018”.
Line 52 to 55, need to be rephrased.
Line 66- add a semicolon before “however”
Review
Line 120- please add a reference
Line 124- what do you mean by “wide environment”
Line 134- move the reference to the end of the sentence
Lines 137 to 139- can you give an example here?
Line 145 – change “flexible, adaptive recovery to “flexible and adaptive recovery”
Line 158- mention the target number
Line 158 to 160 – please rephrase, grammar!
Line 172, add “for example” at the end of the sentence
Line 178, add a “comma” after for example
Line 188 – 189 Where is this happening or planned to happen? “The recent trend towards establishing very large MPAs (greater than 100,000 km2) is accelerating the expansion of their global coverage.”
Line 202 to 206 – Please revise this sentence, grammar.
Line 201 – what do you mean by “effectiveness”, you mean effectiveness of establishing MPA?
Line 240 – 241- Reference?
Line 250 – add the scientific name of the coral after “one coral species”.
Line 257 to 263 – Please rewrite, the sentence is very long and confusing.
Line 281 – Change “being in the USA” with “were in the US”
Line 292 – “but filling these knowledge gaps has become a priority” what are you trying to say here?
Line 300- which habitats?
Line 308- references?
Line 332- remove “that,”
Perspectives
Line 359 – but you have not reviewed the deep-sea except in some minor examples, I would thus recommend the authors to spend a bit more time on collecting literature review from the deep sea and how the targets 6, 11, 15, and 19 have been studied in the deep sea. You can have a look into another paper published from the same mentoring program and cite it, and also look for the literature they have used, you might find them useful (Saeedi, H., Reimer, J. D., Brandt, M. I., Dumais, P. O., Jażdżewska, A. M., Jeffery, N. W., … Costello, M. J. (2019). Global marine biodiversity in the context of achieving the Aichi Targets: ways forward and addressing data gaps. PeerJ, 7, e7221. doi:10.7717/peerj.7221).
Lines 402 to 412 – it might be useful to add some example where citizen science was successful and how it helped the biodiversity maintenance
Line 433 to 443- I see here a lack of references and data repositories such as OBIS and GBIF examples, you should review how these efforts have been done in the past and what are your suggestions to improve them.


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 AICHI BIODIVERSITY TARGETS: ACHIEVEMENTS FOR MARINE CONSERVATION AND PRIORITIES BEYOND 2020
Review round: 2
Reviewer: 1

Output:
Basic reporting: The paper now has been sufficiently revised based on the comments of the referees. This is a review paper based on a mentoring plan in WCMB to review the Aichi targets. The authors chose 4 Aichi targets and reviewed them. The authors finally identified the key priorities that must be addressed for better ocean management.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Please go through the paper one more time and try to revise the English and also the grammar. I started doing this just as an example for the first paragraph. there are many sentences that are not grammatically correct. The authors are not consistent in using the connecting words. For example, one time there is a comma before 'however' and one time a semicolon.


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: SYNOPTIC REVISION OF THE FERN GENUS ELAPHOGLOSSUM SCHOTT EX J.SM. (DRYOPTERIDACEAE) IN MADAGASCAR, WITH THE DESCRIPTION OF 23 NEW TAXA, ALL BUT ONE ENDEMIC
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In the following, I present my review on the manuscript "Synoptic revision of the fern genus Elaphoglossum Schott ex J.Sm. (Dryopteridaceae) in Madagascar, with the description of 23 new taxa, all but one endemic", authored by Dr. Germinal Rouhan.

The manuscript presents a treatment for 55 species from Madagascar, almost half of the newly described in this work. It is an excellent contribution to the Flora of Madagascar and adds valuable information to the genus' diversity as well. The manuscript is well written, and the new species are described following the rules of the International Code of Botanical Nomenclature. The author did a great job illustrating the morphology of new taxa, as well as their distribution in Madagascar. I have made all my suggestions in the manuscript, marked as track changes. Some aspects that I judge more critical I highlight below:

Abstract
1-	Some changes in the abstract could make it easier for the readers to capture the main points of your manuscript (see my suggestions in the marked pdf.).
2-	Still in the abstract, it is said that "six novel dichotomous keys are proposed...". I found only four keys – two of them were combined into a single one. Please, revise.
Introduction
3-	The reference for the Leipzig Catalogue of Vascular Plants is missing.
4-	Lines 86-87: Please, check the correct citation for those references.
5-	Line 92: I suggest changing the sentence "The taxonomy of Elaphoglossum is challenging because the genus is distinctive but, at first sight..." by something like "Although the genus is readily distinguished among the ferns, most of its species are morphologically uniform and difficult to distinguish."
6-	Lines 101-104. I think you could also cite here Vasco et al. (2009) on section Lepidoglossa, and Matos et al. (2019) on Section Polytrichia.
Material and Methods
7-	In the distribution maps, there are dots with distinct colors, some are solids, and some are not. Could you explain what they are? I also think this explanation should be included in the captions, for the ease of understanding.
Keys
8-	I suggest using a "noun-adjective" format, as done for other couplets in the key. For example, in couplet 1, I would replace the sentence "... inconspicuously reduced scales (< 0.5 mm in diam.), arachnoid, scattered, dark brown to black..." by "but with scales that are inconspicuous, reduced (...), arachnoid, ... "and so on.
9-	Couplet 2a: I suggest replacing "Frond scales" with "Laminar scales." This is how it is described for all species.
10-	As for the subulate scales, I suggest describing them as "hairlike or conical, with its margins inrolled for most of their length."
11-	Couplet 2b: I noticed that in some descriptions, like in Elaphoglossum ambrense, there is no mention of whether the scales are subulate or not. I think it is essential to mention in the description of any character that has been used in the key, even if it is missing in a particular species.
12-	I do not understand why the sections I and II were combined into a single key. Is there a particular reason for that? If so, I suggest it be explained what the reason to combine them (as you did for Sections III and IV, lines 270-271) is.
Descriptions and comments
13-	I think the figures need to be cited in more detail. Could you cite the particular figures (e.g., Fig. 1 A) in the diagnosis you provided, or in the descriptions? This would render the figure citation more precise and accessible to the readers.
14-	As for the Holotypes in Paris, I suggest citing them as "holotype: P [P00749250]". I think it is important to keep the Herbarium acronym just as "P", and mention the barcode number between brackets.
15-	In the descriptions, I would start mentioning the habit for each species.
16-	Please, cite the maps right after your comment on "Habitat and Distribution."
17-	In several instances, there are Isotypes in other Herbaria. Could you provide the barcodes for those specimens as well?
18-	When you provide the diagnosis for your new taxa, sometimes you compare them with other similar species. In this case, it is important to mention not only the characters of the new species but also of the species that you are comparing it to. For instance, in the diagnosis for Elaphoglossum brachymischum you compare it to E. pseudovillosum and say that "Elaphoglossum brachymischum clearly differs by short-petiolate fronds, rhizome scales clearer, shorter and narrower, laminae thinner and herbaceous, and laminar scales with several long, ciliform, marginal appendages above the base." Please, include here how these characters are in E. pseudovillosum as well.
19-	Elaphoglossum sabineanum: It is just a suggestion, but why not call it E. sabineae?

Figures:
20-	Please, check whether all the letters in the figure captions are in parenthesis.
21-	Remember to include in the captions an explanation of why the dots are different on the same map.


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: SYNOPTIC REVISION OF THE FERN GENUS ELAPHOGLOSSUM SCHOTT EX J.SM. (DRYOPTERIDACEAE) IN MADAGASCAR, WITH THE DESCRIPTION OF 23 NEW TAXA, ALL BUT ONE ENDEMIC
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript “Synoptic revision of the fern genus Elaphoglossum Schott ex J.Sm. (Dryopteridaceae) in Madagascar, with the description of 23 new taxa, all but one endemic” is a much needed addition to the taxonomy of one of the most complicated fern genus. Elaphoglossum, with more than 600 species, is one of the most complex taxonomically and less studied fern genera. The revision is built on accumulated knowledge of an authority in the group, in a very diverse and understudied area.

The figures are excellent, with images illustrating well all the relevant characters for species recognition in the genus. They are high quality images, well displayed and labelled.
The keys are overall very good, although I suggest making separate keys to each section. A few issues listed below:
In the key to the sections (ln 232), It would be better, if possible, to put a couplet to separate Elaphoglossum section Elaphoglossum and E. section Squamipedia;
In the key to section Polytrichia and Setosa (ln 252): to make this step comparable with the opposing one in the couplet, describe in which parts of the plant these scales occur.
Other minor comments about the keys were made in the file
Regarding the descriptions, they are well standardized, very objective, and well-written. The only information that is not consistent throughout species descriptions is about sporangia. I also think it would be relevant to describe and illustrate the spores of the newly described species, the only information I believe is missing in the description. Although not mandatory, for the subspecies, I think a short description in addition to the diagnosis should be provided. Some suggestions were made in a few species diagnoses. For Elaphoglossum repandum, the diagnosis, which is mandatory, is missing.
Experimental design: As a taxonomic paper describing new taxa, the manuscript question is well-defined, with appropriately described methods
Validity of the findings: The description of so many new taxa, most of them endemic to Madagascar, is a major step in helping preserving plant diversity in a biodiversity hotspot. The keys also are essential to help identify and catalogue the diversity.
Additional comments: The manuscript is well-written, and I have made overall small suggestions or corrections, but I would like to point out I am not a native speaker. The literature cited is well referenced and relevant for the manuscript. Other general minor issues are highlighted below:
Ln 76: There are six numbers but only seven listed sources.
Ln 106: I think this should rephrased to be more assertive. Based on the currently known richness, it either is or isn’t the second center or diversity
Ln 107: Maybe state here how many or which fraction of overall described species occur in Madagascar
Ln 157: QGis reference missing here
Lns 159-160: I recommend this information to be inserted in the maps as a legend
Ln 184: It is not clear what the author meant here, I suggest rephrasing
Ln 197: It is interesting to present here also the number of endemic species
Ln 607: Since it’s the diagnosis, even if it gets redundant, it would be interesting to cite those species here
Ln 564: I do not know political geography of Madagascar, so I highlighted here for the author to check if it’s not erroneously repeated
Ln 569: Maybe “makes” it’s a more appropriate verb here
Ln 770: I believe “similar to” could be more appropriate for the diagnosis
Ln 893: I think this is not a very useful information for the diagnosis


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: EFFECT OF A HIIT PROTOCOL ON THE LOWER LIMB MUSCLE POWER, ANKLE DORSIFLEXION AND DYNAMIC BALANCE IN A SEDENTARY TYPE 1 DIABETES MELLITUS POPULATION: A PILOT STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript aimed to investigate the effects of 6-week high-intensity interval training protocol on lower limb strength, ankle dorsiflexion range of motion and dynamic balance in an inactive T1DM population.
The present topic is new, interesting and relevant for the scientific knowledge, concretely for the readers of PeerJ, since the present results show that a 6-week HIIT program is safe and effective to improve execution velocity in squat movement which is a fundamental skill in daily living activities, as well as ankle dorsiflexion range of motion and dynamic balance to reduce foot ulcers, risk falls and functional impairments.
The authors used a correct English language but it needs to be slightly improved. There are some confusing words, and expression that avoid me to well understand specific answers. I consider that a revision performed by a native English speaker would increase the comprehension of many ideas.
I commend the authors for attaching the raw data.
Experimental design: The authors have met the manuscript structure following PeerJ author guidelines. The methods are correctly explained. Moreover, figures and tables are generally adequate and relevant.
Validity of the findings: The results are robust and support the main conclusion of the manuscript.
Additional comments: This manuscript aimed to investigate the effects of 6-week high-intensity interval training protocol on lower limb strength, ankle dorsiflexion range of motion and dynamic balance in an inactive T1DM population.
The present topic is new, interesting and relevant for the scientific knowledge, concretely for the readers of PeerJ, since the present results show that a 6-week HIIT program is safe and effective to improve execution velocity in squat movement which is a fundamental skill in daily living activities, as well as ankle dorsiflexion range of motion and dynamic balance to reduce foot ulcers, risk falls and functional impairments.
The authors used a correct English language but it needs to be slightly improved. There are some confusing words, and expression that avoid me to well understand specific answers. I consider that a revision performed by a native English speaker would increase the comprehension of many ideas.
The authors have met the manuscript structure following PeerJ author guidelines. Moreover, figures and tables are generally adequate and relevant. The results are robust and support the main conclusion of the manuscript.
Although the manuscript has a high scientific merit and accuracy, minor issues can be addressed to improve the quality and comprehensibility before its publication:
•	Some statements in the introduction section should be supported by references (see lines 51 or 56 among others).
•	Did the authors perform power analysis to determine sample size before the beginning of the study?
•	The authors mentioned that the participants were instructed not to change their nutritional habits and not to perform any regular exercise program out of the study. However, were these variables experimentally controlled?
•	Did the author control the physical activity levels of the participants before the exercise test? This fact could influence data collection.
•	The authors reported that they measured VO2max but they have not reported data of cardiorespiratory fitness after the intervention. I suggest them to include these data.
•	This reviewer recommend that the authors would include a paragraph discussing why a HIIT training program (which is usually applied to improve cardiorespiratory outcomes) is a valid tool to increase muscular strength. Which physiological mechanism are involved in this process?
•	Finally, a specific paragraph including the practical implications of the study’ findings would be acknowledged.


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: EFFECT OF A HIIT PROTOCOL ON THE LOWER LIMB MUSCLE POWER, ANKLE DORSIFLEXION AND DYNAMIC BALANCE IN A SEDENTARY TYPE 1 DIABETES MELLITUS POPULATION: A PILOT STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The reporting of the manuscript is understood, but there are some issues with the use of English language which would be assisted by having a person native to English language proof-read. Mostly the arguments are logical and appropriately referenced.

Within the discussion, there is some re-stating of results. It would be better to summarise the result in the discussion rather than directly re-stating it. There is no need to present data or p values in the discussion.

While the tables are appropriate, they could easily be combined into a single table.

Some more baseline data about the participants are required to better understand the context of the results and assist with interpretation. For example, duration of diagnosis, medications that participants were taking, exercise/physical activity being completed, etc. VO2peak is reported to be measured but has not been reported, it should be.
Experimental design: An appropriate experimental design was implemented, but it is unclear how the sample size was determined. Some reporting on sample size calculation should be included.

The methods are appropriately described but would benefit by some reporting of the variability of measurement, particularly when multiple measures were conducted (e.g. coefficient of variation).

To ensure full reporting and interpretation of the data, it would be useful to include some of the training data to verify that participants complied with the exercise prescription.

The authors claim to measure muscle strength, however the assessments conducted are probably more reflective of muscle power. Suggest changing all reference of muscle strength to muscle power.
Validity of the findings: The findings appear to be valid and mostly based on reported data. Claims of safety of the exercise intervention need to be better supported by well defined data presented in the results.
The discussion is appropriate and proposes more questions and hypotheses. However, the conclusion contains too much speculation and/or unsupported claims. Adding some of the identified data would partially mitigate this.
Additional comments: Line 55 – “endogen” should be ‘endogenous’
Line 69 – which counterparts?
Line 69/70 – Which population?
Line 79 – “dead” should be ‘death’
Line 95 – is “XX” meant to be 20th or something different?
Lines 343-345 - if this is an important finding, there needs to be something reported in the results about this. The remainder of this paragraph is reported more like results than discussion.
Lines 369-370 – better to summarise the result rather than re-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: EFFECT OF A HIIT PROTOCOL ON THE LOWER LIMB MUSCLE POWER, ANKLE DORSIFLEXION AND DYNAMIC BALANCE IN A SEDENTARY TYPE 1 DIABETES MELLITUS POPULATION: A PILOT STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have correctly answered all my concerns.
Experimental design: The authors have correctly answered all my concerns.
Validity of the findings: The authors have correctly answered all my concerns.
Additional comments: The authors have correctly answered all my concerns.


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: EFFECT OF A HIIT PROTOCOL ON THE LOWER LIMB MUSCLE POWER, ANKLE DORSIFLEXION AND DYNAMIC BALANCE IN A SEDENTARY TYPE 1 DIABETES MELLITUS POPULATION: A PILOT STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: The writing is much better following an English language review, however there are still some minor issues. Throughout the manuscripts, there are still regular references to muscle strength as an outcome of this study, when the authors have really measured muscle power outcomes rather than strength. Please read through the manuscript carefully and change.
Experimental design: From the authors response, I understand that as sample size of 11 was predicted to be required. This information has not been included in the manuscript but it should be. The authors should also identify what data they used to estimate the sample size.
Validity of the findings: Information pertaining to adverse events and safety has now been included to support statements, but these findings should be outlined in the results, before being explored in the discussion, not just simply reported in the discussion.

This prompted a closer look at the statistical analyses and results. The authors have indicated that they performed a mixed factorial ANOVA to assess the influence of condition and time, but the results have not been presented that way. From the results, it appears that separate pre-post (potentially t-tests) have been conducted for each group, so it is not clear if there was or was not any influence of condition. The authors should clarify the reporting of results. Particularly as the effect sizes and their (assume 95%) confidence intervals tend to indicate potentially trivial findings.
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: EFFECT OF A HIIT PROTOCOL ON THE LOWER LIMB MUSCLE POWER, ANKLE DORSIFLEXION AND DYNAMIC BALANCE IN A SEDENTARY TYPE 1 DIABETES MELLITUS POPULATION: A PILOT STUDY
Review round: 3
Reviewer: 1

Output:
Basic reporting: The authors have appropriately addressed all of the reviewers comments and the manuscript is acceptable for publication in my opinion.
Experimental design: No additional comment
Validity of the findings: No additional comment
Additional comments: No additional comments


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

Input:
Title: FULL-LENGTH GENOME CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF SARS-COV-2 VIRUS STRAINS FROM YOGYAKARTA AND CENTRAL JAVA, INDONESIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this paper, entitled "Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Indonesia", Gunadi et al. reported new 4 whole genome sequences of SARS-CoV-2 from patients in Yogyakarta region, Indonesia, in addition to the 60 other full sequences from Indonesia that have already been deposited in GISAID. This work may pioneer the full genome analysis reports of SARS-CoV-2 in Indonesia. While I appreciate this paper, I have a number of important comments/suggestions, and questions to the authors.

1. The lack of details on the bioinformatics analysis related to the read mapping and SNP calling is concerning:
a) In line 219, the authors mentioned the use of "BWA or Bowtie" sequence alignment methods. Can the authors elaborate further? Which program did the authors actually use? Were both used? In which manner? Or was just one algorithm used?
b) The base calling program/algorithm was not written in the Methods. I suggest to add information related to this matter, including the calling parameters and thresholds, and whether all SNPs called satisfied the thresholds.
c) What is the mean coverage of each sequence reported here?

2. The focus of this paper is to report the full genome of SARS-CoV-2 in Yogyakarta and its characterization. However, majority of the Results section is about patients' information (Case 1 - 4) in a great detail, which deviates from the focus itself. I suggest to put the patient's information as Supplementary Materials, and instead, develop more on the genetic analysis results in the Main Text.

3. In Figure 3 (Phylogenetic Tree analysis),
a) what is the length unit of the tree?
b) I suggest rooting the tree, to be able to observe the ancestrality.

4. In line 228, the authors claimed that there is an increase of clade GH detection since April 2020 until now. In the sense that the samples sequenced are only 0.02% of all confirmed cases in Indonesia (60/290000), and with the current rate of 4000 new confirmed cases perday, 60+4 samples (over the range of collection date between March-September) cannot robustly conclude about epidemiological pattern (eg. increase vs. decrease of frequency) of a particular clade in indonesia.

5. In line 264, the authors miscited reference number 10 (Dearlove et al. 2020; PNAS). Dearlove et al. mentioned the founder event in Europe, but not globally (see Dearlove et al.'s Figure 2 caption). Meanwhile the global spread of the D614G mutation is more likely due to positive selection (see Korber et al. 2020; Cell).

6. In line 273, the authors' mentioned the correlation between the severity of the cases vs. the 614G mutation pattern, based ONLY on 4 individuals. Furthermore, severity is caused by multi-factors, including host immunity, treatment, etc. that were not considered here. The authors must clearly mention the caveat, or completely remove the sentence.

7. Reference number 12 (Lorenzo-Redondo et al. 2020) was never cited in the Main Text.


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: FULL-LENGTH GENOME CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF SARS-COV-2 VIRUS STRAINS FROM YOGYAKARTA AND CENTRAL JAVA, INDONESIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The Introduction and basic support are not enough.
Experimental design: No comment, I have add in the comments to the authors.
Validity of the findings: If the authors analyzed only 4 genomes, The findings is not enough for publication.
Additional comments: The authors reported and described the four full-length genome sequences of SARS-CoV-2 characterization and compared them with the previous genome in Indonesia from the GISAID. The SARS-CoV-2 with D614G mutation has been the significant circulating strain worldwide since March 2020. We now have the whole genome of more than 10,000 genomes worldwide in GISAID. The analysis of the data should be reanalyzed with the other whole genome in Indonesia. The title should be changed. If you analyze only your four genomes; there is not enough scientific significance for publication. I would suggest you reanalyze all of them in Indonesia with more information on location, date collection and etc.

I have some comments about your MS in this study as follows

Introduction

1. The introductions needed to be more detailed. The authors should explain more about the clinical epidemiology of COVID-19 in Indonesia, for example, How was the first case identified, the peak of transmission, diagnostic tests, public health interventions, etc.
2. Please add a reference (s) at the end of the sentence in Line 98 and 100.
3. Spelling mistakes: sydromecoronavirus
4. Your aim to compare with the other whole genome sequence in Indonesia, but you did not do the molecular characterization for them.

Methods
1. Criteria to select these 4 cases to perform NGS?
2.The authors should describe the clinical criteria of mild, moderate and severe cases of COVID-19

Results
1. The reported 4 cases can be summarized in table 1. The results of point mutations with the other whole genome of Indonesia can be described to see the whole picture of Indonesian strains. Table 1. In the manuscript, the explanation for “Lineage B.1.36 and B” in table 1 is missing.

1. Line 180. what is the full name of NLR.
- (Page 9, line 112). Give manufacturer, city, country for VTM and all the products or reagents should be company, city, country except the USA use the only abbreviation of the state.
- (Page 10, line 141). Why not maximum likelihood?

2. Fig 1 does not provide additional information and justify why you want to show the photos of a circular map of four SARS-CoV-2 genomes; they do not show anything new about the genome, except maybe the presence of the original genome, but even that has already been published for other papers. The authors should consider removing it
2. Clade distribution (Fig 2). The authors should define the unit on the y-axis. Is it percent or number of persons?

Discussion
1.Line 274-276, the authors should discuss in more detail about the mutations of SARS-CoV-2 and clinical severity, especially the part when the authors compare this study's sample size with other studies.
2.(Page 13, line 254-256). If you are making a statement about the increase of GH clade in North America and Africa, please add at least one reference from America or Africa.
3.This paper lacks a statement of the major limitations of the findings before the concluding paragraph.


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: FULL-LENGTH GENOME CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF SARS-COV-2 VIRUS STRAINS FROM YOGYAKARTA AND CENTRAL JAVA, INDONESIA
Review round: 1
Reviewer: 3

Output:
Basic reporting: The study basically reported 4 SARS-CoV-2 genome sequences originating from Yogyakarta, Indonesia. The authors also analyzed global as well as other Indonesian sequence entries.

English is relatively understandable with a few require more clarity and grammatical corrections:
1. What is NLR: Neutrophil-to-Lymphocyte Ratio? Please also check for other unexplained abbreviations.
2. Line 98 in Introduction mentioned an vague expression "major frequency"? Does this mean "most frequently detected"? This statement needs to be more substantiated. How many percent?
3. Line 204-205 should read "He experienced..."

Background is succinct and sufficient. Raw data was not needed because specific accession IDs were given to the database.

Suggestions on figures/tables:
1. Figure 2 is rather confusing. Please explain that D614G mutation is carried by all G clades (G, GH and GR). Does the Y-axis represent percentage or number of genomes?
2. In Table 2, does ID refer to GISAID Accession ID?
Experimental design: The manuscript reported original research within the aims and scope of the journal. Research question as reflected in the objectives should focus on viral genome characteristics in Indonesia, both among different areas and with other countries. There are additional requirements to investigation:
Ethical standard was fulfilled.

There are concerns with regards to methodology:

1. It was not explained why only these 88 genomes were selected, while presumably sequences of all genomes were available. Were the Indonesian sequences all that were submitted as per the retrieval date? My current quick search with GISAID gave 111 sequence entries from Indonesia. I think it is only reasonable to conclude on Indonesian mutation situation based on analyses of all sequences submitted from the country. Besides, I am not sure how much sequences from global entries will add value to this study, except all were analyzed. If analyzing global sequence entries is not possible, perhaps better to focus on providing and analyzing (all) Indonesian sequence data.

2. The biggest concern regarding D614G is that the mutation leads to quicker transmission. I think having more detail patient information leading to this information (especially those reported by the manuscript, as specified in Table 1) will add value to the manuscript: epidemiological tracing data upon detection (how far, how fast), what is the size of the cluster where the patient belongs, how is the transmission pattern of the cluster.
Validity of the findings: I find it difficult to comment on this because of the first concern in methodology. There was unfocused data for analyses. Why these 88? Why only selected Indonesian entries?
Additional comments: I commend efforts by the authors' group for their success in obtaining the viral sequence, analyzing and reporting the data. Few more works are required before the manuscript can be published.


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

Input:
Title: FULL-LENGTH GENOME CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF SARS-COV-2 VIRUS STRAINS FROM YOGYAKARTA AND CENTRAL JAVA, INDONESIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I thank the authors for addressing my comments in previous submission. However there are a couple of (minor) points that still need to be clarified:

1. I'm not familiar with UGENE, but the variant calling parameters and thresholds are still not specified in this revised manuscript. However considering the average depth is high, I am assuming the variants called are correct.

2. The tree unit is still not described. What does "0.0001" mean in the tree scale? What is the unit of that scale?

3. I noticed inconsistencies in the current Figure 1 (previously Figure 2): the "clade distribution of SARS-CoV-2 genomes in Indonesia ...".
	a) the shapes are ambiguous when overlapped, they become indistinguishable. I think It's better to have the graph in color rather than in shapes for this particular case.
	b) many numbers are inconsistent between the two figures.
		b1) in prev Figure, in August, clade GH is at 3, while in the revised Figure, it is at 4. The inconsistency persists in clade GH in September.
		b2) clade GR distribution is *very* different between the two figures.
		b3) similarly, clade L distribution is also inconsistent


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: FULL-LENGTH GENOME CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF SARS-COV-2 VIRUS STRAINS FROM YOGYAKARTA AND CENTRAL JAVA, INDONESIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: Ok. No further comments
Experimental design: Ok. No further comments
Validity of the findings: Limitations were mentioned. No further comments
Additional comments: No further 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: ESTIMATING SALT CONTENT OF VEGETATED SOIL AT DIFFERENT DEPTHS WITH SENTINEL-2 DATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Clear english style
Experimental design: original paper
Validity of the findings: the models were sound and statistically validated
Additional comments: In the present study, the authors have applied and compared four machines learning models namely,   back propagation neural network (BPNN), support vector machine (SVM), extreme learning machine (ELM) and random forest (RF), for predicting soil salt content (SSC) measured at five different depth: (0~20 cm, 20~40 cm, 40~60 cm, 0~40 cm, and 0~60 cm) in the vegetated area. One of the novelties of the present paper is that, the authors reported that predicting SSC at vegetated area is rarely reported in the literature. For developing the models, the authors have used 12 bands and 32 spectral indices based on the Sentinel-2 (Sentinel-2A and 2B) data, as predictor (i.e., independent variables). In addition, the inversion capability of the models was investigated. In total, 117 soil samples were collected from Jiefangzha Irrigation Area (JIA), Inner Mongolia, China. Several well-known performances metrics were used for testing the capabilities of the models: the adjusted (R2), root mean square error (RMSE) and mean absolute error (MAE).

This is an interesting paper, well written and well-structured with a solid scientific research objective, constituting this way an excellent starting point of research paper. The paper needs only fewer amendments before to be accepted.

1.	The introduction should be slightly amended. At the end of the line 102, provide a review of machines learning (ELM, SVM, RF and BPNN) applied in many area of water resources management, for example, for modeling water quality, i.e., water temperature, dissolved oxygen, and for many agricultural application  (modeling of salinity, ET0…).
2.	Provide the scatterplot of measured and calculated SSC using the best four machine learning models.
3.	Improve the theoretical description of the machines learning models, and as possible provide a figure for each model.
4.	Provide a flowchart of the proposed methodology.


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: ESTIMATING SALT CONTENT OF VEGETATED SOIL AT DIFFERENT DEPTHS WITH SENTINEL-2 DATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Review of manuscript 51893, entitled “Estimating salt content of vegetated soil at different depths with Sentinel-2 data” by Y. Chen, Y. Qiu, Z. Zhang, J. Zhang, C. Chen, J. Han, and D. Liu.
This study presents four different machine learning methods for assessing soil salinity in Hetao, China, based on remote sensing data from the Sentinel-2 sensor. The topic certainly merits authors attention as soil salinity is one of the major soil degradation processes in the world. However, authors need to better explain how their study compares with research carried out on other places. They have missed some important references. They have also to improve the level of language used in the text. My suggestion is thus that the paper be sent for major revision.
General comments:
1. The language level needs to be improved. Besides proofreading by a native English speaker, authors need to review the vocabulary sometimes used as it is inadequate for a scientific paper. See L133 as an example where the term “nothing” was used instead of “bare soil”.
2. The introduction section needs to be improved by presenting the different methodologies used for salinity assessment via remote sensing (see comments below).
3. There is a general use of acronyms along the text without explaining their meaning. This needs to be corrected.
Specific comments:
L79-89: More important than referring the different satellites used, authors should focus on the methods and assumptions behind the studies cited here. They are quite different. Authors should also refer to the studies conducted by Lobell et al. (2010), Wu et al. (2014), and Scudiero et al. (2014), which constitute important references in this topic. Additionally, they should consider Ramos et al. (2020) as a first example where Sentinel-2 data was used to assess soil salinity.
L83: Authors should explain what they mean by inversion modelling somewhere in the text.
L88: Some of the advantages of Sentinel-2 are yet to be seen. Spatial resolution seems valid. About temporal resolution not so clear since only multi-year data has been considered so far in salinity assessment studies using Sentinel-2 data. Finally, the spectral offer is vast but only the bands in the visible and NIR range have proven to be related to salinity data. These are offered by most satellite platforms.
L94: Authors need to give the meaning of these acronyms. Also, for L107.
L97-99. This is not true. See Ramos et al. (2020) where Sentinel-2 data was used to assess rootzone salinity.
L127-128: Why is this relevant for a scientific paper?
L128-129: Bui and Henderson (2003) apparently worked in Queensland, Australia. How conditions and practices there relate to your region? This citation makes no sense.
L147: Please briefly explain how this formula was developed. Was that study conducted in Hetao?
L158: Each Sentinel-2 satellite may have a revisiting period of 10 days, but combined that period shortens to 5 days. That should be emphasised instead of the 10 days.
L161: Authors should limit themselves to the bands used in this study. For sure, bands 1, 9 and 10 were not used for salinity assessment.
L166-168: As far as I am aware, the Copernicus Hub already provides the 2019 Sentinel-2 data as a Level-2A product. This step could likely have been skipped.
L168-169: Please elaborate further on the resampling technique used.
L177: Please explain cleared what a “soil line” is. I’m not sure if I understood it.
L178: All acronyms should be given in full the first time they are used in the text.
L210-253: What does BPNN, SVM, ELM, and RF stand for?
L418-419: High SSC can increase the osmotic stress, not water stress. These are different processes. Please correct.
References used:
Lobell, D.B., Lesch, S.M., Corwin, D.L., Ulmer, M.G., Anderson, K.A., Potts, D.J., Doolittle, J.A., Matos, M.R., Baltes, M.J., 2010. Regional-scale assessment of soil salinity in the Red River Valley using multi-year MODIS EVI and NDVI. J. Environ. Qual. 39 (1), 35–41. https://doi.org/10.2134/jeq2009.0140
Ramos, T.B., Castanheira, N., Oliveira, A.R., Paz, A.M., Darouich, H., Simionesei, L., Farzamian, M., Gonçalves, M.C., 2020. Soil salinity assessment using vegetation indices derived from Sentinel-2 multispectral data. Application to Lezíria Gande, Portugal. Agric. Water Manag. 241, 106387, https://doi.org/10.1016/j.agwat.2020.106387
Scudiero, E., Skaggs, T.H., Corwin, D.L., 2014a. Regional scale soil salinity evaluation using landsat 7, western San Joaquin Valley, California USA. Geoderma Reg. 2–3, 82–90. https://doi.org/10.1016/j.geodrs.2014.10.004
Wu, W., Al-Shafie, W., Mhaimeed, A., Ziadat, F., Nangia, V., Payne, W., 2014. Soil salinity mapping by multiscale remote sensing in Mesopotamia. Iraq. IEEE J. Sel. Top. Appl. 7, 4442–4452. https://doi.org/10.1109/jstars.2014.2360411


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: ESTIMATING SALT CONTENT OF VEGETATED SOIL AT DIFFERENT DEPTHS WITH SENTINEL-2 DATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I believe authors have addressed my previous comments in a satisfactory way and that the paper can be now accepted for publication.


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

Input:
Title: SEVOFLURANE PRECONDITIONING ATTENUATES HYPOXIA/REOXYGENATION INJURY OF H9C2 CARDIOMYOCYTES BY ACTIVATION OF THE HIF-1/PDK-1 PATHWAY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript needs to be edited by a reader with an eye towards grammar and English language usage - the science is sound, but it is not well conveyed in English. That said, this is a straightforward manuscript, with a clear hypothesis supported by experiments described.
Experimental design: The experiments are well designed. The controls are appropriate, and the use of multiple endpoints to evaluate cell survival strengthens the conclusions. H9c2s are a limited but appropriate model. The methods are very thorough.
Validity of the findings: The data is provided, and findings are valid, with the caveat that the interpretation of the findings is at times a bit too broad. In particular, H9c2s, although derived from rat cardiomyocytes, are metabolically distinct from primary cardiomyocytes. While this is noted in the limitations, at times in the rest of the manuscript this distinction is blurred (for example, the title should clarify that H9c2 cells are used). Also, the authors should be careful to note the data provided do not demonstrate that SEV-induced upregulation of glycolysis via HIF1a is responsible for the difference in survival rate. HIF blockade may protect cells, and a side effect may be that it upregulates glycolysis.
Additional comments: 1.	The introduction is overly descriptive and may be shortened.  For example, it is not relevant to mention the Nobel Prize in lines 42-44, or the origin of glycolysis studies in yeast in lines 50-51.
2.	How is final O2 (listed as <1%, I believe) measured, and controlled during hypoxia?
3.	Fig 1 – please change the length of the bars to better reflect the duration (i.e. 15 min should be 1/12th the length of the 3 hr incubations. The 48 hr equilibration should be a split bar etc.) Also, please label T1 and T2 here for reference to Fig 3
4.	Please clarify that the Fig 2 flow diagrams are annexin – labeled
5.	Fig 2E: the Bax represenative blot looks overexposed, as well as the blots in Figure 5B. Please choose a less-exposed blot for these images.
6.	Figure 4: please state what red and green represent.
7.	Discussion may be streamlined (for example, it is not necessary to state that ATP is called the energy currency of the cells, lines 247-248).
8.	Discussion (lines 248-259) should clarify that while glucose oxidation occurs to produce ATP, fatty acid oxidation is the main source of ATP in the heart


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: SEVOFLURANE PRECONDITIONING ATTENUATES HYPOXIA/REOXYGENATION INJURY OF H9C2 CARDIOMYOCYTES BY ACTIVATION OF THE HIF-1/PDK-1 PATHWAY
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The manuscript by Tianliang Hou et al. describes an interesting phenomenon that provides mechanistic information for myocardial protective effects of Sevoflurane preconditioning following H9C2 cardiomyocyte hypoxia/reoxygenation model.
The authors demonstrate  Sevoflurane preconditioning significantly increased the expression of HIF-1a, PDK-1, and Bcl-2 and reduced the protein expression of Bax, which markedly decreased the apoptosis ratio and Lactate dehydrogenase (LDH) level, increasing the cell viability, content of key enzymes of glycolysis, ATP concentration of glycolysis and stabilizing the mitochondrial membrane potential.
This study designed well, and the authors’ hypothesis is thoroughly tested. Their conclusions are interesting demonstrates that the cardioprotective effects of Sevoflurane preconditioning are potentially associated with the activation of the HIF-1a/PDK-1 signaling pathway.
My main concern is that thought the manuscript, SPC and HIF-1a inhibitor YC-1 were used as intervention methods for grouping study. Western Blot protein detection technique was used to quantify the content of target protein HIF-1a and PDK-1. The results showed that the contents of HIF-1a and PDK-1 in the SPC group increased significantly, while the contents of HIF-1a and PDK-1 decreased significantly in the S+Y group. The principal claim of the result is that the cardioprotective effects of Sevoflurane preconditioning are associated with the activation of the HIF-1a/PDK-1 signaling pathway.
I suggest the authors’ study confirmed that sevoflurane preconditioning can effectively attenuate the
Hypoxia/Reoxygenation (H/R) injury in H9c2 cells.


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: IMPROVED PLAQUE ASSAY FOR HUMAN CORONAVIRUSES 229E AND OC43
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. The paper is lucid and I did not find any discernible mistakes in grammar or any typos in the spelling which tells of the hard work the authors have put in for preparing the manuscript. Kudos to the team for the presentation.

2. Bracci et al has eloquently described a protocol to perform plaque assay to screen antiviral compounds on non-severe coronavirus strains in a BSL-2 setting. The work is exhaustive given the global limitations imposed on research work in view of the pandemic and comes at an opportune time as well. The study has a solid and clear theoretical/conceptual framework, which makes it relevant to justify the study.

3. The purpose of the introduction is to orient the reader and create an interest in the study. This manuscript excels in that department without overstretching it.
Experimental design: 1. The research question is clear. Furthermore, the rationale for the study is clear The authors have provided a clear statement about the need and relevance of this study.

2. The methods have been well described. Since this is primarily a methods paper, the Methods section should give readers enough information in such a form that they can repeat the experiments independently. In this manuscript, all methods are crystal clear. Thus, the authors deserve credit, since interested readers will surely find it easy to follow the same procedure.
Validity of the findings: 1. The description of the results is also very well written. The data presented are easy to follow.
2. From my perspective, the weakest parts of the study are the images used. The images need to look at for brightness and contrast issues and may be due to the lack of photography skills of the experimenters but few images ESPECIALLY Fig 1 and Fig 7 do not feel professional at all. The authors could look into this aspect of an otherwise beautifully presented manuscript.
Additional comments: This is a very interesting study and kudos to the authors for sending such a manuscript
I would also like the authors to look for some professional help regarding the images for the correction of brightness and contrast.


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: IMPROVED PLAQUE ASSAY FOR HUMAN CORONAVIRUSES 229E AND OC43
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript deals with the development of a new and improved plaque assay for titration of human coronaviruses 229E and OC43. A relevant method that may provide a better understanding about SARS-CoV-2. Very promising study.

Comments and suggestions:
1.	An important advice for the authors is to consult a professional native English-speaking editing service for assistance with the manuscript, as there are several parts through it that should be carefully reviewed. I am attaching the reviewed PDF document with several recommendations that should be done to the manuscript.
2.	From my perspective, the introduction should provide some further information to help readers to appreciate the relevance o the study. Thus, I would recommend adding a paragraph describing the rationale for using plaque assays to determine viral load, could help to improve the manuscript.
3.	Even if scientific writing is not as stringent as before, in general terms it is highly recommended that scientific papers should be written in third person and using past tense, which implies avoiding the use of personal pronouns like "I", "we” or “our." So, several parts of the manuscript use these pronouns. Please, rewrite in a more academic style.
4.	On lines 190 (page 11) and 263 (page 13) authors use the expression “we believe.” Science is not a matter of beliefs but of facts. Please, delete.
5.	From my perspective, the study is very interesting and useful. I just would recommend adding a diagrammatic scheme resuming the more optimal conditions and media for titration of the human coronaviruses 229E and OC43. It may help readers interested in the standardization of this protocol at their laboratories.
Experimental design: No comments
Validity of the findings: The findings may be very relevant.
Additional comments: *** I UNDERSTAND THAT THE TASK OF THE REVIEWER IS TO SEE WHAT THE AUTHORS HAVE NOT SEEN. I THINK I AM PROVIDING AUTHORS WITH CONSTRUCTIVE CRITISISMS, AND I AM CERTAIN THAT THIS PROTOCOL COULD BE VERY RELEVANT FOR THE ADVANCE OF VIROLOGY. IF AUTHORS AGREE THAT THE MANUSCRIPT CAN BE IMPROVED BY CONSIDERING THE ABOVE MENTIONED, AND VERY SIMPLE, SUGGESTIONS, THE STUDY WOULD INCREASE ITS IMPACT.


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: UNCOVERING THE HIDDEN DIVERSITY OF MISSISSIPPIAN CRINOIDS (CRINOIDEA, ECHINODERMATA) FROM POLAND
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is a thorough and detailed description of newly discovered crinoid taxa from the Carboniferous of Poland. It is a much needed look at these taxa, since previous crinoid diversity in the region has only been known from columnal-based taxa, which, as the authors discuss, under represents true diversity in the region. Since finding adequately articulated material for crown-based taxonomy is no easy task, I believe these findings are of significant importance for understanding Carboniferous crinoid diversity. The systematic treatment of the material is thorough, and I find the imaged to be of high quality.
Experimental design: The systematic treatment of these crinoid specimens is rigorous, and the descriptions and imaged provided are highly detailed.
Validity of the findings: I am not an expert of crinoid systematics and therefor cannot comment on the specifics of their assignments.
Additional comments: This is only a minor suggested for a figure enhancement:

Though the description of the stratigraphic setting is highly detailed and thorough, I would have also liked a visual aid of a generalized/composite stratigraphic columns representing the 3 localities studied, with indications of where the crinoid specimens came from. Perhaps something like this might work well as a part of Figure 1?