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: RANDOM ALLOGENEIC BLOOD TRANSFUSION IN PIGS: CHARACTERISATION OF A NOVEL EXPERIMENTAL MODEL
Review round: 2
Reviewer: 2

Output:
Basic reporting: I gladly accept the opportunity to re-review the revised manuscript of Ziebart et al. entitled “Random allogeneic blood transfusion in pigs: characterisation of a novel experimental model”.
Based on the authors’ revision, I have carefully reviewed the tracked-changes version of the manuscript as well as the point-by-point answers to the reviewer’s previous comments. I would like to thank the authors for the detailed answers. While the answers are straight-forward and clear, and the manuscript has been changed and adapted mainly in the methods and results section, I regret to note that the authors have not taken the opportunity to clarify one very crucial and misleading point of their manuscript. And I had included this comment in my previous review:
The crucial point is that the authors study, its design and results, are valid to assess the immunogeneic effects of whole blood transfusion. Therefore, the title is correct by stating that this is description of a (new) animal model. However, the authors’ study is NOT a study investigating organ cross-talk, not at all. And therefore, any mention of organ cross-talk remains purely speculative, is not supported by their results, and should be removed from the manuscript. One single sentence at the end of the discussion, i.e. that immunogeneic effects of blood transfusion may play a role in designing adequate models for the study of organ cross-talk mechanisms during transfusion, is a valid point, and is just enough to make the point.
In their point-by-point reply, the authors argue that upcoming studies (on organ cross-talk) would make use of this model. I agree, that this may be an option for future studies, and that these upcoming studies rely on the basic immunogeneic effect of whole blood transfusion as a “control”. In this context, the present results may represent a basic definition and description of a model,  that – in the future - may be used as a “control” to study whether organ cross-talk may be mediated by whole blood transfusions. Based on the considerations, again, I suggest to rewrite the article, giving it a different perspective and stressing the assessment of immonogeneic effects of transfusion, NOT of organ cross-talk, because the latter is misleading and not supported by the design and the results of the study. Preferably, however, I advised the authors to put two things together in one comprehensive manuscript: 1. the “baseline characteriziation” of the model presented in the present manuscript and 2. their results of upcoming studies investigating whether blood transfusion is involved in the mechanisms of organ cross-talk. I have gotten the impression that the current definition of their (new) transfusion model is just the baseline, and indispensable characterization of a model, that shall be used to study the initial hypothesis. Therefore, these two aspects belong in one manuscript.
Since this is a very basic and major concern I have about the current manuscript, please allow me to refrain from making additional specific comments. In general, there are a few typos; grammar, language should be revised, and comparisons in the results section should be made clearer. Moreover, the discussion should focus on the immunogeneic effects rather than on speculations about organ interactions. Figures 5 and 6 may be clearer, when normalized mRNA expression are being shown relative to controls (controls=1). Sample sizes should be added to tables and figures. Again, I strongly suggest to invest more energy to rewrite the manuscript to make a valid point and transfer a meaningful and clear message to the readers.
Experimental design: no additional comment
Validity of the findings: no additional comment
Additional comments: no additional 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: RISK AND PROGNOSTIC NOMOGRAMS FOR HEPATOCELLULAR CARCINOMA WITH NEWLY-DIAGNOSED PULMONARY METASTASIS USING SEER DATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study attempts to demonstrate risk factors for pulmonary metastasis (PM) from hepatocellular carcinoma (HCC) as well as poor prognosis in HCC patients with PM at initial diagnosis. The data clearly showed significant risk factors using the nomograms with large cohort. Also, their discussion seems well-written and reasonable. Since there are several points that should be revised, I would give some suggestion as following.
Experimental design: Methods seem to be well described.
Validity of the findings: 1)	The data seems very clear, but there is a critical point that the nomograms were not validated using external validation cohort. At this point, it is unclear whether their nomograms can work universally. Thus, they may refer this in the Discussion section.
2)	Then, the data demonstrated that hepatic surgery as well as chemotherapy is a favorable prognostic factors in this cohort. However, it should be noted that performance status that could not be obtained in the SEER database can be a confounding factor that must influence therapeutic decision-making.
3)	There is no evidence whether the early detection of PM can contribute to prolong survival time. So, they may mention this in the Discussion section.
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: RISK AND PROGNOSTIC NOMOGRAMS FOR HEPATOCELLULAR CARCINOMA WITH NEWLY-DIAGNOSED PULMONARY METASTASIS USING SEER DATA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear and unambiguous, professional English is used throughout.

The authors cite relevant literature, citing recent similar research.

The authors have used professional presentation structure including figures and tables.
Experimental design: The research presented here is not novel as the authors also discuss in the manuscript. However the research questions are well defined with relevant limitations of the study.

The authors should describe what T stage and N stage stand for.
Validity of the findings: The authors have assessed the impact and novelty of the study and they discuss the associated limitations.
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: RISK AND PROGNOSTIC NOMOGRAMS FOR HEPATOCELLULAR CARCINOMA WITH NEWLY-DIAGNOSED PULMONARY METASTASIS USING SEER DATA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Title: (Risk and prognostic nomograms for hepatocellular carcinoma with newly diagnosed pulmonary metastasis)
●	The aim clear.
●	Title is informative and relevant.

Introduction:
•	Clear, the research question clearly outlined.
•	I would recommend saying: (Liver cancer is one of the most aggressive malignancies and one of the major cause of 44 cancer death globally) avoid the (Fourth) because of the controversy. Check the following : (Lung cancer is the most commonly diagnosed cancer (11.6% of the total cases) and the leading cause of cancer death (18.4% of the total cancer deaths), closely followed by female breast cancer (11.6%), prostate cancer (7.1%), and colorectal cancer (6.1%) for incidence and colorectal cancer (9.2%), stomach cancer (8.2%), and liver cancer (8.2%) for mortality).
•	 (Check Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries (https://doi.org/10.3322/caac.21492)

Discussion:
●	Discussed from multiple angles and placed into context without being overinterpreted. Answered the aims of the study. There is a good opportunity to repeat this study in future the data are well explained to be repeated by my opinion.  You already referred to in the discussion to the Inclusion and exclusion criteria but I would urge you to write them separately and in very clear way so that would make our research clearer.

references:
•	I would recommend using the numbers for the references in the discussion to avoid putting the article names between the brackets for less distraction and easier reading and following.
Experimental design: Methods:
•	Please make comment about the following in the methods: The possible weakness in this study which I need the authors to comment about is using the (univariate and multivariate Cox regression analysis), as there are suggestions of violation of the proportional hazard assumption in the Cox regression model may lead to creating a false model. that does not include only time-independent predictive factors. For this reason, before the application of a simple hazard model is made, one has to check the above assumption and apply the Cox stratified regression model or time-dependent variable model if necessary.
Validity of the findings: Results:
●	Tables and figures relevant and clearly presented.
●	Table 1/Clinical and pathological features of 30641 patients diagnosed with hepatocellular carcinoma:  There is an obvious the selection bias in that table, please try to make a comment about how we reduced that possible bias to defend and make our case stronger.
Additional comments: Overall:
●	I like the idea of the research and it is new and having some creativity.
●	It would be good add for what we now about the prognosis of hepatocellular carcinoma with newly diagnosed pulmonary metastasis. But they need to work on covering some bases to make the study stronger and more convincing. Would recommend to consider publication after some changes and corrections.


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

Input:
Title: RISK AND PROGNOSTIC NOMOGRAMS FOR HEPATOCELLULAR CARCINOMA WITH NEWLY-DIAGNOSED PULMONARY METASTASIS USING SEER DATA
Review round: 2
Reviewer: 1

Output:
Basic reporting: They did a reasonable changes and for me it looks ready for publication.
Experimental design: I agree with the changes they did
Validity of the findings: Ready
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: EXPLORING THE POTENTIAL OF DEEP-BLUE AUTOFLUORESCENCE FOR MONITORING AMYLOID FIBRIL FORMATION AND DISSOCIATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: The deep-blue autofluorescence in amyloid fibrils even when formed by proteins without aromatic amino acids is an intriguing observation.  Yet the origin of this signal and, therefore, its potential to provide additional information about the amyloid assembly process remain controversial.  Additional experiments to elucidate both the origin and utility of this signal are certainly welcome. The authors try to explore the utility of dbAF for fibril growth kinetics by combining deep-blue autofluorescence measurements with light scattering and ThT measurements of the kinetics of seeded growth, and GuSCN-induced dissociation, of aggregates formed by insulin, lysozyme and human prion protein. One of the intrinsic weaknesses of this paper is that it remains mostly descriptive without providing additional insights into the origin of the dbAF signal. The authors do suggest that aggregate size might play an important role – but don’t provide any independent evidence to support this hypothesis.

Important Concerns/ Requested Changes

1)	Perhaps the biggest omission is the lack of characterization of the morphologies and size distributions of (a) their amyloid seeds under their conditions used for seeded growth or  (b) of the aggregate morphologies at the end of seeded growth. For one, the resulting aggregate populations might actually be quite heterogeneous, which would raise the question which ones are responsible for the observed changes in any of the three readouts. In addition, the growth conditions (pH 6) are quite unusual in particular for insulin and lysozyme. This might further complicate the interpretation if the aggregates are complex mixtures of various distinct populations. Even if fairly uniform, the overall structure/morphology/size of the aggregates prior to and following seeded growth might play an important role in the observed dbAF kinetics.

2)	The authors indicate that the large (50 nm) Stokes shift should preclude a leak from light scattering into their dbAF fluorescence channel. Given that the authors work with probably large aggregates formed during seeded growth and that scattering intensities from short-wavelength excitation can be orders of magnitude larger (even far from the excitation source) than any fluorescence signal, the authors need to confirm this assertion directly. This is particularly important since the light scattering and dbAF signals show noticeable correlations in their time course for all three proteins.
One way to check this would be to measure the actual spectrum of their dbAF emission. If that spectrum rides on a large shoulder that increases towards the short-wavelength cut-off ( i.e. towards the excitation wavelength ) this would indicate that scattered excitation light is leaking into their dbAF emission channel – despite the significant Stokes shift.

Minor Concerns/ Suggestions

3)	Instead of displaying their signals on an arbitrary scale (0-100) without a clear reference point, the authors should represent their signals as fractional change ( i.e. S / S(0) or [S-S(0)] / S(0)).  This permits a comparison of the relative changes of any of these three signals during growth and enables readers to compare results  obtained with different instruments against those of the authors.

4)	The authors provide no clear motivation why they chose to follow seeded growth vs. monitoring the nucleated polymerization of their seeds in the first place.  This deserves some comment.
Validity of the findings: some of the comments above relate to the question whether the reported data are sufficient to support the author's conclusion.
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: EXPLORING THE POTENTIAL OF DEEP-BLUE AUTOFLUORESCENCE FOR MONITORING AMYLOID FIBRIL FORMATION AND DISSOCIATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: Article conforms to the basic reporting guidelines of PeerJ
Experimental design: The research is within the scope of the journal. Research question in relevant for study protein aggregation.
Validity of the findings: Data is provided and is sound and conclusions are stated well.
Additional comments: In the figures1,2 and 3, for the aggregation studies, each of A, B & C have three sets of data points. It may be prudent to plot each of them in a different color to help the reader identify that there are three different kinetic experiments.

Alternatively one could plot them as mean+/SD too.

It may also be useful for the reader to see a quantitative comparison between the three different methods and may be achieved by fitting the data to a kinetic model.


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: EXPLORING THE POTENTIAL OF DEEP-BLUE AUTOFLUORESCENCE FOR MONITORING AMYLOID FIBRIL FORMATION AND DISSOCIATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: see general comments
Experimental design: see general comments
Validity of the findings: see general comments
Additional comments: I have reviewed the revisions of the original manuscript. There are still some short-comings - but I would like to leave it to the authors to address those residual issues at their discretion. I am particularly pleased with the added AFM images which give a nice overview of the changes in aggregate morphology. I would further agree that these images do show predominately fibrillar species.

Residual issues/concerns
1) Concern about contributions from light scattering to dbAF.  The authors have performed the experiments I suggested - but I do disagree with their assessment. Looking at the panels of their supplemental Figures S1D-F, it is obvious that their dbAF signal (black) is indeed riding on a LARGE shoulder towards their excitation wavelengths. It is this exact shoulder in their fluorescence signal that they need to account for - not the relatively minor contributions at the beginning of their experiments (initial condition?). Their (uncontaminated) fluorescence signal should have a nearly flat baseline on either side of the dbAF peak (see the shape of the dbAF peak in S1A). To correct this properly, they should use a two-peak gaussian (or Lorentzian) fit to their fluorescence trace - with one peak centered at the dbAF peak and the other centered at or near the excitation wavelength (which represents the shoulder in their spectra). My rough estimate is that the corresponding contribution to their dbAF peak in eg. panel S1F is closer to 50%. This might significantly affect their interpretation of the dbAF vs. light scattering kinetics.

2)  I could not find any figure captions to the supplemental figures.  The authors should make sure those get included in the final manuscript.

3) Seeded vs. unseeded kinetics: The investigation of exclusively seeded growth kinetics does raise some questions as to whether dbAF is a good readout of amyloid kinetics in the absence of seeding. The authors might want to elude to this issue in their discussion. The reason I add this cautionary note this is that, in our hands, dbAF did NOT replicated unseeded fibril kinetics with either ThT or light scattering.


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: EXPLORING THE POTENTIAL OF DEEP-BLUE AUTOFLUORESCENCE FOR MONITORING AMYLOID FIBRIL FORMATION AND DISSOCIATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: I am satisfied with the response of the authors.


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

Input:
Title: EXPERIMENTAL REMOVAL OF INTRODUCED SLIDER TURTLES OFFERS NEW INSIGHT INTO COMPETITION WITH A NATIVE, THREATENED TURTLE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written and provides mostly sufficient background and context. I have made a few suggestions for improvement in the specific comments to the authors.
Experimental design: Research question is well designed and executed. There are a few points that need improvement and clarification (i.e., body condition index). I specified these concerns in the general comments to the author.
Validity of the findings: Although some results were unexpected, the authors do well to discuss their findings.
Additional comments: General comments: This is a well written paper that addresses an important conservation question regarding the most invasive freshwater turtle species in the world and its effects on a threatened species. I have the following comments that I think would improve the quality of the manuscript.
Line 57: I think the authors can spend a little more time on native and introduced distribution of RES. PeerJ is not a turtle oriented journal and the readership in wide so more info here could be useful. Perhaps talking about introduction to other continents and then introduction to “non-native” states of the US. Saying “central USA” I do not think is accurate enough.
Line 60-61: I feel that going into more details about the results of these studied won’t hurt.
Line 74: Elaborate on these basking structures you mention (Lambert et al. 2013).
Line 86-88: Please provide more explanation about why/how is this a closed system. Is it fenced off completely. Working with turtles for over a decade even in fenced off areas, I learned that their movement is quite underestimated.
The distribution of basking should be further explained instead of just citing a previously published paper.
Line 110: More information about the study site is needed. What do the authors mean by optimal habitat. It is hard for readers to visualize this without further description. How big is the area etc?
Did dip netting and hand capture occur over the same time span?
Line 128-132: More appropriate approach is to use residual values of linear regression of PL to body mass as a body condition index. It looks like that is what the authors did in the figure, but they did not appropriately explain it here. Also were the data normally distributed or log transformed etc.? I like that they used individual WPT as a random effect.
Line 133: Is the model fit better when you removed non-significant variables from the model?
Line 139: This sentence sounds like you were monitoring 16 days before you started a removal. Please clarify/rephrase.
Line 142-146: I am intrigued by the visual survey technique. What was the distance between the observer and the basking structures? Were the turtles by any means disturbed by the observer? Also, how long did it take to complete one survey? In addition, did the same surveyor conduct surveys pre and post removal? This may be important when it comes to the potential biases especially IDing the turtle basking.
Line 154-155: explain the variation west to east as it pertains to both species.
Line 157: with proportional data?
Line 158-159: was the same package and function used as in the previous paragraph. Please specify.
Line 160: what interaction? I would say and if the interaction between treatment and distance was significant….
Line 164-165: Is there any chance these can be labeled on the Figure? If that will make the figure messy then I suggest referencing the supplemental material where we can find more info on the sites.
Line 174: what do you mean by remarked? Does the mark fade so fast?
Line 186-188: You trapped and measured the turtles during different months for each treatment (pre and post removal). Do you think this could affect the measurements given for example female reproductive cycle or the times of highest activity/foraging? Even if those effects were minimal I think this needs to be addressed in the methods or discussion. Also, is it normal for males to be heavier than females?
Line 197-199: Can you please state what were the pre-removal estimates and what were the confidence intervals for both estimates?
Line 208: Was this one site used previously by RES?
Line 234-235, line 270-273, line 274-276, line 280-282: hard to visualize where these sites are. Figure 3 helps with this, maybe refer to them.
Line 289-298: this paragraph may be a good one to mention a possibility of observer bias (or the lack of) or perhaps the area was more heavily used by people that would cause turtle disturbance and affect observations and therefore the number of turtles observed.
Line 301-302: briefly tell us what those preferred characteristics are.
Line 305: Remove the comma before parentheses
Line 337-357: the authors appropriately discuss the potential reasons for these unexpected results. Adding potential for future projects such as dietary studies (especially given they euthanized RES and stomach contents are available) may be something they want to add.
Line 364: For Cossman et al. unpubl. will there be a report available through supplemental material or similar?
Line 388: I would remove “large-scale”


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: EXPERIMENTAL REMOVAL OF INTRODUCED SLIDER TURTLES OFFERS NEW INSIGHT INTO COMPETITION WITH A NATIVE, THREATENED TURTLE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written using clear and unambiguous, professional  english throughout.

The introduction is based in the literature and provides sufficient context for the study. The methods section should have additional citations better rooting the authors work into the published framework.

The article structure, figures and raw data are professional and with some minor changes will be publishable.

The manuscript is mostly self contained. In one or two locations additional description of methods will improve this aspect of the manuscript.  See the attached review.
Experimental design: The work described is original, and seeks to fill a knowledge gap in how an invasive species impacts a native species in more natural settings than previous studies.

As described the authors performed the work to a high technical and ethical standard.

Methods mostly were described well. In a few locations additional information should be provided to better describe the methods.
Validity of the findings: The underlying data have been provided, appear to be robust and statistically sound.

The conclusion is well stated, linked to the original question and mostly limited to supporting results.

Some speculation is made in the manuscript and discussion of alternative explanations of their findings should be expanded.
Additional comments: Overall, this is a well written manuscript that addresses an important question about the interaction between red-eared slider turtles and native turtle species interactions. The work described is suggestive that RES can impact native species in large bodies of water. This work builds on a number of previous studies that addressed this question in mesocosm type experiments.

The manuscript can be improved by providing some additional description about methods and expanding the discussion to better consider alternative explanations of the findings.


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: ONTOGENETIC BRAINCASE DEVELOPMENT IN PSITTACOSAURUS LUJIATUNENSIS (DINOSAURIA: CERATOPSIA) USING MICRO-COMPUTED TOMOGRAPHY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is well written, clear and comprehensive, but not unnecessarily long or wordy. The anatomical description of the three specimens is very detailed and complete. Descriptions are accompanied by very professionally looking figures, which show the anatomy comprehensively and help with the understanding of the otherwise often complex anatomy of the braincase elements.
The introduction provides a good overview of the topic and previous research. Methods and specimen details are sufficiently outlined. The discussion puts the findings for the most part in a good context with previous research. However, a comparison with ontogenetic series of other dinosaur species is missing. I do realise that the manuscript focusses on ceratopsian dinosaurs, for which little data exists, however, there are several examples of reported ontogenetic stages in other ornithischian dinosaurs (e.g. Evans et al. 2009; Lautenschlager & Hübner 2013). A more detailed discussion of these in the context of the current study would be very appropriate.

Evans, D. C., Ridgely, R., & Witmer, L. M. (2009). Endocranial anatomy of lambeosaurine hadrosaurids (Dinosauria: Ornithischia): a sensorineural perspective on cranial crest function. The Anatomical Record, 292(9), 1315-1337.

Lautenschlager, S., & Hübner, T. (2013). Ontogenetic trajectories in the ornithischian endocranium. Journal of Evolutionary Biology, 26(9), 2044-2050.
Experimental design: The experimental design is appropriate and all methodological approaches have been defined/explained in sufficient detail. The research question is stated in the introduction and clearly defined/addressed.
Validity of the findings: The anatomical descriptions are detailed and comprehensive. Findings are supported by appropriate figures and data tables. Conclusions are provided and linked to the outlined research question.
Additional comments: This is a very well-executed and detailed study of three ontogenetic stages of the basal ceratopsian Psittacosaurus. The manuscript is well written, appropriately detailed and accompanied by professional and clear figures. My biggest gripe with the manuscript is the lack of discussion of other ontogenetic series of (ornithischian) dinosaur brain cases/endocasts. I would like to see some comparisons with published studies and how Psittacosaurus differs from other ornithischians. This would allow making inferences beyond a single species and possibly provide some more general patterns for brain/braincase development in dinosaurs more broadly.
A second point, where this study could be improved would be to present a summary figure showing the findings in a morphological context. I wonder if it would be possible to schematically present the ontogenetic changes similar to Figure 3a in Lautenschlager & Hübner 2013 for the braincase (I am aware, that I am shamelessly suggesting one of my own publications, but the authors might find this useful),
In addition, I have a few minor, more specific comments and suggestions listed below. These, however, should be relatively easy to incorporate.
All in all, this is a nice contribution to our knowledge of ornithischian development and ontogenetic patterns, and I am sure it will be of interest to a wider audience of palaeontologists interested in these topics. Based on the well-written and professionally illustrated manuscript, I will recommend publication pending minor revisions.

List of additional comments:
Line 40-42: It would be good to add a brief (e.g. 1-2 sentences) explanation on the relevance of chaoyangsaurids for readers without intimate knowledge on early ceratopsian taxonomy.

Lines 44-45: The two paragraphs feel quite unrelated and it would be helpful to link them together thematically (e.g. psittacosaurs important for understanding of early ceratopsian evolution in particular with regards to locomotion/posture…)

Lines 64-65: As above, these two paragraphs are topically unconnected. Possibly mention the importance of both psittacosaurs and ontogeny to address questions of heterochrony in ceratopsian evolution or similar?

Lines 74-79: Move this to the methods.

Lines 85: I do agree that the models are “visually striking”.  Nevertheless, remove this qualifier as it is not a methodological step and sounds somewhat unprofessional.

Line 113: Abbreviations for basioccipital (BO) missing. Compare with other elements for consistency.

Line 135: You refer to the basisphenoid-parasphenoid complex here, but it is referred to as the basisphenoid only in the corresponding figures.

Lines 161-162: The reference should be to figure 4x not figure 5.

Lines 182-183: In figure 6 only the hypoglossal nerve is indicated to pass through the foramen.

Line 209: “Main trunk” is ambiguous. Do you mean the cochlear duct?

Line 229 “…which is the location of the cerebral hemispheres” – Better “… which represent the space occupied by the cerebral hemispheres of the forebrain”. On that note, are there any impressions of vascular structures or similar recognisable which would hint at a close contact of the brain and the frontals. Either way, this should be mentioned.

Line 264: “of the basioccipital”

Line 306: Remove “unfortunately”. I share the feeling but try to keep a neutral language.

Line 322: “Difficult” is probably more appropriate than “hard”. Is this due to the fusion or the resolution of the scan?

Line 404: “sub-diamond in shape” is unclear. “Circular” or “ovoid” might be a better description?

Line 423: “Nerves X-XII exit medio-ventrally through the exoccipitals…” – showing the foramen for the nerves in the figure would be helpful.

Line 470: Remove “at”.

Line 506-507: Would it be expected that the contribution of the individual bones to the occipital condyle changes? If the condyle is entirely formed by the basioccipital in the hatchling this would mean a relative reduction of the element if the with growth. I know that the contribution of different elements is variable in different species, but is there an example for changes within an ontogenetic sequence?

Line 543: Is this shrinking relative to other elements or in absolute size? This also applies to several other occasions in the text, where a reduction in size is mentioned. I assume this is a relative reduction compared to the rest of the skull, but make sure this is clear.

Line 547-548: “Such large, well-defined hemispheres are unusual within ornithischians.”- I would disagree with this statement. Evans et al. (2009) and Lautenschlager & Huebner (2013) show a few examples with well defined cerebral hemispheres.

Evans, D. C., Ridgely, R., & Witmer, L. M. (2009). Endocranial anatomy of lambeosaurine hadrosaurids (Dinosauria: Ornithischia): a sensorineural perspective on cranial crest function. The Anatomical Record, 292(9), 1315-1337.
Lautenschlager, S., & Hübner, T. (2013). Ontogenetic trajectories in the ornithischian endocranium. Journal of Evolutionary Biology, 26(9), 2044-2050.

Lines 573-575: “They are frequently reconstructed, when adult, as facultative bipeds, dropping their bodies and arms to the ground when feeding, for example, but rearing high to seek danger or feed on leaves high on a tree.” – This sentence is rather convoluted and would benefit from rephrasing. Also, not convinced the adults are seeking danger…

Lines 592-604: Excellent discussion/summary of the current debate regarding head orientation using the LSC. I would stress a bit more that recent studies, such as Schellhorn 2018 actually find a correspondence between hypothesised posture and observations of living specimens.

Figure 4: Abbreviation “pct” not explained in the caption.

Figure 25: Abbreviation “pps” not in the figure.

Figure 30: The outlines are a bit abstract. It would help if a small picture of the specimen or the digital model with the location of the basal tubera is added.

Figure 31: I would like to see a dorsal view of the inner ears as well so that the outline of the LSC and the angle between the ASC and the PSC becomes clear.

Figure 32. This will require some inferences and artistic skills, but would it be possible to add little silhouettes of the whole animal below each skull showing the full body posture?

Table 1: It would be useful to add another table or additional columns to the existing one showing the percentage increase between the three specimens


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: ONTOGENETIC BRAINCASE DEVELOPMENT IN PSITTACOSAURUS LUJIATUNENSIS (DINOSAURIA: CERATOPSIA) USING MICRO-COMPUTED TOMOGRAPHY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well written, but with some errors in structure, spelling, citation and reference.
Experimental design: no comment
Validity of the findings: This is a good manuscript that firstly report the ontogenetic information of the psittacosaur braincase.
Additional comments: Dear Editor, Dear Authors,
This is a good manuscript describing the first ontogenetic information of the psittacosaur braincase. The manuscript is well written, but with some errors in spelling, citation, and so on. I list them as below. Besides these, I would like to highlight some other issues that should be addressed before this manuscript goes to press:

1) As mentioned by the authors, the Lujiatun psittacosuars are deformed more or less, as the juvenile V12617 and the adult V22647; and the hatchling IVPP V15451 is possibly deformed too. Normally, the skull of psittacosaurs is subrectangular in lateral views without a distinct posterior inclination; so that the adult V22647 is more deformed than the juvenile V12617. It is not correct to consider the posteriorly-inclined cranial structure as the natural condition by the authors, as in lines 360-361 “The occipital surface of the skull is orientated postero-ventrally, as in the case in the hatchling”.
   And also, these deformed skulls would impact on the orientation of semicircular canals. The authors should consider how to exclude this influence, especially when the orientation be used to index the head position. The authors should include more undeformed fossils in this study, at least scan one more adult skull to check this influence in V22647. As we know, psittacosaurs are common in many Chinese collections, should also in IVPP.

2)Line 58, About the isotope dating of Lujiatun deposits, Jiang et al. (2011) did not work on the radiometric age. And also, the 124 Ma is replaced by an updated age of 126.0 Ma by Chang et al. (2017). The reference is here, Chang S-C, Gao K-Q, Zhou C-F, Jourdan F. 2017. New chronostratigraphic constraints on the Yixian Formation with implications for the Jehol Biota. Palaeogeography, Palaeoclimatology, Palaeoecology, 487:399-406.

3)Lines 74-79, this paragraph is only about three skulls, should be included in “Materials & Methods”.
4)Line 95, ZMNH is Zhejiang Museum of Natural History, Hangzhou, China. Please correct it.
5)Lines 97-99, the citation should be present in Reference Part.
6)Line 101, “Zhou, 2006” should be “Zhou et al., 2006”
7)Lines 96-102, “Systematic Palaeontology”, the authors should write out the whole thing, such as, paratype, referred specimens, and diagnosis. Alternatively, this part can be deleted.
8)Line114, “5.3 mm” is inconsistent with “5.4 mm” in table 1.
9)Line 125, “constructed” may be “constricted”
10)Lines 223 and 224, “the nasals” and “postorbitals” should be singular form.
11)Line 263, “The occiput” should be “The occipital condyle”; please delete “Psittacosaurus”, its taxonomy is already known in the Materals and methods Part. Do not need to repeat this again.
12)Line 305, “the prootic” should be plural form.
13)Line 312, “paroccipitals” should be singular form.
14)Line 320, “the paroccipital processes” should be singular form.
15)Line 322, “the parietals” is singular form.
16)Line 330, “the frontal” and “the laterosphenoid” should be plural form.
17)Line 331, “the squamosal” should be plural form.
18)Line 334, “prootic” should be “prootics”
19)Lines 341, 342, “the nasals”, “the postorbitals” and “the prefrontals” should be singular form.
20)Line 535, “Holiday, 2009” is not present in the Reference part.
21)Line 553, “Anterior and posterior semicircular canals” should be deleted. This paragraph is about the general information of semicircular canals, not just for the two canals.
22)Line 563, “the anterior semicircular canal is approximately three times taller than the posterior one”, I did not find this feature in Fig. 31B. In Fig. 31B, the anterior canal is taller than the posterior one, but not too much as mentioned by the authors.  Please check it again.
23)Line 570, “including” should be added in front of “IVPP V16902”
24)Lines 581-582, “(LSC, or ‘horizontal’ semicircular canal)” should be moved to Line 569, behind “Lateral semicircular canal”; “our” should be replaced by “the”
25)Lines 582-584, the sentence should be deleted, due to it is meaningless.
26)Lines 596-597, a repeat between “120 in humans” and ”220 in humans”.
27)Lines 597-598, the citations “Graf et al., 1995; Spoor & Zonneveld, 1998” are not in the Reference Part.
28)Line 601, “2016” should be corrected as “2017”
29)Line 621, “Averianov, 2006” should be replaced by “Averianov et al., 2006”
30)Line 627, the description about the number of nerve foramina in three skulls, is inconsistent with that shown in Fig. 33. Please check it.
31)Lines 652-663, this paragraph should be included in the Discussion Part.

With best regards,

Chang-Fu Zhou


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: ONTOGENETIC BRAINCASE DEVELOPMENT IN PSITTACOSAURUS LUJIATUNENSIS (DINOSAURIA: CERATOPSIA) USING MICRO-COMPUTED TOMOGRAPHY
Review round: 1
Reviewer: 3

Output:
Basic reporting: Overview:
The article describes in detail the anatomy of the braincase from an ontogenetic series consisting of three individuals of Psittacosaurus lujiatunensis, a basal Ceratopsian dinosaur from the Barremian of Liaoyang Province, PRC. The anatomy of each element is described based on segmented CT data, and the anatomy of the reconstructed vestibular apparatus (semicircular canals) is described. Semicircular canal orientation is used to infer posture for differing ontogenetic stages of Psittacosaurus.

I would like to begin my review with a reminder that any comments here are intended to be constructive and I apologize in advance if any of my comments strike the readers as anything otherwise.

Basic Reporting

Figures are of good quality, and it is encouraging to see the large number of figures representing the elements in multiple views. It would assist the reader if there were a way to view 3D representations of the renderings. Perhaps 3D pdfs of the individual elements and whole cranial reconstructions could be provided?
In some places in the text, labelling additional features in some figure views would make it easier for the reader to follow the description. Suggestions for additional labels in the figures are made below in the detailed list of comments.
The description notes that segmentation of several of the elements was difficult and that sutural boundaries were inferred (i.e. in the juvenile braincase: the supraoccipital [line 296], basioccipital [line 271], prootic [line 321-322], parietal [line 333-334], in the adult braincase: the basioccipital-exoccipital contact [line 378], the supraoccipital [line 407] and others). I appreciated how the reconstructed areas of the vestibular apparatus were highlighted in red in Fig. 31. The same should be done for all of the contact surfaces that are inferred and have higher uncertainty than the other surfaces of the bones presented in the figures. This way the reader knows exactly whether a surface was observed or inferred.
The citations are somewhat sparse throughout the paper. Though not voluminous, a literature exists on the braincases of Ceratopsian dinosaurs, going back to Hatcher et al., (1907), which is not properly cited. A more recent publication dealing with the external anatomy of the basicranium of Psittacosaurus specifically, and its relationship to the basicranium of more derived ceratopsians is Dodson et al. (2010).
The discussion of ontogenetic changes in Psittacosaurus seems oddly divorced from the literature on ontogenetic change in other Ceratopsian dinosaurs. Extensive growth series exist for Protoceratops (Brown and Schlaikjer, 1940; Dong and Currie, 1993; Fastovsky et al., 2011), Bagaceratops (Maryanska and Osmolska, 1975), and, further afield, Triceratops (Horner and Goodwin, 2006). Less extensive growth series exist for Liaoceratops (Xu et al., 2002), Montanoceratops (Chinnery and Weishampel, 1998; Makovicky, 2010), and Chasmosaurus (Currie et al., 2016). Comparisons between known changes in the elements in these taxa and the patterns seen in this paper would be valuable. Although few of the previous descriptions look at endocranial elements, per se, at least the elements of the occiput and dorsal skull roof could be compared.
Also strangely omitted in the background or introduction is any reference to the previous work on juvenile Psittacosaurus, including Coombs (1982) an extensive description of perinatal Psittacosaurus cranial anatomy and ontogeny in a growth series of Psittacosaurus. Further comments on juvenile Psittacosaurus can be found in Sereno (2010). The introduction need not be vastly expanded, however some comments relative to the previous work on the ontogeny of ceratopsians and previous work on Psittacosaurus would help put the present addition into context.
The literature on the bipedal to quadrupedal transition in ornithischians in general and ceratopsians specifically is also undercited in this manuscript. Work on ceratopsian posture by Chinnery (2004) is directly relevant to the history of inferences of posture in Psittacosaurus and work relating histological features to posture in Chinnery and Horner (2007) may be useful (I leave the use of this second reference up to the authors).
The raw data was not included in the article. As the raw data represents CT data which some repositories view as a risk for unauthorized duplication (e.g. 3D printing), that is understandable. However, the authors should note the repository for the CT data and what institution qualified researchers should contact for access. Presumably the data are housed at IVPP. If not, the data must be placed in an appropriate repository where qualified researchers may access it in perpetuity. Again, it is acceptable for this repository to be curated, as in natural history museums where curators may limit access to specimens while they are under study, but the data should be accessible at some later date. Contacting the authors for data access is unacceptable and not in keeping with modern best-practices.
The structure is well organized. Each element described in a consistent pattern.
The authors should re-read the paper for small errors. I noted that in the institution list ZMNH was listed as “Zigong Museum of Natural History, Zigong, China”. This is incorrect as ZMNH was listed in the paper as the prefix for the holotype of Psittacosaurus lujiatunensis which is housed at the Zhejiang Museum of Natural History in Hangzhou, China. A few minor comments on organization, apparent omissions or mistakes in the text, and grammatical corrections are included in the list of line-by-line comments below.
Experimental design: Experimental Design
This descriptive paper follows the general pattern seen in many vertebrate paleontology articles. Methods for scanning were well described.
Graphing the relative size data of the three skulls as % basal skull length vs. basal skull length may improve the clarity of the comparison of dimensions between the three skulls and the discussion of isometric vs. allometric growth of different bones in the braincase.
Validity of the findings: Validity of the Findings
The conclusion needs to be better organized and slightly expanded in a few places. A common issue with papers that include much anatomical description is so much work goes into the description that the discussion and conclusion sections become neglected. This is something that I’ve done myself, and had reviewers guide me into improving my conclusions.
The discussion of changes in skull proportions would benefit from further comparisons to the ontogenetic series of other ceratopsians. How is Psittacosaurus different? Are there any commonalities. Line 486 mentions that the measurements from the juvenile braincase do not correspond to those from the other individuals. I am unsure what is meant by correspond in this context. If the intent is to say that the juvenile has proportions more unlike either the perinatal individual or the adult, then the sentence should be rephrased. I think that is the most likely intent, but one could also interpret that sentence to mean that the measurements in the juvenile are somehow using different landmarks, or different start and end points and so cannot be compared to the other two. If that is so, it needs further explanation.
The discussion of the lateral semicircular canal needs to be slightly expanded. A discussion of changes in posture through ontogeny for Psittacosaurus requires citation of the relevant literature on the posture of Psittacosaurus, including recent work by Maidment, Barrett and colleagues on ornithischian posture, with citations of the myological modelling, osteological correlate, and center of mass lines of inquiry that they pursued. Citations of older morphometric work is also needed (Chinnery, 2004; Chinnery and Horner, 2007). Citations of reconstructions of Psittacosaurus as a facultative biped mentioned in lines 574-575 are also needed. Even if these are popular works, or outreach sections of museum websites, they are worthy of documentation as they are the product of the thinking of experts in many cases. Also, in this discussion, the expected orientation of the head at neutral position for a quadruped or biped is not mentioned. It is unclear what the meaning of the different alert postures are. There are more specific comments following.
The conclusion section is very difficult to follow. It needs to be reorganized, with clear connections between statements of data from the paper and conclusions. One could describe the logical structure as “we found A, therefore we can say B”. I have more specific comments below, but the section needs to be largely restructured.
There were issues with several references, where Hailu You was referred to by his given name (Hailu) rather than his family name (You), as is traditional in citations. I have noted the corrections.
There are two findings that are quite strange and seem to be only briefly mentioned.
1)	The discussion of the supraoccipital in the adult Psittacosaurus seems to give the element an anatomy that is unlike any other previous reconstruction of that bone in adult Psittacosaurus in the literature. Given that the authors state that the borders of the supraoccipital are unclear in the adult specimen (line 407) would not a morphology incorporating flat material lateral to the thin caudally directed lamina which is currently assigned to the supraoccipital by the authors, be the more conservative approach?  A supraoccipital bearing a ridge but being composed of bone on either side of that ridge is consistent with our understanding of the supraoccipital from other ceratopsians where it is known (e.g. Dodson et al., 2010; Morschhauser, 2012), and from non-ceratopsian neornithischians (e.g. Galton, 1974), which are our closest comparisons from an earlier diverging lineage as all basal ceratopsians lack well-preserved supraoccipitals. All previous interpretations of Psittacosaurus have proposed a larger supraoccipital than is reconstructed here (Dodson et al., 2010; Sereno, 1987; 2010; You et al., 2008).
2)	The additional ossifications reported in the hatchling associated with the frontal (line 234-237) are described and characterized in two sentences as neomorphic bones similar to the epiossifications seen in derived ceratopsids, from which the structures reported here are separated by no small phylogenetic distance, as well as over 30 million years of time. It seems unlikely at first glance that these would have anything to do with epiquamosals and epiparietals, but the authors have not really argued that case. A more thorough discussion of these structures is necessary. The assertion of the authors would be strengthened by a discussion of evidence to disprove alternative hypotheses for these structures (for example, are they artifacts of the scanning process? Are they broken fragments of bone from elsewhere in the skeleton, or elements from another taxon that were taphonomically displaced to their current location? Could this specimen have been a perinate and associated with eggshell? How do these structures look under a light microscope?).
Overall the changes I am requesting are largely for clarity, expanding the review of past work slightly, and organization/grammatical in nature.
Additional comments: Line-by-line comments
Line 4 University of Bristol does not currently list Qi Zhao on its website (which seems quite good as reporting research affiliates and the like). The relationship with Bristol should be clarified (Visiting faculty perhaps?)
Line 19: Abstract states that ontogenetic sequences are relatively rare among ceratopsian dinosaurs. Rare compared to what? Dinosaur ontogenetic series are generally rare, but within dinosaurian, Ceratopsia is one of the better represented clades, with six or seven general with extensive or partial ontogenetic sequences.
Line 24 age of the Yixian Formation should be mentioned here, either in years, or to the age (Barremian)
Line 39: Authors use the informal term Psittacosaur, which is permissible, but it always struck me as odd. This entire group the psittacosaurs are all members of a single genus, why not just call it Psittacosaurus and be done with it?
Line 39-40 Citation needed for the statement “a diverse and geographically widespread suborder of ornithischian dinosaurs.” Perhaps use Dodson et al., 2004 and the relevant biogeography chapters from the Dinosauria 2nd edition to support.
Line 41 Citation mentioning Sereno, 2000; Morschhauser, 2012 should also mention Han et al., 2017 which recovers Psittacosaurus as basal most in some MPTs.
Line 51 P. sibiricus does not appear to be much smaller than the largest P. lujiatunensis.
Line 95 Institution incorrect. ZMNH M8137 is housed in the Zhejiang Museum of Natural History, Hangzhou, China
Line 118 It would improve reader understanding if the basal tubera grove (btg) were labelled on Fig 3C as well.
Line 180 Replace “tab-like” with a more descriptive term. A “tab” is not a shape (though many authors like to use it as such). If rectangular or square is the outline intended, then use those terms.
Line 183-184 “They [Nerve pathways X-XII] are visible when the braincase is viewed posteriorly.” It would be helpful to label these on Fig. 6 where the exoccipital is in posterior view.
Line 189 Change “vcd” to “vcd?” to conform with Fig. 6D.
Line 197-198 Label the portion of the laterosphenoid that makes up the dorsal boundary of Cranial Nerve V on relevant views in Fig. 7.
Line 210-211 For the sentence ending “…the prootic when viewed dorsally.” Add a citation of the portion of Figure 8 where the prootic is in dorsal view and cite the abbreviation for the pathway of the semicircular canal used in the figure.
Line 220-221 Label the indentations formed in the lateral margins of the parietal in Figure 9.
Line 235-237 “We are assuming they [frontal ossicles] are epiossifications much like those seen on the parietosquamosal frill...” Why? Seems like a big assumption. See my previous comment on how this section or a section discussing these features in the discussion needs to go test (even if only by thought experiment) alternative hypotheses for these structures before stating conclusions. Also, this sentence is more interpretation than description, and probably belongs in the discussion section anyway.
Line 260 The L-shape of the basioccipital tubera is unclear from the scans as presented in Fig. 12. Perhaps the direction or angle of the lighting of the scans in the virtual environment can be changed to highlight the rostral extension of the tubera better.
Line 261-262 “Posteriorly, they are almost entirely obscured by the occipital condyle.” In Fig. 12E the tubera seem to clearly sit lateral to the occipital condyle. Clarify this statement.
Line 269 “(Fig. 12: cdn)” This implies that there is a label on Fig. 12, but labels appear to be missing on Fig. 12B, 12C, 12D and 12E.
Line 273 Again, citing an abbreviation on Fig. 12D, but no labels are present on that figure section.
Line 283 Sentence beginning “The basisphenoid-paraspehenoid complex…” repeats something stated in line 280. Delete this sentence here
Line 295 Figure 14A is inverted relative to Fig. 14B. Since PeerJ technically has no pages, “white space” around figures becomes an aesthetic concern, not a space concern. The clarity gained from having both views in the same orientation more than makes up for the slightly less efficient use of space in the image.
Line 311 Label the posterior semicircular canal on the paroccipital figure.
Line 319 Label the antero-dorsal corner of the exit for CN V on Fig. 16.
Line 338 Label the small parietal shelf on Fig. 18
Line 352 It is unclear to me whether the frontal crest or the shallow parasagittal ridges are a product of taphonomic deformation.
Line 370 “The basal tubera are larger than the OC…” In what way are they larger? Dorsoventral depth? Etc.
Line 393 Reference Fig. 20 at the end of the sentence “…and the basioccipital posteriorly.”
Line 395 “It is a deeper…” Deeper in what way? Dorsoventrally? Mediolaterally? Specify in the sentence.
Line 399 Label the paracultriform ridge in Fig. 22.
Line 414-416 “Unlike the supraoccipitals of younger specimens it appears that it does not contribute to the surfaces of the cranial vault surrounding the brain.” This seems odd. The supraoccipital is involved in the external portion of the braincase wall in Protoceratops and Triceratops.
Line 422 “concave anterior surface” The anterior surface of the pop is convex on the lateral half of the process. Is this statement referring to the medial portion of the exoccipitals/opisthotics?
Lines 432-427 Label foramina for cranial nerves X-XII on Fig. 24. Also, go through the document and any place referring to these nerves make sure they are referred to as “cranial nerves X-XII” not “nerves X-XII”.
Line 436 “dorsal-most margin of the anteriolaterally orientated CN V” Change “orientated” to “oriented” Also this is a foramen margin, not a nerve margin. Also, label this border in Figure 25.
Line 456 Label the preprootic strut on more views in Fig. 27
Line 468 “It is unclear where the prefontal contact would sit.” My first inclination would be to place the transition from nasal contact to prefrontal contact at that break in slope in the sutural margin.
Line 475 Add reference to “Fig. 29: fc” at the end of the sentence “A low, blunt sagittal crest…”
Line 486 Explain what is meant by “correspond closely” here.
Line 506 Sereno (2010) also suggests that the exoccipitals contribute to the occipital condyle in juvenile Psittacosaurus. Cite somewhere here and adjust the sentences to include.
Line 511 It is important to note that the exoccipitals contribute significantly to the occipital condyle of derived Ceratopsian dinosaurs (most members of Neoceratopsia), so Averianov et al (2006) were on fairly solid ground when making that suggestion.
Line 520-522 The discussion of the supraoccipital has far more certainty that is warranted by the data. The adult specimen does not give clear indications of where the borders of the supraoccipital are and, given the fact that this adult specimen is known to be dorsoventrally compressed and sheared (Hedrick and Dodson, 2013), it is not the strongest ground to suggest dramatic shape changes from. These changes are possible at best, not even likely given the fact that both juvenile and adult skulls shown here are taphonomically distorted. Rephrase section with less certainty.
Line 529 How is the muscular growth linked to the postural change? Is it more difficult to hold a head essentially horizontally when bipedal vs when quadrupedal?
Line 547-548 Large well-define hemispheres first posited in Coombs, 1982. Do we have other perinatal ornithischians to compare with the current sample to see what shape the brains are at this stage?
Line 549-560 “likely due to thickening of the meninges and expansion of the brain through maturation.” Need to cite a reference indicating that the meninges thicken through ontogeny.
Line 569-570 “It is well-known that…” Even established features of non-ceratopsid ceratopsians are not well-known in the vert paleo community outside a small circle of ceratopsian workers, let alone proposed ontogenetic postural shifts. It has been proposed and supported by a few papers.
Line 572 Citation needed for sentence ending in “…lengths of their forelimbs and hindlimbs.”
Line 573 Citation needed for “Adults were always… half the length of the hindlimbs.”
Line 577 Citation needed for sentence beginning “Bone histology…adapted to bipedality during ontogeny, after age 4.”
Line 582 The sentence “The postural and bone histological analysis… and a definitely bipedal adult” is out of place. Move to later in the discussion.
Line 592 “It is important to be sure that the method is plausible, and indeed our data may contribute to resolving the debate.” This seems like an optimistic appraisal of the value of the data in question. While it certainly meaningfully contributes to the debate, it will only go so far in resolving it.  Rephrase the sentence.
Line 611-614. What do these reconstructed habitual alter postures mean for the stance of Psittacosaurus? Is one more likely for a biped or quadruped? Why? Need to explicitly state what head postures one would expect for a quadruped or a biped and then state what the observed pattern means for Psittacosaurus gait. At the moment the reader does not see why the changes of head posture are highly consistent with the previous study on posture and locomotion. Also, please provide a single sentence summary of those results here. People shouldn’t have to look up another paper to understand what the big picture conclusions are when those conclusions are the basis of the argument. To be sure, I am not suggesting a detailed summary of Zhao et al., 2013, but the points most salient to the argument need to be made in this paper.
Line 627 The authors should explore the implications of the changes in the cranial nerve foramina in the exoccipital more. I feel like this section is too short. Phylogenetically, members of Ceratopsidae have only two openings, while protoceratopsids, basal neoceratopsians, and Psittacosaurus should have three.
Line 630-631 “The CT study reported here… post-processing of the scan data” This is a throw-away line. Many studies have shown this. Either cite a few, or just delete the sentence entirely and adjust the following sentence to be the first sentence in the paragraph.
Line 630-636 This entire paragraph is difficult to follow. I am unclear as to what the message of this paragraph is.
Line 641 “…the LSC orientation is well aligned with expectations of head posture” I am repeating a point, but the authors need to explicitly state what those expectations of head posture for different gaits are.
Line 643-644 “Braincases are often neglected…because they are believed to be static and unvarying” Citation needed. I always thought it was because they were either inaccessible inside articulated skulls or because they weren’t preserved in many disarticulated ones.
Line 645 “…many grew at different rates” Cite the data table which demonstrates this quite clearly.
Line 645-646 “Elements that remain similar in relative size or morphology throughout growth may prove useful phylogenetic characters” Based on what? Presumed consistency in morphology through ontogeny associated with consistent relative size? This sentence appears to be making a point, but it is incomplete at the moment. Complete the thought for what makes a good phylogenetic character and why braincases should be good character sources. The following sentence is also unclear. Clarifying it might help make this point.
Line 649-650 See above long comment on the frontal ossicles.
Line 651 “Such well defined hemispheres are unusual in ornithischians.” Citation needed.
Line 654 Change “(Hailu & Dodson, 2004)” to “(You & Dodson, 2004)” Also change reference. Author’s name is Hailu You (when presented in the western format of given name first, surname second).
Line 655 “This frill becomes large and ornate in ceratopsids.” Citation needed. Perhaps Dodson et al., 2004
Line 661-663 “Ceratopsid braincases appear very different as a whole, as do the individual elements, but the general configuration remains the same as in basal ceratopsians.” This sentence seems vague & unhelpful. Are there specific differences or similarities to highlight?
Just glancing over the references, I’m noticing a lack of DOIs for electronic resources. Those can expedite the process of locating electronic resources and I’d recommend including them in every electronically accessed reference unless PeerJ specifically forbids it. The authors should double-check their references to make sure there are no typos and that the reference format is consistent.
References cited
Brown, B. and E.M. Schlaikjer. 1940. The structure and function of Protoceratops. Annals of the New York Academy of Sciences 40:133–266.
Chinnery, B.J. 2004. Morphometric analysis of evolutionary trends in the ceratopsian postcranial skeleton. Journal of Vertebrate Paleontology 24:591-609.
Chinnery, B.J. and D.B. Weishampel. 1998. Montanoceratops cerorhynchus (Dinosauria: Ceratopsia) and relationships among basal neoceatopsians. Journal of Vertebrate Paleontology 18:569–585.
Chinnery, B.J., and J.R. Horner. 2007. A new neoceratopsian dinosaur linking North American and Asian taxa. Journal of Vertebrate Paleontology 27:625–641.
Coombs, W.P., Jr. 1982. Juvenile specimens of the ornithischian dinosaur Psittacosaurus. Palaeontology 25:89-107.
Currie, P.J., R.B. Holmes, M.J. Ryan, and C. Coy. 2016. A juvenile chasmosaurine ceratopsid (Dinosauria, Ornithischia) from the Dinosaur Park Formation, Alberta, Canada. Journal of Vertebrate Paleontology 36:2 DOI: 10.1080/02724634.2015.1048348.
Dodson, P., C.A. Forster, and S.D. Sampson. 2004. Ceratopsidae; pp. 494–513 in D.B. Weishampel, P. Dodson and H. Osmólska (eds.), The Dinosauria, second edition. California University Press, Berkeley California
Dodson, P., H. You, and K. Tanoue. 2010. Comments on the basicranium and palate of basal ceratopsians. Pp. 221-233 in M.J. Ryan, B.J. Chinnery-Allgeier, and D.A. Eberth (eds.). New Perspectives on Horned Dinosaurs: the Royal Tyrrell Ceratopsian Symposium. Indiana University Press, 624p.
Dong, Z. M., & Currie, P. J. (1993). Protoceratopsian embryos from Inner Mongolia, People's Republic of China. Canadian Journal of Earth Sciences, 30:2248-2254.
Fastovsky, D. E., Weishampel, D. B., Watabe, M., Barsbold, R., Tsogtbaatar, K. H., & Narmandakh, P. (2011). A nest of Protoceratops andrewsi (Dinosauria, Ornithischia). Journal of Paleontology, 85: 1035-1041.
Galton, P.M. 1974. The ornithischian dinosaur Hypsilophodon from the Wealden of the Isle of Wight. Bulletin of the British Museum of Natural History 25:1–152.
Hatcher J.B., O.C. Marsh, and R.S. Lull. 1907. The Ceratopsia. U.S. Geological Survey Monograph 49:1–300.
Hedrick, B. P., & Dodson, P. (2013). Lujiatun psittacosaurids: understanding individual and taphonomic variation using 3D geometric morphometrics. PLoS One, 8(8), e69265.
Horner, J. R., & Goodwin, M. B. (2006). Major cranial changes during Triceratops ontogeny. Proceedings of the Royal Society of London B: Biological Sciences, 273:2757-2761.
Makovicky, P.J. 2010. A redescription of the Montanoceratops cerorhynchus holotype with a review of referred material; pp. 68–82 in M.J. Ryan, B.J. Chinnery-Allgeier and D.A. Eberth (eds.) New perspectives on horned dinosaurs: The Royal Tyrell Museum Ceratopsian Symposium. Bloomington, IN: Indiana University Press.
Morschhauser, E. M. (2012). The anatomy and phylogeny of Auroraceratops (Ornithischia: Ceratopsia) from the Yujingzi Basin of Gansu Province, China. University of Pennsylvania.
Sereno, P.C. 2010. Taxonomy, cranial morphology, and relationships of parrot-beaked dinosaurs (Ceratopsia: Psittacosaurus). Pp. 21-58 in M.J. Ryan, B.J. Chinnery-Allgeier, and D.A. Eberth (eds.). New Perspectives on Horned Dinosaurs: the Royal Tyrrell Ceratopsian Symposium. Indiana University Press, 624p.
Xu, X., P.J. Makovicky, X.-L. Wang, M.A. Norell and H.-L. You. 2002. A ceratopsian dinosaur from China and the early evolution of Ceratopsia. Nature 416: 314–317.
You, H. L., Tanoue, K., & Dodson, P. (2008). New data on cranial anatomy of the ceratopsian dinosaur Psittacosaurus major. Acta Palaeontologica Polonica, 53(2), 183-196.


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: ONTOGENETIC BRAINCASE DEVELOPMENT IN PSITTACOSAURUS LUJIATUNENSIS (DINOSAURIA: CERATOPSIA) USING MICRO-COMPUTED TOMOGRAPHY
Review round: 2
Reviewer: 1

Output:
Basic reporting: See general comments
Experimental design: See general comments
Validity of the findings: See general comments
Additional comments: I find the already well-written manuscript much improved after the changes made by the authors. Most of the suggestions and comments of the reviewers were implemented, although it appears to be a bit selective for some suggestions. This however is a minor issue coming down to individual preferences and opinions, and should not preclude publication.
I am happy to see that the discussion has been revised considerably and provides a broader discussion of ontogenetic changes in ceratopsians and other dinosaurs. The list of morphological changes during ontogeny in the conclusions provides a useful summary New/updated figures are very helpful and support the text a lot better now.
All in all, I find the text and figures to be of a high standard and ready 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: LATITUDINAL VARIATION IN PHLOROTANNIN CONTENTS FROM SOUTHWESTERN ATLANTIC BROWN SEAWEEDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: I find the theme interesting and valid to study, however, the paper is currently rather descriptive of such processes rather than being written as a hypothesis driven study, also, there are several problems related to the design and the interpretation of the results. Furthermore, the authors could link the different aspects phlorotannins production and the enviromental conditions. The paper also needs a thorough revision for improving the quality of English and correcting typos.
Experimental design: It is necessary to differentiate between intertidal and subtidal algae, in order to understand the processes that affect the different algae in the  of phlorotannins production. Furthermore, seasonal measurements and environmental conditions, such as water temperature, salinity and / or incident light, must be carried out in order to make consistent correlations. Authors must standardize the sample number
Validity of the findings: This study is only a photograph of the phlorotannins concentrations in certain brown algae, and although the manuscript speculates on the potential causes of the variations, there is no experimental support that allows such affirmations
Additional comments: I find the theme interesting and valid to study, however, the paper is currently rather descriptive of such processes rather than being written as a hypothesis driven study, also, there are several problems related to the design and the interpretation of the results.  This study is only a photograph of the phlorotannins concentrations in certain brown algae, and although the manuscript speculates on the potential causes of the variations, there is no experimental support that allows such affirmations. The authors could link the different aspects phlorotannins production and the enviromental conditions. The paper also needs a thorough revision for correcting typos.


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: LATITUDINAL VARIATION IN PHLOROTANNIN CONTENTS FROM SOUTHWESTERN ATLANTIC BROWN SEAWEEDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In general, the writing manuscript is clear, and the literature references are relevant and sufficient.

Throughout the text there are many instances of unseparated words, which should be separated. Please correct! Some examples include lines 21,32, 36, 37, 39, 40, 42, 51, 66, 70, 72, 77, 78, 79, 82, 85-9, 93, 96, 99, 103, 105-113, 116, 123-4, 127, 141, 144, 148, 150-1, 155, 157, 159, 161-2, 164-167, 170, 173, 179, 180-3, 188, 190, 198, 204-5, 209, 217, 221-3, 229, 238, 242-5, 250, 253, References list.

Abstract: There are few changes in the English to make. Please, also, check all manuscript.
Line 18 - Instead of “littoral”, change to “coast”
Line 20 – Instead of “dry weight of the species” change to “dry weight for the species”
Line 20 -  Instead of “reaffirming a typical amount of ….” change to “confirming reports of the typical amounts of…”
Line 21 - Instead of “chemicalsin” change to “chemicals in”
Line 23 – Instead of “..analyzed were verified significant differences on the amount of phlorotannins in their different individuals...” change to “analyzed there were verified significant differences on the amount of phlorotannins in different individuals..””
Line 24 - Instead of “coefficient of variation (CV)…” change to “coefficients of variation (CV)…”
Line 26 - Instead of “these aspects have been found…” change to “these variables were found…”
Lines 28/29 - Instead of “probably could easily respond to..” change to “probably as a response to..”

Introduction: The introduction is clear and relevant. It provides the justification for your study. I suggest you to include a clearer definition of the hypothesis.
Line 109 - Instead of “D. mertensii(Martius) Kützing change to “D. mertensii (C. Martius) Kützing”.
Line 111 – Instead of “S. stenophyllumMartius, S. ramifoliumKützing” change to “S. ramifolium Kützing, S. stenophyllum C. Martius”

The Figures and tables were included, as well as the raw data, however the words in the raw data should be translated to english.
Experimental design: Material and Methods
This is an original primary research. The methods are described with sufficient detail and information to permit replication, however, the time of year of collection of each population at each site should also be included.  Also, a better explanation about the “small specimens analyzed” should be given.

Figures and Tables are also relevant. Some details should be improved, for instance:
Table 1.
1.	Line 2 - Instead of “collect places”, change to “collection places”.
2.	In the table column “seaweed species” should include the alphabetical order in the list (Sargassum ramifolium should come before S. stenophyllum)
3.	Compare Table 1 and line 154 of the manuscript. There is a mistake? D. delicatula should be described as local Guarapari - ES and not Armação dos Búzios. Please check!
4.	Compare Table 1 and line 178 of the manuscript. There is a mistake? D. polypodioides should be described as local Porto Seguro – BA, however it is marked only in Guarapari- ES Please check!
Table 2.
1.	Line 3 - Instead of “collect sites” change to “collection sites”
2.	Line 3 – should include the word “coordinates” after ..” including the …”
Validity of the findings: Impact and novelty assessed. Conclusive results. Data is robust, statistically corrected.

The conclusions support the results.

Line 173 – concerning the site Ilhéus : Compare the line 173 - Ilhéus – Back Door, and in  Table 1 Ilhéus – BA.. Which is correct?
Additional comments: There is no question that the theme as such has great relevance, includes original data, and must be published. However, there are some changes that must be made. Please see the above.


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

Input:
Title: BORNEO CORAL REEFS SUBJECT TO HIGH SEDIMENT LOADS SHOW EVIDENCE OF RESILIENCE TO VARIOUS ENVIRONMENTAL STRESSORS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript presents research on a question very relevant to coral reef ecology and conservation. Specifically, the authors seek to:
“1) quantify benthic cover, coral cover and health, 2) compare the prevalence of impaired health in the dominant coral species, 3) identify key parameters related to sediment delivery that influence benthic cover and health along an inshore to offshore gradient, and 4) assess how resilient these inshore reefs are to future changes in sediment supply.”
They present results relevant to these questions, though I have some questions about the collection and interpretation of some of the environmental data—see section on experimental design.
The manuscript is generally well written with clear sentences. There are a few acronyms that were not defined the first time they were used. Appropriate references were used to support most points but there are one or two instances where a key reference was missed (in particular, Storlazzi 2011—see comments in pdf) and several instances where a citation was used incorrectly (e.g. were listed when the reference did not support the statement made in the manuscript). Several references are incomplete in the reference section.
There are several instances in which sentences needs to be clarified, see pdf for specific comments.
Figures are very helpful, but:
Fig. 1: add a box around the Miri area on the small-scale map, to show the area that is enlarged.
Fig. 2: state clearly in the legend which sites these environmental data come from, which is important since you did not measure these parameters at all sites
Fig. 3: change sedimentation rate to “trap accumulation rate” or “trap sedimentation rate”, or other wording to highlight that these measures are from sediment traps, which don’t reflect actual accumulation rate on the benthos
Fig. 4: It would be worthwhile to see the variation in sediment size for each site. As it is presented I’m guessing that we are seeing the mean for all traps at a given site (should specify in legend). Possibly instead of showing all size fraction, show % mud (mean + SE) for each site
Fig. 5: Same comment as Fig. 4 about not seeing a measure of variation
Fig. 6: it is difficult to see feeding scars in 6B. There is no explanation of what is shown in 6D. explain what non-focal bleaching represents.
Fig. 7: Indicate what the error bars represent. Standard error?
Fig. 8: same comment as Fig. 7.
Fig. 9: same comment as figure 5.
Fig. 10: same comment as Figs. 7-8
Fig. 11: consider providing a more thorough explanation of the figure in the legend. Explain the Eigenvectors and what the length and direction means. Explain what the circle represents. Should the legend read “Distance-based redundancy analysis plot” rather than DistLM plot? I would recommend removing the box that automatically comes in PRIMER which highlights the transformation and resemblance analysis; best to put this in the legend.
Fig 12: Same comments as fig. 11
Experimental design: This manuscript presents research in coral reef ecology, which is within the aims and scope of Peer-J (Biological Sciences, Environmental Sciences). It sets the stage clearly for the need for this research (i.e. better understand the dynamics of turbid reefs, and assessing their resilience to future disturbances).

The research questions are defined clearly at the end of the introduction, and the manuscript presents data to answer these questions. Methods are a bit unclear at times, and in some cases some weakness must be addressed (at least in the discussion and interpretation of results should be made in light of these weaknesses).
Line 142: Explain what “odyssey and HOBO” mean.
Line 143: explain why these parameters were only recorded at one site, and implications for extrapolation of these data
Line 144: I worry about how effective light-measuring devices are after 2 weeks in the field—would they get covered by sediment over that time period?
Line 148: weather was found on worldwideweatheronline.com—which site?
Line 153: look up Storlazzi 2011 use and misuse of sediment traps in coral reef environments (journal coral reefs) for a thorough discussion of these traps and what they measure. Did yours include baffles?
Line 154: sediment traps are usually changed much more frequently than 9 months. I worry about organisms settling in the traps over this long time period and influencing the amount/type of sediment collected in the end.
Line 163 (and many other places in the manuscript): refer to “trap accumulation rate” rather than “sediment accumulation rate”, since traps overestimate actual accumulation rate
Line 166: describe in greater details how sediments were homogenized.
Line 167: provide the range of size for each size class
Line 176: explain if you used the entire benthic photos as the “quadrat” that you then analyze with CPCe. How big is this quadrat?
Line 177: are those points completely random, or stratified in some way?
183: how did you quantify bioerosion?
187: define focal and non-focal bleaching
195: coral genera, not species. Why these genera only and not Porites?
208: clarify your analysis and unit of replication
217: unclear why you used a Kruskal-Wallis
226: why did you lump all photosynthetic organisms in algae? At least in the Caribbean it makes some sense to divide into macroalgae, turf algae and filamentous cyanobacteria. It seems odd to me to include H’ and richness in the community assemblage.
231: why Euclidean rather than Bray-Curtis in this case?
241: this statement needs a reference. I’m not sure it’s something that occurs broadly, and across a wide range of % coral cover
242: But couldn't one argue this point the other way? What if a reef has a very low diversity, all with species that are quite susceptible to disease?

More generally on the methods:
•	sediment traps have been used a lot traditionally, but recent work has really highlighting their limitations in coral reef environments. You should reference the Storlazzi et al 2011 paper and make sure that your interpretation of sediment data takes into consideration what they highlight.
•	Your results present chi-square analyses but these are not described in the methods. Clarify and justify why a chi-square analysis.
Validity of the findings: The study provides new and valuable data on the status of coral reefs in this region.

I have questions about some analyses, including why chi-square analyses were performed in what seems better analyzed with an ANOVA (continuous dependent variable). The discussion could be fleshed out in several places, and in some cases a point needs to be reworded so that it accurately reflects the references cited, or to keep the statement within the scope of what can be said based of the data provided.

There are misinterpreted/misreported references in these lines: 396, 448, 463

Please review the first section of the results in Begin et al 2013. Sediment size and composition are not related in this study. Amend your statements that make broad generalizations suggesting that sediment size can be used as an indication of sediment origin.
Similarly, be careful of your statements suggesting that terrigenous sediment always have more organic material, or that the organic material is the cause of their negative impact.

When stating that cover of any benthic component is high or low, try to provide data from other reefs to compare. Similarly when comparing what is found on these inshore turbid reefs (and speculation on the processes causing these patterns) compared to deeper offshore reefs.

Be very careful when comparing sedimentation rate measured here via traps to sedimentation rate reported in other studies, in particular if those rates were measure by other methods. Make sure that you clearly highlight that your results represent trap accumulation rates.

Lines 433-435: reword. This is too strong a statement. You are finding correlation, and don’t have the data necessary to state causation. Additionally, you list “depth” as a “sediment-related factor”, which is arguable.

Generally, the discussion needs to be fleshed out to better explore the various potential causes for the patterns observed here and be more nuanced about the limitations of the study.

Line 283-4: clarify is this is H’ rather than richness
Line 286: was a quantitative analysis performed about this? Provide results.
Line 345: There is no Fig 11a

See pdf for more in-text comments
Additional comments: This study is worthwhile and provides data on reefs in an under-studied area with limited baseline data. It also measures multiple environmental parameters that are related to the study questions, which strengthens the arguments and conclusions. However the limitations of the data need to be made more clear (e.g. that some environmental data are only from some sites; better contextualize the sediment trap accumulations rates), and the authors need to revisit some assumptions (e.g. that fine sediment is of terrestrial origin). More details are needed in the methods and the discussion needs to be fleshed out some more. The authors should also review all references and make sure that they are appropriate as citations for the statement they are cited in. I found several problems on that level and wonder if there are more that I didn’t catch. This study is a worthwhile one that should be published, but it does need more polishing to address the current weaknesses.


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: BORNEO CORAL REEFS SUBJECT TO HIGH SEDIMENT LOADS SHOW EVIDENCE OF RESILIENCE TO VARIOUS ENVIRONMENTAL STRESSORS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is generally well written.  There are minor formatting issues (scientific names are not italicized, the “sp.” after a generic epithet should not be italicized)

The authors cite several studies but I suggest the following key papers in the relevant literature should be included:

Darling, E.S., Alvarez‐Filip, L., Oliver, T.A., McClanahan, T.R. and Côté, I.M., 2012. Evaluating life‐history strategies of reef corals from species traits. Ecology Letters, 15(12), pp.1378-1386.

DeVantier, L.M., De’Ath, G., Turak, E., Done, T.J. and Fabricius, K.E., 2006. Species richness and community structure of reef-building corals on the nearshore Great Barrier Reef. Coral reefs, 25(3), pp.329-340.

DeVantier, L. and Turak, E., 2017. Species richness and relative abundance of reef-building corals in the Indo-West Pacific. Diversity, 9(3), p.25.

Done, T., Turak, E., Wakeford, M., DeVantier, L., McDonald, A. and Fisk, D., 2007. Decadal changes in turbid-water coral communities at Pandora Reef: loss of resilience or too soon to tell?. Coral Reefs, 26(4), pp.789-805.

Flower, J., Ortiz, J.C., Chollett, I., Abdullah, S., Castro-Sanguino, C., Hock, K., Lam, V. and Mumby, P.J., 2017. Interpreting coral reef monitoring data: A guide for improved management decisions. Ecological indicators, 72, pp.848-869.

Johns, K.A., Osborne, K.O. and Logan, M., 2014. Contrasting rates of coral recovery and reassembly in coral communities on the Great Barrier Reef. Coral Reefs, 33(3), pp.553-563.

Licuanan, W.Y., Robles, R., Dygico, M., Songco, A. and van Woesik, R., 2017. Coral benchmarks in the center of biodiversity. Marine pollution bulletin, 114(2), pp.1135-1140.

Smith, J.E., Brainard, R., Carter, A., Grillo, S., Edwards, C., Harris, J., Lewis, L., Obura, D., Rohwer, F., Sala, E. and Vroom, P.S., 2016. Re-evaluating the health of coral reef communities: baselines and evidence for human impacts across the central Pacific. Proc. R. Soc. B, 283(1822), p.20151985.

Vroom, P.S., 2011. “Coral dominance”: a dangerous ecosystem misnomer?. Journal of Marine Biology, 2011.

I suggest assigning numbers to sites (e.g., Eve’s Garden as Site 1, Anemone Garden as Site 2, Siwa Reef as Site 3.  Site numbers related to distance are easier to remember than acronyms.

I suggest the authors organize their findings and discussion better to substantiate the conclusion that the reefs they study are resilient
Experimental design: Please specify the sampling domain and how the domain was sampled to allow us to determine to where the inferences made could be applied.  In particular, please state where in the reef the transects were positioned (i.e., leeward or windward relative to the monsoons of SE Asia; the reef zone sampled (upper reef slope? lagoon?) and identify which are the replicates and which are the subsamples.  Was there randomization or was sampling haphazard? What is the basis for determining transect length used?

Please show a more detailed map showing the reef outlines and where in the reef the transects were located.

The methods section identified the use of the Kruskal Wallis test.  Are these the many instances of the Chi-square values being reported?

Please clarify the substrate categories (particularly algae on rock, algae on rubble, and algae on coral) used with CPCe. Why was this not discussed in the results? Was turf algae lumped with macro-algae? Note that short turf algae is available for coral recruitment (Flower et al 2017).

Please describe in detail how disease, bleaching, bioerosion, pigmentation, mucus production, scars were quantified.
Validity of the findings: I suggest the authors organize their findings and discussion better to substantiate the conclusion that the reefs they study are resilient

Regarding lines 365-375 of the discussion, the papers listed earlier (particularly Smith, Vroom, Licuanan) state coral cover gives indications on suitability of a reef to coral growth but not resilience. The conclusion concerning the latter need to be substantiated.  Personally I think the lower diversity found (lines 382-383) indicates loss of resilience in the Miri reefs studied.  There might have been recovery but not reassembly (using the terminology of Johns et al).  Note that many of the dominant coral genera reported are stress tolerators (see the paper by Darling et al).  Are the Porites listed branching or massive?  The latter paper indicates these two forms of the genus have different life history strategies.  Lines 426-431 indicate life history patterns are more telling than hard coral cover.  However, valid comparisons can be made only if the same reef zones (depth, leeward or windward sides of reefs) and reef habitats (reef slope, lagoon, etc) are being compared.

Please explain what lack of structure (line 392) means.  It appears the reef communities being compared are not comparable given the differences in depth and the absence of information on the locations of the transects.

The authors’ statements about the stability of coral cover (lines 374 to 375) are rather speculative given the typical spatial (within and between) variability of hard coral cover.  Ideally the authors demonstrate that the previous studies cited looked at the same depths, the same zone of the reefs, and the same reefs.
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: BORNEO CORAL REEFS SUBJECT TO HIGH SEDIMENT LOADS SHOW EVIDENCE OF RESILIENCE TO VARIOUS ENVIRONMENTAL STRESSORS
Review round: 1
Reviewer: 3

Output:
Basic reporting: I have read this manuscript very carefully and I find it very difficult to understand the main message that the authors are trying to convey.  I am not certain that they are using the word “resilient” in the strict sense.  At times they maintain the study reefs are resilient and at other times they emphasize their susceptibility to stressors.
It does not make sense to speak of reefs as “resilient” without identifying the stressors they are resisting or re-bounding from.  And they are using the word “health” without defining it
In general, I found a lack of clarity in the writing, with words used in very imprecise ways.  For example, line 106, what is meant by reef “stability”.  What is meant by reef “function”?  What do chlorophyll a and symbiont density indicate?
In general, I think that the lack of precision in the writing may reflect a lack of understanding of some of the basic concepts and mis-interpretation of some of recent scientific literature.
Some of the literature citations do not seem to support the associated statements.
Experimental design: I found it hard to determine exactly how the research was conducted.  Some of the methods are not sufficiently described.
Were the transects selected randomly? ( line 137) That is, independently of each other?  It does not appear so.  In that case, it is not possible to extrapolate the results to entire reef areas.  The data could still be useful, but the fact that the transects were chosen haphazardly should definitely be discussed. If you can not be sure that the sampling units (transects) were representative of the reef area, you can not compare reefs.  If the transects were permanent and data were collected on the two occasions from exactly the same transects, more can perhaps be said with confidence.
If the transects were not selected randomly, then at least some of the statistical analysis is not valid.
And it is not clear without a pilot study if 6 transects is a sufficient number.
Line 153---  I think there are problems leaving sediment traps out for such a long period of time. Were salts rinsed from the sediments?
Line 183—need more explanation as to how each of these signs were identified
Line 190   this is a very small sample size—explain also that overall bleaching was calculated
Validity of the findings: I am not able to evaluate the statistical analyses in the paper.
Some of the conclusions are not well-supported. In general, it appears that the authors are confusing correlation with causation in some of their statements
Line 240--  Higher coral cover is not always associated with greater probability of “impaired health”
Line 241—I think this is an oversimplification of Mydlarz et al’s paper.  If you have a reef with just a few species that are susceptible to diseases, then you have a low diversity reef that is not resistant.
Line 244—requires revision
Line 245--  what are “substrate structure predictors”?
Line 252-- what units were used for PAR?
Line 257  Rogers 1990 suggested further research was needed on sedimentation thresholds and it is not correct to state that this rate, based initially on just a few studies, is a threshold suitable for describing all reefs
Line 302—how was bioerosion identified in the field?
Line 305—what is the reference/citation for a 1evel of 10% of bleaching being low?? If 10% of the coral bleached each year, and it was a different subset of colonies, that would certainly be a sign of high thermal stress
Line 340   what does this really tell us?  62.5%?  not clear what this means
Line 353—so does this say that high diversity is not related to increased bleaching?
Line 365 and on – this discussion of relatively high coral cover is very confusing and not very convincing—
Line 383—once again, not convincing—any suggestion of trends in cover or biodiversity are not based on any real evidence
Once again, the language is not precise
Line 387—so if these reefs are “resilient”, why is there this suggestion that some species are missing because of high sedimentation?
Line 414—can this statement be supported?
Line 434—what is a “gradient” in coral composition?
Line 453—these sediment data cannot “confirm” anything given it is not known if they are terrestrial or not
Line 458—I don’t think 20% is a low prevalence!!
Line 472—I don’t recall a bleaching event being documented at their study sites
Line 480—I don’t understand this statement—and it may contradict what was said earlier in the paper
Line 486-487  doesn’t this also contradict earlier statements?
Line 538--  I would think that there might be some observations available for the time of peak sea water temperatures—from dive tour operators or someone?  It is not appropriate to assume that there was little bleaching on these study reefs
Additional comments: I hope that the authors will be able to substantially revise this paper. I had a very difficult time trying to follow just what was being said.  I think that there is some confusion regarding some of the key recent scientific references.I think that the paper would be substantially improved if the authors very carefully checked on their literature citations to ensure that they are accurately cited.
In some cases, it appears that the authors are confusing correlation with causation in some of their statements.
A few more specific comments follow:
Line 63—requires revision.
Line 85--  What does “fair” indicate?  Did the Reef Check surveys measure coral cover?
If the only coral cover measurements date back to 2000 and then 2002 (with a different method), then we do not know what the trends have been over the last several years. (see related conclusion near end of the paper)
Line 116   I do not understand this statement “why turbid reefs are resilient”--
Line 124--  here it says that the study reefs had 30 to 50% cover but they cite a 2002 paper/reference—
When did the reefs have this cover?  Is this what the authors measured?