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: FEEDING TRACES ATTRIBUTABLE TO JUVENILE TYRANNOSAURUS REX OFFER INSIGHT INTO ONTOGENETIC DIETARY TRENDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: “Feeding traces attributable to juvenile Tyrannosaurus rex offer insights into ontogenetic dietary trends” describes bite marks on a hadrosaurid dinosaur and provides interpretations of these traces in a larger context of dietary niche partitioning (or lack thereof) in T. rex. This study is well written and contributes meaningfully to a growing body of theropod bite mark studies. Figures and tables present the data clearly and fully (Table 2 and Figure 7 are a little redundant, but having the raw data on hand is appreciated). There are a few parts of this paper which need to be strengthened before I can recommend publication.

1) The authors do cite Longrich and colleague’s study on tyrannosaur bite marks, but they do not discuss the paper in much detail. I found this particularly surprising, because Longrich’s study also interprets their bite marks as feeding traces made by a juvenile or subadult T. rex. These traces seem to come from differently aged/sized individuals, and a more complete comparison should be included, especially since the authors are claiming that these new traces are the first published example of juvenile T. rex bite.

Longrich, Nicholas R., et al. "Cannibalism in Tyrannosaurus rex." PloS one 5.10 (2010): e13419.

2) The authors use the word “puncture” to describe the bite marks. Under Binford’s bite mark classification scheme, “puncture” has a very specific meaning relative to pits, scores or furrows. It in unclear if the authors are using the term in this context. If they are, Binford needs to be cited. If they are not, the authors should consider using the classification scheme since it is fairly straightforward and also allows better comparison and uniformity of terminology between their research and other vertebrate bite mark studies.

Binford, Lewis R. Bones: ancient men and modern myths. Academic Press, 2014.

See also D’Amore and Blumenschine, 2009 (full citation below) or the following for an abbreviated explanation of the classification scheme:

Drumheller, Stephanie K., and Christopher A. Brochu. "Phylogenetic taphonomy: a statistical and phylogenetic approach for exploring taphonomic patterns in the fossil record using crocodylians." Palaios 31.10 (2016): 463-478.

A few, minor edits:

Line 43 and elsewhere: I believe that the L in McLain (as in McLain et al., 2018) should be capitalized.

Line 54: Do the authors mean “fauna” rather than “phyla?” While I suppose it’s not technically wrong, using phyla in this context seems oddly broad.

Line 96: I believe there is a formatting hiccup here, with the text reading 23o instead of 23 degrees.
Experimental design: The underlying structure and reasoning of this project are sound, but there are a few areas that need further explanation to add detail and clarity.

1) What other predators are known from the locality? How were they excluded as potential trace makers? I am not necessarily arguing that the authors are incorrect in their identification, I only request that they flesh out their reasoning on how they came to the conclusion that these marks represent juvenile T. rex traces. As written, it sounds like the traces were only ever compared to tyrannosaur dentition. If all other taxa from the locality were too small to make these traces, list them and say so. If other groups’ teeth are morphologically distinct enough to exclude, say that as well. Simple association is a fairly weak argument for associating traces and trace makers, so adding more of this type of discussion would bolster the authors’ argument. The tooth shape and spacing measurements are compelling, but the omission of the rest needs to be addressed.

Along those lines, do any of the tooth marks preserve striations? Serrated teeth do not always leave striations behind, but when they are present, they can be very useful. If so, reference and add discussions addressing the following two papers on how to interpret striated marks and estimate minimum body size from them. This would also bolster the authors’ interpretations.

D'Amore, Domenic C., and Robert J. Blumensehine. "Komodo monitor (Varanus komodoensis) feeding behavior and dental function reflected through tooth marks on bone surfaces, and the application to ziphodont paleobiology." Paleobiology 35.4 (2009): 525-552.

D'Amore, Domenic C., and Robert J. Blumenschine. "Using striated tooth marks on bone to predict body size in theropod dinosaurs: a model based on feeding observations of Varanus komodoensis, the Komodo monitor." Paleobiology 38.1 (2012): 79-100.

If striations are not present, that is also worth mentioning.

2) There are some sections of this paper that I wish had just a bit more detail. For example, on line 43, the authors refer to an anatomical structure as “hadrosaur-like.” As a non-hadrosaur worker, this doesn’t actually tell me much. What is hadrosaur-like about it? Are there apomorphies that can be listed here? On line 105, the authors state that they compare the mark shape and orientation. To what? Were taxa other than T. rex observed in this study? Were the marks compared to other traces in the literature? As written, the authors don’t explain how they arrived at identifying the trace maker as T. rex.

3) The authors suggest that the presence of bite marks on caudal vertebrae suggest early access to the remains. The economy of bones does often guide the order of consumption (higher economy bones, such as femora, support more soft tissue, and are therefore targeted first while low economy bones, like phalanges, have less nutritional value and are therefore targeted last). This results in a predictable "scavenging sequence," in which certain regions of the body are typically consumed before others. Examples:

Hill, Andrew P., and A. K. Behrensmeyer. "Early postmortem damage to the remains of some contemporary East African mammals." Fossils in the making: Vertebrate Taphonomy and Paleoecology (1980): 131-152.

Haglund, William D. "Dogs and coyotes: postmortem involvement with human remains." Forensic taphonomy: the postmortem fate of human remains (1997): 367-381.

This sequence was originally based on mammalian predator and prey species, and deviations from the scavenging sequence are sometimes used to help differentiate predator and prey types. Here is an example involving birds:

Behrensmeyer, Anna K., C. Tristan Stayton, and Ralph E. Chapman. "Taphonomy and ecology of modern avifaunal remains from Amboseli Park, Kenya." Paleobiology 29.1 (2003): 52-70.

As another example, in which bears do seem to target the axial skeleton earlier than other predator groups:

Carson, E. Ann, Vincent H. Stefan, and Joseph F. Powell. "Skeletal manifestations of bear scavenging." Journal of forensic sciences 45.3 (2000): 515-526.

In most groups, viscera and limbs are targeted first while the axial skeleton is targeted last. This would not support the author’s interpretation that bite marks on the centra of cervical vertebrae would suggest early access to remains. Instead, this seems more consistent with late access or at least more complete consumption of the remains (a predator can work through all of the scavenging stages depending on the size of the prey and the duration of access to the remains). Since bite marks are only known on these vertebrae, this pattern would be more consistent with scavenging in the framework of the known scavenging sequence.
Validity of the findings: In the previous section, I discussed why I am not entirely convinced that these traces can be associated with predation over scavenging based on mark location. These two feeding strategies are notoriously difficult to differentiate in the fossil record. In this case, identifying these traces as predation rather than scavenging has bearing on the conclusions the authors draw regarding niche partitioning. If juvenile T. rex could in fact take larger prey, this would suggest less niche partitioning than expected given their relative size. The authors cite several examples using modern crocodylians as examples of groups with significantly different diets across ontogeny.

However, if these marks represent scavenging, the body size of the prey item has little bearing on niche partitioning during predation. To use modern crocodylians as an example again, some modern crocs have been known to scavenge adult elephants, even though they cannot successfully hunt these animals. This has been used to interpret some fossil crocodylian bite marks as incidents of scavenging:

Antunes, Miguel Telles. "Huge Miocene Crocodilians From Western Europe: Predation, Comparisons with the “False Gharial” and Size."

I think that the implications of both scavenging and predation should be discussed in this paper, because I do not think that the authors have adequately argued that the traces represent one behavior to the exclusion of the other.
Additional comments: Overall, I think this is a very interesting study. My suggestions are largely meant to strengthen the authors' existing arguments. I do feel that the addition of a section discussing the implications of scavenging rather than predation is warranted.


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: FEEDING TRACES ATTRIBUTABLE TO JUVENILE TYRANNOSAURUS REX OFFER INSIGHT INTO ONTOGENETIC DIETARY TRENDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript generally meets the criteria for publication. The description of the geological setting can use minor editing and wording changes. Additional citations will improve the discussion of T. rex bite force (Bates and Falkingham 2018), and indention of bone by ziphodont-toothed theropods (Gignac et al. 2010). Also cite Carpenter (1998) and Happ (2008) for records of predation attempts.
Experimental design: The methods are appropriate to the scope of the manuscript. Cite Fahlke (2012) as a study similar to this one.
Validity of the findings: The tooth marks appear to match a specimen of specific size and age. I suggest adding a sentence or two to the discussion about criteria you'd use to identify tooth marks of a tyrannosaur younger or older than one of this exact ontogenetic stage. How would you accommodate different tooth spacing and size?
Additional comments: The figures are clear, but the measurement template (Figure 7) is a dromeosaur tooth.  A tyrannosaur tooth would be far more appropriate.


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: FEEDING TRACES ATTRIBUTABLE TO JUVENILE TYRANNOSAURUS REX OFFER INSIGHT INTO ONTOGENETIC DIETARY TRENDS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have fully addressed all of my previous comments on their manuscript “Feeding traces attributable to juvenile Tyrannosaurus rex offer insights into ontogenetic dietary trends.” The updates have strengthened an already strong study. I only have a very small number of extremely minor comments. Line and page numbers in my comments are based off of the provided Word document with track changes.

Page 2, line 80: insert a space between 4 and m.

Page 3, line 112: caudalm should be caudal

Page 3, line 118: vertebra should be vertebrae

Page 3, line 125: (sensu D’Amore and Blumenschine, 2009) should probably be inserted here, regarding presence/absence of striations in bite marks left by ziphodont teeth. Full citation:

 D'Amore, Domenic C., and Robert J. Blumensehine. "Komodo monitor (Varanus komodoensis) feeding behavior and dental function reflected through tooth marks on bone surfaces, and the application to ziphodont paleobiology." Paleobiology 35.4 (2009): 525-552.

Page 6, lines 236 and 244: Crocodylian (with a y) is technically the correct name for this clade.

Page 6, line 242: crocodile doesn’t need to be capitalized here.
Experimental design: No comment
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: FEEDING TRACES ATTRIBUTABLE TO JUVENILE TYRANNOSAURUS REX OFFER INSIGHT INTO ONTOGENETIC DIETARY TRENDS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The reporting is sound. Another reference is suggested (see 3. Validity of the findings), and a few wording suggestions are on the edited manuscript. The references formatting is inconsistent.
Experimental design: Quite good, as before.
Validity of the findings: The ventrolateral position of the bite marks provides additional support for late-stage carcass consumption. Big Mesozoic dinosaurs had a lot of meat on the tail, unlike that available to modern scavengers on mammal and bird carcasses. That suggests the tail would be an early target. However, if this tyrannosaur was digging into the tail at an early stage from this direction, it would get a mouthful of haemal spine. I'd leave it there; otherwise you risk a speculative whirlpool of suggests, woulds, and ifs. (Do jaguars eat caimans' tails first? Their rostra aren't built to rummage in viscera. What about mammals scavenging on Nile crocs? Nile monitors feeding on Osteolemus? Shrikes on lizards? Komodo dragons go for guts first; crocs seem to eat whatever they want whole.)

Sentences addressing this issue are suggested, and a citation+reference added.
Additional comments: The authors circumspectly incorporate suggestions from both reviewers. They did not fully address the issue of identifying bite marks from a juvenile tyrannosaur whose tooth spacing does not exactly match the Burpee specimen. Happily, adding one word ("morphology"; line 207 of the edited manuscript) resolves the issue, especially with the added discussion of ontogenetic trajectory.

The tyrannosaur tooth template is welcome in Figure 7.


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: MITOCHONDRIAL COMPLEX ACTIVITY IN PERMEABILISED CELLS OF CHRONIC FATIGUE SYNDROME PATIENTS USING TWO CELL TYPES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is generally sound. There are however several typos in the document which need to be corrected.
112	missing word: Diagnostic
147 	Possible typo EGTA
154	Typo injectizon
249	Typo extra work ‘for’
104 Workd- work

References are OK. One is a PhD thesis reference 30
Experimental design: 120	General comment: No information regarding suppliers of materials
126	How was differentiation of myoblast to myotubes established?
132 	Were the wells pre-coated with poly-d-lysine? This may impact cell survival
205	In table 1, the authors state that glutamine was injected however the figure 4 states glutamate. The authors must confirm which compound was used.

I wonder whether the title of the paper is a true reflection of the data?
Validity of the findings: The permeabilised myoblast expt failed to work likely due to insufficient cell/mitochondria.

Not too much should be read into the myoblast data.

239 Successful recordings of the effect of glutamate and malate,
and TMPD and ascorbate were made in control and CFS myotubes  Glutamate does not appear to work in myoblasts (Fig3A).  is this statement correct?

Glutamate and Glutamine are mixed up. The authors need to make sure the correct word is used.

205	In table 1, the authors state that glutamine was injected however the figure 4 states glutamate. The authors must confirm which compound was used.

Did the myoblasts and PBMC used the same glutamine/glutamate substrate
Additional comments: Although on the small side this is a useful study carried out using similar approaches to previous work by the group on PBMCs. The limitations of myoblasts in this type of approach are mentioned and the authors should not over interpret the data based on the myoblasts.

The PBMC data is solid showing no difference between patients and controls with respect to mitochondrial complex activity

One thing to consider for future expts is the mitochondrial burden of pen and strep in conjunction with antifungal amphotericin B. Pen and strep reduces OCR in human fibroblasts. It would be worth investigating how these anitbiotics and fungicides affect the results particularly on PBMCs.


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: MITOCHONDRIAL COMPLEX ACTIVITY IN PERMEABILISED CELLS OF CHRONIC FATIGUE SYNDROME PATIENTS USING TWO CELL TYPES
Review round: 1
Reviewer: 2

Output:
Basic reporting: The paper is well written and most of the references are appropriately cited. The authors have covered the literature and background of the study logically and appropriately. The language of the manuscript explaining results and background reads elegant. The scientific findings are clearly explained in professional English throughout the manuscript. The article conforms to an acceptable format of the journal. Figures legends are well described, and figures are of acceptable quality. However, in line 63-68 quote “Previous studies have shown the energy production, including mitochondrial activity, of whole PBMCs from CFS patients to be significantly impaired compared to a healthy control cohort (4, 15). One study showed CFS PBMCs to have significantly impaired mitochondrial functioning both under basal conditions and when maximally stimulated to respire, under a number of experimental conditions (4).” I would suggest authors to slightly elaborate on the technique used in previous study to draw the conclusion of defective mitochondrial function. Then it will bring the contrast of technological limitation of previous findings and importance of extracellular flux assay as used in the current study.
Experimental design: The present study has clearly and unambiguously laid down the research question and the experiments are well designed to support the claims. The study investigated a plausible mitochondrial dysfunction as a cause of CFS. Authors explored this hypothesis using extracellular flux assay using seahorse. It serves as a great tool to fill in the gap on functional role of mitochondrial ETC complex in the pathogenesis of CFS. The method section has been well described for any independent investigator to repeat the study.
Validity of the findings: Authors have taken good care to include proper control in their data representation. The conclusions in the present study is appropriately stated and authors themselves are cautious in making far stretched conclusion of the study, which is impressive. Small sample sized of the study is also well acknowledged by the authors while drawing conclusion from the experiments.
Additional comments: Though the study shows a negative data, but the authors in the study have used all proper controls to draw their conclusion. I will recommend this work to be accepted for publication with no revision. One thought I ahd was, it would have been nice if authors had used some positive control e.g. say cells with defect in complex 1 activity in their seahorse study to at least show that the assay is working but their experimental setup do not show any positive effects between control and CFS derived myotubes/PBMC.


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

Input:
Title: THE ROLE OF JUVENILE HORMONE IN REGULATING REPRODUCTIVE PHYSIOLOGY AND DOMINANCE IN DINOPONERA QUADRICEPS ANTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The study by Pamminger et al. investigated the role of juvenile hormone (JH) in dominance and fertility in the queenless ant, Dinoponera quadriceps. The researchers applied a juvenile hormone analog (JHa) to dominant workers to measure changes in fertility and dominance rankbehavior. The results showed a decrease in fertility associated with JHa treatment, which is consistent with patterns in other ponerine ants; however, there were no significant effects of JHa treatment on dominance rank or behavior.

The manuscript was well written and conceived, and therefore I recommend a "pass" in this section.
Experimental design: The experiments were well designed. The sample sizes were low, but not outside norm for these types of studies. The authors report that one reason they may not have detected an effect of JHa treatment on dominance rank/behavior was due to insufficient sample size, but they do report a significant effect of JHa treatment on fertility.

The methods were explained in sufficient detail and were reasonable given constraints of the system; therefore, I recommend a "pass" for experimental design.
Validity of the findings: Statistical analyses were sound, and the results were convincing. The conclusions were also well stated, and alternative explanations of negative results were provided.
Additional comments: 34-35 – Why do you think that additional samples would lead to a significant, negative relationship between JHa treatment and dominance behavior? Was there a non-significant trend? If not, this seems too speculative. Other studies have also found effects of JHa treatment on fertility but not behavior, so this result is not so surprising (e.g., Cuvillier-Hot et al. 2004).

57 – Consider starting a new paragraph beginning with, “While most modern ants have a specialized queen caste…”

72-74 – Missing citiations. Consider citing the work of Elizabeth Tibbets and Zachary Huang on paper wasps as well as the work of Sasaki on Polistes chinensis.

109-111 – It would be helpful to lay out predictions here (e.g., “If JH functions similarly to other queenless ant species, then we predict JH will suppress ovarian development and cause high ranking workers to decrease in status. If JH functions as a gonadotropin, similar to solitary insects and social wasps, then we predict…)

170 – The term “aggression” seems imprecise in this context. Two types of aggression exist in this species: defensive aggression towards an intruder, and dominance-based aggression towards another nest mate. Here, you are referring to the former, and at least mentioning this would be helpful.

196 – Is “distal” the correct term here? I’ve also seen this referred to as “proximal.” Maybe leave out this terminology and just say the “end closes to the oviduct with most fully developed eggs if present.”

250 – Should be “decreased.”

267 – Delete extra period.

Discussion – I think there is room here to place these findings in the broader context of ant reproduction, dominance, and fertility signaling. The results presented here are consistent for other gamergate led ant societies (Harpegnathos, Streblognathos, Diacamma). The role of JH therefore seems to be clear in these societies, and there remain more questions about how JH functions in true queens of other ant species. Previous studies have also investigated the connection between JH and signals of fertility. Your clear demonstration that JHa reduces fertility provides an important contribution to this area of research. I would suggest including an additional paragraph that addresses these points, including reference to the role of JH and fertility signaling. Several citations below relate to this in ants, termites, and with respect to signaling the caste of ant brood:

Cuvillier-Hot, V., Lenoir, A., & Peeters, C. (2004). Reproductive monopoly enforced by sterile police workers in a queenless ant. Behavioral Ecology, 15(6), 970-975.

Brent, C. S., Penick, C. A., Trobaugh, B., Moore, D., & Liebig, J. (2016). Induction of a reproductive-specific cuticular hydrocarbon profile by a juvenile hormone analog in the termite Zootermopsis nevadensis. Chemoecology, 26(5), 195-203.

Penick, C. A., & Liebig, J. (2017). A larval ‘princess pheromone’identifies future ant queens based on their juvenile hormone content. Animal Behaviour, 128, 33-40.

Kelstrup, H. C., Hartfelder, K., Nascimento, F. S., & Riddiford, L. M. (2014). The role of juvenile hormone in dominance behavior, reproduction and cuticular pheromone signaling in the caste-flexible epiponine wasp, Synoeca surinama. Frontiers in zoology, 11(1), 78.

284 – “Ectatomma” should be “Streblognathus” if it is consistent with the citation.

Figures – Figures 1&2 are not super intuitive and somewhat obscure the main results. I would prefer to see boxplots of ovarian traits for JHa-treated and control workers. There appears to be a good amount of overlap in Fig. 1, and a boxplot would show this clearer.

Raw data supplement – Please add explanation for “treatments 1 and 2”; also, please add units throughout (e.g., head width, weight, etc.)


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

Input:
Title: THE ROLE OF JUVENILE HORMONE IN REGULATING REPRODUCTIVE PHYSIOLOGY AND DOMINANCE IN DINOPONERA QUADRICEPS ANTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The text is clear and well written. The experiment is well put in context and supported by adequate references.
Experimental design: It is a pity that you measured fertility based on three ovarioles only (is it per ovary or per individual?) (lines 194-199). D. quadriceps has a low fecundity and egg-laying females have few large oocytes in their ovaries hence randomly selecting three ovaries only for measurements may not provide an accurate picture. Given that D. quadriceps has 10 ovarioles per ovary only measuring all ovaries was likely feasible.
Validity of the findings: In the Results section you provide statistical results only. You do not provide values for the variables measured (e.g. actual weight, size and fertility of individual, lines 133-235). This makes for a rather disembodied paper and hinders the perception of the results and their biological significance. I would recommend adding the values of variables.

My main concern is that the results do not strongly support your claim that JH has an effect. Figure 1 shows that there is a difference between the treatment (red) and the control (blue). But it is also clear that a majority of the individuals show no difference and this is not taken into account in your interpretation. This is problematic because this is not a “classic” case where some individuals do not respond to a treatment for whatever reason, so that responding and non-responding treated individuals are split into two groups with non-responding individuals grouped with the control group. Here it is the control group that behaves strangely. The figure shows that all treated individuals responded and are grouped together (although one individual reacts slightly differently to the treatment) and that it is the control individuals that are unexpectedly split into two groups. 75% of control individuals (12/16) responded similarly to treated individuals, which clearly does not support your claim that JH treatment had an effect. In addition, the 4 control individuals responding differently (i.e. as expected from controls) are spread more than the 28 responding individuals (12 controls + 16 treatments) which is also unexpected. All this is clearly problematic and casts a serious doubt on the results.
Additional comments: Some minor comments are listed below:

Line 40-41: rephrase the sentence as “its” currently refers to “animals” rather than to “group” as intended

42: fishes instead of fish

50: eusociality does not imply monogyny and indeed many social insect species are polygynous hence please rephrase, e.g. to “complex societies in which ONE OR SEVERAL QUEENS PRODUCE all females...”

63-66. It could be added here that subordinate workers play a role in stabilizing the dominance hierarchy between top individuals in some species, including D. quadriceps (Monnin et al 2001 Nature)

88-89: Harpegnathos ants do not have queenless colonies! H. saltator colonies are founded by a queen and upon her death some workers mate (i.e. become gamergate) and carry on reproducing. The queen caste has been retained in roughly half of the species where workers can mate (e.g. Monnin & Peeters 2008 Naturwissenschaften) and its biological importance varies from anecdotic to central as in H. saltator. Please rephrase accordingly

115: quadrIceps instead of quadrAceps

237: “CoA” has not been defined yet. Please define it explicitly

281: “we find no measurable effects” would be better than “we did not find here any measurable effects”

366-368: these two references are the same

Fig. S1: move the units in the column titles (weight [mg] ; JHa [µg]) as you did for the concentration of JHa ([µg/mg])


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

Input:
Title: THE ROLE OF JUVENILE HORMONE IN REGULATING REPRODUCTIVE PHYSIOLOGY AND DOMINANCE IN DINOPONERA QUADRICEPS ANTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript examined effects of JH on physiological state and behavior in a queenless ant using topical application of JHA. They found that some individuals treated with JHA reduced their reproductive abilities. These results valuable to understand physiological mechanisms of regulation of reproductive division of labor in ants. However, the authors should answer some points to clarify their findings. And I found that the manuscript has many typos. I strongly recommend you to check again.

Major comments
Introduction:
I imagine that you have data about correlation between JH titer and ovary development/behavior in this species. Please add the information if you have.

Statistical method:
The authors used multivariate analyses to comparisons of effect of JHA treatment on behavior and physiology. However,  in this case, comparisons of effect of JHA on each response variable are more suitable to interpretation of the effect of JHA. Please carry out reanalyses to clarify the effects of JHA.

Minor comments
L. 54: Should rewrote words, “between queens and workers”, because worker-worker conflict also occur in such society.

L. 88: Okada et al., (2005) is incorrect in this context. The study focused on not JH but biogenic amines.

L. 103: Please explain “phenotypic”. Behavioral or/and physiological phenotype?

L. 123: How long observation time per a day? Also please add information about total observation time.

L. 135: Please include “is” before “observed” and “recorded”, respectively.

L. 152: Also please add information about total observation time.

L. 166: AntTrak?

L. 210 Please explain why did you use non-parametric test, although all data has been converted to z-transformation.

L. 229: non-parametric?

L. 267: Defeat a period.

L. 368: Correct??
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: THE ROLE OF JUVENILE HORMONE IN REGULATING REPRODUCTIVE PHYSIOLOGY AND DOMINANCE IN DINOPONERA QUADRICEPS ANTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Following a comment from referee 1 the authors changed figure 1 to Boxplots. This made me realised that I had misunderstood the previous version of Figure 1. My apologies for it! The new version of Figure 1 is much clearer and clarifies my previous concern about controls vs. treated individuals.
Experimental design: OK
Validity of the findings: OK
Additional comments: Some minor comments are listed below:
- Line 51: delete “a” from “in which a one or several queens”
- Line 69: the paper I was previously alluding to is Monnin et al (2002) Pretender punishment induced by chemical signalling in a queenless ant. Nature 419:61-65. Sorry I got the year wrong! It shows that subordinate workers prevent the replacement of the gamergate by a high ranking worker, because it increases their inclusive fitness. It seemed relevant given that this is the species you are experimenting with, but this is up to you
- 207 and 208: this sentence is odd. Does “the ovarioles most end closest to the oviduct” mean “the ovarioles closest to the oviduct”? Does “furthest developed eggs” mean “most developed eggs”? Please rephrase
- 221, 489 and Table 2: Wilcoxon (with capital letter) instead of wilcoxin
- 285: please rephrase this sentence, e.g. “an ‘honest’ signal THAT INFORMS other colony members about their fertility”
- 286-290: if I understand it correctly, this sentence should be “In studies on a gamergate ant society, a social wasp and a termite, topical applications...” (i.e. add “A” termite and replace – by a comma)
Table 1, legend: missing “i” in indivduals


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

Input:
Title: THE ROLE OF JUVENILE HORMONE IN REGULATING REPRODUCTIVE PHYSIOLOGY AND DOMINANCE IN DINOPONERA QUADRICEPS ANTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Some parts of the manuscript were clarified in the current version. However, some problems are still remain. For example, although the authors had analyzed data for effects of JHA on ovary development, there are no the results of statistics in the manuscript. Also, although they were pointed out several typos in previous round, some words still unclear. Therefore, I recommend that the paper should be clarified again.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Line: 184. This software name is described as “AntTrak” (Tranter et al. 2014). However, you wrote the name, “Antrak”. Which is a correct name?
Line 193 and 263: I think that “CoA” and “coA” mean same treatment. If so, please use the same terminology throughout the manuscript.

Line: 222-225. You should analyze the data using GLMM, and please add the results of new statics in the section RESULT.
Line: 222 and 488. “Wilcox"o"n is incorrect name.


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: SYNTHESIS OF LIGHT-INDUCIBLE AND LIGHT-INDEPENDENT ANTHOCYANINS REGULATED BY SPECIFIC GENES IN GRAPE ‘MARSELAN’ (V. VINIFERA L.)
Review round: 1
Reviewer: 1

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: The subject of the paper is very interesting. The article is generally well written and will serve as a valuable resource for our knowledge. I suggest going ahead in a future in such a research line focusing on other bioactive ingredients in plant foods.

Anyway, I feel the authors should comment on some of the related papers on phenolic bioactive compounds in plant foods, such as:
-. “Pattern recognition of three Vitis vinifera L. red grapes varieties based on anthocyanin and flavonol fingerprints, with correlations between their biosynthesis pathways. Food Chemistry, 2012, 130, 9-19”.
-. “Anthocyanins and flavonols berries from Vitis vinifera L. cv. Brancellao separately collected from two different positions within the cluster. Food Chemistry, 2012, 135(1), 47-56”.
-. “Flavonoids in Gran Negro berries collected from shoulders and tips within the cluster, and comparison with Brancellao and Mouratón varieties. Food Chemistry, 2012, 133(3), 806-815”.
-. “Evolution of flavonoids in Mouratón berries taken from both bunch halves. Food Chemistry, 2013, 138(2), 1868-1877”.
-. Relationship between the sensory-determined astringency and the flavanolic composition of red wines. Journal of Agricultural and Food Chemistry, 2012, 60(50), 12355-12361”.
-. “Increasing the added-value of onions as a source of antioxidant flavonoids: a critical review. Critical Reviews in Food Science and Nutrition, 2014, 54(8), 1050-1062”.
-. “Comprehensive identification of walnut polyphenols by liquid chromatography coupled to linear ion trap-Orbitrap mass spectrometry. Food Chemistry, 2014, 152, pp. 340-348”.
-. “A critical review of bioactive food components, and of their functional mechanisms, biological effects and health outcomes. Current Pharmaceutical Design, 2017, 23(19), 2731-2741 (doi: 10.2174/1381612823666170317122913).”
-. “A critical review of the characterization of polyphenol-protein interactions and of their potential use for improving food quality. Current Pharmaceutical Design, 2017, 23(19), 2742-2753 (doi: 10.2174/1381612823666170202112530).”

The science presented is of a high quality with plenty of detail. This is a substantial manuscript that occupies the bounds between food chemistry and analytical chemistry. I do express my positive opinion on the acceptance of the article to be published after minor revision.


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

Input:
Title: SYNTHESIS OF LIGHT-INDUCIBLE AND LIGHT-INDEPENDENT ANTHOCYANINS REGULATED BY SPECIFIC GENES IN GRAPE ‘MARSELAN’ (V. VINIFERA L.)
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1) The English writing should be thoroughly improved. Some of the sentences were so difficult to understand that I could not even guess what the author means. In particular, from library construction to quantitative real time PCR (lines 168 to 230). Some of the terms are not standard, like 'cDNA database' instead of 'cDNA libraries' etc. Most of error prone ones were marked in yellow in details, some were with comments.
2) Carefully check the spellings, like cultivar name 'Marselan' in title page or 'Marselan' in the title, but 'Matheran' in main body context, even in the abstract.
3) Figures were well described and labeled appropriately in the manuscript. All data were appropriate presented too.
Experimental design: Authors investigated the anthocyanin component individuals in berry skins with various light intensity by bagging experiment. The results were interesting and can bring forward our understanding about the relationship between light dependent and light independent synthesized pigments. Coupling with high throughput sequencing, it is expecting to get some useful knowledge in the area.
However, due to bad english writing, I cannot fully understand the details of sample collection of the sequencing samples.
Validity of the findings: Some conclusions should be carefully drawn and it is too speculative in the current version. Examples like:
In the 'Effects of light intensity on anthocyanin composition in grape berry skin' section (line 263 to 265), Pn-3-o-cou and Mv-3-o-cu may be induced by light intensity. This conclusion was not fully supported by the data in suppl. dataset s1. Mv-3-o was not detected in D of S3 stage. But when compare the quantity from CK, A, B, C, the light intensity decreasing, the content of this kind of pigment did not show constant pattern of been light inducible. Again, CHS was considered negatively regulate the synthesis of non-light-inducible anthocyanins (line 452). This conclusion could not be accepted, especially authors only investigate the expression of CHS (a family sometimes with several members, which was not specify or deeply investigated here) with only Mv-3-O-cou. Authors should draw more stringent conclusions.
Additional comments: Detailed concerns
Major points, 1) most of the conclusions were based on the results from table s1, so I suggest you put the table in the main text instead of in supplementary data. In considering that it is a large table, other presentation forms like heatmaps can be applied. 2) Details about the samples collection, replications, corresponding to the library construction should be clear. 3) I do not know how did the authors picked out MYB and bHLH TFs and why they chose the ones listed in the text. If all TF members were included, it is obviously not suitable; if particular ones were selected, put some background information in the introduction section. 4) conclusions should be carefully drawn, for example, Mv-3-O-coumaroylglu (trans) may be induced by light intensity (line 264), why its content decrease when light intensity increase (from table S1)?

line 51, there are more suitable references than that of tomato SB. It is an anthocyanin mutant, not a typical one.
The introduction section from line 48 to 71 and from line 72 to 88 seems to lack logic behind. Recommendations are light intensity and light quality affections, structural genes or regulatory components in either section.
line 130, please add information about why you choose S2 and S3.
line 136, clarify why not choose the collected skins, but from treated plants and explain how you get the fine powder.
line 191, if indexs were used, please indicate the sequence.
line 255, I strongly suggest that Supplementary dataset S1 was used as main results table or as heatmap used in the main text.
line 277, since Pn-3-O-coumaroylglu (trans) only draw from 1% to 0, it is not convincing to get the conclusion
line 290, if your libraries were sequenced 100 bp in length (line 196), how do you get 150 bp reads?
line 295, please provide more information about how do you conducted pairwise comparison.
line 300, we know that Go terms can category genes into three classes, and this was not what we want to know about the data. You should provide detailed information in the three classes, for example, which special go terms in BP or MF or CC category were enriched. That's what authors expected.
line 450 to 452, CHS was negatively regulate the synthesis of non-lint-inducible anthocyanins, it is too speculative to get this conclusion.


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

Input:
Title: AN INTERPRETABLE MACHINE LEARNING MODEL FOR DIAGNOSIS OF ALZHEIMER'S DISEASE
Review round: 1
Reviewer: 1

Output:
Basic reporting: Authors have presented a machine learning model named SHIMR for automated diagnosis of Alzheimer's and tested the proposed system on ADNI dataset. The detailed experimental results show that SHIMR is comparable to the comparative methods in terms of accuracy and it is comparatively more cost-effective and reliable.
1. Text in Figure 2(B) is hard to read. Text size should be increased.
2. Line#73: "He" should be named with citation to avoid ambiguity. Similar ambiguities should be removed.
3. Text in Figure 4(C) and Figure 4(D) is hard to read. Text size should be increased.
Experimental design: Decision tree and traditional machine learning methods are a good choice for this topic. However, authors should also review methods based on state of the art deep learning methods. Hyperspectral imaging can also aid in improving automated diagnosis. The following articles should be cited to improve the literature review: https://www.nature.com/articles/s41598-018-22871-z, https://ieeexplore.ieee.org/document/8314827/, https://arxiv.org/abs/1807.03876, https://ieeexplore.ieee.org/abstract/document/8346384
Validity of the findings: The experimental analysis is comprehensive and nicely concluded. Authors should also mention any possible risks involved in using machine learning for precision medicine and adopting SHIMR for automated diagnosis for Alzheimer's.
Additional comments: No additional comments


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

Input:
Title: AN INTERPRETABLE MACHINE LEARNING MODEL FOR DIAGNOSIS OF ALZHEIMER'S DISEASE
Review round: 1
Reviewer: 2

Output:
Basic reporting: I see only small problems with the writing and presentation. The figures associated with the resulting rule systems are very well done.

Please convert the supplemental documents into PDFs to make them easier to access.

Figure 5 needs to be revised or the associated text changed. I attempted to manually determine the model score from the matched rules, but was only successful on the NC case (part A). I'm guessing that the only rule that matched in Part A was the first rule, thus making the score calculation work with the displayed results. For Part B, I calculated that the model score as displayed should be 0.68 (0.53+0.43-0.28), but the overall model score is 1.1. I'm assuming that some of the other excluded rules match for Part B, but this should be either acknowledged in the figure caption or the figure modified to show the full rule set and associated matches.
Experimental design: The design of novel algorithms/systems for explainable decision making is interesting. The associated source code appears to be complete with appropriate instructions for usage.
Validity of the findings: No major comments, all of the data and results appear to be statistically sound.

Can the authors add a statement concerning the standard runtime of the algorithm? What was the runtime to produce the rule set in Figure 4C?
Additional comments: This system is sufficiently different from a vanilla decision tree to merit publication, but I don't completely agree with the idea that it is somehow more interpretable than a vanilla decision tree. Comparing the rule set in Fig 4C and the decision tree in 4D, the process of using the decision tree seems simpler to me with a more straight forward interpretation.

Another system that produces similarly simple rule sets is the CORELS system that is cited in the paper. How many rules does it take for the CORELS output to reach a similar AUC to the SHIMR output?


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: REMOTE SENSING PIPELINE FOR TREE SEGMENTATION AND CLASSIFICATION IN A MIXED SOFTWOOD AND HARDWOOD SYSTEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is relatively well-written and provides a nice context to the study. The manuscript can benefit from additional review on what has been done to establish such pipeline in the past (such as Kershaw et al., 2016; White et al., 2016;  Hyyppä et al, 2012; van Leeuwen et al., 2010;).
Experimental design: The methods are well-described in most cases, except for omission of some minor details (please see general comments below).

It seems “maxima search” involved lots of visual evaluations before an appropriate set of parameters is arrived upon. Is there any way to present this process in more detail either in the methods or in the results section, so that readers know what exactly is involved in this process and this can be replicated?
Validity of the findings: The whole 'pipeline' required a lot of manual tweaking of the parameters, especially the NDVI/height thresholds and parameters used for local maxima. I am concerned that the pipeline presented here might have limited applicability beyond the current data and study area.

The results section can be improved. For example, in section 3.1, the author provided only an overall J score, but it gives no indication as to how the algorithm performed across trees of different sizes (crown, height) or species. The alignment was evaluated using RMSE and yet the RMSE values (overall or for different tree sizes/species) were not provided. The classification accuracies of different species were also not provided.

The discussion section is also weak. The author assumes that segmentation/ classification is major challenge in the remote sensing community because most participants did not perform well. Over the last two decades, the science of image segmentation/classification has matured enough, and I think the poor performance was solely because none of the participants used industry-standard approaches such as OBIA (e.g. Blaschke et al). The manuscript could benefit from additional comparison of the methods/results against previous tree segmentation/classification literatures (please refer to Zhen et al., 2016 or Blaschke, 2010 for overview)
Additional comments: - The title of the paper should highlight the core content of manuscript. It should be self-descriptive on its own, independent of other manuscripts submitted as part of the challenge.
- Lines 50-54: Are there appropriate citations of these data sets? If so, please cite them accordingly
- Line 55: State the full form of DSM, and that they are used to compute the canopy height model referred elsewhere in the manuscript
- Line 68. For clarity, please refer “the cloud” to something like “the point cloud derived from the raster pixels”
- Line 76: “landcover” to “land covered”
- Line 79: Mention that maxima search was done on NDVI-filtered LiDAR CHM. Also, briefly describe what the TreeTopFinder() does. (Popescu and Wynne, 2004?)
- Line 89: Briefly describe what segmentation algorithm SegmentCrowns()  implements
- Lines 131-139: State how many structural and how many spectral parameters in total were used for PCA.
- Lines 160-162: Can the author also show how the relationship was when the crown height was also included?
- Line 203. Can the author elaborate what specific problem?


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: REMOTE SENSING PIPELINE FOR TREE SEGMENTATION AND CLASSIFICATION IN A MIXED SOFTWOOD AND HARDWOOD SYSTEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a well written manuscript. I enjoyed reading it. The author provided a good background to the problems investigated and used good illustrations to highlight the findings of the study. The data used in this study are publicly available (NEON and the data science competition).
Experimental design: The study has a clear design and the dataset and methods are explained in detail.
Validity of the findings: The segmentation method did not perform well, but the author acknowledged that this remains a challenge in the remote sensing field. The alignment and classification results are promising. The author’s conclusions are grounded in the results presented.
Additional comments: It was a pleasure to read the manuscript – good structure, clear explanations, and relevant background provided. I only have a small set of minor editing suggestions for the author.
Is the spelling LIDAR the most common one? I’ve seen mostly LiDAR and lidar in the literature.
Title: it might be good to make the title a bit more specific (for readers looking for papers on remote sensing and tree identification)
Abstract:
spell out the acronyms (NIST, DSE, NDVI, LIDAR, PCA); replace “compete in the competition” with “participate in the competition”
Background:
Line 20: use plural of aircraft
Line 38: spell out NIST DSE
Line 42: insert comma after “tasks”
Line 45: remove word repetition (“provided”)
Methods:
In 2.1: clarify which datasets are hyperspectral and which lidar; spell out DSM
Line 60: insert “(CHM)” after “canopy height model”
Line 68: spell out NDVI
Line 79: insert “R” before “package”
In Equation (2) is x the CHM value?
Line 81: reword “no ground points were”
Line 118: replace “predicated” with “predicted”
Discussion:
Line 202: Is (Dalponte and Gianelle) a citation? If yes, add year. If not, provide the name of the team mentioned here.
Conclusion:
Line 231: insert “data science” before “competition”
Figure 1 caption: spell out CHM


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

Input:
Title: A DATA SCIENCE CHALLENGE FOR CONVERTING AIRBORNE REMOTE SENSING DATA INTO ECOLOGICAL INFORMATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is concise and clear. The authors provided a good background for the research topics addressed in the manuscript: the data science competition (a concept that I found very interesting) and processing of remotely sensed images to extract tree crown size and location, align images with field reference data (ground truth), and identify individual trees. The figures illustrate well the methods and results of the study. A few editing suggestions for figure captions, to make them more descriptive:
Figure 1 caption: specify which bands (wavelengths) were used create the false-color composite; add the names of the species used in the legend (species codes);
Figure 1 design: why does panel C include three superimposed images?
Figure 2 caption: rephrase “ranked around the median highest in performance”; specify which bands (wavelengths) were used create the composite; include information about the three groups (FEM, Conor, Shawn)
Figure 3 caption: remove the comma after “criteria”; add information about the three groups (FEM, Conor, Shawn) used on X axis
Figure 4 caption: include information about the three groups (FEM, Conor, Shawn)
Figure 4 design: add units on X axis
Figure 5 caption: specify which bands were used create the hyperspectral composite image
Figure 6 caption: include names of species presented in legend as species codes and provide information about the labels used on the images (groups); specify which bands were used create the false-color composite
Figure 7 caption: provide information about the labels used in the figure legend
Figure 8 caption: provide information about the labels used in the figure legend and explain the codes used on X axis (species’ names).
The formatting of tables could also be adjusted to resemble lists (remove vertical and horizontal lines, except for the horizontal line of the header and the end of the table).
Data used in this study are available through NEON portal.
Experimental design: The data science competition was well designed and the analysis of results obtained by various teams seems robust to me. I think that this approach of providing several teams with same data and analyzing the results obtained by teams individually is a good way to compare methods because it pools skills; each team will most likely choose the method(s) that the team has most knowledge of or is most interested in developing.
The methods used to compare the teams’ results are described in detail. The individual team’s methods are not included, but the papers of the teams are cited in this manuscript. It might be useful to add a table that summarizes each team’s methods, capturing just the essential characteristics.
Validity of the findings: The authors discussed the most important aspects of their research but also the possible limitations. One aspect that could be added to the discussion of this study is that the findings apply to NEON AOP hyperspectral data – other hyperspectral datasets (e.g., AVIRIS) might not yield the same conclusions. I think this aspect might be important to mention so that readers are reminded that the ranking of methods in this study may not apply to other hyperspectral data.
Additional comments: I enjoyed reading this manuscript. My review is structured according to the PeerJ format. Additional minor editing suggestions:
Lines 223-224: “widely” is repeated here
Line 240: provide citation for the Hungarian algorithm
Line 317: explain “highly unbalanced data”
Line 584: Anderson 2018 is missing from References list


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

Input:
Title: A DATA SCIENCE CHALLENGE FOR CONVERTING AIRBORNE REMOTE SENSING DATA INTO ECOLOGICAL INFORMATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript describes the results of a data competition organized in 2017 to achieve three important tasks essential for making remote sensing data useful for ecological applications - tree crown delineation, tree stem location and tree species classification. The competition generated broader interest (mainly from US and Europe), albeit only small number of responses (total of six - only 2-3 groups participated in the Task 1 and Task 2 ). The significant outcomes of this effort include a series of manuscripts about algorithms, together with openly-available source codes and data. The manuscript is generally well-written and structured. The raw data is available online.
Experimental design: The competition is designed well with statistical metrics to compare the performance of various algorithms with the baseline. Most of algorithms are described in the accompanying submissions, which are pointed to in the manuscript. The baseline methods (for the three tasks) are however not described in sufficient details. The manuscript could benefit from information as to why particular methodology for baseline prediction was selected compared to other existing approaches.
Validity of the findings: My one concern with the manuscript is the wider applicability of the findings -  both training and test samples were from the same location (NEON Ordway-Swisher Biological Station in Florida). NEON already has similar data available for other stations/biomes. I feel that performance of the algorithms would have been tested more rigorously if the competition provided datasets from multiple sites, or at least the training and test data came from different NEON stations.

Given that most of the participants have also submitted the manuscripts at the PeerJ (McMahon et al., Sumsion et al., Dalponte et al., Anderson) or already published (Zare et al., 2017), this manuscript feel redundant and do not provide any additional insights that these individual manuscripts cannot provide. This is my main concern.
Additional comments: - In 'Introduction' section, the authors describe common data science competition platforms, specifically Kaggle, in detail. However, they fail to describe what platform they used to organize their own challenge. The authors should describe this and provide an URL to the competition website. The original URL to the competition is not provided anywhere in the manuscript.
- Hyperspectral imagery was collected in 2014 and baseline crown delineation field data (ITC) in 2017. The manuscript could benefit from additional discussion on the implications of this three years’ time lapse on the crown delineation, and hence the poor performance for Task 1 (?). Also mention in Section 2.2, which month or season the field data was collected.
- The authors mention possibility of misalignment between the LIDAR/Hyperspectral at several places in the manuscript, but do not state if they really found one. Weren’t these data already co-registered by NEON? Given that both were probably collected in the same flight, was there really a significant misalignment?
- Task1/Task3 in the Table 2 can be combined into one column. They essentially represent same values.
- Line 220: “LiDAR data” should be “LiDAR CHM data”. Can author also provide information on the distribution of the crown sizes?
- Line 240 – What is the “Hungarian algorithm”? Please describe.
- Section 2.5.1.2: Describe briefly the baseline algorithm (Chase-Vese algorithm”
- Lines 522-523 – Please state what exactly was done to transform the data
-  Where is the baseline information for other species (other than PIPA)  in Figure 8? State what the abbreviations mean (LIST, PIEL, QUNI, etc) in the figure caption.


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

Input:
Title: THE EFFECTS OF PILATES VS. AEROBIC TRAINING ON CARDIORESPIRATORY FITNESS, ISOKINETIC MUSCULAR STRENGTH, BODY COMPOSITION, AND FUNCTIONAL TASKS OUTCOMES FOR INDIVIDUALS WHO ARE OVERWEIGHT/OBESE: A CLINICAL TRIAL
Review round: 1
Reviewer: 1

Output:
Basic reporting: I would like to congratulate the authors for their effort invested in this article.
The article has minor English mistakes such as the use of “of” before Pilates in line 23 of the manuscript; line 113 the word “from” is wrongly placed twice. Also consider changing “be sedentary habits” to “had sedentary habits” in line 116. The authors should also be careful to always use past tenses. In lines 119/120 the English should be revised (maybe simplifying e.g., the participants performed a medical exam taking into account x and y).
The background is clear and objective, with valuable references that show the relevance of the study.
Although the structure of the manuscript follows a line of reasoning, lines 133/134 report results (mean ages) that from my point of view, should be placed only in the results section as part of the participants’ characteristics.
Experimental design: The research is within the scope of the journal and is well designed.
The authors brilliantly identified that there is a lack of reliable evidence on Pilates effectiveness in obesity or overweight patients and stated correctly that as previous studies have shown evidence is still needed about cardiorespiratory fitness outcomes.
As a suggestion I believe the article would benefit from a brief explanation (lines 192/193) of why the authors needed to monitor HR during the intervention. Was there any formula used to prescribe intensity? Was the theoretical maximum HR computed just to ensure a safe exercise?

Another great addition to line 203/204 would be an example of a possible adaptation of the exercises to an overweight or obese patient.

The protocol for the CPET was not clearly identified. From line 234 to 239 I encourage the authors to identify the original name of the protocol and the corresponding reference.

It is not clear for the reader why the authors needed 2 different measures for waist circumference. I think it would be helpful if you give a brief explanation.
Validity of the findings: The results are meaningful and their benefit to the literature is clear. However, lines 493-495 could be further explored. As the authors recognized, moderate exercise might not be enough to change body composition. However, it seems to change functional capacity. Why is that important? Is their a relation of functional capacity with other health outcomes in obese/overweight people? Is it a predictor of an important outcome? What are the implications of improving functional performance of obese patients?

In lines 524/525 – The authors should try to reformulate the sentence. Although walking is one of the easiest tasks it is one of the few where almost all musculoskeletal system is working. I think what you tried to state was that walking is not as demanding as Pilates for those specific muscular groups. If not, please try to provide a clearer statement.

In conclusions, it would be helpful to have a paragraph with the authors opinions regarding the need (or not) for future research, and if so, which specific aspects should be adressed.
Additional comments: I would like to thank the editor and the authors for the opportunity to review this work. It is a well-structured manuscript with interesting findings that cover an emergent topic of public health, and an intervention with potential for such population.


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

Input:
Title: THE EFFECTS OF PILATES VS. AEROBIC TRAINING ON CARDIORESPIRATORY FITNESS, ISOKINETIC MUSCULAR STRENGTH, BODY COMPOSITION, AND FUNCTIONAL TASKS OUTCOMES FOR INDIVIDUALS WHO ARE OVERWEIGHT/OBESE: A CLINICAL TRIAL
Review round: 1
Reviewer: 2

Output:
Basic reporting: This article is self-contained, professionally presented and appropriately structured, and is comprehensively and thoroughly embedded in existing literature.

The article is generally well-written in clear and professional English. There are a few occasions where clarity could be improved or grammar is incorrect. These are mostly minor and I have provided some suggested changes below. I feel that the discussion could do with some more extensive rewriting, however.

1. I found the discussion quite long and somewhat convoluted. It would help to perhaps use subheadings for the various outcomes and sharpen the arguments by leaving out details already reported in the results and leaving out extraneous explanations. For example, the explanation in lines 466-471 is not really necessary, and the argument in lines 472-474 could be condensed to something like ‘Due to the small effect size, the results should be viewed with caution’.

2. Additionally, it would be helpful to start the discussion with a summary of the findings, outlining which variables (a) changed significantly over time for each group, and (b) were significantly different between groups at post-test.

3. Minor changes suggested:
Line 23: add ‘has’ before ‘for’
Line 67: change ‘to improve’ to ‘improved’
Line 75: on what specifically has there no consensus been reached?
Line 85: This sentence suggests adherence levels to traditional aerobic programs are not very high only if they are monotone and potentially painful for obese individuals. I wonder if this is what you mean to say (as it seems unlikely that these are the only circumstances where adherence levels are low); perhaps you can add ‘particularly’ if they are monotone…
Line 108/109: could you specify to which outcomes this hypothesis applies? Did you expect similar or higher benefits for all outcomes?
Line 113: delete first ‘from’
Line 120:  change ‘participant first group’ to ‘first group of participants’
Line 133: change ‘that’ to ‘who’
Line 136: it is not clear what you mean by ‘recollections’
Line 152: add ‘to’ after ‘through’
Line 166-168: Please rephrase these sentences. People are blinded to one or more experimental conditions, they are not blinded in themselves (i.e., don’t use blinded as an adjective)
Line 167: change ‘have already’ to ‘had’
Line 183: insert a comma between ‘protocol’ and ‘for’
Line 207: should this be ‘ventilatory’?
Line 213: delete ‘then’
Line 326: change ‘was’ to ‘is’
Line 340: delete ‘of’ before ‘2%’
Line 452: add a comma after ‘Probably’
Line 456: change ‘once’ to ‘as’
Line 613: delete ‘in the baseline’
Experimental design: The study was well-designed and mostly described in excellent detail, sufficient to be reproducible by another investigator. There are a few issues that need further clarification, however:

4. Line 116: the criterion of ‘sedentary habits’ requires clarification. First, although the term ‘sedentary’ used to be common to refer to lack of sufficient physical activity, nowadays it tends to be reserved for actual sedentary behaviours (i.e., “any waking behaviour characterized by an energy expenditure ≤1.5 METs while in a sitting or reclining posture”, see Network SBR. Letter to the Editor: standardized use of the terms “sedentary” and “sedentary behaviours”. Appl Physiol Nutr Me. 2012;37:540–2. doi:10.1139/H2012-024). Second, if the criterion refers to lack of sufficient physical activity, it would be pertinent to know which level of physical activity is not met. I would thus recommend that this criterion is expressed in terms of inactive or insufficiently active in the sense of not meeting specified physical activity guidelines.

5. Lines 118 and 123: I may be missing something here but cardiovascular disease and arrhythmia do not appear to be part of the listed exclusion criteria, yet you have used them for exclusion.

6. Line 136-141: Could you specify when these comorbidities were detected? Was this during the screening exam? How do they relate to the exclusion criteria?

7. Lines 222-229: Please specify when the food intake assessments were conducted.

8. Line 352: you do not appear to have reported the results of these one-way ANOVAs. See also my comment on the possible use of ANCOVAs.
Validity of the findings: 9. I am not a statistician but I believe the potential confounding effect of age differences between the Pilates group and the other groups could be statistically accounted for by conducting Analyses of Covariance rather than Analyses of Variance as the authors have done. I strongly recommend seeking a statistician’s advice on this issue.
Additional comments: I believe this is a good study and deserves publication after the recommended changes. My recommendation of major revision is mostly based on my concern about potential changes to the results when age is included as a covariate.


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

Input:
Title: THE EFFECTS OF PILATES VS. AEROBIC TRAINING ON CARDIORESPIRATORY FITNESS, ISOKINETIC MUSCULAR STRENGTH, BODY COMPOSITION, AND FUNCTIONAL TASKS OUTCOMES FOR INDIVIDUALS WHO ARE OVERWEIGHT/OBESE: A CLINICAL TRIAL
Review round: 1
Reviewer: 3

Output:
Basic reporting: Too many definition-reference mismatches.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: -Manuscript is too long, almost twenty pages or more. Manuscript should be written in fluent, clear and short form. Readers need to be able to easily read, interpret and understand article.
-Abstract- Method section:  Please, indicate which evaluations were made.
- The literature/references should be reviewed again throughout the whole article.  I have given a some examples of definition-reference mismatches below.
Line 76-78, "Moderate walking or  jogging programs have traditionally been suggested to improve variables related to health (Ross  & Janssen, 1999; Pedersen & Saltin, 2015; Santangelo et al., 2016)..."  Santangelo et al 2016 Pathophysiology of obesity on knee joint homeostasis: contributions of the infrapatellar fat pad.  -- this article related to development and progression of OA, and the contribution of fat pads. I could not find any comments about  "moderate walking or  jogging programs".
Line 78-81, "however, randomized controlled trials (RCT) suggest that walking (≥ 12 weeks) results in only a small beneficial effect on body mass, body composition, and aerobic fitness in overweight and obese adults (Gourlan, Trouilloud & Sarrazin, 2011; Aladro-Gonzalvo et al., 2012; Santangelo et al., 2016; Burgess et al., 2017)." Aladro-Gonzalvo et al. The effect of Pilates exercises on body composition: A systematic review.---this reference about Pilates but description about ≥ 12 weeks walking .  Santangelo et al., I could not find any comments about  "moderate walking or  jogging programs".
- Exclusion criteria must be clearly stated.  Line 117-118, Exclusion criteria were present neurological, cognitive, orthopedic, respiratory, and/or endocrine disease. Authors excluded 45 volunteer with cardiovascular disease and one volunteer with arrhythmia. Are cardiovascular disease and heart diseases within the criteria of exclusion?  Line 136-141, diseases such as diabetes mellitus and hypothyroidism are endocrine diseases.  but you indicated that endocrine diseases are in the exclusion criteria. This section is very confusing.
-Line 167-168, "Since previous studies investigating aerobic training effects have already found positive results with eight weeks of training (Ho et al., 2012; Many et al., 2013)..." Ho et al's study about vascular function; Many et al's study about insulin sensitivity and inflammatory markers in obese and insulin-resistant minority adolescents. Your study sample consist of "relatively healthy" adults. For this reason, the studies you have been referring to for the aerobics training protocol (8 week/3times per week...) does not compliance your aim. In addition, one of your outcome measures is body composition. The aerobic training load required to make a change in body composition is clearly indicated by the ACSM criteria (American College of Sports Medicine Position Stand.  doi: 10.1249/MSS.0b013e3181949333 and Matthew A. Exercise Aspects of Obesity Treatment). Although Pilates performed 8 weeks in previous studies, aerobic training is usually performed for 12 weeks. From this point of view, the result seems to be determined at the beginning of the study.
-Line 207-211, authors stated that walking intensity in aerobic training protocol created according to Gourlan, Trouilloud & Sarrazin, 2011 and it did not lead to orthopedic injuries. In this article I cannot find no comment about orthopedic injuries and Gourlan et al stated that " Given these results and the fact that the concept of ‘dose’ of intervention has yet to be explored and developed for educational treatments, it seems that more research is needed in this domain, notably to determine whether or not there is an optimal number or frequency of sessions for a given duration of intervention." The aerobic training protocol should be clearly stated. In addition to this, study sample consist of sedentary overweight and obese. Guidelines usually recommend; instead of starting to walk 180 minutes a week walking time/distance be increased gradually. Please, convey your opinions about this issue.
-In assessment section, please just mention about how assessments are carried out. For example: Line 272-276 and 290-291 authors mention about reliability studies. It is more appropriate to address/discuss them in the discussion section.
-Line 295-296, Colyer et al., 2016 carried out their study on athletes.  Line 485, "considering that DXA—a gold-standard method—was used in our study............"  Are there any studies about the reliability of DXA and about whether DXA is considered gold standard  in overweight and obese ?
-Line 304, abdominal endurance test; Is it sit-up or curl-up test?


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

Input:
Title: THE EFFECTS OF PILATES VS. AEROBIC TRAINING ON CARDIORESPIRATORY FITNESS, ISOKINETIC MUSCULAR STRENGTH, BODY COMPOSITION, AND FUNCTIONAL TASKS OUTCOMES FOR INDIVIDUALS WHO ARE OVERWEIGHT/OBESE: A CLINICAL TRIAL
Review round: 2
Reviewer: 1

Output:
Basic reporting: I congratulate the authors for the improved version of the manuscript. Please try to be coherent through out the body of the manuscript and choose either the term "Pilates" or "Pilates training".
In line 117 please remove the extra dot.
In line 119 please replace "also were" with "were also".
In line 122 also replace the order of medical and physical.
In line 125 replace "presentation" with "presence" and "presence of arrhythmia...". Keep the format (n=x)

Line 172 Please replace the term "physical activity" with exercise, or "apart from the one included in this study."

Simplify line 368-369 (e.g., 90% confidence intervals and percent changes were also calculated).

In line 375 correct "significantly".
Line 429 replace "showed significantly improved" by "showed a significant improvement"

In some references there is no DOI. Try to maintain coherence.

The caption on figures is usually presented after the figure. See figure 1
Experimental design: The authors should consider moving the assessments up in the manuscript before the interventions, as this was the first step.
Validity of the findings: no comment
Additional comments: Overall you should try to shorten the manuscript as it becomes a little difficult for the reader. As a suggestion you may not emphasize as much the importance of effect sizes, as they are now well-recognized in the scientific community.


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

Input:
Title: THE EFFECTS OF PILATES VS. AEROBIC TRAINING ON CARDIORESPIRATORY FITNESS, ISOKINETIC MUSCULAR STRENGTH, BODY COMPOSITION, AND FUNCTIONAL TASKS OUTCOMES FOR INDIVIDUALS WHO ARE OVERWEIGHT/OBESE: A CLINICAL TRIAL
Review round: 2
Reviewer: 2

Output:
Basic reporting: Thank you for including a summary of the findings at the beginning of the discussion. The discussion is still fairly long but the use of sub-headings has made the structure much clearer, and the arguments are more focused.

A few minor changes suggested:
(Please note that where I refer to line numbers, these are the line numbers in the word document with tracked changes [peerj-29176-manuscript_R1_final.docx].)

Line 157: You may want to spell out the full name of IPAQ in the paper for readers not familiar with this abbreviation.

Line 160: Please remove the commas before and after “which were not controlled”. (With the commas, the sentence reads as if all subjects presenting with cardiovascular or endocrine disease were excluded, because for all of them, the diseases were not controlled. Without the commas, the sentence will indicate that only those subjects for whom the diseases were not controlled were excluded, which is what you mean.)

Lines 211-214: The phrasing of “blinded professions” is still awkward. Please revise this to something like: “Professionals who carried out the tests and measurements were blinded to the treatment conditions.” Delete the subsequent sentence starting with “Volunteers…”

Lines 408; 424; 437-442: it would be more logical to report the age differences before noting that the analyses involved age as a covariate. Please consider moving lines 437-442 to a section before line 408. This could potentially be part of the “participants” section. Line 424 should also be part of the information that is moved to before line 408.

Line 531: change “circunference” to “circumference”.

Line 533: I would suggest to change “However” to “Conversely”.
Experimental design: Thank you for clarifying the criteria for categorizing physical activity level. The explanations about exclusion criteria and their link with comorbidities are much clearer now. Just note my comment about commas (in line 160) above.
Validity of the findings: I was pleased to see the authors consulted a statistician to get advice on running an Analysis of Covariance to control for the age differences between the Pilates and other groups. Having accounted for a possible age effect this way, the paragraph in the discussion (lines 714-719) probably does not need to be included.
Additional comments: The authors should be commended on their extensive and detailed response to the reviewers’ suggestions.


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

Input:
Title: THE EFFECTS OF PILATES VS. AEROBIC TRAINING ON CARDIORESPIRATORY FITNESS, ISOKINETIC MUSCULAR STRENGTH, BODY COMPOSITION, AND FUNCTIONAL TASKS OUTCOMES FOR INDIVIDUALS WHO ARE OVERWEIGHT/OBESE: A CLINICAL TRIAL
Review round: 2
Reviewer: 3

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


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

Input:
Title: THE EFFECTS OF PILATES VS. AEROBIC TRAINING ON CARDIORESPIRATORY FITNESS, ISOKINETIC MUSCULAR STRENGTH, BODY COMPOSITION, AND FUNCTIONAL TASKS OUTCOMES FOR INDIVIDUALS WHO ARE OVERWEIGHT/OBESE: A CLINICAL TRIAL
Review round: 3
Reviewer: 1

Output:
Basic reporting: I am happy with the revisions but I think there has been a confusion about which lines to move. I apologise if my earlier instructions were unclear, as it looks like you moved the wrong lines (409-410 rather than 411). (I am referring to the line numbers in the tracked changes document, with all revisions visible, i.e., manuscript_R2_final_tracked_changes.docx, with all markup visible)

To fix this, move lines 164-165 (When the age presented…. was used.) back to lines 409-410. They are more logical there. Perhaps change “When the age presented” with “Where age presented”.  Then move line 411 (One-way ANOVA was used…. intervention.) to line 161, before “The one way ANOVA” (then add the explanation “analysis of variance” after the first mention of ANOVA).
Experimental design: no comments
Validity of the findings: no comments
Additional comments: Thank you for all your efforts in this study. Sorry to ask for one more minor revision.


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

Input:
Title: THE EFFECTS OF PILATES VS. AEROBIC TRAINING ON CARDIORESPIRATORY FITNESS, ISOKINETIC MUSCULAR STRENGTH, BODY COMPOSITION, AND FUNCTIONAL TASKS OUTCOMES FOR INDIVIDUALS WHO ARE OVERWEIGHT/OBESE: A CLINICAL TRIAL
Review round: 4
Reviewer: 1

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


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

Input:
Title: REMOTE SENSING TREE CLASSIFICATION WITH A MULTILAYER PERCEPTRON
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is generally clear but is a bit too concise. It would be good to include in the Introduction a bit of background regarding current progress and challenges in the field of spectral classification of trees. The study and results are represented well by the figures, but I recommend minor edits. For Figure 1, include in the figure caption the genera that are abbreviated. For Figure 2, include two more panels to illustrate accuracy within genus and species (variation by genus and species is of interest, as some genera and species might be more accurately classified than others).
Experimental design: A few important details are missing from Methods section. There is no information regarding the tree dataset (how many samples per species) and any data splitting (for training/testing of classifications). The reader also needs the information regarding evaluation metrics used in the competition (rank accuracy and cross-entropy).
Validity of the findings: The accuracy values are a bit difficult to assess in terms of significance because they are provided at the genus level and species level as averages, I think. I expected genus (5) and species (9) specific accuracy values to be reported, in two matrices (for genus level and for species level analysis). The Discussion section is too short and does not go into the details of the results of this study. It needs to be further developed to highlight the findings of this study and their importance in the context of previous work in the field of tree identification from hyperspectral imagery.
Additional comments: The manuscript can be strengthened by expanding the Introduction and Discussion sections.
I noticed that the authors use “predicted” instead of “classified” when referring to identifying tree genera or species. I suggest revising the use of predicted, predictions, etc.
Abstract:
Line 15: insert “two” before algorithms
Line 16: spell out MLP acronym
Line 21: is 68.8% the average accuracy value, over all 9 species? Please clarify.
Introduction:
Lines 23-27: citations needed in this paragraph
Line 40: “task III” is not relevant in this context, could revise as “one of the tasks”; also, need to include here a paragraph about current progress and problems in the field of tree mapping from hyperspectral data
Line 41: lidar stands for “light detection and ranging”; also here and elsewhere in the manuscript, use LiDAR or lidar spelling (not LIDAR).
Materials and Methods:
Line 50: mention location of NEON data (repository, if readers want to download these data).
Line 57: Marconi et al citation is missing publication year.
Line 58: the section Algorithm Training can me merged into the next section, Classification Algorithms.
Line 59: mention that the function is python
Line 65: cite “Other studies”
Line 71: Scholkopf et al is missing publication year
Line 72: the word frequently is repeated in this sentence
Lines 75-80: citations needed in this paragraph
Line 76: “k features” is unclear to me – what are features in this context?
Line 80: “each tree in the forest” – the use of forest in this context is ambiguous; I think it refers to plants (trees), not classification algorithm; then could be reworded as “each tree species in the forest”
Lines 85-89: this paragraph needs citations
Lines 99-104: this explanation is a bit abstract – is it possible to explain  (briefly) the implications of these parameters?
Line 117: Marconi et al citation is missing publication year; same thing in line 141 (Results(
Discussion
Needs to be further developed; discuss the significance of your results; include the context of previous research. Also, remove “wasn’t” (lines 146 and 151), and reword “hyperspectral images provide the highest accuracy” because it seems vague (highest among other types of imagery?)
line 270: reword “showed different within…”
Conclusions: line 334: reword “wasn’t”


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: REMOTE SENSING TREE CLASSIFICATION WITH A MULTILAYER PERCEPTRON
Review round: 1
Reviewer: 2

Output:
Basic reporting: In this manuscript the authors compared two traditional classification algorithms (SVM,RF) with a neural-network based method (MLP). The authors have also implemented a clever way of aggregating the pixel-level classification to the tree crown level using an ensemble-based method. This should be of value for other remote sensing applications as well.

The introduction section is very brief and do not provide enough context to the study. For example, the authors can discuss previous literatures on species classification, on hyperspectral and LiDAR, and highlight what has been done, what are the key issues and how the current work tries to solve it. The authors can also discuss here why the specific algorithms were selected for this work (SVM, RF, and MLP).
Experimental design: The authors compared the RF and SVM classification algorithms with the MLP – yet have nowhere in the manuscript described what the MLP algorithm is or cite any related literature that does so.
Validity of the findings: The manuscript reports cross-validation classification accuracies for species and genera (Figure 2) but does not report how the algorithms performed with the test samples (30% of the samples were provided as the test by the competition).

I feel that the discussion section can be improved.
Additional comments: Lines 58-61: Please briefly describe how k-fold cross validation works.
Line 65. Please cite which “other studies” that have shown MLP is better for tree classification.
Line 71: Missing year in Scholkopf et al.
Lines 69-74: SVM is also widely used in patterns in remote sensing data! It would be more relevant and interesting to readers to cite the literatures that applies SVM in remote sensing/tree classification than the application in RNA expression
Line 91. Define ‘hyperparameters’
Line 117. Missing year in Marconi et al.


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: HYPERSPECTRAL TREE CROWN CLASSIFICATION USING THE MULTIPLE INSTANCE ADAPTIVE COSINE ESTIMATOR
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript is very well written and conceived – with sufficient context given where needed. I like the overall structure of the manuscript in that it does not focus on the NIST competition itself but rather focuses in describing the method or science behind it.
Experimental design: The paper describes a neural network algorithm to classify trees using hyperspectral data. This method supposedly addresses the issue of mislabeled pixels.

The algorithm is described in detail. The core algorithm is also described in a separate work (Zare et al in press at IEEE) and is open source (available at GitHub). In this manuscript, the authors extend the core algorithm to “one-vs-one” – whereby two classifiers are trained for each pair of class label. A pseudocode for the modified algorithm is also provided.

One suggestion to the authors - since “one classifiers for each pair of class label” is applied in the results section, it may make sense to describe here (in the “Proposed one-vs-one MI-ACE” section), “one classifiers for each pair” instead of current “two classifiers for each pair”.
Validity of the findings: This manuscript is significant contribution to the field. The algorithm should be easily adopted to other data or study areas beyond the competition.  Unlike other approaches, as the parameters are estimated from the training samples, there is no need for parameter optimization – which is a big advantage of this approach.
Additional comments: Line 38: Correct spelling for “absence”
Line 53: “is” missing in “method that based”
Lines 72: Is it “every pair of classes” or “every pair of two classes”?
Lines 75-77: Please describe in detail how the “threshold value” is computed. Since this is an important step of the classification, an equation or pseudo-code would be helpful.
Lines 98-113: Please describe the hyperspectral data used in more detail – for example, how and when was it collected, what sensor was used, spatial/spectral resolution, etc.
Line 105. Was the individual spectral signature the mean of all pixels within the tree crown? If so, please state.
Line 123. State how many of 426 bands were removed.
Line 162. Change “the first row” to “the top row”
Line 155. The “Data Description” section states that the competition only provided “spectral signatures for each tree crown” and “no spatial information was given”. If so, can the authors describe here how was pixel confidence distributions computed?

Figure 1.
- State which bands were used to generate RGB image.
- Provide a label for the LiDAR image so readers know what which color means which height.
- State what X and Y axis are? If it is longitude, latitude It appears the first is different from the last two.
- State what is HSI, and what bands were used to produce the image.
Figure 2. The labels for Figure 2 (b) show the genus instead of species. It should be ACRU, LIST, etc.
Figure 3. State what the vertical blue lines means in the figure caption.


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: HYPERSPECTRAL TREE CROWN CLASSIFICATION USING THE MULTIPLE INSTANCE ADAPTIVE COSINE ESTIMATOR
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear and unambiguous, professional English used throughout.
	- Some sentences need grammatical revision and are highlighted in yellow in the manuscript. The paper should be reviewed for clarity before re-submission.
Literature references, sufficient field background/context provided.
- The Introduction would benefit early on from additional background on the NEON challenge and how and why it came about. This can help tie the work to larger explanation of how the research is relevant and meaningful and fills and identified knowledge gap (see next section, Experimental Design below)
- In addition, some background on the classification algorithm and how it’s design might be better than other algorithms for classifying species. Is the algorithm similar in principal to any other types of machine learning algorithms?
- There are not a lot of references included in the study – some additional background that is narrow in focus and contains references to previous studies would be helpful.
Professional article structure, figs, tables. Raw data shared.
- Abstract: could be expanded from 114 words to up to 500 to include concise descriptions of results and conclusions per abstract journal standards. Also consider Keywords that might help your article appear in more search results (e.g., “NEON”, “species classification”)
- Methods: there is not a clear Methods section and the article will need to be carefully reorganized. Suggest renaming “Proposed Approach” to “Methods” and moving subsections under Experimental Results section such as “Data description” to the “Methods” section.
- This section would also benefit from some sort of a processing flowchart. Also, the code that is provided seems to randomly appear without any background.
Self-contained with relevant results to hypotheses.
-The hypothesis needs to be formulated. Suggest beginning with comment on Line 70. The conclusions section should then be updated to address whether or not results support the hypothesis.
Experimental design: Original primary research within Aims and Scope of the journal.
-Yes
Research question well defined, relevant & meaningful. It is stated how research fills an identified knowledge gap.
-The research question could be better defined and presented earlier on. See comment on line 70. Challenges need to be better developed and more clearly defined. For example, the challenges of “imprecidse labels”, “parameter tuning” and “additional steps for outlier removal” in lines 34 to 35 of the introduction could be expanded to track throughout the paper.
Rigorous investigation performed to a high technical & ethical standard.
- Inputs and image preprocessing steps are unclear. For example, it’s difficult based on Figure 1 and the NEON product descriptions to tell whether or not lidar data were used. See specific comments under Data description.
- It is unclear whether or not validation data that is separate from the training data were used to compute overall classification accuracy since ground truth data were not released in the competition. Along these lines, the number of training samples widely varies for each category, while the rule of thumb is about 50 samples per category (Table 1). This is what was provided in the challenge, but should be pointed out. Validation and Cross validation methods should be described in the Methods section.
Methods described with sufficient detail & information to replicate.
-As of now, no. A start would be to define classification inputs, address whether or not lidar and field data were used and how the classification results were validated. See specific comments in the attached *.pdf.
Validity of the findings: - Can the authors speak to how their classification results compared to results of other competitors, even if based on results that the competitors published? The way the experiment is currently designed, there is no way of comparing results to anything else.
- Do results support a hypothesis or warrant expanded testing – for example, compare performance to another classification method, or extend algorithm to similar datasets acquired in other geographic locations?
- Can the authors identify or discuss any of the study limitations?
Additional comments: Any paper that introduces a new hyperspectral image classification algorithm that is not dependent on subjective thresholding is exciting.It would be great to have some context on why MI-ACE was developed and what classification weaknesses it is designed to address. This may be in the text of other cited work, but worth pulling out.


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: HYPERSPECTRAL TREE CROWN CLASSIFICATION USING THE MULTIPLE INSTANCE ADAPTIVE COSINE ESTIMATOR
Review round: 2
Reviewer: 1

Output:
Basic reporting: Basic reporting criteria satisfied after revisions were made to the article per reviewer comments.
Experimental design: Experimental design criteria satisfied after revisions were made to the article per reviewer comments.
Validity of the findings: Validity of the findings criteria satisfied after revisions were made to the article per reviewer comments.
Additional comments: The article meets PeerJ criteria after revisions in response to reviewer comments.