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: CAN HIGH-INTENSITY INTERVAL TRAINING AND SMALL-SIDED GAMES BE EFFECTIVE FOR IMPROVING PHYSICAL FITNESS AFTER DETRAINING? A PARALLEL STUDY DESIGN IN YOUTH MALE SOCCER PLAYERS
Review round: 2
Reviewer: 3

Output:
Basic reporting: Nice job addressing the requested revisions. The manuscript is much improved and ready for the next phase after one critical read and edit. Thank you for all of your hard work and attention to detail.
Experimental design: Nice job addressing the requested revisions. The manuscript is much improved and ready for the next phase after one critical read and edit. Thank you for all of your hard work and attention to detail.
Validity of the findings: Nice job addressing the requested revisions. The manuscript is much improved and ready for the next phase after one critical read and edit. Thank you for all of your hard work and attention to detail.
Additional comments: Nice job addressing the requested revisions. The manuscript is much improved and ready for the next phase after one critical read and edit. Thank you for all of your hard work and attention to detail.


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: DOPAMINE RECEPTOR ACTIVATION ELICITS A POSSIBLE STRESS-RELATED COPING BEHAVIOR IN A WILD-CAUGHT SONGBIRD
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript by Florkowski and Yorzinski entitled “Dopamine receptor activation elicits a possible stress-related coping behavior in a songbird” assesses the behavioral effects of peripheral administration of dopamine modulators in wild-caught house sparrows. The authors find that a D2 agonist increases “inanimate object biting”, when compared to an antagonist or saline. No other behaviors changed significantly.

Overall, the manuscript is clearly written and structured, experiments were well designed, and data analysis is solid. Raw data were shared.

Some minor comments:
a)	(lines 23-24, 85-86) Please provide rationale for the importance of studying stress responses in this species. The authors state that “few studies have examined[…]” and “there have so far been few studies investigating[…]”, but fail to clearly state the importance of this investigation. In the case of the house sparrow, it could be interesting to make connections between stress responses and their incredible invasiveness (and success) into ultra-urbanized environments. Could their stress responses be adaptive and underlie this? You might find Beaugeard et al., 2018 (Ecology and Evolution) helpful for this.

b)	Figures are mostly clear and well-formatted. Minor stylistic comments:
- Figure 1 would benefit from a legend for the barplot colors. Additionally, plotting individual datapoints (overlaid on top of bars) would give a better sense of variability than only means and SEMs.
- Figure 2 would benefit from larger marker sizes as well as a color scheme to match the one in figure 1
Experimental design: Experiments were well designed and executed. Methods are well described. Data are well analyzed and reported. Statistical tests are appropriate and well-controlled. Overall, authors did a great job here.

Minor comments:
a)	(line 117) Purchase source for PPHT is missing.
b)	(line 134) This could be a good spot to present justification (if it exists) that releasing these birds back into the wild after treatments and captivity is not expected to produce any deficits in fitness.
c)	(line 136) Did you use any specific software for helping score videos?
d)	Weight and body condition could vary significantly in wild-caught birds. Did you record birds’ weights and assess overall body condition? If so, body weight could be used as a random variable in your LMs. Did you administer any anti-parasitic treatment upon lab admittance?
Validity of the findings: The data upon which the conclusions are based are robust and well-controlled. However, my main concern with the manuscript is that the way the data are interpreted does not fully align with the conclusions, such that alternative interpretations cannot be ruled out.
In my opinion, the interpretation of “inanimate object biting” as a stress coping mechanism is somewhat generous and not fully supported by the presented data. The main caveat of this report is that it lacks any direct measures of stress – e.g., chronic stress markers (weight change, feather loss, aggression), or physiological markers such as plasma corticosterone levels.
To be clear, the authors do their due diligence to present relevant literature in support of the possible link between D2 receptor activation and stress-coping behaviors (including biting). I agree this is a possible explanation. However, the authors acknowledge other possible interpretations for this drug-induced behavior (lines 202-210). It is not clear to me why some of these (particularly stereotypy) are not just as likely as stress-coping.
This issue could be mitigated by “toning down” the language that directly connects biting behavior to stress-coping throughout the manuscript (including in the title).
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: DOPAMINE RECEPTOR ACTIVATION ELICITS A POSSIBLE STRESS-RELATED COPING BEHAVIOR IN A WILD-CAUGHT SONGBIRD
Review round: 1
Reviewer: 2

Output:
Basic reporting: This manuscript by Florkowski and Yorzinski investigates the role of the dopaminergic system in coping behaviors in a wild songbird. I found the manuscript to be well-written, with a sound experimental design that allows the authors to answer their research question. The Introduction and Discussion provide good context for the present experiment, and the data strongly suggest that D2 receptor activation increases coping-like behaviors in the absence of major stressors in this species. I had concerns with the statistics and presentation of the data that should be addressed prior to publication. I enjoyed reading the manuscript and thinking about the data, and look forward to the authors’ revisions.
Experimental design: I thought that the research is original and within the aims and scope, that the research question was well defined, relevant & meaningful, that the study design was rigorous. See the "Validity of the findings" section below for some methods details that should be included.
Validity of the findings: Major comments:
•	I didn’t find the statistical analysis to be appropriate for the authors’ data. The large error bars indicate a wide spread of behavior, and figure 2 shows that this might be due to many birds not performing a behavior (i.e., 0-inflated data), as well as the raw data. There was also a possible issue with reporting of pre- and post- treatment behavior. Based on this, I have the following comments:
o	Figure 1 shows that there are possible differences from the pre to post period in selective treatment groups, but the statistics don’t detect this. This is either because these aren’t real differences (i.e., large variances are due to a couple of individuals that did a lot of behavior), or because of the 0-inflated data (i.e., a spread of individuals who did the behavior, but the error is stretched wide because many birds also didn’t do the behavior at all).
o	I am not totally clear on the models that were run from the authors description in the methods. Could they help to clarify? Table 2 helps clear up some, but there should either be a description in the methods or more detail in the results about the “negative” findings.
o	I am not clear on whether the models were nested appropriately. For example, each set of pre- and post- treatment behavior are separate, so it would be inappropriate to run the pre- and post- difference as a main effect. Rather, there are pairs of pre- and post- for each treatment (i.e., three treatments per individual, and one pair of pre- post- specific to each treatment). I don’t believe the random effect controls for this nested design.
	I could see a few ways to address this, including running separate models for the pre- to post- comparisons (and the individual, as well as the pair, would have to be taken into account), or subtracting pre behaviors from post behaviors to get a difference score (or maybe even a normalized Z score to control for the variance between animals in the pre-period for each treatment).
o	I don’t have a specific preference for the way the authors handle the 0-inflated data, but their approach should answer whether the number of animals that do 0 behaviors obscure treatment effects for the proportion of animals that engage in the behavior. Possible approaches include zero-inflated poisson models or negative binomial models, or conducting the current analysis with and without animals with zero behaviors and reporting the results both ways.
o	The authors state that there is no relationship between biting and movement, but this just isn’t true. Figure 2 shows that birds either spend their time moving, or biting depending on the treatment (apart from the many animals that engaged in neither behavior), and do not do intermediate levels of both. This is very interesting and relevant to the authors’ research question.
	As for how to put some kind of statistical test to this relationship, I leave that to the authors to decide what is most appropriate given the data (and my comment about possible analyses above).

•	Given that the data are repeated measures, the figure presentations should reflect this.
o	While readers can download the raw data, I think the authors should plot individual data points on their plots in figure 1 (also see below for comments about visualizing repeated measures data)
o	Bar plots with error bars do not accurately reflect the nature of the data. One approach would be to connect individual data points with lines, laid over bar plots (or next to them). This could be done in many ways depending on how the authors wish to present the data. As examples, data points could be connected between all 6 bars (i.e., keeping the organization of Figure 1), or the authors could rearrange, or only show repeated measures between post- treatment groups, or plot the difference scores between post- and pre- and connect data points between these.

Minor comments:
•	General methods question: Were birds in the same pair given the same treatment each time, or different treatments? If different treatments, could this have any effect on the other partner?
o	Lines 142-145: Correct these sentences to say that all behaviors were scored in both the pre and post periods.
o	Please add a legend to figure 1 for the treatment group colors.
o	Many of the results for the variables the authors included in their models are not presented in the results text. An easy fix would be to say that “no other independent variables significantly predicted time spent engaging in behavior (Table 2).” But see concerns about appropriateness of stats and data visualization.
o	Lines 248-251: I think it would emphasize the rationale of the study to add in a point the authors made in the introduction down here, that there’s a need to test these questions in wild species because domestic species appear to have different physiological responses (and possibly to add in a short discussion of why this might be…totally optional, just a suggestion).
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: DOPAMINE RECEPTOR ACTIVATION ELICITS A POSSIBLE STRESS-RELATED COPING BEHAVIOR IN A WILD-CAUGHT SONGBIRD
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript by Florkowski and Yorzinski entitled “Dopamine receptor activation elicits a possible stress-related coping behavior in a songbird” assesses the behavioral effects of peripheral administration of dopamine modulators in wild-caught house sparrows. The authors find that a D2 agonist increases “inanimate object biting”, when compared to an antagonist or saline. No other behaviors changed significantly. The authors suggest that inanimate object biting could be a  stress-coping behavior; therefore this finding supports that D2 activation induces stress-coping behavior.
Overall, the manuscript is clearly written and structured, experiments were well designed, and data analysis is solid. Raw data were shared.
The authors addressed my previous concerns satisfactorily. I only have some further minor comments to improve readability and clarity.
a)	(line 23) Replace “which are” with “i.e.”
b)	(line 24-25) If you have space in the abstract, summarize the excellent rationale you provided about studying stress in house sparrows (lines 90-91)
c)	(line 85) Italicize the species name
d)	(lines 85-87) Relocate the Lattin 2019 citation to immediately follow the fragment “A study in wild-caught house sparrows (Passer domesticus)”
e)	(line 86) Replace “dopamine” with “D2”
f)	(lines 90-91) Excellent!
g)	(lines 192-193) Add information about on the ratio of how many (x out of N) animals performed biting after treatment
h)	(line 273) If D2 agonists increase stress-coping behaviors which in turn decrease stress, then the logic here would follow that D2 agonists would decrease stress-coping behaviors, therefore increasing stress
Experimental design: Experiments were well designed and executed. Methods are well described. Data are well analyzed and reported. Statistical tests are appropriate and well-controlled. All my minor concerns were addressed. I also liked the addition of the zero-inflation data correction.
Validity of the findings: My major concern was addressed by the authors. The language about linking inanimate object biting to stress-coping was toned down, the caveats of the study are more explicitly stated, and the alternative interpretations are appropriately acknowledged.
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: DOPAMINE RECEPTOR ACTIVATION ELICITS A POSSIBLE STRESS-RELATED COPING BEHAVIOR IN A WILD-CAUGHT SONGBIRD
Review round: 2
Reviewer: 2

Output:
Basic reporting: •	I appreciate the revisions the authors made throughout the manuscript, and I only have minor comments.
•	I think the title could benefit from adding “wild” or “wild-caught” as a descriptor of songbird; it would better describe an important aspect of the authors’ research question.
•	I agree with the addition of ecological context for the species, but would suggest replacing the term “urban invasive” with a more accurate descriptor (with respect to the research question at hand). On line 96, something like “success in non-native urban environments”, and on line 100, something like “urban specialist”.
•	Line 166: Typo: change “we” to “were”
•	Line 184: Typo: add “a” to “as repeated measure”
•	Lines 239-240: It was unclear from the writing what the authors mean by stereotypic behaviors compensating for the unnatural environment.
Experimental design: •	Lines 167-170: clarification, mismatch between wording in data – wording suggests the authors did pre minus post.
•	See below for validity of the findings, but briefly, the authors have addressed the concerns I had related to the statistical analysis.
Validity of the findings: •	I thank the authors for their thorough responses to my feedback. I agree with them that the new analyses have not altered the major findings of the manuscript and that the statistics and data visualization are appropriate and well-executed.
•	With respect to Reviewer 1’s comment from the previous review, please make a change on Line 26 in the abstract…something like changing stress-related coping behavior to “coping-like behavior”.
•	Also with respect to Reviewer 1’s comment, I noted that the dose of PPHT (1 mg/kg) used in the present study, also used in the Balthazart 1997 study, led Balthazart et al. to a pretty vivid description of pecking behavior. I agree their description doesn’t mean the behavior is definitively stereotypy rather than something more akin to coping, but the authors can more directly address this in the discussion in their newly added paragraph about alternative explanations beginning on line 234 (that the same dose in two different bird species elicits a very strong and unique behavior not commonly observed in other conditions, and that the interpretation in the quail study is stereotypy).
•	Line 207: the authors could consider making the following addition “…not yet been demonstrated in any wild species, or in passerines”.
•	Lines 220-223: also with respect to Reviewer 1’s comment about alternative explanations, because the authors did not find a link between weight loss in captivity and biting induced by the agonist, is it equally likely that signaling at D2 leads to biting behavior independent of stress? This wouldn’t be mutually exclusive with the authors’ suggestion that stress may result in increased biting behavior.
Additional comments: No additional comments


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND FUNCTIONAL ANALYSIS OF CLASS III PEROXIDASES IN GOSSYPIUM HIRSUTUM
Review round: 1
Reviewer: 1

Output:
Basic reporting: Class III peroxidases are involved in various stages of plant growth and development. In this work, the authors investigated 166 PRX genes from G. hirsutum on genomic, transcriptomic and functional levels using combinatorial techniques, providing reference for further research on PRX function in plants.
Experimental design: For phylogenetic analysis, maximum likelihood method is usually recommended for publication purpose instead of neighbor-joining.
Validity of the findings: 1. Line 199, could the authors explain how did they come to the conclusion that "the homologous gene pairs of GhPRXs in subgenome A and D mainly exhibited parallel evolution" from Fig 1?

2. Line 205-219, descriptions on group size and number of protein in each group are less relevant, which don't provide much insights. Clustering of some Arabidopsis and cotton PRX genes in the phylogenetic tree could just be resulted from some highly conserved PRXs across plants, doesn't necessary indicate any overall close relation of PRX in this two species from evolution perspective.

3. Fig. 4, by definition, two genes are said to be paralogous if they are derived from a duplication event, but orthologous if they are derived from a speciation event. Apparently the description here is inaccurate.

4. Line 282, for genes that seem to be not expressed, besides loss of function, more often, the reason could be that the expression levels are too low to be detected. Also, gene expression analysis is high restricted to the quality of RNA-seq including sample preparation.

5. Line 301 and Fig. 10, both GhPRX107 and GhPEX128 are higher expressed in sterility line than maintainer line, why does the authors mean by saying "opposite"?

6. ROS level can be affected by many factors, the speculation PRX107 is involved in reproductive process by regulating ROS status lacks solid evidence.

7. Discussion part should dig deeper into the findings and provide more insights instead of repeated description of previous results.

8. Typos and grammars need to be corrected (line 45, 101,104, 176, 190, 195, 201, 222, 228, 274, 279, 289, 302, 317, et al).
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: GENOME-WIDE IDENTIFICATION AND FUNCTIONAL ANALYSIS OF CLASS III PEROXIDASES IN GOSSYPIUM HIRSUTUM
Review round: 1
Reviewer: 2

Output:
Basic reporting: The submitted manuscript analyzes RPX genes, which have been studied in various plants including maize, pears, and Populus. Here the authors specifically focused on one of the unstudied plants, Gossypium hirsutum. The analyses presented here largely follow Zhu et al (2019, https://pubmed.ncbi.nlm.nih.gov/30904716/), with additional analyses on the associations between RPX genes and male fertility. I think in general this is a nice effort. Some suggestions for improvement are provided below.

There are quite a lot of awkward sentences (e.g. lines 33, 38, 190, 199, 244), typos, and grammatical errors (e.g. lines 197, 227, 245, 301, 305) throughout the manuscript, which poses difficulty for readers to clearly understand the text. I suggest the authors use copy editing services or let someone proficient in English to proofread your manuscript. In addition, Fig 10 and Fig 11B need to have higher quality.
Experimental design: In general, the methods for bioinformatic analyses need to be described in much more details so that the readers can reproduce your analyses. In particular, you need to provide the parameters you used for all the bioinformatic analyses you have done. You also need to cite the tools you use correctly: for example, for line 129-132, you should cite the article “PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences” in addition to the website. For GO and KEGG analyses, you will also need to cite the original papers for the databases.

Here are some specific sections that require more details in particular:
Phylogenetic analysis: what specific tools did you use to align the PRXs protein sequences? What parameters did you use? In addition, how did you cluster the genes into different subgroups?

Gene structure analysis: you need to explain what GFF3 profiles are. Also, how did you get the GFF3 files? For the tool you used, what parameters did you choose?

Gene duplication and calculation of Ka/Ks values: how did you find the collinearity gene pairs? Or did you find them using MCScanx? The one sentence explanation in line 124 does not clearly describe what you did.

Analysis of GO and KEGG pathway enrichment: for both GO and KEGG analyses, what background genes and how many did you use? Did you use multiple testing corrections for your p-values?

Expression pattern analysis: write the full name of FPKM. More importantly, how did you process the RNA-seq data to calculate FPKM? What tools and parameters did you use?
Validity of the findings: I suggest the authors to revisit GO and KEGG analyses to make sure they are correct. Here are some specific comments that may help you improve the quality and soundness of your manuscript:

1.	Line 183-185: are there any duplicate PRX genes within this set of 166 genes? Are they non-redundant? It would be nice to check the number of non-redundant genes.
2.	Line 185-187: I believe these are predicted numbers as you don’t actually have the encoded proteins. As in Fig 8, some GhPRX genes are not expressed. It would be better to explicitly say it clearly to avoid confusion. Same with sentences in line 190-194.
3.	Line 188: can you say something quantitative about the similarity? It is difficult to say GhPRXs share high similarity to the maize PRXs proteins without numbers. In addition, how did you compare the similarities between two sets of proteins? I don’t find them in Methods.
4.	Fig 1: “… four genes are located on scaffold” is not very accurate because all GhPRXs are located on 26 chromosomes. “Found” would be a better word as the scaffolds are results of fragmented assembly.
5.	Line 199-200: can you explain more about parallel evolution? The sentence is difficult to understand probably due to its awkwardness.
6.	Line 208-209: how did you determine eight subgroups? Can you add the explanation in Methods?
7.	Fig 2: what do the colors for check marks and stars represent?
8.	Fig 4: (A) It’s only paralogous gene pairs right, as it is within G. hirsutum? (B) The figures do not make sense to me. The x- and y-labels are exactly the same. What are they exactly?
9.	Line 239: < 1 Ka/Ks indicates possible purifying selection, but it does not suggest strong purifying selection. Removal of word “strong” will be better.
10.	Fig 5: is (A) is the same as Fig 3(A)? If so, you can probably combine Fig 3 and Fig 5 into one figure.
11.	Line 246: can you list the number/percentage of regulatory elements related to plant hormones? It is too hard to tell from Fig 5. In addition, you probably need to a supplementary table for this analysis so readers can easily find regulatory elements of GhPRX genes.
12.	Line 258-261: full name of analyses should be listed together with the abbreviations because not all readers are familiar with such kind of analyses. For example, you should say biological process explicitly for GO-BP. Same for GO-MF and GO-CC.
13.	Line 257-264: how many GO terms out of the total are statistically significant? Fig 6 only shows the top 20. You should report all positive hits in a supplementary table.
14.	Fig 6 and Fig 7: explain what rich factor and GeneNumber mean. The legend for GeneNumber in Fig 7 does not make sense – two circles with different sizes have the same numeric value of 33.
15.	Line 256-270: I would re-examine the GO and KEGG analyses again to make sure they are correct. The results don’t look right to me. In particular, both Fig 6 and Fig 7 have extremely low p/q-values. For example, in Fig 6, the lowest reported -log10(p-value) = 200, which means p-value = 10^-200. p-value of 10^-2 = 0.01 is already quite low, and your p-values are extremely small (I don’t think you can calculate p-value to that precision). In Fig 7, is there a reason why you use q-value instead of p-value?
16.	Fig 8: you may want to mention that you split all GhPRXs into two heatmaps as it is confusing to see two figures at the first glance. Besides, please label the legend. What is the unit for expression? Same for Fig 9.
17.	Line 275-284: instead of grouping the expression profiles by hand, you may cluster the expression profiles and see how many groups there are.
18.	Line 298-301: is it statistically significant? Can you use statistical test to make your statement more convincible? You may also want to label the significance in Fig 10.
19.	Line 309: similar to comment 18, statistical test is needed for both text and Fig 11(B).
20.	Fig 10 and Fig 11(B): what do A and B on top of each bar mean?
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: GENOME-WIDE IDENTIFICATION AND FUNCTIONAL ANALYSIS OF CLASS III PEROXIDASES IN GOSSYPIUM HIRSUTUM
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: The major for the article is that there is no directly evidence in the data to support the authors' hypothesis that Class III peroxidase genes are linked to pollen fertility and pollen development. I would suggest the authors to retract that claim or provide further experimental evidence for that claim.
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: GENOME-WIDE IDENTIFICATION AND FUNCTIONAL ANALYSIS OF CLASS III PEROXIDASES IN GOSSYPIUM HIRSUTUM
Review round: 1
Reviewer: 4

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: This study is very interesting and combines bioinformatics and experimental analysis to provide information on the GhPRX gene family in Gossypium hirsutum. Generally, the manuscript is well structured but needs some improvements before publication. I pointed out several comments and suggestions to help you to improve your manuscript:

M&M
- Did you use MUSCLE or CLUSTALW to perform the alignments? Which parameters did you use? These informations should be provided.
 - What substitution model did you use in the NJ analysis? How did you treat the gaps and missing data?
- I would suggest you perform the phylogenetic analysis with Bayesian or ML methods.
- Provide more details of this gene structure analysis.
- Did you test if the EF-1α gene is efficient to be used as a reference gene in this experiment? I would recommend testing more genes or providing the reference that has previously tested it.

RESULTS
- How was the length of the alignment used for the phylogenetic reconstruction? Did you consider codifying the extended gaps before the analysis?
- I suggest including the genes identified in G. raimondii in the phylogeny to compare the groups within the genus Gossypium?

The discussion is very descriptive. You should make an effort to better discuss the results.


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: GENOME-WIDE IDENTIFICATION AND FUNCTIONAL ANALYSIS OF CLASS III PEROXIDASES IN GOSSYPIUM HIRSUTUM
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have well addressed comments from reviewers.
Experimental design: Well.
Validity of the findings: Well.
Additional comments: No


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: GENOME-WIDE IDENTIFICATION AND FUNCTIONAL ANALYSIS OF CLASS III PEROXIDASES IN GOSSYPIUM HIRSUTUM
Review round: 2
Reviewer: 2

Output:
Basic reporting: The English is still awkward -- the manuscript has a lot of awkward/grammatically incorrect sentences that need improvement (e.g. lines 130, 136, 250). Some references are missing for softwares used. For example, I think the authors use CLUSTALW (which they incorrectly spelled as CLUATALW) but they did not cite it.
Experimental design: no comment
Validity of the findings: The methods are more detailed than last time but I still don't know what kind of statistical tests they used.
Additional comments: Figure 3: legend is illegible
Figure 4B: histogram is a better choice for visualizing distributions of a single variable.
Figure 9, 10B: what statistical tests do you use and what significance level is for **?


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: RECENT ADVANCES IN METHODS FOR IN SITU ROOT PHENOTYPING
Review round: 1
Reviewer: 1

Output:
Basic reporting: Comments:
The hidden half of crop plant imparts much important to researchers. Due to difficulties in phenotyping much of the researchers were less interested on its study. Low repeatability and reproducibility of root data is limitation. High plasticity of root traits and GXE interaction limits its application in breeding program. Despite quantitative traits, still this manuscript might help the root phenomics scientists  accustomed with different root system analysis, its advantage, accuracy of data and also software tools available (freely or paid).
-	While going through the manuscript, the comments has been mentioned on manuscript itself. Pl go through comments and incorporate  accordingly.
-	 If possible, kindly insert image of some of the tools to make manuscript  of good quality.
-	Kindly add, mobile base application that can analyze root traits in a paragraph.
-	 In case of software for root analysis, whether scanning based or is of image based.
-	Kindly add some of the reference related to non destructive, forest tree root analysis software (Biovis software).
Some important reference might add flavor to this review:
Tracy, S. R., Nagel, K. A., Postma, J. A., Fassbender, H., Wasson, A., & Watt, M. (2020). Crop improvement from phenotyping roots: highlights reveal expanding opportunities. Trends in plant science, 25(1), 105-118.
Das, A., Schneider, H., Burridge, J., Ascanio, A. K. M., Wojciechowski, T., Topp, C. N., ... & Bucksch, A. (2015). Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics. Plant methods, 11(1), 1-12.
Pioneer work of Foulke et al is missing.
Reference of Rumesh Ranjan on root traits is missing.
Experimental design: NA
Validity of the findings: NA
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: RECENT ADVANCES IN METHODS FOR IN SITU ROOT PHENOTYPING
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article is well written, describing very well about the . The description of the root insitu phenotyping methods and image processing softwares is good. However, information on measurable root traits under each method is to be desired. I have attached pdf with comments for revision
Experimental design: No
Validity of the findings: No
Additional comments: No


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: RECENT ADVANCES IN METHODS FOR IN SITU ROOT PHENOTYPING
Review round: 1
Reviewer: 3

Output:
Basic reporting: The review summarizes a large body of literature on root phenotyping and related image analysis methods. The Introduction adequately introduces the subject matter.

While very few reviews if any are available that focus on both root survey and image analysis methods, I believe there are some very good reviews addressing root phenotyping, or addressing root imaging analysis. I suggest authors to briefly discuss about this in the Introduction.
Experimental design: The study design appears to be comprehensive and unbiased, and the review contents are organized logically.
Validity of the findings: The review provides a good summary of current literature on root phenotyping and imaging, including a discussion of pros and cons of numerous methods. Some of these comments may be based on authors' experience, while others may be based on literature survey; in the latter case, I see that proper citations are provided. So, I think the discussion is useful for readers.
Additional comments: I have only a few minor comments:

(1)  Lines 37-38: Please provide a proper citation of the source of this statement. When was this calculation done and what assumptions were made when making this statement? Why has this been almost accepted as a fact?

(2) Lines 70-71: This disadvantage is too superficial that it is applicable to any other root survey method.

(3) Line 78-79: I don't agree. I think some of these methods for sure can be, and have been, used to examine dynamic changes of roots, even though they are cumbersome and inefficient.

(4) Lines 587-497; Since this is a review, there should not be an "experiment" to design. You can say someone conceived the idea and designed the study, but not the experiment.


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

Input:
Title: GENETIC DIVERSITY OF ENTEROTOXIGENIC BACILLUS CEREUS STRAINS IN CORIANDER IN SOUTHWESTERN MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: This manuscript, entitled “Genetic diversity of enterotoxigenic Bacillus cereus strains in coriander in southwestern Mexico”, had described the toxigenic profile, biofilm production, genes associated with the production of biofilms, sporulation rates, enzymatic profile, psychotropic properties, and genetic diversity of B. cereus strains from coriander in southwestern Mexico. Due to lack of significance and novelty, my suggestion is rejection.
Experimental design: First and most importantly, the samples were collected from a relatively small area within a short period (six-week study period). Also, only 60 coriander samples and 17 B. cereus strains were recovered. The results yield from such samples have limited guidance and significance.
Secondly, only toxigenic profile, biofilm production, genes associated with the production of biofilms, sporulation rates, enzymatic profile, psychotropic properties, and genetic diversity were included in the study. Such phenotype screening is pre-experimental studies upon further in-depth molecular mechanism investigation. The data are insufficient to be published as a scientific manuscript unless there’s novel strain types and genes identified. However, in the current study, none of such types were identified.
Validity of the findings: Thirdly, the results and discussion parts were short and dull, the data presentation is poor. Due to the lack of significance data to be discussed, I suggest the authors to perform more in-depth study.
Additional comments: No additional comments


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

Input:
Title: GENETIC DIVERSITY OF ENTEROTOXIGENIC BACILLUS CEREUS STRAINS IN CORIANDER IN SOUTHWESTERN MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript written by Cástulo-Arcos et al. reports some interesting results. In this work, the authors have discovered that Bacillus cereus strains produce a low amount of bioﬁlm and produce rates sporulation around 80%.
Experimental design: In general, this paper is clearly laid out, well planed and easy to read. The experiments are well designed and appropriate controls are presented.
Validity of the findings: The novelty and significance of the manuscript were not highlighted, please modify the paper more clearly.
Additional comments: Manuscript Title: Genetic diversity of enterotoxigenic Bacillus cereus strains in coriander in southwestern Mexico
Manuscript ID: #71248
The manuscript written by Cástulo-Arcos et al. reports some interesting results. In this work, the authors have discovered that Bacillus cereus strains produce a low amount of bioﬁlm and produce rates sporulation around 80%.
Some specific suggestions or questions are listed below:
1.Abstract: Abstract should be written more precisely and explain novelty of this work.
2.Introduction: Introduction is easy to read but needs a little completed. Bacillus strains are well known for their metabolic capability and environmental versatility as well as for their ability to manage bacterial and fungal pathogens infecting crop plants. Authors should add more information into this section and cite the recent research into the field based on the recent literature (such as doi: 10.3390/plants11030457; doi: doi: 10.3390/microorganisms10020365; 10.3390/microorganisms9122511;  doi: 10.1016/j.jwpe.2020.101712; doi: 10.3390/plants10112342; doi:10.3390/microorganisms8020223; doi: 10.1016/j.postharvbio.2013.10.004; doi: 10.1007/s00253-014-6164-y; doi: 10.1016/j.biortech.2012.01.106; doi: 10.1016/j.chemosphere.2022.133609; doi: 10.1021/jf404908j; doi: 10.3389/fbioe.2020.570307).
3.Introduction: Coriandrum sativum, Please check throughout the manuscript that abbreviations/acronyms are defined the first time they appear in each of three sections: the abstract; the main text; the first figure or table.
4.Introduction: In addition, this part should focus on the research progress related to the topic and emphasize the innovation of this research. However, the novelty and significance of the topic were not highlighted, please modify the introduction more clearly.
5.Material and Methods: please add relative references to support all the methods.
6.Results: This section is too simple. Please add all the results in details.
7.Results: Figure 3 is not clear. Please re-draw the figure and provide high quality one.
8.Discussion: Authors should add more depth discussion into this section and cite the recent research into the field.
9.Conclusions: Authors can add and revise the Conclusions section for the better understanding of the topic and its future research.
References: Many of the references have been superceded and more modern ones are required


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

Input:
Title: MANIPULATION OF LIGHT QUALITY IS AN EFFECTIVE TOOL TO REGULATE PHOTOSYNTHETIC CAPACITY AND FRUIT ANTIOXIDANT PROPERTIES OF SOLANUM LYCOPERSICUM L. CV. ‘MICROTOM’ IN A CONTROLLED ENVIRONMENT
Review round: 1
Reviewer: 1

Output:
Basic reporting: Overall, the manuscript reads well. However there are some sentences which do need to be re-phrased in order to be published.
Experimental design: Please see section 4 for comments
Validity of the findings: Findings are valid and supported by the results presented. Please see section 4 for more comments.
Additional comments: One major concern I have is the way the authors classified the lighting treatments in figure 1. It seems that the authors have placed the FL treatment into many more narrow wavelength ranges. This has not been done with the RB and RGB treatments. While their name suggests they solely emit light in these wavelengths, this is clearly not the case in figure 1. Please revisit these classifications as it may change the results and arguments the authors are presenting in the discussion. I suggest either using only blue, green, red, and far-red as the wavelength classifications, or determining the percentage of the RB and RGB treatments which fall within the more narrow bands presented by the author.

Line 5: There is a space missing between controlled and environment. Potentially just a copying error?
Line 35: change to non-sustainable.
Line 58: remove the.
Line 87-93: Green light has also been shown to drive high rates of photosynthesis (similar to many other wavelengths) as well as support fruit filling through carbon export in tomato. I suggest this be mentioned in a way to strengthen the argument for green light. Suggest a reference to the following in this section as well: doi: 10.3389/fpls.2018.00756.
Line 108-110: This statement is quite awkward. I’m not sure what the authors mean by “finalized” in its current context. Please rephrase the sentence.
Figure 1: I suggest the authors either calculate all the percentages of wavelengths in all lights, or simplify it for the fluorescent light. For example, although the RB light is supposed to be purely red and blue, based on the graph, there is some violet in that spectrum. This is obviously a factor of the LED chip itself, but presenting the table in the way it is done is quite confusing. I suggest the authors use only blue, green, red, and far-red wavelength regions.
Plant material and growth conditions: Please add the number of plants which were place in each light treatment. Also, were there any replications studies performed? Technically, only one replicate seems to be performed with sub-samples (each plant) used for each measurements.
Line 132: When referring to epigeal plant biomass, I’m assuming the authors are speaking of all above ground biomass, however the next line they talk about leaf biomass/epigeal biomass. Please clarify is epigeal biomass is all above ground biomass or non-laminar biomass.
Line 151: Were the fully expanded leaves on separate plants.
Line 153-154: Please state the size of the chamber used for leaf photosynthetic measurements.
Line 155: What was the spectral quality of light used during the measurements?
Line 169: What was the illumination level for the steady-state fluorescence measurements?
Lines 201: Were the seeds of the tomatoes kept for the analysis or were they removed?
Line 254: This sentence is not needed. I suggest it be removed.
Line 259: I’m assuming the statement “Which showed comparable values” is referring to the FL and RB plants. However, it does not read this way and therefore should be changed.
Line 293: Remove indeed.
Heatmap analysis: Related to the wavelength ranges selected, the results may not be valid if correctly adjusted for each lighting source. Only FL light was split into defined wavelengths while RB and RGB was not. Looking at the spectral distribution, it seems that some green from the RGB treatment would be classified as cyan under the authors classification ranges. Perhaps this needs to be looked at again by the authors to ensure their results are conclusive and not a factor of how they classified wavelengths.
Line 327: Again, due to the authors wavelength ranges, these values for the amount of blue light may be different than reported.
Lines 392-394: This needs to be reworded as the beginning of the sentence does not read correctly.
Perhaps consider using subtitles in the discussion to break it into specific sections.


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: MANIPULATION OF LIGHT QUALITY IS AN EFFECTIVE TOOL TO REGULATE PHOTOSYNTHETIC CAPACITY AND FRUIT ANTIOXIDANT PROPERTIES OF SOLANUM LYCOPERSICUM L. CV. ‘MICROTOM’ IN A CONTROLLED ENVIRONMENT
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript by Vitale et al. describes the effect of different light spectra on the photosynthetic activity and fruit bioactive compound synthesis in Solanum lycopersicum L. cv. 'Microtom'. The article is well written with professional English used throughout. The authors have provided sufficient references and they have succeeded in presenting a professional article structure.
Nevertheless, throughout the discussion,  the authors  should add the number of the figure or table to which they refer to.
Experimental design: The research subject  is within the Aims and Scope of the journal and the research question is well defined and meaningful. However, it is not stated how the authors fill an identified knowledge gap. The methods used are very well described  with all the information to replicate.
Validity of the findings: All the data provided are robust and statistically sound and the conclusions are clear, well stated and linked to the original research question.
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: THROMBOCYTOPENIA AND INCREASED RISK OF ADVERSE OUTCOME IN COVID-19 PATIENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is an ambiguous report, however, the authors should revise the English style.
References are ok.
Article structure is correct.
The hypotheses proposed are also correct.
Experimental design: This is a retrospective observational study in which platelet counts were the guide biomarker.
Validity of the findings: Other studies have reported on the importance of thrombocytopenia as a marker of worse outcomes in patients with covid.
Additional comments: This is a multi-centre retrospective study with the aim of evaluating the relationship between thrombocytopenia (defined as platelet count < 100 x 109/L) and disease progression. The outcomes were acute respiratory distress syndrome (ARDS), respiratory failure, intensive care unit (ICU) admission, acute heart injury, septic shock, and disseminated intravascular coagulation (DIC).
The authors included 2,209 patients, of which 127 (5.7%) had thrombocytopenia. Thrombocytopenic patients were older, however, the authors created a matched non-thrombocytopenic group according to age (Table 1).

Criticisms
•	The English style is clear and unambiguous, however, the authors should choose American or British style of spelling, for instance, haematological or hematological, as both are represented in the manuscript.

Results section:
•	lines 176-178, “While thrombocytopenia is a key diagnostic component in DIC, its association with DIC is understandable”, are not clear. Please, rephrase them. The same could be asserted regarding the subsequent lines (178-180), in which the authors state that there was no difference between the two groups regarding some variables, in contrast to what was stated at the beginning of this subsection.
•	Figure 2- I believe it is unnecessary to show percent of cell types, as it overloads the figure (and the message).
•	I think that there are too many figures. The authors could have selected only the altered variables to show in the figures.
Conclusions section can be shortened.


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: THROMBOCYTOPENIA AND INCREASED RISK OF ADVERSE OUTCOME IN COVID-19 PATIENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Clear and unambiguous, professional English used throughout.
Literature references, sufficient field background/context provided.
Professional article structure, figures, tables. Raw data shared.
Self-contained with relevant results to hypotheses.
Experimental design: Original primary research within Aims and Scope of the journal.
Research question well defined, relevant & meaningful.
Rigorous investigation performed to a high technical & ethical standard.
Methods described with sufficient detail & information to replicate.
Validity of the findings: Impact and novelty not assessed. Meaningful replication encouraged where rationale & benefit to literature is clearly stated.
All underlying data have been provided; they are robust, statistically sound, & controlled.
Conclusions are well stated, linked to original research question & limited to supporting results.
Additional comments: Dear Editor,

PeerJ.

Subject: Peer review

I had the pleasure of reviewing the manuscript submitted to your journal, entitled ‘The association between thrombocytopenia and systemic disorders in COVID-19 patients’

The paper needs further major revisions. The paper would be strengthened by:

Major points:
1.	The title ‘systemic disorders’ is misinforming as the paper focuses on clinical outcomes and laboratory values differences among COVID-19 patients with and without thrombocytopenia.
2.	The case to control ratio in propensity match is 1:6. 127 patients in thrombocytopenia and 729 in the non-thrombocytopenia group do not precisely add up to the ratio (127*6=762).
3.	Expand ‘ISTH’ for DIC score.
4.	The term acute heart injury (Table 1) is non-specific. Please clarify.
5.	Figures 2, 3, 4, 5 need P-values as the visual discernment between two groups may be difficult. The P values may be added within the figure for each set of measurements.
6.	Lines 211-215 are most suitable under discussion rather than the results section.
7.	Lines 253-261 talk about ‘both groups.’  Please mention that the two groups are early thrombocytopenia vs. late thrombocytopenia for better understanding.
8.	Explore palusble reasons why the low rates of thrombocytopenia were observed in this cohort compared to other studies on this topic.
9.	Cite the paper by Panyang Xu about the pathogenesis of thrombocytopenia in COVID-19. Ann Hematol. 2020; 99(6): 1205–1208. Published online 2020 Apr 15. doi: 10.1007/s00277-020-04019-0 PMCID: PMC7156897 PMID: 32296910.

Minor points:
1.	Line 171, the phrase ‘higher prevalence of ARDS’ is more appropriate than ‘frequent occurrences of ARDS’.
2.	The phrase PSM database is misleading. Recommend using 'PSM cohort' for better understanding.
3.	Are ARDS and respiratory failure in Table 2 mutually exclusive?


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: THROMBOCYTOPENIA AND INCREASED RISK OF ADVERSE OUTCOME IN COVID-19 PATIENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is a multi-centre retrospective study with the aim of evaluating the relationship between thrombocytopenia (defined as platelet count < 100 x 109/L) and disease progression. The outcomes were acute respiratory distress syndrome (ARDS), respiratory failure, intensive care unit (ICU) admission, acute heart injury, septic shock, and disseminated intravascular coagulation (DIC).
The authors included 2,209 patients, of which 127 (5.7%) had thrombocytopenia. Thrombocytopenic patients were older, however, the authors created a matched non-thrombocytopenic group according to age
Experimental design: This is a multicentre retrospective study in which more than 2,000 hospitalised patients were included.
Validity of the findings: Yes, the findings are well grounded. The results are not exactly new, however, they are sound and useful to the physicians and researchers on this area. Patients with thrombocytopenia had worse outcome.
Additional comments: No comments.


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

Input:
Title: THE NEEDS OF CANCER PATIENTS DURING THE COVID-19 PANDEMIC—PSYCHOSOCIAL, ETHICAL AND SPIRITUAL ASPECTS—SYSTEMATIC REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: I have the following comments for the authors to address. I am happy to review this paper again

1) The authors used "SARS-CoV-2". It is not the most updated term. The authors should use COVID-19.

2) The following statement "The article is intended for professionals who provide support to patients: healthcare personnel, therapists, NGO employees, and social workers. Accurate identification of chronic condition patients’ new needs should also be important for entities in charge of organisation of medical help and assistance on all levels". The above statements are too general and please remove.

3)  The authors stated "SARS-CoV-2 pandemic has caused unprecedented social changes and started rapid healthcare  transformation on the global level [1]". I recommend the authors to state the governments' response based on the following study:

Government response moderates the mental health impact of COVID-19: A systematic review and meta-analysis of depression outcomes across countries. J Affect Disord. 2021 May 27;290:364-377. doi: 10.1016/j.jad.2021.04.050. Epub ahead of print. PMID: 34052584.

4) The authors stated "Its outbreak did not lower the rates of infection with other..." This statement does not make sense and suggests to be removed.

5) The authors stated "Even though the World Health Organisation (WHO) points to the necessity to pay attention to mental health of this population," I suggest the authors to discuss the link between physical and mental health:

Impact of the COVID-19 Pandemic on Physical and Mental Health in Lower and Upper Middle-Income Asian Countries: A Comparison Between the Philippines and China. Front Psychiatry. 2021 Feb 9;11:568929. doi:
10.3389/fpsyt.2020.568929. PMID: 33633595; PMCID: PMC7901572.

6) Before talking about COVID-19 impact on cancer, please discuss how the mental health of COVID-19 patients and other chronic diseases based on the following studies:

A quantitative and qualitative study on the neuropsychiatric sequelae of acutely ill COVID-19 inpatients in isolation facilities. Transl Psychiatry. 2020 Oct 19;10(1):355. doi: 10.1038/s41398-020-01039-2. PMID: 33077738.

Psychological State and Associated Factors During the 2019 Coronavirus Disease (COVID-19) Pandemic Among Filipinos with Rheumatoid Arthritis or Systemic Lupus Erythematosus. Open Access Rheumatol. 2020 Sep 22;12:215-222. doi: 10.2147/OARRR.S269889. PMID: 33061689; PMCID:PMC7520098.

7) Under Contact of Nature, please discuss discuss the findings of the following studies:

Effects of Horticultural Therapy on Asian Older Adults: A Randomized Controlled Trial. Int J Environ Res Public Health. 2018 Aug 9;15(8):1705. doi: 10.3390/ijerph15081705. PMID: 30096932; PMCID: PMC6121514.

 Social connectedness as a mediator for horticultural therapy's biological effect on community-dwelling older adults: Secondary analyses of a randomized controlled trial. Soc Sci Med. 2021 Sep;284:114191. doi: 10.1016/j.socscimed.2021.114191. Epub 2021 Jul 9. PMID: 34271401.
Experimental design: The authors should indicate in the title and the abstract that this is a systematic review.
Validity of the findings: 1) The authors stated "serious obstacles in reaching information by means of the new media – mainly owing to “the digital gap” associated with lack of access to mobile phones or computers, which make use of e.g. online consultation possible". Please provide more details including internet cognitive behavior therapy by adding the following references:

The most evidence-based treatment is cognitive behaviour therapy (CBT), especially Internet CBT that can prevent the spread of infection during the pandemic.

Use of Cognitive Behavior Therapy (CBT) to treat psychiatric symptoms during COVID-19:
Mental Health Strategies to Combat the Psychological Impact of COVID-19 Beyond Paranoia and Panic. Ann Acad Med Singapore. 2020;49(3):155‐160.

Cost-effectiveness of iCBT:
Moodle: The cost effective solution for internet cognitive behavioral therapy (I-CBT) interventions. Technol Health Care. 2017;25(1):163-165. doi: 10.3233/THC-161261. PMID: 27689560.

Internet CBT can treat psychiatric symptoms such as insomnia:
Efficacy of digital cognitive behavioural therapy for insomnia: a meta-analysis of randomised controlled trials. Sleep Med. 2020 Aug 26;75:315-325. doi: 10.1016/j.sleep.2020.08.020. Epub ahead of print. PMID: 32950013.

2) The authors stated "Psychiatry showed that in a group of 6213 patients who had cancer in the period of the pandemic, 23.4% were diagnosed with depression, 17.7% – with anxiety, 9.3% – with PTSD, and 13.5% of patients felt hostility". The authors should compare the prevalence of depression, anxiety and PTSD with general population based on the following study:

A chain mediation model on COVID-19 symptoms and mental health outcomes in Americans, Asians and Europeans. Sci Rep 11, 6481 (2021). https://doi.org/10.1038/s41598-021-85943-7
Additional comments: No additional comments


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

Input:
Title: THE NEEDS OF CANCER PATIENTS DURING THE COVID-19 PANDEMIC—PSYCHOSOCIAL, ETHICAL AND SPIRITUAL ASPECTS—SYSTEMATIC REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article has clear text and conforms to professional standards of courtesy and expression. Some places of improvement are:
Line 55, 56 – Using incl. and ca. is not very common in scientific articles. I suggest at least for the first time use, please use the full form.
Line 66, 67 – Is this a new paragraph? It is too small to be a paragraph on its own.
Line 78 – As ‘of’
Other comments are annotated in the pdf.
The article includes sufficient introduction and background to demonstrate how the work fits into the broader field of knowledge.
Experimental design: This article's content is within the aims and scope of the journal.
The authors describe the field and explain why this review is needed and explain the relevance to readers in the field, and associated areas by citing previous reviews.
However, the methodology excludes the articles and data not published in English. I feel that the authors might be losing some crucial data that is not published in English. COVID19 being a pandemic, there might be some crucial data from other countries.
Additionally, as annotated in the pdf, in lines 78, 229, 560, the authors report statistics from early 2021. In the current pandemic, I think it would be relevant and accurate to report the latest data and statistics.
Validity of the findings: no comment
Additional comments: In the context of a pandemic like COVID19, with ever-changing statistics, it is crucial to report the latest data. The authors in this article mostly report data and numbers from early 2021. Updating and re-visiting the results might be of great value to this literature review.


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 NEEDS OF CANCER PATIENTS DURING THE COVID-19 PANDEMIC—PSYCHOSOCIAL, ETHICAL AND SPIRITUAL ASPECTS—SYSTEMATIC REVIEW
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article covers a very important topic, the psychosocial, ethical and spiritual needs of cancer patients during the SARS-CoV-2 pandemic. I complement the authors for covering this important topic. However, I have some major concerns regarding the reporting and design of the study.
-	Abstract: the abstract is missing structured information about the methodology used, a clear objective and structured information about the major results and conclusions.
-	The introduction, abstract and title describe the objective of this review article slightly different. I think the objective is to assess the psychosocial, ethical and spiritual needs of cancer patients during the pandemic. Please be consequent in the formulation of the objective. For example, in the introduction the authors also mention that they are investigating the medical needs.
-	My major concern is that the previous research on a) psychosocial needs after crisis, and  b) psychosocial needs of cancer patients is missing in the introduction. What has previous research identified as main psychosocial needs after crisis? And what has previous research identified as important needs for cancer patients (for example Chen at al., (2021) developed an instrument measuring important psychosocial needs for cancer patients based on Maslow’s hierarchy of needs)? Regarding the psychosocial needs after crises and disasters many research on this topic exists (for instance a standard work in this area is Hobfoll et al., 2009) as well as  international guideless (for example TENTS guidelines (Bisson et al., 2020) and recent WHO guidelines on psychosocial support). This body of literature can serve the authors as it can function as a framework to identify the most important needs that might be currently missing for cancer victims.  When this framework based on previous research is made clear in the introduction, the specific needs for cancer victims in this specific crisis will follow logically in the result section.
Experimental design: I have some major concerns regarding the methodology.
-	The method section is too brief and is missing detailed and vital information. I miss a clearly described search strategy and screening strategy. Also, there is no information about the methodological strength of the studies included. In this way, it will not be possible to replicate this study or to clearly assess the strength of the results of this study.
-	It is unclear why the used keywords in the search strategy were included. Why are keywords not included that are directly related to the objective, namely psychosocial needs, spiritual needs and ethical needs (or related keywords such as social support, supportive interventions)? Keywords are now used that are not previously introduced to the reader,  such as ‘coping skills’.
-	Psychosocial needs and care is also a psychological topic. It is recommended to include PsycINFO as a database.
-	Please provide a detailed overview of inclusion and exclusion criteria that makes it clear to the reader how the authors arrived at the inclusion of 160 articles (starting with 11999 articles).
-	Please provide a section 'categorization of findings' in the method section that will describe how the results will be categorized and explains to the reader why this categorization had been chosen.
Validity of the findings: -	The article as a whole is very lengthy and this makes it for the reader difficult to read. It will help if the information, especially the results and conclusion section, can be described more structured with subheadings and a clear framework/outline introduced in the introduction or method section. The information can also be described more concise. A table with key results and conclusions can also help the reader.
-	Due to the lack of 1. a clear objective and b. a clearly described methodology, it is not clear to the reader where the results come from and what the strength of the findings is. For example, the section demographic data reads as an introduction instead of research findings on psychosocial needs. And why is mindfulness mentioned as important for treating PTSD (also a citation is missing here) while this not at all first choice of treatments regarding to the guidelines for treatment of PTSD. This should be discussed and a discussion is missing  To me as a reader, it feels like the results and conclusion are missing a clear categorization of findings and discussion of the validity of the findings. It now reads as scattered parts of results.
-	The conclusion does not identify unresolved questions / gaps / future directions.
Additional comments: No additional comments


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

Input:
Title: THE NEEDS OF CANCER PATIENTS DURING THE COVID-19 PANDEMIC—PSYCHOSOCIAL, ETHICAL AND SPIRITUAL ASPECTS—SYSTEMATIC REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: I am satisfied with the amendments.
Experimental design: I am satisfied with the amendments.
Validity of the findings: I am satisfied with the amendments.
Additional comments: I am satisfied with the amendments.


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 NEEDS OF CANCER PATIENTS DURING THE COVID-19 PANDEMIC—PSYCHOSOCIAL, ETHICAL AND SPIRITUAL ASPECTS—SYSTEMATIC REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have taken care of the suggested corrections.


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

Input:
Title: THE EFFECT OF AGE AND SEXUAL MATURATION ON THERMAL PREFERENCES OF HONEY BEE DRONES
Review round: 1
Reviewer: 1

Output:
Basic reporting: I have line notes and a section-by-section commentary that more clearly delineates my opinions here, but broadly speaking, the authors clearly present the background literature, methods, and data using professional English, although some word use and grammatical suggestions are made. The literature review is thorough with context provided, although I have some recommendations about streamlining and improving the logic of the hypothesis. The paper is self-contained and represents a complete experimental unit with a purpose and impact.  The figures and tables are basic, but perfectly adequate for the experiment. There appears to be some data missing pertaining to mucous gland development that I would like to see.
Experimental design: This paper meets the aims and scope of the journal. The research question is well-defined (with the above caveats) and fills a knowledge gap. The design of the experiment is adequate to the question, although arguments about statistical power can be made. I don't strictly think this is a barrier to publication, but is something of which to be aware. Methods are broadly replicable, although I make some recommendations about how to improve this, given that a bespoke apparatus was constructed to perform the described tests.
Validity of the findings: The conclusions are well-stated and largely clear. As mentioned above, some of the data seems to be missing or I'm misunderstanding. Where the experiment does have noticeable pitfalls, these are appropriately called out and analyzed.
Additional comments: This is a very interesting paper, presented in a straightforward and thoughtful manner. I have some items for improvement, but overall I would recommend that this paper be considered for publication after some revisions are performed.

Introduction:
The authors present a fairly detailed literature review that decently summarizes the state of research with regard to drone temperature sensitivity and nest homeostasis more generally. The case for understanding an individual-level variation in age-based preference for temperature is intriguing and has interesting extensions for understanding organismal impacts on sexual development, namely spermiogenesis and spermatozoa transfer to the seminal vesicles. The logic presented in the introduction, however, needs some work to be convincing. There are additionally some elements that appear repetitive or redundant (or I am not understanding the distinctions made). It is unfortunately unclear from the narrative what the exact niche the paper is trying to fill. I therefore recommend some refocusing of the introduction with specific line items noted below.

45: “While drones considerably differ…” This appears to be an incomplete sentence.

63: “A drone is an exceptional example…” I’m not clear on what this sentence is trying to say. It seems redundant with the subsequent review.

64: The “spermatogenesis process…”

66: “Process of gonadal…” It might be wise to define sexual maturity here. If you mean capability to ejaculate, that is a different time point than spermatozoa migration to the seminal vesicles.

78: “In the nest, due to spatial…” I’m not clear on the intended meaning of this sentence. Do you mean that some drones are unable to find their “preferred” temperature? If so, how is this established?

81: “In line with previous…” It would be better to just tell us why nurse bees and young drones should be associated. I assume feeding, but

84: “Previous research…” It seems that this review is somewhat redundant with 58-62 and contradictory with the statement in 53-54. I get that the common scientific trope is, “X is understudied,” but try not to prove yourself wrong in the literature review. I think that you mean that individual variance in age-based temperature variance is an unknown, but you need to emphasize this more.

86: “However, it has been recently reported…” Where please? Also, the three sentences here to line 90 present a logic chain that I’m sympathetic to, but not following. Here’s my interpretation: 1) Age distribution of drones over brood and non-brood areas is different. 2) About 36% of young drones hang out over brood. 3) Therefore, there is individual preference? I don’t think that 3 arises from 1 and 2. Given that this is the rationale of the paper, I need a more convincing logical thread here.

95: “…whose sperms…” I would use spermatozoa instead.

99: “…according to their age and degree of their maturity to mating.”  Here it sounds like you’re suggesting a decoupling of age and sexual maturity. This is very interesting and something that might be worth further exploration, especially if the introduction is refocused as suggested above.

Materials & Methods:
The materials and methods appear adequate for the experimental design, the statistics are reasonable, and any potential shortcomings that I can see are already noted in the text for caveats. The only thing I might wish for is a photo of the testing apparatus, which, while well-described, remains somewhat difficult to visualize. I’m also not capable of evaluating the measurement tolerance (precision particularly) of the camera, so we must trust the authors that the technology is “proven” as it were. I’m not sure there’s a corrective action necessary, but it’s a thought. I have a few notes below.

155: “The emissivity value was” settled…

158: “…was also corrected for during evaluation setting…” This sentence could use some revision for English language clarity.

158-161: The sentence about transferring files to a computer is probably not necessary.

161-162: This sentence implies that the statistics were performed manually in Excel. As this is unlikely to be the case, I assume this statement is redundant with the subsequent statistical methods provided.

162: “…drones went back…” presumably the drones were returned to their cages and foster colonies and did not go there of their own accord.

Results:
Broadly, the results are clearly presented and easy to interpret. I have some concerns about the final, Chi2 square analysis in that it seems to lack the clarity of presentation necessary to properly interpret. This particular analysis further is not represented in the provided data and appears to be incomplete; the reporting seems to only encompass one of the three tested groups. Finally, an n of 5 is likely far too low for a chi square test and an alternative should likely be performed (e.g. Fisher’s exact test).  I would therefore recommend some increased detail and alternative analyses in these areas.

182: I would call the procedure, “Dunn’s test.”

196-200: I rebel in this in my own writing, but it would be helpful, if somewhat redundant, for summary statistics to be provided in the descriptors of the drone group temperature preferences. The sample number is fine, but I would rather have means+standard errors or medians+ IQRs. The sample numbers would be better placed in the statistical table, or as annotations to the accompanying figure.

201-203: since statistically this is a further description of the analyses above, this statement should be within the prior paragraph in my view.

204-209: this appears to be the most novel part of the manuscript, and it unfortunately gets the least page time. I have some concerns that the replication is low (5 per group out of ~1100 drones?). Also, there’s no data table associated with this, or I’m failing to understand what Table 2 is trying to say. My thinking is that the result is suggesting that within age groups, those drones that are at the warmer or colder end show differential qualitative maturity scores based on mucous glands.  If so, there should be a score associated with each drone, which unfortunately is not presented in the provided data. I’m not certain where the Chi2 test is pulling from here. My recommendation is to spend more time on this interesting result and flesh out the analysis and presentation further.

Discussion:
The discussion clearly presents the results and contextualizes the results with the introduction. I have a few notes on focusing, but any other notes are largely matters of taste and style.

213: “Young drones of…” The data show a non-linear trend, but this opening statement suggests a linear trend, consequently misidentifying the oldest age group as being, “younger.”  This should be revised.

229: What discrepancies in results? I’m not clear on the issue.

238: what is “inter alia?”

240: I still prefer “spermatozoa” over sperms. And the spermatozoa are present in the testes at the age groups mentioned, and will migrate to the seminal vesicles, as the authors note in the subsequent sentence.

243-246: This is the most interesting finding of the paper. Highlight this and expand if plausible. Support this statement with improved statistical analyses and reporting.

270-272: I’m not sure what this sentence is trying to say.

References:
The titling of the references need to be made consistent. Some are capitalized (e.g.: 314-316) and some are not (e.g.: 317-319).

Table 1: Please include the test performed in the caption. Also include the test statistic and degrees of freedom in the table for full clarity. I know these tables are somewhat procedural, but it does help in reader interpretation. You might also include significance groups directly in the table.
Table 2: This table should have detailed statistics added in lieu of a Chi2 figure.

Figure 3: Correct “Mediana” to “Median.”


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 EFFECT OF AGE AND SEXUAL MATURATION ON THERMAL PREFERENCES OF HONEY BEE DRONES
Review round: 1
Reviewer: 2

Output:
Basic reporting: I found the manuscript interesting but occasionally confusing and needs some revisions, plus a thorough review of the English language and form.
Title: The title is representative of only part of the work. The manuscript studies the preference in temperature of drones but also the grade of maturation of the sexual glands at different temperatures. I suggest improving the title to cover both aspects.
Abstract: please provide the name of the honey bee sub-species and make the aim of this manuscript more explicit.
Keywords: add Apis mellifera carnica
Introduction: Add the context and a brief description of Apis mellifera carnica to better understand the work to non-specialists.
line 30: add other references if available (e.g., https://doi.org/10.1093/jee/toab023)
lines 45-46: “While …behaviourally” something is clearly missing here.
line 46: explain the drone life cycle (the development of drones from the larvae stage is longer than queen and workers).
line 55: add a comma after i.e.
line 63: specifies that drones are haploid.
lines 65 and 69: please substitute the “emergence” with eclose, here and elsewhere.
lines 90-99: Are these the aims of work? If yes, improve the text to make it more explicit and clearer.
Experimental design: Materials and methods: Materials and methods look quite confusing to me, possibly hampering the reproducibility of the experiment. I would suggest including a drawing of the experimental setup and possibly of the experimental design.
Drones:
line104: where and when did you collect the colonies?
line105: how many broods did you collect for the colony?
Line 107: how many drones did you collect?
Line 108: is there one single cage per colony?
Lines108-111: Why did you put the drones in a different colony?
The temperature platform
Please improve the paragraph with more details and add the photo / drawing of the temperature platform.
Line 119: Which material was used to insulate?
Statistical analysis
This paragraph can be improved with more details (for example, the information at lines 187-188 should be included here).
Validity of the findings: Results
This paragraph should only include the result of the experiment without hastening the discussion.
Lines 187-188: please include this part in M&M (statistical analysis).
Lines 190-192: This belongs to ‘discussion’.
Lines 193-195: This belongs to M&M (statistical analysis).
Lines196-200: This section puzzles me. It looks like the results at Table 1 and Fig 3 (plot with median and CI) refer to the same results, but the information provided by the numbers would suggest otherwise (in Table 1 D5 vs D25 is not significant, whereas D5 vs 25 in Fig 3 is significantly different). Please explain or modify if necessary.
Discussion
I can not comment the discussion because the results are not adequately clear.

Please check all the references of the figures in the main text.
Figures:
•	Figures have been uploaded as single figures, but I believe they were meant to be arranged as combined figures.
•	Photos need a size reference.
•	You could also include some arrows pointing at significant details (the distal part of the reproductive tract).
Additional comments: No additional comments


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

Input:
Title: THE EFFECT OF AGE AND SEXUAL MATURATION ON THERMAL PREFERENCES OF HONEY BEE DRONES
Review round: 2
Reviewer: 1

Output:
Basic reporting: I suggest providing the actual temperature values and range when you mention low and high temperatures in the results and discussion sections, and table 2.

Figures:
•	Figure 1 You could also include some arrows pointing at the main parts of the temperature platform and, if possible, add a new photo with a view from the top.
•	Figure 4 It still needs the bar scale reference.
Experimental design: No further comments
Validity of the findings: No further comments
Additional comments: No further comments


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

Input:
Title: A FRAMEWORK FOR NEAR-REAL TIME MONITORING OF DIVERSITY PATTERNS BASED ON INDIRECT REMOTE SENSING, WITH AN APPLICATION IN THE BRAZILIAN ATLANTIC RAINFOREST
Review round: 1
Reviewer: 1

Output:
Basic reporting: I am going to copy-paste my entire review into 'Additional Comments' below, but here are a few excerpted comments related to this section:

"I also thought the authors could have done more to bring out what’s interesting about the study specifically in contrast to other studies. Predicting diversity from static climate variables is often good and useful, but wouldn’t really have been a new idea. Predicting diversity from remote sensing products that are being measured continuously does seem more novel, although I’m not too familiar with the literature here. So essentially, I wonder whether this approach could be better put into context within the conceptual space of possible approaches to modeling diversity, highlighting its advantages and disadvantages. For example, it could (as the authors say) enable near-real time monitoring of potential change in diversity, which seems tremendously useful—but it might be harder to use for forecasting into the future, given that projected changes in climate or canopy cover would have to be transformed into the specific variables (e.g. NDVI) the model requires.

The large-scale organization of the manuscript seems sound—for the most part, it was easy to follow. There are a few sections (particularly in the Methods and Results) with which I did struggle, and I hope my comments can help the authors clarify them."
Experimental design: No comments.
Validity of the findings: I am going to copy-paste my entire review into 'Additional Comments' below, but here are a few excerpted comments related to this section:

"I have many rather small comments (see below) but few large comments about the concept or framing of the manuscript. One issue that I thought deserved more attention is touched on at the end of the Discussion (454-484). The core of the issue is: Do we have good reason to think the factors that link climate/NDVI and diversity across space up to the present are the same as the ones that will link climate/NDVI and diversity through time in the future? The authors bring up some related concerns, including the importance of dispersal or establishment lags for explaining why we might not see predicted species gains in empirical data (439-448). But I was surprised not to see the matter brought up earlier, given that I think it’s at the crux of whether the model will be useful in practice. The authors wisely suggest that any ecological conclusions/mechanisms from the model should be tested on the ground (466-484), but I still worry that predictions (especially e.g. of PD vs richness residuals) could easily be overinterpreted, which might be worth forestalling."
Additional comments: Thank you for the chance to learn from and share my thoughts on this manuscript submitted to PeerJ. The manuscript builds on a prior study (Paz et al. 2021 Journal of Biogeography) which builds models to predict diversity (species richness and phylogenetic diversity) of nine clades in the Atlantic Forest of Brazil from remotely sensed NDVI and climatic variables. Here, the authors project the model forward to predict biodiversity change through time. The idea seems really interesting—as the authors point out, it could allow near-real time monitoring of potential changes in biodiversity that might guide on-the-ground research. The authors then ‘ground-truth’ the model on datasets collected by other researchers and show that it has some modest success in predicting actual changes in diversity through time. While the results of this ‘ground-truthing’ are not staggering, the procedure is quite a severe test of the approach, for which the authors should be commended.

I have many rather small comments (see below) but few large comments about the concept or framing of the manuscript. One issue that I thought deserved more attention is touched on at the end of the Discussion (454-484). The core of the issue is: Do we have good reason to think the factors that link climate/NDVI and diversity across space up to the present are the same as the ones that will link climate/NDVI and diversity through time in the future? The authors bring up some related concerns, including the importance of dispersal or establishment lags for explaining why we might not see predicted species gains in empirical data (439-448). But I was surprised not to see the matter brought up earlier, given that I think it’s at the crux of whether the model will be useful in practice. The authors wisely suggest that any ecological conclusions/mechanisms from the model should be tested on the ground (466-484), but I still worry that predictions (especially e.g. of PD vs richness residuals) could easily be overinterpreted, which might be worth forestalling.

I also thought the authors could have done more to bring out what’s interesting about the study specifically in contrast to other studies. Predicting diversity from static climate variables is often good and useful, but wouldn’t really have been a new idea. Predicting diversity from remote sensing products that are being measured continuously does seem more novel, although I’m not too familiar with the literature here. So essentially, I wonder whether this approach could be better put into context within the conceptual space of possible approaches to modeling diversity, highlighting its advantages and disadvantages. For example, it could (as the authors say) enable near-real time monitoring of potential change in diversity, which seems tremendously useful—but it might be harder to use for forecasting into the future, given that projected changes in climate or canopy cover would have to be transformed into the specific variables (e.g. NDVI) the model requires.

The large-scale organization of the manuscript seems sound—for the most part, it was easy to follow. There are a few sections (particularly in the Methods and Results) with which I did struggle, and I hope my comments can help the authors clarify them.

Shan Kothari
shan.kothari@umontreal.ca

Major comments:
76-83: I think this line of reasoning could appear suspect to many readers in light of the case presented Mayfield & Levine (2010 Ecol Lett). In particular, Mayfield & Levine show that competition can also lead to clustering, while (as Cavender-Bares et al. 2009 Ecol Lett point out) environmental filtering can lead to phylogenetic overdispersion if trait evolution is convergent. Any given pattern can thus have multiple plausible explanations in the absence of other context that rules some out. I would also be concerned that the spatial resolution of the data (~10 km) in this study would make it hard to pick up on the signatures of local species interactions (e.g. see Cavender-Bares et al. 2018 American Journal of Botany). This isn’t a problem for the authors’ decision to look at phylogenetic diversity, since we have more reason to care about phylogenetic diversity than just as a guide to local community assembly processes; but it might be more convincing to put some of those other reasons in the foreground instead.
208-241: I realize it’s often hard to describe model calibration and validation procedures in a clear way, but I struggle to understand this section. My understanding is that the static diversity maps were combined with the remote sensing/climate products from the 2002-2014 period, but I’m not sure how the temporal aspect within the 2002-2014 period is handled (or if the predictors were just combined via summary statistics). The paragraph makes continual references to ‘projection through time,’ but I can’t tell whether that refers to something within the 2002-2014 period or to the projections to the 2015-2019 period that are described in the next paragraph. Then follows cross-validation across spatial partitions, which makes sense, but it’s unclear whether the only output from these models used in to build the ‘full’ models for each algorithm is some set of optimal settings, or something else besides. The terms can also be a bit confusing, e.g. line 235 refers to “final tuned models” (presumably for each fold of CV) while line 236 refers to “a full model” (across all data after CV). I think a bit of rewriting could make this section much easier to follow.
225-233: I like the idea behind this spatial partition procedure, but it would be interesting to know what it looks like. How were the regions determined?
288-290: I think this whole ground-truthing approach is commendable, and I really appreciate the thought that went into it. That said—while this comparison to a coin flip (essentially) makes sense, I’m not sure it ends up providing the strongest test of the models’ power. While reading this section, I thought about what my uninformed baseline guess would be about biodiversity change would be—and I decided I would guess that biodiversity is declining in each pixel (here and in most of the world, at large enough spatial scales). Based on the results (367-391), my baseline ‘model’ that every pixel is declining in species richness would outperform the epiphyte model and come quite close to the performance of the amphibian model. This isn’t meant as a criticism, and certainly there must be value to having a more spatially targeted prediction, but I wonder if there’s a way to describe the results here that makes these advantages clearer? I don’t have a specific suggestion, and I don’t mean for this comment to obligate any response, but perhaps it gives something to think about.
331-342: It could be interesting (if not too burdensome) to create similar maps of the change in important predictor variables from 2015-2019 so that we can see by eye how they relate to the predicted outcomes for diversity.
Fig. 2: Based on the caption, does this mean that some pixel(s) have predicted local loss of ~36 Miconieae species between 2015 and 2019? That number seems very large, so I just want to check that I’m understanding correctly.

Minor comments:
Here, I use the → symbol to represent a textual change that may be easier to read. Of course, each of these comments is just a suggestion!

26: “periodical” → “periodic” (periodical most often means a newspaper/magazine)
39: “difficulty to establish” → “difficulty of establishing”
48: “what can be now done” → “what can now be done”
69: “hereon” → “henceforth”
69-72: This sentence is a little ambiguous. The intended meaning, I’m sure, is that species richness and phylogenetic diversity are both correlated with climate and habitat configuration. But I first read it to mean that species richness is correlated with climate, habitat configuration, and phylogenetic diversity. One solution would be to change “also” (70) to “so have.”
101-102: Presumably the studies listed in this parenthetical are now the published studies listed at the end of the sentence? (If so, congratulations!)
103-104: I might recommend taking this clause that begins “but not…” and turning it into a separate sentence so that this sentence coheres a bit better.
108: “machine-learning reproducible framework” → “reproducible machine learning framework”
111-115: Since this list is spelled out in the Methods, it may be fine to cut it here.
112: “Mealastomataceae” → “Melastomataceae”
127-128: “expect that those groups… to be” → “expect that those groups… will be” or “expect those groups… to be”
164-165: It might help to briefly explain what this flexibility constitutes, e.g. is it in general true that alpha hulls around a given set of points will be no larger than the corresponding convex hull? Can they be disjoint?
165: The referent of “they” here is a little unclear. The specific alpha hulls used to create the maps in this (and the prior) study?
166: It’s hard for me to put this note that the datasets “lacked information about the date of observation of each sample” into context. What follows from this fact?
175: What metric of phylogenetic diversity? Faith’s PD?
183: It seems legitimate for the study to claim that its framework would allow near-real time modeling of biodiversity, but I’m not sure it makes sense to describe this set of models demonstrating the framework as “near real-time models.” To me, that term implies that the estimates are being made about the present or very recent past.
184: “the conditions experience” → “the conditions experienced”
188-189: I would write “The two MODIS data products” (or some variant) rather than “Data from MODIS” so that the note on spatial resolution is easier to follow. I might also suggest just writing CHIRPS rather than “the latter.”
195: “NDIV” → “NDVI”
215: “one” → “an” (or vice versa in the previous line)
220: Pluralize “neural network”?
242-245: This sentence was a bit hard to follow and might be better split up into two.
245: “each yearly” → “each year’s” or “each set of yearly”
274: It took me a while to understand exactly what was meant by “had some coverage of the forest.” Perhaps something like “had relatively broad coverage of the region”?
299: Here and in the abstract, the manuscript says that the variables describe change in temperature and precipitation, which seems to leave out NDVI. Perhaps not a big issue, but I would imagine that change in canopy cover as shown by NDVI might explain a major part of the models’ predictive power.
303-304: This clause “few exceptions happened when individual fit was poor ensemble fit was worse” is very hard to understand.
304-306: It might be worth showing some formal statistics if appropriate.
306-307: “The models with good fit for both diversity measures (R2 > 0.5) were observed” → “Models had good fit for both diversity measures”
349: I’m not sure what it means to say “where the Atlantic Dry forests are found up to 2018.”
352: Extra period after “richness.”
360: “as” → “a”?
361: “somehow consistently” → “somewhat consistently”?
383: “has” → “have”
389: Missing word before “an”?
411: “result” → “results”; I’m not really sure what “overestimation of diversity patterns” means.
436: “direction of magnitude of change” → “direction or magnitude of change” or “direction of change”
441: “more difficult documented” → “more difficult to document”
463: Perhaps “suggested by” rather than “enabled by”?
467: “and tested” → “and test them”; “While patterns…, yet the predicted residuals” →  “Patterns…, yet the predicted residuals” or “While patterns…, the predicted residuals”


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 FRAMEWORK FOR NEAR-REAL TIME MONITORING OF DIVERSITY PATTERNS BASED ON INDIRECT REMOTE SENSING, WITH AN APPLICATION IN THE BRAZILIAN ATLANTIC RAINFOREST
Review round: 1
Reviewer: 2

Output:
Basic reporting: Very good.
Experimental design: Very good.
Validity of the findings: Very good.
Additional comments: Review of MS: A framework for near-real time monitoring of diversity patterns based on indirect remote sensing, with an application in the Brazilian Atlantic rainforest (#70910)
1.	The introduction is good and but it should draw parallels with relevant studies from the peer-reviewed literature covering novel concept of essential biodiversity variables and multiple components of biodiversity. Authors may cite the following highly applicable works.

Skidmore, A. K., Coops, N. C., Neinavaz, E., Ali, A., Schaepman, M. E., Paganini, M., ... & Wingate, V. 2021. Priority list of biodiversity metrics to observe from space. Nature ecology & evolution, 5(7), 896-906.

Reddy, C.S. 2021. Remote Sensing of Biodiversity: What to measure and monitor from Space to Species? Biodiversity and Conservation, 30, 2617–2631.

2.	The methods section should spell out clearly the multi-source species data, linkage of remote sensing based environmental datasets and validation of results. Towards this, I suggest authors to prepare a flow chart showing methodological framework.