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 MICROPHENOTRON: A NOVEL METHOD FOR SCREENING PLANT GROWTH-PROMOTING RHIZOBACTERIA
Review round: 3
Reviewer: 1

Output:
Basic reporting: The text requires a number of revisions for format and style. I gave up after Introduction because Abstract and Introduction are jumbled. Abstract should follow the convention of background, unmet need, methods, results, discussion/conclusion. Introduction should follow this outline.
1.	Field of study:
a.	PGPR play a critical role
b.	Variations influence field performance
c.	We need to screen lots of them to find ones that work
2.	Unmet need – reliable high throughput, low cost PGPR assay
a.	PGPR can be characterized on the basis of beneficial biochemical attributes but these in vitro assays do not consistently predict field performance
b.	Pot trials are expensive and fraught with bias
c.	Large scale robotic phenotyping systems work great but they are expensive
3.	Microphenotron system shows promise
a.	Works with metabolites
b.	Hasn’t been applied to isolates
c.	Hasn’t been validated with pot trials
4.	In this study we
a.	Isolated rhizobacteria
b.	Screened them with all of the above
c.	Observed that ___
Experimental design: I think it is great that the authors included pot trials in this manuscript; however, the number of replicate pots (three) seems low and I do not understand Figure 7. Methods states pots were inoculated with bacteria. I presume there was some sort of negative control too but those categories are not shown in Figure 7 and even then the authors should show the relationship between the response in the microphenotron versus the response in potted plant trials.  I suggest a biplot, with the x-axis a metric derived from microphenotron data (like root growth) and the y-axis a metric (like fresh weight) derived from the potted plant trials. This graph would show if the microphenotron predicted plant growth response.
Validity of the findings: See above
Additional comments: Specific comments on first 65 lines.
Replace bars in Figures 4 and 5 with box/whisker plots like Figure 7.  Box is almost always better than bar.
Line 25. Revise to “that uses 96-well”
Line 26. Delete “of Arabidopsis” (I bet you could use other plants).
Line 29. Replace “or” with “and”
Line 30. Format is Genus species. Revise to “Acacia arabica”
Line 30. Replace “The final taxonomic status of bacterial strains was confirmed through” with “The phylogeny of these rhizobacteria was determined by...”

Line 34. Here and throughout, write actively and define strains. Replace “and the highest activity was exhibited by Bacillus endophyticus S-6” with “A strain (S-6) of Bacillus endophyticus exhibited the highest activity”

Line 35. Describe all the methods used in one section (16S sequencing, PGPR traits (ACC deaminase...) UPLC, microphenotron, and pot trials) and then summarize results observed.

Line 38. As above, the reader doesn’t know these strains and write actively. Revise to “Two strains (S-7 and S-11) of Psychrobacter alimentarius procuded the most IAA, ICA and ILA.”

Line 54. Revise to “(PGPR) play a critical role in soil fertility.” Delete “and plant growth promotion”

Line 55. Write actively. Revise to “An incomplete understanding of the mechanisms of plant growth promotion hinders the application....”

Line 57. Delete “the” here and wherever you can.

Line 60. Delete “bacterial metabolites” (ACC demaminase is an enzyme not a metabolite) and replace “has” with “have”

Line 61. Replcae with “does not consistently predict”

Line 62. Greenhouse trials are not an in vitro technique, so you cannot use them as an ex

Line 65. Reorder these sentences to “ It can...in A. thaliana. In the present study...” and move them to the end of Introduction.

Line 69. This paragraph appears to contradict the previous one. You just said in vitro assays do not always produce a desirable outcome.

Line 345. To make it clear who developed the method, revise to “Forde et al. (2013) developed ...


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 MICROPHENOTRON: A NOVEL METHOD FOR SCREENING PLANT GROWTH-PROMOTING RHIZOBACTERIA
Review round: 4
Reviewer: 1

Output:
Basic reporting: The manuscript has been improved and remains very interesting to me; however, I have a few significant suggestions. Introduction requires revision, as it doesn’t follow a coherent outline. I suggest the order. To illustrate this structure of revision I have attached a pdf.
1.	(Background) PGPR and their applications
2.	(Justification) Current screening methods are inadequate
3.	Microphenotron
Experimental design: No comment
Validity of the findings: I think I failed to communicate what I mean by “biplot” for Figure 9. I meant that the manuscript needs to show a plot that compares growth response as measure by Microphenotron versus pot trials. That plot would have rosette weight, measured in pot trials, on the x-axis and root length, measured with in Microphenotron, on the y-axis. Each point would correspond to the strains and control and show the variation, in x and y directions, for each variable. That plot would allow readers to determine if the microphenotron and pot trials correlate with each other. To facilitate discussion, I suggest that symbols indicate strain or traits associated with sets of strains.
Additional comments: Line 262. Why cap “Indolic?” Also revise to “….supernatants: indol-..”
Line 280. Do not just tell the reader a figure exists. State the result and direct the reader to the data. Delete “Figure 5 …bioassay.”
Line 282. Again, state the result (All tested strains increased….(Fig. 6).”
Line 288. As above, state result, don’t announce that a figure exists.


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: LIPOPOLYSACCHARIDE-ACTIVATED MACROPHAGES REGULATE THE OSTEOGENIC DIFFERENTIATION OF BONE MARROW MESENCHYMAL STEM CELLS THROUGH EXOSOMES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript entitled “Lipopolysaccharide-activated macrophages regulate osteogenic differentiation of bone marrow mesenchymal stem cells through exosomes” by Xiao Song et al. investigated that how inflammatory macrophage-derived exosomes affected osteogenic differentiation. Exosomes was extracted from lipopolysaccharide (LPS) -treated macrophages and characterized using transmission electron microscopy, particle size analysis, and Western blotting. Exosome uptake was verified by bone marrow mesenchymal stem cells (BMSCs) using fluorescence microscopy. They have found that LPS-treated macrophage-derived exosomes increased the mRNA and protein levels of the inflammatory factors, such as interleukin-6 and tumour necrosis factor-alpha in BMSCs. Inflammatory exosomes also suppressed osteogenic genes, including alkaline phosphatase, type I collagen, and Runt-related transcription factor 2 as well as the alkaline phosphatase activity. They concluded that inhibition of exosome secretion is a potential therapy to suppress bone tissue destruction during inflammation.
Experimental design: 1.	Key experiments should have three biological replicates (n=3). It was not described in the manuscript.
2.	In Methods, statistical analysis should be elaborated. It is too simply just stating “One-way ANOVA was used to analyze differences among more than 2 groups”. One-way ANOVA is used to test whether it is statistically different among all compared groups. Multiple comparison is followed to test which two groups are different.
Validity of the findings: 1.	In Figure 2C-F, authors did not describe what comparisons the asterisks annotated.  While authors stated the level of TNF-α protein remained stable, it showed significant (**) in Figure 2C.
2.	Figure 2D showed that the protein level of IL-6 was significantly increased by inflammatory exosome. However, authors stated that “there was no significant difference in IL-6 protein levels between the two groups”.
3.	Authors measured mRNA and protein expression of osteogenic markers using RT-PCR and Western blot. However, there are no phenotypic experiments to support the effect of inflammatory exosomes on osteogenic differentiation of BMSCs. They could perform direct staining of matrix components.
4.	Why did authors use mouse mononuclear RAW264.7 macrophage as the model? The most relevant model is human macrophage isolated from healthy subjects and periodontitis patients.
5.	The key experiments should be reproduced and validated in a second cell line.
Additional comments: The manuscript will benefit from English editing.


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: LIPOPOLYSACCHARIDE-ACTIVATED MACROPHAGES REGULATE THE OSTEOGENIC DIFFERENTIATION OF BONE MARROW MESENCHYMAL STEM CELLS THROUGH EXOSOMES
Review round: 1
Reviewer: 2

Output:
Basic reporting: .
Experimental design: .
Validity of the findings: .
Additional comments: Review of article: "Lipopolysaccharide-activated macrophages regulate osteogenic differentiation of bone marrow mesenchymal stem cells through exosomes”
In this manuscript by Song et al, the authors examine the effects of exosomes secreted from inflammatory macrophages on the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSC). The authors showed that BMSC uptake exosomes and thereby leading to increased expression of proinflammatory cytokines such as IL-6 and TNF-alpha. Moreover, authors also found that exosomes are responsible for inhibiting the osteogenic differentiation of BMSC as confirmed by downregulation of expression of several genes (alkaline phosphatase, type 1 collagen and RUNX2) involved in osteogenic differentiation of BMSC.
The manuscript could be strengthened by addressing the below listed points.
The main concerns regarding the manuscript are the experimental design, the lack of some important controls and the methods are not properly described in detail which creates great difficulty for the readers to understand. Several important references are missing throughout the manuscript and there are several places in manuscript where the sentences are unclear or incomplete. There are numerous minor errors in English expression and punctuation, and general typographic errors, throughout. I suggest the authors should check the entire manuscript carefully and make corrections.
Method section was written very vaguely and not well explained and hence need to improve to clarify for the reader.
Line 119 pretreated time point?
Line 121-126: Authors need to clarify for the readers that what method was used to analyze expression of IL-6 and TNF-alpha at different time points and moreover cell lysate or cell supernatant was used to analyze expression of genes? What do authors mean by remaining cells is it the cells left after the supernatant collection? And they were further incubated for another 24h or 48h? what is the stimulation time for LPS is unclear.
Line 138: Authors need to specify what was the method used to quantify mRNA or cite the reference of article for the method being used.
Line 141: Authors need to clearly specify the time of LPS stimulation since it is very confusing for the readers as it says 24h or 48h stimulation or did the author mean time of supernatant harvest after 6h LPS stimulation since according to figure legends it is not consistent.
Line 147: Specify the name of cell. What was the composition of exosome clearance medium? Or cite reference article.
Line 169: Authors need to specify how much amount of lysate was used to quantify protein expression by western blot? Also, need to mention that Calnexin was used as a negative marker for exosomes.
Line173: name of the fluorescent probe is missing
Line178: what time point Hoechst stain was added?
Line 180: Authors need to mention the name of the microscope, magnification lens used and describe in detail the method used to analyze the images
Line 188-190: Need to describe the method briefly to clarify readers and What reagent was used for transfection?
Line 200: Authors need to specify the secondary antibodies used.
Line 209: Authors need to specify what groups or refer to method section where already written.
Line 221-222: Authors need to readdress the results (Fig 1A-B) as IL-6 levels were still elevated at both 12h and 24h which is very much comparable to 3h. Any explanations since both cytokines show completely different pattern of gene expression at different time points. TNF-alpha has highest expression levels at 3h when compared to IL-6 which is highly expressed at 6h. Authors need to give strong evidence why they choose 6h timepoint for LPS stimulation in most experiments.
Line 226-227: How can the authors reach this conclusion from Fig 1C-D if the experiment was not performed beyond 48h timepoint. To demonstrate this author, need to perform ELISA at 72h timepoint and confirm whether the inflammatory state truly lasted only up to 48h.
Authors should also harvest cell culture supernatant samples at similar timepoints 1h,3h,6h,12h and 24h for performing ELISA. Any explanations why chosen different timepoints for mRNA and ELISA analysis (Fig1).
In Fig1H authors need to explain the control in western blot in figure legend.
Authors need to discuss this result why CD81 shows no expression on the exosomes when compared to control and CD9 showed lower expression levels when compared to control?
Figure legends are written very ambiguously and not well explained and hence need to improve to clarify for the reader. Correct ‘ns means non-significant’
Fig1D replace H by h in figure labelling
In Fig2C-D keep the figure labelling consistent in all graphs like in Fig2E-F. Similarly change in Fig 3.
I strongly recommend seeing the effect of exosomes when BMSC and macrophages are co-cultured in vitro since it will strengthen the significance and conclusions.
Additionally, authors should perform the experiment using TLR signaling blockers/inhibitors and observe the effects of exosomes on BMSC.
Authors need to discuss in detail the limitations of the study and what do they interpret from their 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: LIPOPOLYSACCHARIDE-ACTIVATED MACROPHAGES REGULATE THE OSTEOGENIC DIFFERENTIATION OF BONE MARROW MESENCHYMAL STEM CELLS THROUGH EXOSOMES
Review round: 1
Reviewer: 3

Output:
Basic reporting: This manuscript aims to understand how inflammatory macrophage-derived exosomes regulate osteogenic differentiation of bone marrow mesenchymal stem cells. To achieve this, the authors utilized P. gingivalis LPS to stimulate mouse macrophages, then they used ultrafast centrifugation to extract macrophage-derived exosomes. After characterizing the exosomes, the authors further looked at the effects of exosomes on the BMSC inflammatory response and osteogenic differentiation by qPCR and Western blot, and they found that exosomes upregulated the expression levels of two inflammatory factors and decreased the expression of several osteogenic markers in BMSCs. At last, the authors demonstrated that exosome inhibitor GW4869 could attenuate the effect. While the results generally support the conclusion, the manuscript lacks more solid data, and the data analysis in this manuscript is flawed.
Experimental design: 1 A major negative aspect of the work is that it does not have supportive data looking at the fundamental biological functions of BMSCs upon the uptake of inflammatory exosomes. Though the authors thoroughly checked the expression of osteogenically marker genes as well as ALP activity, and found statistical differences, this does not necessary mean that there would be biological differences. Especially by comparing the data from cells treated with CM to those from cells treated with CM+GW4869, the differences of protein expression were minor. It would strengthen this study a lot if the authors could also look at the biological functions of BMSCs, such as their migration and mineralization, et al.
2 Please indicate in line 149 what concentration of GW4869 was used.
Validity of the findings: 1 The most important issue is the statistical analysis:
a.	If one-way ANOVA is used, the authors should clearly point out the difference between each pair of samples in the figures. For example, figure 2,3 and 5 from Han et al.’s manuscript (Stem Cell Res Ther, 2017 Sep 29;8(1):210. doi: 10.1186/s13287-017-0663-6) showed how the significant difference should be labeled when one-way ANOVA is used.  Please also indicate in the method section which post hoc test was used for one-way ANOVA.
b.	Please carefully interpret the data, as several statements in the results section are not true. For example, the statement in line 222-223 is not true. Figure 1 panels A and B clearly show that even at 12 and 24h, the TNF-alpha and IL-6 levels were significantly higher than the baseline, which indicate that the inflammatory state of the cells did not return to normal. The statement in line 252-253 is not true. Figure 2D shows that IL-6 protein level was increased in the inflammatory exosome group. The statement in line 255-256 is not true. Figure 2C shows that TNF-α protein level was decreased in the CM+GW4869 group.
2 Please indicate what “control” is in figure 1H. Why the extracted exosomes showed no CD81 expression?
3 I have a hard time understanding figure 1G. It would be help if the authors could provide some elaborations in the results section.
4 In figure 2A, it would be better if the authors could provide pictures of the staining of BMSCs before they were treated with exosomes as negative control.
5 In the abstract, the conclusion the authors drew in line 53 is not supported by the evidence the authors provided. Bone tissue destruction is mainly caused by osteoclast-mediated bone resorption. It would be more proper to say “a promising method for bone tissue regeneration in inflammatory states”.
Additional comments: 1 The discussion section should provide in depth discussion of the results. However, the current discussion was written in a way that is more like an introduction. Many literatures were cited on the purpose to provide broad and general information. In my opinion, more relevant literatures that show similar or contradictory results to the current study should be cited and discussed. In additional, the discussion should be concise. There is no need to repeat the content that is already involved in the results section.
2 I don’t think the statement in line 268 is true. It is the activity of osteoclasts that matters.
3 Please have the manuscript thoroughly checked by an editor. As currently written, the manuscript contains numerous grammar mistakes and awkwardly structured sentences.


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: LIPOPOLYSACCHARIDE-ACTIVATED MACROPHAGES REGULATE THE OSTEOGENIC DIFFERENTIATION OF BONE MARROW MESENCHYMAL STEM CELLS THROUGH EXOSOMES
Review round: 1
Reviewer: 4

Output:
Basic reporting: The manuscript meets PeerJ's  publication standards and the content is relevant to the the topics published by PeerJ.
The authors provided sufficient background to highlight the importance of this work and help the audience understand the key context of this study
Experimental design: The authors did a great job at documenting all the methods and materials used for this study. Experimental designs were clearly laid out. The key research question (exploring the role of macrophage-derived exosome on osteogenic differentiation of BMSC) is clearly defined and will fill the knowledge gap with the findings from this study.

I only have a few minor comments on the appropriate control:
1. for Figure 2A: it is difficult to tell whether the PHK67-labeled exosomes are actually concentrated around the nuclei of BMSCs or just randomly distributed in the cytoplasm; providing additional background staining as control would help clarify this (e.g. F-actin staining to show the cell body of BMSCs, ER staining to show the area adjacent to the nuclei); a negative control with just the PKH67 antibody and the plain medium / solvent used to suspend the exosomes should also be provided

2. for Figure 2B-2F: a baseline control of TNFa and IL-6 levels in untreated BMSCs is needed (i.e., BMSCs treated with the plain medium / solvent used to suspend the exosomes, and BMSCs treated with the plain medium used to make conditional medium); adding such baseline control will provide more context for the change in TNFa and IL-6 levels because it looks like just adding the ordinary exosomes also increased TNFa and IL-6 levels

3. Labeling in Figure 2B-2F: Com-exo is not clearly documented / explained in the rest of the manuscript, also not a straightforward abbreviation for ordinary exosome. It would be great if the authors can add the appropriate labeling during the revision process.
Validity of the findings: This study have provided some very interesting findings on what roles macrophages play in the process of BMSC osteogenic differentiation. It's clear that the exosomes secreted by macrophages after inflammatory response suppress osteogenic gene expression in BMSCs.

The only unclear link is whether this suppression is caused by the inflammatory response: i.e., inflammatory exosomes led to increased inflammatory gene expression in BMSCs, which led to decreased ALP, Col1, and Runx2 expression; or it is something else in the inflammatory macrophage that led to the increase of osteogenic expression. The current conclusion points to the former but the author did not provide sufficient evidence to validate this causal relationship.

To fully validate this, the authors should consider treating the BMSCs with just TNFa or IL-6, to see if that alone suppressed the osteogenic gene expression.
Additional comments: No comment. Great job on this study!


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

Input:
Title: LIPOPOLYSACCHARIDE-ACTIVATED MACROPHAGES REGULATE THE OSTEOGENIC DIFFERENTIATION OF BONE MARROW MESENCHYMAL STEM CELLS THROUGH EXOSOMES
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have successfully responded to my comments.
Experimental design: None.
Validity of the findings: None.
Additional comments: None.


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

Input:
Title: LIPOPOLYSACCHARIDE-ACTIVATED MACROPHAGES REGULATE THE OSTEOGENIC DIFFERENTIATION OF BONE MARROW MESENCHYMAL STEM CELLS THROUGH EXOSOMES
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors appropriately answered all the comments.
Experimental design: Authors appropriately answered all the comments.
Validity of the findings: Authors appropriately answered all the comments.
Additional comments: Authors appropriately answered all the 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 FIELD TEST OF FOREST CANOPY STRUCTURE MEASUREMENTS WITH THE CANOPYCAPTURE SMARTPHONE APPLICATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: 1.	Comparing this App with other Apps
This is the most efficient way to show how good this App is.

2.	Canopy closure, canopy cover and leaf area index (LAI) are three different canopy properties.
Canopy closure (=1- canopy openness), canopy cover and leaf area index are related to each other, but they are not identical (Chen et al. 1997; Jennings et al. 1999). Canopy openness shouldn’t be used interchangeably with canopy cover (in Figures 2 and 4). It is improper to use LAI (acquired with LAI-2200s as a benchmark) to evaluate canopy cover of CanopyCapture. Since the confusion between canopy closure and canopy cover is ubiquitous, and canopy closure (rather than canopy cover) is the most direct result of canopy image analysis, it is better to confirm with the CanopyCapture developer which canopy property is actually estimated by this APP. In the indirect methods (such as hemispherical photography and LAI-2200c) for measuring light availability, percent light availability is derived from gap fraction (LI-COR Biosciences 2021; Rich 1990). Before revising this manuscript, it is strongly suggested to understand the definitions of canopy closure, canopy cover, leaf area index, gap fraction and light availability.

3.	The field of view should be controlled.
The poor performance in Figure 2b and Figure 4 will discourage the use of this App. The poor relationships may be attributed to that the field of view of LAI-2200 is much higher than that of smartphone cameras. Using a wide-angle adapter (such as https://www.amazon.com/Camera-Adapter-SourceTon-Samsung-Smartphones/dp/B07415BD9B) can increase the field of view of smartphones. Hopefully, this approach can raise the performance.

4.	Using RMSE rather than R-squared
Please use RMSE (root mean square error) rather than R-squared to evaluate the performance of this App. R-squared is to quantify the extent that a dependent variable is explained by a regression model. RMSE is to quantify the differences between two variables (in this manuscript, variable measured with CanopyCapture and variable measured with LAI-2200s) (Confalonieri et al. 2013).

5.	The problem of being unable to measure light availability > 5% should be solved.
The understorey light availability of many vegetation types (such as young plantations, forests recovering from clearing ) is higher than 5% (Beaudet et al. 2004). The existing methods (e.g. hemispherical photography, LAI-2200s, quantum sensors, GLAMA app) don’t have such problem. The use of this App will be greatly limited if this problem isn’t solved.

6.	The misclassification problem of canopy and sky should be solved.
This problem was shown in Figures 6 and 7 and will considerably reduce the performance of this App in a high light environment. This problem can be mostly eliminated through thresholding, but this App doesn’t include this function. Please elucidate whether this problem can be solved through any approach.

References
I.	Beaudet, M., Messier, C., and Leduc, A. (2004). "Understorey light profiles in temperate deciduous forests: recovery process following selection cutting." J. Ecol., 92(2), 328-338.
II.	Chen, J. M., Rich, P. M., Gower, S. T., Norman, J. M., and Plummer, S. (1997). "Leaf area index of boreal forests: Theory, techniques, and measurements." Journal of Geophysical Research-Atmospheres, 102(D24), 29429-29443.
III.	Confalonieri, R., Foi, M., Casa, R., Aquaro, S., Tona, E., Peterle, M., Boldini, A., De Carli, G., Ferrari, A., Finotto, G., Guarneri, T., Manzoni, V., Movedi, E., Nisoli, A., Paleari, L., Radici, I., Suardi, M., Veronesi, D., Bregaglio, S., Cappelli, G., Chiodini, M. E., Dorninoni, P., Francone, C., Frasso, N., Stella, T., and Acutis, M. (2013). "Development of an app for estimating leaf area index using a smartphone. Trueness and precision determination and comparison with other indirect methods." Comput. Electron. Agric., 96, 67-74.
IV.	Jennings, S. B., Brown, N. D., and Sheil, D. (1999). "Assessing forest canopies and understorey illumination: canopy closure, canopy cover and other measures." Forestry, 72(1), 59-73.
V.	LI-COR Biosciences (2021). LAI-2200C- Plant Canopy Analyzer instruction manual, LI-COR Biosciences, Lincoln, Nebraska, USA.
VI.	Rich, P. M. (1990). "Characterizing plant canopies with hemispherical photographs." Remote Sens. Rev., 5, 13–29.
Validity of the findings: No comment
Additional comments: 1.	There is no Figure 3. The figure below Figure 3 is Panel b of Figure 2.
2.	Putting the line of X=Y in Figure 4 will show whether the relationship of the two variables varies along the gradient of canopy cover.
3.	In Figure 2, the dots were round, and the legends were square. Please be consistent.
4.	In Table 1, standard deviations should be provided.
5.	In the caption of Figure 2, please mention that the X and Y axes are both in log scale.
6. L 175-176: The result (Figure 2a) is not enough to support this conclusion.


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

Input:
Title: A FIELD TEST OF FOREST CANOPY STRUCTURE MEASUREMENTS WITH THE CANOPYCAPTURE SMARTPHONE APPLICATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a useful comparison and validation of a smartphone canopy measurement application (CanopyCapture) that might be an alternative to more traditional methods. The author makes three comparisons: 1.) They compare the canopy closure estimate from CanopyCapture app with ‘light availability’ from a LiCore LAI-2200c instrument. They also compare canopy cover from CanopyCapture 2.) across clear or overcast days and 3.) among phone models.
	The statistical methods are sound and well-reasoned. Overall, the writing is clear.
	I have two primary concerns with the study. First, I think the framing is spurious. Second, I have a hard time evaluating the results of the comparison between the LAI-2200 and CanopyCapture because it seems two different measurements are used.
Experimental design: One concern is in the comparison between LAI-2200c “light availability” and CanopyCapture’s “canopy cover.” It is not clear from the methods section what exactly is being estimated with “light availability.” It would be useful to explain this clearly and perhaps provide the equation from which it is derived in order to know if a comparison with canopy cover is justified. Because hemispherical projections like LAI-2200 measure canopy CLOSURE, not canopy COVER, it is confusing (see Jennings, S. B., Brown, N. D., and Sheil, D. (1999). Assessing forest canopies and understory illumination: canopy closure, canopy cover and other measures. Forestry 72, 59–74.). All estimates of LAI, canopy cover, closure, and (I assume) light availability are based on estimates of gap fraction, so it seems that gap fraction would be a better statistic for comparison.
Validity of the findings: The framing of the introduction sets up the relative advantage and disadvantages of canopy measurement methods as a comparison of the LAI-2200, the CanopyCapture app, hemispherical photography (HP), and densiometers. However, these aren’t mutually exclusive methods and some of the contrasts are spurious. The LAI-2200c is essentially just a small hemispherical camera in which all estimates are computed under-the-hood. Treating them as separate methods is misleading. For instance, HP also requires calibration from a clearing or second sensor (line 52-53) and the LAI-2200c also requires overcast conditions (line 56-57, lines 229-231) unless direct sun is blocked and additional measures of light scatter are acquired (https://www.licor.com/env/support/LAI-2200C/topics/sun.html) (which is also true for HP). Similarly, both HP and LAI-2200c need to be leveled (line 58). The author mentions that HP needs to be carefully oriented (line 58) but this is only true if one is plotting sun paths. For estimates relying solely on gap fraction (like canopy closure and LAI) orientation doesn’t matter for HP, either. I believe that the author needs to more clearly articulate exactly where the advantages and disadvantage lie for different methods while being careful not to conflate methodological difference origination from using the tools to measure different things (i.e. light environment like Site Factors versus canopy structure like gap fraction or canopy cover).
	Along the same lines, I think that the author needs to address the fact that not all HP methods are the same. The disadvantages of traditional methods of HP with SLR cameras (as in Rich 1990) differ from those using single-shot estimates from smartphones (as in Bianchi et al 2017) and many problems have been obviated by HP generated from spherical panoramas captured on smartphones (as in Arietta 2021).
	The framing that thresholding “normally involves some degree of subjectivity” (line 69) with Canopy Capture as an objective exception (line 71) is misleading. All of the comparisons that the author cites (line 68) use objective, algorithmic thresholding. Tichy (2016) and Arietta (2021) use histogram-based threshold algorithms. Patrignani & Ochsner (2015) use automatic color-based thresholds. Bianchi et al (2017) use both. The only difference is that all of this happens in a “black box” with CanopyCapture, but that isn’t a question of more or less objective.
Additional comments: Line 66-69. I think it would be useful to summarize the smartphone applications available. Of the citations listed for this sentence, only Buchi et al (2018) present a smartphone app (GLAMA); the others are all methods that use smartphones but are not smartphone apps themselves.

Line 72-73. I don’t think that the leveling mechanism is very important. Hand-leveling doesn’t introduce noticeable bias in traditional HP (see: Origo, N., Calders, K., Nightingale, J., and Disney, M. (2017). Influence of levelling technique on the retrieval of canopy structural parameters from digital hemispherical photography. Agric. For. Meteorol. 237-238, 143–149.) and Arietta’s (2021) method with smartphone spheres obviates the need to level at all.

Line 127-152. These two parts of the study are sound and I really appreciate that the authors included them. These analyses are important in understanding the limits of this method.

Line 153-166. The statistical analyses are appropriate. I especially think that the use of SMA rather than OLS is wise.

Line 244-251. In addition to hardware differences between phones, it is important to mention that software difference likely play a much larger role. In contrast to traditional cameras, smartphones rely on computational photography to capture images. The difference in software routines has a much larger effect than difference in hardware.

Line 252-260. The conclusions make good sense. I agree with the author’s appraisal.

The figures and table look good. I especially appreciate the example outputs from CanopyCapture.


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 FIELD TEST OF FOREST CANOPY STRUCTURE MEASUREMENTS WITH THE CANOPYCAPTURE SMARTPHONE APPLICATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: - Clear and unambiguous professional English used throughout the manuscript.
- Literature references and sufficient field background/context not provided. I have specific comments on this this in the attached document.
- I don't see any raw data shared but the author maintained professional article structure and tables/figures.
- I don' think the application/software of interest has the merit to be the centre point of a scientific article. However, the author asked good research questions and presented data accordingly.
Experimental design: I have a lot of questions and concerns related to the experimental design. I have shared them in the attached document in the relevant sections.
Validity of the findings: I am not convinced that the overall merit of this article is novel. I have made several comments in the relevant sections.
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: A FIELD TEST OF FOREST CANOPY STRUCTURE MEASUREMENTS WITH THE CANOPYCAPTURE SMARTPHONE APPLICATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: I appreciate the author’s effort in revising the manuscript. I especially think that the additional analysis with a wide-angle lens adapter strengthens the study. However, I have major concerns that terminology is being used incorrectly and the relative strengths and weaknesses of different approaches are somewhat opaque and misleading.
Experimental design: I understand that the author’s purpose is to test how well CanopyCapture compares to the industry-standard LAI-2200C instrument. However, this is only possible if the same metrics are compared. As written, it is impossible to determine if this is the case. Despite all three reviewers pointing out the issues comparing very different instruments and very different metrics, the author has not addressed this sufficiently in the manuscript.
Validity of the findings: In their rebuttal to the initial review, the author states, “I wanted to see if CanopyCapture measurements can serve as a proxy for actual measurements of (a) leaf area index and (b) understorey illumination, which is why I report correlations with those variables and not gap fraction.” However, the LAI-2200C are also just a proxy for LAI and light, not “actual measurements” which would be far more difficult. Since both methods are using Gap Fraction estimates to calculate proxy measures of LAI and light, it makes far more sense to compare Gap Fraction. (See comments on specific lines below).

In any case, because misusing terms can lead to a lot of confusion, the author needs to clearly define the metrics that they are using. Again, I think it would be useful to explain this clearly and perhaps provide the equations from which the metrics are derived in order to know if a comparison with canopy cover is justified. This could easily go into the appendix and referenced in the methods section.
Additional comments: Lines 54-55. This statement is factually incorrect. HP also requires calibration from a clearing for accurate measurements. Many practitioners use an estimate (either from a single image from a clearing or from point estimates within the stand) rather than simultaneously capturing two images, but the same practice can be used with LAI-2200C to avoid the second sensor.

Lines 61-63. This statement is factually incorrect. Not all HP based methods require exogenous leveling. Arietta’s (2021) method automatically levels the hemispherical images. Perhaps add this as a caveat.

Lines 88-91. I’m not sure if the app is measuring canopy closure either. When canopy closure is measured with an optical device with a projection other than perfect equasolid angle, it has to be corrected for zenith angle. This is because the gap area is distorted by the lens projection. Since the CanopyCapture app doesn’t seem to require any input about lens projections or field-of-view, the estimate must be uncorrected Gap Fraction. Frazer (1997) explains this well: “gap fractions must be corrected for area distortion before calculations of canopy openness or cover are made. Percent open sky is defined as the percentage area of the sky hemisphere that is unobstructed by vegetation, and can be calculated as the sum of all area corrected gap fractions multiplied by 100% (ter Steege 1993).”

Lines 129-134. I appreciate that the author included the additional analysis with the wide-angle lens adapter. This strengthens the manuscript in my opinion. Was the projection of the adapter/lens combination calibrated and used to correct the area distortion for Canopy Closure estimates? If not this need to be stated. Also, if not, then the metric is uncorrected Gap Fraction, not Canopy Closure.

Lines 228-229. I think this sentence implies that the phone camera adjusts exposure according to the average brightness of the field of view? That is not how any modern cell phone made in the last decade works. Cell phones use computational photography and HDR to adjust individual pixel to normalize the luminance histogram of the image. Only older single-shot point-and-shoot or (sometimes) DSLRs adjust overall exposure based on average brightness.

Lines 243-244. This is largely obviated by HP methods derived from smartphone images (as in Arietta, 2021) because those methods expose for restricted portions of the viewing field at a time and utilize the camera’s built-in HDR methods.


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 FIELD TEST OF FOREST CANOPY STRUCTURE MEASUREMENTS WITH THE CANOPYCAPTURE SMARTPHONE APPLICATION
Review round: 3
Reviewer: 1

Output:
Basic reporting: I appreciate that the author persisted through these reviews. I think the final product is very good and a useful addition to the literature.
Experimental design: With the canopy metrics of comparison now clarified, the experimental design is warranted and appropriately reported.
Validity of the findings: No comment.
Additional comments: None.


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

Input:
Title: SOIL PROPERTIES AND MICROBIAL COMMUNITIES OF SPRING MAIZE FILED IN RESPONSE TO TILLAGE WITH STRAW INCORPORATION AND NITROGEN FERTILIZATION IN NORTHEAST CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English language should be improved in all text.
Experimental design: The experiment design is not clearly, in my mind it is a two facters split–plot
design, and straw is not a factor. However, in introduction part, I feel clearly it is a three factors experiment. The experiment design should be clearly.
Validity of the findings: This study evaluates the effect of tillage with straw incorporation and N levels on soil environment factors, enzyme activities, microbial abundance, diversity and community composition and explore the relationships between soil microbial communities, enzyme activities and environment factors. It has some important data should be published after major revising.
Additional comments: Line 6:“researching the relationships....”is Chinese English, the English language should be better
Line 24-25: in fact, the soil microbial diversity and community composition has been evaluated such as Lu et al. 2018.
Line 64-66: The English language should be improved. And I think “study” is not good, experiment should be better.
Line 249-252: “However, at jointing stage of maize, decomposition of straw and SOM released minerals, such as amino acids and amino sugars, which could be acquired by microorganisms, then mineralized to NH4+ or NO3– , utilized by crop roots” is this true?
The discussion part should be improved.
You have many treatment, while you used “between” in all table title.


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: SOIL PROPERTIES AND MICROBIAL COMMUNITIES OF SPRING MAIZE FILED IN RESPONSE TO TILLAGE WITH STRAW INCORPORATION AND NITROGEN FERTILIZATION IN NORTHEAST CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study reported the effects of tillage practices (rotary tillage and plow tillage) with straw incorporation with three N fertilization levels on soil microbial communities and enzyme activities. The language is of sufficient quality. However, the data analysis for the 16S rRNA sequencing result is not accurate and needed to be improved. For these details, please refer to the general comments.
Experimental design: The experimental design is clear and reasonable. However, there is no control group included. The best way is to add a control group without any treatments or without the application of straw. In that case, the data should be sufficient to reflect the effect of tillage practices and the straw incorporation.
Validity of the findings: The study is really helpful and supportive for the agriculture application and practices.
Additional comments: Line 7. The whole microbial community has a stronger relationship with these different factors, rather than only microbial diversity.

Line 9. A practical measure? Or approach?

Line 67, I suggested that you can draw a figure to show the plots design, which can indicate where is the main plots and where is the subplots, as well as which treatment on the different plots.

Line 124. It is accurate number for the amplicon length of bacteria based on 338F and 806R? Please correct it.

Lin196-197. You mentioned that PTS improved Chao1 and Shannon index in fungi, however, the figure 3E didn’t indicate the same result. Chao1 index also showed that there is no significant difference between RTS with CK and MN, and PTS. The description of fungi is not correct.

Line 198-199. There is no difference among PTS+CK, PTS+MN, PTS+HN, RTS+CK and RTS+MN in Fungal Chao 1 analysis. It is not correct to describe that fungal Chao 1 was the highest values in PTS+CK.

Line 216. How do you know RTS treatments significantly increased …? Did you measure the PERMANOVA? What is the result that indicated the significant increase?

Line 217. The word “Quantities” is not correct. You measured the relative abundance, rather than absolute abundance. How do you quantify the abundance? What is the meaning of quantities?

Line 218. Also here, how do you know significantly decreased? Without statistical analysis, you cannot say significantly… If you did any statistical analysis for the bacterial community compositions, please emphasize here.

Please add information What is the total read of the 16S rRNA sequencing result? How much remaining after filtering? How do you process the sequence read? After the quality control, how many sequences reads remain? You should mention this information of the 16S rRNA sequence at either methods or result parts in your manuscript. It is the main focus of your manuscript. Without this detailed information, it is hard to trust the data and results.

Line 295-296. How do you know RTS treatments increased the bacterial and fungal abundance compared with PTS treatments? The bacterial Chao 1 analysis indicated that PTS+MN has the highest bacteria abundance than RTS. The description didn’t match with the results shown in the figure.

Line 323-324. Which data indicated microbial diversity was significantly influenced by all factors? Which factors were involved in the analysis? Also, the next sentence is not accurate. Not all PTS or RTS treatments were increased/decreased. You also should discuss why PTS+MN showed the highest richness, rather than CK or HN. Is it related to soil nutrition, or other reasons?


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: SOIL PROPERTIES AND MICROBIAL COMMUNITIES OF SPRING MAIZE FILED IN RESPONSE TO TILLAGE WITH STRAW INCORPORATION AND NITROGEN FERTILIZATION IN NORTHEAST CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: Introduction should be presented in present sentence unless examples are cited to support the stated facts and background. Accordingly, authors should rewrite the introduction section from the second paragraph.

In most of the (sub)sections, the language is not clear: the main area of focus for the authors to work on before resubmitting.

Authors should avoid unnecessary usage of comma and phrases that create ambiguity. Also, avoid non-scientific words and contractions like wasn’t, don’t, etc. Grammar should be double checked.

Authors need to clearly state the existing problem(s) related to the land management activities in the area and why the current interventions (treatments) were sought.
Experimental design: In the site description,  the last sentence (Line 99-101) is not complete; authors should rewrite it.

Why these levels of N? Authors would justify this.

The experiment was established in 2015 and the samples were collected in 2019? Readers would miss information on whether the treatments were applied only once (in 2015) or repeated every year (season) till 2019. Similarly, whether the soil samples were collected only once (in 2019) or every season after harvest from 2015 to 2019. I think authors need to indicate this in this section.
Validity of the findings: This study addressed important aspects of land management activities on soil properties and microbial communities. Authors have put great effort to acquire rich data and presented the results in tables and figures.

However, the manuscript is not well organized and needs to be rewritten.

Some sentences are not complete or complexed with unnecessary phrases. There is also repetition, and authors would consider combining results and discussions sections to minimize this.

It's better to combine the two subsections: 'Effect of tillage with straw incorporation and N levels on microbial abundance' and 'Effect of tillage with straw incorporation and N levels on microbial composition'. Abundance and composition are both measures of  diversity.

Line 205-209: Not clear sentences, please rewrite them.

Line 213: ‘improvements’ is not the right term here. Instead, you can use ‘increment’?

Line 288-290: I couldn’t understand the meaning; the grammar is not correct, either. Consider deleting this sentence.

Line 295: amino acids and amino sugars are not minerals. Authors need to be careful in using terms across the manuscript and avoid using non-scientific words.
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: SOIL PROPERTIES AND MICROBIAL COMMUNITIES OF SPRING MAIZE FILED IN RESPONSE TO TILLAGE WITH STRAW INCORPORATION AND NITROGEN FERTILIZATION IN NORTHEAST CHINA
Review round: 3
Reviewer: 1

Output:
Basic reporting: The manuscript has been improved very well.
Experimental design: Authors responded as to why they chose the N rates in the rebuttal. It would be better if they add this justification in the Experimental Design section.
Validity of the findings: The manuscript is well improved now after the authors have incorporated the comments provided in the first round review.
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: NON-DESTRUCTIVE MONITORING OF 3D CELL CULTURES: NEW TECHNOLOGIES AND APPLICATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: -In introduction section, limitations related to conventional 2D culture systems were missed. Please add relevant information.
-In Figure 1 legend, the term SB should be defined.
-For scaffold free 3D culture authors can refer to previously published articles as follows; https://doi.org/10.1186/s12645-020-00074-4
-The limitations to SF cellular aggregation were missed in this review article.
-There are some typos errors within the manuscript. Please consider the issues
-Authors are asked to debate about SB culture systems such as spherical hydrogels such as microspheres used in different experiments.
-The role of cell alignment, orientation and cell-to-cell interaction within 3D SB cultures should be debated in detail.
-The effect of micro and nanopattering in 2D and 3D culture system should be also considered.
Experimental design: -
Validity of the findings: -
Additional comments: -


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

Input:
Title: NON-DESTRUCTIVE MONITORING OF 3D CELL CULTURES: NEW TECHNOLOGIES AND APPLICATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the current review, Marilisa Cortesi and Emanuele Giordano summarize and compared the different methods for 3D cell cultures, which is very promising methodology to mimic the in vivo micro-environment during in vitro study. Especially, when the 3D fell culture were combined with high-through out drug screening and live Real-Time visualization. Therefore, I agree and favor this review very much. Although the 3D culture  was initialed from 1980s, this technology was really restricted to popular utilization due to technical issues.
Experimental design: The background literature and study rationale clearly articulated.
Validity of the findings: No comment
Additional comments: No additional comments


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

Input:
Title: NON-DESTRUCTIVE MONITORING OF 3D CELL CULTURES: NEW TECHNOLOGIES AND APPLICATIONS
Review round: 1
Reviewer: 3

Output:
Basic reporting: In the manuscript by Cortesi et al., the authors summarized the recent advances in the field of non-destructive monitoring of 3D cell cultures. The authors first gave a brief introduction to the 3D cell culture model, and then systematically reviewed the techniques to monitor the 3D cell culturing and the cell-matrix interactions. The reviewer has some minor comments:

1. The pink color of the matrix in Fig 1a and Fig 1c is similar to that of the cells. It is suggested to change the matrix color to blue for better presentation.
2. The DNA content-based techniques for cell viability evaluation are missing, such as Picogreen assay. The most common technique to determine cell proliferation, BrdU assay, is missing.
3. Fig. 2 should summarize all the techniques for the evaluation of cell viability and proliferation, not only showing the EIT technique.
4. There are too many simple lists of the techniques throughout this review. The authors should add more comparison and their opinion on these techniques. It is suggested to change the summary paragraphs to tables for easier reading, for example, Line 200-208. Page 5.
5. The citations are too old. Most of the citations are published three years ago. Although it is important to give the readers an outline of technique development, it’s better to add more recent publications to give up-to-date information.
Experimental design: Nil
Validity of the findings: Nil
Additional comments: Nil


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: NON-DESTRUCTIVE MONITORING OF 3D CELL CULTURES: NEW TECHNOLOGIES AND APPLICATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Good
Experimental design: not applicable
Validity of the findings: inteperations are valid
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: NON-DESTRUCTIVE MONITORING OF 3D CELL CULTURES: NEW TECHNOLOGIES AND APPLICATIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors have made all the appropriate changes in this revision. This manuscript could be accepted in its current form.
Experimental design: Nil
Validity of the findings: Nil
Additional comments: Nil


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: COMPARATIVE PROTEOMIC ANALYSIS BETWEEN MATURE AND GERMINATING SEEDS IN PARIS POLYPHYLLA VAR. YUNNANENSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The balance between ABA and GA is crucial for seed dormancy. Zhang and Li showed us that the levels of several GAs were significantly increased in germinating Chonglou seeds, whereas the amount of ABA was sharply reduced. Through proteomic and transcriptome analysis, the authors have pointed out that the ABA synthetic related enzymes and their responsible genes have altered in germinating Chonglou seeds. The results were consistent with previously study. However, the article is not well written, and some results need to be discussed.
Experimental design: The metods are detail described. Experimental design should be completion: the transcriptome should be verified by real-time quantitative reverse transcription-PCR.
Validity of the findings: The conclusions is appropriately.
Additional comments: Comments to author,
I have some concerns.
Major concerns:
1.	The English language must be improved to ensure that an international audience can clearly understand your text.
Examples: Line 42, this species; Line 93, germinating; Line19-20, 44-45, I could not get what the authors wanted to say. There are too many such incomprehensible sentences in the whole manuscript.
2.	How about the GA synthetic enzymes in germinating Chonglou seeds
3.	The transcriptome should be verified by real-time quantitative reverse transcription-PCR, and also the expression level of GA synthetic genes.
Minor concerns:
1.	Paris polyphylla var. yunnanensis is known as Chonglou in China. It is better using Latin and Chinese names in the beginning and then only using Chonglou.
2.	Figures should be improved:
The resolution of all figures is poor;
It is better to show the data in descending order for Figures 1 and 2;
Figure legends should be detail.
3.	Through Table 2, I see that the levels of serval GAs was changed. However, the authors only GA3 and GA7 were significantly increased, how about the orthers?
4.	Also in Table 2, statistical analysis and significance labeling should be presented conventionally.
5.	The discussion is poorly written. The state of seed dormancy is correlated with ABA/GA ratio (White et al., 2000; Penfield and King, 2009; Liu et al., 2014). The authors should carefully read these articles and fully discussed the relevance between ABA/GA ratio and the germination of Chonglou.


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: COMPARATIVE PROTEOMIC ANALYSIS BETWEEN MATURE AND GERMINATING SEEDS IN PARIS POLYPHYLLA VAR. YUNNANENSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: In the discussion part, I suggest the authors discuss the significance of their findings, for example, how their findings will benefit the seed germination in the field.

Even though it is a supplementary figure, figure S1 doesn’t seem very necessary. It looks like only part of the figure S2 is shown in the file. More information such as the meaning of green/red is needed. In figure 4, the dot of “metabolic pathways” is not fully shown in the figure.

The language needs improvement to make sure the manuscript clear, unambiguous, and professional. For example, in line 23-24, DEPs (differentially expressed proteins) are comparison between two groups, but the authors only mentioned the germinating group. In line 34, the word “underly” is not professional, consider revision.
Also, minor typos are present in the manuscript. Some examples are: In line 41, a space between “saponins” and “are” is missing; In line 67, there are two periods.

The English language of this manuscript needs improvement to make sure international audience understand it. Some examples are line 45, 102, 268.
Experimental design: "No comment".
The authors of the manuscript entitled “Comparative proteomic analysis between mature and germinating seeds in Paris polyphylla var. yunnanensis” filled the knowledge gap of the difference between proteome and transcriptome of mature and germinating seeds of Paris polyphylla var. yunnanensis. The experiment design is logical and sound.
Validity of the findings: Conclusions are too tedious, try to focus on important results/findings.
Additional comments: No additional comments


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

Input:
Title: COMPARATIVE PROTEOMIC ANALYSIS BETWEEN MATURE AND GERMINATING SEEDS IN PARIS POLYPHYLLA VAR. YUNNANENSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed almost all my concern. However, the writing needs to be further improved.
Experimental design: The metods are detail described.
Validity of the findings: The conclusions is appropriately
Additional comments: I suggest authors ask a language service.


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: COMPARATIVE PROTEOMIC ANALYSIS BETWEEN MATURE AND GERMINATING SEEDS IN PARIS POLYPHYLLA VAR. YUNNANENSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: Even though the authors have revised the manuscript, the language still needs improvement to make sure the manuscript clear, unambiguous and professional. For example, in the abstract, past tense should be used when the authors were describing the method they used. Through the paper, the author used some present perfect that doesn't seem appropriate.

The figures still seem fussy to me. Please provide figures with higher resolution.
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: COMPARATIVE PROTEOMIC ANALYSIS BETWEEN MATURE AND GERMINATING SEEDS IN PARIS POLYPHYLLA VAR. YUNNANENSIS
Review round: 3
Reviewer: 1

Output:
Basic reporting: The language of the manuscript improved after revision. I don't have other comments.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: No additional comments


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

Input:
Title: QTL MAPPING AND CANDIDATE GENE ANALYSIS OF LOW TEMPERATURE GERMINATION IN RICE (ORYZA SATIVA L.) USING A GENOME WIDE ASSOCIATION STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: The thesis is well organized and described logically.

But, It is necessary to review recent papers related to low-temperature germination.
Moreover, there are many articles for GWAS related to low-temperature germination,

There are some errors in some references.
line 160; not in the reference.
line 315 & line 317: need to be moved over line 337.
Experimental design: In GWAS, the plant population is very important.
Authors need to describe how to select a mini core collection (276)  from 3K-RG.
Validity of the findings: The authors need to add the results of the GWAS using GEMMA analysis for 2020D7 in Figure 3.
Please describe how to select two genes out of 13 genes.

Need to modify.
4.1% in line 129 and 22% in line 133 should be modified to 3.5% and 24% according to Table 1, respectively.
Additional comments: In fig 4. please check the variety accessions. The names differ in footnote and picture.


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: QTL MAPPING AND CANDIDATE GENE ANALYSIS OF LOW TEMPERATURE GERMINATION IN RICE (ORYZA SATIVA L.) USING A GENOME WIDE ASSOCIATION STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: - The authors should devote a paragraph or so introducing LTG and why it is an important agronomic trait. - The introduction should answer quite obvious questions that come to mind for someone not familiar with this trait, for example:  what is its biology? Why should I care for this trait? Why do the authors care for this trait? Why did you use this approach to dissect the trait architecture? What other approaches could you have used-why didn’t you use those approaches? etc.
- L 37: What makes rice the MOST IMPORTANT staple? Provide more recent and relevant support for your statement, otherwise, revise accordingly.
- It makes little sense to write the Introduction in the past tense – Lines: 39,41,52,53, etc
- Present a coherent discussion of the studies you list in the introduction – why are they relevant to the reader?
Experimental design: - L 71 / L 122: Be consistent - is this a mini core collection? Cite or provide a description of the collection if it is.
- L 73: “… Meanwhile each accession was treated equally as much as possible in two consecutive years …” what do you mean by this?
- L 128: “… Germination is defined as the seed shoot or root exceeding 0.1 cm from the seed coat …” Why 0.1 cm? Provide relevant support.
L 129: Justify the choice of time points: why D6 to D10 – why not D5 or D4 to D10 or more?
L 130: Why could this have been the case – do you have any speculations?
- How did you use the transcriptome datasets for haplotype analysis?
Validity of the findings: - Can you clarify what the percentages mean? For example, L 133 – 134: “… average germination rates were 22% and 31% with a medium of 10% and 22% in 2019 and 2020, respectively …” What does the medium statistic represent?
- L 150 – 156: This is an interesting result. How much variation do PC 1 and 2 account for together? Is this the correspondence between subgroup membership 100% consistent with Japonica and Indica – how do you explain the discrepancy if any?

- L 158: “… A total of 136,276 validated SNPs were calculated in silico. …” what do you mean by calculated in silico?
- L 159: “… Based on the calculation of P value, 5.13 was set as the threshold in this study for the full population. …” What P value calculation are you referring to??
Additional comments: L 150 - 156: Since this is quite an interesting result ( the correspondence between these ~270 accessions with rice sub-classification Japonica and Indica, it would make sense to include in the introduction brief material about the botany of rice.


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: QTL MAPPING AND CANDIDATE GENE ANALYSIS OF LOW TEMPERATURE GERMINATION IN RICE (ORYZA SATIVA L.) USING A GENOME WIDE ASSOCIATION STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript could benefit from professional English translation. Grammatical errors are a major distraction from an otherwise good paper.

The authors responded well to suggestions for more background with a sufficient review of relevant literature on the subject of study.
Experimental design: Sound and valid experimental design were used.
Validity of the findings: Valid but not novel.
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: COMBINATIONS OF ACTION OBSERVATION AND MOTOR IMAGERY ON GOLF PUTTING’S PERFORMANCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript reports a result of a comparison of different action observation and motor imagery and intervention combined both techniques to demonstrate the beneficial effects on golf putting performance. Three strategies were used to differentiate the AO and MI, namely, arranging the participants into either S-AOMI group (Simultaneous-AOMI), A-AOMI group (Alternate-AOMI), and A-S-AOMI group (Synthesis-AOMI). The results suggested that, after six weeks of intervention, the participants in the S-AOMI, A-AOMI, and A-S-AOMI groups performed better in the putting task in the post-test when compared to the pre-test. The superior performance was also found in comparing the MI-AO combined groups to the counterparts in the control group. This manuscript is reasonably clear and concise, and the authors show a revealing command of future studies. The authors have done a great job of providing an informative and meaningful addition to the literature of AO and MI in sport psychology.
However, there are several changes that the authors are encouraged to revise to elevate the overall contribution of the paper to this research field.
Experimental design: General comments:
1.	Firstly, the authors are recommended to add more information regarding the rationale of conducting the current study, especially why is the rationale behind comparing three different kinds of AO-MI combined tasks and why chose golf putting performance as the designed motor task.
2.	Please make the introduction more concise. The authors may want to streamline the theoretical background in the introduction section to elevate the conciseness. One helpful suggestion might be moving some information from the introduction to the discussion to balance the overall information flow.
3.	The abstract requires a conclusive implication at the end. It would be nice to see how the authors elucidate the overall findings in the abstract.
4.	The overall findings in the current study may require further discussions in sport psychology. For instance, how does the AO/MI relate to motor performance, though which kinds of possible mechanisms? Does the AO/MI approach alter the attentional focus?
Validity of the findings: Specific comments:
1.	Line 109, is investigating the optimal order of AO and MI the primary focus in this study? However, the relevant studies cited in this paragraph did not fairly match this point. The authors may want to collect and specify more evidence surrounding the optimal order of AO and MI.
2.	Line 115, please specify the type of participants from the study of Romano-Smith. It would make a more precise point to establish the previous findings.
3.	Line 123, a more robust rationale is expected than merely comparing the S-AOMI or A-AOMI difference in another motor task. The readers might wonder why the golf putting task set a different tone from the dart-throwing task when taking S-AOMI or A-AOMI into consideration.
4.	Line 129, again, it might be nice to explain why the authors chose the golf putting task before introducing it.
5.	Line 147, did the gender balance exist in all groups?
6.	Line 177, the PETTLEP approach. The authors may want to add additional information regarding PETTLEP approach. Furthermore, why chose this approach?
7.	Line 188, the readers might be curious about why using Stimulus-Response Training here. Add more information concerning why and how this training connected to the current study is encouraged.
8.	Line 224, is there any supportive evidence to the retention test after one week from the post-test? Moreover, any deliberate control was adopted to ensure the participants did not continuously practice the golf putting?
9.	Line 234, the Research Tools section seems a bit redundant. Many pieces of information can be integrated into either the study design section or the experiment procedure section.
10.	Line 272, the skill performance scoring. Did all the participants perceive a similar difficulty when performing the putting task? 180 cm from the hole might be a good start for the novices. However, some might feel hard to put the ball into the hall because the distance might not be the factor to introduce the difficulties for novices. Furthermore, was the artificial turf inclined or having any curves?
11.	Line 279, the readers might wonder why scoring 1 and 2 are two different stories. Was the putting performance accessed to exemplify the accuracy or something else?
12.	Line 303, please keep the stats in a consistent format throughout the manuscript.
13.	Line 356. The explanation should be careful as the studies cited above do not provide collective support to this interpretation. That is, Wang et al. (2020) made the comparison on elite golfers, not novices. These findings may not follow the following findings, which suggested that enhancing motor cortical activity in the brain resulted from AO and MI (Avanzino et al., 2011; Jeannerod, 2001; Tani et al., 2018). Hence, the enhanced motor performance after the intervention may require further evidence to support this claim.
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: COMBINATIONS OF ACTION OBSERVATION AND MOTOR IMAGERY ON GOLF PUTTING’S PERFORMANCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overview
This is a neat study which addresses a relevant and contemporary topic in this field of research. I think this work makes a useful contribution to the field because, and as the authors state, previous AO+MI golf studies have not included a retention test, and you did. The authors employed a between group pre- post – retention (1 and 2) design to compare three types of mental practice against each other and a no practice control group. At the important second retention test, synchronous AO+MI does not perform as well as asynchronous AO+MI or a group where these two AO+MI instructions are combined. I think the main components of a good study are reported in the manuscript, but I recommend the authors consider the points I raise below as a means to improve the write up further prior to publication.

Introduction
I don’t think it is necessary to recapitulate several dated theories at the start of your intro (line 57 – 76). You don’t test these theories directly and some are not well supported by empirical work (and you don’t include an evaluation of the available evidence supporting each theory. My suggestion would be to remove at least the first two (psychoneuromuscular and symbolic learning theory). I would briefly add some empirical support for bioinformational theory – please see earlier work e.g., by Jenn Cummings (University of Birmingham)

For further clarity and improve readability in the main terms you use, I would recommend using:
-	Synchronous AO+MI (instead of S-AOMI)
-	Asynchronous AO+MI (instead of A-AOMI)
-	I don’t think the term ‘synthesised’ really captures the methodology you used in the third condition. Instead of synthesised AOMI (also quite similar to my new suggestion of synchronous) you could consider terms like: graduated or progressive AO+MI

Line 57: imagery works… to achieve what? Please expand
Line 83: needs a reference, e.g.:
Rizzolatti, G., Maddalena, F.D., Arturo, N., Gatti, R. & Pietro, A. (2021). The role of mirror mechanism in the recovery, maintenance, and acquisition of motor abilities. Neuroscience and Biobehavioral Reviews.

Line 102: the word ‘then’ implies that the two processes (AO and MI) occur in a sequential fashion, when this is not the meaning you intend – consider replacing, e.g., with ‘and imagining’ … ‘either / or‘ ?

Line 128: I would not say that you extend Romano-Smith’s study, as you use a completely different task. Please re-phrase

To support hypothesis 2, I would suggest adding a little extra detail on the rationale behind the order of presentation used in A-S-AOMI… namely that you place alternating first – do you presume this is less demanding and more helpful in early learning than S-AOMI? If so, two studies support the idea that extra neurocognitive demands are involved in the latter:

-	Emerson, J. R., Scott, M. W., Van Schaik, P., Kenny, R. P. W., & Eaves, D.L. (2022). A neural signature for combined action observation and motor imagery? An fNIRS study into prefrontal activation, automatic imitation, and self-other perceptions. Brain and Behaviour. e2407.

-	Eaves, D. L., Behmer, L. P., & Vogt, S. (2016b). EEG and behavioural correlates of different forms of motor imagery during action observation in rhythmical actions. Brain and Cognition, 106, 90-103.

the writing style is mainly approriate throughout - take care to avoid small typos throughout
Experimental design: methodology
Line 176 – please include the sample imagery script in your supplementary materials and make it clear how this follows the pettlep principles in context. Was the imagery assessment used as a screening tool for inclusion in the study? If so, please describe the cut off for inclusion?

Line 186 do you mean 6 blocks of trials comprising 5 trials each (n= 30)?

Line 207. Please add more detail to the imagery instruction component of the S-AOMI condition – what specifically did you ask them to imagine during the video, for e.g., the kinaesthetic physical sensation of effort and force? Did this include trunk rotation, and body/head position and also did the imagery end when the visual component related to ball trajectory in the video – did they see the ball go in the hole on each trial and if so, what were they imagining at that point?

Line 209: what were the observation instructions exactly? Did you say just watch, or did you direct them to observe the same components of action described in the imagery? Importantly – did you take any steps to ask participants not to undertake imagery in the AO phase of each trial? Please state in the paper if you believe this could be an explanation for the main findings. This point also applies to A-S-AOMI.
Please state the total number of AO and MI trials in A-S-AOMI as well as the total number of AOMI trials in this group. It is important to be able to compare the number of trials across all groups… I presume all groups had 30 trials per intervention session, but it will be good to see the break down (to allow for assessing dose response

Please make it clear in the methods section that the intervention comprised purely of mental practice in the absence of physical practice throughout the intervention period (not withstanding the physical execution required at the repeat baseline testing points

Pre test and post test – please state the number of physical trials undertake at each of these two time points.  For retention test please identify each time point as described in the results section (retention test 1 and retention test 2)
Validity of the findings: Results
Table 2. it is not good to present the same data twice. To avoid this, please add the SD bars on to figure 3 and remove table 2.
From your stats reports it is not clear if there is a significant difference between the four groups at the initial pre-test – please report… looking at figure 3 it seems there is an imbalance in the scores at this time point (despite the fact you have not added comparison bars to highlight sig difs.
Please report the post hoc analysis to follow up on the main effect of test (i.e., time)
It is also difficult to see in your stats what the results are for the comparisons within each group – e.g., do they all increase performance over time to the same extent?
Given the unstated analysis of differences between groups at the pre-test, please could you explain why you have opted not to run an analysis of co-variance on the data, using the base line score as the co-variant? This will be necessary if there are indeed differences between groups at the baseline
Discussion
Limitations: please comment on the possible confound of spontaneous MI during the so-called AO only phases of the methodology – what actions did you take to reduce this possibility and what impact might this potential confound have on your data?

How do you account for the finding that the S-AOMI group performed worse than the A-AOMI group, given the large number of neuro imaging studies that show the neural involvement is very different between these two instructions? The general pattern of results is that AOMI significantly increases motor cortical involvement compared to AO or MI alone, and this is assumed to be a good thing for motor learning see:

Ruffieux, J., Mouthon, A., Keller, M., Mouthon, M., Annoni, J.M. & Taube, W. (2018). Balance training reduces brain activity during motor simulation of a challenging balance task in older adults: an fMRI study. Frontiers in Behavioral Neuroscience, 12, 10.

Taube, W., Mouthon, M., Leukel, C., Hoogewood, H., Annoni, J., & Keller, M. (2015). Brain activity during observation and motor imagery of different balance tasks: An fMRI study. Cortex, 64, 102-114.

The conclusion starting in line 408 is wrong or at least too blunt – you did find sig differences between these three conditions at both retention tests. Clearly the second delayed retention test is the most crucial time point to highlight in your discussion section for evaluating your findings. Here you show:
A-AOMI and A-S-AOMI >  control group
A-S-AOMI > S-AOMI
I think the latter finding specifically speaks to the advantage offered early in learning from asynchronous AO and then MI… this also suggests that your task was suitably novel / challenging for your participants… it could be anticipated (based on these results) that as motor skill develops, performers can graduate toward using S-AOMI and then perhaps favour MI alone, but this remains to be tested at advanced skill levels
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: COMBINATIONS OF ACTION OBSERVATION AND MOTOR IMAGERY ON GOLF PUTTING’S PERFORMANCE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revised manuscript is more concise and clear than the previous version. My compliments to the authors.
Just a few revisions should take into account before the final decision.

Line 136. The study contained AOMI (S-AOMI) and AOMI (A-AOMI) approaches. The readers might wonder how these two approaches affect the psychological and cognitive processes after the training. More supportive inferences might be helpful to explain the results which using AOMI (S-AOMI) and AOMI (A-AOMI).

Figure 2 looks like it can be upgraded by using more proper software to display the results. Please reform Figure 2.

The study design. The authors are recommended to implement a flowchart or framework to showcase the study design. This addition would make the readers understand the design of the current study more easily.
Experimental design: No further comments on this part.
Validity of the findings: Line 519-520. I would expect an informative indication of the main results here...before simply introducing the optimal combination of AOMI for future study. Again, similar to the previous comments, the results should be linked with the inference to the psychological or cognitive processing of motor performance.
Additional comments: Taken together, the authors did an excellent job of elevating the overall quality of the current manuscript. However, based on the spirit of advancing the boundary of AO/MI fields in sports, more theoretical evidence and interpretation should be provided and added to explain the findings.


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

Input:
Title: COMBINATIONS OF ACTION OBSERVATION AND MOTOR IMAGERY ON GOLF PUTTING’S PERFORMANCE
Review round: 2
Reviewer: 2

Output:
Basic reporting: I am happy that the authors have revised the manuscript in accordance with and to address my initial concerns
Experimental design: .
Validity of the findings: .
Additional comments: .


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

Input:
Title: COMBINATIONS OF ACTION OBSERVATION AND MOTOR IMAGERY ON GOLF PUTTING’S PERFORMANCE
Review round: 3
Reviewer: 1

Output:
Basic reporting: I have no further issues with the manuscript and I recommend the manuscript for PeerJ publication.
Experimental design: This parts sounds good to me.
Validity of the findings: The authors have revised our comments accordingly.
Additional comments: No additional comments


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

Input:
Title: EFFECTS OF FIRE DISTURBANCE ON SPECIES AND FUNCTIONAL COMPOSITIONS VARY WITH TREE SIZES IN A TROPICAL DRY FOREST
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is clearly written and easy to understand, although there are minor grammatical English errors throughout.

The paper is well organized, has good literature review and sufficient background, and results and discussion stick to the questions posed in the introduction.

It is clear what the figures show and they are good quality, and relevant to the questions being explored in this analysis.
Experimental design: A 50 ha mapped plot with census of trees every 5 years provides an excellent basis for the study, with 1250 20 x 20 m quadrats in which species composition is followed.

This is original research on an important topic with respect to dry tropical forests. The research questions are well defined and important, namely how surface fire affect the species composition, size class distribution and functional trait composition of the forest over 20 years.

The methods are well explained and the way in which functional traits were determined in the field and used in the statistical analysis for the 49 species followed were very good.

The results are rigorous and because repeated observations over 20 years in the same forest after fire is uncommon in tropical dry forests, it does fill a knowledge gap.
Validity of the findings: The findings presented are valid. However, I don't think the data was fully analyzed. In addition to 5, 10, 15 and 20 year time periods, all starting in 1994, the study could also use the same data to do four 5-year periods within the total 20-year period of observation (1994-1999, 2000-2004, 2005-2009, 2010-2014). This is important because the 1994-1999 results (shape of curves in Figures 1 and 2) is much different than the curves for 1994-2004, 1994-2009, 1994-2014. To really understand what is going on, we should also see if the remaining 5-year periods after 1994-1999 also have curves shaped the same, or if the five-year periods look progressively more like the 1994-2014 curves. In other words, is 1994-1999 a typical 5-year period or is there progression in successive 5-year periods toward the shapes of the curves for the full 20-year period, so that the analysis mostly represents forest recovery from the 1998 fire? With this addition the conclusions would be stronger.

Conclusions are linked to the questions posed in the introduction. The data presented is adequate to verify the results and conclusions.
Additional comments: The role of fire is not integrated into the abstract--although it does mention that surface fires play an important role in dry tropical forests, the occurrence of fire during the 20 years of observation and its role in the results are not mentioned.


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

Input:
Title: EFFECTS OF FIRE DISTURBANCE ON SPECIES AND FUNCTIONAL COMPOSITIONS VARY WITH TREE SIZES IN A TROPICAL DRY FOREST
Review round: 1
Reviewer: 2

Output:
Basic reporting: Comment 1: In community ecology, one important goal is to understand the processes of community assembly and the underlying mechanisms. Therefore, many processes have been proposed to explain the patterns of plant diversity, including stochastic and deterministic processes, which can be determined by evaluating temporal turnover in species and functional composition. Fire disturbance is an important driving force of forest turnover, affecting ecosystem functioning in tropical forests. The authors aimed to address two important questions: 1) what are the pattern of temporal turnover in species and functional composition in a community with frequent fire disturbance? And 2) how did the temporal turnover vary with tree size? The topic of this study is interesting and important. However, the statements are at time unclear, especially for the fire effects on temporal species and functional turnover for tree species.
Comment 2:  The title is “How does surface fire disturbance affect temporal species and functional turnover for tree species in a tropical dry evergreen forest?”. However, I failed to find how fire (e.g. burn severity, burned area or fire return interval) affected temporal species and functional turnover for tree species. The authors did not test the direct effects of fire on post-fire temporal species and functional turnover. And in the conclusion, the author stated that they did not assess the effects of fire regimes like fire intensity. In my opinion, I recommend changing the title.
Comment 3: In lines 57-58, the authors took an example to support above statement “Optimal functional traits of tree species vary along environmental gradients”. The example is related to the trees that survive in high mountainous areas with low temperatures tend to have small leaves adapted to low temperature communities. I think it would be better to take an example which is related to how functional traits of tropical trees respond to environmental changes.
Comment 4: In general, fire is a random event in landscape-scale and is therefore difficult to predict. In the manuscript, the author stated that “fire can contribute to both stochastic and deterministic processes” and explained this statement from lines 98 to 107. From the statements, the authors explained how fire caused the stochastic process, but did not introduce the deterministic process clearly. The statement “while a high intensity canopy fire such large canopy fire is more likely to kill almost all trees indiscriminately” is confusing. Whether there is a mistake in the statement of “high intensity canopy fire such large canopy fire”. Furthermore, the authors stated that “because of the non-random mortality, temporal turnover in functional composition should be non-random”. Please provide related references for this. Although tree mortality is random with a high intensity fire, the post-fire recruitment process may be random as the seed dispersal is random from the unburned forest.
Comment 5: In the introduction, the authors stated the underlying effects of fire intensity on temporal species and functional turnover. However, they did not test the effects of fire intensity on temporal species and functional turnover. So the introduction seems to be redundant.
Experimental design: No comments
Validity of the findings: Comment 1: The author stated that “we quantified the effects of fire disturbance on species and functional composition of tree species”. Whereas in the conclusion, they stated “we could not assess the effects of intraspecific trait variation and fire regimes like fire intensity”. The statements seem to be contradictory.
Comment 2:Comment 7: It is hard for readers to see how the quadrats which exhibited functional turnover significantly different from random primarily distributed in the 50-ha study plot in the figure S1 due to the similar green colors. Same comments for figure S2.
Comment 3: In the discussion section, the two subheadings of “The effect of tree size on species temporal compositional changes” and “The effect of tree size on temporal functional turnover” discussed the effects of tree size on species temporal compositional changes and functional turnover, not related to fire effects. This also suggested that the title was not appropriate.
Additional comments: Comment 1: line 112 There was a mistake for “be help”. Maybe "helpful"?
Comment 2：line 228 and 230 There was a mistake for the word“high”. Maybe “higher”?


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

Input:
Title: EFFECTS OF FIRE DISTURBANCE ON SPECIES AND FUNCTIONAL COMPOSITIONS VARY WITH TREE SIZES IN A TROPICAL DRY FOREST
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1）The references cited in the Introduction section should be updated and added. There are few cited references of recent five years in the manuscript. The newest references could better describe the novelty and make the readers who focus on related research field understand the importance of current research.

2)	L211-212. How authors reached this conclusion? Please provide the detailed information here. This statement is not apparent in Fig.2.

3)	Fig. S1 and S2 are critical for current research because authors referred these two figures so many times in the manuscript. I suggest that authors move these two figures into the manuscript instead of putting it in the supplementary materials.

4)	Result section. Why the results with high DBH (>10cm) of Fig.4 are not presented in here? Besides, the results of Fig.4 are abnormal due to extremely high numbers of quadrats appeared in the second, third and fourth column. Can you explain or provide more detail?
Experimental design: no comment
Validity of the findings: 5)	The novelty and contribution should be clearly bolded in the discussion section. Therefore, the structure of Discussion needs to be modified to better answer two questions raised in the Introduction. I suggest that authors clearly summarize the results by dividing the discussion into three parts, which mainly discuss the turnover pattern (Fig.1 and 3), the effect of sizes (Fig.2 and 4) and changes of functional trait distribution (Fig.5).
Additional comments: 1)	L32. Should be “investigated”
2)	L50. Missing words: “new recruits this forest” should be “new recruits of this forest”
3)	L55. Should be “affect”
4)	L65. Please add the reference.
5)	The forms of Fig.2 and Fig.3 should be uniform. There should be one title of x-axis and y-axis.
6)	The caption of figures should be adjusted. The names of Fig.1 and Fig,2, Fig.3 and Fig.4 are identical.


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

Input:
Title: EFFECTS OF FIRE DISTURBANCE ON SPECIES AND FUNCTIONAL COMPOSITIONS VARY WITH TREE SIZES IN A TROPICAL DRY FOREST
Review round: 2
Reviewer: 1

Output:
Basic reporting: Improvements made in response to previous review are very good
Experimental design: No comment
Validity of the findings: Revisions in response to previous review make it clear that findings have high validty.
Additional comments: Changes in response to my previous review comments seem well done. I have no additional comments at this time.