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

Input:
Title: A FRAMEWORK FOR NEAR-REAL TIME MONITORING OF DIVERSITY PATTERNS BASED ON INDIRECT REMOTE SENSING, WITH AN APPLICATION IN THE BRAZILIAN ATLANTIC RAINFOREST
Review round: 1
Reviewer: 3

Output:
Basic reporting: Dear authors, I enjoyed revision and apologize for delays! You link remotely sensed climate data with presence-absence data from nine taxonomic groups and validate with extensive monitoring datasets. The combination of techniques results in a robust framework to estimate alterations in the distribution ranges, and provides an important contribution to enhance biodiversity monitoring. I recommend highly the publication of the manuscript, although some revision is necessary:

Main point: What about cumulative effects of climate? Physiologically, climate severity (e.g., a dry year)  may reduce fitness and reproduction of a population, but may be compensated by a following, less severe year, in which the population recovers, while an additional severe year may indeed cause (temporary) local extinction of the population. So I wonder if the consideration of middle-term climatic effects (such as ENSO anomalies) may enhance the predictions.

I would welcome some speculations about underlying mechanisms for mismatches in between observed and modelled data (Figure 4). It seems that matches are concentrated in regions with higher forest cover/less fragmentation, which would indicate higher dispersal abilities for the taxa (although colonization may lag behind environmental alterations as stated in discussion)!

Furthermore, I would welcome Table S2 in the main text, to give the reader a better idea about the model parameters. Consequently, some details about the models may be withdrawn from the result section.

Legend Figure 2: Can slope variation be incorporated in the Figure?

To finish: I am not a native speaker, but some spelling/grammar/editing issues: References in l. 101, Melastomataceae in l. 112, word duplication in l. 298
Experimental design: As stated above: What about cumulative effects of climate? Physiologically, climate severity (e.g., a dry year)  may reduce fitness of a population, but may be compensated by a following, less severe year, while an additional severe year may indeed cause (temporary) local extinction of the population. So I wonder if the consideration of middle-term climatic effects (such as ENSO anomalies) may enhance the predictions.
Validity of the findings: OK
Additional comments: Non


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: FUNGAL DIVERSITY IN SHADE-COFFEE PLANTATIONS IN SOCONUSCO, MEXICO
Review round: 1
Reviewer: 1

Output:
Basic reporting: Fungal diversity in coffee plantations was studied in a variety of different ‘habitat’ types on the coffee trees and bushes. This is a novel study and provides interesting information on understudied habitat types for an economically and culturally important plant species. The dataset is relatively rich, but additional analyses and statistical reporting are required for publication.

Introduction
Overall the introduction is sufficient. However, additional detail on the rationale for finding orchid mycorrhiza on bark is necessary. This is an interesting idea but not sufficiently explored in the introduction at present

Additional studies have uncovered a diverse suite of endophytic taxa on branches or tree bark, and the authors could situate their study in this literature as well. For example Lynn Boddy, Pellitier et al., etc

Line 91: it is not clear what mycorrhizae forming endophytic fungi means. Mycorrhizal fungi inhabiting an endophytic niche? The authors could consult literature by M.A. Selosse exploring the evolution of the mycorrhizal niche (i.e. the ‘waiting room hypothesis).

Methods
Please provide additional information regarding the proximity of each site to one another.
Additionally, please provide information regarding what is an ‘upper’ or ‘lower’ branch. Information on the relative age of the host trees, years since clearing of the forest, overstory composition, soil type, and other site level information is necessary. Were the bark samples surface sterilized, if not why? Were there epiphytic plants growing on the sampled tissue, or was it bare? A photograph could be added to the supplement.

This data is essential for reproducibility and context.

-The parameters used in the DADA2 command should be reported.
-Which UNITE database version was used? Please report

-Overall I am missing a section in the methods discussing the statistical tests that were employed. It appears that certain tests for alpha and beta diversity were conducted? The statistical tests need to align with the questions of interest proposed in the introduction. Please consider some of the recommendations regarding presentation of results (below) that may assist in guiding the analysis. For example, instead of an occurrence test, perhaps the relative sequence abundance of ‘orchid mycorrhiza’ across each sampling type could be provided.

Recommendations for the presentation and analysis of the results:
In the introduction, the authors stress that coffee plantations may be a ‘reservoir’ for fungal diversity. This seems plausible, however, the results do not provide context to evaluate this possibility. Comparison of overall alpha diversity after rarefaction could be provided and then compared to other studies from this region. Moreover, the relative alpha diversity of the different habitat types could be reported as a nice box plot and analyzed with ANOVA.

Consider presenting an ordination (NMDS or PCoA) visually orienting the reader to differences in beta diversity among the sample types (i.e. tree vs shrub, and upper vs lower branch). A PERMANOVA implemented using the Adonis function in vegan is suitable for such an analysis.

It would be interesting to know, given that the two sites span such a wide latitude gradient if elevation figures as a driver of overall alpha or beta diversity

Table 1 is great but can be moved to the supplement.

Table 2, 3 and 4 are useful to display the data, but i might recommend adding additional information regarding which habitat type each sample is derived (i.e. where on the bark).Especially for table 2 and 3, an indicator taxa analysis could be a useful way to assess this data.

The insights derived from Figure 1 are relatively minimal when Fungal sequences are clustered at the Phylum level. The authors could perhaps consider remaking the figure with fungal Class taxonomic assignments, which may provide more nuance to the findings. The authors say in line 206 that no other trends were observed in lower taxonomic levels? Is this a statistical result? What is driving the trend in the Figure 1 at present? Are the distinctions between Asco and Basidiomycota among the samples a function of elevation? Sampling location?

Figure 2 could be improved by collapsing the stacked bar plots into box and whiskers displaying sequences assigned to each habitat type, not necessarily presenting data for every single sample.
Experimental design: Overall the experimental design is sufficient, however few samples were analyzed, and at present the overall analysis remains relatively weak with many areas for improvement. See above.
Validity of the findings: Validity of the findings is sufficient Molecular sequencing methods are solid. Statistical method are not reported, and clear findings therefore are missing.
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: FUNGAL DIVERSITY IN SHADE-COFFEE PLANTATIONS IN SOCONUSCO, MEXICO
Review round: 1
Reviewer: 2

Output:
Basic reporting: a.	Table2: “Sequence counts” – is this OUT or ASV?
b.	Table3: “Sequences counts”
c.	Line215-220: I suggest two figures to illustrate this result.
Experimental design: Line119: I suggest describing the forward and reverse primers separately and including the primer sequence.
Validity of the findings: a.	I suggest PCoA plots to discuss the beta diversity results.
b.	This is a well-structured manuscript. My concern is the study used unequal numbers of samples of coffee and tree. This may rise bias.
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: FUNGAL DIVERSITY IN SHADE-COFFEE PLANTATIONS IN SOCONUSCO, MEXICO
Review round: 2
Reviewer: 1

Output:
Basic reporting: This is well structured and written manuscript studying the fungal community in shade-coffee plantations with ITS amplicon analysis.

References: please add DOIs to several references, e.g. Line534, Line567, Line641.

Table 1: please add the column header.
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: INTEGRATED TRANSCRIPTOME AND METABOLOME ANALYSES REVEALED REGULATORY MECHANISMS OF FLAVONOID BIOSYNTHESIS IN RADIX ARDISIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: Some figures have low definition (e.g. Fig. 6). There is also a lot of room for improvement in writing.
Experimental design: I think it is probably an important contribution to the traditional medical field, but the authors could do a better job to make the results attractive to the general audience. In addition, the methods section can be elaborated to include many details.
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: INTEGRATED TRANSCRIPTOME AND METABOLOME ANALYSES REVEALED REGULATORY MECHANISMS OF FLAVONOID BIOSYNTHESIS IN RADIX ARDISIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: Throughout the manuscript there are significant issues with English grammar and syntax to the point where it is sometimes difficult to understand the meaning of phrases. Aside from relatively minor problems such as missing direct and indirect articles (“a”, “the”) there are more serious problems with phrasing that make reading difficult. Below I have offered a few examples with suggestions for how to correct language issues. I would suggest, if possible, passing this manuscript along to a colleague with fluent English language mastery who can help to revise the writing throughout the paper. I believe this would help considerably with clarity and readability.

Lines 58-59:  “Pharmacological studies showed that the AC possess anti-inflammatory, anti-arthritic, anti-tumor,
and inhibiting angiogenesis (Wen et al., 2019; Hamid et al., 2017; Sulaiman et al., 2012; Hamsin et al., 2013).”

Example of language revision: Pharmacological studies showed that AC exhibits anti-inflammatory, anti-arthritic, and anti-tumor activitity, and can inhibit angiogenesis.

Lines 71-73: “Flavonoids are naturally occurring compounds that possess many pharmacological effects, containing anti-tumor, anti-oxidant, anti-inflammatory and so on (Maleki et al., 2005; Maleki et al., 2019; Zhang et al., 2021).”

Example of language revision: Flavonoids are naturally occurring compounds that display many pharmacological effects such as anti-tumor, antioxidant, and anti-inflammatory activities.

Lines 109-110: “The analysis of total phenolic content (TPC) was used to Folin–Ciocalteau spectrophotometric method, with some modifications.” This statement is unclear to the point that I can’t tell exactly what it means.

Example of language revision: “The analysis of total phenolic content (TPC) was carried out according to the  Folin–Ciocalteau spectrophotometric method, with some modifications.” I think this is what is meant here, but I am not 100% sure.

A related issue is that there a large number of typos such as missing spaces, extra articles (“the the...”), etc throughout the manuscript. I recommend a detailed review of the entire document to find and fix these issues.

Lines 41-43 of the introduction. Terms such as “heat meridian”, “stasis pain”, and “dispelling wind” are not familiar to me and I suspect they will not be familiar to many readers. I think these terms, and their origins, should be explained or that the the terms should be replaced with more commonplace medical terms. A further issue here is that there are not citations for the assertions made in this opening statement. I think it would be best to include some references that support these statements.

Lines 79-80 of the Introduction. Species names here and throughout the manuscript should be italicized to be consistent with the convention.

Lines 185-186 of the Results. It is stated that “The results indicated that the assembly quality was better in this study.” The assembly quality is better in comparison to what? Is this compared to another dataset? If so, that study should be cited here. Also, here the NCBI BioProject number for the raw reads is provided, which is great, but will the transcriptome assemblies also be made available somewhere for the sake of reproducibility?

Lines 196-205 of the Results (sub-header “DEG Function Enrichment Analysis”) is essentially just a single long list of ontology terms that were enriched in the KEGG pathways. This information would probably be better condensed into a table. Instead, this sub-section could be used to contextualize this information rather than simply listing categories.

Lines 285-289 of the Discussion. There is a fairly long discussion here of the steps in the upstream part of the flavonoid pathway. I think it would be very helpful for most readers to have a figure showing a simple diagram of the the pathway so that the logic is easier to visualize.

Lines 294-296 of the Discussion. It is stated that “The regulatory network and CCA analysis shown that Naringenin, Luteolin, Catechin, Quercetin was more likely to be key compound in the flavonoid biosynthesis pathway, involving in 4CL, AOMT, CHS, CHI, DFR, F3’5’H, FLS, LAR, and so on.” It is not clear to me what exactly is being argued here. How does the correlation analysis show that these flavonoids are more likely to be “key compounds” and what is the link to the list of genes that is provided? Is it saying that these flavonoids form a module (defined by correlation) with these particular pathway genes, which was identified by the CCA analysis? This needs to be rephrased and/or expanded to make the logic clearer.

Throughout the Methods section TFC is used to indicate “Total Flavonoid Content”, which makes sense to me, because a variety of flavonoids (including flavonols and flavones) are listed and discussed. However, through the Disscussion (and in the Abbreviations section) TFC is used to indicate “Total Flavone Content”. Based on the compounds that are discussed, I believe the authors still mean Flavonoid, but this should be checked and confirmed throughout the manuscript.

The image quality for some of the figures, such as Fig. 2, Fig. 4, and Fig. 6, is quite poor. This makes it difficult to see certain information. Also, I would recommend putting lines around the bars in the bar plots in Fig. 2, because  the neighboring bars bleed together and are difficult to see clearly.

Figure captions, particularly for figures such as Fig. 3, Fig. 4, and Fig. 5, need to contain more detailed information about what is shown. These are complex figures and there is not enough information in the captions for readers to parse them efficiently. I also recommend declarative titles for the captions that state the takeaway messages.

In Fig. 7, the unigenes (blue ellipses) and the metabolites (red triangles? This information needs to be included in the captions!) are only labeled with numbers and unique IDs that are not meaningful to the reader. How should these results (e.g. the apparent clusters/modules in the network) be interpreted? It would also be very helpful to highlight the genes and metabolites that are elaborated on in the subsequent analysis and in the text (i.e. those that are associated with flavonoid biosynthesis). And again, the image quality of Fig. 7 is very poor and needs to be improved before incorporation into any final version of this manuscript.

I have a similar critique to Fig. 7 for Fig. 8. What is the identity of the genes and metabolites shown in this heatmap figure (i.e. which one is a CHS gene or the quercetin compound). Not having this information clearly communicated in the figure makes it extremely difficult to parse and to link what is being shown with the statements that are made in the text.
Experimental design: Lines 107-108 of the Methods. Why was methanol used as blank in this spec measurement? As far as I can tell from the description, there is no methanol in the solution used for the procedure? This should be explained. In this same procedure it is stated that “a calibration curve was plotted to calculated the TFC”. What was used to generate this calibration curve? A single flavonoid? A mixture of flavonoids? Different flavonoid compounds have very different absorption spectra, so it is necessary to know what was used for calibration in order to interpret the absolute values calculated from the calibration curve.

Lines 110-112 of the Methods. It is stated that “The 1 mL of gallic acid (standard solution) or ACS and AC extract and 3 mL of the Folin–Ciocalteau solution (10% in water) were pipetted into the wells of a microplate. After 5 min, 6 mL of a 10 % sodium carbonate aqueous solution were added to each well.” This does not seem to be possible. How can 6mL of solution fit into each well of a micro-plate? I am guessing this is supposed to be microliters?

Lines 117-118 of the Methods. It is stated that “In this study, 12 samples produced from Ardisia crenata Sims (ACS) and Ardisia Crispa (Thunb.) DC (AC) (six biological replicates) were tested by using RNA-seq. Total RNA was extracted with the RNAprep Pure Plant Kit (Tiangen, China) and detected on a 1% agarose gel.” What tissue was used here? Was it root tissue? This is important, because the qRT-PCR validation of the RNA-seq data is done with root tissue. It is stated later (in the results) that these were root samples, but this type of detail should definitely be included in the methods section.

Lines 119-120 of the Methods. It is stated that “The purity, concentration, and integrity of the
total RNA samples were assessed prior to further analysis.” How was this done? Qubit for concentration? Tape Station or similar to look at integrity? This information should be specified.

Lines 121-125 of the Methods. It is stated that “In this work, twelve cDNA libraries
produced from the ACS and AC were sequenced by using the Illumina HiSeqTM 4000 platform and paired-end reads were generated, and clean reads were obtained by removing raw reads containing adapter, reads containing ploy-N and lower quality reads. Transcriptome assemblies for the twelve libraries were performed separately using Trinity (Garber et al., 2011).”. Again, there is insufficient information here to gauge exactly what was done. What kind of adapter sequences were used? Was a library prep kit used? If so, what kind? Was PCR amplification used during the library prep? How long were the paired-end reads? What settings were used with Trinity?

Lines 129-132 of the Methods. It is stated that “We used KOBAS 2.0 (Xie et al.,
2011 ) software to test the statistical enrichment of DEGs in KEGG pathways. After further investigation, we selected the flavonoid biosynthesis pathways for more detailed analysis.” What was the “further investigation” that was done here. In other words, what were the criteria for determining that the flavonoid pathway would be further investigated?

Line 163 of the Methods. It is stated that “The KEGG database was employ to analyze the metabolites and metabolic pathways.” Again, this is not enough information for a reader to really understand or judge what was done. How was KEGG used to analyze pathways? Some degree of detail is needed here.

Line 165 of the Methods. It is stated that “We performed conjoint analyses on DEGs and DEMs to ascertain the degree pathways.” What does this mean? Again, need more detail. What are “degree pathways”? How are they relevant to the analysis? What tools were used for this analysis?

Lines 165-167 of the Methods. It is stated that “To uncover the regulatory mechanism of flavonoid biosynthesis, we measured the relevance between metabolome and gene by calculating the Correlation Coefficient (CC). ” What correlation coefficient was used here? Spearman? Pearson? How was it calculated? It’s not clear from this statement what sets of values are being correlated.  Likewise, the canonical correlation analysis is not explained in adequate detail.
Validity of the findings: Lines 241-254 of the Results (sub-header “Correlation analysis between RNA-seq and metabolite uncovers the regulatory of flavonoid biosynthesis”) is stated to have the goal to “unveil the underlying regulatory mechanism in flavonoid biosynthesis metabolism between ACS and AC, we performed correlation analyses of the metabolites related to flavonoid biosynthesis and the transcripts.” I do not think that the results presented in this section reach this goal. They certainly demonstrate that there are correlations between metabolites and gene expression that make sense based on what we know about the structure of the flavonoid pathway. However, there is no clear demonstration of a regulatory mechanism, rather there are only correlations. Furthermore, these correlations don’t have any clear evidence of directionality or interrelationships between genes/metabolites (i.e. co-regulatory relationships), which we know do exist systems where flavnoid regulation has been looked at in some detail. This is not to say that the correlation analysis here does not have value, but rather that it doesn’t meet the stated goal of unveiling the underlying regulatory mechanism. Doing this would require some sort of functional experiment. So, I think that the language discussing the idea of an "underlying mechanism" should be tempered and reflect that only correlations between gene expression and metabolite profile is shown here.
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: INTEGRATED TRANSCRIPTOME AND METABOLOME ANALYSES REVEALED REGULATORY MECHANISMS OF FLAVONOID BIOSYNTHESIS IN RADIX ARDISIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The article is greatly improved from the first version. The data and methods are communicated much more clearly and the language has been clarified. I still feel that it would be better to show the names of the flavonoid pathway genes in Figures 8 and 9, rather than the alphanumeric Unigene codes. Not having the gene names makes it much harder to interpret and relate to what is going on and what is being said in the text. I am also still confused by the volumes described in lines 137-145. It seems to me that if these were pipetted into a "microplate", that the units should be uL (microliters) and not mL (millileters).
Experimental design: no comment
Validity of the findings: I think the findings are valid and the justification and interpretation of the results is now much clearer.
Additional comments: I think that this is now publishable with some minor revisions to clarify issues that I mention above.


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

Input:
Title: INTEGRATED TRANSCRIPTOME AND METABOLOME ANALYSES REVEALED REGULATORY MECHANISMS OF FLAVONOID BIOSYNTHESIS IN RADIX ARDISIA
Review round: 3
Reviewer: 1

Output:
Basic reporting: The modifications made to the manuscript have fixed the points that I found confusing and made the presentation clearer. Adding the gene names to figures 8 and 9 make them much easier to interpret. I think the manuscript is now suitable for publication.
Experimental design: NA
Validity of the findings: NA
Additional comments: NA


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: AGRICULTURAL BIG DATA AND METHODS AND MODELS FOR FOOD SECURITY ANALYSIS—A MINI-REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: The present study reviews Big Data, methods, and models in Agriculture for Food Security. I appreciate the work of the authors.

Specific Comments to the Authors:

1-	After reading the manuscript, I see the title should be: Big Data, methods, and models in Agriculture for Food Security – A mini-review.

2-	Keywords must be relevant for database search and different from those already appearing in the title. The function of keywords is to supplement the information given in the title. The title's keywords are automatically included in indexes, and keywords serve as additional pointers. The author should pay good attention to the keywords they provide.

3-	From Lines 14-15, "about 150 articles were selected", and from Lines 331-332, "122 papers were reviewed", Line 131 "a total of 130 papers were chosen": which papers count is correct?.

4-	Line 20: what do you mean about "Approximately 122 models were examined"?

5-	Many abbreviations have been used without prior declaration through the manuscript, which made the revision uncomfortable, such as Line 75, 210, 274, and so on.

6-	However, it is a review article; there is a lack of citations; see Lines 105-178.

7-	Line 185: "the two research questions" please compare with Lines 128-131.

8-	Lines 196-197: "Data of Landsat images could be accessed by Sentinel-2 in the European Union" this is wrong technically: how Landsat can be accessed by Sentinel-2?.

9-	Line 269: (http://www.chinatrace.org/index.html) is not in English.

10-	Many English corrections have to change (Big Data, big data, bigdata), and the majority of citations in text are incorrect; see Line 2016, 218.

11-	By Section 2.2, it is not enough to add UAE to the title of the manuscript.

12-	However, the manuscript reviews big data, which mainly refers to raster and vector data formats (shp, tif, cn, netcdf); they are not included in Section 2.3.

13-	Generally, authors have to move from the literature-review style to the review-article style, for instance: https://doi.org/10.2136/vzj2015.09.0131
Experimental design: no comment
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: AGRICULTURAL BIG DATA AND METHODS AND MODELS FOR FOOD SECURITY ANALYSIS—A MINI-REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: The review paper "Big Data, Methods, and Models in Agriculture for Food Security – A Review for Global and UAE Contexts" is very interesting because it investigates the available and required datasets, methods, and models for food security studies in arid environments. Given the importance of the current study as an initial and genuine start in food security studies, there is a significant gap in this type of research in both UAE and GCC countries. Furthermore, the paper identified food security gaps in the global and UAE contexts, which could serve as a foundation for future directions to close such gaps.

Therefore, I do recommend it for publication after addressing some comments below.

-          Sometimes you mention big data and bigdata elsewhere, please be consistent through the text

-          Lines 81-86 should include the most common ML models used for food security, as well as the relevant references.

-          Headings number after the Introduction section looks confused, please check, and correct wherever. For instance, number 2 is the survey methodology, and this part should be separated from other headings.

-          The section Agricultural Bigdata (potential, current status, and limitations), requires much information and references. There are many methods, models and datasets used in agriculture in different environments, please extend this section.

-          Please correct any grammar errors and improve the language as needed.
Experimental design: 1- The Survey Methodology is consistent with a comprehensive, unbiased coverage of the subject,

2-      The sources are properly cited and quoted or paraphrased as needed.

3-      The review organized logically into coherent paragraphs/subsections
Validity of the findings: 1- There is a well-developed and well-supported argument that meets the objectives stated in the Introduction.

2- The conclusion identifies unanswered questions, gaps, and future directions.
Additional comments: The review paper "Big Data, Methods, and Models in Agriculture for Food Security – A Review for Global and UAE Contexts" is very interesting because it investigates the available and required datasets, methods, and models for food security studies in arid environments. Given the importance of the current study as an initial and genuine start in food security studies, there is a significant gap in this type of research in both UAE and GCC countries. Furthermore, the paper identified food security gaps in the global and UAE contexts, which could serve as a foundation for future directions to close such gaps.

Therefore, I do recommend it for publication after addressing some comments below.

-	Sometimes you mention big data and bigdata elsewhere, please be consistent through the text
-	Lines 81-86 should include the most common ML models used for food security, as well as the relevant references.
-	Headings number after Introduction section looks confused, please check, and correct wherever. For instance, number 2 is the survey methodology, and this part should be separated from other headings.
-	The section Agricultural Bigdata (potential, current status, and limitations), require much information and references. There are many methods, models and dataset used in agriculture in different environments, please extend this section.
-	Please correct any grammar errors and improve the language as needed.


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: AGRICULTURAL BIG DATA AND METHODS AND MODELS FOR FOOD SECURITY ANALYSIS—A MINI-REVIEW
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a very interesting paper; I recommend that it be published as a review of the broad and cross-disciplinary interest and within the scope of the journal, and the Introduction adequately introduces the subject and makes it clear who the audience is/what the motivation is. However, some comments below must be addressed first.
1-	Abstract is OK, but at the end of line 24, you should add another sentence as a future direction message.
2-	Lines 31-32, global hunger happened due to many factors not only population, income, and dietary changes change, but also due to climate change, pandemics, as well as limited natural resources. So, please add them with further references.
3-	Line 34, Large dataset or Big dataset? And what is the difference? please be consistent thoroughly.
4-	Line 53-54, please add a supplementary Figure for FS dimensions.
1-	Lines 62-63 " Different countries, in particular poor and low income, suffering from limited data of agricultural, and food security statistics, even though sound decisions are based on accurate data and information," I think that you need to rewrite this sentence as GCC countries should be included in countries with limited data sources.
2-	Lines 79-81, how can you prove that, add the appropriate reference. Furthermore, you need to extend this sentence with other sentences to explain the importance and significance of dynamic models in food security over different environments. There are many sources in the literature that explained that, so go through them and specify the knowledge gap.
3-	Survey methodology, presented very well, thank you.
4-	Line 263, add the appropriate reference
5-	Section 2.4. Agricultural Bigdata (potential, current status, and limitations), to be consistent, please specify if it is for global or UAE context
6-	Section 2.5. Methods and Models for FS Should add the word "used" so, the correct should be " 2.5.Methods and Models  used for FS"
7-	Line 377, add a future research need by mentioning the other subjects required for food security studies, such as analytical framework, drivers, indicators, and scenario development. This will assist scientists and policymakers inadequately addressing FS in the UAE.
Experimental design: 1-	The Survey Methodology is consistent with a thorough, unbiased examination of the topic.
2-	The sources are properly cited and paraphrased or quoted as needed.
3-	The review is divided into logical paragraphs and subsections.
Validity of the findings: 1- The argument is well-developed and well-supported, and it meets the goals stated in the introduction, but further references are needed.
2- The conclusion identifies unanswered questions, gaps, but future directions are required.
Additional comments: Language needs improvement through the text.


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

Input:
Title: AGRICULTURAL BIG DATA AND METHODS AND MODELS FOR FOOD SECURITY ANALYSIS—A MINI-REVIEW
Review round: 2
Reviewer: 1

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


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

Input:
Title: AGRICULTURAL BIG DATA AND METHODS AND MODELS FOR FOOD SECURITY ANALYSIS—A MINI-REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: After responding to all of the comments, the paper improved significantly.


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: PUBLIC AWARENESS OF SEAFOOD MISLABELING
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is largely well written in English and uses clear and technically correct terms. Occasionally, the authors speak in sweeping all-inclusive statements and this phrasing should be reconsidered (example: Line 27, 'seafood awareness is unknown'). Similarly, from lines 101 to 104, the authors state seafood mislabeling is commonly reported through major media outlets, but then again state it is unknown by the public. The sweeping statements seem contradicted.

 Introduction and background are provided, however, there are concerns with how well the literature was reviewed by the authors due to potential inaccuracies and citation of some references that don't seem to match the intent of the current paper. For example, Line 74, Willette et al. 2017 paper was not on toxins, heavy metals or human health risk, Ray 1989 speaks about slavery but not in the context of IUU fishing which I don't believe was coined as a term until more recently in the early 2000s (see FAO's IPOA-IUU), and some references can not be checked because they are incompletely cited (e.g. Stiles et al. 2013). Furthermore, other use of references are misleading. For example Line 61-63, the authors state few studies have been conducted in China, Peru, and Thailand, and cite a single review by Luque & Donlan 2019. This 2019 paper was extensive, however, the authors should also screen the literature themselves before making such a claim. Peru, for example, has a growing number of studies on seafood labeling, including from their government institutions such as IMARPE.

The article structure, figures and tables are professionally done. Raw data is shared & appreciated.
Experimental design: The research question is well defined. It is stated how it could fill the research gap of gauging public awareness of seafood mislabeling.

Although the concept of the study is solid, the implementation of the study seems narrow and at risk of bias due to the way the survey was conducted. A major concern is how survey participants were included. Details are somewhat vague and potentially skewed. For example, on lines 143-149, the authors state that it was shared via social media, but it is unclear how? Were paid advertisements put out or was the survey shared only through the authors individual social media accounts? Given the authors are at a university and state 40% of participants were students, this seems skewed. Additionally, 62% of participants were from 4 North Carolina cities that are all in-land, away from coastal cities where seafood issues may be more familiar. The authors state signs were posted, but in how many locations, and why only in local markets and healthcare facilities? Why choose these locations over fish markets, seafood restaurants, etc.? More details are needed on postings in Miami and Seattle, notably because only 4 respondents were from Washington State based on supplemental data. Further, based on the supplemental data provided, only 22% of participants were from coastal states (excluding respondents from NC). Does this matter that the survey seems to exclude coastal towns and cities?

Line 138-139 - Please more clearly explain what human-research ethic standards means, particularly because in line 141 the authors state it is exempt from IRB authorization.

Line 140-142 - Which Office of Human Research Ethics? UNC?

More generally, I feel the study is limited in its reach and I strongly encourage them to consider broadening the number of participants included. The authors cite a nice example of how to set up such a survey study as this by using Sicherer et al. 2004. Examples like this should be modelled from for increased rigor.
Validity of the findings: Major concern - Data lacks statistical analysis, but are largely reported as percentages only from the survey responses. This weakens the data. Rather authors should include 95% confidence intervals for all reported percentages. I find the lack of 95% CI particularly curious as it was a major issue in seafood mislabeling studies discussed by Luque & Donlan 2019 that the authors cite early in this manuscript.

Authors should more clearly and directly state the scope of the study and the limits of the experimental design. I would suggest the title be modified to speak to the geographic scope of the study area. Arguably states with very low respondent numbers (<10) could be dropped. A suggestion would be 'Public Awareness of Seafood Mislabeling in North Carolina' or '... in the Southwest United States'.  As the authors state, major media outlets may indeed pick up on this study and sensationalize the results & conclusions without considering the limits of the research (majority of respondents from inland North Carolina, a plurality are students, surveys conducted through social media channels, etc.).
Additional comments: I do feel this could be an important contribution to the PeerJ readership and the larger scientific audience, however, the study lacks enough rigor and statistical foundation to have confidence in the conclusions. I feel with major revisions and re-focusing on the geographic scope of the study, it would be well suited for publication.


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

Input:
Title: PUBLIC AWARENESS OF SEAFOOD MISLABELING
Review round: 1
Reviewer: 2

Output:
Basic reporting: In my opinion, this work is clear and easy to read. I think the context shown in the introduction is correct and the objective is clear. The material offered (raw data, figures, and tables) is adequate and clear. I detected only a few errors (probably errata) that I have detailed in my comments.
Experimental design: I think the experimental design is good and the analysis and statistics were fine. However, there are some small issues that I think the authors should review before publishing. I add a few proposals that I miss in the analysis and/or results.
- L128-130: I do not agree with the definition of mislabeling. Mislabeling and fraud are not sinonims. Fraud implies intentionality. When a product is unintentionally mislabeled, it should not be called fraud. In the case of mislabeling, on many occasions, it is impossible (although it can be supposed) to ensure that there has been a fraud, except when it is impossible that the species had been captured at the same time and had not coincided during their supply chain.
On the other hand, I do not understand exactly the position of the definition in the survey. It is between Q3 and Q4. Does it mean you consider that Q3 was answered without knowing the definition?  Did it appear after answering? Or the definition was to clarify the mislabeling before Q3 responses? This is important because knowing what is mislabeling (definition) sure will change the response of Q3.
- L132-136: The statement showed before the Q6 clearly conditions the response of the sixth question. If you do not use any statement there probably the participant's responses would probably be less inclined to attach such importance to independent verification of products. But if you tell them previously that mislabeling is enormous, they will obviously reply that they would prefer to be sure of what they are buying. This is good to know that if the population were aware of the problem, they would really value such verification and control. But in no case can it be taken as a reflection of current society when in the first questions of the test it is clear that the population is not aware that mislabeling is a problem. For the rest of the people (non-participants who have not this information), it is still an unknown risk and therefore they would not give so much importance to the independent validation. I think you need to explain better the intention of the question and the potential conclusions of the responses.
- L137: For future studies, it is also interesting to ask “what is the educational level” in order to know if it is correlated to the concern, knowledge, or interest about mislabeling or the news related with. I also miss some calculations about the relationship between age and the responses.
Validity of the findings: I think this study is useful and a great view of society's awareness about seafood mislabeling. The article shows that much work is still needed to do for spreading properly the knowledge about mislabeling and its important consequences. I think the authors should add to the discussion some aspects such as “who should be responsible for the control and validation tools”, etc. I have detailed these proposals in my general comments. But, despite this, this article has a lot of potentials, it is clear and direct and as a point to highlight, towards the end, the authors transform the lack of knowledge and awareness about mislabeling into a call to society to empower itself and be aware of mislabeling, saying that everyone, as consumers, can change the market and its failures. This hopeful message seems really important.
Additional comments: Introduction
- L51: “can be difficult to detect for consumers” instead “can be difficult for consumers to detect”
- L52: fillets
- L52-L53: several species are difficult to recognize by consumers: in some cases because the species are really similar and even for an expert is difficult but other times because many people do not know the natural appearance of the species, only in the market and many times only after any processing.
- L59: studied species
- L79: I miss some connector: “On the other hand”, …
- L85: The same, I miss some connectors as “In addition” or similar
- L89: Since fish IS …
- L101: Yes, seafood mislabeling is commonly reported on media (correct, you have two prepositions). But in my opinion, not enough compared with the real frequency of mislabeling currently. Maybe in the US seafood mislabeling is on regular media (not specialized) every day but in my country, we can see news about it once every 4 or 5 months hopefully. Even though it happens every day. It is because for me it is not surprising that people really not be aware of the huge problem that it is and the huge consequences that it has.

Results
- Table 1: The percentages are not the same as in the main text (L161-165). Please review and correct to have the same percentages in both places.
- Figure 3: Is the percentage in the medium of the bars the “moderately concerned”? Please add it to the figure legend.

Discussion
- L194: the percentage is not the same in the text (38%) as in the Table (37%). Please check it.
- L208-209: Another reason can be the people see the social justice issues as slavery as a problem really far from their country so … many times “if you do not see that it does not exist ...”.
- L210-211: I understand the sentence but I think the expression is weird. Please, review and rewrite it.
- L215: “states” instead “state”
- L212-2019: in addition, several times consumers do not know the verified labels available and their characteristics or requirements. That is another problem about people's awareness. There are sustainable certifications that none knows …
- L223225: So the development of more tools to identify more species and detect fraud is extremely needed.
- I miss some points in the final section of the discussion that maybe you can add (a few sentences). (1) Who should create the verified labels or verification systems? Governments, associations, volunteers, all, … All these systems mean money. (2) I miss some proposals to increase the general public’s education on seafood mislabeling (opinion or original proposal and comparison with some bibliography).

Supplements
- Supplement 2 graph: in the bar of 18-24 years old say 8-24. Please correct it.


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: LONGITUDINAL STUDY ON THE EFFECT OF KERATINIZED MUCOSAL AUGMENTATION SURROUNDING DENTAL IMPLANTS IN PREVENTING PERI-IMPLANT BONE LOSS
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: Please see the additional comments
Additional comments: The article addresses a very important topic in Periodontology?Oral implantology that is the need of keratinized tissues around implants to maintain mucosal health.
This restrospective study assessed only the radiographical bone loss around implants in regards to the amount of keratinized tissues. The paper needs improvement especially in the interpretation of the results and the discussion. Please find below my suggestions and questions:
Line 40: Please correct word: “Background”
Abstract: abbreviations are used without the whole words the first time (KMW etc.)
Line 45: Please rephrase, it seems inaccurate to say that this study aims to clarify the
 importance of KMW as it does not give any explanation regarding this role, the aim of this study is to assess the correlation between bone loss and the amount of keratinized tissue etc.
Line 60-63:Abstract’s conclusion: ‘the importance of keratinized mucosa in maintaining the health of peri-implant tissues’: The results show a reduction in Peri-implant bone loss but no indicators about peri-implant health were assessed so please modify the conclusion by limiting it to bone loss
Line 70: is a well-established method to rehabilitate
Line 73-75 : However, peri-implantitis, a complication, involves the loss of surrounding tissue accompanied by an inflammatory reaction, culminating in implant removal in severe cases : Very brief and expeditive introduction to peri-implant (PI) disease. Please explain shortly the evolution from PI health to PI mucositis then to Peri-implantitis and the plaque-associated type of these disease, in order to link it to oral hygiene performance and the role of keratinized tissues in it
Line 96: contralateral side : please replace contralateral side by the anatomical term : ‘oral’ or’ Palatal/Lingual’
Line 115 : where are the 6 dental office situated, also in Japan?
Line 134: Please explain the choice of this definition of Periodontitis and why not to adopt the current international classification's definition?
Line 150: KMW was defined as the minimum: not clear what minimum means here
Line 152: 'APF was judged necessary when the KMW was between 1 mm and 2 mm, and FGG was judged 153 necessary when the KMW was less than 1 mm': These criteria were the same followed during 19 years in 8 centers? Or just at the University centers?
Line 214: please rephrase as this study didn’t “clarify” the importance of keratinized tissue but showed in a retrospective manner a reduction of Bone loss correlated with keratinized tissues
Table1: No  analysis was done for each confounder  to determine if the difference between each group is significant? For instance, did you see if the higher plaque score of group C was statistically significant in comparaison to A and B.

The discussion needs substantial modifications, especially related to the obtained results: Is the bone loss between Group A and B significant? The values of bone loss should be compared to other described studies in the discussion especially between (an emphasis on the comparison of group B and C is important as these two groups are more comparable than the group A which have only 66 patients, and less KMW than the group B). The Mean endpoint assessment (functional time) between the groups is high especially between group A and C and this should be discussed and potentially compared to other 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: LONGITUDINAL STUDY ON THE EFFECT OF KERATINIZED MUCOSAL AUGMENTATION SURROUNDING DENTAL IMPLANTS IN PREVENTING PERI-IMPLANT BONE LOSS
Review round: 1
Reviewer: 2

Output:
Basic reporting: 1. It is better if you can add keywords (after the abstract) for this paper.
2. Please italic the symbol 'P' in P-value
Experimental design: no comment
Validity of the findings: 1. Please re-check the total number in group A (line 193) because it is stated differently in the table provided.
2. Please re-structured tables 1 and 2 so that you can have a better result presentation
Additional comments: 1. See the manuscript for the further correction
2. Little bit of grammatical errors


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: LONGITUDINAL STUDY ON THE EFFECT OF KERATINIZED MUCOSAL AUGMENTATION SURROUNDING DENTAL IMPLANTS IN PREVENTING PERI-IMPLANT BONE LOSS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The title was relevant and appropriate and supported the study

Introduction or background covered the relevant aspects related to the study done

Minimal errors and typing mistakes in the text need to be clarified and corrected respectively. Please refer to the attached file and please make all paragraphs in the text in the “justified form”

Need some corrections and a bit of rearrangement in tables and figure. Please refer to the attached file
Experimental design: Objectives were clearly stated and the methodology was well described

Results were sufficient to reach a clear conclusion
Validity of the findings: Well written discussion and conclusion

Be careful with the references in the text. Should follow the standard guideline

References range until 2021 which were adequate and up to date
Additional comments: The manuscript is good and easy to understand and the contents are well presented

Several authors advocate that a 5-year follow-up is still short for more reliable information for survival and complication rates (Jung et al., 2008). A more recent systematic review has reported that it has been recommended to have a study with a minimum of 5 years of follow-up as stated in the Proceedings of the Third European Workshop on Periodontology (Needleman et al., 2012)


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: LONGITUDINAL STUDY ON THE EFFECT OF KERATINIZED MUCOSAL AUGMENTATION SURROUNDING DENTAL IMPLANTS IN PREVENTING PERI-IMPLANT BONE LOSS
Review round: 2
Reviewer: 1

Output:
Basic reporting: ..
Experimental design: ..
Validity of the findings: ..
Additional comments: Dear authors
Thank you for the modifications, the paper seems publishable to me. Please add the explanation to your choice of Perio classification in the manuscript (that the study design was done according to another study, so that the readers could understand that you followed another paper. Also i couldn't find in the references the Derks et al. 2016 you are refering to, so please add it

Best Regards


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: PROVIDING CHOICE OF FEEDBACK AFFECTS PERCEIVED CHOICE BUT DOES NOT AFFECT PERFORMANCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors provide a well-written and concise manuscript describing an experiment that tested the OPTIMAL theory hypothesis that autonomy would benefit learning and performance. Additional hypotheses pertaining to positive affect (greater with autonomy support), feedback (performance greater with 100% feedback frequency), and feedback preference-performance dissociation (some learners would prefer a feedback schedule that was less effective).
The authors should be commended for a) preregistering their study, b) providing the raw data from their experiment, and c) conducting an a priori power calculation in an effort to adequately power their experiment. While I do have a number of comments/concerns that may need addressing before publication, I do believe this paper provides a contribution to the literature.

1.	Basic Reporting

The manuscript provides a clear description of the experimental design and results. I was easily able to evaluate the methods in this paper and the authors should be commended for this.

My comments:

1.	Perhaps the most important concern I have with respect to the rationale for this experiment is the use of reaction time task to test predictions from motor learning theory. The task required perceptual decision making, not motor skill. Indeed, with almost any motor skill there would be a highly significant block effect during acquisition (especially with a sample of this size). In this experiment there was no evidence of improvement across blocks, although there was a difference between pre- and post-tests suggesting some improvement did occur.

While I think that testing the impact of choice and feedback schedule on a perceptual decision-making task is worthy of investigation – real world motor behavior often involves rapid decision making, after all – I do think the authors should acknowledge that they are not testing the motor learning and performance predictions forwarded in OPTIMAL theory. Indeed, Wulf and Lewthwaite write in their theory (2016, pg. 1383):

“The foundation of our theory is motor behavior. That is, we are less concerned with skills that have a strong cognitive or decision-making component (i.e., learning “what”; see Shmuelof & Krakauer, 2011). Rather, of concern is primarily the learning of “how” to bring about the coordinated or skilled control of (complex) movement, for which the quality of movement execution is of primary importance (Shmuelof & Krakauer, 2011).”

2.	It is unclear on what basis the authors form their predictions that positive affect will be influenced by autonomy support.
3.	It is also unclear why the authors predicted a dissociation between chosen feedback schedule and the most effective schedule.
4.	I assume that the authors predicted online (or 100%) feedback would be more effective than summary based on the guidance hypothesis (Salmoni et al., 1984), but I don’t see reference to that or an alternate rationale.
5.	The authors should expand on their discussion that the that their post-test is an immediate retention test and discuss the potential implications of this measurement choice compared to a delayed retention test. See for example Kantak & Winstein, 2012 but also McKay et al., 2022 for discussions.
Experimental design: Experimental Design

The authors designed an experiment that appropriately addressed their research questions. I have minor quibbles that may be useful for the authors to consider, either in this paper or future papers.

1.	Power analysis: I appreciate that the authors conducted an a priori power analysis to determine the sample size for this study. However, I have a couple points to consider. First, as the authors note in their discussion, there was a meta-analysis of self-controlled practice research available. Instead of using the estimates from that meta-analysis, the authors relied on a single estimate from a previous study that was obviously too large to be the true population parameter. To their credit, the authors reduced the estimate by 20%, but even still they powered for an effect of f = .30 or d = .60. Even the published experiments in the meta-analysis by McKay et al. (2021) only estimated an effect of d = .54, so the estimate in this power analysis was a bit optimistic.
2.	Power analysis 2: As a technical follow up, I noted that the authors use partial eta-squared from a previous study to calculate the effect size in G*Power. Please be aware that the default settings in G*Power are not the same as in SPSS when it comes to partial eta-squared. As such, unless the settings are changed in G*Power to “as in SPSS,” the resultant sample size calculations in G*Power are substantially under-estimated.
3.	My points above are meant only to facilitate a more accurate estimate of the a priori power the present study had to detect a range of effects. Of course, we do not know the true effect so we cannot know the actual power of the study.
4.	Analyses: First, while I can understand why the authors chose to create a yoked-group from their two feedback groups, I think overall this strategy was quite inefficient. Why not compare the autonomy group to both groups combined, for example? The unequal sample sizes can be handled a variety of ways. Also, why not compare the three groups and follow up with pairwise comparisons? I think either method would have had some benefits compared to the approach the authors landed on – though I should be clear I do not think the authors’ approach was invalid.
5.	Similarly, while not invalid, the mixed ANOVA approach to pre-post data is not ideal and ANCOVA is the preferred method (see Senn, 2006).
6.	As a final note, I appreciate the analyses were preregistered and I support the authors sticking with their originally planned analyses as their primary results. If the authors choose to take my comments above into account, they may consider adding them as supplemental results or exploratory analyses.
Validity of the findings: The findings reported in this manuscript appear valid. The discussion of those findings with respect to OPTIMAL theory, while warranted, need to be better contextualized to acknowledge the difference between the task used in the present study and the type of movements OPTIMAL theory makes predictions about. Most previous research on autonomy and motor performance has focused on motor skills rather than decision making, so the authors should help the reader understand the gap the present research fills.
Additional comments: I appreciate the opportunity to review this paper.

References:

Kantak, S. S., & Winstein, C. J. (2012). Learning–performance distinction and memory processes for motor skills: A focused review and perspective. Behavioural brain research, 228(1), 219-231.
McKay, B., Hussien, J., Vinh, M. A., Mir-Orefice, A., Brooks, H., & Ste-Marie, D. M. (2022). Meta-analysis of the reduced relative feedback frequency effect on motor learning and performance. Psychology of Sport and Exercise, 102165.
Senn, S. (2006). Change from baseline and analysis of covariance revisited. Statistics in medicine, 25(24), 4334-4344.


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: PROVIDING CHOICE OF FEEDBACK AFFECTS PERCEIVED CHOICE BUT DOES NOT AFFECT PERFORMANCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a well-powered study that was conducted online. Pre-registration and data transparency are especially appreciated. The authors found that autonomy support by providing choice of feedback during performance leads to enhanced agency or autonomy but did not result in improvements in performance or affect. The use of remote online testing is also appreciated. While relevant and useful for remote human subject testing under current (pandemic) difficulties of in-person testing, it does have important drawbacks (see next section). The most important issue is related to establishing appropriate controls (see next section).

Other important issues concern the definition of certain terms and methodological description are listed here:

First, the use of the term “yoked,” to describe the two feedback groups is inaccurate. Yoking does not simply mean that the same number of participants be in the autonomy and feedback groups, but rather the order and manner of stimulus presentation. Any assignment to group that is performed ex post facto (as was done in this study) is non-experimental and should not be characterized using the same terminology as from an experimental paradigm. Therefore, this reviewer suggests that the feedback groups be described as they are and if they were combined for analysis, that that be described appropriately as well. It is noted that this is a drawback of online testing, however, conflating the feedback groups with a traditional yoked group is misleading (e.g., Line 100). Once again, this raises the larger issue of setting appropriate controls in this experiment, and it is my opinion that for the online mode of testing, a within-group control (by setting control/baseline conditions) will be more fruitful and convincing rather than a between-group control (however, there may be other clever ways of setting up between-group control). In this regard, the pre-post design used in this study is useful, but falls short for purposes of determining the effect of the task itself.

Second, the result that self-reported perceived choice was enhanced in the autonomy support group should be clearly distinguished as a check of experimental manipulation and not a hypothesized effect. In other words, that individuals in the autonomy perceived greater choice is (and should be) an expected effect; if this weren’t the case, then there wouldn’t by definition be an experimental group.

Third, there is no clear rationale in the Introduction for why the authors hypothesized a change in affect. By what means might autonomy support enhance affect? Appropriate literature must be cited, and the use of PANAS should be justified.

Lastly, although the raw data are provided, it seems that it was filtered for outliers. For full transparency, please provide data with outliers. Critically, there is no mention outlier detection or their treatment in the paper It is acceptable to perform outlier detection and removal, but a clear a comprehensive explanation for the reason and method for doing so should be described in the Methods section.
Experimental design: One important consideration for online tests across disciplines, but especially for cognitive and psychological experiments, is the timing and circumstance of testing. For instance, the attention paid by a participant to an online task can greatly modify the timing of responses, such as reaction time. Given that participants were given unlimited time to respond, and that reaction times reported in the study were in the ~1250ms (>1sec) range might perhaps suggest that people may not have been paying attention to the task. To me, this is a fatal error in experimental design because it directly confounds the main outcome measure in this study. Experimentally, one way to circumvent this problem is to introduce catch trials or trials with attention probes, which can help determine if participants were in fact paying attention to the task at hand. How did the authors deal with this issue? It is not clear from the Methods if online data collection was remote, or in-person? This should be specified along with detailed description of instructions etc. Was there supervision by an examiner, such as a proctor, or did people do this at their own leisure?

Along these lines, the finding that RT variability is significantly smaller in the autonomy group might indicate that participants in this group (owing to the need to make choices at every trial) may have become better at paying attention to the task—perhaps something of interest as it shows a different route through which such active decision making might help make performance more consistent and less variable.

On a related note, the alternate task switching was described as “difficult” and likened elsewhere in the Discussion as being “complex.” This may very well be true. However, as described above, a control condition is required to infer that. Indeed, a rather straightforward control condition would have been to have all participants perform a short block of simple reaction time task for the same keys. This would not only provide a baseline for comparison with the alternate-task switching task but could also be used to infer regarding attention (an issue discussed in the previous paragraph). In other words, if SRT>CRT (in the alternate task) then one could be more certain that the experimental alternate-switching task was not only more difficult but warranted more attention by participants (who exhibited longer RTs) thus suggesting that they were in fact paying more attention to this task.

However, there is no mention that any of the above or similar control measures were taken.
Validity of the findings: All in all, the lack of appropriate controls and sufficient methodological description (especially considering that online testing is a fairly new arena for psychological, psychomotor and cognitive fields), do not allow clear conclusions to be drawn from this study.
Additional comments: No additional comments


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

Input:
Title: PROVIDING CHOICE OF FEEDBACK AFFECTS PERCEIVED CHOICE BUT DOES NOT AFFECT PERFORMANCE
Review round: 2
Reviewer: 1

Output:
Basic reporting: I believe the authors have addressed all of my comments. The revised version of the manuscript is clear and well reasoned.
Experimental design: The added limitations and updated exploratory analyses are welcomed.
Validity of the findings: The study provides an unbiased estimate of the effect it sought to study and augments the extant literature.
Additional comments: I thank the authors for their revisions and for their patience in waiting for my review. I recommend accepting the manuscript.


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

Input:
Title: COMPARATIVE TRANSCRIPTOMICS REVEALS NEW INSIGHTS INTO MELATONIN-ENHANCED DROUGHT TOLERANCE IN NAKED OAT SEEDLINGS
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study investigated the regulatory mechanism of melatonin in naked oat seedlings under drought stress. The following aspects could be considered for revision.

1.Much more details should be added in the Methods section, most of current methods are too simple, especially for RNA-seq.
2.The correlation between RNA-seq data and physiological analysis should be analyzed and discussed.
3.Most of current discussion are the repeated results, some real discussion based on this study and other published references should be added.
Experimental design: No
Validity of the findings: No
Additional comments: No


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

Input:
Title: COMPARATIVE TRANSCRIPTOMICS REVEALS NEW INSIGHTS INTO MELATONIN-ENHANCED DROUGHT TOLERANCE IN NAKED OAT SEEDLINGS
Review round: 1
Reviewer: 2

Output:
Basic reporting: This research demonstrated physiological responses and transcriptomic analysis associated with melatonin-regulated drought tolerance in naked oat seedlings.
Major concerns:
1. Trascriptomic data need to be further analysis, and many analyse were unclear. For example, Table 1 only showed basic information about the transcriptome and should be removed to supplemental materials. Table S6 showed comparison of differential gene expression enriched in plant hormone signal transduction pathway between DS + MT and DS, which have been discussed in Discussion section in details associated with melatonin-regulated drought tolerance. So Table S6 should be added in the main body of the manuscript.
2. Please add DEGs between DS+MT and DS (DS+MT vs DS) in the FIg. 3, because the DS+MT vs DS presents the effect of MT in plants under drought stress.
3. Fig. 4 or Fig. 5 showed the GO enrichment analysis or the KEGG pathway enrichment, which was analyzed by using all DEGs? It was unclear in the manuscript. It is better to do the GO and KEGG pathway enrichment using the DEGs between DS+MT vs DS.
4. DEGs in the table 5 and 7 were identified from the DS+MT vs DS? It was unclear.
5. Many unclear or wrong sentences were observed in the Discussion section. For example, line 235-237, and Please delete "being"; add "to" between "crops" and "overcome"; line 241-242; line 252-254;.... The correction and improvement in English should be done throughout the entire paper again.
6. For the Fig. 6, the gene names should be added in this figure. Why were these genes chosen for qTR-PCR validation?
Experimental design: No problems about the experimental design.
Validity of the findings: This research demonstrated the melatonin-regulated drought tolerance in naked oat seedlings associated with plant hormone signal transmission pathways including ABA and IAA pathways.
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 TRANSCRIPTOMICS REVEALS NEW INSIGHTS INTO MELATONIN-ENHANCED DROUGHT TOLERANCE IN NAKED OAT SEEDLINGS
Review round: 1
Reviewer: 3

Output:
Basic reporting: - Language is clear, unambiguous, and professional
- Sufficient and relevant literature is cited
- Article structure, figures, and tables are professional and properly structured
- Confirmed that raw RNA-Seq data is available in the NIH SRA as indicated in the paper
- Article is self contained with a clear research question and appropriate background to understand the research question and motivation for it
- Results, methods, and conclusions are clearly described and easily understood
Experimental design: - Scope is appropriate
- Research question is clear, well-defined, relevant, and meaningful.  Connection to existing literature is made
- Methods are detailed (save one issue, explained below) and clear
- Design of the RNA-Seq experiment is appropriate for the question
- Analysis and interpretation of the RNA-Seq results are clear and reasonable

My one caveat is that the Methods section on the RNA-Seq experiment does not explain how the actual sequencing was done.  In other papers, there is usually some text such as:

"mRNA selection, library preparation and sequencing was performed by the Cornell University Life Sciences Core Facilities on an Illumina GAIIx sequencer according to manufacturer specifications. Briefly, mRNA was selected using oligo(dT) probes and then fragmented using divalent cations. cDNA was synthesized using random primers, modified and enriched for attachment to the Illumina flowcell. We sequenced one 60-cycle paired-end lane and two 87-cycle paired-end lanes, generating ∼102.6 million reads for a total of 8,150 MB of sequence." (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014202#s2)

"After checking for the quality of RNA with an Agilent 2100 bioanalyzer, samples of nine resistant and nine susceptible mosquitoes were pooled and one RNA-seq library was prepared from each pool. Paired-end Illumina libraries were prepared and run for 80 cycles each end by the Expression Analysis Core at the UC-Davis Genome Center using standard Illumina procedures. Libraries were run at a concentration of 4–5 pM." (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044607#s2)

Secondly, there was no discussion of how the sequencing data were processed prior to running DESeq2.    How were the data filtered to remove low quality reads?  Were they trimmed?  How did you do the alignment and/or transcriptome assembly?

I would propose that the authors deposit their generated transcriptomes and associated transcript counts in an archive such as NIH GEO.
Validity of the findings: - Underlying  data have been provided
- Statistical analyses are robust and valid
- Conclusions are well-stated, linked to the original research question, and supported by the results
Additional comments: Thank you for the opportunity to read your paper.  It was a very interesting study and clear from your results that melatonin could provide to be a valuable resource for drought stress resistance.  I appreciate your emphasis on explaining the mechanisms behind its actions.  The paper is well written and easy to read.


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 TRANSCRIPTOMICS REVEALS NEW INSIGHTS INTO MELATONIN-ENHANCED DROUGHT TOLERANCE IN NAKED OAT SEEDLINGS
Review round: 2
Reviewer: 1

Output:
Basic reporting: OK
Experimental design: OK
Validity of the findings: OK
Additional comments: OK


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 TRANSCRIPTOMICS REVEALS NEW INSIGHTS INTO MELATONIN-ENHANCED DROUGHT TOLERANCE IN NAKED OAT SEEDLINGS
Review round: 2
Reviewer: 2

Output:
Basic reporting: All my questions have been addressed.
Experimental design: No additional comments
Validity of the findings: No additional comments
Additional comments: No additional comments


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

Input:
Title: COMPARATIVE TRANSCRIPTOMICS REVEALS NEW INSIGHTS INTO MELATONIN-ENHANCED DROUGHT TOLERANCE IN NAKED OAT SEEDLINGS
Review round: 2
Reviewer: 3

Output:
Basic reporting: - Lines 118 - 122 are very repetitive and could be explained more succinctly

- I was able to access the raw sequencing data in the NCBI SRA using the provided project number.
Experimental design: - The methods are still insufficiently detailed and
    - Need to give the database, accession number, genome / gene set versions, and any relevant citations on line 129
    - How were the reads cleaned?  With what program?  What parameters were used?
    - Need details on the qRT-PCR experiments beyond just the generation of primers.

- The Results subsection for the transcriptome analysis described a de novo assembly with Trinity.  This does NOT match the methods which describes aligning the reads to the genome.  Further, Trinity is not cited.
Validity of the findings: - I do not see statistical analyses supporting the conclusions in the first two result subsections.  The increase or decrease is maybe less important than whether the differences are statistically significant.
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 TRANSCRIPTOMICS REVEALS NEW INSIGHTS INTO MELATONIN-ENHANCED DROUGHT TOLERANCE IN NAKED OAT SEEDLINGS
Review round: 3
Reviewer: 1

Output:
Basic reporting: No comment
Experimental design: Description of analysis of RNA-Seq data in the Methods is now consistent with the Results.  Trinity is mentioned in both places.
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: HAPPINESS, DEPRESSION, PHYSICAL ACTIVITY AND COGNITION AMONG THE MIDDLE AND OLD-AGED POPULATION IN CHINA: A CONDITIONAL PROCESS ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Authors reported on a conditional process analysis on the happiness, depression, physical activity and cognition among middle and older people in China.

I went through the manuscript and I found that overall, it is suitable for publishing in the Peer J, but I have some major methodological concerns and other issues that the authors need to address before I can accept the manuscript for publication.

Though the paper seems properly organised, it is not and easy to follow. Some issues are not clearly defined or presented (e.g., hypotheses/research questions), which makes it difficult to understand the various parts of the manuscript.

The problem is the lack of proper familiarity with the English language and recommend that the entire article should be corrected by someone who is a professional editor (lines 14-15, 41-42, 48, 53, 56, 58 contains errors and others have no meaning like lines 54-55 or it seems they do not have a common tense, is it present or present perfect; also, lines 61-67 need to be rephrased and the hypothesis needs to be distinctively formulated).

Authors should consider adding more info on background and methods units of the abstract (i.e., questions used in the questionnaire - how many/what kind, procedure they used in the study).

In the entire manuscript the info should be better presented as to raise the interest of the readers. The methods and the results sections look like a string of numbers/percentages, instead they should be presented in an attractive way.

The quality of the images is good enough, but they are quite small. I don’t know if this version has lower resolution than the final version. If not, images should have better resolution in its final size.
Experimental design: The methods seem sufficiently described in this section.
The date of the approval is not given by the authors.
The tense of the used verbs should all be in past (line 93 – “happiness is…”)
Line 96 needs rephrasing, something like The...scale was used to assess depression.
For the control variables it would be better to use a figure/table to illustrate them, maybe using colours or other attractive issues. The paragraph here is somehow boring when it should be presented in an interesting and attractive way to the reader.
Validity of the findings: In Results section, the authors should consider trying to make explanations here less boring and in a better English.

It would be better to have seen more use of terms like 'originality' and 'significance'. Identify what is new in this study that may benefit readers or how it may advance existing knowledge or create new knowledge on this subject. There should be a clear conclusion on why the research findings are significant for health subject and could be used for the help of people in this situation.
Additional comments: Thank you for the opportunity to read your work. This is an interesting topic that can be considered by readers. Nevertheless, there are some concerns with the present manuscript that would need to be addressed for the paper to be able to achieve its potential.

Though the paper is properly organised, it is not and easy to follow. Some issues are not clearly defined or presented (e.g., hypotheses/research questions, methods, results), which makes it difficult to understand the various parts of the manuscript.


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

Input:
Title: HAPPINESS, DEPRESSION, PHYSICAL ACTIVITY AND COGNITION AMONG THE MIDDLE AND OLD-AGED POPULATION IN CHINA: A CONDITIONAL PROCESS ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The idea of the article is good, but the research is sloppy by the authors. The article needs a major overhaul. Beyond the information in the content of the article, the general framework should be reconstructed. I would like to review the article again after the authors have carefully reconsidered the research.

The introduction should be rewritten. The material and method are sloppy. Completely rewrite. Rewrite Table 1.
Experimental design: Experimental design needs to be explained in more detail.
Validity of the findings: Findings need to be rearranged.
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: HAPPINESS, DEPRESSION, PHYSICAL ACTIVITY AND COGNITION AMONG THE MIDDLE AND OLD-AGED POPULATION IN CHINA: A CONDITIONAL PROCESS ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article is written in english satisfactory and it has sufficient studied literature.
I consider a more rigorous explanation  of figures and tables is welcome.
Experimental design: In my opinion the experimental design is within normal limits.
I suggest just a little bit accurate description to the questionaire.
Validity of the findings: Validity is ok. Like I said before is an interesting result of correlation beetween happiness, depression and physical activities, in this country.
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: HAPPINESS, DEPRESSION, PHYSICAL ACTIVITY AND COGNITION AMONG THE MIDDLE AND OLD-AGED POPULATION IN CHINA: A CONDITIONAL PROCESS ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Thank you for providing this comprehensive work.
The authors have presented an improved version of the manuscript.

The introduction provides a proper background of the topic. The manuscript is well-structured, and it is easy to follow the sections.
The quality of the images is good enough, but I don’t know if the reviewing version has lower resolution than the final version. If not, images should have better resolution in its final size.
It seems that the English is technically correct.

I can see that the key words are missing.
Experimental design: The experimental design meets the scope of the journal, and it is relevant to the community.
Methods are described detailed enough.
Validity of the findings: The results and the conclusions are quite interesting and well-discussed. All data are provided.

The authors have adequately addressed all my comments. I have no further suggestions.
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: HAPPINESS, DEPRESSION, PHYSICAL ACTIVITY AND COGNITION AMONG THE MIDDLE AND OLD-AGED POPULATION IN CHINA: A CONDITIONAL PROCESS ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: First of all, congratulations to the authors. The research idea and design is nice. The research design looks good.

Introduction, method, statistical analysis and discussion of the findings in the research were done very well. The results of the research provide an innovative perspective by contributing to the literature.

I think that the quality and content of the pictures in the text should be improved
Experimental design: Really good.
Validity of the findings: Really good.
Additional comments: No additional comments