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: EVALUATING ACOUSTIC SIGNALS TO REDUCE AVIAN COLLISION RISK
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. Questionable relevance of experimental context for window and light-mediated collisions

The authors frame their paper in the context of declines in bird populations due to people, stating that collisions make up a meaningful part of that mortality. I don't disagree; collisions lead to hundreds of millions of deaths annually in the US along (e.g. Loss et al. 2015). However, the vast, vast majority of those collisions occur because of glass, light, or a combination of the two. Unfortunately, the results of this study don't seem applicable to these scenarios--as the authors state in the discussion, "sound is unlikely to reduce (or may even increase) the risk of a collision" with windows (lines 376-377) or when artificial light is involved (line 381). And the experimental set up (a looming black object in a flight chamber) is very different than, e.g., a window.

Relatively speaking, a tiny amount of collisions occur because of birds striking a solid, non reflective object. For example, Loss et al. 2015 estimate that there are 234,000 annual collisions with wind turbines in the US, compared to 599 million collisions with building windows. Mitigating these collisions is of course a worthwhile endeavor, but I find it disingenuous to frame the study in the context of the "hundreds of millions of bird deaths" (line 43) when sound doesn't have relevance for--or may even worsen--the vast majority of those events.
Experimental design: The experiment seems well designed.
Validity of the findings: 2. Statistical reporting

I found it odd that there were no figures or tables corresponding to the main results of treatment vs control flights (described in the text on lines 262-268). Please provide both figures and tabular results for these comparisons.

Especially in an experimental context, reporting estimated effect sizes (and confidence intervals) of the results is important. In the main text, the authors report F- and p-values but not effect size estimates and confidence intervals. I would ask the authors to please report effect estimates in every instance where F- and p-values are reported, and to provide confidence intervals in tabular form (e.g. in Table 3).

I reviewed the provided R script and data.
- The authors provide summarized measures for each flight (those given in Table 2), but not the original instantaneous data from which they derived these summaries. The data given is enough to reproduce the statistics, but not the calculation of those original metrics. Therefore, I am not sure if "all underlying data have been provided" as required by PeerJ.
- The statistical models from which the authors calculated whether the frequency and shape of the sound have an effect are mixed-effects models with bird ID as a random effect. This is not reported anywhere in the main text. The authors should fully describe their modeling approach.
- I was not able to run the code for any of the anova_test functions - all of the tests gave me errors.
- I did not see code corresponding to the main results of treatment vs control flights (described in the text on lines 262-268), but I may have missed it because of the errors.

3. Are birds just avoiding a loud noise?

From the results of the experiment, it is difficult to disentangle whether the behaviors the authors report when sound was played were due to the birds recognizing the obstacle earlier in their flight, or whether they were just avoiding the loud noise. The latter scenario would still be useful, but the authors frame their study largely with the former. Indeed, in lines 239-241, the authors state, "assessing distance from the speaker and from the obstacle separately allowed
insight into whether avoidance behaviors were in response to the warning signal or visual detection of the flight hazard." In the results, they report statistically significant effects on both measures (lines 264-268). The larger F-value for the distance from the speaker (28.6, vs 21.4 for the obstacle) suggests that birds may have more consistently avoided the speaker, although it seems like the average effect was likely very similar. So it seems essentially impossible to distinguish these two scenarios. Therefore, I am unconvinced when on lines 323-325 the authors conclude that the birds were "aware of the obstacle."

I also wonder if measuring distance from speaker is of limited use if "the speaker emitted a highly directional sound field that was approximately constant in amplitude at all distances from the speaker" (lines 162-163). If the sound was equally loud at all distances, how could the bird judge where the sound was coming from?
Additional comments: Line 79 - what is the evidence that insufficient visual perception is why those methods (decals, lights, lasers) don't work as well?

In the introduction, the authors talk generally about "birds" when discussing eye and skull morphology. I would prefer that they specify the groups of birds to which they refer (e.g. songbirds), as many birds do have excellent binocular vision (e.g. birds of prey).

Line 219: should be "for EACH FRAME of the flight" - it currently sounds like these metrics were calculated only once per flight.

Fig 4 - I like that all the data points are shown in addition to the error bars (although they are hard to see - suggest making the points a little lighter and the error bars bolder).


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: EVALUATING ACOUSTIC SIGNALS TO REDUCE AVIAN COLLISION RISK
Review round: 1
Reviewer: 2

Output:
Basic reporting: The is a well written and presented ms. It meets all of the criteria for  basic reporting.
Experimental design: The ms. fulfills all of the requirements of good experimental design as defined by the journal. The research question is well defined and  placed in a clear context and the analysis is rigorous.  However, I do have some concerns which are described in section 4.
Validity of the findings: This ms. meets all of the criteria
Additional comments: I have a concern about what the results actually show. Certainly in the presence of an obstacle the presentation of a sound does result in a change in the birds' flight paths. However,  is this necessarily an effect that occurs only in the presence of an obstacle? What is the basic mechanism that is operating? The authors have not shown that the sound results in the birds actually avoiding the obstacle, they have simply shown that their flight behaviour changes when a sound is present but this could actually enhance the probability of collision.

The assumption seems to be that projecting the sound at the bird increases its awareness of the obstacle. This may work by making a bird more visually aware of its surroundings, and in consequence the bird takes more note of what lies ahead. However, the sound may simply be changing a bird's flight behaviour through avoidance of the sound. A further control condition, in which the tarp obstacle is absent, may sort out whether the birds are seeking to avoid the sound rather than the sound  acting to alert the bird  to detect an obstacle using visual cues. If a bird behaves the same when sound is given regardless of the presence of the obstacle then this would suggest that its effect is not specifically to do with collision avoidance.

A related problem arises in the use of the term "warning signal", as in lines 99 and 113, but also elsewhere.  To be a "warning" signal  the bird needs to learn a pairing of the sound with the obstacle. The experimenter assumes that a sound will warn the bird, but what can it warn the bird of? The association between a sound and a sheet of tarpaulin is unlikely to be innate, such an association would have to be learned. In humans, warning signals are culturally determined, we learn  what a warning signal is, we learn that it is a sound that carries specific information. If we have not learnt the association then an un-predicted acoustic signal may simply alert/arouse our attention, but it does not warn us.  I would suggest the authors consider rewriting some of the ms. so as not to use the idea of warning. At root, this is getting at the difference between the sensory salience of a signal (that is the features that are most likely to be detected; e.g. manipulation of  frequency, sound shape, volume) and its cognitive salience,  i.e. what does the bird interpret that signal to be?.  Does it actually warn of something specific or does it have a non-specific arousal function?


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: EVALUATING ACOUSTIC SIGNALS TO REDUCE AVIAN COLLISION RISK
Review round: 1
Reviewer: 3

Output:
Basic reporting: It is an interesting manuscript on collision avoidance in birds. A not so common experimental approach which must be acknowledgment
Experimental design: I did not find any shortcoming in general. They provide a good enough description
the only problem for my is that they did not conducted any experiment on habituation,

The potential individual variability in responses must be adressed
Validity of the findings: I have some doubt about habituation and the effect of individulas varience in behaviour
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: EVALUATING ACOUSTIC SIGNALS TO REDUCE AVIAN COLLISION RISK
Review round: 2
Reviewer: 1

Output:
Basic reporting: Please mention in the abstract that the results of this study most applicable to collision scenarios with solid non reflective objects, and not for window/glass or when artificial light is involved.

Regarding the R script:

(1) All the code ran successfully on my machine.

(2) The data paths are given as local paths on Robin Thady’s computer. For example:

deltaV <- read.csv("/Users/robinthady/Desktop/Thady manuscript/Raw Data/deltaV.csv")

I would suggest rewriting the code so only relative paths are used, which will make it easier for a user to run the script on their own machine after specifying a working directory.

Regarding the raw data provided:

I had a look at the “Bird_tracking” data folder. I thank the authors for including the raw data. However, I found the data difficult to decipher. I could not find a readme or any other document describing how the data are structured and what each directory and file represents. Please provide this information, otherwise having provided the data will ultimately of limited use. It would be helpful to provide a script showing how the flight data can be processed to obtain the summaries that went into the main analysis.
Experimental design: The paper satisfies all primary requirements.
Validity of the findings: The paper satisfies all primary requirements.
Additional comments: I think the authors for a thorough and well done revision.


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

Input:
Title: ESR2 GENE VARIANTS (RS1256049, RS4986938, AND RS1256030) AND THEIR ASSOCIATION WITH BREAST CANCER RISK
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript titled as “ESR2 gene variants (rs1256049, rs4986938, and rs1256030) and their association with breast cancer risk” is reviewed and the points that need to be checked are listed below:

-Eventhough the language used in the article in general is clear the terminology used in some parts are not mentioned in a traditional way (for example Line 60-61 bound sites, Line 66-67 cancers express progesterone receptors, line 183-184 cirrhosis biliary, etc) .

-Also in line 46 a nonrelated statement “Add your abstract here” was found in the mansucript.

-In the case of haplogenotype it is strongly suggested to use the regular haplotype or haplogroup terminology. And also in results and discussion part it is better to  show this haplogroups by defining the order of the SNPs. For example in line 139 haplotype GGGACT, in here it would be better to show the order of the SNPs and/or only alleles may be included, in general literature it is not common to show it this way. The whole text should be checked for the mentioning of  haplogroups/haplotypes.
Experimental design: In materials and methods section in order to understand the method well text may include the full method used in experimental approach. Restriction digestion  analysis was not mentioned in the text but in the table. So the explanation of the technique is weak. It would have been also good to see the restriction digestion results on the gel as a figure /figures for each SNP.
Validity of the findings: The aim of the study was stated clearly, there wasn’t any problem with the statistical approach that was used in the text.
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: ESR2 GENE VARIANTS (RS1256049, RS4986938, AND RS1256030) AND THEIR ASSOCIATION WITH BREAST CANCER RISK
Review round: 1
Reviewer: 2

Output:
Basic reporting: Overall, the manuscript is well written with a clear and concise English. The structure, figures and tables are relevant to the text. Mainly the introduction is relevant and almost all publications were referred. The 4 publication I listed below are missing in introduction and discussion parts. It would be better if the authors will refer these articles:
1. Al-Eitan LN, Rababa'h DM, Alghamdi MA, Khasawneh RH. Association between ESR1, ESR2, HER2, UGT1A4, and UGT2B7 polymorphisms and breast Cancer in Jordan: a case-control study. BMC Cancer. 2019 Dec 30;19(1):1257. doi: 10.1186/s12885-019-6490-7.
2. Gallicchio L, Berndt SI, McSorley MA, Newschaffer CJ, Thuita LW, Argani P, Hoffman SC, Helzlsouer KJ. Polymorphisms in estrogen-metabolizing and estrogen receptor genes and the risk of developing breast cancer among a cohort of women with benign breast disease. BMC Cancer. 2006 Jun 29;6:173. doi: 10.1186/1471-2407-6-173.
3. Treeck O, Elemenler E, Kriener C, Horn F, Springwald A, Hartmann A, Ortmann O. Polymorphisms in the promoter region of ESR2 gene and breast cancer susceptibility. J Steroid Biochem Mol Biol. 2009 Apr;114(3-5):207-11.
4. Tsezou A, Tzetis M, Gennatas C, Giannatou E, Pampanos A, Malamis G, Kanavakis E, Kitsiou S. Association of repeat polymorphisms in the estrogen receptors alpha, beta (ESR1, ESR2) and androgen receptor (AR) genes with the occurrence of breast cancer. Breast. 2008 Apr;17(2):159-66.
Experimental design: Even though the overall description of Method and statistical analyses are sufficient, there is a missing point in "Materials&Method" part: It was not clearly indicated which method was used after PCR during genotyping of variants.
Even though the sample size of healthy and patient samples are not low, it would be better if the authors indicate the power analysis of the study.
Validity of the findings: Even though there are many studies that search the association between the ESR2 gene variants and breast cancer in various populations, the manuscript shows this association for the first time in Mexican population.
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: ESR2 GENE VARIANTS (RS1256049, RS4986938, AND RS1256030) AND THEIR ASSOCIATION WITH BREAST CANCER RISK
Review round: 1
Reviewer: 3

Output:
Basic reporting: No comment
Experimental design: The larger population size is always powerful for associaton studies, the studied population size  is relatively big enough for this study compared the cohorts with similar studies. The selection criteria of the patients and genotyping methods were well defined and successfully obtained. The selected poplymorphisms and allele frequencies are as important as the size of the population.
The selected polymorphisms such as rs1256049 has very low MAF values in Mexican population . Considering very low number of cases for carrying this allele , population size creates limitation. Therefore, the selection criteria of studied polymorphisms should be explained.
Validity of the findings: Estrogens hormones with their regulating roles in the development of  mammary gland and overexpression patterns in breast cancer makes these hormones as a strong candidate for cancer pathogenesis. ESR2 gene have been associated with breast cancer and this gene is a favourable target for these studies.

ESR2  gene polymorphisms and and BC risk have been inconclusive since the regulatory roles of different polymorphic variants on the expression of ESR2 gene is mainly uncertain. Although  there are associations, the opposite finding are also available in different studies.
In this study, the research group investigates the association of ESR2 variants (rs1256049, rs4986938, and rs1256030) in breast cancer for Mexican women population with breast cancer risk. Thus, the aim of this investigation was to determine the frequency and association of ESR2 variants (rs1256049, rs4986938, and rs1256030) in Mexican women with breast cancer risk.

For 22 studies including 22,994 cases and 30,514 controls, There was no significant association between rs1256049 and cancer risk in the overall population but not in Asians  whereas negative results were obtained for breast cancer in any genetic model.

Considering the allele frequencies, the MAF value in the study cohort of the rs1256049 variant appears to be very low. Therefore, the distribution of alleles within the cohort may be considered insufficient to determine the genotype-phenotype correlation. This limitation may be the main reason why a significant association was not found for this variant.

Authors found that rs1256049 and rs1256030 were found to be strong linkage disequilibrium in the control samples. The available number of cases for carrying different variations with this allele is very limited and LD studies should be reconsidered for this variant. This could have been highlighted in the article.
The application of haplotype and haplogenotype analysis in the study was a very good approach. However, the ESR2 gene is highly polymorphic with 720 SNPs (www.snpper.chip.org). There are many studies of association of ESR2 gene variants with breast cancer in the literature. Other variations located close to the LD could have been taken into account when performing the haplotype and haplogenotype analysis. The number of analyzed variations maybe limited to reflect more extensional results on the haplogenotype in a given population.

Different studies were also conducted in different population cohorts regarding the variations within the scope of the study. Conflicting results have been obtained regarding its association with breast cancer. This study conducted in the Mexican population should have been compared with the data from other individuals on a population basis. The similarities and differences should be discussed in the article and comparative  analysis methods may useful to reveal population based differences.
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: DIFFERENT PRUNING LEVEL EFFECTS ON FLOWERING PERIOD AND CHLOROPHYLL FLUORESCENCE PARAMETERS OF LOROPETALUM CHINENSE VAR. RUBRUM
Review round: 1
Reviewer: 1

Output:
Basic reporting: Level of langauge is acptable and literature  reference is sufficiend to describe problem which presented by authors
Experimental design: There is some problem in part of materials and method. Detailed comments and suggestions were added in atached file
Validity of the findings: Article is interesting and quite good and will be better with added suggested information
Additional comments: Interesting work for those who like ornamental plants

Review of peerj-69279 manuscript – suggestion for authors (from the attached PDF)
 In part Materials & Methods Plant material and experimental layout authors only how the plant
were look before trimming process but they do not show it after it. There is also lack of
information how the plant material was protected for drying process. In line 93-94 authors also
write they used home compost but they forget to put information about pH of it and some basic
chemical characteristic such C:N ratio content of N, C, P and K. Authors used in experiment also
organic fertilizer but they do not write what was it and it chemical characteristic. There is also
lack of information about size of pot which were used and how much medium was putted to each
pot. In section measurements authors write they measured chlorophyll fluorescence but they
didn’t write what was the fluorimeter they used and described the measurement protocol and
haven’t write information did they adapt leaves. If yes for how long.


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: DIFFERENT PRUNING LEVEL EFFECTS ON FLOWERING PERIOD AND CHLOROPHYLL FLUORESCENCE PARAMETERS OF LOROPETALUM CHINENSE VAR. RUBRUM
Review round: 1
Reviewer: 2

Output:
Basic reporting: "Pruning" is a simple and efficient way to control the flowering period, in this paper, Loropetalum chinense var. rubrum was pruned in different degrees. This result has certain significance for regulating the flowering of woody ornamental plants, but there are some problems in the article that need to be revised and improved.
1. Materials and methods
1) The description of pruning is not clear, and the difference between the methods of various pruning degrees is not clearly indicated. It is recommended to add a schematic diagram of pruning method. In particular, it is necessary to explain the state of the plant before pruning, whether it has no flower bud or has a flower bud? And also, the age of the plant materials, the reasons for selecting these varieties etc. should be explained in detail. These will affect whether the conclusions of the experiment are generalizable.
2. In the results
1) The error value in Figure 2 is too large, it is recommended to increase the repetition to reduce the error.
2) Please check the description of the data in Table 1 carefully. First, no unit is added in the table. Second, does the 0 day in the table mean that the flower began to bloom after 0 days of pruning? This result is unconvincing.
3) There is no clear description of 'the early, peak and final flowering stages' in JIP-test curve during anthesis.
Experimental design: The materials and methods used should be described in detail, especially the choice of materials.
Validity of the findings: no comment
Additional comments: Pruning is very important for woody ornamental plants to control flowering and plant type. The results of this paper can provide a good theoretical support for the cultivation and management of woody ornamental plants. However, the data and detailed description need to be further deepened in the article, and it is also suggested to increase the flowering phenotype of the pruned plants, so that readers can intuitively have a perceptual understanding of the pruning 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: DIFFERENT PRUNING LEVEL EFFECTS ON FLOWERING PERIOD AND CHLOROPHYLL FLUORESCENCE PARAMETERS OF LOROPETALUM CHINENSE VAR. RUBRUM
Review round: 2
Reviewer: 1

Output:
Basic reporting: English language is correct and literature references well choosen to describe problem which is presented in paper
Experimental design: All previous mention mistakes and problems which were noticed was corrected and eliminated by authors
Validity of the findings: Very interesting paper for producers of ornamental plants
Additional comments: You prepare very interesting paper which some scientific potential for people who are interested in subject of ornamental plants


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 IMPACTS OF BOVINE MILK, SOY BEVERAGE, OR ALMOND BEVERAGE ON THE GROWING RAT MICROBIOME
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. I could not access https://gitea.agresearch.co.nz/JAUREGUIR/Microbiomics

2. I did not see a link to a public repository in which the authors deposited their data.
Experimental design: 1. While the manuscript is of potential interest, this choice of dietary treatment greatly distracts from its significance. The authors should have chosen milk, milk formula and soy formula.

2. Both males and females mut be studied.

3. The authors need to state how random assignment to groups was achieved.

4. The authors need to test for heterogeneity of variances prior to conducting statistical analysis.

5. Why use rats as a model? This study should have been conducted in humans.

6. The observation that diet alters the gut microbiome is not novel.

7. I might have overlooked it, but how did the authors account for cage effects.

8. The study is descriptive and does not offer insights into functional consequences.
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: THE IMPACTS OF BOVINE MILK, SOY BEVERAGE, OR ALMOND BEVERAGE ON THE GROWING RAT MICROBIOME
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see "additional comments" below to see all my comments and suggestions.
Experimental design: Please see "additional comments" below to see all my comments and suggestions.
Validity of the findings: Please see "additional comments" below to see all my comments and suggestions.
Additional comments: Cakebread et al. investigated the impact of bovine milk, soy beverage, or almond beverage on the growing rat microbiome. Two control groups were used (AIN-93G food, 20% casein protein; AIN-93G amino acids food). Animals on AIN-93G AA food were offered three diets (ultra-heat treatment [UHT] milk, and UHT soy and almond beverages) were offered for a period of 4 weeks.

General comments
Please make sure that you allow an easy identification of all 5 groups. For instance, it is difficult for me to guess which group in Figure 1 match the description of groups in the abstract and in the methods. I assume that AA water is the group with AIN-93G AA food that was not supplemented with either milk, soy or almond?
I did not see anything about cecum weight or cecum weight contents, could you please explain why you did not study these variables? See this for a reference about these variables: https://pubmed.ncbi.nlm.nih.gov/28815303/

Line 59. It is Bifidobacteriaceae, as the authors rightfully placed in other areas.
Lines 145-147. Why exactly did you choose to offer the diets to the animals on AA food and not to the casein control group?
Line 155. Is there any reason why you choose caecum samples only?
Line 159. Caecum contents? Or did you use the whole tissue?
Line 177. QIIME, with capital letters.
Line 183. The incorporation of covariates is somehow complex (https://genstat.kb.vsni.co.uk/knowledge-base/tancova/; https://www.stat.purdue.edu/~bacraig/notes514/topic10a.pdf), in part for the possible differences in slopes among treatments. However, I do not see anything in the results or discussion about differences among slopes. See the barley paper mentioned above. Also, is there any reason why you decided not to use baseline microbiota composition as a covariate in the microbiota analysis?
Lines 198-199. Is the casein water group the same as the UHT milk treatment group? How do you explain this finding? In other words, how the AA water and AA almond groups ended up related to lower body weights?

Lines 257-258. Please re-structure the discussion, these two lines look odd by themselves. Also, the next paragraph of 5 lines could also be incorporated more nicely with other parts of the discussion.
Line 259. Please make sure you only use the correct names associated with the right taxonomic level. Bifidobacteria is incorrect.
Line 260. Why do you talk about UHT milk fed groups, in plural? I had the impression that only one treatment group received AIN-93G AA food plus UHT milk.
Line 324. Effects? Bacteroidetes? You are talking about taxa at the phylum level, am I correct?
Line 325. Does not this paragraph contradict the previous statement in lines 257-258? Please explain.
Line 337. What do you mean by “linear labelling”?
It would be nice to incorporate a paragraph describing the limitations of this study, for example the use of only one technique to analyze the microbiota, or the fact that the authors decided not looking at the prediction of metagenome functional content, e.g. using PICRUSt.

References
Please be consistent with the references, in some the first letter of each word is capitalized.


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: METAGENOMIC INSIGHTS INTO SURFACE WATER MICROBIAL COMMUNITIES OF A SOUTH ASIAN MANGROVE ECOSYSTEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript titled “Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem” describes the structure and function of microbial communities in the surface water of selected sampling stations with comparable salinity in Sundarbans mangrove estuary situated in the north-eastern coast of India. The authors took a metagenomic approach and used nanopore sequencing chemistry to decipher the microbial structure and function in the above-mentioned samples. The detailed metagenomic analyses revealed the widespread dominance of proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes, and Cyanobacteria showed site-specific abundance. Moreover, Prasinophyceae, Saccharyomycetes, and Sardariomycetes were found to be the abundant eukaryotic class in the studied samples. Functional annotation analyses revealed the identification of metabolic pathways for carbohydrate, amino acid, nitrogen, and phosphorus metabolism across all the studied stations. Furthermore, antibiotic resistance and heavy metal resistance/mobilization pathways were also identified within the dataset. Together the results presented in the manuscript are important and can be explored further through extensive laboratory experiments. Unfortunately, authors completely ignored published and available pieces of literature from the same mangrove wetland estuary and this makes the present study considerably weak. They have only cited their own research works and have not even considered discussing other published research articles on mangrove microbial community analysis in India (Sundarbans, Goa, Kerala, etc.).  A comparative analysis with published and available microbial community diversity analysis from this and other mangrove wetland systems might help authors to strengthen their results. The manuscript in its present form is not acceptable and warrants further comparative analysis with existing pieces of literature.
Experimental design: 1.	Please describe the logic behind the selection of sampling stations based on comparable salinity. In Sundarbans, salinity has a temporal behavior and therefore raises a question of why authors didn’t look into the temporal variability of microbial communities in these sampling stations?
2.	Line 117: “pristine region”--- what does this mean? Did the authors use any marker to select this as a pristine environment?
3. Line 119-120: “No human activities are permitted within the pristine regions.”---
Please define pristine area? Moreover, as per the site selection, they are not in the core area, where human activity is restricted. Also, many of the sampled locations are often used for tourist activities. Please clarify and amend accordingly.
4.	Line 125: ’11 stations’--- I couldn’t find any mention of biological or technical replicates? Did the authors consider the collection, processing, and sequencing replicates???
5.	Line 114: When in pre-monsoon 2019? Please mention the month as the pre-monsoon extends for a few months!!!
Validity of the findings: Major comments:
1.	Figure 1: The map of the sampling sites lacks proper annotations and wrongly represents the name of estuaries.  What is shown here as the Thakuran estuary is actually the Matla and vice-versa. Also, the name of the rivers in the upper reaches is omitted, making it incoherent. The map scale is too low is unable to accurately determine the character of the sampling stations. Moreover, the coordinates of the 11 sampling sites are missing and it is unclear how the other sites among the 250 do not have comparable salinity levels. Also, there is a slight conflict in statements in lines 117-119 where the region is referred to be under 'heavily protected reserved forest' region yet states that they are inhabited and also geomorphologically this region is predominantly under the influence of tidal estuarine ecosystem rather than the coastal ecosystem. Even the statement of the entire region being inaccessible during the monsoons is largely exaggerated.
2.	In the Abstract, the authors mention that besides Proteobacteria and Firmicutes, other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes, and Cyanobacteria showed site-specific abundance. However, this has not been extensively addressed further in the manuscript. For example, finding an abundance of Euryarchaeota in Sundarban mangrove has been reported previously and has been implicated for bioremediation [Bhattacharyya et al. (2015), Archaea (DOI: 10.1155/2015/968582); Mukherji et al. (2020), Ecotox. Env. Safety 195:110481]. Please discuss such possibilities in the present study.
3.	Introduction (line 90-91): “Even though the instances…., very little is known about factors responsible for rapidly increasing abundances of acquired pathogenesis….the Indian Sundarbans.” --- Several articles are available on microbial community diversity and their correlation with the anthropogenic activities in the sediments of Sundarban (Mukherji et al, Ecotox. Env. safety 2020; Bhattacharyya et al. Sci Total Env 2019; Basak et al. Genomics Data 2016; Bhattacharyya et al. Archaea 2015; Basak et al. Genomics Data 2015; Basak et al. Microbiol Ecol 2015). It’s clear from the published literature and the data presented in the present manuscript that there exists considerable similarity in the microbial communities of the sediment and surface water of Sundarbans mangrove. Please discuss and compare published datasets while introducing your hypothesis. This will not dilute your contribution rather give strength to it.
4.	Line 193-197: Unit of salinity is not clear from descriptions. In line 193, it seems salinity is presented in PSU (Practical Salinity Units). While in line 196, salinity is presented in mg/L. Please clarify and maintain uniformity throughout the manuscript.
5.	Line 217-225: Please provide a quantitative comparative assessment (% reads etc.) to facilitate readers to understand variations comparatively.
6.	Section ‘Microbial community structure’ (line 214-242): Although archaea are reported as significantly abundant in the microbial community, no detail has been provided about their spatial variation or abundance. Please provide details.
7.	Line 270: Description of genes responsible for ‘anaerobic degradation is provided. However, no genes involved in aerobic degradation have been discussed. Didn’t the authors find any such metabolic genes within the dataset? As this study involves surface water, it is expected to identify genes involved in aerobic metabolism. In any case, please discuss this in detail.

Minor comments:
1.	BioProject number PRJNA786468 is not accessible for review purposes.
2.	Please check the language throughout and remove typos.
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: METAGENOMIC INSIGHTS INTO SURFACE WATER MICROBIAL COMMUNITIES OF A SOUTH ASIAN MANGROVE ECOSYSTEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: Methods:

Sunderban has a number of estuaries, what is the specific reason for sampling from Thakuran and Matla estuaries?

The accession number of the samples in MG-RAST is missing. Raw reads submissions to NCBI are also missing.

As per the methods, samples were collected from 250 stations, however, the results indicate that there are only 11 datasets. Kindly provide how were the samples pooled or managed.

Results:

In the results section, functional annotation identified "cold and heat shock" resistance, what could be the reason?

Have you done Differently Abundant Genera/Gene (DAG) analysis? It seems to be missing. Or what is the reason for avoiding DAG analysis?

Discussion:

Several ARGs were identified in this study, was there any association between the abundance of those ARGs and the antibiotics used in the Sunderban (or nearby areas)?
Experimental design: The MS is interesting since it's one of the first metagenomic studies to do waste analysis from mangrove forests in India (Sunderban). However, there seems to be a lack of experimental design as no proper comparative analysis could be seen throughout the MS. Furthermore, statistical analysis is also lacking.
Validity of the findings: The beginning part of the abstract seems to convey the message that ARG and heavy metal resistance are enriched due to climate change. Although it could be true to some extent, the enrichment could be mainly due to pollution rather than climate change.

The reporting is simply a catalogue of the microbiome and the diversity of ARGs, it does not provide any information on the reasons or the patterns of occurrence. Hence, the abstract should be more informative and novelty is needed.
Additional comments: The MS may send for a major revision


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

Input:
Title: METAGENOMIC INSIGHTS INTO SURFACE WATER MICROBIAL COMMUNITIES OF A SOUTH ASIAN MANGROVE ECOSYSTEM
Review round: 1
Reviewer: 3

Output:
Basic reporting: The article was well-written in clear and unambiguous, professional English throughout the main text. Nonetheless, a few scientific names were misspelled (please, verify).
The cited references are adequate, up-to-date, and cover the main theme of the article (Mangroves, Microbiome, and Metagenomics). The article is well-structured, the figures are clear, self-explained, and sufficient to graphically depict the main obtained results. Furthermore, Supplementary Table details the metagenomic results. Raw data is shared as a BioSample deposit in NICBI. The objectives are clear and are achieved and well-discussed.
Experimental design: This is an original primary research study and falls within the aims and scope of the PeerJ journal. The research question is well-defined, is original, and relevant, clearing stating how the study fills the posed knowledge gaps. The study is carried out using rigorous technical standards (e.g.: adequate sampling sufficiency, and replicates), the methodology is described in detail and permits the replicability of the study.
Validity of the findings: I consider this is an original study, clearly demonstrating the feasibility of the use of Nanopore Technology to shotgun metagenomics. The results are robust and statistically controlled, and the conclusions respond to the posed objectives in an adequately manner.
Additional comments: I would like that the authors clarify to me the following doubts:

1. Why did the community structure analysis was restricted to the more inclusive taxonomical categories (genera are not analyzed and discussed, for instance)? Is there any technical restriction? If yes, why?

2. How may this study be used by policymakers in order to avoid or mitigate more environmental problems (e.g.: pollutants) in this important area?

3. How do you compare the Nanopore technology with Illumina Technology for performing shotgun metagenomics. How the former can be ameliorated?


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: METAGENOMIC INSIGHTS INTO SURFACE WATER MICROBIAL COMMUNITIES OF A SOUTH ASIAN MANGROVE ECOSYSTEM
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors have sufficiently addressed the reviewers' 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: METAGENOMIC INSIGHTS INTO SURFACE WATER MICROBIAL COMMUNITIES OF A SOUTH ASIAN MANGROVE ECOSYSTEM
Review round: 2
Reviewer: 2

Output:
Basic reporting: Authors addressed all the comments which i have raised previous review
Experimental design: Improved
Validity of the findings: Improved
Additional comments: No comments


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

Input:
Title: EFFECT OF NAPPING ON A BEAN BAG CHAIR ON SLEEP STAGE, MUSCLE ACTIVITY, AND HEART RATE VARIABILITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: This study evaluated effects of daytime napping comparing bean bag chair and urethan bed with multiple objective testing methods. The result of muscle relaxation and parasympathetic activation of bean bag napping was interesting.
However, the authors should address issues below.

1. In 'Participants and setting', authors employed power analysis. Although I understood that power analysis was employed to calculate sample size for this study, the expression is seemed to be unclear for the readers. Please make it clearer.

2. In Study design, authors should make a figure to explain how they employed this study. They employed multiple testing before and after napping, had testing during the napping and napping was consisted by 2 different types of bedding. This study is very complex. A figure explaining the study design will be very helpful for readers.

3. In Electroencephalogram and sleep stage scoring, authors noted that they did sleep stage scoring according to AASM rules. However, I believe that AASM manual recommends 6 EEG plus EOG and EMG with Mastoid reference, sleep stage 1,2,3,REM detection, 30s epoching. Therefore the method of scoring  should be different from AASM's. The authors should clarify how they scored. And they noted that their method is validated as Nonoue et al., 2017. If so, they should note that their method is same as Nonoue's.

4. The authors noted that they did not distinguish N1 and N2. However, in table 2, there are N1 and N2 both. Please be consistent.
Experimental design: Experimental design is excellent. Nothing to 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: EFFECT OF NAPPING ON A BEAN BAG CHAIR ON SLEEP STAGE, MUSCLE ACTIVITY, AND HEART RATE VARIABILITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The authors use clear, unambiguous and professional English throughout their article. They provide references and sufficient background information. The article is well structured. The layout and content of figures and tables is correct. The necessary research data is supplied. The article is self-contained with relevant results to the research question.
Experimental design: The topic of the article is within the scope of the journal. The research question is well defined, relevant and meaningful. The authors contribute to fill the identified knowledge gap and follow ethical and technical standards. Using the described methods the results can be replicated.
Validity of the findings: The underlying data is shared online and open to the public. The conclusions are well stated and connected to the research question.
Additional comments: The authors provide an excellent scientific article.


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: EFFECT OF NAPPING ON A BEAN BAG CHAIR ON SLEEP STAGE, MUSCLE ACTIVITY, AND HEART RATE VARIABILITY
Review round: 1
Reviewer: 3

Output:
Basic reporting: General comments:
I reviewed the article “Effect of napping on a bean bag chair on sleep stage, muscle activity, and heart rate variability”. The article aims to evaluate the effect of an bean bag chair compared with a traditional sofa-type chair manufactured with urethane on daytime napping and physiological parameters related to sleep.
Despite the present study indicated that the sleep architecture showed no significant difference between the two bedding conditions, the muscle activity of trapezium decreased and the LF/HF ratio during sleep decreased used an bean bag chair.
The manuscript is interesting and the topic has the potential to be interesting and useful from a scientific point of view. However, additional clarifications about the study design should be added. The main problem is that, in my opinion, is not clear when the authors made the actigraphic monitoring. In some parts of the article seems that is made at home the night preceding the experiment while in other parts seems that is made also during the nap in the laboratory. Clarify this aspect is extremely important to understand the results even if there are no differences for the sleep architecture.
Here below some specific comments.
Experimental design: MATERIALS AND METHODS
Participants and setting
How many participants for each group (BC vs UR)?
Line 124: please report Morningness-Eveningness Questionnaire instead of Morning-Eveningness Questionnaire.
Lines 126-128: specify the units of measure for all the variables.

Actigraphy recording
I don’t understand when the authors made the actigraphic monitoring. Reading the material and methods, I understood that it was made at home the night preceding the experiment while reading the results seems that was made also during the nap in the laboratory.
Validity of the findings: RESULTS
As I said previously, I don’t understand properly the results about sleep and related parameters. In fact in table 1 the authors said to report the comparison between sleep parameters from the preceding night and subjective scale scores for each bedding condition but I saw only the comparison between actigraphic sleep parameters in the two bedding conditions. Where were the sleep parameters of the preceding night? Where were the subjective scale scores? To obtain the actigraphic sleep parameters for the two bedding condition the authors used the actigraphy also during the nap in laboratory? If yes, they have to declare it in the study design. In addition, in the caption as well as in the description of the table 1 remove “No statistical differences…..” because was a repetition of the results and add the numerosity of the participants for each group (BC and UR).
Table 2 the same problem because there were the actigraphic sleep parameters for the two bedding conditions and the authors didn’t report that the actigraphic monitoring was made also during the nap in the laboratory. In case, add it. In addition, in the caption as well as in the description of the table 2 remove “Sleep efficiency-TST/SPT”, add the numerosity of the participants for each group (BC and UR), add units of measure when missing. Add in the description of the table 2 N1 and change in table 2 Flicker into CFF.
Table 3 add units of measure when missing and the numerosity of the participants for each group (BC and UR). Change type into napping condition.
Figure 2 specify that the red histogram was for BC group instead the blue histogram was for UR group and delete the period “The trapezius muscle demonstrates……” because was a repetition of the results.
Figure 3 specify that the red line was for BC group instead the blue line was for UR group and delete the period “Values in the panel……” because was a repetition of the results.
Additional comments: No comments


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

Input:
Title: EFFECT OF NAPPING ON A BEAN BAG CHAIR ON SLEEP STAGE, MUSCLE ACTIVITY, AND HEART RATE VARIABILITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript was properly revised.
Experimental design: nothing to point out
Validity of the findings: nothing to correct
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: EFFECT OF NAPPING ON A BEAN BAG CHAIR ON SLEEP STAGE, MUSCLE ACTIVITY, AND HEART RATE VARIABILITY
Review round: 2
Reviewer: 2

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


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 TYPE AND FERTILIZER RATE AFFECT WHEAT (TRITICUM AESTIVUM L.) YIELD, QUALITY AND NUTRIENT USE EFFICIENCY IN AYIBA, NORTHERN ETHIOPIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: General Comment
The research study is an extensive investigation that covers a much-needed area of knowledge. It commendably seeks to solve the issue of fertilizer use and application with regards to soil fertility and the quality of wheat grown in a part of Ethiopia.
However, several issues should be revised before the manuscript gets published.
Experimental design: Scope and concept

In the abstract, the authors stated that “Bread wheat (Triticum aestivum) is the most important staple crop…” This claim is seemingly untrue and should be completely removed. Though the region where this claim was intended for was not mentioned, the claim is invalid for world and for Ethiopia. Global rankings of the most important staple foods place Maize Corn and Rice above Wheat (https://www.worldatlas.com/articles/most-important-staple-foods-in-the-world.html). In Ethiopia, maize was reportedly more produced in the 90’s and 2000’s than wheat [Rashid, Shahidur. (2010). Staple Food Prices in Ethiopia. Michigan State University, Department of Agricultural, Food, and Resource Economics, Food Security Collaborative Working Papers.] Even the authors listed (in order) sorghum, teff, and maize ahead of wheat for the study region (line 153). Contrastingly, the authors mentioned in lines 44- 46 “Bread wheat (Triticum aestivum) is ONE OF THE MAJOR CEREALS, along with maize (Zea mays), teff (Eragrostis teff Zucc), barley (Hordeum vulgare) and sorghum  (Sorghum bicolor).” WHERE? IN THE WORLD? OR IN ETHIOPIA?

In lines 52-54, authors stated “However, wheat yields are WOEFULLY LOW, with a national average of 2.97 t ha-1 under farmers conditions”. How is “woefully low” defined? The word woeful should be removed

The study was conducted in a region of the Northern part of Ethiopia. In lines 140-141, it was only stated that “The area is among the potential wheat-producing regions in Tigray furnished with tepid to cool semi-arid agro-ecological zone”. The authors are yet to establish a good justification to use a research study conducted in that one region of the country to conclude for the whole country (lines 663-665). I think a more brief but effective justification should be included after line 141.
Validity of the findings: Lengthy manuscript
The manuscript is seemingly too wordy. Every section contains too much information; some of which are not required, and the required ones missing. The introduction covers 3 pages. The materials and methods cover 4. Results and discussions take around 13.5 pages. The conclusion consumes 1.5 pages with 3 massive paragraphs. This should be totally reviewed. The entire manuscript should be rid-off of information and data that is excessive or do not drive any point. An example is for lines 153-157 which speaks “extremely extensively” on the too-many crops (13) grown in the study region.

Discussions and unanswered questions.

The results and discussions section are summarily a declaration of the results obtained and results obtained in other published studies. Detailed descriptions that answer the question of “WHY?” where hardly mentioned. This should be revised in the entire discussion section.
For example, lines 323-324 states “The increase in the number of tillers in response to an increasing rate of NPSZnB blended fertilizer indicated the importance of balanced nutrients for better vegetative growth and crop development. In addition, all fertilized treatments significantly improved wheat total and productive tillers compared to the unfertilized control.” The question is WHY? Why the increase? What caused it? How did the fertilizers improve wheat production? Did they regulate the soil pH? Which micronutrients did they supply? Did they affect any soil circulation?

Same concerns are for the following lines amongst several others:
Line 332: “…the application of blended fertilizer has an advantage on 333 tillering capacity of bread wheat over the conventional application under Ayiba conditions…” HOW? WHY?
Lines 376-378: “The highest NKS and TKW may be due to the provision of balanced nutrients, which enhanced spike elongation and accumulation of assimilating in the grains and thus resulting in more spikelets per spike and heavier grains.” This looks like a technical discussion. It should be expatiated with reference to quality literature.
Line 387: “…The variation in NKS and TKW in both soil types as a function of fertilization indicated that different soils have various responses to different fertilizer rates and types.” HOW? WHY?
Lines 501-502: “Increasing grain protein and its strength has recently received greater attention due to their positive effect on bread and pasta products” HOW? WHY?
Additional comments: Grammatical disconnect and incomplete sentences

The introduction and several parts of the manuscript have twisted or unlinked sentences. These sections should be entirely revised for technicality and grammatical soundness and meaningfulness. Few are mentioned below:

Line 54: “…reasons for the low levels of wheat, yields are declining soil” The comma after wheat should be removed
Line 63-64: “In addition, at present, population rising and dietary pattern shifting linked to urbanization are causing to surpasses the demand for national wheat supply (6.3 Mt demand Vs. 4.6 Mt supply)”. This sentence should be re-written for clarity
Line 67: “… for the last several years” Should be removed and re-written with proper grammatical expression.
Line 68: “Although demand and production are not related yet, there is…” HOW?
Line 72: “…2023 (MoA, 2019). Thus, increasing domestic wheat…” The period should be removed. The latter sentence cannot stand without the former
Line 79: “The problem with fertilization indicated that the need for great…” “that” should be removed.
Line 80: “By doing so it is possible to increase the nutrient use…” A comma should be added after “so”

In addition, the use of professional titles for the cover page abstract "Prof." and "Dr.", except required by the journal is apparently unethical. Reviewers can view such as a case for winning favor or bias.


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 TYPE AND FERTILIZER RATE AFFECT WHEAT (TRITICUM AESTIVUM L.) YIELD, QUALITY AND NUTRIENT USE EFFICIENCY IN AYIBA, NORTHERN ETHIOPIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: I think this manuscript is interested and provide good findings. Unlike developed countries, Sub Saharan Africa lacks literatures and specialized systems which regularly monitor changes in nutrient budget. Therefore, it is an important contribution to the filed. Therefore, I suggest accepting the manuscript after considering my following suggestions and comments.
1.	The English language should be improved to ensure that an international audience can clearly understand your text. For example, the title which is the most important sentence for the manuscript has a mistake (affect NOT affects). I strongly suggest the author to do a very careful proofreading for the entire manuscript. There are so many problems in writing that it is difficult to continue reading the paper. I suggest you have a colleague who is proficient in English and familiar with the subject matter review your manuscript, or contact a professional editing service.
2.	The introduction is good and contains good information that paves the way for reaching the idea of the research. But this is a manuscript and not a doctoral thesis. I strongly suggest the authors to reduce this introduction to the half and only information that confirms the idea of the research. I also greatly missed the discussion of the recent findings of Elrys et al. (2019, 2020, 2021) which dealt with the nitrogen budget in Africa during the past five decades, as well as calculating the nitrogen fertilizer rate needed to achieve self-sufficiency of Africa by 2050. Please indicate their important results in the introduction and discuss their accuracy in the discussion section based on some of your results. You can find their papers through the following references:
a.	10. Elrys, A. S., M. K. Abdel-Fattah, S. Raza, Z. Chen, J. Zhou (2019). Spatial trends in the budget of nitrogen flows in the African agro-food system over the past five decades. Environmental Research Letters, 14: 124091.
b.	Elrys, A. S., Metwally, M. S., Raza, S., Alnaimy, M. A., Shaheen, S. M., Chen, Z., & Zhou, J. (2020). How much nitrogen does Africa need to feed itself by 2050? Journal of Environmental Management, 268.
c.	Elrys, A.S., E.-S.M. Desoky, M.A. Alnaimy, H. Zhang, J.-b. Zhang, Z.-c. Cai,…, Cheng, Y. (2021). The food nitrogen footprint for African countries under fertilized and unfertilized farms. Journal of Environmental Management, 279: 111599.
3.	Results and Discussion: I highly recommend the authors to separate this section into two sections. I mean the authors must introduce the results in a separate section and Discussion in another section. Regarding results, there is no need to present each attribute in a separate title. Please group them into groups and show readers your important findings to help them understand the message of your study.
For the discussion section, you can separate it into two subsections, the first section should discuss your important findings but please avoid repeating the results again. The second part of the discussion should be the implications of this study, you have good implications but the authors have to discuss them and not just mention it. Don't forget to link your repercussions with the large scale of Africa because, you know, nutrient depletion is not only a problem for Ethiopia, but for most of sub-Saharan Africa.
Experimental design: I think this manuscript is interested and provide good findings. Unlike developed countries, Sub Saharan Africa lacks literatures and specialized systems which regularly monitor changes in nutrient budget. Therefore, it is an important contribution to the filed. Therefore, I suggest accepting the manuscript after considering my following suggestions and comments.
1.	The English language should be improved to ensure that an international audience can clearly understand your text. For example, the title which is the most important sentence for the manuscript has a mistake (affect NOT affects). I strongly suggest the author to do a very careful proofreading for the entire manuscript. There are so many problems in writing that it is difficult to continue reading the paper. I suggest you have a colleague who is proficient in English and familiar with the subject matter review your manuscript, or contact a professional editing service.
2.	The introduction is good and contains good information that paves the way for reaching the idea of the research. But this is a manuscript and not a doctoral thesis. I strongly suggest the authors to reduce this introduction to the half and only information that confirms the idea of the research. I also greatly missed the discussion of the recent findings of Elrys et al. (2019, 2020, 2021) which dealt with the nitrogen budget in Africa during the past five decades, as well as calculating the nitrogen fertilizer rate needed to achieve self-sufficiency of Africa by 2050. Please indicate their important results in the introduction and discuss their accuracy in the discussion section based on some of your results. You can find their papers through the following references:
a.	10. Elrys, A. S., M. K. Abdel-Fattah, S. Raza, Z. Chen, J. Zhou (2019). Spatial trends in the budget of nitrogen flows in the African agro-food system over the past five decades. Environmental Research Letters, 14: 124091.
b.	Elrys, A. S., Metwally, M. S., Raza, S., Alnaimy, M. A., Shaheen, S. M., Chen, Z., & Zhou, J. (2020). How much nitrogen does Africa need to feed itself by 2050? Journal of Environmental Management, 268.
c.	Elrys, A.S., E.-S.M. Desoky, M.A. Alnaimy, H. Zhang, J.-b. Zhang, Z.-c. Cai,…, Cheng, Y. (2021). The food nitrogen footprint for African countries under fertilized and unfertilized farms. Journal of Environmental Management, 279: 111599.
3.	Results and Discussion: I highly recommend the authors to separate this section into two sections. I mean the authors must introduce the results in a separate section and Discussion in another section. Regarding results, there is no need to present each attribute in a separate title. Please group them into groups and show readers your important findings to help them understand the message of your study.
For the discussion section, you can separate it into two subsections, the first section should discuss your important findings but please avoid repeating the results again. The second part of the discussion should be the implications of this study, you have good implications but the authors have to discuss them and not just mention it. Don't forget to link your repercussions with the large scale of Africa because, you know, nutrient depletion is not only a problem for Ethiopia, but for most of sub-Saharan Africa.
Validity of the findings: I think this manuscript is interested and provide good findings. Unlike developed countries, Sub Saharan Africa lacks literatures and specialized systems which regularly monitor changes in nutrient budget. Therefore, it is an important contribution to the filed. Therefore, I suggest accepting the manuscript after considering my following suggestions and comments.
1.	The English language should be improved to ensure that an international audience can clearly understand your text. For example, the title which is the most important sentence for the manuscript has a mistake (affect NOT affects). I strongly suggest the author to do a very careful proofreading for the entire manuscript. There are so many problems in writing that it is difficult to continue reading the paper. I suggest you have a colleague who is proficient in English and familiar with the subject matter review your manuscript, or contact a professional editing service.
2.	The introduction is good and contains good information that paves the way for reaching the idea of the research. But this is a manuscript and not a doctoral thesis. I strongly suggest the authors to reduce this introduction to the half and only information that confirms the idea of the research. I also greatly missed the discussion of the recent findings of Elrys et al. (2019, 2020, 2021) which dealt with the nitrogen budget in Africa during the past five decades, as well as calculating the nitrogen fertilizer rate needed to achieve self-sufficiency of Africa by 2050. Please indicate their important results in the introduction and discuss their accuracy in the discussion section based on some of your results. You can find their papers through the following references:
a.	10. Elrys, A. S., M. K. Abdel-Fattah, S. Raza, Z. Chen, J. Zhou (2019). Spatial trends in the budget of nitrogen flows in the African agro-food system over the past five decades. Environmental Research Letters, 14: 124091.
b.	Elrys, A. S., Metwally, M. S., Raza, S., Alnaimy, M. A., Shaheen, S. M., Chen, Z., & Zhou, J. (2020). How much nitrogen does Africa need to feed itself by 2050? Journal of Environmental Management, 268.
c.	Elrys, A.S., E.-S.M. Desoky, M.A. Alnaimy, H. Zhang, J.-b. Zhang, Z.-c. Cai,…, Cheng, Y. (2021). The food nitrogen footprint for African countries under fertilized and unfertilized farms. Journal of Environmental Management, 279: 111599.
3.	Results and Discussion: I highly recommend the authors to separate this section into two sections. I mean the authors must introduce the results in a separate section and Discussion in another section. Regarding results, there is no need to present each attribute in a separate title. Please group them into groups and show readers your important findings to help them understand the message of your study.
For the discussion section, you can separate it into two subsections, the first section should discuss your important findings but please avoid repeating the results again. The second part of the discussion should be the implications of this study, you have good implications but the authors have to discuss them and not just mention it. Don't forget to link your repercussions with the large scale of Africa because, you know, nutrient depletion is not only a problem for Ethiopia, but for most of sub-Saharan Africa.
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 TYPE AND FERTILIZER RATE AFFECT WHEAT (TRITICUM AESTIVUM L.) YIELD, QUALITY AND NUTRIENT USE EFFICIENCY IN AYIBA, NORTHERN ETHIOPIA
Review round: 1
Reviewer: 3

Output:
Basic reporting: This is a very well written manuscript; a pleasure to read. This unique, innovative and creative study interestingly examined the effect of NPSZnB blended fertilizer on bread wheat yield, quality traits and use 19 efficiency in two soil types under rainfed conditions in Ayiba, northern Ethiopia.
Experimental design: The focus is well maintained throughout the manuscript. The methods and analyses are well done and results logically presented. Just few comments on  Figure 1 : Author can improve this figure and include grids and other  elements of a complete map.
Validity of the findings: The results and discussions of this study are well elabolated and are aligned with the previous studies. Conclusions are well stated, linked to original research question and limited to supporting result.
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 TYPE AND FERTILIZER RATE AFFECT WHEAT (TRITICUM AESTIVUM L.) YIELD, QUALITY AND NUTRIENT USE EFFICIENCY IN AYIBA, NORTHERN ETHIOPIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript has been greatly improved, but there are some minor concerns that can be considered for a more effective technical delivery of the research message.

The abstract still looks seemingly too lengthy. Several sentences therein would fit in the introduction and discussion sections. The authors should consider minimizing the abstract. The technical abstract should be a crisp but concise summary of the whole research in the fewest words possible.
Experimental design: The design looks better. However, a graphical abstract that summarizes the whole study methodology in one simplified figure would be suggested since it will be highly beneficial to the technical audience perusing this research.
Validity of the findings: The results presented are seemingly satisfactory.
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 TYPE AND FERTILIZER RATE AFFECT WHEAT (TRITICUM AESTIVUM L.) YIELD, QUALITY AND NUTRIENT USE EFFICIENCY IN AYIBA, NORTHERN ETHIOPIA
Review round: 2
Reviewer: 2

Output:
Basic reporting: The manuscript has been greatly improved and is recommended for acceptance. Thanks to the authors.
Experimental design: It is OK
Validity of the findings: It is OK
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 TYPE AND FERTILIZER RATE AFFECT WHEAT (TRITICUM AESTIVUM L.) YIELD, QUALITY AND NUTRIENT USE EFFICIENCY IN AYIBA, NORTHERN ETHIOPIA
Review round: 2
Reviewer: 3

Output:
Basic reporting: This is a very well written manuscript; it is a pleasure to read. This unique, innovative, and creative study interestingly examined the effects of NPSZnB blended fertilizer on bread wheat yield, quality traits, and use 19 efficiency in two soil types under rainfed conditions in Ayiba, northern Ethiopia.
Experimental design: The focus is well maintained throughout the manuscript. The methods and analyses are well done, and the results are logically presented. The authors have improved the manuscript.
Validity of the findings: The results and discussions of this study are well elabolated and aligned with the previous studies. Conclusions are well stated, linked to the original research question and limited to supporting results.
Additional comments: No additional comments


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

Input:
Title: AN ASSESSMENT OF SENSORY SENSITIVITY IN WOMEN SUFFERING FROM DEPRESSION USING TRANSCUTANEOUS ELECTRICAL NERVE STIMULATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: This is, in summary, an interesting paper aimed to investigate whether women who suffer from depression experience an electrical stimulus applied during electrotherapy treatments in the same way as women who are mentally healthy. The authors found that Median sensing threshold of electric current (depression vs. control: 7.75mA vs. 8.35mA; no significant), type of sensation evoked (depression vs. control: tingling 90.9% vs. 92.7%, no significant), hedonic rating (depression vs. control: unpleasant 11.4% vs. 2.4%; p=0.003), hedonic rating (mildly ill vs. moderately ill vs. markedly ill: unpleasant 5.3% vs. 6.3% vs. 33.3%; p=0.066).
Experimental design: As the most relevant aims/objectives of this study have been reported, the main hypotheses underlying the present study could be briefly specified by the authors.

In addition, the conditions of the 19 women suffer from depression need to be described within the Results section rather than within the Methods section as in the current version of the manuscript.
Validity of the findings: The authors should present and discuss, in the first lines of the Discussion section, the most relevant study findings of this paper instead of focusing on the main literature gaps upon the main topic that have been adequately stressed within the main text.

Importantly, the most relevant study limitations/shortcomings should be described in a more detailed manner as the the main caveats have been only partially reported.
Additional comments: Finally, what is the take-home message of this paper? While the authors reported that females suffering from depression present a similar threshold of sensitivity as mentally healthy females to an electrical stimulus, they failed, in my opinion, to focus on some conclusive remarks to this specific regard. Specifically, what are the main implications of this paper according to these findings? How the mentioned results may be generalized? Here, some additional details might be useful for the general readership and should be provided by the authors based on their expertise.


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

Input:
Title: AN ASSESSMENT OF SENSORY SENSITIVITY IN WOMEN SUFFERING FROM DEPRESSION USING TRANSCUTANEOUS ELECTRICAL NERVE STIMULATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: Some improvement in the writing and referencing is required , but this is essentially a well-written paper which needs some revision to overcome some problems, which are detailed below.
Experimental design: The design is good but some improvement in the description of the methods is required.
Validity of the findings: The findings are valid, interesting and increase our understanding about TENS but some of the statements in the discussion include unreferenced over-generalisation and should be improved.
Additional comments: I think that this is an interesting study with new insights into the experience of potential TENS users. The findings could help to explain limited benefits from TENS in patients with depression. However some of the detail requires improvement, and I have provided a detailed description of these problems below.
Line 21: “Beckground.” This is a typo, it should be Background.

Lines 21-23: “Perception is the result of experiences arising from the mental
interpretation of the phenomena occurring, therefore it depends not only on physiology or biology, but is also psychically conditioned.”
Please could you review the meanings of the words experience, perception and psychically? It could be possible to state that our lived experiences are the result of perception (if perception is the process by which sensations are processed, organised and interpreted). Perception also has a dual meaning, describing both the process and the end result of the process, and this second meaning is equivalent to “experience”.
These definitions might be helpful: https://dictionary.apa.org/perception and https://dictionary.apa.org/experience

I suspect that you mean “psychologically conditioned” not psychically conditioned, but do check: https://dictionary.cambridge.org/dictionary/english/psychically

Physiology is a subset of biology, so you could perhaps remove one of these words.

Line 44: “Sensory perception is based on the subjective evaluation of a stimulus acting on the
human body, thus it is an individual variable.”
Please could you review this sentence, based on the comments made above about the definition of perception as a process? Is part of the process of sensory perception separate from subjective experience, for example could we identify processing of TENS stimulation within the nervous system of a person who was asleep, and therefore this aspect is not subjective? Is it possible that the subjective evaluation is the final stage of sensory perception? Some psychologists (e.g. Albert Bandura) conceptualise subjective experience as an emergent property of biological systems, and this concept might be helpful here. A reference is: https://www.annualreviews.org/doi/abs/10.1146/annurev.psych.52.1.1

Line 45: “psychically” here is probably best changed to “psychologically”.

Lines 55-57: “Therefore, differences in tactile or pain sensitivity assessed only in terms of physiology are insufficient and must be obligatorily combined with an assessment of the overall "satisfaction with life" of the person examined.”
The word obligatorily could be removed. I’m not sure that “satisfaction with life” is the best term to use here: “quality of life” however is a term that is commonly used in terms of patient experience and health outcomes. Would this work better?

Lines 75-77: “Depression is one of the most common psychiatric illnesses, as well as being both a major cause of diseases and a leading cause of disease-related disability throughout the worldwide.”
I think the statement that depression is a major cause of diseases should be referenced.
I think the word “worldwide” should be changed to “world”.

Lines 93-96: “This study aimed to assess if there is a difference in the sensory sensitivity to an electrical stimulus in women suffering from depression and what the hedonic rating is when the stimulus acts on the organism’s tissues.”
I think this could be altered to focus more on the TENS experience, such as:
“This study aimed to assess if there is a difference in the sensory sensitivity to an electrical stimulus in women suffering from depression and what the hedonic rating is of the lived experience of TENS.”

Line 100: were the women inpatients, outpatients or both?

Line 107: I think that the Clinical Global Impression - Severity Scale should be referenced.

Line 139: I have not been able to find an explanation of the intensity of the TENS stimulation when the participants were asked to make a hedonic rating. What instructions were given regarding turning up the TENS intensity?

Line 143: “organism’s tissues” could perhaps be replaced by the words “human nervous system”.

Line 195-6: “Moreover, it seems that in the scientific field there is no direct practical
references to the effects of electrotherapy in people suffering from depression.”
I think that there are references to this: you could review papers reporting clinical audits such as Lampl et al 1998: https://journals.lww.com/clinicalpain/Abstract/1998/06000/Transcutaneous_Electrical_Nerve__Stimulation_in.8.aspx

I tried a search of Google Scholar on “transcutaneous electrical nerve stimulation AND depression” and found several papers of interest on this subject.

Line 209-10: “Namely, if physical treatments are unpleasant for the patient, does the organism still perceive them as healing?”
I suggest that this is reworded to:
Namely, if physical treatments are unpleasant for the patient, does the person still
perceive them as therapeutic? I don’t think we should be calling people “organisms” (even if we are!), and I don’t think that TENS is “healing” even if it might be therapeutic.

Line 211-13: “All electrotherapy is based on ascending and descending analgesic mechanisms, but are these mechanisms activated when the procedure brings discomfort to the patient?”
I think that mentioning secondary hyperalgesia at this point might be helpful.

Line 239: The paper by Leo is quite old now (2005) and I think a more up to date reference should be included.
I spent a minute or two looking for newer articles, and there are plenty. This review might be a good start: https://www.iasp-pain.org/publications/relief-news/article/depression-pain-changes/

Lines 255-7: “It is highly probable that people suffering from depression and who are being given physical treatments, do not divulge information about their mental health to the physiotherapist.”
I think that this is a significant assertion and is not referenced. Can you provide evidence for this statement? Physiotherapists can offer a holistic, biopsychosocial assessment which includes an enquiry about the presence of any mental health issues, and the impact of pain on mood and morale.

Line 257: “…any actual somatic disorder.”
It could be argued that patients who experience pain associated with depression are experiencing a somatic disorder, especially if we think about the mind and body being integrated rather than a mind-body dualist view. I wondered if replacing “somatic” with “musculoskeletal” might be helpful here?

Lines 275-7: “The sensory threshold test, however, showed a tendency to a more frequent unpleasant perception of TENS stimulation in the group of women suffering from depression, especially in those with a higher degree of severity according to the CGI-S scale.”
I think that this needs to be corrected, as the sensory threshold test showed no difference. I think you mean the hedonic rating?

Lines 296-8: “The effect of psychotropic drugs on the human organism is mainly based on the reuptake of norepinephrine and serotonin, increasing the levels of these neurotransmitters (Klauenberg et al., 2008).”
This seems to me to be a significant over-generalisation. Is this really true for ALL psychotropic drugs? See the statement in line 307 about benzodiazepines.

Line 303: “as well as unacceptable for health reasons.”
Not all depressed people take anti-depressants, due to lack of efficacy and intolerable side-effects. It should be possible to recruit from this population.

Line 311-3: “Unfortunately, pain has a negative impact on the diagnosis of depression, as it often moves to the fore so much that it completely captivates the attention of doctors and physiotherapists.”
This is another significant over-generalisation. Can you provide evidence to support this statement? I suggest that you search the literature on secondary depression due to pain.

Lines 317-19: “If the patient's somatic pain is the result of psychological issues, it is very unlikely that physical treatments will bring a particular therapeutic effect.”
Is it VERY unlikely? What is the evidence for this statement? We know that depression can affect treatment outcomes, but within that there is a complex picture of variable outcomes for different patients. Some will have primary depression, others secondary depression due to pain.

Line 342: “Group D” might be better stated as “depressed women” in the conclusion.

General point regarding the discussion. Anhedonia is a key feature of depression. Many of these depressed women will be experiencing reduced pleasure in many experiences which would normally be pleasant. This might apply (for example) to social contact, music, exercise and chocolate. The reduced hedonic rating of TENS might just be part of this general phenomena: I cannot find any discussion of this key point.

Figure 4: “markedely” should be corrected to “markedly”


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

Input:
Title: AN ASSESSMENT OF SENSORY SENSITIVITY IN WOMEN SUFFERING FROM DEPRESSION USING TRANSCUTANEOUS ELECTRICAL NERVE STIMULATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have responded constructively to the review and have produced a paper which is clear, well referenced and well structured.
Experimental design: The authors have clarified the sections in the methods which were picked up in the first review, and this section is now satisfactory.
Validity of the findings: The authors have again responded well to the first review, and the findings and interpretation are now  more robust.
Additional comments: I am satisfied with the second draft, and would support its 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: DISCOVERY OF PROTEIN-BASED NATURAL HYDROGEL FROM THE GIRDLE OF THE ‘SEA COCKROACH’ CHITON ARTICULATUS (CHITONIDA: CHITONIDAE)
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this article Cakmak et al., report their discovery of a protein-based natural hydrogel from the girdle of a chiton species, Chiton articulatus. Further, they analyze the chiton hydrogel  to study the thermal stability, surface morphology, chemical composition, swelling behavior and cytotoxicity. This chiton hydrogel could be a good alternative to the synthetic hydrogels and the so called ‘natural hydrogels’  due to their potential for being environmentally safe , non-toxic  and sustainable. While a good amount of characterization has been performed it will be valuable to report the mechanical properties of the chiton hydrogel especially because the other ‘natural hydrogels’ have poor mechanical properties. In addition to this there are other minor issues such as text being difficult to read at some parts.

1)	Describe fig 3F further.

2)	Make sure the scientific names of the organisms are italicized. For example in line 199.

3)	The last sentence in the abstract ends as “….and helping to regulate”. It would be useful if you the authors can specify what process they speculate is being regulated or revise the sentence.

4)	Raw data files need to be titled and annotated clearly. It is difficult to understand them in their current form.

5)	In figures and text, the terms chiton hydrogel and protein-based hydrogel seem to be used interchangeably. The authors should be consistent and use one term throughout the text. This would help with the flow of the article.

6)	In line 321, the biological function section could be removed and the text added to the discussion.

7)	In line 255, “previous protein studies” are mentioned. Please elaborate on how the results from this study are compatible with these previous protein studies and cite them.

8)	Typo in line 264, Fig.S instead of Figs.

9)	Revise the sentences 269 and 270. Their purpose is not clear. I assume the idea is to indicate that protein concentrations in the chiton hydrogels are higher than other hydrogels.

10)	Rephrase sentences 307 and 308. As MTT assay is already mentioned in the preceding paragraph you could simply state “The MTT assay results were then validated with a real-time experiment examining cell viability…….”

11)	In line 70, it is mentioned that ‘natural’ hydrogels are non-toxic but in line 77 increased toxicity is noted as one of the disadvantages of these ‘natural’ hydrogels. This is a bit confusing. It would be useful to explain or revise these statements further.
Experimental design: 1)	The paper refers to the so called ‘natural’ hydrogels which are prepared in the lab by crosslinking of natural polymers as having poor mechanical properties. It would be valuable if you can test and present the mechanical properties of the chiton hydrogel.
Validity of the findings: 1)	In line 339, mention the maximum decomposition temperature values and explain the issues if any related to this slightly lower decomposition temperature.

2)	For the MTT assay results in figure 4, report the standard deviations rather than standard error of the mean. Standard deviation shows the variability from the individual data values to the mean which is appropriate here.

3)	In paragraph Cytotoxicity assay, line 427, expand more on how chitin hydrogel can be used in biomedical field and the limitations of it based on the toxicity observed at higher concentrations.

4)	In lines 390, 391 and 392, mention the maximum swelling capacity either as percentages or times. In addition, it would be useful for the reader to note the maximum swelling capacity of chitin hydrogel in this context.

5)	Can you address if any difficulties in obtaining enough of this chitin hydrogel for different applications and possible environmental impact?

6)	In lines 378 and 379, the purposes of these sentences without any reference to the chiton or protein-hydrogel is not clear. Revising them would help the reader to understand it better.
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: DISCOVERY OF PROTEIN-BASED NATURAL HYDROGEL FROM THE GIRDLE OF THE ‘SEA COCKROACH’ CHITON ARTICULATUS (CHITONIDA: CHITONIDAE)
Review round: 1
Reviewer: 2

Output:
Basic reporting: Emel et al., developed protein-based hydrogels from the girdle of the sea cockroach.
Experimental design: The selected topic was very interesting and the authors presented it in a good manner way.
Validity of the findings: The selected topic was very interesting
Additional comments: Minor comments:
•	The extracted material needs to compare with standard materials.
•	Abstract: use this sentence “predominantly 83.93% of protein”
•	Remove these “Chiton articulatus; Chitonidae”, if there are synonyms
•	Add the following reference at Line 49: 10.1016/j.msec.2017.05.096; line 53: 10.1016/j.ijbiomac.2019.01.145; line 84: 10.1016/j.molliq.2019.112087 with explanation


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF FIBRILLIN (FBN) GENE FAMILY IN TOMATO (SOLANUM LYCOPERSICUM L.)
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: FBN play important roles in tomato development, and they also involved in response to phytohormone and different stresses. This paper mainly explore their function with qRT-PCR in differernt samples. There are some questions need to be answered.
(1 )In your paper, SlFBN1, SlFBN2b and SlFBN7a were highly expressed in flowers, but the three genes were located in chloroplast, and chloroplast content in flowers may not so high, please present your viewpoint.
(2) As known that FBN in tomato may originated from a common ancestor, there is no gene duplication among 14 SlFBNs, please give your opinion.
(3) SlFBNs have no collinearity with rice, and present collinearity with Arabidopsis, but rice has bigger genome size than Arabidopsis, please state your standpoint.


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF FIBRILLIN (FBN) GENE FAMILY IN TOMATO (SOLANUM LYCOPERSICUM L.)
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: several minor comments,
1. please add note of the legend in Fig.6 and Fig.8 what dose -1.5, 0 and 1.5 means?
2. P value should be p value.
3. several formatting errors in references, such as Line 408-410,"2020" appeared twice, Line365-367, "37(web server issue)"?


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

Input:
Title: GENOME-WIDE IDENTIFICATION AND EXPRESSION ANALYSIS OF FIBRILLIN (FBN) GENE FAMILY IN TOMATO (SOLANUM LYCOPERSICUM L.)
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: In this article, the authors identified 14 FBN genes in the genomes of tomato, which divided into 11 subgroups, studied the phylogenetical and collinearity relationship among the subfamilies of FBN from different species, and found 8 homologous gene pairs between tomato and Arabidopsis. Furthermore, the authors provided detailed expression data of SlFBNs in tomato through transcriptomic data analysis and qRT-PCR. The major interesting findings were that: 1. The cis-acting elements of hormone (especially ethylene, MeJA and ABA) were widely distributed in the SlFBN promoters. 2. most of SlFBNs were preferentially expressed in leaves and showed higher expression in mature or senescent leaves than in young leaves ". 3. SlFBN1, SlFBN7a and SlFBN2b with high expressional levels in flower showed significantly higher expressions in three NILs than wild type. 4. All of SlFBNs were responded to Pst DC3000 and ABA treatments. These results provide some useful information for the next step of exploring the functions and molecular mechanisms of SlFBNs in leaf development, fruit differentiation, stress and hormone responses. However, with some shortcomings, the present vision needs improvements for publication.
1.	In materials & methods section: Line 116-117 provides the genomic data of tomato. But at present, there are different genome assembles of tomato. It is necessary to showed the version information of tomato genome.
2.	In materials & methods section: The authors should provide the detailed information on biological duplications of tomato samples under different treatments.
3.	In introduction section: Line 81 showed the fbi4 mutants in apple and Arabidopsis. The “apple” should provide the Latin name as first appearance.
4.	In materials & methods section: in Identification of FBNs in tomato paragraph, line 123, the authors mentioned that using the SMART "to screened FBN genes in tomato genome", didn't mention which mode of SMART. Since two mode applied different algorithm, it may cause different results in analysis.
5.	In materials & methods section: in RNA extraction and quantitative real-time PCR (qRT-PCR) paragraph, line 173, the authors mentioned that ACTIN gene was used as internal reference gene. There are many ACTIN genes in tomato genome. So, the authors should provide the gene accession No. of ACTIN used in this article.
6.	In results section: in Cis-element analysis of SlFBN promoter regions paragraph, line 238-239, the authors found “The hormone responsive elements, especially ethylene, MeJA and ABA, were widely distributed in the SlFBN promotes.” by cis-acting element analysis. The authors need to explain why they choose ABA, when they analyzed the expression profiles of SlFNBs under plant hormones.
7.	There are many format errors in references. For example, Line 404, the Latin name of tomato " Solanum lycopersicum " in the title " Hormonal changes in relation to biomass partitioning and shoot growth impairment in salinized tomato (Solanum lycopersicum L.) plants "need to be italic. The same questions are in Line 426, 435, 442, 473 and so on. The For the name of journals, in some journals the first letter of each word is capitalized (e.g., Nucleic Acids Research, Journal of Bacteriology), while in others, not all the same (e.g., Molecular plant, Journal of experimental botany, The Plant cell). Some journals are used full name (e.g., Plant Physiology, Plant Science.) while others are abbreviated (Plant Sci, Plant Physiol, et al.).
8.	The extra blanks occurred multiple times in whole article.
9.	The Figure 2 and 3: the names of chromosomes are different with Table 2. The authors should unify the chromosome names.
10.	The Figure 4: the font of legends in figure 4-A and B is too small to read.
11.	The legend of Figure 6: There no statement about the meaning that three red asterisks represent in Figure 6-C. The authors need to provide additional explanation.