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: FUNCTIONAL ANALYSIS OF A PHYTOPHTHORA HOST-TRANSLOCATED EFFECTOR USING THE YEAST MODEL SYSTEM
Review round: 2
Reviewer: 1

Output:
Basic reporting: This manuscript shows that six P. sojae effector that suppress PAMP- and effector-triggered programmed cell death in planta inhibit yeast growth, which suggests effector may perform similar molecular function in two different species. It can provide some clues about potentially key regulatory genes in plants and lays the foundation for future work thought the yeast model system that explores the function of phytophthora effector. There is no doubt that there are some differences between the yeast system and phytophthora-plant interaction system. But in the face of the large number of effectors secreted by pathogens, the yeast system also provides us with a way to quickly screen for potentially functional effectors and explore their possible molecular mechanisms providing support for studies on plant-pathogen interactions. Overall, the manuscript is well written and the results are easy to follow.
Experimental design: Several aspects of the study need further interpretation or additional experimentation.
1.	These six effectors can inhibit yeast growth, which is probably caused by the experimental system. To exclude this possibility, author should add effectors that can’t suppress PAMP- and effector-triggered programmed cell death as a control to make the results more persuasive.
2.	The transcriptome analysis found PHO4 may be a potential target of PsAvh110. The RT-qPCR related experiments about PHO4-regulated genes expression in yeast should be performed, which can verify whether these transcriptome analysis data are reliable to a certain extent.
3.	Analysis data related software helps us analyze and provide convenience. With reliable data, we also have the responsibility to do our best to show it. So the pictures shown in Figure 2 and Figure 3 should be drawn with related drawing software or displayed in a new way instead of screenshots.
Validity of the findings: no comment
Additional comments: no comment


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

Input:
Title: LEAF SPOT OF HOSTA VENTRICOSA CAUSED BY FUSARIUM OXYSPORUM IN CHINA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors isolated and identified a new pathogen causing leaf spot of Hosta ventricosa in China. The morphological and molecular characters of the isolates indicated that the pathogen causing leaf spot of Hosta ventricosa is Fusarium oxysporum. Additionally, Koch’s postulates were also fulfilled by artificially inoculation. I appreciate the works done in this research.  However, the manuscript will benefit from editing by a native English speaker to polish the language.
1. For the figure legend of  Figure 3,  Should it be "Fusarium proliferatum" or "Fusarium oxysporum"
Experimental design: 1. For Sampling and isolation methods (Line49), the deatiled informations of three sampling places should be provided (including the longitude and latitude)
 2. For Pathogenicity test (Line59), how many plants were used for pathogenicity test should be clarified.
3. For line105, The author isolated fifty fungal samples and divided them into seven types base on the colony morphology, The results and the detailed classification standard should be provided.
Validity of the findings: 1. F. oxysporum is important  and destructive pathogen with a broad host. This is the first report of H. ventricosa leaf spot in China and Chinese H. ventricosa is a new host of F. oxysporum.  Therefore,The incidence and the epidemic features of the leaf spot  disease caused by the F. oxysporum should be provided in the results part.

2. ZE-1b and ZE-2b  are all  Fusarium oxysporum, but the disease symptomes caused by  ZE-1b and ZE-2b were not the same (Figure 1). Are there any discrepancies in pathogenicity among the isolates.
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: LEAF SPOT OF HOSTA VENTRICOSA CAUSED BY FUSARIUM OXYSPORUM IN CHINA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript titled "Leaf spot of Hosta ventricosa 1 caused by Fusarium oxysporum in China" was submitted for publication in the PeerJ. It reports the first occurrence of leaf spot disease caused by this particular pathogen in China.
Experimental design: no comment
Validity of the findings: The findings seem valid; however, a single pathogen first report cannot be published in PeerJ.
Additional comments: The article fails to meet our standards as the authors have just provided a first national report of a disease in an ornamental plant. This kind of work could be sent for publication to Plant pathology journals like "Plant Disease" or "Plant pathology" and some other related journals which publish first disease notes from various countries. I regret to state that this paper could not be published in the PeerJ as it is a short first disease report based on only morphological, molecular, and pathogenicity characterization.


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: LEAF SPOT OF HOSTA VENTRICOSA CAUSED BY FUSARIUM OXYSPORUM IN CHINA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Basic Reporting:
Leaf spot disease of ornamental plant,  H. ventricosa caused by fungal pathogen F. oxysporum is reported. For more confidence in results, the experiment was designed to perform on three places.  The reporting is based on two important techniques, infection tests under control conditions on host plants and identification of Pathogenic isolate with sequencing by targeting multiple genes.
This is good data for first report. But For a journal having repute of publishing extensive research, the other parameters like passage of pathogen in the plant, lab and field management through modern pathogen approaches are important.
Experimental design: Since, disease was just confirmed through identification of the pathogen on the basis of physical characteristics and infection tests, so up to these two points the experiment designing is good. At the same time, our previous knowledge directs that Fusarium oxysporum is mainly a soil borne fungus and causes rots and wilts more commonly but exceptional diseases leaf spots are interesting.
Validity of the findings: Findings are straightforward and easily reproducible. Usually F. oxyxporum causes rots and wilts. The proposed study is novel regarding leaf spot role of fusarium as less number of such reports are available.
Additional comments: I would suggest accepting the paper after revising the grammar and English language and will also suggest including one or two more genes to target for sequence which will definitely put some weight to publish this manuscript in this prestigious journal.


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: LEAF SPOT OF HOSTA VENTRICOSA CAUSED BY FUSARIUM OXYSPORUM IN CHINA
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: There is another question for Figure 1G, the authors inoculated  two mycelial plugs of ZE-1b on the leaves of H. ventricosa, why does the plug on the left side not infect the leaf.
Additional comments: The authors properly addressed some the comments that I made. However, I think the pathogenicity experiment lacked enough trust. The detailed comment that I feel they need clarification is as follows.
There is another question for Figure 1G, the authors inoculated  two mycelial plugs of ZE-1b on the leaves of H. ventricosa, why does the plug on the left side not infect the leaf?


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: LEAF SPOT OF HOSTA VENTRICOSA CAUSED BY FUSARIUM OXYSPORUM IN CHINA
Review round: 2
Reviewer: 2

Output:
Basic reporting: I have read the whole revised manuscript. The new version is improved. Professional English has been incorporated throughout the article. References are updated. Whole story is presented precisely and in a good way. All the figures and tables are mentioned in the text and properly numbered. Raw data regarding accession number of the sequences etc. is provided with valid links.
Experimental design: The research fit well into scope of the journal. Since such reports are rare, so it would be a good addition in the coming issue/s. Research question was raised as hypothesis and then answered with valid results. The research addresses the important problem of Leaf spot disease which was noticed by authors and his team during survey and was later monitored for isolation of the pathogen and its valid identification. It was proved that the disease caused by Fusarium oxysporum in the Hosta ventricosa through infection tests and through sequencing of multiple genes fusarium was declared as causal organism. The hypothesis was further answered through infection tests  on the host plant and microscopy strengthened, which not only validate Fusarium as causal organism but also provide enough information regarding its virulence against H. ventricosa. The data provided was replicated and the method could be reproduced easily in any lab having enough facilities.
Validity of the findings: According to my knowledge, it is novel work, since it is being reported first time which is enough proof for its novelty and need. As I mentioned earlier, the authors incorporated all the doable suggestions which I humbly suggested during the review of initial draft. The word file clearly shows the technical incorporations and improvement in the write up.
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: EXTRACTION BEHAVIORS OF AQUEOUS PEG IMPREGNATED RESIN SYSTEM IN TERMS OF IMPREGNATION STABILITY AND RECOVERY VIA PROTEIN IMPREGNATED RESIN INTERACTIONS ON BOVINE SERUM ALBUMIN
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors report the application of AIRS for the separation of BSA. The factors influencing the performance of protein adsorption by the resin were studied systematically. As compared to ATPS and adsorption techniques, the recovery of protein by AIRS was the highest. The data and experiment design could be useful as a reference to future studies adopting AIRS as the purification method. The manuscript is recommended for publication, after consideration of the comments given below:
Experimental design: •	Title: The mention of “biological product” is redundant, as BSA is commonly known as a biological product. AIRS can be mentioned in the title.
•	Abbreviation. The abbreviation shall be first defined, followed by its consistent use. Please check them, e.g., AIRS, BSA, PEG. The English grammar shall be improved. A number of obvious grammar mistakes were spotted.
•	Lines 62-64: The description of method is not clear. Is the salt phase responsible for biomolecule extraction? More information about AIRS can be provided in Introduction.
•	Why BSA is used as an exemplary target product? Typically, BSA is the undesirable protein contaminant. Does the study intend to examine the influence of this protein in the performance AIRS? Similarly, what is the rationale behind selection of sodium citrate as the salt phase?
•	Line 95: What does the ‘sample’ refer to? Solution or the impregnated resin? In Eq. 1, the absorbance of impregnated PEG is needed, but how can this be measured? Does it require the release of PEG from the resin? Besides, is 180 min sufficient to evaluate the stability of PEG impregnated on the resin?
•	Line 114: What is the justification for using these 3 types of solid materials?
Validity of the findings: •	Table 1: There are quite a number of interesting leaching trends exhibited by different resins. Suggest to discuss them and explain the phenomenon.
•	Line 135: Is the claim on the relationship between pore size and impregnation stability based on this study? If yes, what are the pore sizes of resins used in this study?
•	Line 144 and 192: Where are the results implying that 30 min of contact time is sufficient?
•	Lines 206 and 207: What are the concentrations of PEG impregnated on the resin? Is there a saturation point in resin for impregnating PEG on the surface?
•	Line 221: Provide reference for the pI of BSA.
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: EXTRACTION BEHAVIORS OF AQUEOUS PEG IMPREGNATED RESIN SYSTEM IN TERMS OF IMPREGNATION STABILITY AND RECOVERY VIA PROTEIN IMPREGNATED RESIN INTERACTIONS ON BOVINE SERUM ALBUMIN
Review round: 1
Reviewer: 2

Output:
Basic reporting: The English language needs to be improved to ensure that an international audience can clearly understand your text.
some examples where the language could be improved include lines 48, 60, 64, 105, 111, 116, 132, 133, 148,173, 186, 202, 204, 209, 210, 211, 222 and 226.
I suggest you have a proficient English colleague and familiar with the subject matter, reviews your manuscript, or use grammar checking tools.
one example can be described as line 48, "are" need to change to "is."

Figures are appropriately Figure 2, Y axes label is missing %.

The literature references are listed without title and the end of the manuscript. Hence its is recommended to authors revise them appropriately.
Experimental design: The experimental design is well organized and appropriately addressed the aim of the study.
Validity of the findings: The results are solid, well organized and valid.
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: EXTRACTION BEHAVIORS OF AQUEOUS PEG IMPREGNATED RESIN SYSTEM IN TERMS OF IMPREGNATION STABILITY AND RECOVERY VIA PROTEIN IMPREGNATED RESIN INTERACTIONS ON BOVINE SERUM ALBUMIN
Review round: 2
Reviewer: 1

Output:
Basic reporting: It is acceptable after the revision made.
Experimental design: It is acceptable after the revision made.
Validity of the findings: It is acceptable after the revision made.
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: EXTRACTION BEHAVIORS OF AQUEOUS PEG IMPREGNATED RESIN SYSTEM IN TERMS OF IMPREGNATION STABILITY AND RECOVERY VIA PROTEIN IMPREGNATED RESIN INTERACTIONS ON BOVINE SERUM ALBUMIN
Review round: 2
Reviewer: 2

Output:
Basic reporting: The punctuations and grammatical errors need to be reviewed again. Please correct the list below:
Line 68 and 77, change salt aqueous solution to appropriate order as "aqueous salt solution/ phase."
Line 89 and 162, weight needs to be changed to " weights"
Line 113, please correct " Switzerland"
Line 128, the solid's surface is the correct form.
Line 164, sizes needs to be changed as " sizes"
Line 173, percentage + s = "percentages".
Line 200, following however, a comma is missing.
Line 205, slight need to be changed to " slightly"
Line 218, type +s = types.

line 147-153, Analytical methods are exactly copy-pasted from "4.5. Total Protein Content Determination" paper " Abdul Aziz, Nur Fazrin Husna, et al. "Recovery of a Bacteriocin-Like Inhibitory Substance from Lactobacillus bulgaricus FTDC 1211 Using Polyethylene-Glycol Impregnated Amberlite XAD-4 Resins System." Molecules 25.22 (2020): 5332"

Please do not copy-paste the same content and try to paraphrase it.

For lines 129-131, please indicate "Ribeiro Alves, Márcia Regina, et al. "The process of separating bovine serum albumin using hydroxyapatite and active babassu coal (Orbignya Martiana)." The Scientific World Journal 2016 (2016)." as a reference.
Experimental design: In the excel file, the model is linearized while there is no justification for such a decision. In other studies, several models of adsorption kinetics were used to fit the experimental data: the pseudo-first-order, the intraparticle diffusion model, and the pseudo-second-order kinetic model. There needs to be a justification for why the authors did not take into account other fitting models.

In the chemical and reagents part, more information regarding materials is used in the experiment. Specifying just the location of obtaining BSA does not provide the necessary information. please use this format for the chemical and reagents: (≥ 99.0%, BP671-10, Hampton, NH, USA)
Validity of the findings: If there is enough justification for why linearization instead of pseudo-first-order or pseudo-second-order is used, the linearization can be accepted. Otherwise, other fitting methods gained momentum in the literature and can be applied in this study too.
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: EXTRACTION BEHAVIORS OF AQUEOUS PEG IMPREGNATED RESIN SYSTEM IN TERMS OF IMPREGNATION STABILITY AND RECOVERY VIA PROTEIN IMPREGNATED RESIN INTERACTIONS ON BOVINE SERUM ALBUMIN
Review round: 3
Reviewer: 1

Output:
Basic reporting: It is accepted after the requested revisions are made.
Experimental design: It is accepted after the requested revisions are made.
Validity of the findings: It is accepted after the requested revisions are made.
Additional comments: It is accepted after the requested revisions are made.


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 MYCORRHIZAL FUNGI OF CYMBIDIUM PROMOTE THE GROWTH OF DENDROBIUMOFFICINALE BY INCREASING ENVIRONMENTAL STRESS TOLERANCE
Review round: 1
Reviewer: 1

Output:
Basic reporting: In their study, Li et al. used four mycorrhizal fungi isolated from Cymbidium to inoculate with Dendrobium officinale under biotic and abiotic stresses.The results showed that the four Cymbidium mycorrhizal fungi are compatible strains for improving the growth rate of D. officinale by increasing its environmental stress tolerance, providing an effective way to supply resources through artificial reproduction.The nature of the study is technical as it provides information about mycorrhizal fungi can improving the growth rate of D. officinale by increasing its environmental stress tolerance on the basis of the results.
Experimental design: After reading your manuscript, it was not really clear for me, what is your main obtained result. For me the manuscript is quite confusing, especially “four mycorrhizal fungi isolated from Cymbidium”.
Validity of the findings: First I strongly suggest you to search in available literature for information. Than I recommend to add some nice pictures showing the morphological characteristics of studied plants and fungi. The English language should be improved and I suggest that give us more clearly information in section of “Material and methods”
Additional comments: Below I state some comments/suggestions that could improve their study.
1.	L43-L46 We suggests that you may provide more relevant information about Orchidaceae mycorrhizal fungi (OMF). Orchidaceae mycorrhizal fungi are a large group with specific genera and species.
2.	L74-75, In this paper, authors showed the hosts of strains GDB162, GDB254, GS222 and MLX102, but not give more information about these four strains. You have to identify these strains, and give the corresponding information.
3.	L90, Please tell us why choose “60 days” for data determination?
4.	L91 , What do you mean” other parameters” ? Please write in detail.
5.	L94  What do you mean “4 leaves of D. officinale”?
6.	L97 Why do you know “infected the root of the plant (about 15 days)”? I suggest that you need to provide tissue sections of the root to determine the colonization time.
7.	L98-100, What are the test conditions? Pot?or MS medium？What do you mean”The first” and ”The second” ? I think it should be “Group I” and “Group II”.
8.	L132, How do you measure “symptoms and death rate”? I suggest that you need to provide references.
9.	L148, I suggest that you should add the “method of acid phosphatase activity “ in the section of “material and method”.
10.	Figure 1, I recommend to add some nice pictures.
11.	L165-L174, in figure3, You did not mention “5 month” and “bud number” in the section of “material and method” , please give us more information.
12.	L179, What do you mean” in the early, middle, and late periods of drought conditions”? In supplements, 15,30,60 days, Does it mean the same thing? I recommend to describe clearly.
13.	Please add the rulers in figure 5A and D.
14.	L189-L200, I recommend to use shorter but more exact sentences, or you can delete it, as it adds nothing to the study.
15.	L209, What do you mean “most seedlings withered”? Please give the statistics. Please add the rulers in figure 6.
16.	L213, “four Rhizoctonia spp”? Four strains used in this study belonged to genus “Rhizoctonia”? or other four Rhizoctonia spp.?
17.	L248-255, I suggest that you need to use shorter but more exact sentences to describe the pathogens information. We want to know more details about the function of mycorrhizal fungi, instead of pathogens.
18.	L265 “mainly caused by antibiotics and lytic enzymes produced by the fungi on the plates”, Please provide more references.
19.	L274-L293, Many literatures have shown that mycorrhizal fungi can promote the growth of orchids. Please explain the similarities and differences between your research and others' research.
20.	L284, “Mycorrhizal fungi that have dissolving abilities should provide additional phosphorus for usage”, please provide references. There are many types of mycorrhizal fungi. The interaction mechanisms between plants and fungi are different. What kinds of mycorrhizal fungi do you mean?


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 MYCORRHIZAL FUNGI OF CYMBIDIUM PROMOTE THE GROWTH OF DENDROBIUMOFFICINALE BY INCREASING ENVIRONMENTAL STRESS TOLERANCE
Review round: 1
Reviewer: 2

Output:
Basic reporting: Language is fluent. but background of the mycorrhizal fungi GDB162, GDB254, GS222 and MLX102 are not enough!
Experimental design: 1) In materials & methods,the author have not designed the mrcorrhizal fungi proof for GDB162, GDB254, GS222.
2)  In materials & methods,the author designed the content "Determination of chlorophyll and MDA contents",but no results were given. the author only mentioned it in discussion.
Validity of the findings: no comment
Additional comments: 74-75line: Because GDB162, GDB254, and GS222 are mycorrhizal fungi, you should give the reference about GDB162, GDB254, and GS222. If you first report you should draw a cluster tree diagram and give the proof of mycorrhiza.
102line: I have not found the results about the content “Determination of chlorophyll and MDA contents”
140-141 line: what is the concentration of mycorrhizal fungus to inoculate into D. officinale?
142 line: “the seedlings were inoculated with pathogenic fungi”. The fungal spores or colony, which one was used to inoculate? What is the concentration of pathogenic fungi?
207-211 line: please give the picture “most seedlings withered”;on the other hand, please mark the diseased roots with arrows.
212 You mentioned “Mycorrhizal fungi are competitive with pathogenic fungi”, can GDB162, GDB254, GS222 and MLX102 colonize the D. officinale? But you have not given the proof.
221-239 line: you give the result “Mycorrhizal fungi improve root rot resistance of D. officinale”by chart. Can you give the picture for pot experiment?


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

Input:
Title: THE MYCORRHIZAL FUNGI OF CYMBIDIUM PROMOTE THE GROWTH OF DENDROBIUMOFFICINALE BY INCREASING ENVIRONMENTAL STRESS TOLERANCE
Review round: 2
Reviewer: 1

Output:
Basic reporting: This manuscript describes that four mycorrhizal fungi of Cymbidium can promote the growth of plants and increase environmental stress tolerance on Dendroium offcinale. One regrettable thing is that whether the four mycorrhizal fungi can colonized on roots of D. offcinale had not been directly varified. However, the study can guide agronomic operation to enhance production of D. offcinale to some extent.
Experimental design: no comments
Validity of the findings: no comments
Additional comments: 1. In materials & methods, the information of GDB162, GDB254, GS222, MX102 has already provided on the manuscript. But I want to know that whether has some references reported for these four strains? If yes, please provide?
2. line 105-106: why did the experiment use leaves to inoculate mycorrhizal fungi? Please provide references if possible. Moreover, on the part: the effect of mycorrhizal fungi on pathogens (line163), you used 5mm diameter blocks of agar containing fungi.
3. line 109-111: there are three group on here，but only two group (adequate and limited water) were showed in figure 4. why?
4. line157-161: Whether this protocol has been reported previously, and if available, please provide the literature.
5. line 196-198: According to figuer3B-D, the fungus with the best growth-promoting effect is GDB162, not GDB254.
6. line 201-203: There are three group in material & method, which experiment groups are described by this result ?
7. line219-220: Pathogenicity tests were conducted on medium and pot conditions. However, figure 6 showed only plants in pot, please provide information on medium. In addtion, the material & method  about this test should be revised clearly.
8. line 235-238: Likely Pahtogenicity, this experiment were conducted on medium and pot conditions, but figure 8 seemed to show only plants in mediumt, please provide more information on another condition. In addtion, the material & method  about this test should be revised clearly.
9. The materials & methods section of the manuscript should be revised for clearer.
10. Another comment, please see the attachment.


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: DISENTANGLING DIRECT AND INDIRECT EFFECTS OF LOCAL TEMPERATURE ON ABUNDANCE OF MOUNTAIN BIRDS AND IMPLICATIONS FOR UNDERSTANDING GLOBAL CHANGE IMPACTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The paper is generally clear and the English is good (there are a few grammatical errors that could be corrected at the editing stage). The structure is correct, figures and data are in order.

I have a few minor comments on the context and background.

1.	L37-39 – This is a bit confusing – studies addressing both land-use and climate change effects over time (i.e. with long-term data) are scarce, but there are many studies (like this one) that consider both of these under a space-for-time substitution approach (e.g. those cited on L50-51). I think you need to expand a bit here – “there are few studies that have really tried to partition the interactive effects of climate and land-use” would be more accurate.
2.	L48 – Give a reference to support the statement that specialist species of these ecosystems are highly threatened. The implication is that Cheviron and Brumfield says this, but in fact, this citation is relevant to only the second part of the sentence.
3.	L72-74 – as per comment 1, I do not agree with this statement. There have been several studies that have considered the relative contributions of direct climate effects (i.e. distributions modelled in relation to temperature and precipitation) and indirect effects (as expressed by vegetation zones along the elevation gradient), many of which are cited. The goal here is a little more subtle than described – previous studies have looked at these effects, but I guess you would argue that your approach better addresses the interaction between them and hence can better measure their independent effects – so say this!
4.	L122-127 – the approach of using temperature loggers in conjunction with point counts is pretty much the same as used by Jähnig et al. 2020 (DOI 10.1007/s10336-020-01778-5). This paper also has some highly relevant results. I am surprised it is not cited.
5.	In general, I don’t think that the paper is placed in the correct context of the existing literature. You need to be clear on what the paper replicates and what it provides that is new.
Experimental design: I have some major comments on this section.

1.	By using all points for each species, you will be including habitats that are completely unsuitable. For example, we know that Crested and Coal Tits require trees for nesting and they are not found in open treeless areas. Similarly, a Water Pipit will not occur in the middle of a forest. Absences in unsuitable habitat in these cases may be seen as ‘naughty naughts’ or ‘redundant zeros’ (see Zuur et al. 2009 Mixed Effects Models and Extensions in Ecology with R). I suspect the models are to some extent just describing the well-known division between ‘open’ and ‘closed’ habitats rather than telling us anything more interesting. Several papers that you cite have divided the alpine bird community into open and closed habitat species before analysis in order to avoid this issue. I think what you have done is worth keeping, but I think follow-up analyses, restricting each species to it’s likely potential nesting habitat, is needed.
2.	Several published papers considering bird-habitat associations in alpine landscapes have included topographic variables (slope and aspect), and in some cases, these have proven to be important predictors. Moreover, it seems plausible that they may have interaction effects with temperature and thus are likely to be highly relevant to the current study. There is no reference at all to the potential importance of topography. These data can be readily extracted at a pretty high resolution from existing DTMs. I think they need to be included.
3.	Spatial autocorrelation may be an issue and should be tested for (again, most of the cited papers analysing alpine species distributions have tested for spatial autocorrelation, although it seems rare that there are important effects).
Validity of the findings: Some minor comments on the Discussion.

1.	L207-208 – What is meant by ‘high interspecific variability’. There was variation in significance, but for those species that showed a significant effect, it was always positive. Only significant effects are reported in Table 2, so we can’t tell whether effects were generally positive (whether significant or not). Re-word this sentence.
2.	L212-213 – I would argue that there is only one mountain specialist, the water pipit (possibly also the wheatear, although this can occur in a wider range of open habitats). It needs to be stressed that you cannot really conclude anything about mountain specialists more broadly.
3.	L230-233 – I agree with this statement, but you should acknowledge that this is hardly original. It has been proposed several times (by many of the papers cited here). Rather you should say that the work supports previous research that has suggested grazing as a conservation tool to maintain open habitats in the face of shifting treelines.
4.	L235-247 – There are better papers to cite that deal specifically with the Water Pipit. In particular, Rauter et al. 2002 (Ibis 144, 433–444) considers how micro-climate and topography interact to affect nesting success (this is also relevant to EXPERIMENTAL DESIGN comment 2). Related papers from the same group should also be considered.
5.	L251 – including topography.
6.	L284-286 – Again, this statement supports several other studies and I think this should be acknowledged.
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: DISENTANGLING DIRECT AND INDIRECT EFFECTS OF LOCAL TEMPERATURE ON ABUNDANCE OF MOUNTAIN BIRDS AND IMPLICATIONS FOR UNDERSTANDING GLOBAL CHANGE IMPACTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The article completely satisfies basic reporting requests. I have not further comments to add apart from the minor comments highlighted in the review (please see pdf).
Experimental design: The article completely satisfies  experimental design requests. I have not further comments to add apart from the minor comments highlighted in the review (please see pdf).
Validity of the findings: The article attempts to disentangle habitat vs climatic drivers influencing bird occurrence/abundance across a wide elevation gradient. This is a major and very relevant topic for climate change-related studies. The authors have correctly highlighted the novelty factor of this work throughout the manuscript.
Additional comments: Congratulation to the authors for submitting this very interesting manuscript. Most of my comments are minor (see attached pdf) and I have few major comments to make:

- Given the wise elevation gradient used I was expecting to see habitat & temperature relationships to be non-linear (i.e. quadratic) but authors have opted for linear structural equation model. I wonder if this choice might explain some of the unexpected results emerged in the study (relationship between temperature and some mountain specialist birds). Can the authors explain their rationale for choosing only linear structural equation model.

- Precipitation were not modelled in this study and authors have provided a reasonable argument why this choice is unlikely to be a major issue for the final results. However, I argue that the use of the world “climate” in the title and throughout the manuscript (i.e. “we modelled climate”) is not correct and should be changed with “temperature”.

- It will be very informative to plot mean season temperature across elevation (whilst accounting for aspect) to make the reader understand how much variation occurs across the study site .

Thanks a lot for the opportunity in reviewing this important work


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: DISENTANGLING DIRECT AND INDIRECT EFFECTS OF LOCAL TEMPERATURE ON ABUNDANCE OF MOUNTAIN BIRDS AND IMPLICATIONS FOR UNDERSTANDING GLOBAL CHANGE IMPACTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The basic report is good. Previous queries have been adequately dealt with. Just a few comments on the text (line numbers refer to the tracked changes Word Document)

1. L9 - "in 2018" rather than "In year 2018".
L134 - it's not clear what is meant by "are indeed hardly to occur". You mean there is hardly any evidence that topographic features have effects on alpine birds?
L168 - it should be "..not aimed at quantitatively disentangling...".
L209 - "intrepreted with caution" would be better than "cautiously considered".
L211 - I agree that chiffchaff should still be included, despite the relatively high spatial autocorrelation. The caveat provided is sufficient.
Experimental design: All is now clear - the additions to the text have clarified the authors' approach.
Validity of the findings: No further comment - all issues addressed adequately.
Additional comments: Nothing further to add.


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: DISENTANGLING DIRECT AND INDIRECT EFFECTS OF LOCAL TEMPERATURE ON ABUNDANCE OF MOUNTAIN BIRDS AND IMPLICATIONS FOR UNDERSTANDING GLOBAL CHANGE IMPACTS
Review round: 2
Reviewer: 2

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: NA
Additional comments: I thank the authors for the substantial changes made to the manuscript. Congratulations for your work!


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: ESTIMATING THE IMPACT OF INFLUENZA ON THE EPIDEMIOLOGICAL DYNAMICS OF SARS-COV-2
Review round: 1
Reviewer: 1

Output:
Basic reporting: Authors showed the possible impacts of seasonal influenza on the SARS-CoV-2 transmissions, by fitting the compartment model with the number of COVID-19 deaths in European countries. The manuscript is well written and provides insight into interrelationship between the transmission dynamics of influenza and COVID-19. However, I have some major concerns in terms of the model design and evaluation. I hope this suggestion make this manuscript to have the highest impact.
Experimental design: 1. I am not convinced that the actual transmission dynamics of COVID-19 can be reconstructed by fitting the age-aggregated model with the number of deaths. As authors mentioned in the Limitation part, the infection fatality risk of COVID-19 is suggested to considerably increase by age, moreover, young adults contracted with COVID-19 are likely to be a mild case (but they are infectious). Thus, considering this crucial characteristic of COVID-19, without using the age-structured model, I believe reconstructing the actual dynamics by fitting with the number of deaths might be highly limited.

2. I would be inclined to mention why authors assumed the negative binomial distribution in death reporting. I think the most crucial advantage of death data is under-ascertainment issue can be partially removed, since the COVID-19 death cases are highly likely to be observed. Did the countries in this study have huge difficulties in death reporting? or were there any circumstance with huge under-reporting in the number of deaths? It would be great if authors can clarify the reason of introducing the negative binomial distribution in death reporting.
Validity of the findings: 1. The model evaluation was conducted by comparing the number of observed and modeled deaths. However, authors did not show that the model integrated with the influenza dynamics can provide better insight into actual COVID-19 dynamics, compared to the conventional COVID-19 model. The fitting results looks plausible and authors also show some published papers about the possible impacts of influenza. However, I think it is not enough to say the model incorporated with the influenza can provide a better performance and can be used as an evidence. I suggest authors to compare the AIC value between the proposed and conventional model to show the performance of model.
Additional comments: [Minor comments]
1. L142: I would like to suggest to change the abbreviation of the stringency index to other word. Since s(t) seems like the number of susceptible at time t (in the compartment model), it can make readers confused.
2. Could authors show the estimated overdispersion parameter in death reporting (k_D) in the Table 2?


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: ESTIMATING THE IMPACT OF INFLUENZA ON THE EPIDEMIOLOGICAL DYNAMICS OF SARS-COV-2
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript meets all basic reporting standards.
Experimental design: While I find the results of the study intriguing, I think there are some further assessments needed to make the results more conclusive.

1. Similar to the study showing suppression of SARS-CoV-2 infections by rhinovirus (Dee et al. cited in the current manuscript), there is a study indicating that SARS-CoV-2 infections could be suppressed by influenza (Pinky and Dobrovolny, (2020) J. Med. Virol.). How does this fit into the assumption that SARS-CoV-2 transmission is enhanced by influenza?

2. The authors mention that they fit the model with beta_f = 0 to the data, but they do not present these results in the manuscript. I think the parameter estimates and log likelihoods for this model need to be included in the manuscript (or supplementary material with the other models). After all, if the log likelihood for a model without the effect of influenza is similar to the log likelihood of the model with influenza, then the case for the effect of influenza is pretty weak.

3. I think the authors also need to include correlation plots of the estimated parameters. It could be that the assumed effect of influenza can be compensated for by altering other model parameters.

4. The set range for some of the estimated parameters might be too small. The 95% CI for b and R0 are hitting the lower boundary for some of the data sets.

5. Why are two different methods used to estimate 95% CI for the estimated parameters (Table 2 caption)?

6. This wasn't entirely clear to me, but was the model fit only to daily deaths? Or were case counts also included?

7. The discussion around lines 345-354 is actually presenting a new result and should probably be included in the results section.

8. The authors should perform additional sensitivity analysis on the number of stages assumed in each of the transitions. As n --> infinity, the number of stages has little effect on the estimated parameters, but the authors have fixed each transition to 2 stages, so even a change to 3 stages might change the estimated parameter values.
Validity of the findings: The conclusions are well stated, although as outlined above, I think more evidence is needed to support their claim.
Additional comments: No additional comments


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

Input:
Title: ESTIMATING THE IMPACT OF INFLUENZA ON THE EPIDEMIOLOGICAL DYNAMICS OF SARS-COV-2
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors revised the manuscript and overall the revised manuscript is well written in accordance to comments. I appreciate authors' effort on it. However, I am not still convinced that the validity of proposed model is sufficiently secured to assess the impact of seasonal influenza on the transmission dynamics of COVID-19.
Experimental design: Unlike the early phase of epidemic, detailed information on the characteristics of SARS-CoV-2 transmission has been identified. Thus, at this stage, I do not fully agree that reconstructing the transmission dynamics of COVID-19 by fitting the age-aggregated model with daily deaths using an identical infection fatality risk across all age is sufficient, especially, to explore the possible association with the seasonal influenza. In addition, although the estimated confidence interval of proportion of infected individuals among all population includes the estimated value from sereprevalence data (Table 2), considering an absolute number of the 1% of total population in each countries, I think the estimates with the broad confidence intervals is not so informative to show the validity of the reconstructed model.
Validity of the findings: I fully understood that the present study relies on the likelihood-based inference, however, considering the different number of used parameters, I do not think that only showing the likelihood can clearly clarify that the incorporation of seasonal influenza can significantly improve the model. Despite of my opinion, the shown table shows the model incorporated with seasonal influenza shows better performances, although I still have some worries on the validity of model as mentioned in the upper 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: ESTIMATING THE IMPACT OF INFLUENZA ON THE EPIDEMIOLOGICAL DYNAMICS OF SARS-COV-2
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: The authors have incorporated many of the additional checks, strengthening the support for their findings.
Validity of the findings: No comment
Additional comments: The authors have addressed my concerns to my satisfaction.


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: BOLL CHARACTERISTICS AND YIELD OF COTTON IN RELATION TO THE CANOPY MICROCLIMATE UNDER VARYING PLANT DENSITIES IN AN ARID AREA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript need English editing.
Experimental design: OK
Validity of the findings: OK
Additional comments: English should improve by a native person. The paper suffers from a poor English structure throughout and cannot be published or reviewed properly in the current format. The manuscript requires a thorough proofread by a native person whose first language is English. The instances of the problem are numerous and this reviewer cannot individually mention them. It is the responsibility of the author(s) to present their work in an acceptable format. Unless the paper is in a reasonable format, it should not have been submitted.
2.    The novelty of the study needs to be highlighted compare to other similar studies.
3.    Discussion is weak. The discussion needs enhancement with real explanations not only agreements and disagreements. Authors should improve it by the demonstration of biochemical/physiological causes of obtained results. Instead of just justifying results, results should be interpreted, explained to appropriately elaborate inferences. Discussion seems to be poor, didn't give good explanations of the results obtained. I think that it must be really improved. Where possible please discuss potential mechanisms behind your observations. You should also expand the links with prior publications in the area, but try to be careful to not over-reach. For the latter, you should highlight potential areas of future study.
4.    The scientific background of the topic is poor. In "Introduction" and "Discussion", the authors should cite recent references between 2016-2020 from JCR journals.
Fahad, S., Sönmez, O., Saud, S., Wang, D., Wu, C., Adnan, M., Turan, V. (Eds.), 2021a. Plant growth regulators for climate-smart agriculture, First edition. ed, Footprints of climate variability on plant diversity. CRC Press, Boca Raton, FL.
Fahad, S., Sonmez, O., Saud, S., Wang, D., Wu, C., Adnan, M., Turan, V. (Eds.), 2021b. Climate change and plants: biodiversity, growth and interactions, First edition. ed, Footprints of climate variability on plant diversity. CRC Press, Boca Raton.
Fahad, S., Sonmez, O., Saud, S., Wang, D., Wu, C., Adnan, M., Turan, V. (Eds.), 2021c. Developing climate resilient crops: improving global food security and safety, First edition. ed, Footprints of climate variability on plant diversity. CRC Press, Boca Raton.
Fahad, S., Sönmez, O., Turan, V., Adnan, M., Saud, S., Wu, C., Wang, D. (Eds.), 2021d. Sustainable soil and land management and climate change, First edition. ed, Footprints of climate variability on plant diversity. CRC Press, Boca Raton


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: BOLL CHARACTERISTICS AND YIELD OF COTTON IN RELATION TO THE CANOPY MICROCLIMATE UNDER VARYING PLANT DENSITIES IN AN ARID AREA
Review round: 1
Reviewer: 2

Output:
Basic reporting: I must congratulate to the authors of this manuscript for conducting this study, I mean such study are very limited in the literature. I have gone through this article, when I just the file sentence of "ABSTRACT" portion, that confused me, where it is mentioned "making full use of the group effect are the keys to achieving high-efficiency ". This is not clear to anyone, this indicate the re-phrase of such sentence to remove the ambiguity (if any). It allowed me for mentioning that, this article must ne edited for English Native Speaker before publication.
Likewise, the author should elaborate the RESULTS and DISCUSSION portion, and this is possible after see critical review of tables, figure and statistical analysis.
Experimental design: Well designed
Validity of the findings: I have also gone through the data and its statistical analysis, this portion is acceptable to me
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: BOLL CHARACTERISTICS AND YIELD OF COTTON IN RELATION TO THE CANOPY MICROCLIMATE UNDER VARYING PLANT DENSITIES IN AN ARID AREA
Review round: 2
Reviewer: 1

Output:
Basic reporting: ok
Experimental design: ok
Validity of the findings: ok
Additional comments: Accepted as it is


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: CNV-P: A MACHINE-LEARNING FRAMEWORK FOR PREDICTING HIGH CONFIDENT COPY NUMBER VARIATIONS
Review round: 1
Reviewer: 1

Output:
Basic reporting: In this manuscript, Wang et al. proposed a machine learning framework, CNV-P, for predicting high confident copy number variations (CNV). The computational detection of CNVs using genome sequencing data is an important task and should be of general interest to the community.  I think this work may be helpful to the CNV data end-users.
Experimental design: The current CNV calling methods are suffering from low  accuracy with high false positive rates. Different from the conventional methods which use hard cutoff to select high confidence callings, the authors proposed a machine learning method based on random forest to predict high confidence CNVs using multiple features such as read depth, split reads  and read pair around the putative CNV fragments.
Validity of the findings: The authors validated their method on synthesized and real data sets. The proposed method showed high precisions with good sensitivity.
Additional comments: Minor Comment:
It is interesting to know the contributions by each feature in the random forest prediction model, and compared performance with the hard cutoff method using the eminent feature.


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: CNV-P: A MACHINE-LEARNING FRAMEWORK FOR PREDICTING HIGH CONFIDENT COPY NUMBER VARIATIONS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The detailed method of training in real sample is understandable by Table S1 and S2 but it should be written in the method section in the main text with similar details.
Experimental design: no comment
Validity of the findings: Integrate SV calls from multiple algorithms and extract better calls by using supporting evidences based on random forest learning of PE, SR, RD and so on, is not a new idea (for example, Werling et al. Nat Genet 2018; 50: 727-36. or Zhuang et al. NAR genom bioinform 2020; 2: Iqaa071, possibly more?) While the details were somehow different each other.

This reviewer asks the authors to compare the performance. It would also be valuable to see the comparison of the performance with other integrative CV callers such as MetaSV.
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: CNV-P: A MACHINE-LEARNING FRAMEWORK FOR PREDICTING HIGH CONFIDENT COPY NUMBER VARIATIONS
Review round: 2
Reviewer: 1

Output:
Basic reporting: All my questions are addressed.
Experimental design: All my questions are addressed.
Validity of the findings: All my questions are addressed.
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: CNV-P: A MACHINE-LEARNING FRAMEWORK FOR PREDICTING HIGH CONFIDENT COPY NUMBER VARIATIONS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors appropriately addressed my concern
Experimental design: no comment
Validity of the findings: The authors mostly addressed my concern, this reviewer appreciated it. However, in my original comment, I also asked the authors to compare with Werling et al. method

(now merged to) https://github.com/broadinstitute/gatk-sv#gather-sample-evidence

Please mention it and compare, or if there is difficulty to compare with it, please explain.

Also this reviewer would request the authors to describe the comparison pipeline at the authors' github space or somewhere, for the readers to be able to replicate it.
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: CNV-P: A MACHINE-LEARNING FRAMEWORK FOR PREDICTING HIGH CONFIDENT COPY NUMBER VARIATIONS
Review round: 3
Reviewer: 1

Output:
Basic reporting: NA
Experimental design: NA
Validity of the findings: I've checked the authors' github space

https://github.com/wonderful1/CNV-P

and confirmed that they successfully addressed the point of concern.
Additional comments: NA


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

Input:
Title: IDENTIFICATION AND PATHOGENICITY OF ALTERNARIA SPECIES ASSOCIATED WITH LEAF BLOTCH DISEASE AND PREMATURE DEFOLIATION IN FRENCH APPLE ORCHARDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is well written and easy to read. While the introduction is slightly on the longer side, it does contain important information to build an understanding for the next sections. I would suggest that the section would be divided into smaller paragraphs as it currently appears to have only two paragraphs. Smaller sections would make it easier to follow the text and separate the different topics.
The manuscript is well structured and illustrated with a range of informative figures and tables. Adding the supplementary data provides further information which might also be useful to some readers.
Experimental design: The study included a large number of samples from a range of geographic areas, collected over three years. That results in a sufficiently representative collection to make conclusions about the pathogen populations and authors have provided sufficient detail about the methodology they have used for sequence data generation and analysis, as well as for pathogenicity testing.
Validity of the findings: The results and conclusions from the study are well supported and presented. Publishing these results will be useful to a range of professionals working in apple orchards. It is important to make these findings publicly available so we could better understand the role of different Alternaria species in leaf blotch and fruit spot disease.
Additional comments: There are a few minor aspects that would be good to revisit and clarify. Please see some small suggestions below:
- Line 142 - could you please clarify what do you mean by "malt medium"? Was this malt extract agar?
- Line 288 – the first part of the sentence reads a bit odd. Maybe “resulted in a 900 bp long alignment” or “Concatenated Alta-1 and Endo-PG were in total 900 bp long”?
- Line 303 – remove word “only”
- Line 352 – modify the sentence as follows “… examples of the results from the pathogenicity tests…”
- The introductory section in the beginning of the discussion (lines 356-360) do not add much value, in my opinion. I would suggest removing it and moving straight to discussing the results.
- I would also suggest to remove the conclusions section as it is very similar to the abstract and the well structured discussion section already allows to find the three main points about the findings of this study.


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

Input:
Title: IDENTIFICATION AND PATHOGENICITY OF ALTERNARIA SPECIES ASSOCIATED WITH LEAF BLOTCH DISEASE AND PREMATURE DEFOLIATION IN FRENCH APPLE ORCHARDS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is very well written. Literature references are adequate. Very well structured manuscript.
Experimental design: The experiments are very well carried out. No further comments.
Validity of the findings: The data are robust and sound. Conclusions are clear. No further comments
Additional comments: Dear authors, a very good manuscript. I have made a number of suggestions in the attached pdf. These are mainly edits (e.g. cultivar instead of variety).


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: COMPOSITION, RICHNESS AND NESTEDNESS OF GALLERY FOREST BIRD ASSEMBLAGES IN AN AMAZONIAN SAVANNA LANDSCAPE: LESSONS FOR CONSERVATION
Review round: 1
Reviewer: 1

Output:
Basic reporting: No comments.
Experimental design: No comments.
Validity of the findings: No comments.
Additional comments: The manuscript is very interesting, with clearly stated objectives and conclusions. It represents a good addition to the literature regarding gallery forests and savanna ecosystems. Below I present suggestions on specific parts of the manuscript. Of major concern are some aspects of the methods that need clarification and/or reevaluation. Specifically, I do not consider the proxy for dispersal ability a good choice as the measure could be correlated to several other species-specific traits and I suggest its removal from the analysis. I hope the authors will find my comments useful to improve their manuscript.

Abstract:
(1) change “porcentage” to “percentage”

Introduction:
Line 56: remove ‘s’ from “savannas”
Line 68: remove ‘s’ from “centers”
Lines 69-74: “Regions” are repeated a lot in these phrases, and it could be reworked to read better. I suggest briefly stating that gallery forests are part of savanna ecosystems (i.e. of the savanna regions) as it would possibly make it easier to rework the statements.
Lines 87-91: It is important to note that, as mentioned by the authors, Forman (1995) also considers other functional traits – not only dispersal ability – by mentioning that generalists would dominate the GF communities. Therefore, it is important to mention “generalism” in addition to dispersal ability. Also, I think that it would interesting if the authors present about the expected drivers of the differences in community composition and its expected nestedness, more specifically regarding the habitat attributes (e.g. proximity to adjacent forest?).

Methods:
Line 175: add ‘,’ between “lianas” and “dead trees”
Lines 188-191: In every transect (site) there were 21 measurements of litter depth (3 plots x 7 measurements/plot). Please, double check the total of 63 measurements per transect (site).
Line 198: change “was” to “were”
Line 203-204: Was the sampling order of point counts randomly assigned such that the time of sampling would not interfere in the results (e.g. one site is always sampled at 6am and has higher species richness than a site that has always been sampled at 10am due to reduced species activity)?
Line 216: Please, cite the literature from where the body mass data was obtained.
Lines 218-221: I consider that it is not a good measure of species dispersal ability as many other specific traits might influence how far a species can move into the savanna. For example, in the dataset there are species that are well adapted to open vegetation areas with scattered trees, like Elaenia flavogaster, Myiarchus ferox, Thraupis spp., among others, for which this proxy for dispersal ability would not make sense. Therefore, I suggest removing it from the analyses (even though a correlation was found between this variable and abundance and occupancy) or removing species characteristic of open vegetation and reanalyzing a subset of the data composed only of forest-dwelling species. Also, I could not find Sousa’s dissertation to evaluate their methods, not even at Universidade Federal do Amapa’s online library system. On the other hand, the authors already have a proxy for dispersal ability, the HWI data taken from Sheard et al. (2020). Yet, it also is important to note that, although Sheard et al. (2020) calls it HWI, they actually measured the Kipp’s Index (1959), not the HWI as presented by Claramunt & Wright (2017) and Claramunt et al. (2012). Claramunt & Wright’s HWI has a standardization for body size (wing length) in their formula, not used by Sheard et al. (2020).
Line 230: Please, add the conditions that determined if a species well-sampled.
Lines 237-239: Please, cite a reference for this standardization. If it was not taken from the literature, but is a common practice, it should be explained further.
Line 252: Should it be VIF < 3? If not, how much higher than 3? If VIFs are too high, one or some of the variables should be removed from the analyses.
PGLS, AICc, and model selection: (1) To compute the model average presented in Tables 1 and 2, were only the models with delta < 2 used? If not, would you consider using only those models with delta < 2, as those are considered the most informative?
(2) In the PGLS analyses, categorical variables should be added to the models by dummy coding them (Mundry, 2014), but it seems that was not the case for foraging stratum groups. I suggest performing the analyses again and using dummy coded variables for foraging stratum.
Mundry R. (2014). Statistical issues and assumptions of phylogenetic generalized least squares. In
Modern phylogenetic comparative methods and their application in evolutionary biology (ed. LZ Garamszegi), pp. 131–153. Berlin: Springer.

Results:
Line 338: italicize Dendrocolaptes certhia
Line 354: The sample size is small (26) and the number of models tested is too high, reducing the power of the AIC to detect the best model (check Burnham & Anderson [2002] book and their discussion about it – number of models x number of variables x sample size). I believe this issue is reflected in the low values of the AIC weights for the models (or, alternatively, all models are performing poorly in describing the data). Therefore, I would suggest that the authors select a smaller set of biologically meaningful models for testing, instead of using all the possible model combinations as it has been done. In the way the analysis was performed it is impossible to tell models apart and determine which factors are correlated with taxonomic, functional, and phylogenetic diversity in the study system.

Discussion:
Lines 384-386: I still am unconvinced that the distance is correlated with, or a proxy for dispersal ability. I think other functional traits might be affecting how far a species move into the open savanna, i.e. habitat preferences, diet, or foraging behavior. In other words, the traits that would make the species tolerance to the savanna ecosystem higher (a generalist), but not necessarily dispersal capability.
Line 409: Add a period (.) after “(Mustin et al., 2017)”
Line 417: change “gallery forest” to “birds”

Conclusion:
Lines 453-454: the correlation between PD and understory foliage density is not presented in the discussion. Please, add a discussion about the processes that might be driving it and its significance in the study.

Figures and tables:
Figure 1: in the box within the map, change anthropism for anthropogenic, disturbed, or similar word.
Tables 1 and 2: these tables results from similar analyses, thus I suggest standardizing their format.


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: COMPOSITION, RICHNESS AND NESTEDNESS OF GALLERY FOREST BIRD ASSEMBLAGES IN AN AMAZONIAN SAVANNA LANDSCAPE: LESSONS FOR CONSERVATION
Review round: 1
Reviewer: 2

Output:
Basic reporting: Generally clearly written and well constructed, historical literature appropriately treated and figures OK - note Fig 1 will be inaccessible for R-G colourblind readers.
Experimental design: MS within the scope of the journal and fairly novel. It would have been useful to understand whether the community composition is a nested subset of surrounding terra firme forests, or a novel community of fragmentation tolerant and edge species. Looking at the list more species seem to be the latter - the two most abundant species are Tolmomyias flaviventris and Turdus leucomelas which are not associated with undisturbed forest habitat in Amazonia and Formicivora grisea is a not a forest-associated species at all. The sample size is rather small and the sample contains a long tail of rare species, several of which I wouldn't expect to be rare, so good to emphasize the knowledge of the surveyor.

A lot of the paper hangs on the 'species' dispersal ability' scores taken from an unpublished MSc thesis. A much better rationale needs to be made for using these scores which are opaque. Several of the species e.g. Formicivora breed in the savannas so I don't see how this is measuring dispersal and not just tolerance of non-forest habitats. It seems odd to have Querula have a 'dispersal score' of 0 when it is a large bodied bird which is a very strong flyer with a mid-range HWI. The HWI is itself a measure of dispersal capacity. I would seek to categorise species by habitat preference using an external dataset.

I did wonder about using unlimited radius point counts with only 200m between points - some Amazonian species can easily be detected at 200m risking double-counting and hence pseudoreplication when summing data across points.

The landscape scale habitat coverage section is poorly treated, many of the corridors are situated a long way from forest nodes, it might be useful to capture both this variation and habitat availability at wider buffer widths - also corridor width seems important and in combination may explain the presence/absence of forest-associated suboscines. I have generally found that investing lots of effort in local habitat variables explains little as they vary so much in space and birds often have large territories, the authors should seek to glean more information about habitat at landscape scales.
Validity of the findings: The section on general traits of species in the study area e.g. L342 seems out of place when the authors have had to constrain their community due to sampling issues - bigger species will have been excluded for example.

The lack of predictive power of the env variables could be improved by considering more landscape variables describing habitat amount, habitat quality and connectivity.

I struggle with the 'selective colonization' paradigm - how is this different from habitat filtering?
Additional comments: Abstract 'porcentage' = 'percentage', nestedness pattern = nested pattern
L52 are Neotropical savannas 'regions' or 'habitats'
L53 also silvioculture - e.g. in AP eucalyptus and in PA oil palm
L60 do gallery forests sustain savanna species? Is Burhinus in the galley forest?
L79 surely gallery forests are also totally structurally distinct from terra firme forest - hence habitat filtering.
L112 the MAPITIOBA frontier also vies for this title.
L200 4 visits isn't enough to capture most species - the regional species pool includes lots of species that were not recorded.


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: COMPOSITION, RICHNESS AND NESTEDNESS OF GALLERY FOREST BIRD ASSEMBLAGES IN AN AMAZONIAN SAVANNA LANDSCAPE: LESSONS FOR CONSERVATION
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript is well structured and clearly written. Sufficient field background/theoretical context is provided. The structure in terms of tables, figures and raw data is apropriated. The questions are clear and the authors found relevant results to them.
Experimental design: The study is original and in the scope of the journal. The research questions are clear, relevant and meaningful. It is stated how the study fills an identified knowledge gap. The investigation was performed to a high technical standard. The methods are described in detail and can be replicable.
In Methods, in the sub-item "Species functional traits" the authors mentioned that the body mass for all species was gathered from the literature, but did not include the references used for that, which need be added. In the sub-item "Species Selection" it will be good to include what is the minimum amount used to consider a species as "well sampled".
Validity of the findings: The underlying data have been provided and they are robust and statistically sound. The discussion is appropriated, the conclusions were well stated and linked to the research questions. The second part of the conclusion (Lines 460 to 481) seems more appropriated to be included at the end of the discussion instead as in "conclusion."
Additional comments: The manuscript approaches a relevant issue for biodiversity conservation. The authors proposed strategies on how gallery forests can be managed to maintain bird species assemblages in face of the fast anthropogenic activity in the tropical landscape. A result to be highlighted as a new finding is that increased human activities in the landscape was negatively correlated with taxonomic and functional diversity of gallery forests. This supports the idea that in tropical landscapes, extrinsic factors (e.g. matrix dynamics), are as important as intrinsic factors to explain the ecological processes occurring within habitat patches. Based on their results, the authors indicated recommendations for conservation of gallery forests, which are important to the maintenance of a substantial part of the biodiversity in neotropical savannas.
Specific suggestions/comments were included in the PDF file of the manuscript.


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

Input:
Title: COMPOSITION, RICHNESS AND NESTEDNESS OF GALLERY FOREST BIRD ASSEMBLAGES IN AN AMAZONIAN SAVANNA LANDSCAPE: LESSONS FOR CONSERVATION
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments.
Experimental design: No comments.
Validity of the findings: No comments.
Additional comments: The authors addressed all of the reviewers' comments, including those regarding the analyses and parameters used, and the manuscript has improved substantially. The manuscript is easy to read and draws interesting conclusions, especially regarding the conservation of gallery forests/savannas. I found only one minor sentence that needs to be fixed in Lines 383-384 where it reads "Indicators of landscape structure explained more the variation of the three biodiversity dimensions that indicators of vegetation structure." which could be fixed as "Indicators of landscape structure explained more of the variation in the three biodiversity dimensions than indicators of vegetation structure."

Good luck on your future research, sincerely,


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: COMPOSITION, RICHNESS AND NESTEDNESS OF GALLERY FOREST BIRD ASSEMBLAGES IN AN AMAZONIAN SAVANNA LANDSCAPE: LESSONS FOR CONSERVATION
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I am generally happy with the efforts by the authors to attend to my comments and those of the other reviewers which have resulted in a strengthened manuscript.


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

Input:
Title: COMPOSITION, RICHNESS AND NESTEDNESS OF GALLERY FOREST BIRD ASSEMBLAGES IN AN AMAZONIAN SAVANNA LANDSCAPE: LESSONS FOR CONSERVATION
Review round: 2
Reviewer: 3

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The manuscript has greatly improved with the authors' review. I only have two small changes:
L 163: replace "(4)" with "(3)"
L 478: replace "Maria Alice Alves" with "Maria Alice S. Alves"


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

Input:
Title: EFFECTS OF PROBIOTIC SUPPLEMENTS ON GROWTH PERFORMANCE AND INTESTINAL MICROBIOTA OF PARTRIDGE SHANK BROILER CHICKS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article must be written in English and must use clear, unambiguous, technically correct text. The article must conform to professional standards of courtesy and expression.
Experimental design: The design was poor. All the study were just 2 groups, without positive control group. How to compare the advantage of your EM without the ruler. Hence, the data was unconfident.
Validity of the findings: In section of Background: “to our knowledge, there is no report of EM on the growth performance and the modulation in GM of Partridge Shank broiler chickens: were wrong. EM have been used in poultry chicks, also in Partridge Shank broiler chickens. The authors must read more references on direct supplementary probiotic feed.
Additional comments: Although this work was carried out with efforts. The related research was very heavy. And the innovation of this study was few. There was no corrected analysis on the data of growth performance and intestinal micro structure. The most issue was the uncorrected group design cause the inappropriate data.


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

Input:
Title: EFFECTS OF PROBIOTIC SUPPLEMENTS ON GROWTH PERFORMANCE AND INTESTINAL MICROBIOTA OF PARTRIDGE SHANK BROILER CHICKS
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript describes a study to investigate the efficacy of probiotic supplementation on growth performance and intestinal microbiota of partridge shank broiler chickens between 10-30 days of age. The novelty of the manuscript is fair, but there are several problems. First, the author's description of significance is not particularly clear, including the writing and description of the P value. When the comparison between the test group and the control group is significant in a certain parameter, the P value needs to be added to the end of the sentence. For example, line 258. On the contrary, there is no need to add P value. And in general, there is no need to report or discuss non-significant results because they do not contribute to the research results.
Experimental design: .
Validity of the findings: .
Additional comments: Line 31-33: There is only one in the experimental group. If you can do two more experiments with different EM additions, the discussion of the results may be richer and have practical guiding significance.
Line 78-79: The connection between these two paragraphs is a bit awkward, you may need to add one sentence.
Line 202-203: Do not use the first paragraph for each of the results subsections to indicate what was done (as this is already included in materials and methods section) and a caption of the representative table. Instead, directly and concisely report the results and refer to the table as appropriate in the text.
Line 205: The P value should be presented P < 0.05, P < 0.01 or P < 0.001. Please change this consistently within the manuscript. Moreover, non-significant results do not need to be reported.
Line 216-220: Same as the problem presented in line 202-203.
Line 222-223: Delete the sentence “However, the indices of Shannon, Simpson, Chao1 and Ace tended to be higher as the broilers grew up”
Line 264-275: No P value was presented in the paragraph.
Line 285: Whether the word “Partridge Shank” need to be italicized, please unify it.
Line 290: “(Sohail et al., 2012)” should be presented as “(2012)”.
Line 290-291: Inconsistent statements and references.
The latest references should be added in your manuscript. You can check the work in
1. Production performance, egg quality, plasma biochemical constituents and lipid metabolites of aged laying hens supplemented with incomplete degradation products of galactomannan
2. A sustainable process for procuring biologically active fractions of high-purity xylooligosaccharides and water-soluble lignin from Moso bamboo prehydrolyzate


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

Input:
Title: EFFECTS OF PROBIOTIC SUPPLEMENTS ON GROWTH PERFORMANCE AND INTESTINAL MICROBIOTA OF PARTRIDGE SHANK BROILER CHICKS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The research background is introduced in detail in the preface, being there are few studies about the impact of EM on local chicken breeds, so this article was carried out to evaluate the effects of EM on the growth performance, gut health and microbiota of Partridge Shank broiler chickens.The reason and basis are sufficient, and the previous research literature references are also included. The structure, figures and tables are put in correctly. All appropriate raw data have been made available. The submission include the results relevant to the hypothesis that the EM would improve the structure and composition of gut microbiota of EM-treated broiler chickens, perhaps via a mechanism of inhibiting the colonization of bad bacteria. The language is clear and intelligible, but not professional. Some examples where the language could be improved include lines 71,72,79,80, 81, the current phrasing makes comprehension difficult . I suggest you have a colleague who is proficient in English and familiar with the subject matter review your manuscript.
Experimental design: The article aimed to evaluate the effects of a basal diet with the supplementation of an EM mixture on the growth performance and gut health in Partridge Shank broiler chickens. The experiment was performed to a high technical and ethical standard.
All procedures involving live animals were verified and approved by the Office of Animal Care and Use of Jiangxi Agricultural University (protocol number JXAU-LL-2020-0018). Methods were described with sufficient detail and information to be reproducible by another investigator. But the number of replication and the replication per are too few. According the experimental design, 6 replications are necessary, and 30-50 chickens per replication are more suitable.
Validity of the findings: All underling data have been provided, and they are robust, statistically sound and controlled. Some meaningful research results are obtained, i.e when compared with the control group, in cecal the abundances of Firmicutes, Euryarchaeota, and Ruminococcus were significantly reduced, while the abundances of Actinobacteria and WPS-2 were significantly increased. But in the discussion, there is no explanation for the significance of this change in intestinal microbiota. Please add it. Moreover, the microbiome in feces is very different from the intestinal microbiome, the study of intestinal microbiome is more meaningful than fecal microbiome. Why does this study focus on fecal microbiome? The conclusions are not well stated, it is too long, should be accurately summarized.
Additional comments: 1. Line 28 Methods: It is too simply, we don't know which indicators have been sampled and tested.
2. Line 37 results: the results of gut microbiota,come form feces or cecal? We donot know.
3. Line 81: According to reports, local breeds of broiler chicken account for 46.52% of broiler slaughter in China, 2017, and this proportion will continue to increase in 2018 (Zhao et al., 2019), are there any up-to-date references? It's too old.
4. Line 108: vaccines against Marek’s disease, Newcastle disease, and Infectious bursal disease，the specific immunization date should be given.
5. Partridge shank chicken, a local broiler breed in China, using NRC (1994) standard is not suitable, do you think?
6. line 121: basal diet supplemented with 2.5 x 109 colony-forming unit (cfu) of EM per bird/day for 20 days, how to do it, add it to the feed?
7. Line 127: Then the feed intake was calculated from the differences between the offered and residual feed and was used to calculate average daily intake (ADFI), average daily gain(ADG), and feed/gain ratio (F/G). How to calculate the ADG through the feed intake?
8. Line 132: excreta at the 1st, designated as EM0, why not designated as EM1? Same as B0.
9. Line 135: Fecal samples and cecal contents from 3 chickens in each coop were pooled as one test specimen. Since five chickens in each group were sampled, how to deal with remaining two?
10. Line 153: What is the composition of the PCR reaction system?Please in detail.
11. Line 158: with Nextera XT Index primers, what is primers sequence？
12. Line 220:“No significant variation was observed between”, “was “ should be “were”.
13. The result is sometimes in the past tense and sometimes in the present tense. Such as Line224 and line 231.
14. Line 290: Controversially, Falaki et al observed that the feed intake was decreased by the addition of prebiotics (Sarangi et al., 2016). Prebiotics are not probiotics, it is inappropriate to compare the two together.
15. “ Chantsawang, 1999; Wondmeneh et al., 2015”, these two references were not found in the reference.


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

Input:
Title: EFFECTS OF PROBIOTIC SUPPLEMENTS ON GROWTH PERFORMANCE AND INTESTINAL MICROBIOTA OF PARTRIDGE SHANK BROILER CHICKS
Review round: 2
Reviewer: 1

Output:
Basic reporting: It is ok now.
Experimental design: It is ok now.
Validity of the findings: It is ok now.
Additional comments: The authors have revised the manuscript according to the reviewers. It can be accepted now


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

Input:
Title: EFFECTS OF PROBIOTIC SUPPLEMENTS ON GROWTH PERFORMANCE AND INTESTINAL MICROBIOTA OF PARTRIDGE SHANK BROILER CHICKS
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The discussion is not deep enough. However, all the amendments mentioned have been revised. It is ok.


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

Input:
Title: ACHIEVING PHYSICAL EXAMINATION COMPETENCE THROUGH OPTIMIZING HANDS-ON PRACTICE CYCLES: A PROSPECTIVE COHORT COMPARATIVE STUDY OF MEDICAL STUDENTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The theme of the reported study is focused on a specific topic (standardized physical examination training) of the medical undegraduate students, which I believe is within the scope of PeerJ publication. The manuscript was generally easy to read and is targeted for the international audience. The authors have provided informative data on regarding the research

However,  I think there is still room for improvement regarding the use of terms in area of medical education. And some description in the Methods section needs further clarification.

I feel that contents of Figure 1 can be illustrated in words, therefore Figure 1 seems unnecessary. On the other hand, it would be nice if the authors could include a figure that actually demonstrate the learning curve.

Line 65, "behavioral learning theory" should be "behaviorism".
Lines 125-127, the description of "groups" vs "cohorts" is quite confusing, the authors might need to rephrase this part to allow easier undertstanding for the readers.

Mis-spelling in Figure 2, "Dyas" should be "Days".
Experimental design: The general research focus of the study is on the repetition of the DP. The authors did not seem to present strong rationale regarding the relationship the questionaire part towards the rest of the study, therfore I feel that it's not necessary to include the first part (to determine the reasons why the students cannot master PE skills well in a training course , we conducted a questionnaire survey to the PE instructors and students on their views on the PE courses and the effects of teaching/learning) in the study. Further explaination might be needed as why the survey should be included in the study.

The authors did not provide the reason for why 60 days and 15 days were determined to conduct follow-up assessment and the final exam on abdominal PE respectively in lines 136 and 139.
Validity of the findings: The authors compared their study results regarding repetition cycles of PE towards other procedural trainings in lines 243-248, I think there is a degree of consistency among different studys, therefore, the authors should take the opportunity to expand ond descripbing such consistency and search for further support with learning theories and/or principles. I believe this is the holy grail of this study.

And I feel that the authors failed to explain why "high-frequency hands-on training" is effective or efficient.

Also, I would carefully consider how the result of this study can by broadly applied in other areas of the world (lines 254-255).
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: ACHIEVING PHYSICAL EXAMINATION COMPETENCE THROUGH OPTIMIZING HANDS-ON PRACTICE CYCLES: A PROSPECTIVE COHORT COMPARATIVE STUDY OF MEDICAL STUDENTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Is there any clear definition made by the PE experts about what "mastery" is when it comes to PE conducted by medical students?
Experimental design: It is not clear to me how the students were distributed into 10 groups (line 125) to assure randomisation.
The 60 days following the practice sessions, were students able to practice PE (line 136)? and how were these 25 students recruited?
What randomisation method was used to pick up the 95 students for the final exam (line 139)?
Knowledge of these methods can help understand any potential bias more and also help replicated the study if needed.
Validity of the findings: No comment.
Additional comments: I praise the authors for conducting this study to look into how DP can be incorporated into PE training in medical school, an important topic that we need more data about. They clearly stated the limitations of the study, highlighting how baise can potentially affect 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: ACHIEVING PHYSICAL EXAMINATION COMPETENCE THROUGH OPTIMIZING HANDS-ON PRACTICE CYCLES: A PROSPECTIVE COHORT COMPARATIVE STUDY OF MEDICAL STUDENTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: This article had a lot to report and I found the flow a bit hard to follow.
Should re-organize to meet the 3 aims of the paper:
1) determine the reasons why the students cannot master PE skills well in a training course.
2) find the optimal practice times in a PE training course
3) validate the threshold (cut-off times)

Too many tables/figures. Could definitely cut back and focus on the main outcome.

Minor English corrections such as use of "hand-on" on line 85.
Typo in Figure 2 "Dyas" instead of "Days"
Other minor grammatical corrections

Background is fine, but flow could be improved to go along with the aims of the current study. Also, could add some info about PE and what the requirement is for learning.
Experimental design: As above, this article had A LOT to report and I found the flow a bit hard to follow.
Should re-organize to meet the 3 aims of the paper:
1) determine the reasons why the students cannot master PE skills well in a training course.
2) find the optimal practice times in a PE training course
3) validate the threshold (cut-off times)

You also reported on setting that Aim 3 threshold, but don't really mention it in the methods.  I think this may be the missing link? First you did a survey on PE skills and what learners and teachers were missing, then you did training for a group of students and looked at practice session numbers and validated the thresholds. Where does the standard fit?

There were methods mixed in with background (and AIMs), and results mixed in with methods.  It was hard to figure out what the actual MAIN outcome/goal of this study was since it seems like it all took place simultaneously?

The methods and results need a major re-organization so a reader could follow what is done when and WHY.

The title of the article mentions "MASTERY", however, this is not an example of "mastery-learning" as described in the literature.
1) It was mentioned in the limitations that there was no baseline assessment- this is a key feature of mastery learning
2) all trainees need to reach the "standard", set by experts, which isnt entirely clear in this article in order to achieve "mastery"
3) Need more info in the methods on how the standard is set- the study mentions angoff method. It also seems as though 5 "experts" helped to set the standard- there should technically be at least 8, and how were they selected? who were they? specialties, etc.

None of the other survey findings were addressed? the second highest suggestion from both teachers and learners was enriching the content?  Was anything done in that sense?
Validity of the findings: This is hard to assess without the improvement of the other areas. I think the data is there, it just needs to be sorted out and focused. Maybe there are too many Aims and the authors should nail down what's most important.
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: ACHIEVING PHYSICAL EXAMINATION COMPETENCE THROUGH OPTIMIZING HANDS-ON PRACTICE CYCLES: A PROSPECTIVE COHORT COMPARATIVE STUDY OF MEDICAL STUDENTS
Review round: 2
Reviewer: 1

Output:
Basic reporting: 1. Language: This version of manuscript has significant improvement in language, however, minor language issues still exist, some of which are concerned with professionial expression in medical education. I would suggest a thorough language check of the manuscript performed with the aid of a (near) native English speaker.

2. Figures: The current presentation of the figures are much easier to comprehend. However, figure legends of the manuscript are not presented in the current version (interestingly, you do have the figure legends in the supplemental materials). A relatively detailed description of the 3 figures should be available; otherwise, it would be quite impossible for the readers to find out the meaning the the axises and other elements in the figures.

For the flowchart (figure 3), I would suggest the authors to keep with the two arms after randomization, instead of combining the two arms during assessment.
Experimental design: Since the authros have got rid of the the questionaire in the main text, the previous Aim 1 was excluded . This makes the article more logical to read.

Do the authors keep record of the time spent in each teaching/learning session for both Cohorts? What was the portion of time spent on learner practicing vs learner receiving feedback? Such result could potentially help you with answering the impact of feedback vs repetion of practice in DP.
Validity of the findings: How to determine whether "the threshold (cut-off cycle) defined by the learning curve" has been validated (Aim 2 in current version)? What are the outcome measures that supports this validation process? The authors are suggested provide further explaination in the Discussion Session to answer this question.

Also, since the authors has mentioned other studies (in Lines 176-179) that was trying to address the repetition components of DP (although not focusing on abominal PE), what are the similarities and differences regarding the findings of your research compared with those previously reported ones? You only mentioned afew in Lines 187-193, but the ones from McGaghie and Bursk et al. are also worth further discussion.

The authors mentioned the the potential bias of more repetition that resulted in more feedback (Lines 213-215), I think this is worth extend your discussion, not just as a limitation, but as an association, or benefit of having repetition of high frequency practice.

Since this is an interesting topic of study, have you considered further research to be performed in the future? Future directions of your reseach, as well as the strength of your study should also be included in your manuscript.
Additional comments: No additional comments