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: MOLECULAR PHYLOGENY OF MULBERRIES RECONSTRUCTED FROM ITS AND TWO CPDNA SEQUENCES
Review round: 2
Reviewer: 3

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: This manuscript has been improved substantially after the authors have accepted most of the comments and advices in the first round review. The English is clearer in the new version. However, they still did not claim their scientific questions in the main text, which may confuse the readers. The authors found ITS pseudogenes in muberry and suggested that polyploid, hybridization and concerted evoluiton shaped the evolution of Morus. This study improved our understanding of the evolution of mulberry. I hereby have several minor suggestions.
Line 76, it would be better to mention which genus in Moraceae
Line 83, it would be better to avoid words like “impossible” in a scientific article. It may hard to solve some scientific question for now, or only in the context of this study, but we can hardly say it is “impossible” to solve it, considering the whole history of modern science.
Line 164, Thank you for following my advice in the phylogenetic reconstruction part of Materials and methods. However, it is odd to me that two different criteria were used to select best substitution models in two reconstruction approaches. Please justify this or use the same criterion.
Line 275-284, reads like results for me.
Line 335, please tell the full name of an abbreviation at the first time you mention it.


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

Input:
Title: MEMCAT: A NEW CATEGORY-BASED IMAGE SET QUANTIFIED ON MEMORABILITY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Generally good. Please see the "small points" section of the general comments for a few suggestions.
Experimental design: Fine.
Validity of the findings: Please see items 2 and 3 of the general comments.
Additional comments: The authors provide a 10,000-image dataset that is organized by broad semantic category (5 superordinate-level categories) and normed in terms of memorability by an average of ~100 observers per image. This is a lovely effort and a great service to the community. I am generally pleased with the writeup of this work, but I do have a few suggestions.

-1- Motivating the database
As I stated, I believe that this database is a great tool for the field, but I feel that the uses and implications are not clearly stated early on in the introduction where most folks might start to read. For example, the framing of the manuscript in the first paragraph is a little unusual. Most of the cited papers are not studying how photographs “differ” (line 38) for their own sake, but studying how perception, attention, and memory work in the context of naturalistic visual inputs. I feel like the current motivation (to paraphrase: photography is popular, we should study it) actually cheapens the value of this work, which is of broad use to the cognitive science community. More broadly, the hierarchical category structure of the database is an untapped asset. The authors could ground this in terms of the cognitive science of hierarchical concepts (e.g. Rosch etc) and/or known neuroscientific concept distinctions such as animacy, real-world size, etc.

-2- Possible confound in sports category
Line 179-182: I am not following the logic here. I am assuming that the authors mean that non-incidental images of people were only allowed in the sports category. However, this might be an issue for two reasons: (1) if people are more intrinsically memorable, this could artificially inflate the memorability of this category; (2) if the people depicted in the sports images are famous, this would further artificially inflate memorability and/or increase variability in memorability because some (but not all) participants may recognize the players.

-3- Memorability scores
Lines 227-240: These memorability scores are somewhat non-standard. I am unsure of why the authors chose to combine two previous scores rather than more accepted precision/recall, and/or sensitivity/specificity.

-4- Black boxes
Lines 63-64: There are two types of “understanding” that the authors might be referring to, and it would provide clarity to know which one is intended. The “black box” argument often refers to the lack of human interpretability of dCNNs. However, dCNNs can also be critiqued for not having a full, semantic understanding of a picture. I suggest a clarification and a reference to help the reader understand which of these interpretations is intended.

-5- Small points
--Abstract, line 30 final sentence: suggested re-phrase “allows the study of” rather than “allows to study”
--Line 62: what is being predicted? I assume memorability score, but the sentence is a bit ambiguous
--Line 102: I suggest that the authors hyphenate “memory-relevant”
--Line 103: Citation needed about studies that show that these categories differ in terms of memorability.
--Line 112: No comma needed after “there”


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: MEMCAT: A NEW CATEGORY-BASED IMAGE SET QUANTIFIED ON MEMORABILITY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The narrative is easily understood and fits the scope of the work, all in all a well-written text with a clear structure. I only have three recommendations (ranked by importance from most to least important) for further improvement according to PeerJ guidelines.

1. Much of the current literature concerning memorability is presented although one important paper is ignored: https://ieeexplore.ieee.org/abstract/document/8704932.  Ideally many members of the community will use this image set (it certainly deserves to be used). To increase understanding of memorability as a concept and how it may vary *within* semantic categories,  I think it would be of benefit if the potential role of Visual Memory Schema is shortly addressed in the introduction, for instance in page 4 after line 80 when goodness of image organisation is introduced.
2. The concept of memorability relevance (page 5, line 96) is introduced but only explained three sentences later. Comprehensibility of the paragraph would be improved if memorability relevance were explained immediately.
3. Data visualisations are informative and aesthetically pleasing. Captions only include basic descriptions of what is shown but results could be communicated even more effectively if captions include a short summary of the meaning of the figure/results.
Experimental design: The methods are very well explained and fit the overarching research question. No further comment.
Validity of the findings: Analyses are statistically appropriate and accessibility to and composition of the stimulus set and (raw) data files are exemplary. No further 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: MEMCAT: A NEW CATEGORY-BASED IMAGE SET QUANTIFIED ON MEMORABILITY
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: I would like to thank the authors for their revision. I feel that the new structure of the paper will give it the attention it deserves.


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 OF KEY GENES IN NON-SMALL CELL LUNG CANCER BY BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article entitles “Identification of target genes in non-small cell lung cancer by bioinformatics analysis “ by Zhang et al is interesting and has potential for publication. However, there are few concerns as listed below and authors need to address these issues properly before the article is accepted.

1)	 The authors have followed the methods applied in Xiao et al., 2018 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928621/) and Zhang X. 2018. Identification of Candidate Biomarkers Correlated With the Pathogenesis and Prognosis of Non-small Cell Lung Cancer via Integrated Bioinformatics Analysis. Front Genet 9:469. 10.3389/fgene.2018.00469. However, in this article, the method described is unclear, how the tools were used and the detailed description of each analysis need to be provided.

2)	In title, authors have mentioned “target genes”. What the target means? Is it drug target/ Marker for prognosis/ anything else please clarify or remove from the title.

3)	It is well established that markers are ethnicity specific. Authors have not described the used datasets properly, what the stages of the cancers, what the ethnicity of the patients etc.

4)	Further, it is unclear why the authors have selected these particular datasets from GEO, also in the used datasets, the number of controls are less. Therefore, larger and additional datasets to be incorporated in the analysis.

5)	It is also unclear about the novelty of the findings. The identified markers are already reported in various literature as following. Therefore, its require to clearly mention the novelty of the work in respect to used method and or outcomes.
CDK1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5356732/)
CCNB1 (https://www.ncbi.nlm.nih.gov/pubmed/10945597)
CCNA2 (https://www.frontiersin.org/articles/10.3389/fgene.2018.00469/full)
BIRC5 (https://link.springer.com/article/10.1134/S0026893308040146)
CCNB2  (https://www.ncbi.nlm.nih.gov/pubmed/26349989)
KIAA0101 (https://www.ncbi.nlm.nih.gov/pubmed/21689861)
MELK (https://elifesciences.org/articles/32838)

6)	In conclusion, authors have mentioned “However, further molecular and biological experiments are required to confirm the functions of the key genes in NSCLC.” As mentioned in the above points, all the selected 7 markers are  reported previously with validation, what the other experiments the authors propose to conduct to validate? Please elaborate.
Experimental design: 1) The authors have followed the methods applied in Xiao et al., 2018 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928621/) and Zhang X. 2018. Identification of Candidate Biomarkers Correlated With the Pathogenesis and Prognosis of Non-small Cell Lung Cancer via Integrated Bioinformatics Analysis. Front Genet 9:469. 10.3389/fgene.2018.00469. However, in this article, the method described is unclear, how the tools were used and the detailed description of each analysis need to be provided

2) It is well established that markers are ethnicity specific. Authors have not described the used datasets properly, what the stages of the cancers, what the ethnicity of the patients etc.

3) It is unclear why the authors have selected these particular datasets from GEO, also in the used datasets, the number of controls are less. Therefore, larger and additional datasets to be incorporated in the analysis.
Validity of the findings: 1) It is also unclear about the novelty of the findings. The identified markers are already reported in various literature as following. Therefore, its require to clearly mention the novelty of the work in respect to used method and or outcomes.
CDK1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5356732/)
CCNB1 (https://www.ncbi.nlm.nih.gov/pubmed/10945597)
CCNA2 (https://www.frontiersin.org/articles/10.3389/fgene.2018.00469/full)
BIRC5 (https://link.springer.com/article/10.1134/S0026893308040146)
CCNB2  (https://www.ncbi.nlm.nih.gov/pubmed/26349989)
KIAA0101 (https://www.ncbi.nlm.nih.gov/pubmed/21689861)
MELK (https://elifesciences.org/articles/32838)

2) In conclusion, authors have mentioned “However, further molecular and biological experiments are required to confirm the functions of the key genes in NSCLC.” As mentioned in the above points, all the selected 7 markers are  reported previously with validation, what the other experiments the authors propose to conduct to validate? Please elaborate.
Additional comments: Improvement in description of method so that it can be reproducible.
Improvement in description of Result section so that it can be better interpritable.


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 OF KEY GENES IN NON-SMALL CELL LUNG CANCER BY BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 2

Output:
Basic reporting: Figure 2A and 2B - Dear authors, increase font size for easier viewing and reading.

Figure 3A and 3B - PPI network images containing some dozens of nodes and interactions, although didactic, are difficult to visualize and analyze.I strongly suggest increasing the font size of the gene name as well as transferring the image from main article to supplementary material in .PDF format.

Figure 4A and 4B - The font size of the x and y axes should be increased to facilitate visualization and reading for both the four centrality measures and the values.

Line 106 - Please, cite DAVID and version
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009;4(1):44-57.

Line 115 - Please, cite STRING and version
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 Jan; 47:D607-613.D

Line 118 - Please, cite Cytoscape and version
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Research 2003 Nov; 13(11):2498-504

Line 119 - Please, cite MCODE and version
BADER, Gary D.; HOGUE, Christopher WV. An automated method for finding molecular complexes in large protein interaction networks. BMC bioinformatics, v. 4, n. 1, p. 2, 2003.

Line 127 - Please, cite Network Analyzer and version
ASSENOV, Yassen et al. Computing topological parameters of biological networks. Bioinformatics, v. 24, n. 2, p. 282-284, 2007.

Line 128 - Please, cite CytoNCA and version
Yu Tang, Min Li, Jianxin Wang, Yi Pan, Fang-Xiang Wu. CytoNCA: a cytoscape plugin for centrality analysis and evaluation of biological networks. BioSystems, 2014, DOI: 10.1016/j.biosystems.2014.11.005

Line 142 - Please, cite GEPIA and version
TANG, Zefang et al. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic acids research, v. 45, n. W1, p. W98-W102, 2017.

Line 150 - Caros autores, creio que o valor de "585 DEGs..." deve ser substituido por "685 DEGs..."

Line 150 - Dear authors, the value of "585 DEGss ..." should be replaced by "685 DEGs ..."
Experimental design: Dear authors, the PPI network was constructed based on the differentially expressed genes identified in previous experiments, after the four centrality measures were calculated.According to Dilluca (2017), in bacteria, the degree of interaction has correlation with essential proteins, an assertion supported by other articles including experimental ones. However, this statement is true when the PPI network is constructed with all the genes of the organism. Thus, a sub-network of differentially expressed genes does not reflect the dynamics and the biological condition of the organism, consequently generates bias in the measures of centrality.

The STRING version database has 5.879.727 interactions for Homo sapiens, 420.534 having score >= 0.7, and all must be used to calculate the measures of centrality, even if only DEGs genes are described in the results. I also suggest uses score >= 0.7 from STRING because it reflects very reliable interactions.

Reference: DILUCCA, Maddalena; CIMINI, Giulio; GIANSANTI, Andrea. Topological transition in bacterial protein-protein interaction networks ruled by gene conservation, essentiality and function. arXiv preprint arXiv:1708.02299, 2017.
Validity of the findings: Dear authors, the enrichment analysis was performed for 685 DEGs, however, the final result concentrates on seven out of eight genes identified. Thus, I suggest transferring the "GO and KEGG pathway enrichment analysis" step to the end of the "Materials and Methods", analyzing seven target genes found in previous steps, allowing the reader to know in which these seven genes stand out in comparison to the other DEGs .

Line 192 and Figura 4A - The degree interaction of biological networks tends to present a power-law distribution, whose graph can be generated directly in the Network Analyzer plugin of Cytoscape. With a partial network of 685 DEGs many interactions were disregarded, probably generating heavy-tailed distribution graph.
Additional comments: The article uses systems biology techniques to correlate data of gene expression, annotation and interaction networks in order to identify possible relevant genes in the article context.

The main contribution of an Bioinformatics work is to reduce the sample field and to suggest genes for future experimental works. Thus, the article fulfills its role, however it follows some suggestions to improve the 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: IDENTIFICATION OF KEY GENES IN NON-SMALL CELL LUNG CANCER BY BIOINFORMATICS ANALYSIS
Review round: 1
Reviewer: 3

Output:
Basic reporting: Language is generally OK. However, another check will be better
Line 105-106: which is an online program that can provides should be "provide".
Experimental design: Line 109-110: Sorting was conducted according to the P-value from small to large, and the top 25 GO terms and the KEGG pathways were selected.

This is not the ideal way. You should not choose or sort based on p-value only. The p-values just give a significance level (p<0.05 and p<0.01 doesn't tell the latter is better).  A better way is to calculate the enrichment factor. Also, check if the genes in identified GO terms are common or specific.

Line 115: The STRING database (http://string.embl.de/) provides the method which can construct a PPI network of DEGs.
The string database can construct a network of any given gene list. The authors have created a network of DEGS. Perhaps a rephrasing of the sentence would be better.

Line 172: Module analysis of the NSCLC related network
This analysis needs to be improved.
How many genes are there in different modules that are related to enriched GO terms and pathways?
What is the role of the modules in the NSCLC carcinogenesis and patient's survival?

Centrality analysis of PPI network.
Only four centralities have been calculated. This section can be improved as well.
1. What are the centralities that have the highest resolution?
2. What is the rank intercorrelation among centralities?
3. It is also not clear how the final selection (16) was arrived at?

Line 194: 16 molecules? (or DEGs?) with high topological features were obtained with high degree, betweenness, closeness, and eigenvector
Validity of the findings: It has to be clearly stated what is the novelty of the work, and how will it be helpful to other researchers.
The findings can also be validated through the search of the literature where others might have reported some of the genes for involvement in NSCLC.
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: IDENTIFICATION OF KEY GENES IN NON-SMALL CELL LUNG CANCER BY BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 1

Output:
Basic reporting: Authors have implemented most of the suggestions and may be accepted now for publication
Experimental design: OK
Validity of the findings: OK
Additional comments: Authors have implemented most of the suggestions and may be accepted now for publication


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

Input:
Title: IDENTIFICATION OF KEY GENES IN NON-SMALL CELL LUNG CANCER BY BIOINFORMATICS ANALYSIS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The authors accepted and executed the recommendations of the first review, or justified the reasons.
Experimental design: The authors accepted and executed the recommendations of the first review, or justified the reasons.
Validity of the findings: The authors accepted and executed the recommendations of the first review, or justified the reasons.
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: FOSSIL FERN RHIZOMES AS A MODEL SYSTEM FOR EXPLORING EPIPHYTE COMMUNITY STRUCTURE ACROSS GEOLOGIC TIME: EVIDENCE FROM PATAGONIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: See general comments to the editor
Experimental design: See general comments to the editor
Validity of the findings: See general comments to the editor
Additional comments: Review of Fossil fern rhizomes as a model system for biotic interactions across geologic time: Evidence from Patagonia (#21919)

This study introduces and documents an exciting approach for characterizing epiphytic ecosystems and separating them from detrital ecosystems in a relatively consistent environment over an extensive segment of the Phanerozoic fossil record.  The paper is well organized and clearly written in excellent English.  With the exception of one figure, it is well illustrated with the appropriate photos and one table of excellent quality.  Identifications and characterizations of the different organisms appear to be sound.  They are appropriately documented with photographic evidence and citations to the appropriate literature.  Overall, the literature is appropriate and up to date.

I find this to be an important paper for demonstrating the potential of the fossil record of plants.  It extends further into the realm of extinct ecosystems the types of studies that can be accomplished with fossils.  The paper will be of interest to a broad spectrum of paleobotanists, paleobiologists, and paleoecologists.

Figure 1A needs to be improved in quality and possibly increased in size to show better the features of the osmundaceous stem, and of the various mircoenvironments present within a fern trunk.  It would be helpful if the authors could offer a genetic identification of the osmundaceous fern.  In addition, a few edits have been offered on the accompanying PDF of the submitted manuscript.  Otherwise, this is an excellent contribution that I recommend be accepted with minor revisions.  A few minor suggestions follow:

Lines 124-133 – Fossil osmundaceous fern trunks with anatomical preservation are well known, and well characterized to genus.  What is this?  If possible, please identify to genus and figure features that will document more than merely the ordinal identification of this fern. None of the characters listed on lines 130-132 (except phyllotaxis) are clearly illustrated in Figure 1A.

Line 233 – Fern rhizomes may be growing at the apex and dead below.  In fact, most tree ferns have stems that are dead and rotting at the base, but are kept upright and nurished by the stem-borne adventitious roots.  As a result, whether the fern was alive or dead at the time of fossilization isn’t as important as whether this section of the stem was alive or dead at the time of fossilization. Please clarify this in the text.

GWR


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: FOSSIL FERN RHIZOMES AS A MODEL SYSTEM FOR EXPLORING EPIPHYTE COMMUNITY STRUCTURE ACROSS GEOLOGIC TIME: EVIDENCE FROM PATAGONIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This study presents a new record of an Eocene permineralized osmundaceous rhizome that contains abundant evidence of bryophytes growing on the rhizome surface and several different fungal remains associated with the peripheral, partially decayed regions and tissue systems of the rhizome. The discovery is interpreted as an interaction system, and it is concluded that osmundaceous stems in general may represent paleoecological model systems providing insights into biotic interactions across geologic time.

The ms meets the basic professional requirements for article structure, language use, and data sharing.
Experimental design: No comments
Validity of the findings: The findings are potentially worthy of being considered for publication in PeerJ, but I feel that the ms as stands is insufficient. My gravest concern relates to the fact that the word ‘interactions’ is used to circumscribe and qualify the assemblage of organisms seen in this fossil. But what the fossil actually shows are ill-preserved bryophytes that grew on the surface of the rhizome, as well as several different types of fungal spores, hyphae, and microsclerotia that were produced by some fungi, which perhaps lived in close association with the fern (within the tissues or on the surface), but could equally well be fungi that occurred in the substrate surrounding the fern, with propagules accidentally transported into the degrading periphery of the rhizome. Speaking of ‘interactions’ therefore is over-interpreting the data! The bryophytes are associated with the fern – ok. Conversely, the fungal hyphae, spores, and sclerotia, based on the evidence provided, just occur and co-occur in the partially degraded periphery of the rhizome. As to whether the fungi that produced the hyphae, spores, and sclerotia actually interacted (i.e. entered into some form of specifiable relationship) with the fern cannot be determined based on the material at hand. Part of the problem results from the lack of information regarding the number of specimens of the individual fungal remains. (1) Has each of the types of fungal remains only been found once or a few times, or do all these different remains occur frequently in the rhizome periphery? (2) If the latter is accurate, then, where exactly do they occur? Randomly distributed or in specific areas of the rhizome, perhaps in areas into which they could not accidentally become washed and that would indicate spore production within host tissue? (3) What exactly does the mapping of the different remains on a single cross section of the rhizome tell us? To provide any meaningful insight into what you call a “model system” (e.g., with regard to infection and distribution pathways of the fungi; tissue preferences etc.), a quantitative analysis and mapping of the whole series of sections is needed.

Permineralized osmundaceous rhizomes are referred to as a “paleoecological model system” that can be used to explore plant biotic interactions across geologic time. As stated above, there is no easy way to establish based on the data at hand that interaction actually occurred between either of the organisms found on and in this rhizome. Moreover, I do not quite understand what exactly the ‘model’ character is? I am thinking, if you take three rhizomes, one from the Permian, the second from the Triassic, and the third from the Neogene, analyse all three for microbial content, and plot the results, what exactly is this going to tell you? You will likely see differences in the number and quality of remains, along perhaps some similarities. So what? As stands, it reads as if you view the rhizome-bryophyte-microorganism assemblage as a super organism with a very long evolutionary history, and thus that changes in the assemblage of organism reflect something that has to do with paleoecology. But is it really that easy?
In conclusion, I feel that much more work is needed to evaluate in full the many different and interesting aspects preserved in this rhizome. I strongly feel that the original research results presently are too slight to vindicate publication. It will be necessary to provide a more extensive description and photographic documentation of the bryophytes and microbial remains, especially with regard to their spatial distribution. Finally, the technical flaws of the writing (e.g., amalgamation of descriptive and discussion items in the Results section) need to be removed.
Additional comments: See above


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

Input:
Title: FOSSIL FERN RHIZOMES AS A MODEL SYSTEM FOR EXPLORING EPIPHYTE COMMUNITY STRUCTURE ACROSS GEOLOGIC TIME: EVIDENCE FROM PATAGONIA
Review round: 2
Reviewer: 1

Output:
Basic reporting: see attached pdf
Experimental design: see attached pdf
Validity of the findings: This is my first review of this manuscript altogether.
I base my suggestion on an evaluation of the manuscript in its present form in light of the comments and suggestions accompanying the previous editorial decision and of the revision notes of the authors accompanying this revised submission.
In general, I understand this project to be more of a pilot study. Having worked on this particular fossil myself, I can agree to the authors’ decision to refrain from a more in-depth and more quantitative analysis, as reviewer 2 has (justifiably) requested earlier. The preservation of the fossil is simply too incomplete and too imperfect to provide sufficiently adequate material for a more detailed analysis. As we state in our description of the fossil, which has only just been published, “[…]preservation of the fossil material presented here is imperfect: most of the stem parenchyma appears to have been degraded and replaced by silica, and many of the more robust, lignified or sclerified structural elements in the stem appear crushed or variably displaced, which makes precise interpretation of many of the structural features commonly used for species delimitation in Osmundaceae (e.g., numbers of leaf traces in cortical regions or of xylem strands per stem cross section) difficult.” (Bomfleur and Escapa, 2019). This would apply similarly to  studying the inventory and distribution of epiphytic organisms.
Still, even though the authors present largely qualitative data and an only informal systematic treatment of the epiphytic organisms, I do see great merit in publication of this revised manuscript version pretty much as is, if only to provide a survey of the evidence of biotic interactions in the fossil, and to provide an impetus for further study of similar material from different localities and different stratigraphic ages.
In this context and with this scope, I find this manuscript to present novel and interesting findings that contribute significantly to our understanding of such complex component communities in the geological past. The manuscript is well-written and well-prepared; the structure has been revised, and results and discussion more clearly separated during revision following previous editorial suggestions. Some key issues that the previous reviewers put forward, such as the request for a more detailed description and taxonomic placement of the host fern, have become obsolete with the separate formal systematic treatment of the fossil (Bomfleur and Escapa, 2019).
All in all, I come to suggest publication following a minor final revision; I only have a few remaining issues that I think should be addressed (see comments and suggestions in the attached annotated pdf file).
Hoping I could be of assistance, I remain
Yours sincerely,

Benjamin Bomfleur
Additional comments: Dear Alex Bippus, dear co-authors,

I have reviewed (only) the revised of your manuscript and come to suggest publication following just a minor reviison of a few remaining issues.

Best wishes,

Benni


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: UNPROFESSIONAL PEER REVIEWS DISPROPORTIONATELY HARM UNDERREPRESENTED GROUPS IN STEM
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article meets the basic reporting criteria very well.
Experimental design: Experimental design is excellent.
Validity of the findings: Findings are valid.
Additional comments: This is a very important and useful survey.  It provides empirical evidence for what this reviewer has suspected for many years--that unprofessional reviews can negatively impact career advancement and discourage researchers.  It affirms the importance of training researchers on how to do professional reviews and for editors to pay close attention to peer reviewer comments and edit them.


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: UNPROFESSIONAL PEER REVIEWS DISPROPORTIONATELY HARM UNDERREPRESENTED GROUPS IN STEM
Review round: 1
Reviewer: 2

Output:
Basic reporting: Please see below. I would suggest adding the entire survey in an appendix. This is an exploratory study so no specific hypotheses were given.
Experimental design: Please see feedback below. The research is appropriate to the scope of the journal.
Validity of the findings: The findings are novel. I cannot comment on statistical validity or reporting.
Additional comments: The manuscript aims to assess the impact of unethical peer review among STEM participants specifically capturing participants’ perceptions of scientific aptitude, overall productivity and delays in career advancement.

The authors have done a terrific job clearly outlining the gap in the literature surrounding the ethics of peer review, namely that there is little known about the downstream impact of unprofessional reviews on the researchers. Therefore, the findings reported here are of great value to researchers interested in research integrity and I applaud the researchers for undertaking this study. I have outlined several areas that I believe could benefit from greater clarity or explanation which I hope serves to strengthen the manuscript.

The introduction reads well and sets the stage nicely for undertaking the study. Certainly it could be further expanded but it is well written, clear and concise. I have no comments here.

Materials and Methods:

1) Thank you for doing a nice job explaining the ethics and the protections to research participants. I am interested in knowing more about the recruitment strategy including its rationale. Why were social media platforms used, especially as there is some data suggesting that not all academics in all positions use social media uniformly. Why twitter and Facebook specifically? Which listservs and how was it decided who to invite by email. The current recruitment method seems very unsystematic. In addition, there are no details on how contact was initiated, e.g., was recruitment done to a specific Facebook group(s)? And if so why? Were secondary emails sent to invitees (basically was there any follow-up to initial recruitment)? Details about recruitment are important not only for readers to assess the rigor of the methods, but also to reproduce the research.

2) There seems to be no information pertaining to how many people were contacted and what was the response rate. Is this because the researchers didn’t start with a known number of potential participants (because of recruitment through social media) and so the denominator remains unknown? Please explain.

3) While I understand the brief rationale given in the Introduction surrounding why specifically scientific aptitude, productivity and career advancement were chosen, I am unsure about how these items and scales were designed. I presume these are not borrowed scales and no such scales could be identified. I would explain this. So how were these items designed? Was this based on the existing literature, was any pretesting of questions done using interviews prior to survey dissemination? My reason for asking for such details is that the terms “scientific aptitude,” “overall productivity,” and “career advancement” are likely to mean different things for different respondents. There is also a temporal element as certainly a bad review when I was a trainee might impact me temporarily as an Associate Professor responding today. Can more of a description be given for choosing the language used in these items? The design of this instrument might be considered a limitation.

4) Thank you for adding a limitations section. In my experience, limitations for empirical social science studies are provided in the Discussion section usually as a last paragraph before the Conclusion. This is a formatting issue so I will leave it to the authors/editors to decide where it is best placed.

5) I understand that first authors of papers were invited. How was this determined? There was no bibliometric method used to identify first authors so how was this determined? In addition, were these authors of single blinded peer review, double or open? I presume judging from the comments in Fig 1 that the respondents were part of a single blind or open review process because reviewers knew the names. If this is unknown, please state this in the paper.

6) I am a bit confused as to how the survey was conducted. When the first set of questions about whether the respondents received an unprofessional review was asked among 1106 respondents, only 642 said yes which meant the remainder only gave demographic info and no further questions were given. To me, this is a presurvey question literally as a way to screen for the inclusion of participants. So at the end of the day, you are working with 642 participants. Is this correct? If so can the method simply not be written as we prescreened participants based on whether they answered “yes” to having received an unprofessional peer review based on the screening criteria?

Results
7) There is language in the results and in the discussion that I would like clarification on. The intersectional comparisons showed no significant differences as indicated on lines 202-3 and the statement in the discussion line 246-8 “while there were no difference in the perception of receiving unprofessional comments among the four intersectional groups in our study, there were clear and consistent differences in downstream effects across groups.” These statements can be confusing to a general academic science audience who would be interested in this paper. Firstly, what the researchers are doing is to capture the perceptions of participants who have experienced unprofessional reviews so saying there were no differences in perceptions of receiving unprofessional comments among intersectional groups, but then saying there were difference in downstream effects is confusing and sounds contradicting. Please help me understand the meaning of the above sentence.

Discussion
8) Would it be possible to unpack some of the ethics surrounding unprofessional reviews? I have once in my life received an unethical review which did impact me and I was struck by the types of comments in Figure 1. In fact, I would ask the authors to consider calling these even unethical reviews. My comment is whether the authors might consider discussing further the impact of open peer review practices and how this might (or might not) curtail unethical peer reviews.

9) Another area I think is worth discussing is the role of Associate Editors/Editors when receiving unethical peer reviews. What should editors do in such cases beyond simply redacting such useless and unprofessional comments when providing feedback to the authors? As an AE for a couple of journals, I have never come across such comments from reviewers. Personally, I would consider removing the reviewer from our database completely, making it known to the senior editorial team, and would probably send an email to the reviewer personally. But this is a weak reprimand. In addition, the suggestions provided in the final paragraph of the discussion are all about ensuring practice of peer review is known to reviewers and does not touch upon how to deal with reviewers who commit such misbehaviors. While these positively framed suggestions are worthwhile to explain, positive attributes can only go so far and sometimes, reprimands are necessary to guide ethical behavior. Can the authors identify editorial responsibilities in the context of receiving unethical peer reviews? And also, can the authors perhaps consider what types of reprimands could be given to reviewers of unethical peer reviews. Should editors contact institutions and if so whom within the institution should be contacted. This paper has obvious implications for editorial teams interested in ensuring the ethical practice of peer review and editorial conduct. Greater discussion here would certainly be helpful.


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: QUANTITATIVE ESTIMATION OF WASTEWATER QUALITY PARAMETERS BY HYPERSPECTRAL BAND SCREENING USING GC, VIP AND SPA
Review round: 1
Reviewer: 1

Output:
Basic reporting: 1. Manuscript is lacking a good English. The language should be improved to ensure that it can be in publishable form and clear to reader. Some examples where the language could be improved include lines 59, 63, 81, 97, 101, 93, 94, 109, 116- the current phrasing makes comprehension unclear and difficult.
Line 81: it should be “water sampling at fixed points” for “in fixed”, "physical and chemical examinations" for “experiments”
Line 97: Authors have written “particles” for COD and BOD “main pollutant particles (COD, BOD)”. Please describe is it “parameters”? or How these can be particles?
Line 101:  Hyper-spectral techniques are still being widely used for various monitoring of natural resources. This line needs to be corrected.
Line 160: Seems incomplete and contains spelling mistake.
Line 169: Needs to be revised and corrected with “water taking” for "water taken", "were shown" should be replaced by “are shown”.
There is no space between the word and bracket (eg. substances(TDS)), that needs to be corrected.
2. Literature references are not sufficient and have not been focused on latest findings.
3. Figure and table legends need to be revised and explained. Units should be in standard format and representation of data corrected (eg “90%-98%” should be as “90-98%”).
Experimental design: Material and methods sections needs some latest references. What was the purpose of adding pure water to the wastewater samples before the analysis, please explain?
Please explain “what is the Table 1 for?” Is it chemically estimated values of the wastewater? This should be properly mentioned in the material method section.
Validity of the findings: Result and discussions is lacking sufficient and proper references in support of the findings, that needs to be addressed in the MS.
Compared representation of chemically estimated and hyper-spectral analysis values is lacking in MS and this needs to be addressed.
Additional comments: Figure and table legends needs to be revised and explained. Units should be in standard format and representation of data corrected (eg “90%-98%” should be as “90-98%”). Axis title “Wavelength/nm” is confusing, please explain what it is for or correct it as “Wavelength (nm)”. Other axis titles also need correction. Following the published paper of the journal will be helpful in this regard.


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: QUANTITATIVE ESTIMATION OF WASTEWATER QUALITY PARAMETERS BY HYPERSPECTRAL BAND SCREENING USING GC, VIP AND SPA
Review round: 1
Reviewer: 2

Output:
Basic reporting: The language and grammar of the manuscript needs to be improved. The references, figures, tables are alright.
Experimental design: The manuscript deals with original research and falls within the aim and scope of the journal. The research question is well defined, meaningful, and relevant. Methodology has been described that could be replicated.
Validity of the findings: The data provided are robust, statistically sound and controlled. Conclusions are well stated and supports the result.
Additional comments: Line # 97: In the water, some of the main pollutant particles (COD, BOD)
Comment: COD and BOD are not pollutant particles. Instead, they are pollution indicators.
Line # 175-176: The laboratory was kept in constant temperature and protected during the experiments.
Comment: What does the statement ‘laboratory was kept in constant temperature...’ refers to.


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: QUANTITATIVE ESTIMATION OF WASTEWATER QUALITY PARAMETERS BY HYPERSPECTRAL BAND SCREENING USING GC, VIP AND SPA
Review round: 1
Reviewer: 3

Output:
Basic reporting: Environmental pollution is one of the most challenging problem against mankind. The measurement of water quality parameter regularly is a challenging job. The regular measurement is costly affair. Keeping this fact in mind. the present work is quite promising.
Experimental design: Experimental design part is ok.
Validity of the findings: The model results showing good agreement with experimental data but the source of data and data used for model development is from same source. It is not clear that the model will work for any other set of sample taken from different source. Rigorous validation using waste water from different sources is required to establish the efficacy and applicability of this method.
Additional comments: The authors should include validation of best model taking waste water from different sources.


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: ORGAN HEALTH AND DEVELOPMENT IN LARVAL KINGFISH ARE UNAFFECTED BY OCEAN ACIDIFICATION AND WARMING
Review round: 1
Reviewer: 1

Output:
Basic reporting: The English used in the MS is excellent.  One thing that could be improved is removal of redundant statements such as "Previous studies have found significant effects of 	elevated CO2 concentrations in some or all of these tissues" which could be edited to "Elevated CO2 concentrations have significant effects on some or all of these tissues" and use of "as well as" where "and" would suffice.

The background, references and context are very good, and more than adequate.  The structure is excellent and the presentation is appropriate.  Data are available and the MS is self-contained.
Experimental design: These are all appropriate for the contents and findings.
Validity of the findings: The findings in general are excellent.

The most important factor in larval development of kingfish that manifests in hatchery culture is development of the swim bladder and adequate vascularisation of the swim bladder.  Swim bladder pathologies are described in the background, but are not examined in the study.  If this can be analysed it should be, but the choice of the organs and why they were chosen should also be described.

Vacuolation of the retina is consistent with viral nervous necrosis caused by betanodaviruses.  These are common in hatcheries and are recorded from carangids such as Pseudocaranx dentex (silver trevally/striped jack) - the striped jack nervous necrosis virus causes losses in hatchery culture of striped jack in Japan.  These viruses typically also cause brain vacuolation - were the brains examined?  Were the fish screened for nodaviruses?  If any materials remain they should examined for these viruses.

Mortality and the "normality" of the batch is not described.  This needs to be established to ensure that the findings are valid.
Additional comments: Line 201 - Aqui-S is not 50% isoeugenol (it is 99+% isoeugenol).  It is better to cite it as a proprietary product and name the manufacturer.


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: ORGAN HEALTH AND DEVELOPMENT IN LARVAL KINGFISH ARE UNAFFECTED BY OCEAN ACIDIFICATION AND WARMING
Review round: 1
Reviewer: 2

Output:
Basic reporting: This is a very well written manuscript. The experiment appears solid and the histology expertly done. I did not find many issues and I think this will be a nice addition to the ocean acidification literature. Publication of negative results doesn't happen enough. Negatives results are generally more difficult to publish, and much research ends up unpublished, so it was nice to read this manuscript. It is also positive to see a fish larvae not seriously affected by CO2 and warming.

The manuscript is well referenced.

The figures are very good with boxplots, lnRR, MDS, and pretty histology. I wonder if figure 2 could be nicer in colour? What is the reason it is presented in black and white?
Experimental design: The experimental design is is good but it may have an issue. The warm groups were heated 7°C over 24 hours. That means the warm group got an acute heat shock that the two cold groups didn't get. Normally, chronic thermal exposures are applied gradually to the treatment groups so that the factor is chronic and not a confounded mix of acute and chronic. If there are references showing that the embryos are thermally tolerant, then that should be presented. Otherwise this potential issue should be acknowledged.
Validity of the findings: The negative results are compared with the relevant literature and the interpretations are sound.
Additional comments: Minor comments for the authors:

Line 100. Higher than what?

Line 122. Why did the two control treatments differ in pCO2. That is not predicted by the ipcc models.

Line 148. An acute seven degree increase sounds potentially damaging. Was this rate of warming validated? This potentially harmful heat shock was applied to only one of the temperatures and could thus have introduced a confound.

Line 210. Great to see blinded scoring used here.

Line 205. How many sections were scored per fish?

Line 223. LnRR is a great way of visualizing effect sizes and isn’t used nearly enough, so I’m pleased to see that used here.

Line 267. All four treatments had temperature and co2, so their "combination" doesn’t make sense here. Elevated co2 and warming, and the combination would make sense.

284. I don’t understand “eco physiology of fish to OA”. Rephrase.

293. Preference and physiologically optimal temperatures can differ so it’s not certain that 21 is the more optimal temperature. Especially as the high temperature is used in aquaculture of the species.

Line 313. The authors discuss non-significant trends and while some may advice against that, I think it’s correct in this case. The binary thinking of significance testing should be a thing of the past.

Line 229. Why was this under a JCU ethics permit? Shouldn’t the host institute and host country review the ethics of their experiments?


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: ORGAN HEALTH AND DEVELOPMENT IN LARVAL KINGFISH ARE UNAFFECTED BY OCEAN ACIDIFICATION AND WARMING
Review round: 2
Reviewer: 1

Output:
Basic reporting: The ms is now mostly suitable for publication.
Experimental design: The experiment is well designed.
Validity of the findings: The findings are valid, but the authors need to describe the “water sterilisation” if they are relying on it for assurance the fish were virus free.  Also, nodaviruses are often pseudo vertically transmitted, so the status or surveillance of the parents should be described, or it should be stated that their status is unknown.
Additional comments: The ms is much improved but could benefit from a final edit for flow and sense.


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

Input:
Title: EFFECT OF TEMPERATURE ON POLLEN GERMINATION FOR SEVERAL ROSACEAE SPECIES: INFLUENCE OF FREEZING CONSERVATION TIME ON GERMINATION PATTERNS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript that entitled: Effect of temperature on pollen germination for several Rosaceae species. Influence of freezing conservation time on germination patterns (#38121) carefully read and could help researcher and fruit breeder to improvement of genotypes against environmental conditions (Abiotic stress) for example temperature which the author explored of the research on eight Rosaceae species.
Overall the article is suitable but the English language should be improved to ensure that an international audience can clearly understand your text. Some parts of the text in the manuscript unclear and need to be again checked it by one Speck -English native English around the whole of document.
The authors need to be introduce litterateur review on current references on Prunus species, which is not issued and need to be developed by recent reference of these studied species. For example:
Sorkheh et al. (2011) Influence of temperature on the in vitro pollen germination and pollen tube growth of various native Iranian almonds (Prunus L. spp.) species. Trees (2011) 25:809–822.
Sorkheh et al. (2011) Response of in vitro pollen germination and pollen tube growth of almond (Prunus dulcis Mill.) to temperature, polyamines and polyamine synthesis inhibitor. Biochemical Systematics and Ecology 39 (2011) 749–757.
Sorkheh et al. (2018) Interactive effects of temperature and genotype on almond (Prunus dulcis L.)
pollen germination and tube length. Scientia Horticulturae 227 (2018) 162–168.
The structure of Tables and Figures need to be minor revision for clearly understand your text. For example: Table 1 provides information on Latitude N, Longitude E, Elevation (m), Annual rainfall (mm) from each location that’s you are selected the species.
In Table 2, 3 and 4; please characterized each abbreviation as superscript in the Tables and so described them below of the Tables. This is importance clearly understand your text.
Please revised the title of Table 2: the percentage; Cydonia blonga

Figure 1-6 need to be added standard error bar for each point (temperature, block times). This is could help reader to clear find significant times for each species.
Experimental design: The research relevant suitable results and could helpful in fruit breeding. In this part suggested that’s calculated relative injury, pollen viability and so completed M&M on measurements. Methods need to be completed on details.
Validity of the findings: The validity is good and applied using statistics software. But the authors when working of pollen germination and pollen tube under temperature need to be clarified. For example; Relative injury (RI) to cell membranes resulting from the temperature treatments was calculated according to Kakani et al. (2002) and Acar and Kakani (2010).
Pollen viability; this index is very significant and need to be authors of the paper described of it under different treatments.
I would be like know the authors classified the species according to Sorkheh et all (2011) and Kakani et al. (2005) as tolerant, moderate and susceptible species. Because it’s very importance for fruit breeding and development of tolerant genotypes for different environmental conditions.
Additional comments: The manuscript that entitled: Effect of temperature on pollen germination for several Rosaceae species. Influence of freezing conservation time on germination patterns (#38121) carefully read and could help researcher and fruit breeder to improvement of genotypes against environmental conditions (Abiotic stress) for example temperature which the author explored of the research on eight Rosaceae species.
Overall the article is suitable but the English language should be improved to ensure that an international audience can clearly understand your text. Some parts of the text in the manuscript unclear and need to be again checked it by one Speck -English native English around the whole of document.
The authors need to be introduce litterateur review on current references on Prunus species, which is not issued and need to be developed by recent reference of these studied species. For example:
Sorkheh et al. (2011) Influence of temperature on the in vitro pollen germination and pollen tube growth of various native Iranian almonds (Prunus L. spp.) species. Trees (2011) 25:809–822.
Sorkheh et al. (2011) Response of in vitro pollen germination and pollen tube growth of almond (Prunus dulcis Mill.) to temperature, polyamines and polyamine synthesis inhibitor. Biochemical Systematics and Ecology 39 (2011) 749–757.
Sorkheh et al. (2018) Interactive effects of temperature and genotype on almond (Prunus dulcis L.)
pollen germination and tube length. Scientia Horticulturae 227 (2018) 162–168.
The structure of Tables and Figures need to be minor revision for clearly understand your text. For example: Table 1 provides information on Latitude N, Longitude E, Elevation (m), Annual rainfall (mm) from each location that’s you are selected the species.
In Table 2, 3 and 4; please characterized each abbreviation as superscript in the Tables and so described them below of the Tables. This is importance clearly understand your text.
Please revised the title of Table 2: the percentage; Cydonia blonga

Figure 1-6 need to be added standard error bar for each point (temperature, block times). This is could help reader to clear find significant times for each species.

The research relevant suitable results and could helpful in fruit breeding. In this part suggested that’s calculated relative injury, pollen viability and so completed M&M on measurements. Methods need to be completed on details.

The validity is good and applied using statistics software. But the authors when working of pollen germination and pollen tube under temperature need to be clarified. For example; Relative injury (RI) to cell membranes resulting from the temperature treatments was calculated according to Kakani et al. (2002) and Acar and Kakani (2010).
Pollen viability; this index is very significant and need to be authors of the paper described of it under different treatments.
I would be like know the authors classified the species according to Sorkheh et all (2011) and Kakani et al. (2005) as tolerant, moderate and susceptible species. Because it’s very importance for fruit breeding and development of tolerant genotypes for different environmental conditions.

The manuscript have suitable results and could be accepted /published in Peer J. after revision.


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

Input:
Title: EFFECT OF TEMPERATURE ON POLLEN GERMINATION FOR SEVERAL ROSACEAE SPECIES: INFLUENCE OF FREEZING CONSERVATION TIME ON GERMINATION PATTERNS
Review round: 1
Reviewer: 2

Output:
Basic reporting: It is interesting to read the article and I would like to thank the authors for their work. The authors have evaluated how temperature and freezing time affect pollen germination and mean and maximum pollen tube length in 9 species of Rosaceae. They show that different species have different optimums and that in general terms freezing time was negatively correlated with pollen tube length (showed graphically). However, there are some major concerns after reading the manuscript that need to be addressed.

The English needs more work, I’m not native English speaker so I cannot comment much on it, but some phrases are difficult to understand. There are some references from Spanish journals, this makes difficult to international readers to follow them if necessary, I suggest to find these references in English. There are also phrases that need referencing. Moreover, there are some citations that need better explanation in the text. The text need to be clearer and everything better explained. I cannot comment on the literature much because I’m not very familiar with it. However, I have added few suggestions below.

The tables and figures need more work. Improve axis labels, italicise species names, improve captions… In example, Figure 7 has bars that are not described, what it is, confidence intervals, sd, sem?  There are just 3 tables with stats results and there are 9 species. It seems that is based on the significance of the results. I suggest here to make a table with all the species just showing that there are differences or not with the Anova output and maybe add Tukey test but no need to report all the basic statistics, they are informative before the analysis to understand the data but not as main result of the study. If you do believe that is necessary to show these data, I think that showing it graphically will make it easier for the reader.

Moreover, the analysis just tests differences of pollen germination rate with different temperatures. Why not on mean and maximum pollen tube length? Compare it statistically too. How do you know if freezing time and temperature is affecting the different proxies, if you don’t have a control? How can we know that the selected temperature to store the samples is good or bad? Why not testing different freezing temperatures too? The comparisons of the effect of temperature are with the same freezing times or different or grouping all of them? This is very relevant and should be clearly specified.

Here I add some comments in detail about the abstract and the introduction. Methods, results and discussion are commented on sections 2 and 3.

Abstract

The abstract lacks an intro to your research. State your questions and highlight your findings. What do you test? Lack of consistency with the scientific names. Instead of name the freezing times “blocks”, treatments sound better for me, at the end you are testing that, different treatments. The underscore of block, for the r script makes sense but not for a paper presentation. So, what about state your results like: Pollen germination was maximum for all species between 15 and 30 degrees. For xxx species maximum pollen germination was… Germination did not change significantly for xxx species with freezing time but we found significant …

Line 22: Even though you mention that you have used eight species here, but in the methodology section you tested nine species including E. Japonica? Therefore, please check this and change it accordingly.

Introduction

The first paragraph of the introduction should be catchier… You already describe what your species are in table 1.  If you want to mention the species, maybe in the last paragraph of the intro or in methods you can describe them with more detail. You need to introduce the topic to your reader in a more elegant way.

For me is lacking that you state clearly what the knowledge gap is and how this research can help in the field of pollen biology. For example, knowing the correct store methodology can help breeders or research of pollen biology to be performed at any time during the year without reduction in success of pollen germination… I’m lacking this on the text, the practicality of it and more exhaustive description of what we do know and do not know.

The second paragraph of the intro I think is find there just need to be improved and replace the Spanish reference for an English one. Ref for Rosaceae flowers are actinomorphic and hermaphrodite. Sargent 2003 will do the work for the symmetry. You should find other ref for compatibility. Scientific names! Make it consistent.

Third paragraph, if you talk about the studies, mention what they have done and found. So, we will know what past literature has found and what needs to be addressed. Could be interesting to link the different temperature ranges of the species with the maximum pollen germination and pollen tube length.  I would consider to move the first paragraph of methods to the intro and develop this idea as a research question that could help the paper to grow.

Fifth paragraph, different temperatures are tested in the different studies, what did they find? Any temperature is better? If so, explain it. Rajasekharan & Ganeshan 1994, journal of Horticultural Science showed that with liquid nitrogen, cryostored pollen maintained its ability to produced seeds on roses. This could help to build this paragraph… Why you test just one temperature? Is any reason? Nath & Anderson 1975 Cryobiology, talk about the cooling rate… As a variable that affect pollen germination, I’m not very familiar as I said with the literature but everything should be expanded and more variables consider.

Last paragraph of the intro, you don’t test temperature conservation conditions… Build your research question with the correct terminology.
Experimental design: I think that the article fits the aims and scope of the journal and I I do believe, that their research can help the field of pollen biology. However, their research questions are not clearly tested and their methodology lacks detail to make this study reproducible.

The methods section needs more detail:

I will not use E. japonica due to is from 2017 and not 2018 like the rest… Better to avoid the lack of consistency to have less noisy results.

How did you storage the samples? Tube, bag?

Again, don’t call it block call it treatment.

Delete lines 99 to 102. Don’t include loquat. This makes your research inconsistent.

The analysis needs better explanation and structure. If you compare the differences with Anova’s between pairs with Tukey test, explain it together, don’t say that you use Tukey at the end with the CRAN packages. It’s good that you do basic descriptive stats for understanding your data but I won’t mention them in methods. You can show that graphically with means and confidence intervals and is more elegant that a table full of numbers in case you really want to add them.

Please mention sample size in the text. Why in the table of results is a different N for each temperature. Any reason of the different sample sizes?

How do you consider that a pollen grain has germinated or not? Any minimal length? We should help future work to make it reproducible. And please we need the units and how you measured it. From all the pollen grains which ones you counted or measured? all? subset?

The results are very chaotic, is important to make the life easier to the reader. Divide your results in your research questions and reference figures and analysis outputs.

Seems that pollen tube maximum and average length decrease with freezing time as seen in the figures. This is interesting! Sell it. However, the percentage of germinated pollen grains seems to don’t change that much. We need stats to confirm this, add them. Again, instead of calling it block, “Treatment” sounds better and remove underscore.
Validity of the findings: The hypothesis need to be clearly tested, at the moment the discussion is lacking substance. Moreover, the conclusions don't fit the results. How it can be the conclusion that conserving pollen at -20 degrees Celsius is good? You are not testing that, you are testing different freezing periods and different ranges of temperatures for germination and pollen tube length... I guess that is said because the germination rate is not low... But you should mention what you are really testing. The discussion needs more though, better explanation and going from the bigger picture to the specific detail.
Additional comments: Other comments:

Why pollen tube length decreased with freezing time but no germination? I'm lacking more discussion about this.

I like the idea that the results are trying to be matched with the climatic regions this could be converted to a research question and tested explicitly.

Figure 1 Y axis, maybe better “Germination rate”? I guess is an average, so describe it in the caption.

In the Figures 1 to 6 explain why you have a line that links the points… Visualization purposes?

Line 40: after worldwide “like”

Line 51: Why they behave differently if they are self-compatible or self-incompatible. Explain it.

Line 59 to 67: So, you say there are several studies with Rosaceae but what do they say or conclude? Is that relevant to your research?

Line 68/69: Linked with the last paragraph (59/67), now you talk about more studies are the same ones? Reference them.

Line 86 to 88: So, you test pollen germination with different temperatures and different freezing times? What about pollen tube length?

Line 91: Rosaceae family species, fix English.

Line 92: Fix English and add reference to the temperature range.

Line 110/112: Rephrase.

Line 118/119:  Fix English.

Line 124: E#ect, fix.


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

Input:
Title: EFFECT OF TEMPERATURE ON POLLEN GERMINATION FOR SEVERAL ROSACEAE SPECIES: INFLUENCE OF FREEZING CONSERVATION TIME ON GERMINATION PATTERNS
Review round: 2
Reviewer: 1

Output:
Basic reporting: The manuscript is revised based on the comments of respectful reviewers and I think the manuscript could be considering for publication in PeerJ.
Experimental design: The experimental information on M&M are suitable and with sufficient detail and information.
Validity of the findings: the validity of findings have done using statistics but so important parameters that's completed the work and could be beneficent for fruit breeding Relative injury (RI) and pollen viability, which the authors have not calculated.
Additional comments: The manuscript has suitable information on effect of temperature on pollen germination for several Rosaceae species this is very important for next experimental that's could help fruit breeder in the selection of tolerant and sensitive cultivars for different environmental conditions. Thus, the manuscript could be considering for publication in PreeJ.


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: DIFFERENTIAL RESPONSES OF THE ACIDOBACTERIAL COMMUNITY IN THE TOPSOIL AND SUBSOIL TO FIRE DISTURBANCE IN PINUS TABULAEFORMIS STANDS
Review round: 1
Reviewer: 1

Output:
Basic reporting: Please, include “Conclusion” to summarized the results and suggests the meaning of study or further study. Some citations are inappropriate, so please check again as mentioned below.
Experimental design: Experimental design was well designed, while the rationale of the study to focus on Acidobacteria is insufficient. I understand that Acidobacteria is abundant in soil and has important roles in soil ecosystem. However, other bacteria (e.g. Proteobacteria) are also abundant and have some roles in forest. Why other bacteria are not need to be studied? It is also important in soil ecosystem. Comparing responses of different bacterial phyla depend on wildfire severities can be interesting subject. Covering all bacteria is not essentially required, but authors should provide the reason to focus on Acidobacteria in this study.
Validity of the findings: Results are interesting, but some statistical methods are concered. All statistical tests in this study are parametric analysis, But, boxplots in Fig. 2 looks non-normal distribution and there is none of mention about testing assumptions for parametric test (e.g. normality test). Is it tested appropriately? Then please mention about it in the manuscript.
Additional comments: # Major comments
1. Rationales of study is needed as mentioned above.
2. Authors used Bray-Curtis dissimilarities on ordination analysis. It is not considered phylogenetic relationships of the species (OTUs) in communities, thus it can miss some aspect of natural community structures. Unifrac dissimilarity is recommended to be included additionally in analysis.
3. The abundance of other bacterial phyla is not provided. Is Acidobacteria most abundant in all samples? Although Acidobacteria is main focus in this study, supplementary information for other phyla is informative for readers.

# Minor comments
Acidobacteria is italicized in all part of the manuscript. But, the names of higher taxonomic levels (family, order, class, phylum or division, and kingdom) should not be italicized.

Line 94: Please provide the reference of classification standard.
L126-127: Citation of primers is not relevant. Please provide references appropriately.
L144-145: This sentence is repetition of following sentence (L14-146).
L146: The meaning of “300 bp reads” is ambiguous.
L152: Citation is wrong (UCLUST).
L153: please provide citation for Usearch (Edgar 2010).
L153-154: What kind of algorithm was used for chimera detection. De novo or reference based?
L154-156: Is it correct to use UCLUST for taxonomic assignment? Then, what is the meaning of a confidence threshold?
L155: Wrong citation for SILVA.
L164-166: What is the meaning of relationship? Diversity or abundance?
L179-180: Citation of vegan package and R. Please use a command “citation()” or “citation(“vegan”)” on R.
L190-195, 201-203: Interpretation of the results is not appropriate in Results parts. Please move to Discussion part.
L254-255: What is the meaning of close relationship? Between what?
L272: P. tabulaeformis forest is better.

Figure 2. Insufficient legend (“different capital letters ?”)
Figure 3. Please change the color of M10 for better recognition. The legend of 3b is incorrect (e.g. H10 > H20).
Figure 4. A-F in venn diagram are not need in this Figure. It is no meaning and distractive.