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: GYNOMONOECY IN A MYCOHETEROTROPHIC ORCHID EULOPHIA ZOLLINGERI WITH AUTONOMOUS SELFING HERMAPHRODITIC FLOWERS AND PUTATIVELY OUTCROSSING FEMALE FLOWERS
Review round: 1
Reviewer: 3

Output:
Basic reporting: An intriguing study that is basically well conceived and carefully undertaken, but it does tend to over-interpret the data and make unnecessarily grand claims. The Results are written in a rather discursive style; the original data should be integrated more thoroughly with the text to strengthen the inferences drawn.

Individual grammatical and stylistic suggestions are given below.
Experimental design: Essentially fine to explore the ecological subject described, although the inferences are a little over-interpreted in an evolutionary context in the Discussion.
Validity of the findings: A very intriguing subject matter and clearly a rare example of gynomonoecy in the Orchidaceae. However, the Discussion tends to over-interpret the data, making rather grand conclusions from a limited – albeit intriguing – sample set. I think a more guarded approach should be adopted, particularly with using embryo presence to infer seed viability, since the two are not necessarily correlated, and in deriving support for the hypothesis that the observed mixed mating strategy is important for maintaining the species’ symbiotic (“antagonistic”) interactions. If the latter is to be viewed as a solid interpretation for the data at hand, I feel the author should consider why this reproductive strategy is not more generally prevalent within the orchid family as a whole, since many of its species are obligately mycorrhizal, many occur in pollinator-poor habitats and many exhibit pollinator-limitation. Clearly there are other important factors that also play a role.
Additional comments: Additional minor comments are listed below.

Abstract
Line 18. End first sentence with a full stop after “gynostemium”. Start second sentence with “Exceptions to this rule…”.
Line 19. Change to “Here, I report an”.
Line 23. Insert “an” before “investigation” and change following “on” to “of”.
Line 24. Insert “the” before “reproductive” and change “in” to “of”.
Line 25. Insert “a” before gynomonoecious”.
Line 28. Insert “a” before “lack”.
Line 29. Insert “documented” before “example”. Why do you claim this to be the first documented example if, as you state in the Introduction, the same phenomenon has been reported previously in Satyrium ciliatum?
Line 30. Delete “The”, and start the sentence with “Gynomonoecy…”.
Line 32. Change “These” to “This”.
Line 35. I don’t understand the meaning of “such as mycoheterotrophic plants and its fungal victims”. Change to “such as those with fungal associates”.

Introduction
Line 40. Change “is” to “are”.
Line 41. “Change “species, which are distributed among” to “species classified into”.
Line 42. Delete “The” and start sentence with “Variation in floral characteristics”.
Line 44. Insert “while” before “the vast majority”.
Line 46. Delete “while”.
Line 48. Insert “as a whole” after “flowering plants”.
Line 50. End sentence with full stop after “2002)”. Start new sentence with “Exceptions”.
Line 54. Change “dioecies” to “dioecious”.
Line 60. Change “The females of” to “Female flowers of”.
Line 65. Change “discovered” to “report”.
Line 81. Why would female flowers be more attractive to pollinators? Please explain.
Line 84. Delete “The” and start the sentence with “Current”.
Line 94. Perhaps change “The preliminary…” to “My preliminary…” otherwise it is ambiguous to which investigation you are referring.
Line 98. It is not clear what you mean here. Why do you refer to “female” flowers having male function?
Line 103. Insert “s” at end of “observation”.
Line 104. Delete “s” at end of “assurances”.
Lines 87–105. In this discussion of the mating system of Eulophia zollingeri, I am surprised you do not refer to the study of Zhang et al. (Guihaia 34: 541–547. 2014), who report data for crossing experiments and observations of pollinators in this species in China.

Materials and Methods
Line 124. Change “kept” to “enclosed”.
Line 125. Change “non-manipulated” to “left unmanipulated”
Line 132. Change “At 3–4 months” to “Three to four months”.
Line 133. Change “weighted” to “weighed”.
Line 136. By what method or measure was seed viability assessed? Since there are different assumptions involved in the different methods available (presence of an embryo, TTC-staining, in vitro germinability testing, in situ seed-baiting, etc.), you need to be more precise in describing your approach. Simple presence of an embryo should not be misconstrued as viability.

Results
Line 142. Embellishments such as “the seed-feeding fly” should be left to the Discussion, as they need a citation.
Line 145–146. Embellishments such as “It is also noteworthy…” should be avoided in the Results. Just state your findings.
Line 148. The presence of an embryo alone should not be misconstrued as viability, which would require germination experiments to verify.
Line 147. 60% is not necessarily a “high proportion”. Perhaps “More than half” is more accurate. And to which experiment are you referring here? Is this as a result of artificial self- or cross-pollination or through open pollination?
Line 150. What do you mean by “most”? Where are the data showing the results of the crossing experiments?
Lines 147–156. Please refer to Table 2 earlier in this paragraph so it obvious from what raw data you are basing these inferences.
Line 156. Change “the” to “a”.

Discussion
Line 159. To avoid confusion with the description of separate female and hermaphroditic flowers in Satyrium ciliatum that you provide in the Introduction, I think it would good to emphasise the distinguishing features of the breeding system identified here.
Line 162. Delete “a’ before “severe” and insert “s” at end of “improve”. It is not clear what the “this” refers to here. Perhaps better to restructure this sentence.
Lines 165–166. Change to ”the size of floral parts did not differ significantly in the female and hermaphroditic flowers of E. zollingeri measured in the present study.”
Line 166–167. Change to “female flowers were not only produced at the apex of the inflorescence.”
Line 169. This statement needs a citation.
Line 170. Delete “should”.
Line 180. Change “can be” to “is” or “represents”.
Lines 170–187. How does this discussion gel with the findings of Zhang et al. (Guihaia 34: 541–547. 2014), who claim E. zollingeri is food-deceptive?
Line 188. Insert “s” at end of “advantage”.
Lines 188–190. This sentence is not grammatical. Restructure.
Line 190. What is meant by “should” here? Why should it be low?
Line 193. Change to “in one female flower.”
Lines 202–205. But you have not measured actual viability in terms of germinability.
Lines 206–208. If this is the case, why is this strategy not more widely prevalent throughout the Orchidaceae, given that the vast majority of its species are obligately mycorrhizal, and that many occur in pollinator-poor habitats and exhibit pollinator-limitation? I suspect there are other factors other than those you mention here. This interpretation is a little simplistic.


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: GYNOMONOECY IN A MYCOHETEROTROPHIC ORCHID EULOPHIA ZOLLINGERI WITH AUTONOMOUS SELFING HERMAPHRODITIC FLOWERS AND PUTATIVELY OUTCROSSING FEMALE FLOWERS
Review round: 2
Reviewer: 1

Output:
Basic reporting: A few more typos and minor grammatical errors to be corrected as listed below. I would also suggest simplifying the title a bit, if possible.
Experimental design: Fine.
Validity of the findings: Basically as before. I feel the author should underscore the fact that what he reports for his study populations of E. zollingeri in Japan may not (in fact appears not to) be the case for the species elsewhere in its range, as evidenced by the findings of Zhang et al. (2014).
Additional comments: The title is a bit of a mouthful. Can it be simplified?

Abstract
Lines 19–20: Eulophia zollingeri is actually very widespread in Asia and Australasia, not purely a Japanese species as this line suggests. This is an important point, because the reader should be informed that the data presented here concern only a tiny fraction of the global population, and what occurs in these few Japanese populations may not reflect the situation in other parts of the species’ range. Change to “…example of Japanese populations of a widespread Asiatic orchid species whose…”.
Line 23: Add “s” at end of “observation”.
Line 31: I think you need to state what the tradeoff is in – for example, “…tradeoff in reproductive potential between female…”.
Line 33: Although I neglected to mention this in my first review of this paper, I am reticent to consider this species “fully mycoheterotrophic” – as your photos in Fig. 1 show, many populations I’ve seen of this species in Asia have green stems which probably permit a degree of nutrient gain via photosynthesis, albeit probably rather limited. In the context of the argument that you put forward in terms of gynomonoecy being differentially advantageous for such species so heavily reliant on a symbiotic partner, I would counter that, in that case, why do we not see this strategy in other truly non-photosynthetic orchids?

Introduction
Lines 95–97: I suggest rewording to “Intriguingly, Zhang et al. (2014) revealed Chinese populations of E. zollingeri to be non-rewarding, self-compatible and dependent on the Halictid bee Nomia viridicinctula Cockerell for pollination through food deception. Although those Chinese populations consequently experienced strong pollinator limitation, my preliminary investigation revealed that Japanese populations consistently exhibit high fruit set.” It is interesting to note that the Chinese study populations exhibited a significant difference in fruit-set between forest edge and forest populations (perhaps something to consider in your Discussion – e.g. were your study populations in deep forest or at the forest edge?).

Results
Line 163: Change “begged” to “bagged”.
Line 169: Change “differ” to “differed”.
Line 172: Change “while” to “although”.
Line 174–175: Delete “and lost the ability to physically separate the stigma and pollinaria”, and change “them” to “the stigma and pollinaria”.
Line 176: Insert “to be” before “autogamous”.
Line 177: Insert “a” before “column”.

Discussion
Line 182: Consistency – use “I” instead of “we”. Insert “Japanese populations of” before “Eulophia”. Change “develops” to “develop”. I think it is important to underscore that what you report in these Japanese populations of E. zollingeri is clearly not a universal strategy within the species as a whole, since it was not reported in the Chinese study (Zhang et al. 2014). In this sense, it differs from the fixed systems in Catasetum, Cycnoches and Satyrium.
Line 216: You may also wish to cite Zhang et al. (2019, BMC Plant Biology 19: 597) here.
Line 220: Insert “in China” after “viridicinctula” as you didn’t record this as the pollinator in your study populations. Does this bee species occur in Japan?
Lines 252–253: Change “system” to “systems” and “occurs” to “occur”.
Lines 254–255: Change “which have independently evolved mycoheterotrophy from E. zollingeri” to “which evolved mycoheterotrophy independently from E. zollingeri”.
Line 258: Change “can” to “might”.
Line 260: Change to “concluded that the Japanese populations of E. zollingeri studied here preserve”.
Line 271:  Change “suggested” to “suggest”.
Lines 279–281: I would also add that it would be interesting to clarify how common this strategy is in different E. zollingeri populations across its range – could it be more prevalent where its effective pollinator is less abundant or absent?

Acknowledgements
Line 284: Change “Th” to “The”.


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 CHANGES IN ISOTOPIC BASELINES ON THE EVALUATION OF FOOD WEB STRUCTURE USING ISOTOPIC FUNCTIONAL INDICES
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript by Belle and Cabana entitled “Effects of changes in isotopic baselines on the evaluation of food web structure using isotopic functional indices” tested the validity of Layman’s IFIs in natural streams. The results indicated that some indices strongly depend on isotopic baselines, but some were not. The information is useful in applying “isotope space” study in food web research.
Experimental design: The use of waterfall as a controlled experiment in natural streams is a good idea. The experimental design is simple and straightforward.
One uncertain point is the authors sampled DIC in early May and late June 2016, but stream invertebrates in early June. As the environmental condition seems to change drastically from snow melting season to summer in Canada, the growth of each living organism seems to be high. Concentrations and isotope ratios of DIC are instantaneous, and short-lived algae may change their isotope ratio rapidly, but long-lived predator may integrate the signals through time. Do the author consider that the isotope ratios of DIC and invertebrate communities are comparable as in Fig. 5 and 6?
Validity of the findings: The final conclusion is clear. I agree with the authors that we need to test various isotopic indices to compare for relevant types of questions.
Additional comments: Minor comments below
L. 120 the same environmental conditions: Could you add simple descriptions among sites? Readers may want to make use of similar settings.
L. 152 delta-definition: The factor 1000 is an extraneous numerical factor and should be deleted (Coplen2011 Rapid Commun. Mass Spectrom).
L. 153 and other standards, too. Internal standards (C1 = -3 ‰, and C5 = -22 ‰): We don’t know each value itself, but the values should be written with significant figures, like -3.0 ‰.
L. 158 benthic invertebrates were sampled: Exact where did the authors sample invertebrates? Riffles, pools, or mixed?
L. 162 A small isotopic deviation can be observed using this technique: Indicate the reasons why the methods may cause the deviation.
L. 190 Remove “calculate”.
L. 205 “increase of -2.2 ‰” should be “increase of 2.2 ‰”.
L. 212 displayed high similarity: How did the authors identify “high similarity”?
L. 221: (Fig. 6): Fig. 5 comes later. Thus Fig. 6 should change to Fig. 5.
L. 271 (Fig. 4): Fig. 6?
L. 272 (Fig. 5.B): (Fig. 7.B)?
L. 284 and/or over time with fluctuating isotopic baselines: This seems true, but the authors didn’t test the hypothesis (see 2. Experimental design).

Table 1 Explain “1” and “0”, also “A” and “B”.
Fig. 5 Trophic guilds are abbreviated to the first four letters (e.g., Herbivore becomes “Herb”): but not abbreviated.


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 CHANGES IN ISOTOPIC BASELINES ON THE EVALUATION OF FOOD WEB STRUCTURE USING ISOTOPIC FUNCTIONAL INDICES
Review round: 1
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: It seems that this manuscript is the revised version I have reviewed previously in another journal. The content has been improved considerably with newly added analyses such as NMDS, PCA, and IFIs, all of which were not shown in the previous manuscript. The results suggest that these indices are not very much sensitive to environmental change between above- and below-water falls. I think that the authors did a good job to wrap up their research, except for one critical issue as follows.

The main aim (Lines 93-94) and conclusion (Lines 286-288) of this study should be reframed, because both autochthonous and allochthonous baseline data (e.g., algae and terrestrial plants) were unfortunately not present. I strongly disagree to use DIC as baseline, because there is isotopic fractionation against 13C between DIC and algae. Its size and variation are both greater than the delta13C difference in DIC between above- and below-water falls. However, this criticism might be avoidable if the authors used herbivores and detritivores as aquatic- and terrestrial-baselines, respectively (Post 2002 Ecology). This is advantageous over using benthic algae as baseline, which show a large variation in delta13C depending on environmental heterogeneity such as water velocity (Finlay et al. 1999 L&O) and on DI13C variation (Lines 67-70).


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 CHANGES IN ISOTOPIC BASELINES ON THE EVALUATION OF FOOD WEB STRUCTURE USING ISOTOPIC FUNCTIONAL INDICES
Review round: 1
Reviewer: 3

Output:
Basic reporting: This study performed the analysis of isotopic functional indices (IFIs) for  a natural experimental set-up to quantify impacts of changes in algal isotopic baselines on ecological inference. This study was well conducted and very interesting for isotope ecology. However I have few minor comments.

For NMDS, please describe NMDS stress for the Figure 2.

Figure 4 I could not see x and y ticks.

Figure 5 What  the error bar means here?
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


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

Input:
Title: EFFECTS OF CHANGES IN ISOTOPIC BASELINES ON THE EVALUATION OF FOOD WEB STRUCTURE USING ISOTOPIC FUNCTIONAL INDICES
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: Thank you for your revision. I think the manuscript has been improved substantially.


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: NEW RECORD OF PODOCOPID OSTRACODS FROM CRETACEOUS AMBER
Review round: 1
Reviewer: 1

Output:
Basic reporting: The article is clear, concise and well structured. The English is generally of a reasonable standard, but sounds a bit awkward here and there, e.g. line 24, 29, 39 etc. The last author should be able to sort out the English.

The literature references are mostly fine, apart from the following;
I suggest that original sources of data for specific facts should be cited rather than general review chapters on ostracods. For example (line 28–39),
“…the marine Gigantocypris can be up to 32 mm (Horne et al., 2002; Brusca & Brusca, 2003).”
The original data for the size of Gigantocypris probably came from Poulsen 1962, who recorded a maximum size of 34 mm for Gigantocypris agassizi (credit where credit is due).
Poulsen, E. M. 1962. Ostracoda-Myodocopa, 1: Cypridiformes-Cypridinidae. In Dana Report, 57:1-414, 181 figures. Copenhagen: Carlsberg Foundation.

One reference is missing: Line 47–48.
“However, most of the relatively few records of ostracods preserved in amber (e.g., Keyser & Friedrich, 2017; Matzke-Karasz et al., 2019)…”
There is also Keyser, D. & Weitschat, W. 2005. First record of ostracods (Crustacea) in Baltic amber. Hydrobiologia, 538, 107–114.

The references need checking through. Smith et al. 2011 is not cited in the text. Smith et al. 2015 (line 82) is not listed in the references. I'm not sure either Smith paper is an appropriate citation for the higher classification of ostracods.

The figures are of good quality, but there is a mistake on the scale bar of Figure 1A. Additionally, the red-cyan stereo anaglyphs (Fig. 2, D and I) didn’t work for me. A photograph of the whole amber piece would also be a good idea.
Experimental design: With the ethical controversy surrounding Burmese amber, further details about how this piece was obtained should be given, such as its provenance, date of purchase by previous owners, and date of donation/purchase by the Natural History Museum of Vienna. Whether this is an ethically sourced specimen needs to ascertained before this paper is published. The Journal of Systematic Palaeontology is now refusing to publish any articles on Burmese amber, but of course, this is a matter for the editor.
Validity of the findings: This is an interesting article about (possible non-marine) ostracods from Burmese amber. The authors have been quite conservative in their conclusions about what the ostracods can tell us and which taxa they represent, which is a good thing.  I agree with their assessment, although I think they have missed some possible ‘clues’ about these ostracods (see below).

There does seem to be a small discrepancy about possible taxonomic affinities in the article. The Remarks section of Taxon A concludes “… perhaps favours an assignment to the group Cypridoidea but this is not conclusive.” (line 122).
However, the Discussion (line 170) says:
“Nevertheless, we can speculate, on the basis of gross morphological similarities, that at least taxa A and B belong to either of two ingroups of Cypridocopina, namely Pontocypridoidea and Cypridoidea.”

One thing I would mention in the Discussion is that we don’t know if the specimens are adults. They are all quite small, and the shape of Taxon A could be a juvenile, which tend to have less inflated posterior margins.
If we assume Taxon A is an adult, then it resembles a Pontocypridoidea or Cypridoidea (maybe even a Paracypridinae of the Candonidae: Cypridoidea).

The ostracods were living in the same environment as the isopod, so does the isopod give any clues to the palaeo-environment? (e.g. a marine, brackish or freshwater taxon?). The main problem with Burmese amber is the lack of stratigraphic data with the pieces recovered. Some think that Burmese amber may span at least 5 million years (according to Science, 24 May 2019 issue, p. 725).  So it is unknown if this piece came from the same time period as the ammonite or the marine myodocopid ostracod.  Therefore, previous finds may not be that informative (or even misleading) with respect to the palaeo-environment of isolated amber pieces. I would therefore place more weight on syninclusions; the Diptera and Coleoptera would suggest non-marine for this piece, which in turn nudges the possible taxonomic affinities of the ostracods towards the Cypridoidea.

The fact that the ostracods are totally surrounded by amber, with no evidence of a substrate near them, suggests that they were capable of swimming above the substrate and they ‘landed’ on the resin. (It also suggests that the ostracods were alive when trapped as it would not be possible for dead ostracods on a substrate to be cleanly separated out like this.) This would exclude the Cytheroidea, and Candoninae (can’t swim).  Could the ostracods have been feeding on, or drawn to, a trapped isopod, and consequently been trapped themselves? I think that one study of all the inclusions in this piece, rather than being split in different publications, would have been a better approach to understanding the palaeo-environment. But ultimately that is up to the authors.

Other records of ostracods in amber typically have a gape to the valves and appendages protruding. These ostracds don’t, but are instead tightly closed. I don’t know the significance of this, but perhaps it should be noted somewhere.
Additional comments: Other small issues with the manuscript style include:

Line 22
The first line of the abstract is a bit limp, and could be changed to something like:
“Burmese Cretaceous amber (~99 Ma, Myanmar) is famous for the preservation of a wide range of fauna and flora, including representatives of marine, freshwater and terrestrial groups.

Line 30
“Taphonomic and palaeoenvironmental implications are also discussed.”
Rather than just saying they are discussed, the authors should outline their conclusions.

I suggest adding that tomography was used to study the ostracods to the abstract.

Line 39.
“Ostracods are also the most common fossil arthropods during the geological history of the group, which can be dated back to Early Ordovician (Horne, 2005).”
A clearer way to say this is perhaps “Ostracods are the most commonly preserved fossil arthropods…”.

Line 61.
What is the size of the amber piece?

Line 97.
“Fig. 1A; Fig. 2; Suppl. 1”
Should note that it is marked by the arrow in fig.1A (not the whole plate).

Line 101
There are dimensions for Taxon A, but not for B and C. Is it possible to get a e.g. length, if not all dimensions for the other two?

Line 103
“Locality and horizon.”
Add latitude and longitude (also for the other two taxa).

Line 118
“Remarks: The right valve shows shallow indentation near the anterior end of the ventral margin…”
Surely you mean the left valve, as seen in Fig. 2H?
An arrow on the figure, and the figure number would help here. This shallow indentation is not mentioned in the description. OK, so you think it is possibly an artefact, but I think it should be included.

Line 160
“Alavesia sp. (Dipera);”
Should be Diptera.

Line 177
“However, we cannot rule out the possibility that it may belong to the group Cytheroidea…”
Unlikely to be Cytheroidea because they don’t swim. See comment under Validity of the findings.

Line 204
Better to write
“The three specimens are the first podocopan ostracods to be reported from Burmese Cretaceous amber”


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: NEW RECORD OF PODOCOPID OSTRACODS FROM CRETACEOUS AMBER
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript reports three ostracods preserved in Cretaceous age amber from Burma. Relatively few ostracods have been described from amber and similar deposits and, as the authors observe, more from Cenozoic age deposits than from Mesozoic. The material is of international interest, although that I predict in a few years time interest will focus only on ostracod specimens with soft parts preserved.
Experimental design: Aims simple - to document a currently rather rare record.
Methods clearly described and appropriate.

The manuscript is concise, suitably structured, generally well written, the experimental design and methodology are appropriate, reference citations are relevant and up-to-date, and the figures are both necessary and of good quality.
Validity of the findings: See my comments (attached) on the identifications. Otherwise data justify conclusions.
Additional comments: This is a rather simple piece of science but, as I note in my attached comments, of current international interest.


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: SPATIAL MODELING COULD NOT DIFFERENTIATE EARLY SARS-COV-2 CASES FROM THE DISTRIBUTION OF HUMANS ON THE BASIS OF CLIMATE IN THE UNITED STATES
Review round: 1
Reviewer: 1

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
Additional comments: N/A


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: SPATIAL MODELING COULD NOT DIFFERENTIATE EARLY SARS-COV-2 CASES FROM THE DISTRIBUTION OF HUMANS ON THE BASIS OF CLIMATE IN THE UNITED STATES
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper seeks to determine whether climate data can contribute to predicting the range of SARS-CoV-2 in addition to human population distribution patterns. They found little evidence that climatic variables contribute much predictive power not explained by human population distribution. The paper is written with appropriate caution and the authors outline the caveats well.

However, there is much detail missing from the Methods, and the wording is so confusing that it's difficult to determine exactly what was done. This is despite the authors' own claims about the good level of methodological information they reported.

Further, some crucial elements were missing or lacking from either the Introduction or Discussion:
1) a clear acknowledgment that viral distribution patterns are also heavily driven by regional politics (i.e., country-specific responses to public health). Doesn't this also need to be accounted for (especially in the US)? High transmission rates, regardless of climate or human behavior, may be higher somewhere just because a particular gov't did not prepare sufficiently, or because they are reporting cases more accurately, etc.
2) a brief review of how SDMs have been used to model pathogen distributions, the difficulties they faced, how they overcame them, etc.

As a whole, although the topic may be of interest to those studying SARS-CoV-2 distributional patterns and the paper does call out some preprints claiming that the viral distribution can be properly explained by climate, key elements are missing that make for potential confusion, and these need to be addressed.
Experimental design: The main research question was well-defined, but the way key results were referred to was inconsistent (please use the same names for data products throughout), key methodological details were missing, and some confusion regarding model evaluation appeared to exist. I explain in the line-by-line comments, but selection of a model via AIC does not consider cross validation results, despite the authors' claims they used spatial cross validation to choose models. Table 1 is appreciated, but these same details must be referred to somewhere in the Methods text.
Validity of the findings: This paper does help to dispel the notion that viral distributions can be predicted solely with climate, but the analysis itself does not include enough human-specific variables to make a convincing model prediction. For example, some effect of regional politics is sure to play a role in infection rates, especially in the US, but this is glossed over in a single sentence in the Discussion. Nonetheless, the findings of this study will contribute overall to the understanding of the biogeography of SARS-CoV-2, and the authors are entirely transparent about data sources.
Additional comments: Line-by-line comments:

L65: Change to: "appear to explain much of the viral distribution".
L69-70: If SARS-CoV-2 is dependent on human hosts, what kinds of abiotic variables might shape its niche? Wouldn't most of these niche factors relate to the host's internal environment? How would knowledge of the "abiotic preferences" of the virus help contain its spread. Please explain more clearly.
L73: Remove "of".
L76: Maybe "foundation" instead of jumping-off point?
L86: lipid-enveloped
L112: Remove colon
L121: Isn't it "to at least some extent reflect the habitat patterns of their host"?
L136: self-isolation
L140: Needs updating
L164: Change to "interpolated climate data". Can you at least verify that using a more up-to-date interpolated climate dataset like CHELSA would not have affected results very much? More importantly, how good is Worldclim at predicting current weather? This pandemic just occurred. Wouldn't using PRISM have made more sense?
L166: Min and max of what? Avg monthly? Of warmest quarter, etc.?
L175: What is the purpose of this section? Please outline the logic behind your methods at the end of the intro.
 L177: Probability of what? What exactly is the function of this kernel density grid? Why does it use climate variables? It looks from Fig. 1 that you took the kernel densities of cases and human pop, not climate (which would not make sense anyway). At this stage in the paper I am confused.
L180: population-scaled
L189: By "climate record", do you mean county record associated with climate? Also, what is a "raw SDM"?
L190-193: I don't follow this at all. What does it mean to "expand" a record? Why would any counties have fewer than one data point?
L195: It is not clear what the difference between these two is. Please explain more clearly. Also, where is the description of the "human population SDM"? Not even sure what that means, as SDMs are based on presence data, not abundance.
L195-199: It looks like you selected model settings for Maxent based on two datasets (but not clear what you did if the two were different), then used these settings to make models with other datasets. This makes little methodological sense, so I think I must be misunderstanding. Please clarify. Also, was maxnet used in your ENMeval run?
L202: Please explain briefly why this is preferred for models with regularization. From my understanding, it is best practice for the purposes of interpretation and to avoid extrapolation errors due to changes in covariance. Also, where do you discuss model evaluation?
L205: Please rephrase for correct grammar and fix spelling.
L209: Please explain the niche overlap and similarity tests. What do they do? How are they different?
L218: record(s)
L238: Please clarify "for people". As there are multiple variables considered, please reference them explicitly to avoid confusion.
L271-272: The model does not indicate that raw values should not be used as inputs. You infer that after analyzing the results.
L302-304: This seems like a relatively trivial exercise given you have the data in hand. Why didn't you do this and briefly compare it to your other results?
L324:324: If we are missing lots of data from more tropical areas, this would certainly affect global climate models. Why such uncertainty?
L325: What "best practices" are you referring to? The lead author on the paper criticized is the same one in the best practices paper you cite. Shouldn't this person, of all people, adhere to best practices? That seems like a valid criticism.
L328: A number of these best practices are missing from your Methods.
L351: Needs updating: https://www.who.int/news-room/commentaries/detail/bacille-calmette-gu%C3%A9rin-(bcg)-vaccination-and-covid-19

Table 1. Using AICc for model selection does not consider the results of cross validation at all. So regardless of the fact that you used spatial block cross validation with ENMeval, you did not consider the cross validation results unless you also considered test stats like testing AUC or omission rates, etc. Key details like which Maxent parameters you considered, etc., are missing from the Methods.

Fig 1. Nowhere in the text do you explain the relevance of wind speed, water vapor pressure, or solar radiation to SARS-CoV-2 distribution.


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: SPATIAL MODELING COULD NOT DIFFERENTIATE EARLY SARS-COV-2 CASES FROM THE DISTRIBUTION OF HUMANS ON THE BASIS OF CLIMATE IN THE UNITED STATES
Review round: 1
Reviewer: 3

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors use an SDM model to compare suitability for SARS-CoV-2 with human population suitability. The aim of the study is partly to critique earlier work using similar models which found a more conclusive effect of climate on SARS-CoV-2. I think the paper is well-written, well-argued and important. I recommend the study be published by PeerJ. I have only minor comments:

92 is this “scientists” or ecologists or some other sub-group? There are lot of scientists who do not use these methods so I think you need to be more specific.

139, remove “our” here as you haven’t introduced your model yet, suggest “While epidemiological models are highly uncertain, COVID-19 may peak…”

141 This sentence is confusing. It seems you are trying to state the purpose of the paper here? “Baseline” could mean a lot of things. I think the purpose of the paper is better stated in the abstract and some version of this should be re-stated here e.g. “Here we develop a SDM model using both climate and human population data to determine whether the effect of climate can be appropriately disentangled from other drivers…” – some better version of this.

155 I think the authors should clearly state that they are only take one value per county: total cumulative cases as of March 30th.  Are call counties reporting? Would be nice to know the sample size.

169 5km buffer is very small, aren’t most counties much larger than this? You could have used a county shapefile to take averages over the climate data. Or by county center do you mean the population center? If you mean the county centroid, then that isn’t necessarily representative of where people live? In general, I don’t think this will matter too much, as climate data tends to be highly correlated over short distances. Perhaps mention this to justify using the small area.

176 (similar to line 155 comment) Are you using the total cases as of March 31ST 2020? State this clearly. Lots of the climate-regression studies use the whole time series of cases and compare variations in county-level climate with county-level cases over time. I think you need to make clear that you are using a purely cross-sectional approach.

Discussion: Probably worth citing this recent paper in Science suggesting even if climate can impact transmission, it will have minimal impact compared to population susceptibility. This may explain higher case numbers in Florida and other warmer locations.

Baker, Rachel E., et al. "Susceptible supply limits the role of climate in the early SARS-CoV-2 pandemic." Science (2020).


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: SPATIAL MODELING COULD NOT DIFFERENTIATE EARLY SARS-COV-2 CASES FROM THE DISTRIBUTION OF HUMANS ON THE BASIS OF CLIMATE IN THE UNITED STATES
Review round: 2
Reviewer: 1

Output:
Basic reporting: The paper is much easier to follow now, but there are still some sentences phrased awkwardly, grammatical mistakes, and unclear statements. I made suggestions in my line-by-line edits. Much better coverage of literature now.
Experimental design: This revision made the methods more clear, but lingering questions remain (see line-by-line edits). The authors need to use consistent language when referring to results, explain the methods in a bit more detail, better outline the methods in the introduction to prepare the reader for them, and in general take care to be consistent with the order and manner in which different results are reported (else it gets confusing).
Validity of the findings: The findings here are important for the field, as the authors demonstrated that climate-based SDMs are not appropriate to model the range of a novel pathogen spread by humans, and that human population density is a much better predictor. The authors just need to be more emphatic that this is the best way forward. The conclusions are clear and there is an appropriate amount of uncertainty outlined.
Additional comments: Good job on this latest revision -- I think the paper has improved considerably.

Line-by-line comments:

L29: "not in population equilibrium"
L32: "population-scaled" -- all instances need hyphens
L52: What is a "basic distribution"?
L70: Spelling
L97: Format
L102: Please finish the sentence.
L103: If the abbreviation SDM refers to "modeling", then SDMs becomes "species distribution modelings".
L106: Please cite something more recent and general, like 2011 Peterson et al. book.
L109: Grammar
L108-113: Not clear what the difference here is. A model of potential distribution is making correlations with climate data. Please be more clear about the distinction you are drawing.
L117: I would say "environmental variables correlated with its occurrence exist" because you can project to unsuitable conditions too.
L129: No capitalization mid-sentence.
L130: Why do you cite the standards paper here? Seems not relevant.
L142: "Still, the climate-based SDMs for SARS-CoV-2 presented recently..."
L143: Can we really use "habitat preferences" for modern humans? Can't you say "climatic preferences"? This is more accurate anyway because climate does not define habitat.
L146: "..., and may help to better ensure..."
L158-159: You do not mention here the niche overlap analyses. Please prepare the reader adequately for all the methods you undertake and explain why you're doing them.
L204: "were produced" -- please make sure to stay in past tense for the Methods section
L209: If "total cases per county" = "raw case data", say it like this to avoid confusion "Raw case data (i.e., total cases per county)"
L215: "we calculated non-parametric Spearman's rank correlation coefficients in R" (the code is not necessary)
L221-223: Rephrasing like this may be less confusing, and includes the expansion factor: "while occurrence data for population-scaled SDMs were generated the same way as for the raw SDM except that county climate records were multiplied by the total case count divided by the county population, such that no county had fewer than one record, then multiplied by an expansion factor." Please why you use the expansion factor.
L224: Use "total virus cases", not just "cases".
L227: Please cite Maxent here and introduce it as an SDM algorithm for presence-only data with complexity settings that can be tuned.
L230: After "feature classes", put "(constraints on model fit)" and after "regularization multipliers", put "(penalizes complexity)" for those who don't already know.
L231: Not "best", but "optimal", which emphasizes that you did not pick the absolute best but the best of the set explored.
L232: Rephrase to: "Optimal model parameters were chosen by maximizing the average test AUC calculated with cross validation using the spatial ‘block’ partitioning method, and minimizing AICc in the case of ties."
L234: "including those tested within ENMeval" -- not needed?
L236: Does "human density" here mean "human population"? Later in the Results you refer to "human population model" -- is that this human density SDM? Please use consistent terms.
L237: What does "clearly linked" mean? Can't you easily quantify their correlation?
L244-245: It is crucial to mention here which particular methodological decisions brought you to bronze, else readers cannot appreciate what is so commendable about your study.
L245: "inherently imperfect" is very vague. Can you be more specific as to why this data is imperfect for SDMs?
L260: "during the latest date in March" -> "for March 30"
L280: What are the results for the human pop model? They should be here.
L287: Not sure this interpretation is correct. I would interpret mean test AUC as a measure of average transferability and the variance as variation in transferability, as the AUC itself is measuring how well the trained model predicts the new data. Further, a difference of 0.0068 in variance is very small -- perhaps "slight difference"?
L290: Please report the results for the human pop model -- they seem to be missing. What were the optimal model settings? Also, I think they belong in the preceding paragraph where you discuss the pop scaled case model.
L311: "At least some human-focused data" is not really strong enough here when you just demonstrated that the observed infection patterns reflect human population density. Shouldn't this be the main kind of variable used?
L315-316: "inline" should be "in line"
L336: What does "statistically identical" mean? Aren't these different models with different complexity settings and different training data?
L338: Please quantify this, as the data exists.
L341: The models are different, and are certainly "statistically distinguishable" even though the niche similarity test was significant. Figure 3 shows the differences clearly. You might say they are "very similar".
L371: Which papers? Do you mean specifically those doing SDM analyses, or those doing SDM analyses on disease vectors? Please be more specific.
L392: Just say "individuals".
L398: Perhaps "while conducting an analysis on global data would have been ideal, we avoided this because..."
L435: What "heartbreaking statistic"? Might want to avoid using such emotional language.


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: SPATIAL MODELING COULD NOT DIFFERENTIATE EARLY SARS-COV-2 CASES FROM THE DISTRIBUTION OF HUMANS ON THE BASIS OF CLIMATE IN THE UNITED STATES
Review round: 2
Reviewer: 2

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: I am happy with the authors' response to my questions and the changes made. I suggest the authors double-check spelling/grammar before submitting the final version e.g. Line 102 "once the endemic phase is reached" and Line 315 inline should be in line.


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: TOWARDS A UNIFIED GENERIC FRAMEWORK TO DEFINE AND OBSERVE CONTACTS BETWEEN LIVESTOCK AND WILDLIFE: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: The MS meet standards
Experimental design: The  approach, literature search,  filtering and analysis meet the standards
Validity of the findings: A relevant stop forward on standardizing contact data art the wildlife-livestock interface
Additional comments: The aim of this study was to systematically review the reasons for, and observational methods used in, studies investigating livestock-wildlife contacts, and to propose a generalized framework for defining contacts between livestock and wildlife. Definitively, as the authors claim, a standardized generic template for defining livestock-wildlife contacts is needed. And this MS is an important step forward.
The MS is excellent as a comprehensive review on the topic.The authors show in the results section the novel generic framework to categorise wildlife-livestock contacts (Fig. 4), based on the locations of individuals in space and over time. It shroud previously be introduced also in Material and Methods (the general approach)
L123: legend for Figure S1 (two categories by column??) explain).

L129. Remark that research addressing resource use by wildlife and livestock, but not directly the contacts, is included.

L147. Define “study power”: ability to detect rare contacts??

L148. Authors mention: “Conclusions were robust and directly derived from the results in 109 (89%) publications. Is that subjective”. Provide indication how you assessed this (they all are peer-reviewed papers), did you question conclusions in 11% remaining?

L160: do you include wild boar as wild pig? Specify since it is used over the MS (e.g. fig. 3).

Further analyses (i..e according to system, or geography) of paper scores can provide interesting results.

L202. What about locations first visited by livestock?

L229. The proposed unified framework to define direct and indirect contacts must be introduced (the approach) in Mat & Met), and briefly commented in the summary.

L236: define SC (critical distance between animals, depending on the system being studied as well as the specific objectives of each study, I only found the definition in legend of figure 34) and Tc (critical time over which critical distance happens between 2 individuals, depending on the system being studied as well as the specific objectives of each study) (maybe in Mat & Met).

Discussion.
Proposed unified framework: I agree the approach of this generic framework to define direct and indirect contacts will help ensure results between studies are more easily comparable. However, the main problem: the definition of Sc1, Sc2, Tc2, and Tc2 according to the system and specific conditions. This, itself, needs a common framework (guidance or rules) which is not addressed here and vaguely commented. Then, studies can be comparable. For discussion and future research: I encourage authors to discuss if it can be developed a generic framework to define Sc1,2, Tc1,2 as a function of objective characteristics of the pathogen- host-environmental systems and objectives. This would be also very useful for researchers to approach their study systems to generate comparable values and use the appropriate methodology (and not to make the definition on contact dependent on methods or other practical issues). Provide any clue for what is near or different in Figure 4 for a specific system (this distinction, as it is presented, is vague). Most discussion could be part of the introduction. I encourage authors to expand discussion on the abovementioned, on the limitations of this framework, which need more detail (e.g. definition on near and different) and a parallel framework for definition of Sc1,2, Tc1,2 (in a separate research)

L251: Meaningful comparison only to a certain extend. See my previous comment.

L329: Agree! This is a necessary step forward.


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: TOWARDS A UNIFIED GENERIC FRAMEWORK TO DEFINE AND OBSERVE CONTACTS BETWEEN LIVESTOCK AND WILDLIFE: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: No comment
Experimental design: No comment
Validity of the findings: No comment
Additional comments: The present manuscript performs a systematic review of papers studying wildlife-livestock contacts, and subsequently propose a generalised framework for defining direct and indirect contacts between domestic and wild mammals (Figure 4). The manuscript addresses a highly relevant topic, especially in the current situation of sanitary uncertainty, in which we must increase efforts in sanitary surveillance and in the implementation of control measures of zoonotic diseases. Besides, the review includes the most important published studies of the topic.
However, I have some concerns about the methodology, discussion and the applicability of the proposed framework:

Methodology:
1.	Line 88-89: As stated at the end of the paragraph, a contact could be an association between animals and farms, so, this must be included in the formal definition of the contact.
2.	Line 96-97 and (Table S1). Just curiosity: regarding the terms included in the searching process, why did you specify so much wild species (lion, antelopes, buffalo, wolf……….) when the most important concepts were also included (i.e. carnivore, herbivore, wildlife….). By being so specific, many species will be forgotten (as for example: giraffe).
3.	Line 126: what is the point of defining the quality of the papers? I suggest being more precise on what you mean with quality, since this is a very broad term, and (probably) all of the papers considered in the revision have been published after a peer review, so the quality of all of them is implied.
4.	The development of the “generic unified framework” is my major concern. I agree that this is a major weakness in the study of contacts, since many studies are not comparable between them, so the proposal of a unified framework appears like a great solution. However, your proposed framework does not really contribute to the consensus of a generic definition of direct/indirect contacts. This definition has to go beyond a spatio-temporal agreement of what it will be considered as a contact, since this definition will depend on the pathogen (in the case of disease studies), the species, the aim of the study, the methodology employed… For example, an indirect contact (see Figure 4) could be “near in time”; according to this, the temporal window could be 1 hour or 1 day, and this not make comparable the studies using such different windows.

You should also include the problem of the representativeness of the individuals, especially when the contacts have been recorded with a methodology that requires the marking of individuals (GPS, proximity loggers, VHF…). This representativeness will also modify how comparable are two studies.

It is also very important to relativize the number of contacts (both direct and indirect) with regards to the total population. Two studies won’t be comparable if study A only uses 3 camera traps and study B uses 100 camera traps.

I suggest to improve the “proposed unified framework” by including all these considerations, for example, proposing a definition of contact regarding the topic of the study (disease, behaviour…), or regarding the pathogen studied, or the species included….

Results:
1.	Line 224: what do you mean with “power”? Explain (maybe in the methodology section?)
Discussion:
2.	Line 253: however, you don’t give a real range either
3.	Line 271 – 273: this is not precise, since sometimes, the species involved or the study area will condition the methodology employed. For example, we can’t use GPS devices if our study area doesn’t have a proper signal; or we cannot observe directly the contacts if the visibility of our study area is not good. So, the choice of the methodology will depend on many factors, and not only on the spatio-temporal window employed to define contact.
4	Line 273: be careful with the term “observation method” because it could be confused with the direct observation of the contacts (as for example in the case of Richomme et al. 2006)
5.	Line 332-333: the direct observation of the contact (which is a methodology included in the review) could be applied in this case

Figures:
1.	Figure S1: what does represent the numbers in the bars? The sum of these numbers is higher than 122 (which is the total number of papers included in the review). Besides, what does represent the two themes or categories in this figure (primary and secondary theme)?
2.	Figure 4: the title of Figure 4 is too long, especially if we consider that almost all this information appears in the Results section

Minor comments:
1.	Line 10: maybe not so surprising, since (as you estate below throughout the text) the definition of contact will depend on many factor: the pathogen under study [transmission route, survival capability…], the species involved, the methodology applied for the recording of contacts….


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: TOWARDS A UNIFIED GENERIC FRAMEWORK TO DEFINE AND OBSERVE CONTACTS BETWEEN LIVESTOCK AND WILDLIFE: A SYSTEMATIC REVIEW
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1.	The introduction and background were clear, provided a good foundation for the review, and generally well-referenced. There were several points where clarification was needed (see comments in PDF) in the abstract and results:
a.	Lines 13 – 14: 30,080 unique publications were eligible for screening, based on Figure 1. It's more accurate to report the 30,080 rather than 43,000 since many of these were duplicates.
b.	Lines 14 – 16 (abstract) vs. 160 – 161 (results): it’s unclear what the most studied wildlife species were (and in what order): deer, wild pigs, or badgers?

2.	There are several errors, omissions, typos that need to be fixed in the tables. Please see notes in the PDF. Particular attention should be paid to Table 4, which currently has several errors ranging from issues of formatting to statistical reporting.
a.	Your reporting of descriptive statistics needs attention. I'm unsure how you arrived at your summary statistics (mean, median, range). For example, are you reporting the mean number of direct contacts within a single study or are you calculating the mean number of observations within multiple studies? For example, the mean, median, and range are often reported to be the exact same numbers. This is odd and suggests that there is only a single value, in which case there is no need for summary statistics. Also, the range, by definition, has two numbers: a lower limit and an upper limit. Just reporting one number is confusing and incorrect (e.g. PRISMA Checklist #13 is “State the principal summary measures (e.g., risk ratio, difference in means)” and all you say is “Descriptive”).
b.	Can you clarify what you mean by “Number of studies” and “References” as column headings (and what the difference is?). For example, on row 3 – 4, I'm confused why the livestock camelid + wildlife camelid rows say that there is only one study, but two different references? Same question applies to numerous rows in the table.
c.	A table should be used to summarize and this table is too large and doesn’t condense information effectively. One possible solution is to just reserve this table for actual summarizing of studies involving > 2 studies? Can you further edit or summarize the last column (type of contact). Or perhaps just include publications that actually provide information on the frequency of contacts (i.e. no rows with “-" in them?)
d.	I am unsure why “models” are included as methods used to observe contact. Models are either based on empirical data (from observation methods like the ones you mentioned) or theoretical information. Can you explain why you consider “models” an observational method?

3.	I think it’s important to mention what “themes” emerged in the actual text of the paper (lines 122 – 123) and then refer the reader to the Supplemental figure to see the breakdown. For example, I didn’t know what themes you were referring to until the results section, but it should be mentioned earlier.

4.	Please use caution when reporting percentages and mention in the text when they sum to > 100% due to overlap or non-mutually-exclusive outcomes (e.g. lines 153 – 156). The caption for figure 3 was useful and a similar note should be made in the text where appropriate (e.g. “Many publications used more than one method to monitor contacts, and therefore the numbers of studies exceed 100% for some groups.”)

5.	Table 2 also had numerous minor calculation errors, please see individual notes in the PDF and change accordingly. Recommend using more concise language in Tables 2 and 3 (see PDFs for specific suggestions).

6.	Figure 3 (and supplemental figure S4): I recommend increasing the contrast between the shades of blue for the dots. It does not stand out very well currently.

7.	Figure and table captions/legends should provide more information, in general. The figures and tables should provide enough information to stand on their own (see notes in PDF). The exception is Figure 4, which contains far too much information and is taken verbatim from the text. This should be simplified and redundancy removed.

8.	It is already implied that findings in this paper are "agreed upon by the authors" and it’s not necessary to mention this "agreement" several times (e.g. lines 106, 116, 123).

9.	There was no problem accessing the raw data provided (Supplementary_File_3)
a.	It’s unclear why the first reference says “no author name available.”

10.	Supplemental tables and figures do not have titles or captions. Tables S4 and S5 do not match the text of lines 156 – 158 (the text has a denominator of 80 for both diseases, while the total bacterial diseases in Table S4 is 58 and the total viral diseases in Table S5 is 13) and Table S5 has a typo (should read 62% cumulative for foot-and-mouth disease).

11.	Manuscript structure and organization were clear and easy to follow; however, it would be helpful to add some additional subheadings to organize the flow of the paper (see PeerJ  Literature Review standard sections: https://peerj.com/about/author-instructions/#literature-review-sections)
Experimental design: 1.	The research question and aims were generally well-defined and clearly stated; however, there are some points of clarification or further discussion needed either in the introduction or discussion.
a.	The systemic review question (lines 90-92) includes “risk factors for contacts between wild animals and livestock”, but risk factors were not addressed clearly in this review. Can this be included/addressed or else removed from this sentence?
b.	The systemic review question also said, “… contacts between wild animals and livestock or livestock farms worldwide?”. A brief discussion on reporting/ publishing bias is important for any review article. It was useful that you included a geographic breakdown of where articles were published (e.g. Table S3), but it is important to point out that the predominant countries where livestock-wildlife articles were published was the U.S. and U.K., which is hardly representative of the world at large. In order to promote critical thinking and transparency, it recommended that they include the potential bias this introduces into their review in the discussion section. It could be interesting to combine Table S1 (regional distribution) with Figure 2 (yearly distribution) in the same figure with 2 panels, particularly since both space and time are prominent themes of the review.
c.	The aims of the review (lines 11-13) included investigating “which livestock-wildlife contacts have been studied and why,” but this did not receive as much attention as the second aim, which was to investigate the observational methods used. More time and thought should go into the discussion of “why” certain livestock-wildlife contacts have been studied. In addition, it’s unclear whether they are referring to the types of contact (e.g. direct vs. indirect) or the species of livestock and wildlife that have been studied.

2.	The methods were well described, with sufficient detail and information to replicate. The adherence to PRISMA reporting guidelines was very helpful. Some clarification is needed:
a.	Lines 116 – 121: can you clarify whether or not your working/provisional definitions of direct and indirect contact fail to mention space and time considerations? And I’m assuming that these were developed a priori before performing the literature review, but can you confirm?

3.	The description of the development of a generic unified framework (lines 131 – 134) in the Methods section is currently quite vague and more detail is warranted. For example, was this framework used to refine your provisional definitions of direct and indirect contact and if so, what is the improved/revised definition? How did you define “meaningful” contacts in each study? In contrast, the results section is overly complicated in its explanation of the framework, both in the text (lines 235 – 244) and Figure 4 (as noted above, the wording is redundant). The way it is currently written is not intuitive and makes the topic more complicated than it needs to be. Also, lines 233 – 235 and 244 – 247 are very similar and these ideas only need to be conveyed once in a single sentence. Some of the scenarios in Figure 4 are somewhat helpful, but I don't understand why scenarios B and D are both considered "near in space" when both involve badgers, but scenario B space is 10-15 m, while scenario D space is >50 m. This seems like a substantial difference in "space."
4.	This review article fits within the scope of PeerJ since it is focused on the biological sciences. I commend you for utilizing the most current PRIMSA checklist for literature reviews (and thank you for including it in the supplemental materials). Inclusion and exclusion criteria were clearly defined in the text and Table 1.
Validity of the findings: 1.	In the abstract (lines 2 –4) and discussion (lines 312 – 314), COVID-19 is mentioned very briefly, although your paper focuses on diseases arising from contact between wildlife and livestock, not humans. It would be more beneficial to highlight emerging infectious zoonotic diseases that impact people directly through livestock that were infected from wildlife (e.g. as you mentioned, Hendra and Nipah are good examples of this). Although COVID-19 is an important emerging infectious zoonotic disease, the most recent evidence of spillover is from bats and potentially other wildlife species in wet markets. I’m not aware of any evidence that livestock played a role in disease transmission. It is misleading to begin your abstract with COVID-19 simply because it's a current public health emergency with international attention, when your paper has a different focus. If you are going to mention it in the discussion, please elaborate more.

2.	I was initially concerned that your paper excluded small mammals (rodents, bats) and birds, particularly given their global importance in disease spill-over dynamics. For example, Wiethoelter et al (PNAS, 2015) states, “The bird–poultry interface was the most frequently cited wildlife–livestock interface worldwide.” I was grateful to see this omission partially addressed later in the discussion (lines 329 – 333), but additional explanation would make the paper much stronger. Simply stating that your research does not address avian influenza is insufficient. It is likely that other readers will have similar concerns and will expect more in-depth discussion of this point. I don't think you need to re-do your entire study, but more time must be devoted to justifying why these important animals were omitted, and how your findings may not be reflective of these other important wildlife taxa (e.g. how to interpret your results, recognizing the bias this contributes, etc.). Also, reconsider whether you should use the term “most” wildlife and livestock interfaces throughout the paper because I question whether this is accurate, given your omission of several key taxa.

3.	Your discussion section and study conclusions need revisions that include a more in-depth examination of this broad topic and future directions.
a.	I think that more persuasive arguments need to be made as to why a unified generic framework is necessary. Lines 252 – 253 give a reason of “wide-ranging definitions describing contacts,” but this is not surprising given the fact that the details or livestock-wildlife contacts are highly context-dependent and variable based on the species of wildlife and livestock (as well as demographics like age and sex), the pathogen (infectious dose, mode of transmission, half-life, etc.), and environmental conditions (temperature, humidity, weather, region, etc.). You do a nice job mentioning some of this in lines 204 – 206, but more is needed. One of the more important points that you make (lines 215 – 216 and 225) is the complete lack of definition of contact, omission of a space or time component, and conflicting or overlapping definitions of direct and indirect contact. These are fundamental problems that make comparisons between studies impossible and necessitates the use of a generic framework like the one you suggest. This needs to be emphasized in the discussion/conclusion of your paper.
b.	Lines 22 – 24 mention that this framework “may aid the development of better disease transmission models and improve the design and effectiveness of interventions to reduce or prevent disease transmission.” This sounds great, but is not addressed anywhere else besides your abstract. Further elaboration on this point in your discussion section would be worthwhile.
c.	Try to identify unresolved questions, remaining knowledge gaps, and future directions for research pertaining to the livestock-wildlife interface. This will help fit your review into the greater context.

4.	I applaud the fact that you mentioned study power and uncertainty in the publications, since this is important for interpretation of findings. You report the number and percentage of studies with low power (lines 147 – 148), but you do not indicate the number or percentage that reported adequate power, or the total number that assessed statistical power (unfortunately, this is commonly omitted from studies, so it would be helpful to know how many even addressed the topic). Can you provide more information here, especially since you mention that power assessment was a criterion for your publication quality score? Also, in lines 322 – 324, you mention low power, but I’m unsure what you meant by “considering the relatively rare nature of certain types of direct contact.” Are you referring to cryptic wildlife species and our inability to capture or document instances of direct contact using current observational methods? Can you clarify and be more specific?

5.	Thank you for acknowledging that diseases can also go the other way, from livestock to wildlife. Lines 285 – 287 provide some examples that are much needed. I think more recognition of this bidirectionality aspect is crucial. You mention that there is “little (if any) focus on the value of wildlife,” so I recommend you take this opportunity in the introduction and discussion of your own review paper to highlight the conservation implications of disease spillover into wildlife.
Additional comments: I commend you for your thorough review and adherence to the PRISM reporting guidelines. You have summarized a lot of information in a fairly efficient manner that was clear and easy to follow. You stated how the research fills an identified knowledge gap. Potential weakness of the manuscript include the statistical summaries provided in Table 4 (as I have noted above), the description of the unified generic framework and its utility, and the discussion section, which should be improved upon before Acceptance.


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: TOWARDS A UNIFIED GENERIC FRAMEWORK TO DEFINE AND OBSERVE CONTACTS BETWEEN LIVESTOCK AND WILDLIFE: A SYSTEMATIC REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: No comments
Experimental design: No comments
Validity of the findings: No comments
Additional comments: I would like to congratulate the authors on the clear effort they have made to improve the manuscript. I really enjoyed reading the document. The ideas are now much clearer and discussion allows understand both the aim of the study avoiding misunderstandings. Congratulations.


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: TOWARDS A UNIFIED GENERIC FRAMEWORK TO DEFINE AND OBSERVE CONTACTS BETWEEN LIVESTOCK AND WILDLIFE: A SYSTEMATIC REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: No comment.
Experimental design: No comment.
Validity of the findings: No comment.
Additional comments: The authors have done a very nice job incorporating our suggestions and responding to our questions. The tables and figures (especially Table 4) are much improved and the discussion is significantly more thorough and well-organized. Thank you for the opportunity to provide feedback on your 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: ZFPM2-AS1 PROMOTES THE PROLIFERATION, MIGRATION, AND INVASION OF HUMAN NON-SMALL CELL LUNG CANCER CELLS INVOLVING THE JAK-STAT AND AKT PATHWAYS
Review round: 1
Reviewer: 1

Output:
Basic reporting: The manuscript needs careful editing by English native speaker OR professional language editing service.
Experimental design: Most experiments perform with rigorous design. only one experiment may need more evidence.
Validity of the findings: The conclusion needs to be re-written.
Additional comments: Wang et. al. submitted the manuscript ” ZFPM2-AS1 promotes the proliferation, migration and invasion in human non-small cell lung cancer cells by targeting JAK/AKT/STAT pathway” The authors provide clinical evidence to show the correlation between ZFPM2-AS1 and NSCLC and use multiple methods (MTT, colony forming, wound healing, and Transwell assay and Flow cytometry,) to confirm that ZFPM2-AS1 regulates the proliferation/colony formation, migration, and invasion of lung cancer cell lines. In addition, they employed ZFPM2-AS1-siRNA and western blot to show ZFPM2-AS1 might regulate via JAK-STAT and AKT pathway and PD-L1. The data is enough to support the ZFPM2-AS1 is involved in NSCLC. The ZFPM2-AS1 might serve as a potential target of lung cancer treatment/immunotherapy in the future. However, the whole manuscript was poorly written, and results/figures are not well-organized, and it still needs more evidence to prove ZFPM2-AS1 involved in the JAK-STAT and AKT pathway. The manuscript requires substantial revision before acceptance. Here I have some suggestions and comments that may be helpful to improve the manuscript.

Major point:
A.	Your most important issue is scientific paper writing.
your manuscript needs careful editing by English native speaker OR professional language editing service. Please pay attention to sentence structure, verb tense, and clause construction. Additionally, the authors should write the paper in logistic order, especially the result section (Figure 7).

B.	The next most important item is Figure 6.
It still needs more convincing evidence to support ZFPM2-AS1 involved in JAK-STAT and AKT pathway. JAK-STAT and AKT pathway is the new and most important finding of ZFPM2-AS function in your study.

C.	All the figures need to be carefully edited.

All details are listed below:
1.	The author should use “targeting” carefully in the title. According to the results you presented, you did not figure out the real target (gene/miRNAs) of LncRNA ZFPM2-AS1. In addition, it is generally believed that JAK-STAT and AKT are two distinct signaling pathways, and the AKT pathway is not the direct upstream of STAT, although these signaling pathways can be integrated in some cases.
2.	Line 29. Please make sure if you use “RT-PCR” rather than “qRT-PCR” to examine the transcription level of ZFPM2-AS1.
3.	Line 41, the author mentioned the “PD-1” in abstract, but there is no description concerning PD-1 in the result section.
4.	Line 64” warranted” in here is very confused.
5.	There are many sentences with sentence structure problems, i.e. Line 51-53, line 62-64… please addressed these issues in the whole manuscript.
6.	The introduction was not well-written, your need to make a comprehensive review on the LncRNA of your interest (ZFPM2-AS1)[there are more than 10 papers in PubMed (https://pubmed.ncbi.nlm.nih.gov/?term=ZFPM2-AS1)], and don’t pay too much attention to other unrelated lncRNAs in JAK-STAT and AKT pathway(line 71-85). And it needs some background information about IFN-γ to make your audience clear about your study.
7.	Line 97 “different ”
8.	Line 110 &131, ”CO2” (“2” here should be subscript)
9.	Line 125, 4x103; (“3” here should be superscript), please carefully check the same issues in otherwhere, line 135, line 143…etc.
10.	Line 165, please indicated the manufacture information of “IP lysis”, check if “IP lysis” is the correct name of this reagent.
11.	line 198, “one lung normal epithelial cell line, four NSCLC cell lines, and one tool cell line ”, avoid this kind of usage in a scientific paper, please state the specific name of cell lines.
12.	Line 202, “including H1299 and H292”, should be “including H1299 cells and H292 cells”, please carefully proofread the similar issues in otherwhere, line 218, line 219, line 229, line 232, line233…...
13.	Line 206, please indicate the abbreviation” TNM” information.
14.	Line 216, please add a short description of why you use IFN-γ for your study, and there is no description in introduction and otherwhere (result and discussion), which will make the readers very confused.
15.	Another confusing point: The whole paper focused on the ZFPM2-AS1 rather than ZFPM2 (although ZFPM2 is a potential target of ZFPM2-AS1 lncRNA). The authors present lots of data to prove the role of ZFPM2-AS1 in NSCLC, but at the end of the results (Result-3.8), the authors tried to explain the role of ZFPM2 in tumor immune infiltration. Please explain it OR re-organize the results to make readers clear about the object of your research.
16.	Line 253 “Meanwhile, the expression of JAK2, p-STAT3 and p-AKT was decreased, compared with the control group. However, there was no significant differential expression in STAT3 and AKT”. Typically, phosphorylated JAK2 (pJAK2), rather than JAK2, represents “active status” in the signaling study, in my opinion, you should check the pJAK2 (the ratio of pJAK2/total JAK2).
17.	Result 3.7, The most important finding in this article is ZFPM2-AS1 involved with JAK-STAT and AKT pathway. I guess the authors try to use the IFN-γ to activate the JAK-STAT pathway (not stated in the manuscript), however, it still cannot exclude that ZFPM2-AS1 regulate NSCLC by other pathways(like p53 pathways), in my opinion, you should use JAK inhibitors to block the JAK-STAT pathway, and then check if the inhibitors can abolish (at least attenuate) the effect of ZFPM2-AS1 on proliferation/migration/invasion of lung cancer cells. You may present at least one piece of data in this section.
18.	Line 287-299. Please don’t overstate the JAK-STAT pathway that is well-known signaling in cancer, this paper focused on ZFPM2-AS1, you may discuss how ZFPM2-AS1 regulates JAK-STAT pathway and whether other pathways (for example, p53 pathway that you mentioned in the introduction) involved in ZFPM2-AS1 regulatory network.
19.	Conclusion. Usually, the conclusion just briefly summarizes your finding, which differs from the abstract and result.
20.	Please provide a brief title for each figure and avoid unnecessary descriptions in the text. According to the Journal requirement, use ”Figure x” rather than all capital ” FIGURE x”.
21.	Figure 3, panel E is already in Figure 3, please remove figure 3E on Page 31.
22.	Figure 4, there are 5 panels (A.B.C.D.E) in Figure 4, which located on different pages. The authors should re-organize the layout and combine all panels in one page OR divide them into two figures.
23.	Figure 5. Combine all panels in one page. Figure 5B, please use “IFN-γ” instead of “γ”.
24.	Figure 6. Combine all panels in one page. Figure 6B, I cannot see a significant difference(as the author wrote, line 259-260) of pSTAT3 level in groups, please confirm. In addition, the author should add a bar graph to each protein in Figure 6. For the phosphorylated protein, a phospho/total ratio (i.e., p-STAT3/STAT3…) need to be presented.
25.	Figure 7. Combine all panels in one page.


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: ZFPM2-AS1 PROMOTES THE PROLIFERATION, MIGRATION, AND INVASION OF HUMAN NON-SMALL CELL LUNG CANCER CELLS INVOLVING THE JAK-STAT AND AKT PATHWAYS
Review round: 1
Reviewer: 2

Output:
Basic reporting: a.	The overall language used is acceptable however minor grammatical and typological errors need to be fixed. For example, in lines #59, #67, #81– words like mounting, frustrate and sponging are out of context and provide ambiguous meaning. I would recommend that the authors restructure these sentences to make it clear.

b.	It is not clearly stated that the authors consider both lung adenocarcinomas and lung squamous cell carcinomas for their work presented here. It is to be assumed based on their results. However, I would recommend adding a clear statement to their methods section to remove any ambiguity.
Experimental design: a.	The authors choose to focus specifically on signaling driven by phosphorylation of Akt on Ser47 vs Thr308. However studies have shown activation at these sites have different phenotypic effects and consequences in cancer cells such as https://doi.org/10.1038/bjc.2011.132 . The authors should address this by looking at Akt phosphorylation at this site via western blotting. (If possible).

b.	The data shown in figures 3C and 3D do not seem very convincing. There is significant inconsistency in the data presented with some experiments performed in only H460 and some only in A549. Specifically, in figure 3C and 3D, the difference in proliferation between the control and sample (either siZFPM-AS1 or overexpression of AFPKM-AS1) seems too small to be significant. The raw data provided show much variation in their values. I would recommend that the authors verify their statistical tests keeping the variation between replicated in mind. The authors should also address why only one cell line was chosen for certain experiments vs others or provide data for both to make their study more robust.

c.	There is a lack of explanation on the relevance of the JAK-STAT pathway and the use of IFN-gamma induction of this pathway in NSCLC specifically. The authors do try to expand on this in the discussion but some further expansion on  this may be helpful. The authors can refer to reviews like 10.1080/21623996.2014.999503 and https://doi.org/10.3390/cancers6020708 to further supplement the introduction and discussion.

d.	In their TCGA data analysis, the authors do not mention what studies were included in their 535 lung cancer cohort. What criteria was used to be included in their study compared to normal. If this analysis was based off their previous publication that should be mentioned here.

e.	The analysis/ data used for the calculation of the ROC in Figure 1B is not explained. If this is part of the TCGA provided analysis it needs to be clearly stated. Furthermore, the ROC curve is depicted in an unusual manner with the AUC shaded and the random guess line is not shown. Can the authors please comment as to why they chose to depict the results in such a manner over the conventional representation?

f.	In their RNA,qRT-PCR methods section, the authors fail to mention how the relative gene expression was calculated and which housekeeping gene was used. (Lines 120-122)

g.	The authors need to mention if the colonies were counted manually or under a microscope for their colony formation assay. (Line 133)

h.	Lines 147-148. This is ambiguous. Please provide information on the magnification and the specifications of the microscope.

i.	In figures 4D and 4E the bottom panel of the quantification of results should be H460, not A549 again. Please correct this typographical error in your figures.

j.	In Figure 7A the color legend is missing to indicate what the red, blue and purple mean.
Validity of the findings: None.
Additional comments: The article ZFPM2-AS1 promotes the proliferation, migration and invasion in human non-small cell lung cancer cells by targeting JAK/AKT/STAT pathway by Wang et al is a generally well-put together article aimed at elucidating the molecular mechanism of lncRNA ZFPKM-AS1 on the tumorigenic characteristics of NSCLC. I commend the authors on testing the effects of both loss and overexpression of ZFPKM-AS1 on multiple characteristics of tumor cells. I was specifically impressed by their assessment of 50 clinical samples in this context. I further appreciate the efforts of the authors in sharing the raw data for almost figure represented in the paper to aid transparency and provide confidence in their results. However, there are some concerns with the paper in its current version as detailed 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: ZFPM2-AS1 PROMOTES THE PROLIFERATION, MIGRATION, AND INVASION OF HUMAN NON-SMALL CELL LUNG CANCER CELLS INVOLVING THE JAK-STAT AND AKT PATHWAYS
Review round: 1
Reviewer: 3

Output:
Basic reporting: 1. The most important issue is the English language used throughout the manuscript. I suggest the authors carefully proof-read and further improve the quality. Many sentences were grammatically incorrect. Some examples include line 60(…lncRNAs might role…), line 61 (…differential expression lncRNAs…), line 237(…in the nuclear...), etc. Some other phrases, albeit grammatically correct, were scientifically confusing. Examples include line 63 (...biological behavior of NSCLC cells...), line 86(...proliferation, migration, and invasion capacity of ZFPM2-AS1 in NSCLC cells), line 215(...the decreased efficiency...), line 261 (...distinctly inhibited...), etc.

2. Please define and spell out acronyms where they appeared for the first time. Some examples include ZFPM2-AS1, MIF, NC, etc.

3. I think it would be helpful to briefly summarize/conclude at the end of each Results subsection. The last sentence of section 3.4 was a good example.

4. Some figure labels are barely visible.

5. Line 283 needs reference
Experimental design: 1. It would be helpful to explain the rationales of different analyses done in Figures 1B and 1C, either in the legends or text.

2. Could the authors explain why they used IFN-γ in the proliferation experiments. Because this was used extensively throughout the manuscript, it might be worth mentioning in the introduction. Along the same line, could the authors comment on why some differences were only significant in the presence of IFN-γ, e.g. Figure 3C?
Validity of the findings: I appreciate that this manuscript had extensive amount of results, most of which are well controlled. My biggest concern, however, is that the differential expression of the lncRNA ZFPM2-AS1 in various NSCLC samples and cell lines. In fact, as the authors reported, ZFPM2-AS1 was significantly downregulated in two out of four cell lines experimented. This should not be overlooked and should be commented on, given that the authors proposed this to be a promising prognostic marker and even a therapeutic target.

Please include quantification of the western blotting results in Figures 6A and 6B, normalized to internal controls.
Additional comments: N/A


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: ZFPM2-AS1 PROMOTES THE PROLIFERATION, MIGRATION, AND INVASION OF HUMAN NON-SMALL CELL LUNG CANCER CELLS INVOLVING THE JAK-STAT AND AKT PATHWAYS
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors submitted the revised manuscript ” ZFPM2-AS1 promotes the proliferation, migration, and invasion of human non-small cell lung cancer cells via the JAK-STAT and AKT pathways”. Thank you for a point-to-point response to my comments, the current manuscript had a great improvement in language and data presentation, which makes readers clearer about the object of the research. Here, I have several concerns that need to be addressed.

1.  the authors presented excellent data to prove the ZFPM2-AS1 regulates proliferation, migration, and invasion of NSCLC cell lines and correlate with NSCLC clinical characteristics. Additionally, the readers can also make a clear conclusion from your data:
(1) ZFPM2-AS1 enhance the IFN-gamma effect on proliferation/ migration/ invasion of NSCLC cells
(2) ZFPM2-AS1 negatively regulate ZFPM2
(3) ZFPM2-AS1 positively regulate PD-L1
(4) ZFPM2-AS1 activates JAK-STAT3 and AKT pathway.
However, the current data is not enough to prove ZFPM2-AS1 regulates its downstream effector (ZFPM2, PD-L1) through JAK-STAT3 and AKT pathway. It is a good thing to prove JAK-STAT3 and AKT pathways are the factors that contribute to proliferation/ migration/ invasion as well as the change of PD-L1 and ZFPM2, but you do not have to prove them, you just need a more comprehensive and accurate title.
If you want to prove them, the most helpful experiment is the JAK inhibitors(and/or AKT inhibitors) assay (I mentioned in the last comments), I also reviewed the supplemental figure 1, you didn’t perform the assay in incorrect way. The following cohorts may be used for validating ZFPM2-AS regulate cell proliferation/ migration/ via the JAK-STAT pathway.
a.	Vector
b.	ZFPM2-AS
c.	Vector + JAK inhibitors
d.	ZFPM2-AS+JAK inhibitors
And if you want to further prove its association with PD-L1, these 4 cohorts need to be performed in the presence OR absence of IFN-gamma (Totally 8 groups).

2. There are still have some typos/grammar/tense need to be corrected, although the revised manuscript was greatly improved in language.

3. The revised Figure 3C is different from the previous version, please confirm and explain.


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: ZFPM2-AS1 PROMOTES THE PROLIFERATION, MIGRATION, AND INVASION OF HUMAN NON-SMALL CELL LUNG CANCER CELLS INVOLVING THE JAK-STAT AND AKT PATHWAYS
Review round: 2
Reviewer: 2

Output:
Basic reporting: The revised manuscript is much better written and easier to follow. I would like to thank the authors for taking my concerns into account and sufficiently addressing them specifically in the aspect of language and grammar. These revisions make the science and the rationale provided by these authors easier to follow for a wider, more international audience. The pdf version of their manuscripts requires some minor edits as pointed out below
(1) Lines 92-94 , lines 134 and 180 : missing letters "fl" in words like influence, confluence etc. Please double check

(2) Line 135 : please change "applied" to "used"

(3) Line 150 : Remove the phrase "following that". Unnecessary and causes ambiguity.

Apart from these changes in the text, the following minor edits need to be addressed in the figures
(1) Figures 3E, 3G : please add the cell line labels to the images of the Colony formation assay

(2) Please move figure 3D to panel H and group all the siRNA data consecutively. Figure 3D is the only one that has overexpression data

(3) Figures 4E, G, I, K : please add cell line labels to the crystal violet images and magnification bars

(4) Figure 5G, H - Please add the percentages associated with each cell cycle stage consistent with the other panels in the figure.
Experimental design: All comments have been addressed.
Validity of the findings: All comments have been addressed.
Additional comments: I would like to thank the authors for their effort in addressing all the concerns raised. The experiments designed and conducted add credence to their data. The written language better supports the data presented .


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: ZFPM2-AS1 PROMOTES THE PROLIFERATION, MIGRATION, AND INVASION OF HUMAN NON-SMALL CELL LUNG CANCER CELLS INVOLVING THE JAK-STAT AND AKT PATHWAYS
Review round: 3
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: The authors submitted the revised manuscript” ZFPM2-AS1 promotes the proliferation, migration, and invasion of human non-small cell lung cancer cells involving the JAK-STAT and AKT pathways”，I really appreciate the authors responded to my comments. The author uses a more accurate title. To make sure it is consistent in the whole paper, you still need to avoid these conclusive sentences line 42-45; Line 264-265; Line 278-279; line 327-328, or similar sentences in the whole paper.  [Please keep in mind, “the current data is not enough to prove ZFPM2-AS1 regulate its downstream effectors (proliferation/migration/invasion, ZFPM2, PD-L1) through JAK-STAT3 and AKT pathway, although they showed similar change pattern. The only way to prove them is using pathway inhibitors to block the signaling, and then check if the inhibitors can abolish/attenuate the effect of ZFPM2-AS1 on its effectors.”.]


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: ZFPM2-AS1 PROMOTES THE PROLIFERATION, MIGRATION, AND INVASION OF HUMAN NON-SMALL CELL LUNG CANCER CELLS INVOLVING THE JAK-STAT AND AKT PATHWAYS
Review round: 3
Reviewer: 2

Output:
Basic reporting: No comments. All issues have been addressed
Experimental design: No Comments. All issues have been addressed.
Validity of the findings: No comments. All issues have been 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: ZFPM2-AS1 PROMOTES THE PROLIFERATION, MIGRATION, AND INVASION OF HUMAN NON-SMALL CELL LUNG CANCER CELLS INVOLVING THE JAK-STAT AND AKT PATHWAYS
Review round: 3
Reviewer: 3

Output:
Basic reporting: N/A
Experimental design: N/A
Validity of the findings: N/A
Additional comments: I would like to thank the authors to address reviewer's comments. The revised manuscript is clearly improved and easier for follow. I recommend this manuscript to be accepted and published as 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: MOLECULAR DETECTION MAPPING AND ANALYSIS PLATFORM FOR R (MDMAPR) FACILITATING THE STANDARDIZATION, ANALYSIS, VISUALIZATION, AND SHARING OF QPCR DATA AND METADATA
Review round: 1
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: First, this is a great product and I am happy to support the publication of your manuscript following my review. See my notes in the Reviewer Comments pdf as to where I think you have been particularly successful or could use some expansion (nothing rose to the level of failing to meet the PeerJ review criteria).

As an end-user who would appreciate and benefit from this work, I was a bit curious as to why the Platform, tasked at allowing multiple datasets to be co-analyzed, was designed to integrate output data from 3 relatively new, specialized (compact/low throughput and/or field ready) qPCR systems as opposed to systems that are present in a majority of labs around the world. Using BioRad, ThermoFisher/Applied Biosystems, etc. output files would make this Platform immediately applicable to a large number of labs and would presumably allow for immediate integration and analysis of years of previously collected data. While I don’t think this point in any way precludes the work from being publishable, I can assure you that some detail on the thought process would be desired from researchers that will read this article, even if it just happened to be availability of the systems in your lab. I am heartened by your desire to develop R script to help broaden the outputs available to be integrated into the Platform.

Another major question that arises from reading this manuscript is what will become of the Platform after this (Lines 334 to 343)? You suggest that users will have the ability to adapt the Platform to various qPCR software programs, but a centralized database still needs to be established, and the standards chosen as data fields did not seem to come from the qPCR community. Can you expand on these a bit more?

An excellent feature is the ability to save a dataset from the Data File Preparation for re-analysis and to reproduce results. This aspect of data management is becoming vitally important in fields where new data are added to databases. I commend your effort to ensure FAIR principles and the inclusion of DwC-compatible identifiers.

Best of luck!