JerMa88/TPR_Peer_Reviews huggingface dataset:
Peer review of: Stereospecific Si-C coupling and remote control of axial chirality by enantioselective (2020)



REVIEWERS' COMMENTS: 

Reviewer #3 (Remarks to the Author): 

Hydrosilylation of unsaturated carbon-carbon bonds with hydrosilanes is one of the most important 
processes and can rank one of the most fundamental reactions in organsilicon chemistry. In this 
manuscript, Xu and co-workers reported a highly enantioselective Si-C coupling hydrosilylation of 
carbonyl-activated alkenes using palladium catalysis with excellent enantioselectivity and yields 
(up to 99% yield, >99:1 e.r.) for the synthesis of a wide of functionalized succinimides with or 
without axial C-N bond. And this process is quite useful because the Si-C coupling approach could 
be applied in in synthetic chemistry and photocatalysis for the enantioselective construction of 
unprecedentedly reported N-heterocycles bearing one to three carbon-stereogenic centres. These 
obtained results are particularly original and interesting. The authors also answered all the 
questions in a quite satisfactory manner. Now I recommend to publish this article in Nature 
Communications without any further modifications.
Peer review of: Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize (2018)



REVIEWERS' COMMENTS: 

Reviewer #3 (Remarks to the Author): 

Dear Authors, 

Compared to the manuscript a year ago, a lot of supplementary data have been added, making 
the revise version an attractive article. 

1) Quantitative data for fertility/sterility (Fig4, SupFig16 and Sup Table1) 
I’m interested in the swap analysis between the high and low temperature of Supplementary Fig 
16. But it is unclear to distinguish which tassels are fertile or sterile, because the anthers in most 
tassels were detected in these figures photo. I recommend a quantitative indicator to show the 
fertility rate using pollen fertility rate or seed fertility rate etc, NOT PHOTO. I recommend the 
quantitative fertility data for swap analysis is added in the main Fig. 4, because these data are 
important. 

In Fig4, I detected (D, E, H and I) are fertile and (G) is sterile. However, it is unclear in (F) photo. 

in Sup table1, there is no quantitative data for fertility/sterility with segregation of siblings. For 
example, how about seeds fertility rate? I don’t know whether seeds fertility of “+/+” and “+/-
“ siblings are 100%, and those of “-/-“ are 0%. 

2) Fig. 2 E and Supplementary Fig 15 
The numbers of binucleated tapetal cells in DCL5/DCL5, which showed fertility is low, around 15% 
under permissive temperature in Supplementary Fig 15. 
This rate (15% of DCL5/DCL5) is less than the rates (28%) of dcl5-1/dcl5-1, which shows sterile 
(in Fig2 E). Is it correct? 

3) Supplementary Fig 12 
It seems that the total expression patterns of dcl5-1 restrictive are higher than those of dcl5-1 
permissive (log2 of abundance). But it seems that box-plots (right) are opposite between dcl5-1 
restrictive and dcl5-1 permissive. 

4) Supplementary Fig 9 C and D 
The pictures of C and D were not clear, please change the photos (if you could do)
Peer review of: Mode of action of teixobactins in cellular membranes (2020)


  

REVIEWERS' COMMENTS second round: 
 
Reviewer #1 (Remarks to the Author): 
 
I am satisfied with the authors' thoughtful efforts to address our concerns and those of the other 
reviewer, particularly in light of the COVID-19 shutdown, and recommend publication as is. The 
PDB structure will be a particularly valuable contribution and is a good addition. 
James S. Nowick 
 
 
Reviewer #2 (Remarks to the Author): 
 
The authors has addressed all my concerns. In particular, I would like to mention that the use of 
“cellular membranes” in the current title is appropriate. It also connects to the previous studies by 
the authors using cellular membrane systems. The ambiguous aspects of the technical details are 
now clarified. The maintext and Supplementary Information files have also been reshaped. 
 
The revised manuscript is clear, novel, and technically sound.
Peer review of: Labeled oxytocin administered via the intranasal route reaches the brain in rhesus (2020)


Reviewer #1 (Remarks to the Author): 

The manuscript has been significantly improved and deserves publication. 

Reviewer #2 (Remarks to the Author): 

The authors have addressed many of our concerns in this revised manuscript. The data are important to 
present since this is the first measurement and comparison of IV and intranasal OT penetrance in the 
primate brain. 

That said, several concerns with the manuscript remain: 

1. The finding of no difference in CSF OT concentration between IN OT administration and IV 
administration does not align with findings from previous studies (e.g. Chang et al. 2014; Dal Monte et 
al. 2014; Striepens et al. 2013). The authors need to more fully defend this result against the findings of 
prior studies. Is this a limitation of their method or the use of deuterated OT? Deuteration is known to 
affect the pharmacokinetics of drugs. 

2. The figures are a mess. In figures 1 and 2 the 40 IU plots are missing from the figures. In figure 3, the 
y-axes are all on different scales, apparently chosen arbitrarily, making comparison difficult. For all 
figures in which the reader is invited to compare conditions, the data should be plotted on the same y-
axes. 

3. The text is still awkward in places, with some tortured construction, misplaced commas, missing 
spaces, etc. I don't have time to go through line by line, but this paper could use some proof-reading. 

Reviewer #4 (Remarks to the Author): 

The authors responded to the reviewer comments in detail. The comments involved several technical 
questions, presentation issues and finally some advice on additional citations and organization to aid the 
clarity of the work. The authors well addressed the technical issues and unclear presentations. There are 
no further issues. In addition, the authors have added clarifying statements and citations as requested. 
Overall, the manuscript as been improved. As all four reviewers stated, the work is important and 
exciting, and the revised manuscript does a much better job at conveying the importance of the work.
Peer review of: A nanobody-based fluorescent reporter reveals human α-synuclein in the cell cytosol (2019)



REVIEWERS' COMMENTS: 
 
Reviewer #1 (Remarks to the Author): 
 
In this revised version and/or in their rebuttal letter, authors meet all comments and critics raised 
by reviewers. 
 
 
Reviewer #2 (Remarks to the Author): 
 
Thank you for the clarification re what forms of aSyn the reporter recognizes. This is an important 
point for use cases of this tool. 
 
I suggest adding the figure provided in the rebuttal letter (relating Fluoresyn readout to IF for 
aSyn) as a supplemental figure; I found the information valuable, as may others thinking of 
adopting this tool. 
 
The addition of Supplemental Fig 6 is valuable in interpreting results, even though the cases do 
not have PD. For both the figure suggested above (relating Fluoresyn readout to IF for aSyn) and 
Supplemental Fig 6b, please provide both p-value and correlation coefficients for the relationships 
shown. 
 
Alice Chen-Plotkin 
 
 
Reviewer #3 (Remarks to the Author): 
 
The changes that were made have clarified several issues, and expanded on others. 
This increases the value of this paper.
Peer review of: Hunting strategies to increase detection of chronic wasting disease in cervids (2020)



Reviewers' Comments: 
 
Reviewer #1: 
Remarks to the Author: 
I have read the response to reviewers comments and the updated manuscript. The authors have done 
a fine job responding to the comments and revising their manuscript accordingly. When the authors 
were unable to adjust their framework in response to a comment (e.g., Reviewer 2's main concern), 
the authors included text within their revision that identifies the caveat within their study. Otherwise, 
all comments were basically integrated into the revision.
Peer review of: American mastodon mitochondrial genomes suggest multiple dispersal events in response (2020)



REVIEWERS' COMMENTS: 

Reviewer #1 (Remarks to the Author): 

My previous comments have been thoroughly addressed by the authors and I have no further 
suggestions. 

Reviewer #2 (Remarks to the Author): 

I was a reviewer for the earlier version of this manuscript. I thought the previous submission had 
substantial value as it represented the first large scale mitochondrial study of extinct North American 
mastodons and provide interesting results that expanded our knowledge of understanding of 
mastodon origins and evolutionary history. My criticisms of the earlier version focused on issues 
related to 1) nature of the discussion of these results, and 2) what I interepretated as the the over 
interpretations of the mastodon age estimates, which had high very broad 95% HPD. 

This new submission is a substantial improvement on the original manuscript. This version does a 
much better job in their discussion of clades and their revised methodologies (Bayesian age estimates 
and LOO analysis) resulted in improved reliability in their results discussion. The authors have 
adequately responded to my concerns and comments, and I have no further reservations for the 
publication of this manuscript. I expect this manuscript will be of great interest to a broad audience of 
Nature Communication readers. 

Matthew Hill 

Reviewer #3 (Remarks to the Author): 

The authors made significant improvements to the manuscript. I believe that the new molecular dating 
analyses strengthen the argument for multiple re-expansions to Beringia and thanks to the changes in 
the text, results are now delivered more clearly and their potential to contribute to understanding the 
general issues outlined in the Introduction is more straightforward. I don't have any further 
comments.
Peer review of: Incorporating hydrology into climate suitability models changes projections of malaria (2020)


 

 

 

Reviewers' Comments: 
 
Reviewer #1: 
None 
 
Reviewer #2: 
Remarks to the Author: 
The authors have revised the paper to include a sensitivity analysis as I suggested, this 
analysis is well described and benefits from the inclusion of two figures (S13 and S14). I 
would also add that the inclusion of a detailed evaluation of the model in the supplementary 
material is a valuable addition to the paper. I'm happy to recommend this for publication in 
Nature Communications. 
 
Best wishes, 
Liz Stephens 
 
 
 
Reviewer #3: 
Remarks to the Author: 
The authors have thoroughly addressed each of my comments. I am happy to recommend 
the publication of this manuscript.
Peer review of: Untangling the seasonal dynamics of plant-pollinator communities (2020)



Reviewers' Comments: 
 
Reviewer #1: 
Remarks to the Author: 
I’ve now reviewed the authors’ revision and response letter. I think the authors have done a solid job 
of addressing my previous concerns. I especially appreciate the inclusion of statistical details and the 
expanded treatment of sampling/abundance. As I remember from the previous version, the paper was 
well written, and it continued to be in this revision. 
 
The only detail that gave me pause was Supplementary Figure 14. If we look at the ‘Hill’ model, it 
appears that the majority of pollinator observations fall within the region where there is a strong 
positive relationship with ‘relative degree’ (e.g., less than 10 observations). At the end of the day 
though, I thought the authors did a nice job of addressing this issue in their new discussion paragraph 
when they talked about the “two ends of an interesting conceptual spectrum”. This isn’t so much of a 
major comment to be addressed, but I just want to mention that I think this is an unsolvable concern 
for this manuscript, and I appreciate that the authors have devoted a nice paragraph in their 
discussion to this issue. They have at least addressed my previous concern on this topic. 
 
I only have some minor comments remaining, which I include below. I don’t think they are strictly 
necessary to address, but I think they could be helpful in clarifying some details for other readers: 
 
L244--245: what does “loss of interactions” exactly mean? I assume it means qualitative interactions, 
as there is necessarily a loss of interactions with removing observations, right? 
 
L245--250: I was initially lost here. I think the reason was that the verbal description was immediately 
followed by the mathematical description, but without any distinction of the two. Perhaps just a 
comma to separate the two, or putting the math in parentheses (i.e., ….) would make this more clear. 
 
L309: ‘effect’ instead of ‘affect’? 
 
L338-344: specialists pollinators interacting with generalist plants, right? I think it could be helpful to 
be explicit here. The same could be done for L362-364. 
 
Legend of Supp. Fig. 3: don’t you mean top-left corner? 
 
Legend of Supp. Fig. 10: vii)? Or should it be vi)? Also, this figure is a little difficult to understand. I 
would consider including less information. I’m also surprised by the very high weight of model iv) 
despite some models having similar WAIC values (unless I’m misinterpreting the figure). 
 
I detected a couple of minor grammatical errors (e.g., delete ‘an’ on L345; delete “d” at end of 
“calculated” on p. 2 of Supplementary Material after description of priors). 
 
 
 
Reviewer #2: 
Remarks to the Author: 
The authors have addressed all my concerns and this version reads really good. Thank you. The only 
missing detail is that it would be great if the code is provided directly in a code repository or as 
supplementary material, and not upon request.
Peer review of: Extreme environmental conditions reduce coral reef fish biodiversity and productivity (2020)


 

Reviewers' Comments: 
 
Reviewer #2: 
None 
 
Reviewer #3: 
Remarks to the Author: 
The manuscript titled ‘Organismal responses to extreme temperature reduce 
coral reef biodiversity and functioning’ has now been revised and the authors 
addressed my main concern about possible other factors but temperature 
playing a role here. It is a massive piece of work and adds an important puzzle 
piece to how coral reefs might ‘adjust’ to future environmental changes. 
I only have small comments and one comment on a part of the discussion that 
was changed since the first review: 
Line 54: Not sure ’extreme’ is the correct word. You could refer to 
environmental ‘changes’ or environmental 
Line 101: food availability? 
Line 284:’notable’ 
Line 396: Big jump here – provide an introductory sentence? 
Line 400: at what depth was this temperature measured? 
Line 424: the conditions were unfavorable also in the past or is there a change 
in temperature for that area more recently? 
Line 512: you just mention five species by name above – why is it 6 in total? 
You could add anomolus to line 509. “And one species specific to the Arabian 
Gulf”. 
Line 690: ‘coral’ reef. 
Line 832-392: 
I am not sure I follow this argument: 
Genetic adaptation and transgenerational plasticity isn’t necessarily an either – 
or scenario. Ultimately adaptation needs to happen through allele frequency 
changes – but plasticity (transgenerational or not) can allow for survival 
especially in rapidly changing environmental conditions. I don’t think that the 
fact that you found lesser body condition at the hotter reefs is evidence of 
transgenerational acclimation not playing a role here. 
I had a quick look at the three papers that the authors mentioned in response 
to another reviewer (who asked about the fact that the body condition was 
based on winter temperatures) and I don’t see that those studies look at the 
fish going back to a lower temperature (after high temperature exposure). In 
particular for a short-lived species experiencing very different environmental 
conditions through even a year from generation to the next my guess (!) would 

be that carry-over effects, parental effects and transgenerational plasticity 
would play a role as well. That being said, it is obvious that lesser amounts of 
food (or worse quality) might be a more dominating issue. 
It is logical that C.anomalous might be doing better as it has ancestors that live 
in more extreme conditions, hence, possibly having a genetic background that is 
favorable to extreme temperature conditions. However, the argument about 
resource limitation would also need to be considered here - does the genetic 
background aid the species to forage better – live better of less food 
availability/restricted food etc.?
Peer review of: The role of calcium in regulating marine phosphorus burial and atmospheric oxygenation (2020)

REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The paper is now in very good shape. However, I am still not happy about the treatment of CFA
solubility in the model. Equations 4 and 5 in the main text imply that an increase in the concentration
of dissolved carbonate ions in porewater ([CO32-]) causes a decrease in the rate of CFA formation.
This counterintuitive behavior arises because the solubility of CFA (KspCFA) rapidly increases with
[CO32-] (Eq. 5) such that the saturation state (ΩCFA) decreases with [CO32-] (Eq. 4).
I agree that the solubility of CFA increases with the carbonate ion content of CFA (SCO3). It is also
likely that SCO3 somehow increases with [CO32-]. However, the relationship between these variables
is complicated and not fully understood.
The authors apply a constant CFA stoichiometry in Eq. 4. Thus, they ignore the increase in SCO3 that
may be induced by a rise in [CO32-] even though this change in CFA composition drives the increase
in CFA solubility expressed via Eq. 5. This is clearly not a consistent approach.
Moreover, the assumption that CFA does not dissolve when ΩCFA < 1 (lines 243-244) is not valid from
a thermodynamic perspective. It is in fact possible that CFA formed at depth dissolves when it is
transported to the surface via e.g. bioturbation. The assumption may be valid if the kinetics of CFA
dissolution is extremely slow but I am not aware of any data supporting this assumption.
The additional simulations with constant KspCFA show that the [CO32-] –dependency assumed in Eq.
(5) has no strong effect on the model results possibly because of the low carbonate content of CFA
defined in Eq. 4. Nevertheless, I would like to suggest that the authors either change their concept or
at least clearly highlight the consequences, uncertainties and inconsistencies of their approach.
Peer review of: Mantle data imply a decline of oxidizable volcanic gases could have triggered the Great (2020)


REVIEWERS' COMMENTS: 
 
Reviewer #1 (Remarks to the Author): 
 
The authors addressed all reviewers' comments and provided additional useful information about their 
calculations. I am not fully satisfied with considering volcanic gases and magma fo2 as both reflecting the 
mantle source fo2. But, I must conclude that this is not the paper solving this enigma. 
Therefore, I strongly support the publication of this paper. 
 
Best wishes, 
Vincenzo Stagno 
 
 

 
Reviewer #2 (Remarks to the Author): 
 
The revised version reads well, as the first one. The paper is an interesting modelling exercise, which will 
be useful to scientists working on the oxygenation of the atmosphere, although not everyone will agree 
with model outcomes. 
 
I have the following comments: 
 
1. The authors now quote our work (Moussallam et al 2019) stating (line 258) that we claim that the 
cooling of the earth and ensuing oxidation of volcanic gases trigerred the GOE. This formulation is 
incorrect. We said that such a change could have facilitated, not trigerred, the transition toward oxidizing 
conditions along with other factors, because we are quite aware that this important transition was 
possibly driven by a number of mechanisms. The authors state the same in their paper in press in GPL 
but I guess that it is to late at this stage to correct this overstatement. 
 
2. The authors claim that we did a conceptual error in our analysis. I obviously do not agree. What we did 
is simply to use the f factor derived by Holland to illustrate how the change in gas speciation as affected 
by temperature changes this parameter (which could be wrong, but this is an other issue). The gas data 
we show are what they are, as long as one believes they represent some equilibrium. It is, in my opinion, 
a matter of what temperature you select to mix your volcanic gases with the ambiant atmosphere. This is 
just a comment however, since that part belongs more to the GPL paper. 
 
3. On line 129, it is said that basalts are more evolved than komatiite and this would result in these melts 
being more reduced than komatiite due to sulfur degassing. Please be more specific? Is it because you 
believe that basalts are richer in S than komatiite ? 
 
4. lines 276-278. As I understand it, your melt buffered stage assumes that nothing happens (in terms of 
redox evolution) during decompression. Obviously, I also disagree here, in view of the growing evidence 
provided by several groups in various settings on that matter (see last paper of Moussallam et al on hot 
spots). This is the main weakness, and quite a severe one, of this otherwise interesting paper. 
 
5. line 313. I guess you want to say decomposition of water ? (not the composition) 
 
Bruno Scaillet. 
 
 
 
Reviewer #3 (Remarks to the Author): 
 
I am satisfied with the changes made in this revised manuscript.
Peer review of: Mutualist and pathogen traits interact to affect plant community structure in a spatially (2020)

Reviewers' Comments: 
 
Reviewer #1: 
Remarks to the Author: 
I thank the authors for producing thoughtful responses and edits to their manuscript. My comments 
have been fully addressed. The two added boxes are especially helpful additions. 
 
 
 
Reviewer #2: 
Remarks to the Author: 
The revised version clarifies a number of questions I had with the original version. I have a few further 
minor comments. 
 
Lines 27-28. I suggest revising ‘that, in turn, differentially affect’ to ‘which, in turn, differentially 
affects’ because ‘affects’ refers back to ‘the composition of the local soil microbiome’. 
 
Lines 118-122. This doesn’t appear to be a sentence. Maybe remove the ‘that’. 
 
Line 182. ‘Figureb’. I think this must be Figure 5b, as the figure shows negative feedback increasing as 
the host specificity increases, in agreement with the text. 
 
Line 257. The sentence (Lines 255-257) would be a bit clearer if ‘their’ in Line 257 was identified as 
the common plant, as, at least grammatically, the ‘their’ could apply to the rare plant, which is the 
closer antecedent. 
 
Lines 372, 385, 464. Change ‘Where’ to ‘where’ 
 
The results of the manuscript are interesting and non-intuitive and are an important step in 
understanding effects of plant-soil microbiome interactions on plant community structure.
Peer review of: Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal (2020)


 

REVIEWERS' COMMENTS: 

Reviewer #1 (Remarks to the Author): 

All my concerns/suggestions/questions were addressed in this revised version of the paper, and I want 
to thank the authors for their detailed replies, and work on the manuscript. I now fully recommend 
this article for publication. 

Here are a few minor typos/suggestions: 

Line 55: maybe remove extra “and”? 
L. 61: italicize species names. 
L. 88: include a missing “as”? (“referred to as the”) 
L. 327: one occurrence left for “artifact” instead of “artefact”. Should “artifactual” on line 600 also be 
changed for “artefactual”? 
L. 354: remove an extra “and”? 
L. 558: I believe this sentence could start without the “But”. 
L. 608: replace the unusual word “clading” by a more classical “grouping”? 
L. 824: “used genomes” seems odd to me? Please check. Maybe “genomes used” instead? Same 
comment on line 828. 
L. 860-862: HMM is an acronym and should thus be spelled in upper case: “HMM”. 
Line: 864-865: this hmmsearch command-line seems odd to me (“Table”?). The authors may want to 
check it.