JerMa88/TPR_Peer_Reviews huggingface dataset:
Peer review of: Androgens predispose males to monocyte-mediated immunopathology by inducing the expression (2020)


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Revision 2 NCOMMS-19-26999A
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have comprehensively answered the concerns from the prior review and the manuscript is improved as a result. I have no further critiques.
Reviewer #2 (Remarks to the Author):
The authors adequately addressed my major concerns.
A few modifications that the authors should consider:
1. I would not use a slang term like 'trans' in a manuscript. Replace with 'transgender'. 2. In Figure 5g, the conceptual cartoon image would benefit from showing how androgen receptor signaling interacts with TLR4 signaling to make the cartoon more relevant to this manuscript. 3. In Figure 7d and related text, I would suggest replacing 'lymphocyte isolation' with 'immune cell isolation' because monocytes are not lymphocytes.
Reviewer #3 (Remarks to the Author):
The manuscript has improved. However, to still use student t test for small sample groups is not acceptable and inconsistent even if the authors now used another test to evaluate potential normal distribution in small samples. Non-parametric test must be used for these groups with lees than 10-20 animals/independent samples.
Peer review of: Refinement of pore size at sub-angstrom precision in robust metal–organic frameworks for separa (2020)


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REVIEWER COMMENTS
Reviewer #1 (Remarks to the Author):
It seems that all the concerns have been appropriately addressed, so I would suggest publication of this paper in current form.
Reviewer #3 (Remarks to the Author):
The article has been well revised and some questions has been solved. But there are still some questions that needs to be answered.
1.As I mentioned before, in the revised Figure S9, the breakthrough curves with different flow rates (0.5 and 1.0 mL/min) on MFM-300 (In) in figure a and b, the retention time of p-, m-, and o-xylene are almost the same. And the caption of a-axis is the eluted volume. But how can the retention time in figure c and d (MFM-300(V)) be different with different flow rate?
2.The amount of sample is only 0.005 g for each batch for single-component liquid-phase adsorption. And the concentration of the xylene solution is very dilute. The uptake capacity was up to 3.45-3.88 mmol/g for MFM-300(V). I am wondering why the authors take such incontrollable conditions to measure the single-component adsorption.
3.For the Table S4-7, the structural data of xylene-loaded MFM-300. The formula weight of different xylene-loaded was the same, but the formula of these materials was almost different. Please clarify.
4.Since the authors mentioned that it is very complex and difficult to compare the kinetic separation due to the surface barriers and also influenced by the amount of substrate adsorbed. But the title of this manuscript is kinetic separation of xylenes. It is better to give direct evidence to clear understand this mechanism, not just comparison of the pore size. And I did see any difference from the results of Figure S16 (normalized kinetic profiles of xylene-loaded).
Reviewer #4 (Remarks to the Author):

In this revised version, the authors have satisfactorily addressed all the raised points. I thus recommend its publication.
Peer review of: Modulating oxygen coverage of Ti3C2Tx MXenes to boost catalytic activity for HCOOH dehydroge (2020)


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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors responded all my comments satisfactorily apart from one point about the counter ion effect, and the response is totally unacceptable. Probably the reviewer did not make this point clear enough or the authors did not understand this point correctly. From the experimental point of view (preparation procedure), it is not possible to have atomic H, Al and F on the surfaces. For H and Al, their right form should be their positively charged species, like H(+) and Al(3+), while for F, the right form should bd the negatively charged species, like F(-). For keep the charge balanced, they need the counter ions, i.e.; anions to balance H(+) and Al(3+), and cation to balance F(-). The authors should check this possibility.Otherwise, the reaction becomes radical process
The response that “Considering that H, Al and F atoms might exist and adsorb on the surface of catalysts” is just a joke and this does not reflect the chemical reality. Please delete this before making any joke
Reviewer #4 (Remarks to the Author):
The manuscript contains significant novel results. The authors have performed a serious work to change their manuscript. I am happy with the additional changes and support publication of this manuscript.
Peer review of: Taf14 recognizes a common motif in transcriptional machineries and facilitates their clustering by (2020)


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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
Reviewer #3 (Remarks to the Author):
Reviewer #4 (Remarks to the Author):
  The authors have made numerous changes to the revised manuscript that clarify their findings and
 resolve most of the questions raised in the previous round of review. The manuscript is greatly
 improved and I have no other recommendations or suggested revisions for this submission.
  The authors made efforts to faithfully address all reviewers comments. These efforts reinforced the
 conclusions made by the authors. As such, it is this reviewers opinion that the manuscript should
 be accepted for publication.
  I would like to thank the authors for addressing all my points, and congratulations on a beautiful
 manuscript!
  The author revised the manuscript well, and the current manuscript has been greatly improved.
 Besides some minor issues, I would in principle recommend publication.
 Minor comments:
 1. For Supplementary Figure 3d: Error bars were largely missing in the presentation of the
 experimental data. I could hardly find the error bars from this figure.
 2. Figure 3b, Line 472, 492, 549, 550, 570, 610, 629: There should be a space between the unit
 and the value, please check the manuscript and revise them.
 3. Line 259: I suggest the author to unify the form with ‘Figure.’ or ‘Fig.’ in the manuscript.
 4. Line 495, 485: unify the form with ‘μL.’ or ‘μl’
 Ling Jiang
Peer review of: Unique universal scaling in nanoindentation pop-ins (2020)


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Reviewers' Comments:
 Reviewer #1:
 Remarks to the Author:
 I believe that the authors meticulously addressed all comments, inquiries and suggestions that all
 the referees posed. I believe the work is an excellent contribution to the field and should be
 published in Nature Communications.
 Reviewer #2:
 Remarks to the Author:
 The authors have work very hard to answer the constructive remarks of the referees considerably
 improving their manuscript. I am satisfied by the corrections and suggest to accept the paper in
 the present form.
 Reviewer #3:
 Remarks to the Author:
 Manuscript ID: NCOMMS-19-41235
 Title of Article: Unique universal scaling in nanoindentation pop-ins
 Since this is the second round of reviews, I will dispense with the customary summary of the
 manuscript contents.
 The authors have made a substantial effort to address my earlier concerns, and in particular have
 greatly expanded the analysis of the MD results and the discussion of what properties of the
 dislocation arrangements could lead to the observed power-law scaling. I now believe that, while
 this does not report on any scientific breakthrough of general interest, the research is well-done
 and should attract the attention of those concerned with the mechanics of materials and avalanche
 processes.
 I still have several concerns which are enumerated below:
 1. The language can be difficult to follow in places. I trust that the editorial staff would be able to
 address these difficulties though.
 2. Some of the added material does not feel very focused. In particular, the comparison with the
 micropillar experiments in p11 and the discussion of the MD simulations on p14,15 could be make
 more concise. This would not only shorten the manuscript, but make the author's points clearer.
 3. Some of the material that was added to Results should be moved to the Methods section. For
 example, the discussion of the area function could be moved. Similarly, the discussion of
 displacement vs load control in the MD simulations should be moved to the Methods section.
 4. There appears to be a missing factor of $g$ in the exponent in Eq. 5 of S13, and the authors
 should consider replacing Eq. 5 with an integral of the log probability. Then the passage to the
 logarithm in Eq. 6 could be made exact.
Peer review of: OTUD5 cooperates with TRIM25 in transcriptional regulation and tumor progression via deubiquity (2020)


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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author): The manuscript is ready for publication.
Reviewer #2 (Remarks to the Author):
    The manuscript has been improved again and the authors have provided appropriate answers to
 all the points I raised and they have provided relevant revisions.
 Some style issues might be still corrected, as in the abstract, line 31-32:
 �the growth-promoting effect of OTUD5 depletion was dependent on its interaction with TRIM25.�
 �its interaction with� should be removed, or the sentence rephrased.
 All together, according to me, the manuscript is now suited for publication by Nature
 Communication.
Peer review of: Proton irradiation-decelerated intergranular corrosion of Ni-Cr alloys in molten salt (2020)

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 Reviewers' Comments:
 Reviewer #2:
 Remarks to the Author:
 The author satisfactorily addressed all of my comments and made appropriate changes to the manuscript.
 Reviewer #3:
 Remarks to the Author:
 All my comments are well addressed, therefore, I recommend publishing the paper
Peer review of: The Rad53CHK1/CHK2-Spt21NPAT and Tel1ATM axes couple glucose tolerance to histone dosage (2020)


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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
All my major concerns were thoroughly addressed and the text has been revised to remove overly
 broad statements
Reviewer #2 (Remarks to the Author):
The authors have performed several additional experiments to clarify the links between glucose
 metabolism, histone levels, Rad53 checkpoint function, and metabolites in the presence of acetate.
 The authors have also rewritten much of the text. While the manuscript remains complex and
 dense, the message is much clearer now and represents new insights into metabolic alterations,
 gene silencing and glucose metabolism and the role of Rad53/CHK1 in regulating this.
Reviewer #3 (Remarks to the Author):
The revised version adequately addressed my specific points. Eric Gilson
Peer review of: Cholesterol metabolism drives regulatory B cell IL-10 through provision of geranylgeranyl pyropho (2020)

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 Reviewers' comments:
Reviewer #1 (Remarks to the Author): Review of NCOMMS-19-37939A
   Bibby et al have addressed some of my concerns and the manuscript has improved accordingly.
 However, I still have considerable problems with the concept that all B cell populations contribute
 to IL-10 production and do so via Blimp1. Conceptionally, this just does not make sense to me. I
 am prepared to believe that B cells produce IL-10 in a GGPP-dependent manner. Similarly, I am
 fundamentally convinced that Blimp1 regulates IL-10 production in B cells. The conceptional
 problem I have is that the authors claim that the GGPP and Blimp1 pathway are linked (for which I
 don't see evidence) and that it applies to all B cell populations.
 For example, naïve B cells don't express Blimp1, but according to the authors express Il-10. Of
 course, a lot may depend on how one defines ‘naïve B cells’. After naive B cells have been
 stimulated for 48h they may well express Blimp1 and IL-10. But after 48h stimulation, naïve B
 cells are not naïve B cells anymore, they are activated B cells. This is not just semantics.
 Some of these interpretations hinge on the tSNE plot in Suppl. Fig. 4. It shows essentially no
 resolution of the various B cell populations. There is just one large cluster and an additional small
 cluster, neither appears to correlate to any marker used in the analysis. Neither naïve B cells, nor
 memory, B10 or plasmablast constitute a discrete population in the tSNE plot. How can that be?
 One way of addressing the ongoing issue of which populations express IL10 under which
 conditions would be to sort human B cell populations into the relevant populations before culture.
 In this case, it would also be useful to CTV label the cells to allow measuring whether or not cell
 division parallels the acquisitions of IL-10 production capacity.
 In this regard, it would also be useful to do these experiments with other ligands that induce B cell
 activation and differentiation. What about LPS and CD40L plus cytokine stimulation? Do these
 stimuli induce IL-10 in a GGPP-dependent manner? Is IL-10 production from MKD patients
 impaired?
 A technical concern: after 48h of stimulation memory B cells should differentiate into plasma blasts.
 Based on their FACS analysis, this does not appear to happen in the cultures of the authors. Is
 that because they gate on CD20+ cells? It should be noted that CD20 is downregulated on
 plasmablasts. Thus, gating should not use CD20high.
 Reviewer #2 (Remarks to the Author):
The authors have adequately addressed my concerns in their revised manuscript.
Peer review of: Cholesterol metabolism drives regulatory B cell IL-10 through provision of geranylgeranyl pyropho (2020)

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 Reviewer #1 (Remarks to the Author):
 Bibby et al have provided extensive explanation for their data and model. It is clear that there is in
 some ways a fundamentally different understanding of some of the data. A good example is the
 tSNE plot in Suppl. Fig. 4. The authors interpret these results as supportive of their argument that
 IL-10 producing cells do not constitute a separate population. I would argue it show exactly that:
 IL-10+ B cells sit separate from all other cells and do not or hardly overlap with any of the other
 populations. Thus, our interpretations of the data differ quiet fundamentally.
 I also argue that the current way of showing the data to some degree defies the purpose of tSNE
 plots. After clustering, these plots should display the expression levels of certain markers, such as
 IL-10, CD24, CD38 etc within these plots. That would allow readers to assess the data. At present,
 the authors gate populations manually and then overlay them onto their tSNE plot. This is not
 helpful, and I would suggest to change that.
 I am also not convinced of the data that show induction of Blimp1 by GGPP (Fig. 5). The only
 evidence is the RNAseq data; however, this should have been confirmed by an independent
 method.
 Having said all of that, I am prepared to accept that the study is fundamentally interesting and
 provides an expansion of the model as to how IL-10 production from B cells is regulated. As such,
 it will be of interest to the community and will undoubtedly stimulate discussion and follow-up
 studies.
 I suggest to include most of the data and figures provided to the reviewer as Suppl. Data.
Peer review of: Single cell electron collectors for highly efficient wiring-up electronic abiotic/biotic interfaces (2020)

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 REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
  The reviewer is satisfied with the revisions made by the authors. Thus, publication of this revised
 manuscript is recommended after polishing its English expression.
  The authors have addressed all my concerns reasonably well. I do not have further comments.
 Congratulations to the authors for the nice piece of contribution.
Peer review of: Transition metal-like carbocatalyst (2020)


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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Ref. The manuscript “Transition Metal-Like Carbocatalyst" by Wang et al, NCOMMS-20-07371A
The authors prepared a careful response to the comments raised by the referees, including myself. However, the activity of the catalyst in the targeted process (reactions carried out between 32 and 80h) with modest selectivities in the most important reaction products is not competitive. Therefore I am still not convinced that this manuscript is at the level of exigency reached by Nature Communications.
Reviewer #2 (Remarks to the Author):
The manuscript has been improved and I support its publication in Nature Communications.
Reviewer #3 (Remarks to the Author):
In my opinion the authors have addressed satisfactorily all the issues that were raised in my evaluation and also by the other two reviewers. I find their full response very detailed, convincing and also from other perspective intellectually very much entertaining. I propose the publication of the study.
Peer review of: Genome-wide specificity of dCpf1 cytidine base editors (2023)



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 Reviewers' Comments:
 Reviewer #1:
 Remarks to the Author:
 As had been pointed out by the both reviewers, the present method largely depends on mismatch
 filtering. In the authors responses, they argued that many of the previous methods also did the
 same way, and the sequence-independent off-target study should be done elsewhere. This
 argument does not gain novelty nor superiority of this study. The authors also argued that their
 Digenome-seq identified testable number of candidates. However, it seems that the mismatch
 filtering parameters were set in such a way that the number should be reduced to a good size in
 combination with their Digenome-seq results. Although this reviewer appreciates uniqueness of
 their method, it is hard to say “unbiased” and “genome wide" at the current standard of this field.
 Reviewer #2:
 Remarks to the Author:
 The authors have answered all questions and demonstrated reproducibility of their method. The
 author have demonstrated the use of this in-vitro method to look at dCpf1-guided base editors.
 This is an alternative to SNV analysis performed by other groups. dCpf-independent off-targets
 could be detected by SNV analysis, but not by the method described in this manuscript. The
 authors could perform SNV analysis on the whole genome data sets used in this study for
 comparison and discussion.
Peer review of: Genome-wide specificity of dCpf1 cytidine base editors (2023)


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 Reviewers' Comments:
 Reviewer #1 (Remarks to the Author)
Reviewer #2 (Remarks to the Author)
 The weakness of this study is an arbitrary (or not explained) parameter setting for mismatch
 filtering and the lack of quantitative correlation with in vivo results, which raise concerns of both
 incomprehensiveness and false positives. For “unbiased” and “genome wide” studies, the readers
 today would expect more comprehensive anaylses that include gRNA-independent off-targets or
 SNV. If these points are beyond the scope of this study, usability of the method would be limited,
 even though this reviewer acknowledges its uniqueness, and the difficult situation to perform
 additional experiments.
  The authors have demonstrated a creative off-target detection method that is worthy of publishing
 and of great interest to the community. The only thing this reviewer asks is that the authors put
 their work in context of published SNV off-target analysis in the discussion. How is this in-vitro
 manipulation followed by WGS better or a good alternative to simply performing WGS (without
 additional manipulation)and determining SNVs? I think this is a fair question and an important one
 to inform other scientists that want to perform similar experiments.
Peer review of: Turn-on chemiluminescence probes and dual-amplification of signal for detection of amyloid beta (2020)


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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Martina Zangheri
Reviewer #2 (Remarks to the Author):
  The authors have carefully reviewed the paper according to the referees' comments, thus I think it
 can be considered for pubblication.
   I thank the authors for providing a revised manuscript that mostly satisfies my original comments
 and questions. The one issue that remains, however, is the inconsistency in the cartoons shown in
 Figure 7A and the TOC graphic. The authors propose based on calculations that ADLumin-1 binds
 across the different Abeta strands rather than intercalating in between the strands. This
 orientation is correct in the cartoon in Figure 7A, but not in the TOC graphic. For CRANAD-3, the
 authors state in the response letter that this molecule intercalates between the individual Abeta
 strands in fibrils. This orientation for CRANAD-3 is NOT correct in Figure 7A, but is correct in the
 TOC graphic. I would recommend the authors correct these inconsistencies before publication.
 Jerry Yang
Reviewer #3 (Remarks to the Author):
  I think the authors have addressed most of my concerns in the revised manuscript.
 I have only one small question. The author mentioned that ADLumin-1 is luminescent in the
 presence of 10% DMSO DMSO or in pure DMSO. What about other solutions?
Peer review of: Contactless probing of polycrystalline methane hydrate at pore scale suggests weaker tensile prop (2020)


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 REVIEWERS' COMMENTS:
Reviewer #3 (Remarks to the Author):
  The authors have appropriately answers to all may major and minor questions. Since my general
 opinion about the paper was positive and leaning towards publication, now I could firmly
 recommend to accept th epaper as it is.
Peer review of: Adsorption and activation of molecular oxygen over atomic copper(I/II) site on ceria (2020)


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 Reviewers' comments:
Reviewer #1 (Remarks to the Author):
  In this revised manuscript, the authors have addressed some of my issues. I now feel that this work
 has the potential to be published in Nature Communications. However, some issues in my previous
 comment are still unsolved. Particularly, the causality between the HOMO energy and the activity of
 the Cu sites is still unclear. As a result, although the selective activation of O2 over the atomic
 Cu(I/II) site on CeO2 is observed, the most important conclusion in this work, i.e., “low HOMO energy
 enables the selective O2 adsorption and activation, which then improves the CO oxidation activity”, is
 not convincing. Thus, the authors should address the following points before a recommendation can
 be made.
 1. The author claimed that “η2-O2 is not observed in the 20wt% CuO-CeO2, possibly due to the
 higher HOMO level of the CuO clusters which breaks the O=O double bond”. This statement is just a
 speculation without any convincing evidence. Because calculations of the energy level for HOMO at
 first-principles levels are routine nowadays, the authors should provide direct evidence for their
 statement of the effect of low HOMO energy on CO oxidation activity with proper modeling (see
 below).
 2. In the revised manuscript, the authors tried to estimate the charge transfer among Cu, O and Ce
 for the [Cu(I)O2]3- and [Cu(II)O4]6- sites via the Bader charge analysis. However, the authors put a
 neutral Cu atom on the CeO2(111) surface to model [Cu(I)O2]3-. In this model, the formal oxidation
 state of Cu is 0 rather than the expected +1, which is not a proper electronic structure for [Cu(I)O2]3-
 . Thus, the authors should use a proper model for [Cu(I)O2]3-. Furthermore, the CuO2 cluster was
 put on the CeO2(111) surface to model [Cu(II)O4]6-, where two O-O bonds have to be formed to
 keep the Cu(II) oxidation state. The justification of the formation of O-O bonds in [Cu(II)O4]6- should
 be provided. Overall, the electron withdrawing effect of Ce4+ to Cu(I/II) is still ambiguous and should
 be more properly addressed.
 3. The relationship in Figure X5 is interesting. Nevertheless, it is neither in the revised manuscript nor
 in the revised Supplementary Materials. I strongly recommend that the authors shall add Figure X5
 and its related discussions in the revised manuscript.
 Reviewer #2 (Remarks to the Author):
 The authors have adequately responded to my comments and I consider that the manuscript is
 appropriate for publication.