JerMa88/TPR_Peer_Reviews huggingface dataset:
Peer review of: Structural characterization of a novel human adeno-associated virus capsid with neurotropic prop (2020)

RR2
Reviewers' Comments:
 Reviewer #1:
 Remarks to the Author:
 The authors have responded most of concerns raised previously in this revision.
 Authors have demonstrated that AAVv66 has halved BBB penetrating ability
 compared to AAV9, while significantly stronger ability than AAV2. They also
 demonstrated that the serology of AAVv66 is partially distinct from yet similar with
 AAV2.
 I still have some minor concerns:
 1) The authors used neonatal mice(P0-P1) facial-vein injection method to compare
 AAVv66’s and AAV2’s BBB penetrating ability during systematic administration. But
 I am very curious that would there be any alternate outcomes when administrate
 these vectors with adult mice tail-vein injection? Considering there have been
 reports demonstrated that administrating AAV-9 at different development timepoint
 (neonatal or adult mice) could lead to different cell type transduction or tissue
 tropism. Some reference are appended here: (1) doi: 10.1038/nbt.1515 ; (2)
 doi:10.1038/sj.gt.3303029
 2)Since authors propose that the side chain of 499E and 488T; 585S and 588T
 have potential interactions. I think it would be informative to provide molecular
 distances of these side chains in Fig.6c and Fig. 6f.
Peer review of: The MiDAC histone deacetylase complex is essential for embryonic development and has a unique (2020)

R2
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Most of the concerns raised previously have been taken into account and the manuscript has now been much improved.
I can therefore recommend this manuscript for publication.
Saadi Khochbin
Reviewer #3 (Remarks to the Author):
Most of the issues have been well responded. Overall, this is an excellent paper.
1. As a response to question 6-(2) of the third reviewer, Supp. Fig. 10B was provided. Some labels could be added in this panel to improve the clarity, including labels for “the shorter helix”, “a non- polar groove” and “the end of the long helices”.
3. As to the question 6-(4), the “7Å vs 4.5 Å” looks like “7.7 Å vs 4.5 Å” or “8 Å vs 4.5 Å” according to the added Supp. Fig. 8.
Peer review of: Reconstruction of evolving nanostructures in ultrathin films with X-ray waveguide fluorescence ho (2020)


RR3
 Reviewers' comments third round: Reviewer #1 (Remarks to the Author):
  I would like to thank the authors for their valuable and detailed response to my questions. The
 explanations given for the uncertainty analysis regarding statistical and physical constants related
 aspects are very much appreciated. The corresponding additions to the manuscript and supporting
 Information are fine as well.
 I recommend the manuscript for publication without any further revision.
Peer review of: Deconstructing sarcomeric structure–function relations in titin-BioID knock-in mice (2021)


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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The author have addressed my concerns, although I am confused as to the information provided in the Excel file titled fig 3a, fig 3b, fig 5a, fig 5b. These appear to be iBAQ values, but there are no protein identifiers for the values.
Reviewer #2 (Remarks to the Author):
The authors of Rudolph et al. “Deconstructing sarcomeric structure/function relations in titin-BioID knock-in mice” have substantially improved their manuscript by adding and amending text and figures. The imaging part can now be judged and understood by the reader. All essential information is now present in the manuscript and the accompanying extended material.
A few minor points should be addressed before publication:
- Text page 7 line 6: “Fig 2h,i” should read “Fig2i,j” and “Fig 2j,k” should read “Fig 2k,l”
- Fig2i and Fig2k: The line profile indicated in the image is parallel to the border of the figure. It is standard practice to measure the line profile perpendicular to the structure of interest(please also see image attached to this letter) and this should be corrected before publication. Fig 2j and Fig 2l should be updated accordingly.
In addition: The authors might want to consider improving readability of protein names/abbreviations in Fig4 and Ext. Fig 3d.
We hope that the interesting findings regarding the force generating mechanism in muscle will be followed up in future work and extend this elegant study.

Marko Lampe
with substantial support by Muzamil Majid Khan
Peer review of: Sub-picosecond thermalization dynamics in condensation of strongly coupled lattice plasmons (2020)


RR3
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author): Dear editor and authors,
Reviewer #2 (Remarks to the Author):
Reviewer #3 (Remarks to the Author):
   my concerns have been addressed, I am happy to recommend the paper for publication in Nature
 Communications.
  I already supported publication in the previous round, and after reviewing the responses to the
 comments of the other referees, I believe the paper is even stronger now, and thus even more
 support publication in Nature Communications.
  As a result of the second revision process the authors have further refined both the manuscript
 and the supplemental material by incorporating the criticisms of the referees point by point. This
 has been accomplished to such a level of detail that now the manuscript is ready for being
 published at the journal „Nature Communications“.
Peer review of: Non-cooperative 4E-BP2 folding with exchange between eIF4E-binding and binding-incompatible (2020)



RR2
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have satisfactorily addressed all of my previous concerns.
One minor comment. In the Supplemental Methods "Bioinformatic assessment of pTPGGT motif structure and sequences" section, the following sentence should be rewritten (or at least include an extra comma after "PSSM"), because its meaning was not immediately clear to me:
"Now, while the negative data does not overlap with the sequences used to define the PSSM the positive data does, having come from 570 of the 5611 nonredundant protein clusters identified previously."
This could be simplified to "Unlike the negative data, the positive data overlap with the sequences used to define the PSSM. This is because the positive data come from 570 of the ..."
Reviewer #2 (Remarks to the Author):
The new denaturation experiments of non-phosphorylated 4E-BP2 in Fig. S2B clearly show a uniform upfield shift with increasing temperature, in contrast to phosphorylated 4E-BP2. Therefore, my previous comment regarding this control has been addressed. In addition, the authors clarified the sources of errors throughout the text, which was also a concern from Review #1. They also improved the readability of the FRET/FCS sections, removed the redundant equation S12 and added the necessary FCS equations for R_{H}. I just have two minor comments:
1. The color codes of temperatures need to be added in Fig. S2B legend or caption.
2. The github links to analysis scripts are not available at the moment. They should be available after publication.
To sum up, the authors have satisfactorily addressed my comments in this version.

Reviewer #3 (Remarks to the Author):
The authors have greatly improved manuscript clarity. They've also made a number of compelling arguments supporting their conclusions and more clearly outlined novelty of their work. I think that the manuscript can be accepted for publication in its current form.
I only have a minor suggestion. I still think that smFRET experiments with chemical denaturation make interpretation of smFRET experiments done in the absence of denaturants more convoluted. I would argue that smFRET experiments with chemical denaturation are redundant because NMR and DSC experiments already demonstrate non-cooperative unfolding of 4E-BP2. Therefore, smFRET experiments with chemical denaturation could be removed for clarity.
Peer review of: Protonic solid-state electrochemical synapse for physical neural networks (2020)


RR2
 REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
the revision answers my questions adequately, paper can be published now
Reviewer #2 (Remarks to the Author):
    The authors have made a good revision of my previous comments, and I think the manuscript
 reaches the level of other papers published in Nature Communications in this field of research. I
 believe publishing this manuscript is a good choice.
 Just one minor point. I recommended the authors to remove the word “computing” form the title
 and they did. But they replaced by “neural network”. I think this manuscript demonstrates in a
 very clear way that the devices exhibit some synaptic behaviors, but they do not go beyond that. I
 think the authors should still modify the title and remove any work that points to association of
 devices (such as computing or neural network), otherwise the readers is going to be confused and
 overall gives the impression that the authors try to oversell their work. The work is already
 excellent in its field, such overselling is not necessary. So, better to change the title and make it
 more descriptive of the content.
 Other than this, the paper is excellent. Congratulations to the authors for this excellent
 achievement.
 Reviewer #3 (Remarks to the Author):
 The authors have addressed my questions satisfactorily in the revision, which is recommended for
 publication as is now.
Peer review of: Mitochondria-adaptor TRAK1 promotes kinesin-1 driven transport in crowded environments (2020)


RR2
 Peer Review File
Reviewers' comments second round: Reviewer #2 (Remarks to the Author):
Reviewer #3 (Remarks to the Author):
   The authors have addressed all concerns adequately and I have no objections to the publication of
 this work.
  The authors have addressed my concerns either entirely or to the best of their ability, and I
 support publication of this study in Nature Communications. The new data with the TRAKdeltaC
 that lacks the microtubule binding domain is incredibly exciting. The dual mode of allosteric
 activation and tethering of kinesin-1 opens up many exciting avenues of future research. My only
 other suggestion would be to move certain data from the supplement, such as Figure S1c-e, to the
 main figures, but this is at the discretion of the authors.
Peer review of: Structural basis of host protein hijacking in human T-cell leukemia virus integration (2020)


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 REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
  This is a revised manuscript describing the cryo-EM structure of the HTLV-1 IN:DNA intasome bound
 to the B56 subunit of the host PP2A protein. This structure is significant and show the interaction of
 two PP2A B56 subunits bound to the IN tetramer in the presence of a branched DNA substrate. The
 novel feature of the structure is that the interaction is through a loop region between the IN CCD and
 CTD domains, which has previously not been identified to function in other IN:host factor interactions.
 The authors have responded to a majority of the previous comments.
 These two points remain:
 1) Order of supplemental Figures should remain in order of citing (line 54) in the text.
 3) Line 76. Change the text regarding the "strong stimulatory effect on deltaretroviral concerted
 integration reactions".
 The authors in their response dedicated an entire paragraph indicating that "the biochemical activities
 of HTLV IN are highly dependent on the buffer condition and protein construct used." Simply citing this
 manuscript ignores the entire rebuttal presented by the authors.
 Reviewer #2 (Remarks to the Author):
 The structure of the HTLV1 intasome is an important contribution to the scientific community and the
 determination of its structure bound to the cellular factor B56y is a plus. However, the inconsistence in
 the biology does not allow authors to confidently claim that B56y is required for intasome assembly
 and integration of the HTLV1 genome into the host DNA. In vitro experiments suggest B56y is
 essential for intasome assembly, but both in vitro and in vivo assays show integration of HTLV1 in
 absence of B56y. Is B56y essential or an enhancer for HTLV1 cell infection? The impact on infectivity
 by HTLV1 mutants (L194A/R197A) that should have either none or minor interaction with virus
 integrase also leave important open questions.
Peer review of: Strain-induced room-temperature ferroelectricity in SrTiO3 membranes (2020)


RR3
 REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
  I commend authors for providing details of derivation according to my question. I am satisfied with
 their answer; the paper can be published.
 I notice possible typos in equations 7 (possibly c44 instead of c11) and equation 9 (possibly g12
 c12/c11 instead of g12/c11). I trust authors to make appropriate changes; no additional review is
 required, in my opinion.
Peer review of: Strain-induced room-temperature ferroelectricity in SrTiO3 membranes (2020)



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REVIEWER COMMENTS</B> Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
Authors have answered my questions satisfactorily.
  In the revised version of the manuscript, the authors have addressed all my concerns properly and I
 would highly recommend publication in Nature Communications.
   Additionally, I would like authors to explain how the value of alpha_11^prime, alpha_1^prime and C
 in equation (3) is derived form (2) explicitly, if require show steps in the supplementary materials.
 Seems like authors have not used these parameters (g12 and C12) anyway.
 Right below, equation 3, I believe the value (expression involving cotangent) belongs to
 alpha_1^prime; please correct it. Please include the used value of alpha_11^prime.
 Reviewer #3 (Remarks to the Author):
 The authors replied to all of my questions carefully and addressed the according issues in the revised
 manuscript. I recommend accepting the paper for publication.
Peer review of: Unconventional Hund metal in a weak itinerant ferromagnet (2020)


RR2
 REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
  With their revised manuscript submission, the authors have answered all my questions and added the
 suggested changes. Therefore, I fully support the publication of this important work in Nature
 Communications.
  I can see that the authors addressed my questions in the proper manner.
 Therefore, I recommend the manuscript for the publication now.
Peer review of: Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins provide insights into coronavirus (2020)


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Reviewers' Comments:
 Reviewer #1:
 Remarks to the Author:
 All of my concerns have been adequately addressed by the authors.
 Reviewer #2:
 Remarks to the Author:
 The authors have appropriately and carefully addressed all comments and suggestions. The comment
 and model they provided for asian leopard cat S in their rebuttal letter is greatly appreciated.
Peer review of: Imaging the kinetics of anisotropic dissolution of bimetallic core–shell nanocubes using graphene (2020)


RR2
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
In the revised manuscript, the authors addressed the reviewers' comments satisfactorily. Therefore, the manuscript can be accepted for publication in Nat.Commun.
Reviewer #2 (Remarks to the Author):
The authors have satisfied my original critique.
Reviewer #3 (Remarks to the Author):
In this revision, the authors have adequately addressed my questions, comments, and critical feedback, and I believe the work is acceptable for publication. I will observe that the new STEM-EDX maps of the Cu@Au nanocages (Figure S11) do not seem too informative relative to the STEM-EELS already included in Figure 6a and apologize for the experimental difficulty and time spent in acquiring this additional data.
Peer review of: Structure and mechanism of DNA delivery of a gene transfer agent (2020)


RR2
 Reviewers' Comments:
 Reviewer #1:
 Remarks to the Author:
 Thank you to the authors for carefully addressing the points raised during my initial review. With
 removed speculation and cleaner, more streamlined language the new manuscript is much improved.
 Congratulations on such nice work!
 Reviewer #2:
 Remarks to the Author:
 The MS by Bardy and co-authors was significantly improved and much easier to read and follow the
 logistic of the results.
 There are only very minor comments
 Lines 25-27 -> abstract
 �The opening of a constriction within the RcGTA baseplate is mechanically linked to the exposure of
 membrane-penetration helices at the tip of the tail and enables the ejection of DNA into the periplasm
 of recipient bacteria.� It should be made clear, that this is a hypothesis, since the resolution of the
 distal end of the tail was not brilliant (~ 15A?).
 Lines 102-104
 �Additional differences among the capsid proteins are in residues 217-222 from the axial domain,
 which form a loop in a hexamer, but are disordered in the major capsid proteins that constitute
 pentamers�. Apparently the authors talking of the A-loops, but in all conformers they look exactly the
 same -> figure Fig. S6C (like in hk97).
 Would be useful to show this loop in the figure S6C (related to pentamers) -> in this figure in atomic
 models all A-loops are rather well defined, but possibly not in the map? So it is difficult to understand
 which loops are disordered.
 Lines 230-232
 �The structure of tail tube proteins does not change after DNA ejection (Fig. S11), providing evidence
 that conformational changes of the tail do not propagate a signal about baseplate binding to a cell to
 trigger DNA ejection.� It would be recommended to rephrase the sentence. The authors did not
 observe changes in the tail after DNA ejection. There are a few reasons: it may be due to the fact,
 that the tail is short; the authors should be aware that some conformational changes are reversible,
 so after DNA ejection proteins may restore their initial stable conformation, especially in situ
 conditions. So far no changes were found in podoviridae phages, at least nothing was reported. The
 hypothesis of signalling by tails in all types of phage should still be verified, although such signalling
 really exists in myoviridae phages.
 Possibly it would be better to rephrase the sentence in the following way: �The structure of tail tube
 did not reveal any changes after DNA ejection (Fig. S11), suggesting that the tail is not involved into
 signalling to trigger DNA ejection after attachment to a cell.�
 Lines 321-332
 Conformational changes of RcGTA baseplate regulate DNA release. -> It seems that this paragraph is
 too speculative: a resolution of this part of the structure was rather low. So conformational changes
 were actually not observed. Possibly it would be more safe to avoid unnecessary suggestions, which
 were not supported by real observations. Projections were not very convincing,
Peer review of: Spectral cross-cumulants for multicolor super-resolved SOFI imaging (2020)

Reviewers' Comments: 
 
Reviewer #1: 
Remarks to the Author: 
The SOFI technique, like all fluorescence SR methods, makes use of the independence of individual 
fluorophores’ fluorescent state. It is certainly possible, and has been demonstrated, that a two-
channel system can be used to classify several different isolated fluorophores by their ratio in the 
two channels. What is described here is the analogous approach under the framework of the SOFI 
method. Although the mathematics might seem somewhat involved, this is the simplest and most 
straightforward approach to take. Still, it is a clever idea that is also practically useful for those 
that are using the SOFI method because many TIRF or widefield systems have a two-channel 
splitter system (they are cheaper and more ubiquitous commercially, and easier to custom build) 
but much fewer would have three or more channels. 
 
I enjoyed reading the manuscript. It is well written with the method laid out in a straightforward 
manner. Every question that occurred to me as I started reading was addressed somewhere in the 
manuscript or SI. I did simulate data and verify that eq 2 is correct and works. The following 
analyses after eq 2 are not particular to this paper and have been demonstrated previously. The SI 
explores the performance under realistic situations. 
 
 
 
Reviewer #2: 
Remarks to the Author: 
This paper described a method to do 3 color super-resolution SOFI images using two physical 
detection channels. It generalized a previously described spatial-temporal cross-cumulant 
approach between pixels on the same camera, to cross-cumulant between spectrally different 
channels. The authors demonstrated the principle using simulation and illustrated the application 
with fixed sample imaging. The theory behind the approach was clearly explained and application 
was sufficient to demonstrate the point of color unmixing. However, the reviewer has concerns 
about the novelty and proper benchmarking. 
1. The concept of cross-cumulant is not that new and has been applied previously by the authors 
and other group. The value provided in the paper is a generalization to multi-color. If the authors 
provided software packages that help users performing such analysis, it would be a plus. 
2. There are many existing super-resolution methods capable of doing what the current method 
can do, for example, structural illumination, DNA-paint, etc. The 3 color imaging can be done even 
with sequential SOFI with 3 different colors. The simultaneous 2-channel acquisition can save 
some time, but for fixed sample, this advantage is marginal. So the authors should really provide 
some applications that illustrate the unique advantages that other methods cannot do or this 
method can do much better. 
Minor 
1. In Figure 3, the authors could add some analysis to the performance of the method, rather than 
just the figure and the zoom. 
2. Figure 3 and 4 provided similar points of color unmixing and did not add much.
Peer review of: Spectral cross-cumulants for multicolor super-resolved SOFI imaging (2020)


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 Reviewers' Comments:
 Reviewer #2:
 Remarks to the Author:
 In response to my previous comment, the authors made considerable efforts in improving the
 paper, mostly by adding the proof-of-principle live cell 3-color experiment. However, it is still hard
 to evaluate the performance of the technique without some quantitative measurement. What is the
 resolution in each color (experimental and theoretical)? What is the registration accuracy between
 different color? How long does it take to take an image and how does movement of fluorophore
 blur the super-resolution image? How does it compare with other super-resolution techniques and
 what are the unique advantages? As a method paper, I think it is important to give these
 characteristics for the reader to decide whether to use the method.
Peer review of: Single-molecule photoreaction quantitation through intraparticle-surface energy transfer (i-SET) s  (2020)



RR3
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
  Thank You for clarifications and comments. Herein I conclude the manuscript can be accepted for
 publication in Nature Communication.
 Short comments of mine, with no influence on the above decision and with no need to respond.
 1. It is a pity the authors have decided to remove Figure S20, as this discussion and forward
 looking thinking is valuable
 2. The DEX discussion is really interesting. I suggest also to consider non homogenous distribution
 of Tb3+ ions in the NP volume, which we found to be responsible for some spectral nuances in our
 own studies.
 Reviewer #3 (Remarks to the Author):
All of my concerns have been addressed. Nice paper.