JerMa88/TPR_Peer_Reviews huggingface dataset:
Peer review of: Use of ratiometrically designed nanocarrier targeting CDK4/6 and autophagy pathways for effecti (2020)


RR2
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have properly answered my concerns. I have no more questions for this manuscript.
Reviewer #2 (Remarks to the Author):
The authors have addressed the majority of the concerns. Now the paper is substantially improved with key details. With a recent surge of interest to use CDK4/6 inhibitor for pancreatic cancer treatment, this study offers an improved drug delivery method and a combinatorial drug formulation that may benefit human patients. The following minor concerns should be addressed in the revised manuscript.
1) In the rebuttal letter (comment 2D), the authors have shown that the KPC PDA cell line has low RB and phospho-RB(pRB) compared to the human cancer cell lines they have used in their study. They have expressed their skepticism on using KPC PDA animal models to investigate CDK4/6 inhibitors. However, employing KPC animal model, Ruscetti et al (Cell, Volume 181, Issue 2, 16 April 2020, Pages 424-441.e21) have shown that CDK 4/6 inhibitor (in combination with trametinib) can increase senescence through RB, and generate a sensitive background for immunotherapy. Hence it is not clear if the low RB/pRB showed by authors is an in-vitro phenomenon. The author should publish the low RB/pRB level in KPC-PDA cells in the supplemental Fig 1A with other RB Positive cell lines. As there is an emerging interest to test CDK4/6 inhibitors with various drug combinations for pancreatic cancer, this information can be useful to choose the right cell lines and help the scientific community in future research.
2)Comment 5: Figure 4C: For clarity, the authors should mention that the experiment B and C were done with single IV injection ( or add “the experiment was performed as 4B” to the 4C figure legend).
Peer review of: Green light triggered [2+2] cycloaddition of halochromic styrylquinoxaline—controlling photoreac  (2020)


RR2
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have satisfied my initial concerns, and I thank them for digging deeper into the prior literature to frame this exciting work in the best light. I only have one lingering request, which is for the authors to specifically state what the current "record" is in terms of low-energy excitation to trigger the dimerization in solution, to the best of their knowledge/awareness. They mention crystalline example at 530 nm, but it would be good to put the solution value here of 550 nm into context of where other solution studies have pushed to. is the cited 470 nm reported in their prior work considered the low energy number to beat, or has this been pushed longer by other groups/chromophores?
Reviewer #2 (Remarks to the Author):
The authors have thoroughly addressed the the comments/suggestions of all reviewers. I suggest accepting the manuscript in its revised form.
Peer review of: Surface oxygenation of multicomponent nanoparticles toward active and stable oxidation catalyst (2020)

RR2
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
Reviewer #3 (Remarks to the Author):
The manuscript is satisfied for acceptance after the revision.
  The authors have addressed my comments, the paper can now be published pending one comment.
 The axis labels in the plots in Figs. 1, 3 and 4 are microscopic, please use a larger font.
Peer review of: NIR-II bioluminescence for in vivo high contrast imaging and in situ ATP-mediated metastases trac  (2020)

RR2
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
In the revised manuscript, the authors discussed concentration dependency of the dyes in micelles as the component of the bioluminescent probe and potential limitations of this bioluminescence probe. The authors also explained in detail about the differences of the best timing of the probe injection for each in vivo imaging experiments.
These modifications sufficiently addressed my concerns on the original manuscript. After addressing one minor comment below, I recommend the acceptance of this manuscript for publication in Nature Communications.
Minor comment
In Figure 2A, the chemical structure of the reactant N-[(3-(Anilinomethylene)-2-chloro-1-cyclohexen- 1-yl)methylene]aniline monohydrochloride should be added in the scheme.
Reviewer #2 (Remarks to the Author):
The authors addressed the reviewer's comments and the revised manuscript is acceptable for publication.
Peer review of: Preparation of TiH1.924 nanodots by liquid-phase exfoliation for enhanced sonodynamic cancer t (2020)



RR2

 Reviewers' Comments:
 Reviewer #1:
 Remarks to the Author:
 The authors carefully adddressed all concerns raised by the referees. The manuscript has improved
 a lot and I suggest to publish it in the current form.
 Reviewer #2:
 Remarks to the Author:
 The revised version is well prepared by reflecting the reviewers' comments. It can be published as
 it is.
Peer review of: Fast growth of large-grain and continuous MoS2 films through a self-capping vapor-liquid-solid me (2020)

RR4
 REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
  The authors addressed the first three of the comments. However, the last two comments were not
 answered correctly. The figure quality and style in Fig.5 and 6c are far below the standard
 microelectronic device characteristics. Specifically, Fig. 5b doesn't reveal any information of the
 device structure with poor image contrast. Fig.5c and 5d shows channel conductance without
 normalization while 5e and 5f are normalized current. The correct notation for gate voltage is Vgs
 for gate-to-source voltage instead of VG. The source to drain voltage should be denoted as VDS
 instead of VSD. The Vgs is 40V, 45V, 50V and 50 V in Fig 5c to 5f, respectively. And even in Fig 5f
 along, the x-axis for black and red curves are not measured within the same range of VG. And
 typically, the channel length should not be L, but Lch or Lg. In the caption of Fig. 5f, this should be
 called transfer characteristics in semi-log plot, not Log-plot of the gate-dependent current density.
 In Fig.6b, the optical image provides little information of the device. In Fig.6c, the transfer
 characteristics are considered pretty poor quality for any such devices. In a word, the reviewer
 feels such electrical data of the devices would not get anywhere close to publication in any device
 related journals, let alone prestigious journals like NCOMM. The authors should at least be
 consistent with device measurement, make the correct plot, name the right notations and they can
 find any of those information in classic semiconductor textbooks.
Peer review of: Fast growth of large-grain and continuous MoS2 films through a self-capping vapor-liquid-solid me (2020)


RR3
REVIEWER COMMENTS
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
  All the comments are well addressed, I would like to recommend publication in Nature
 Communications.
  The authors provided some useful data in this round of review. However, it still fall short of a high
 quality paper, especially for a material intended for electronic devices.
 1, The authors stressed several times that the grain size is record high. However, it is only twice
 large compared to previous results. In the material growth area, this is typically considered as
 incremental.
 2, The novelty from the growth method itself, it is not the first time using spatially confined
 decomposition of metal fluorides from reviewer 1’s comment. BaF2 and NaF essentially play the
 same role in the growth and thus the difference is minimal.
 3, How to eliminate the multilayer region is a huge problem. The authors only provide a hypothesis
 of using H2S(g) which is groundless without any supporting data.
 4, The electronic device data in figure 5 is quite poor even compared to previous work, especially
 in Fig. 6c. This dispersion is far from uniform as the authors claimed.
 5, As shown in table 1, the data from this work has only incremental advantage compared to other
 work. The current is from a device biased at Vds=8V, which clearly is very high in the common
 device applications, and very likely exceeding those from other references.
 Overall, this work shows little advances in terms of material growth method, the material quality,
 and the devices based on this material. As a result, the reviewer does not suggest its publication in
 Nature Communications.
Peer review of: Interaction of the pioneer transcription factor GATA3 with nucleosomes (2020)


RR2
 REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
  The authors have adequately addressed my previous questions and concerns. It is unfortunate
 that they were unsuccessful at obtaining structures of GATA3 bound to its cognate site at the SHL2
 positions given their data suggesting this is likely to be the more biologically relevant in terms of
 enhancer function. It will also be important for the authors to note the recent publication from
 Patrick Cramer�s lab on the structure of two other pioneer factors, SOX2 and SOX11, bound to
 nucleosomes at the SHL2 position published last month in the journal Nature. Cramer�s data
 supports several aspects mentioned at the end of their discussion. The subject of their article is
 very timely and will be of broad interest.
 Reviewer #2 (Remarks to the Author):
Reviewer #3 (Remarks to the Author):
 The authors have adequately revised the manuscript in response to this reviewer's comments. The
 extended discussion finishes with the challenging biological question of sequence requirements for
 pioneer action.
  In the revised version of their manuscript the authors have addressed all of my comments
 satisfactorily. I believe this work should be accepted for publication in Nature Communications.
Peer review of: A nanomaterials discovery robot for the Darwinian evolution of shape programmable gold nanop (2019)


RR2
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The authors report an autonomous platform to explore the chemical space of gold nanoparticles. They built a GA-driven robotic system to prepare and analyze optically the performance of the particle synthesis. The workflow is controlled by an in-house developed software.
The authors addressed all my questions and concerns, and the paper is ready to be published.
Reviewer #2 (Remarks to the Author):
The authors have made a number of changes to improve the readability of the paper. However, the concerns raised in my previous review remain. The introduction still inadequately cites the existing literature on self-optimizing reactors. The justification for using a genetic algorithm remains weak. The authors have added missing information relating to the experimental procedure. However, the description of the genetic algorithm is still incomplete, lacking for instance information concerning the cross-over probabilities, mutation probabilities and penalty functions. As noted, in my previous comments, Fig. 4d does not show “a final UV/Vis spectrum” – presumably the authors mean Fig. 4e? As far as I can tell, the manuscript still contains no data to support the claims made about reproducibility. The labelling of the raw spectra in the SI is unchanged and remains uninformative – what were the experimental conditions corresponding to these spectra? The claim in the abstract of “discovering entirely new systems” seems to me to be overstated.
Peer review of: Spontaneous creation and annihilation dynamics and strain-limited stability of magnetic skyrmion  (2020)


RR2
 Reviewers' Comments:
 Reviewer #1:
 Remarks to the Author:
 The authors went through great efforts and in my opinion have improved the manuscript. I still
 think that the findings are a bit speculative since they are based on essentially a two dimensional
 treatment at zero temperature of a three dimensional problem at elevated temperatures (even
 though the authors mention in the manuscript and in the rebuttal that they do not expect the
 magnetization profile to change much across the film thickness). This makes me less convinced
 that the authors indeed found a new mechanism (antiskyrmion generation and annihilation vs.
 “zippers”), but it may well be possible. I just think that the paper does not provide a stringent
 proof.
 But, as I have mentioned in my first report, the data is of high quality and the discussion is
 adequate. So probably this paper brings something new for the experts in the field. I still think
 that the mechanism is so similar to the one observed for vortex core reversal where the same
 problem has to be discussed, namely the conservation of topological charge, that I think this work
 should be cited. Quite a few papers also discuss the energetic contributions to this very similar
 reversal process and in fact figure 4 resembles the sketch known for vortex core reversal.
 In my opinion this a bit a borderline case since in my view the (reasonable) arguments that the
 authors bring forward are not 100% backed by the experiments for the reasons mentioned above.
 I leave it to the editor to decide.
 Reviewer #2:
 Remarks to the Author:
 I am satisfied that the authors have addressed my comments carefully. The revised explanation
 and the modified discussion sufficiently provide valuable data set, information for reproducibility,
 and interesting insight. The interpretation of data and suggested transition mechanism are based
 on some assumptions, but they are plausible at the present point. Thus, I now recommend the
 manuscript for publication.
 Reviewer #3:
 Remarks to the Author:
 The resubmitted manuscript addresses my questions and doubts correctly enough, though I don't
 feel like it's worthy enough for the DPC data to put it in the main text. So, I can recommend
 publication in Nature Communications.
Peer review of: Machine learning accurate exchange and correlation functionals of the electronic density (2019)


RR3
 REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
Two last points should be considered:
I leave these suggestions to the authors and editor.
  The authors provided an updated manuscript where they have responded to all comments, most of their
 bold statements about their method have been rewritten in order to reflect the true capabilities, while some
 of the issues that have been identified by the reviewers were not addressed but left as future work. I am
 also confused about Table II. They mention that they "have replaced Table II by what is now Table III in the
 SI", but table II is still in the main document. I do not have any further comments.
  The authors have done a reasonably good job of addressing the issues raised by the referees, and with the
 additional examples generated, this paper should now be accepted for publication.
  1. The abstract was not revised as requested. It still lacks specific detail about what has been accomplished
 in this work, and what a reader may hope to use the method for. 80% of it is background generalities.
 2. There is quite extensive new material and discussion, some of it confined to the supp info and briefly
 mentioned in the main text. These mentionings should be more specific (say where in supp info the material
 is) and describe the results and conclusions in a sentence or two in the main text.
Peer review of: Structural basis of seamless excision and specific targeting by piggyBac transposase (2020)


RR2
REVIEWER COMMENTS
Reviewer #1 (Remarks to the Author):
  The authors have fully addressed my questions and concerns. The quality of the manuscript has
 improved substantially and I recommend publication in Nature Communications.
Reviewer #2 (Remarks to the Author):
Large magnetoelectric coupling in multiferroic oxide heterostructures assembled via epitaxial lift-off Pesquera et al.
  The revised manuscript is much clearer and precise than the first version. The authors clearly state
 that their results reveal a strain mediated magnetoelectric coupling between an electroactive substrate
 and strain released epitaxial film of LSMO.
 The process is complex and appears to depend on the fortunate but reproducible formation of an
 amorphous glue transmitting the strain induced by the converse piezoelectric effect in the substrate.
 The two strain states in the (011)pc oriented PMN-PT give rise to twofold magnetic anisotropy.
 The enhanced magnetism and the increase in the Curie temperature occurs via stronger double
 exchange. The switching occurs via the structural orthorhombic to rhombohedral phase transition in
 the PMN-PT substrate.
 Thus, the authors present a fascinating and quite complete picture of strain tuning magnetic
 anisotropy using electrical control of a piezo substrate. The success of the lift-off method should
 stimulate further research.
 The manuscript can be published as it stands. There are just a few minor questions to be
 addressed/corrected.
 On page 5 line 2 when the authors mention the film microstructure they mean (I think) the
 appearance of cracks. They should say so because otherwise one might think that the film is not a
 single crystal film.
 The role of the amorphous layer in fixing the film and transmitting the substrate strain is well
 described. The authors should also discuss succinctly how the Pt electrodes might affect the coupling.
 Pt is neither amorphous nor will the thin Pt electrode have the same train response as the amorphous
 “glue”.
 A minor point on the presentation pf the PEEM analysis, it is not necessarily the 20 micron field of view
 which implies the 50 nm resolution but the overall settings of the microscope and above all the fact
 that the resolution in PEEM is in any case always poorer than in LEEM (latter uses monochromatic
 electrons). My guess is that the 50 nm resolution comes from the fact that it is a PEEM experiment
 and that even with a smaller field of view the spatial resolution would bethe same.
 The PEEM images are very nice, it is a pity they are not included in the main manuscript but I think
 there are space limitations.
 Reviewer #3 (Remarks to the Author):
 I am glad that the authors have settled all doubts of mine in the previous review, thus I recommend
 the publication.
Peer review of: Spatial defects nanoengineering for bipolar conductivity in MoS2 (2020)



RR3
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have addressed my concerns. I recommend the publication of this matter.
Reviewer #2 (Remarks to the Author):
    The Authors have addressed all comments and in my opinion the manuscript can be published in
 its current form.
Peer review of: Quantum-dot assisted spectroscopy of degeneracy-lifted Landau levels in graphene (2020)


RR2
 REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
  The authors have nicely addressed the points I mentioned in my review. The new Fig. S2 has a
 typo in the scale bar: it says 10 um^2 where I suppose it was meant to say 10 um. This should be
 fixed prior to publication.
  The authors have answered my and the other referee's comments and questions well, in my
 opinion. I recommend the publication of this manuscript in Nature Communications.
Peer review of: Ultra-fast vortex motion in a direct-write Nb-C superconductor (2020)


RR2
 <b>REVIEWER COMMENTS</B> Reviewer #1 (Remarks to the Author):
  The revised version has been improved and some of the points of my previous report have been
 addressed. In my opinion this work is interesting and addresses important issues of superfast
 dynamics of vortices so I could recommend it for publication in Nat. Comm. Although the arguments
 of the authors appear convincing, I think that they should not ascribe their results exclusively to the
 edge-barrier mechanism but mention other possibilities. As I pointed out in my first report, the well-
 known I_c \propto 1/(B0+B) of the Kim model of bulk pinning fits the observations of this work as well,
 giving a linear dependence of Ic(B) an B < B0 and Ic \propto 1/B at B >> B0. (Kim and Stephen in
 Superconductivity v. 2, ed. by Parks, p. 1107 (1969); Campbell and Evets, Adv. Phys. 21, 199 (1972)].
 Perhaps, the authors should soften their categorical claim that their observations are “fingerprints of
 the edge barrier model...”, replacing it with something like “the totality of our experimental data
 indicates ...” while mentioning other potential scenarios along with corresponding references. For
 instance, it would be worth mentioning in the introduction and discussion sections that jumps on the
 V-I curves could also result from the hotspot formation unrelated to the LO instability. The Joule
 heating in these films at low T can be pretty strong: at 4.2K, I = 20 uA and V= 5 mV, the heat flux
 from the film q = IV/lw = 15 kW/m^2. For typical values of the Kapitza interface thermal conductance
 of the order of 10 kW/m^2 and not very effective diffusive heat removal across the Si substrate with
 thermal conductivity some 2 orders of magnitude smaller than those of good metals, the Joule heating
 could cause phonon overheating of a few K.
 The description of the TDGL equations in the Methods is still incomplete as div(J^Us -J^GL) was not
 specified. The whole point of giving these equations in the Methods (particularly in this journal aimed
 at a more general physics audience) is that the reader can see the full set of equations used in the
 simulations without going to original papers. Using the rather technical notions of J^Us and J^GL
 without explaining what they are and directing the reader to Ref. 32 defies the purpose of giving these
 eqs in the first place. The authors could just have shown the results in Fig. 5 and stated that they
 were obtained using the model eqs of Ref. 32.
Peer review of: AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex (2020)

RR2 
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
 In this manuscript, Hirschi et al. describe the cryo-EM structures of Csy-AcrIF9 complex and Csy-
 AcrIF9-dsDNA complex. Under structural and biochemical data, the authors show AcrIF9 not only
 sterically blocks the binding of target DNA to crRNA, but also promotes nonspecific recruitment of
 dsDNA, potentially sequestering the complex from target DNA. The authors have addressed all my
 concerns by adding new text during revision.

 Reviewer #3 (Remarks to the Author):
 The comments have been addressed by the authors.
 However, should the EMSA protocol in the Methods not be updated with the optimized conditions
 presented in the revised manuscript?
Peer review of: Glycan-dependent cell adhesion mechanism of Tc toxins (2019)


RR2
 REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The revised manuscript improves in a number of aspects on the original version.
   The logic behind the decision to pursue heparin binding is now more clearly described. I think the
 paper would be still be clearer if there was a single, coherent numbering scheme in the compounds
 used, rather than having to cross-reference different numbering schemes in supplementary Tables.
 I understand that renumbering the compounds for the paper would be a frustrating exercise, but I
 think it would improve the clarity of the paper for the reader.
 The visualisation of heparin binding in two different TcA subunits certainly bolsters the claim that it
 is a mechanism of initial cell surface recognition in some (but not all) members of the TcA family,
 and the lack of conservation of the binding site implies that the recognition of heparin has evolved
 independently at least twice in the TcA family. This itself is an intriguing new finding. I still think
 the heparin screening experiment would be improved by the addition of: 1) a known heparin-
 binding protein as a positive control, and 2) another negative control that contains a positively
 charged surface patch. These controls would give information about the specificity of binding, but I
 accept that they would involve a reasonable amount of extra work and would do little to change
 the overall conclusions of the paper, so are not strictly required.