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Reviewer #1:
Remarks to the Author:
Prof. Katona and colleagues proposed developmental anoikis and the molecular player that
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Reviewer #1:
Remarks to the Author:
Prof. Katona and colleagues proposed developmental anoikis and the molecular player that
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Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors addressed all of points and the manuscript reads well.
Reviewer #2:
Remarks to the Author:
The revised version of László et al. addresses the points raised during the previous round of
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I appreciate the fact that in the pre... |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors addressed all of points and the manuscript reads well.
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The revised version of László et al. addresses the points raised during the previous round of
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Reviewer #1 (Remarks to the Author):
Giansanti et al. - Dynamic remodeling of the human host cell (phospho)proteome upon enterovirus
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GENERAL COMMENTS
This manuscript explores the altered proteome in cells infected with Coxsackievirus B3. The authors
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Reviewer #1 (Remarks to the Author):
Giansanti et al. - Dynamic remodeling of the human host cell (phospho)proteome upon enterovirus
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GENERAL COMMENTS
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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The revised version of this manuscript address all the questions and suggestions by the authors and
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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The revised version of this manuscript address all the questions and suggestions by the authors and
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REVIEWERS' COMMENTS:
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I am totally satisfied with the revisions made by the authors, in which all my comments have been
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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
I am totally satisfied with the revisions made by the authors, in which all my comments have been
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0 | 0 | Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The manuscript “Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase” by
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Reviewer #1 (Remarks to the Author):
The manuscript “Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase” by
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0 | 0 | Ion mobility collision cross-section atlas for known and unknown metabolite annotation in |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have done a very thorough job of responding to my comments. I particularly welcome
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(which is, I think, a more common use-case).
I woul... |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have done a very thorough job of responding to my comments. I particularly welcome
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0 | 0 | Ion mobility collision cross-section atlas for known and unknown metabolite annotation in | REVIEWER COMMENTS
Reviewer #1 (Remarks to the Author):
This paper described the creation and validation of an atlas of CCS values. The atlas is created using a
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Reviewer #1 (Remarks to the Author):
This paper described the creation and validation of an atlas of CCS values. The atlas is created using a
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0 | 0 | Complete chemical structures of human mitochondrial tRNAs | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
tRNAs are central to the decoding process and the post-transcriptional modifications of tRNA are critical
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Reviewer #1 (Remarks to the Author):
tRNAs are central to the decoding process and the post-transcriptional modifications of tRNA are critical
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0 | 0 | Complete chemical structures of human mitochondrial tRNAs |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have addressed all my previous concerns and the revised manuscript has been improved. I
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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have addressed all my previous concerns and the revised manuscript has been improved. I
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0 | 0 | Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Having read the revised version, we are convinced that the manuscript warrants publication in
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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Having read the revised version, we are convinced that the manuscript warrants publication in
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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
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REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
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0 | 0 | Caveolin-1-mediated sphingolipid oncometabolism underlies a metabolic vulnerability of | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript reports the association between plasma sphingolipid profile and disease progression
in low risk localized prostate cancer, and attempts to link this observation to a targetable biology in
the cancer cells involving scavenging and meta... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript reports the association between plasma sphingolipid profile and disease progression
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REVIEWERS' COMMENTS:
Reviewer#1:
The authors have thoughtfully addressed the critiques. I recommend this article for publication.
|
REVIEWERS' COMMENTS:
Reviewer#1:
The authors have thoughtfully addressed the critiques. I recommend this article for publication.
| TPR | NC_BS_BIOCH_009_RR3.txt | {
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0 | 0 | Caveolin-1-mediated sphingolipid oncometabolism underlies a metabolic vulnerability of |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The revisions to the manuscript have enhanced the clarity and quality of the manuscript text and key
figures. The critical amendments I requested to the clinical descriptors are now accurate and there is
greater detail about the key experiment... |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The revisions to the manuscript have enhanced the clarity and quality of the manuscript text and key
figures. The critical amendments I requested to the clinical descriptors are now accurate and there is
greater detail about the key experiment... | TPR | NC_BS_BIOCH_009_RR2.txt | {
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0 | 0 | Structural mechanism for replication origin binding and remodeling by a metazoan origin | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
JM Schmidt and F Bleichert report a structural mechanism for replication origin binding and remodeling
by the Drosophyla melanogaster’s Origin Recognition Complex (ORC) and its co-loader Cdc6. While
ORC recognizes consensus DNA sequences in S. cerevisiae, ... | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
JM Schmidt and F Bleichert report a structural mechanism for replication origin binding and remodeling
by the Drosophyla melanogaster’s Origin Recognition Complex (ORC) and its co-loader Cdc6. While
ORC recognizes consensus DNA sequences in S. cerevisiae, ... | TPR | NC_BS_BIOCH_010_RR1.txt | {
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0 | 0 | Enhancing intracellular accumulation and target engagement of PROTACs with reversible |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have adequately dealt with the previous comments that I raised.
Reviewer #2 (Remarks to the Author):
The authors have done a nice job to carefully address questions raised by all reviewers by
performing ... |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have adequately dealt with the previous comments that I raised.
Reviewer #2 (Remarks to the Author):
The authors have done a nice job to carefully address questions raised by all reviewers by
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0 | 0 | Enhancing intracellular accumulation and target engagement of PROTACs with reversible | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This is an interesting study of the effect of reversible covalent Protac ligands on protein degradation.
The authors provide compelling data for the effectiveness of their RC-1 ligand in producing BTK
degradation. I cannot comment on the underlying... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This is an interesting study of the effect of reversible covalent Protac ligands on protein degradation.
The authors provide compelling data for the effectiveness of their RC-1 ligand in producing BTK
degradation. I cannot comment on the underlying... | TPR | NC_BS_BIOCH_011_RR1.txt | {
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0 | 0 | Orthophosphate increases the efficiency of slow muscle-myosin isoform in the presence of | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The authors have resubmitted a greatly improved version of their manuscript. I only have a few additional comments on the rebuttal responses and associated manuscript updates.
Major comments:
1. The authors justify their choice to use permeabilized rabbit soleus... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The authors have resubmitted a greatly improved version of their manuscript. I only have a few additional comments on the rebuttal responses and associated manuscript updates.
Major comments:
1. The authors justify their choice to use permeabilized rabbit soleus... | TPR | NC_BS_BIOPH_002_RR2.txt | {
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0 | 0 | Orthophosphate increases the efficiency of slow muscle-myosin isoform in the presence of | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Summary: The authors of the submitted manuscript present data investigating the mechanism by which the systolic heart failure (HF) drug, Omecamtiv Mecarbil (OM), affects the force output and cycling kinetic of rabbit soleus muscle in situ. Mechanical experiments... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Summary: The authors of the submitted manuscript present data investigating the mechanism by which the systolic heart failure (HF) drug, Omecamtiv Mecarbil (OM), affects the force output and cycling kinetic of rabbit soleus muscle in situ. Mechanical experiments... | TPR | NC_BS_BIOPH_002_RR1.txt | {
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"content": "Reviewers' comments:\nReviewer #1 (Remarks to the Author):\nSummary: The authors of the submitted manuscript present data investigating the mechanism by which the systolic heart failure (HF) drug, Omecamtiv Mecarbil (OM), affe... | 2,020 | |||
0 | 0 | TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in mem |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Zhang et al. provide a revised manuscript, which improved in readability and clarity (also about
the limitations of their study). I am satisfied with most of their replies. The only remaining
problem for me is the link to physiology. First, it is ... |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Zhang et al. provide a revised manuscript, which improved in readability and clarity (also about
the limitations of their study). I am satisfied with most of their replies. The only remaining
problem for me is the link to physiology. First, it is ... | TPR | NC_BS_BIOPH_003_RR2.txt | {
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0 | 0 | TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in mem | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Based on three new structures of the TrkAH complex in the presence of ADP, ATP and
ATPgammaS, respectively, Zhang et al suggest a novel mechanism of nucleotide-dependent gating
of an RCK protein-regulated K+ channel. This is particularly interesting as f... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Based on three new structures of the TrkAH complex in the presence of ADP, ATP and
ATPgammaS, respectively, Zhang et al suggest a novel mechanism of nucleotide-dependent gating
of an RCK protein-regulated K+ channel. This is particularly interesting as f... | TPR | NC_BS_BIOPH_003_RR1.txt | {
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"content": "Reviewers' comments: \n \nReviewer #1 (Remarks to the Author): \n \nBased on three new structures of the TrkAH complex in the presence of ADP, ATP and \nATPgammaS, respectively, Zhang et al suggest a novel mechanism of nucleot... | 2,020 | |||
0 | 0 | Talin dissociates from RIAM and associates to vinculin sequentially in response to the | REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The authors have satisfactorily addressed my comments. | REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The authors have satisfactorily addressed my comments. | TPR | NC_BS_BIOPH_004_RR2.txt | {
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0 | 0 | Talin dissociates from RIAM and associates to vinculin sequentially in response to the | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This technically very elegant study analyzes the force-dependent interaction of the two adhesion
proteins RIAM and vinculin to talin, a crucial integrin activator and force transducer. By further
developing a previously established in vitro reconstitution assay,... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This technically very elegant study analyzes the force-dependent interaction of the two adhesion
proteins RIAM and vinculin to talin, a crucial integrin activator and force transducer. By further
developing a previously established in vitro reconstitution assay,... | TPR | NC_BS_BIOPH_004_RR1.txt | {
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0 | 0 | A dietary fatty acid counteracts neuronal mechanical sensitization | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
“A dietary fatty acid counteracts neuronal mechanical sensitization”
SUMMARY: This manuscript presents a thoughtful and rigorous characterization of the effects of
margaric acid (MA) enrichment of the plasma membrane on PIEZO2-dependent
mechanotransduction in ... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
“A dietary fatty acid counteracts neuronal mechanical sensitization”
SUMMARY: This manuscript presents a thoughtful and rigorous characterization of the effects of
margaric acid (MA) enrichment of the plasma membrane on PIEZO2-dependent
mechanotransduction in ... | TPR | NC_BS_BIOPH_005_RR1.txt | {
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0 | 0 | A dietary fatty acid counteracts neuronal mechanical sensitization | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have made substantial text changes and added new data analyses and results that
greatly strengthen the manuscript. They have directly addressed all of our concerns highlighted in
our initial review. It is our opinion that the data now fully support th... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have made substantial text changes and added new data analyses and results that
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0 | 0 | Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The revised version of the work “Redox-Coupled Proton Pumping Drives Carbon Concentration in
thePhotosynthetic Complex I “ presents a significant improved and corrected version of the
manuscript. Authors have adressed and/or adressed most of my previ... |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The revised version of the work “Redox-Coupled Proton Pumping Drives Carbon Concentration in
thePhotosynthetic Complex I “ presents a significant improved and corrected version of the
manuscript. Authors have adressed and/or adressed most of my previ... | TPR | NC_BS_BIOPH_006_RR2.txt | {
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0 | 0 | Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The work entitled “Redox-Coupled Proton Pumping Drives Carbon Concentration in the
Photosynthetic Complex I “ presents a structural study which combines CrioEM data, with
Structural modeling, Molecular Dynamics (MD) and QM based calculations to analyze sev... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The work entitled “Redox-Coupled Proton Pumping Drives Carbon Concentration in the
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Structural modeling, Molecular Dynamics (MD) and QM based calculations to analyze sev... | TPR | NC_BS_BIOPH_006_RR1.txt | {
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0 | 0 | Tug-of-war between actomyosin-driven antagonistic forces determines the positioning | Reports from round 1:
Rev#1
The authors have done an excellent job addressing the reviewer concerns, including addition of significant new experiments, all of which support their model. All critiques have been addressed, this is a lovely paper.
Rev#2
The authors have sufficiently addressed referee concerns. The manuscr... | Reports from round 1:
Rev#1
The authors have done an excellent job addressing the reviewer concerns, including addition of significant new experiments, all of which support their model. All critiques have been addressed, this is a lovely paper.
Rev#2
The authors have sufficiently addressed referee concerns. The manuscr... | TPR | NC_BS_BIOPH_007_RR1.txt | {
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"content": "Reports from round 1:\nRev#1\nThe authors have done an excellent job addressing the reviewer concerns, including addition of significant new experiments, all of which support their model. All critiques have been addressed, thi... | 2,020 | |||
0 | 0 | Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism | Reviewers' comments first round: Reviewer #1 (Remarks to the Author):
Carulla and co-workers employed various biophysical techniques - NMR, SEC/IM-MS (size exclusion
chromatography coupled with ion-mobility mass spectrometry), MALDI-MS, electrical recordings,
as well as MD (molecular dynamics) simulations - to determin... | Reviewers' comments first round: Reviewer #1 (Remarks to the Author):
Carulla and co-workers employed various biophysical techniques - NMR, SEC/IM-MS (size exclusion
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0 | 0 | Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism | REVIEWERS' COMMENTS second round: Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
Reviewer #3 (Remarks to the Author):
The authors addressed the comments of all reviewers with great care. With regard to my
comments I can confirm that they were also addressed satisfactorily. I have no further... | REVIEWERS' COMMENTS second round: Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
Reviewer #3 (Remarks to the Author):
The authors addressed the comments of all reviewers with great care. With regard to my
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0 | 0 | Single molecule secondary structure determination of proteins through infrared absorption | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The manuscript by Ruggeri and co-authors reports on structural determination of single proteins
using AFM-IR. Specifically, the aurthors showed that using this highly sensitive technique they
could probe secondary structure of thyroglobulin and apoferritin deter... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The manuscript by Ruggeri and co-authors reports on structural determination of single proteins
using AFM-IR. Specifically, the aurthors showed that using this highly sensitive technique they
could probe secondary structure of thyroglobulin and apoferritin deter... | TPR | NC_BS_BIOPH_009_RR1.txt | {
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0 | 0 | Single molecule secondary structure determination of proteins through infrared absorption | REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The manuscript was revised very well.
I recommend to accept it for publication.
technical comments:
- The authors should consider to check if the maximum of signal as given in the text in connection
with Figure 1 f) is at ~-2kHz off-resonance.
- Fig S4; "F... | REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The manuscript was revised very well.
I recommend to accept it for publication.
technical comments:
- The authors should consider to check if the maximum of signal as given in the text in connection
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- Fig S4; "F... | TPR | NC_BS_BIOPH_009_RR2.txt | {
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0 | 0 | Polyamine regulation of ion channel assembly and implications for nicotinic acetylcholine | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Novel genome-wide screening was used to discover an unlikely candidate for selectively and efficiently
promoting expression of alpha 7 and alpha 4 beta 2 AChRs through a novel mechanism. The small
cytoplasmic protein SAT1 encodes the rate limiting enzyme for poly... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Novel genome-wide screening was used to discover an unlikely candidate for selectively and efficiently
promoting expression of alpha 7 and alpha 4 beta 2 AChRs through a novel mechanism. The small
cytoplasmic protein SAT1 encodes the rate limiting enzyme for poly... | TPR | NC_BS_BIOPH_010_RR1.txt | {
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0 | 0 | Polyamine regulation of ion channel assembly and implications for nicotinic acetylcholine | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
This paper reports novel discoveries about the role of polyamines in regulating the expression of alpha
7 and alpha 4 beta 2 AChRs but not alpha 6 beta 4 AChRs. Extensive data are provided. The authors
were responsive to reviewer comments. This is an interesting ... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
This paper reports novel discoveries about the role of polyamines in regulating the expression of alpha
7 and alpha 4 beta 2 AChRs but not alpha 6 beta 4 AChRs. Extensive data are provided. The authors
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0 | 0 | Kinesin-14 motors drive a right-handed helical motion of antiparallel microtubules around | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
The revised manuscript by Mitra et al. has now been greatly improved by editing and new data.
The authors now demonstrated that Ncd can actually generate torque that is large enough to
cause microtubule twisting and coiling. ... | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
The revised manuscript by Mitra et al. has now been greatly improved by editing and new data.
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0 | 0 | Kinesin-14 motors drive a right-handed helical motion of antiparallel microtubules around | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The authors systematically compare the rotational motion of microtubules that Ncd motors
crosslink in vitro. It is well known that several mitotic kinesins such as kinesin-5 and kinesin-14
crosslink two microtubules. An emerging view is that they exhibit off-axi... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The authors systematically compare the rotational motion of microtubules that Ncd motors
crosslink in vitro. It is well known that several mitotic kinesins such as kinesin-5 and kinesin-14
crosslink two microtubules. An emerging view is that they exhibit off-axi... | TPR | NC_BS_BIOPH_011_RR1.txt | {
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0 | 0 | Cooperative transport mechanism of human monocarboxylate transporter 2 |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
I think authors have addressed the issues regarding functional characterization of the transporters to
a reasonable extent, including new experiements. A pity that pCMBS assays were not possible.
Structural aspects are beyond my expertise.
... |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
I think authors have addressed the issues regarding functional characterization of the transporters to
a reasonable extent, including new experiements. A pity that pCMBS assays were not possible.
Structural aspects are beyond my expertise.
... | TPR | NC_BS_BIOPH_012_RR2.txt | {
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0 | 0 | Backmapping triangulated surfaces to coarse-grained membrane models |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
All of my points have been more than adequately addressed.
Reviewer #2 (Remarks to the Author):
The authors have done a great job replying to reviews and the paper is suitable for publication.
|
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
All of my points have been more than adequately addressed.
Reviewer #2 (Remarks to the Author):
The authors have done a great job replying to reviews and the paper is suitable for publication.
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0 | 0 | Backmapping triangulated surfaces to coarse-grained membrane models | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Overall this is an excellent manuscript on what I think is a game-changing tool; it will be highly
useful in taking molecular level simulations to the next level in terms of system size. I have no
problem with the methods - they are demonstrated in the man... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Overall this is an excellent manuscript on what I think is a game-changing tool; it will be highly
useful in taking molecular level simulations to the next level in terms of system size. I have no
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0 | 0 | ucleoplasmic signals promote directed transmembrane protein import simultaneously via | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Mudumbi et al combine a toolbox of advanced microscopy methods aiming to resolve the long-lasting
debate about the nature of different INM protein groups in the peripheral channels in the NPC and
their integration within the nuclear pore membrane.
Overall, I ... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Mudumbi et al combine a toolbox of advanced microscopy methods aiming to resolve the long-lasting
debate about the nature of different INM protein groups in the peripheral channels in the NPC and
their integration within the nuclear pore membrane.
Overall, I ... | TPR | NC_BS_BIOPH_014_RR1.txt | {
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0 | 0 | ucleoplasmic signals promote directed transmembrane protein import simultaneously via |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors addressed satisfactorily my previously raised concerns, and therefore recommend to
accept the manuscript for publication in Nature Communications.
Reviewer #2 (Remarks to the Author):
My concerns have been dealt with satisfactory an... |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors addressed satisfactorily my previously raised concerns, and therefore recommend to
accept the manuscript for publication in Nature Communications.
Reviewer #2 (Remarks to the Author):
My concerns have been dealt with satisfactory an... | TPR | NC_BS_BIOPH_014_RR2.txt | {
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0 | 0 | Lipid-protein interactions modulate the conformational equilibrium of a potassium channel | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
All questions are answered satisfactory. I have no further comment and therefore recommend this
paper to be published in Nature Communications.
Reviewer #2 (Remarks to the Author):
In the revised manuscript the authors addressed to all reviewer c... | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
All questions are answered satisfactory. I have no further comment and therefore recommend this
paper to be published in Nature Communications.
Reviewer #2 (Remarks to the Author):
In the revised manuscript the authors addressed to all reviewer c... | TPR | NC_BS_BIOPH_015_RR2.txt | {
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0 | 0 | Lipid-protein interactions modulate the conformational equilibrium of a potassium channel | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
In this study, the authors investigated the effect of different membrane environment on the
channel permeation rates using molecular dynamics simulations. The authors found that the
thickness of the bilayer, lipid unsaturation as well as cholesterol cont... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
In this study, the authors investigated the effect of different membrane environment on the
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thickness of the bilayer, lipid unsaturation as well as cholesterol cont... | TPR | NC_BS_BIOPH_015_RR1.txt | {
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0 | 0 | Selective flexible packaging pathways of the segmented genome of influenza A virus |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
In the revised manuscript entitled, “Selective, flexible packaging pathways of the segmented genome
of Influenza A Virus”, the authors utilized sequential FISH staining to visualize all 8 segments within
single cells at a single timepoint (10hpi) a... |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
In the revised manuscript entitled, “Selective, flexible packaging pathways of the segmented genome
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0 | 0 | Selective flexible packaging pathways of the segmented genome of influenza A virus | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
In the manuscript entitled, “Selective, flexible packaging pathways of the segmented genome of
Influenza A Virus”, the authors utilized sequential FISH staining to visualize all eight influenza viral
segments within a single infected cell at a single timep... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
In the manuscript entitled, “Selective, flexible packaging pathways of the segmented genome of
Influenza A Virus”, the authors utilized sequential FISH staining to visualize all eight influenza viral
segments within a single infected cell at a single timep... | TPR | NC_BS_BIOTEC_001_RR1.txt | {
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"content": "Reviewers' Comments: \n \nReviewer #1: \nRemarks to the Author: \nIn the manuscript entitled, “Selective, flexible packaging pathways of the segmented genome of \nInfluenza A Virus”, the authors utilized sequential FISH staini... | 2,020 | |||
0 | 0 | BRCA1-associated structural variations are a consequence of polymerase theta-mediated |
Reviewer #1 (Remarks to the Author):
In this investigation, Kamp et al. report that C. elegans lacking the mammalian BRCA1 and BARD1
orthologs accumulate mutations similar to those seen in human brca1-deficient tumors. These
mutations include relative small (<30 bp) deletions and large (1-1000kb) tandem duplica... |
Reviewer #1 (Remarks to the Author):
In this investigation, Kamp et al. report that C. elegans lacking the mammalian BRCA1 and BARD1
orthologs accumulate mutations similar to those seen in human brca1-deficient tumors. These
mutations include relative small (<30 bp) deletions and large (1-1000kb) tandem duplica... | TPR | NC_BS_BIOTEC_002_RR1.txt | {
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"content": "\n \nReviewer #1 (Remarks to the Author): \n \nIn this investigation, Kamp et al. report that C. elegans lacking the mammalian BRCA1 and BARD1 \northologs accumulate mutations similar to those seen in human brca1-deficient tum... | 2,020 | |||
0 | 0 | Fast and multiplexed superresolution imaging with DNA-PAINT-ERS | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Civitci et al. report an effort to improve the imaging speed of DNA-PAINT by the addition of
ethylene carbonate (EC) into the imaging buffer. EC helped increase the unbinding speed of the
imaging strand from the docking strand, and with the addition of r... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Civitci et al. report an effort to improve the imaging speed of DNA-PAINT by the addition of
ethylene carbonate (EC) into the imaging buffer. EC helped increase the unbinding speed of the
imaging strand from the docking strand, and with the addition of r... | TPR | NC_BS_BIOTEC_003_RR1.txt | {
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"content": "Reviewers' comments: \n \nReviewer #1 (Remarks to the Author): \n \nCivitci et al. report an effort to improve the imaging speed of DNA-PAINT by the addition of \nethylene carbonate (EC) into the imaging buffer. EC helped incr... | 2,020 | |||
0 | 0 | Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The is a very mature and clearly written manuscript. The authors present an approach for SNP
based demultiplexing of single cell RNA-seq data to measure transcriptional effects of
perturbations. This is a very active research field and the contribution is ... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The is a very mature and clearly written manuscript. The authors present an approach for SNP
based demultiplexing of single cell RNA-seq data to measure transcriptional effects of
perturbations. This is a very active research field and the contribution is ... | TPR | NC_BS_BIOTEC_004_RR1.txt | {
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0 | 0 | Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Silivia et al. utilized isotope tracing based metabolomics to discover a syntrophic relationship
between Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp). In general, it is found that Lp
provided lactate for Ap as a precursor to synthesize... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Silivia et al. utilized isotope tracing based metabolomics to discover a syntrophic relationship
between Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp). In general, it is found that Lp
provided lactate for Ap as a precursor to synthesize... | TPR | NC_BS_BIOTEC_005_RR1.txt | {
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"content": "Reviewers' comments: \n\n \n\nReviewer #1 (Remarks to the Author): \n\n \n\nSilivia et al. utilized isotope tracing based metabolomics to discover a syntrophic relationship \nbetween Acetobacter pomorum (Ap) and Lactobacillu... | 2,020 | |||
0 | 0 | Single cell transcriptomics of human epidermis identifies basal stem cell transition states | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
In this manuscript by Wang et al. the authors utilize Single-Cell-RNA-Sequencing by 10X genomics
to explore cellular heterogeneity of human neonatal foreskin epidermis. To my knowledge this is
one of the first single-cell-RNA-seq analysis of the epidermis ... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
In this manuscript by Wang et al. the authors utilize Single-Cell-RNA-Sequencing by 10X genomics
to explore cellular heterogeneity of human neonatal foreskin epidermis. To my knowledge this is
one of the first single-cell-RNA-seq analysis of the epidermis ... | TPR | NC_BS_BIOTEC_006_RR1.txt | {
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"content": "Reviewers' Comments: \n \nReviewer #1: \nRemarks to the Author: \nIn this manuscript by Wang et al. the authors utilize Single-Cell-RNA-Sequencing by 10X genomics \nto explore cellular heterogeneity of human neonatal foreskin ... | 2,020 | |||
0 | 0 | A machine learning-based chemoproteomic approach to identify drug targets and binding |
Reviewers' Comments:
Reviewer #2:
Remarks to the Author:
In this work, Piazza and Beaton et al. improve their previous limited proteolysis approach to identify
targets of small molecules in cell lysates. Compared to previous studies, the authors used a dose-
response approach that allows the use of a more str... |
Reviewers' Comments:
Reviewer #2:
Remarks to the Author:
In this work, Piazza and Beaton et al. improve their previous limited proteolysis approach to identify
targets of small molecules in cell lysates. Compared to previous studies, the authors used a dose-
response approach that allows the use of a more str... | TPR | NC_BS_BIOTEC_008_RR1.txt | {
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"content": "\n \n\nReviewers' Comments: \n \nReviewer #2: \nRemarks to the Author: \nIn this work, Piazza and Beaton et al. improve their previous limited proteolysis approach to identify \ntargets of small molecules in cell lysates. Comp... | 2,020 | |||
0 | 0 | Widespread protein lysine acetylation in gut microbiome and its alterations in patients with |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have addressed the critiques raised.
Reviewer #2:
Remarks to the Author:
In general, the authors have done a careful and diligent job in considering and responding to the
various review comments. This included some new work to addres... |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have addressed the critiques raised.
Reviewer #2:
Remarks to the Author:
In general, the authors have done a careful and diligent job in considering and responding to the
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"content": "\n\n\fReviewers' Comments: \n \nReviewer #1: \nRemarks to the Author: \nThe authors have addressed the critiques raised. \n \n \n \nReviewer #2: \nRemarks to the Author: \nIn general, the authors have done a careful and dilige... | 2,020 | |||
0 | 0 | Widespread protein lysine acetylation in gut microbiome and its alterations in patients with | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
This paper is novel for presenting a large-scale look at human intestinal microbiome (in situ colonic
mucosal wash) protein modification (K-Ac), which is an important frontier issue in microbiome
ecology. The data is analyzed to describe microbial composit... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
This paper is novel for presenting a large-scale look at human intestinal microbiome (in situ colonic
mucosal wash) protein modification (K-Ac), which is an important frontier issue in microbiome
ecology. The data is analyzed to describe microbial composit... | TPR | NC_BS_BIOTEC_010_RR1.txt | {
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"role": "user"
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"content": "Reviewers' Comments: \n \nReviewer #1: \nRemarks to the Author: \nThis paper is novel for presenting a large-scale look at human intestinal microbiome (in situ colonic \nmucosal wash) protein modification (K-Ac), which is an i... | 2,020 | |||
0 | 0 | A scalable CRISPR/Cas9-based fluorescent reporter assay to study DNA double-strand break |
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The authors have overall addressed my queries.
|
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The authors have overall addressed my queries.
| TPR | NC_BS_BIOTEC_011_RR3.txt | {
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0 | 0 | A scalable CRISPR/Cas9-based fluorescent reporter assay to study DNA double-strand break | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The manuscript from Dr. Mardin’s group describes a colorimetric assay system (color assay tracing
repair (CAT-R)) to simultaneously monitor outcomes of DSB repair via end-protection and end-
resection pathways. This method relies on CRISPR/Cas9 to introd... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The manuscript from Dr. Mardin’s group describes a colorimetric assay system (color assay tracing
repair (CAT-R)) to simultaneously monitor outcomes of DSB repair via end-protection and end-
resection pathways. This method relies on CRISPR/Cas9 to introd... | TPR | NC_BS_BIOTEC_011_RR1.txt | {
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"role": "user"
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"content": "Reviewers' comments: \n \nReviewer #1 (Remarks to the Author): \n \nThe manuscript from Dr. Mardin’s group describes a colorimetric assay system (color assay tracing \nrepair (CAT-R)) to simultaneously monitor outcomes of DSB... | 2,020 | |||
0 | 0 | A scalable CRISPR/Cas9-based fluorescent reporter assay to study DNA double-strand break |
REVIEWER COMMENTS
Reviewer #1 (Remarks to the Author):
The authors have addressed most of my comments.
Reviewer #2 (Remarks to the Author):
The manuscript has improved significantly and the authors have addressed a significant fraction of
the queries. However, I still have the following issues. ... |
REVIEWER COMMENTS
Reviewer #1 (Remarks to the Author):
The authors have addressed most of my comments.
Reviewer #2 (Remarks to the Author):
The manuscript has improved significantly and the authors have addressed a significant fraction of
the queries. However, I still have the following issues. ... | TPR | NC_BS_BIOTEC_011_RR2.txt | {
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0 | 0 | High throughput error corrected Nanopore single cell transcriptome sequencing |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have addressed my concerns on the description of the transcript novelty. It was nice to
see that novel transcripts are detected at least by 2 cells.
However, I would strongly suggest they use SQANTI categories to describe the novelty as t... |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have addressed my concerns on the description of the transcript novelty. It was nice to
see that novel transcripts are detected at least by 2 cells.
However, I would strongly suggest they use SQANTI categories to describe the novelty as t... | TPR | NC_BS_BIOTEC_014_RR1.txt | {
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0 | 0 | Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
I have no further comments following a review of the authors’ response to reviewers’ comments
Reviewer #2 (Remarks to the Author):
1. One of my primary concerns was that all patients underwent a bowel prep which puts the sham
group at a disadvantage as... |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
I have no further comments following a review of the authors’ response to reviewers’ comments
Reviewer #2 (Remarks to the Author):
1. One of my primary concerns was that all patients underwent a bowel prep which puts the sham
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0 | 0 | ITGB3-mediated uptake of small extracellular vesicles facilitates intercellular communication | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript from the yCajal lab describes experiments aimed at determining a role for avb3
integrin in internalisation of extracellular vesicles (EVs) . The authors have found that knocking
down b3 integrin reduced the level of EV uptake by MDA-MB-23... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript from the yCajal lab describes experiments aimed at determining a role for avb3
integrin in internalisation of extracellular vesicles (EVs) . The authors have found that knocking
down b3 integrin reduced the level of EV uptake by MDA-MB-23... | TPR | NC_BS_CAN_002_RR1.txt | {
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0 | 0 | ITGB3-mediated uptake of small extracellular vesicles facilitates intercellular communication |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This revision has significantly improved the paper and I appreciate the authors taking my
suggestions on board. I feel, however, that some issues remain as the paper stands, particularly
regarding the visualisation of internalised EVs in recipient cel... |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This revision has significantly improved the paper and I appreciate the authors taking my
suggestions on board. I feel, however, that some issues remain as the paper stands, particularly
regarding the visualisation of internalised EVs in recipient cel... | TPR | NC_BS_CAN_002_RR2.txt | {
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0 | 0 | ITGB3-mediated uptake of small extracellular vesicles facilitates intercellular communication |
Reviewer #1 (Remarks to the Author):
Although I feel that this 2nd revision is an incremental improvement on the previous revision,
there are still a number of questions that remain unanswered – such as the mechanism by which
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Reviewer #1 (Remarks to the Author):
Although I feel that this 2nd revision is an incremental improvement on the previous revision,
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0 | 0 | T cell exhaustion and a failure in antigen presentation drive resistance to the graft-versus- | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Zhou et al report on graft-versus-leukemia studies in a model system that relies on T cells that
recognize the minor histocompatibility antigen H60. The authors show that Leukemia-derived H60
was inefficiently cross-presented and they use different approac... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
Zhou et al report on graft-versus-leukemia studies in a model system that relies on T cells that
recognize the minor histocompatibility antigen H60. The authors show that Leukemia-derived H60
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"role": "user"
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"content": "Reviewers' comments: \n\nReviewer #1 (Remarks to the Author): \n\nZhou et al report on graft-versus-leukemia studies in a model system that relies on T cells that \nrecognize the minor histocompatibility antigen H60. The autho... | 2,020 | |||
0 | 0 | T cell exhaustion and a failure in antigen presentation drive resistance to the graft-versus- |
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The authors answered all concerns/issues raised by the reviewer.
|
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The authors answered all concerns/issues raised by the reviewer.
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0 | 0 | A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This study explores the potential role of a rare SNP that is seen at highest frequency in African
populations and associated with a twofold prostate cancer risk as comparted to non-SNP carriers. The
authors posit that there is a functional role that enab... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This study explores the potential role of a rare SNP that is seen at highest frequency in African
populations and associated with a twofold prostate cancer risk as comparted to non-SNP carriers. The
authors posit that there is a functional role that enab... | TPR | NC_BS_CAN_004_RR1.txt | {
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"content": "Reviewers' comments: \n \nReviewer #1 (Remarks to the Author): \n \nThis study explores the potential role of a rare SNP that is seen at highest frequency in African \npopulations and associated with a twofold prostate cancer ... | 2,020 | |||
0 | 0 | A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have addressed my questions.
Reviewer #3 (Reviewer Replacement to comment on behalf of Reviewer #2, Remarks to the
Author):
The authors have provided thorough responses to the reviewer comments.
|
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have addressed my questions.
Reviewer #3 (Reviewer Replacement to comment on behalf of Reviewer #2, Remarks to the
Author):
The authors have provided thorough responses to the reviewer comments.
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0 | 0 | Engineering AvidCARs for combinatorial antigen recognition and reversible control of CAR |
9
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Thank you - the authors have addressed my comments to my satisfaction. Very nice work.
Reviewer #2:
Remarks to the Author:
All the issues and concerns are addressed properly. I have no any further questions.
|
9
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Thank you - the authors have addressed my comments to my satisfaction. Very nice work.
Reviewer #2:
Remarks to the Author:
All the issues and concerns are addressed properly. I have no any further questions.
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0 | 0 | Engineering AvidCARs for combinatorial antigen recognition and reversible control of CAR | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Salzer et al. present a new spin on the CAR platform that is based on coupling reduced-affinity
targeting domains to exogenous CAR dimerization. The authors propose this as a better system
than other published modalities for combinatorial targeting.
Ove... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Salzer et al. present a new spin on the CAR platform that is based on coupling reduced-affinity
targeting domains to exogenous CAR dimerization. The authors propose this as a better system
than other published modalities for combinatorial targeting.
Ove... | TPR | NC_BS_CAN_005_RR1.txt | {
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0 | 0 | OSMR controls glioma stem cell respiration and confers resistance of glioblastoma to | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Sharanek and colleagues describe very convincingly that the cytokine receptor for Oncostatin M
(OSMR) is localized in mitochondria of brain tumor stem cells (BTSCs) and regulates oxidative
phosphorylation and thereby confers resistance to ionizing radiatio... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Sharanek and colleagues describe very convincingly that the cytokine receptor for Oncostatin M
(OSMR) is localized in mitochondria of brain tumor stem cells (BTSCs) and regulates oxidative
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0 | 0 | OSMR controls glioma stem cell respiration and confers resistance of glioblastoma to |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
My concerns have been sufficiently expressed.
signed: Christel Herold-Mende
Reviewer #2:
Remarks to the Author:
The revised paper has been much improved showing the localization of OSMR in mitochondria of
different cellular types. However, this... |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
My concerns have been sufficiently expressed.
signed: Christel Herold-Mende
Reviewer #2:
Remarks to the Author:
The revised paper has been much improved showing the localization of OSMR in mitochondria of
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0 | 0 | Genomic characterization of malignant progression in neoplastic pancreatic cysts |
REVIEWERS' COMMENTS:
Reviewer#1:
the authors addressed all my concerns adequately.
Reviewer#2:
I appreciate the extensive comments made by the authors made on exactly delineating why this
study demonstrates novelty compared to prior data. Also the clarification on ATM is accepted.
|
REVIEWERS' COMMENTS:
Reviewer#1:
the authors addressed all my concerns adequately.
Reviewer#2:
I appreciate the extensive comments made by the authors made on exactly delineating why this
study demonstrates novelty compared to prior data. Also the clarification on ATM is accepted.
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0 | 0 | Genomic characterization of malignant progression in neoplastic pancreatic cysts | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The authors claim that their data “established that both IPMNs and MCNs are direct precursors of
invasive pancreatic cancer“. This would be the most important conclusion of this manuscript and, if
true, it is a significant observation. An important l... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
The authors claim that their data “established that both IPMNs and MCNs are direct precursors of
invasive pancreatic cancer“. This would be the most important conclusion of this manuscript and, if
true, it is a significant observation. An important l... | TPR | NC_BS_CAN_007_RR1.txt | {
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0 | 0 | Pancreatic cancers suppress negative feedback of glucose transport to reprogram chromatin | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
This study by Bechard et al builds on the authors’ previous findings that cells derived from distant metastases of pancreatic
ductal adenocarcinoma (PDAC) are specifically dependent on the oxidative pentose phosphate pathway (ox-PPP) enzyme,
phosphoglucona... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
This study by Bechard et al builds on the authors’ previous findings that cells derived from distant metastases of pancreatic
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phosphoglucona... | TPR | NC_BS_CAN_008_RR1.txt | {
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0 | 0 | Pancreatic cancers suppress negative feedback of glucose transport to reprogram chromatin |
Reviewers' Comments:
Reviewer #3:
Remarks to the Author:
The authors sufficiently addressed my concerns.
Reviewer #4:
Remarks to the Author:
The authors have answered most of the questions raised during the first course of reviewing. The manuscript has
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|
Reviewers' Comments:
Reviewer #3:
Remarks to the Author:
The authors sufficiently addressed my concerns.
Reviewer #4:
Remarks to the Author:
The authors have answered most of the questions raised during the first course of reviewing. The manuscript has
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0 | 0 | FGF2 alters macrophage polarization, tumour immunity and growth and can be targeted | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The manuscript by Buzzelli at al. focuses on understanding the contributions of host-derived
FGF2LMW to tumor growth and macrophage polarization using various tumor models. Initial
studies demonstrate a significant decrease in tumor growth following subcut... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The manuscript by Buzzelli at al. focuses on understanding the contributions of host-derived
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0 | 0 | FGF2 alters macrophage polarization, tumour immunity and growth and can be targeted |
3
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have addressed reviewer concerns.
|
3
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have addressed reviewer concerns.
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0 | 0 | FGF2 alters macrophage polarization, tumour immunity and growth and can be targeted |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Overall, the authors have incorporated many changes and the manuscript has been improved. One
concern is regarding the experiments provided in response to the suggestion to demonstrate that
FGF2 directly activates FGFR signaling in TAMs. The authors hav... |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
Overall, the authors have incorporated many changes and the manuscript has been improved. One
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0 | 0 | Reversal of pre-existing NGFR-driven tumor and immune therapy resistance | Reviewers' comments:
Reviewer #1 (Remarks to the Author); expert on mouse models for melanoma and signaling:
This paper by Boshuizen and colleagues demonstrates a convincing correlation of high
CD271/NGFR expression in melanoma cells with (MART-1) T cell resistance and resistance to other
melanoma drugs. High CD2... | Reviewers' comments:
Reviewer #1 (Remarks to the Author); expert on mouse models for melanoma and signaling:
This paper by Boshuizen and colleagues demonstrates a convincing correlation of high
CD271/NGFR expression in melanoma cells with (MART-1) T cell resistance and resistance to other
melanoma drugs. High CD2... | TPR | NC_BS_CAN_010_RR1.txt | {
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"content": "Reviewers' comments: \n\nReviewer #1 (Remarks to the Author); expert on mouse models for melanoma and signaling: \n\nThis paper by Boshuizen and colleagues demonstrates a convincing correlation of high \nCD271/NGFR expression ... | 2,020 | |||
0 | 0 | Reversal of pre-existing NGFR-driven tumor and immune therapy resistance |
REVIEWER COMMENTS
Reviewer #1 (Remarks to the Author):
In the revised version of their manuscript, Boshuizen and colleagues have incorporated an
extensive set of additional experiments, including CRISPR/Cas9-mediated NGFR KOs and ectopic
NGFR expression, which all in all considerably strengthened their s... |
REVIEWER COMMENTS
Reviewer #1 (Remarks to the Author):
In the revised version of their manuscript, Boshuizen and colleagues have incorporated an
extensive set of additional experiments, including CRISPR/Cas9-mediated NGFR KOs and ectopic
NGFR expression, which all in all considerably strengthened their s... | TPR | NC_BS_CAN_010_RR2.txt | {
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"content": "\n \n \n \n\n\fREVIEWER COMMENTS \n\nReviewer #1 (Remarks to the Author): \n\nIn the revised version of their manuscript, Boshuizen and colleagues have incorporated an \nextensive set of additional experiments, including CRISP... | 2,020 | |||
0 | 0 | Reversal of pre-existing NGFR-driven tumor and immune therapy resistance |
REVIEWERS' COMMENTS:
Reviewer #3 (Remarks to the Author):
The authors have satisfactorily answered all queries from this reviewer.
|
REVIEWERS' COMMENTS:
Reviewer #3 (Remarks to the Author):
The authors have satisfactorily answered all queries from this reviewer.
| TPR | NC_BS_CAN_010_RR3.txt | {
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0 | 0 | ABL1-dependent OTULIN phosphorylation promotes genotoxic Wnt/β-catenin activation to |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have addressed most of the major concerns raised by the reviewers. The paper is now
appropriate for publication.
Reviewer #2:
Remarks to the Author:
According to our criticisms, the authors dramatically improved the manuscript. The f... |
Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
The authors have addressed most of the major concerns raised by the reviewers. The paper is now
appropriate for publication.
Reviewer #2:
Remarks to the Author:
According to our criticisms, the authors dramatically improved the manuscript. The f... | TPR | NC_BS_CAN_011_RR2.txt | {
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"content": "\n\n\fReviewers' Comments: \n \nReviewer #1: \nRemarks to the Author: \nThe authors have addressed most of the major concerns raised by the reviewers. The paper is now \nappropriate for publication. \n \n \n \nReviewer #2: \nR... | 2,020 | |||
0 | 0 | ABL1-dependent OTULIN phosphorylation promotes genotoxic Wnt/β-catenin activation to |
Reviewers' Comments:
Reviewer #2:
Remarks to the Author:
The new data supports the important finding that Wnt reduces linear ubiquitination of β-catenin,
thereby controlling Wnt signaling. This reviewer has no further question.
|
Reviewers' Comments:
Reviewer #2:
Remarks to the Author:
The new data supports the important finding that Wnt reduces linear ubiquitination of β-catenin,
thereby controlling Wnt signaling. This reviewer has no further question.
| TPR | NC_BS_CAN_011_RR3.txt | {
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"content": "\n \n\n\fReviewers' Comments: \n \nReviewer #2: \nRemarks to the Author: \nThe new data supports the important finding that Wnt reduces linear ubiquitination of β-catenin, \nthereby controlling Wnt signaling. This reviewer has... | 2,020 | |||
0 | 0 | ABL1-dependent OTULIN phosphorylation promotes genotoxic Wnt/β-catenin activation to | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
In the manuscript submitted by Wang et al., the authors provide evidence for the DNA damage-
induced activation of Wnt/-catenin signaling through a mechanism which is independent of
canonical signaling through FZD/LRP heterodimeric receptors and Wnt ligand... | Reviewers' Comments:
Reviewer #1:
Remarks to the Author:
In the manuscript submitted by Wang et al., the authors provide evidence for the DNA damage-
induced activation of Wnt/-catenin signaling through a mechanism which is independent of
canonical signaling through FZD/LRP heterodimeric receptors and Wnt ligand... | TPR | NC_BS_CAN_011_RR1.txt | {
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"content": "Reviewers' Comments: \n \nReviewer #1: \nRemarks to the Author: \nIn the manuscript submitted by Wang et al., the authors provide evidence for the DNA damage-\ninduced activation of Wnt/-catenin signaling through a mechanism ... | 2,020 | |||
0 | 0 | The REGγ inhibitor NIP30 increases sensitivity to chemotherapy in p53-deficient tumor cells |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
This manuscript has been revised in response to my previous comments. Some responses are
satisfactory, but others, in my opinion, remain unsatisfactory. I continue to believe that
acknowledgment of earlier work (ref 32) is inadequate with respect to t... |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
This manuscript has been revised in response to my previous comments. Some responses are
satisfactory, but others, in my opinion, remain unsatisfactory. I continue to believe that
acknowledgment of earlier work (ref 32) is inadequate with respect to t... | TPR | NC_BS_CAN_012_RR3.txt | {
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"content": "\n \n\n\fREVIEWERS' COMMENTS: \n\nReviewer #1 (Remarks to the Author): \n\nThis manuscript has been revised in response to my previous comments. Some responses are \nsatisfactory, but others, in my opinion, remain unsatisfacto... | 2,020 | |||
0 | 0 | The REGγ inhibitor NIP30 increases sensitivity to chemotherapy in p53-deficient tumor cells | Reviewers' comments:
Reviewer #1 (Remarks to the Author); expert in proteasome regulation:
This is an interesting and potentially important report that describes regulation of REG gamma
function via the action of two proteins: NIP30 and CDC25. The authors present data showing that
NIP30 directly binds to REG gamm... | Reviewers' comments:
Reviewer #1 (Remarks to the Author); expert in proteasome regulation:
This is an interesting and potentially important report that describes regulation of REG gamma
function via the action of two proteins: NIP30 and CDC25. The authors present data showing that
NIP30 directly binds to REG gamm... | TPR | NC_BS_CAN_012_RR1.txt | {
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"content": "Reviewers' comments: \n\nReviewer #1 (Remarks to the Author); expert in proteasome regulation: \n\nThis is an interesting and potentially important report that describes regulation of REG gamma \nfunction via the action of two... | 2,020 | |||
0 | 0 | The REGγ inhibitor NIP30 increases sensitivity to chemotherapy in p53-deficient tumor cells |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This is a revised manuscript that examines the relative roles of CDC25, NIP30, and REGγ on
proteasome-dependent degradation of p21 and consequent cell growth. As with the previous
version of the manuscript, the results allow the authors to present a mod... |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This is a revised manuscript that examines the relative roles of CDC25, NIP30, and REGγ on
proteasome-dependent degradation of p21 and consequent cell growth. As with the previous
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"content": "\n\n\fReviewers' comments: \n\nReviewer #1 (Remarks to the Author): \n\nThis is a revised manuscript that examines the relative roles of CDC25, NIP30, and REGγ on \nproteasome-dependent degradation of p21 and consequent cell g... | 2,020 | |||
0 | 0 | MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
I have no further issues with this manuscript. I commend the authors on a job well done.
Reviewer #2 (Remarks to the Author):
my previous concerns have been adequately addressed
|
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
I have no further issues with this manuscript. I commend the authors on a job well done.
Reviewer #2 (Remarks to the Author):
my previous concerns have been adequately addressed
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0 | 0 | MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript describes a potential resistance mechanism in temozolomide-treated glioblastoma
(GBM). In a genomic profiling of recurrent GBMs, the authors identify fusions involving the DNA
repair enzyme MGMT, associated with a small percentage of tumors. They... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript describes a potential resistance mechanism in temozolomide-treated glioblastoma
(GBM). In a genomic profiling of recurrent GBMs, the authors identify fusions involving the DNA
repair enzyme MGMT, associated with a small percentage of tumors. They... | TPR | NC_BS_CAN_014_RR1.txt | {
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"content": "Reviewers' comments:\nReviewer #1 (Remarks to the Author):\nThis manuscript describes a potential resistance mechanism in temozolomide-treated glioblastoma\n(GBM). In a genomic profiling of recurrent GBMs, the authors identify... | 2,020 | |||
0 | 0 | European polygenic risk score for prediction of breast cancer shows similar performance in | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript presents a very large and fairly comprehensive analysis studying the application of
a polygenic risk score derived using data from European women to characterize risk in Asian
women. The components of the paper are well developed but the actu... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript presents a very large and fairly comprehensive analysis studying the application of
a polygenic risk score derived using data from European women to characterize risk in Asian
women. The components of the paper are well developed but the actu... | TPR | NC_BS_CAN_015_RR1.txt | {
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"content": "Reviewers' comments:\n\nReviewer #1 (Remarks to the Author):\n\nThis manuscript presents a very large and fairly comprehensive analysis studying the application of \na polygenic risk score derived using data from European wome... | 2,015 | |||
0 | 0 | European polygenic risk score for prediction of breast cancer shows similar performance in |
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The authors have addressed my comments adequately
Reviewer #3 (Remarks to the Author):
The authors have made a comprehensive response to the questions raised by the reviewers. The
addition of explanatory comments and re-editing has improved the cla... |
REVIEWERS' COMMENTS:
Reviewer #2 (Remarks to the Author):
The authors have addressed my comments adequately
Reviewer #3 (Remarks to the Author):
The authors have made a comprehensive response to the questions raised by the reviewers. The
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0 | 0 | AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript is improved over the previous version, but a few issues remain to be resolved
before the work is complete
1) The method of quantifying PLA signal seems odd (total average intensity versus number of
puncta). The method of analysis does ... |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This manuscript is improved over the previous version, but a few issues remain to be resolved
before the work is complete
1) The method of quantifying PLA signal seems odd (total average intensity versus number of
puncta). The method of analysis does ... | TPR | NC_BS_CBIO_003_RR2.txt | {
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0 | 0 | AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This is an involved study that implicates receptor tyrosine kinase organized by the enzyme AXL as
a potential mechanism to enhance metastasis and acquisition of resistance to cancer drugs. This is
a very complicated study with many parts that is compounded... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
This is an involved study that implicates receptor tyrosine kinase organized by the enzyme AXL as
a potential mechanism to enhance metastasis and acquisition of resistance to cancer drugs. This is
a very complicated study with many parts that is compounded... | TPR | NC_BS_CBIO_003_RR1.txt | {
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"content": "Reviewers' comments: \n\nReviewer #1 (Remarks to the Author): \n\nThis is an involved study that implicates receptor tyrosine kinase organized by the enzyme AXL as \na potential mechanism to enhance metastasis and acquisition ... | 2,020 | |||
0 | 0 | AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have satisfactorily addressed all of the points necessary for publication.
Reviewer #2 (Remarks to the Author):
The authors state that now on page 6 that there is minimal phosphatidylserine due to apoptotic
cells in their assay. Nonethele... |
REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have satisfactorily addressed all of the points necessary for publication.
Reviewer #2 (Remarks to the Author):
The authors state that now on page 6 that there is minimal phosphatidylserine due to apoptotic
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"content": "\n\n\fREVIEWERS' COMMENTS: \n\nReviewer #1 (Remarks to the Author): \n\nThe authors have satisfactorily addressed all of the points necessary for publication. \n\nReviewer #2 (Remarks to the Author): \n\nThe authors state that... | 2,020 | |||
0 | 0 | Micro-environmental sensing by bone marrow stroma identifies IL-6 and TGFβ1 as | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have adequately addressed the comments of all reviewers, and have considerabley
improved the manuscript.
Reviewer #2 (Remarks to the Author):
The authors have satisfactorily addressed my concerns.
Reviewer #3 (Remarks to the Author):
In... | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
The authors have adequately addressed the comments of all reviewers, and have considerabley
improved the manuscript.
Reviewer #2 (Remarks to the Author):
The authors have satisfactorily addressed my concerns.
Reviewer #3 (Remarks to the Author):
In... | TPR | NC_BS_CBIO_008_RR2.txt | {
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0 | 0 | Micro-environmental sensing by bone marrow stroma identifies IL-6 and TGFβ1 as | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
In this manuscript, Valletta et al. analyzed the stromal cells of the bone marrow to address the decline
of erythropoiesis and lymphopoiesis upon ageing. They found upregulation of IL-6 and TGFb signaling
induced gene expression in BM stromal cells of aged... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
In this manuscript, Valletta et al. analyzed the stromal cells of the bone marrow to address the decline
of erythropoiesis and lymphopoiesis upon ageing. They found upregulation of IL-6 and TGFb signaling
induced gene expression in BM stromal cells of aged... | TPR | NC_BS_CBIO_008_RR1.txt | {
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0 | 0 | E2F-dependent transcription determines replication capacity and S phase length | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
In this manuscript, Pennycook et al. intend to propose a new concept, called ‘replication capacity’,
which the authors define as the maximum amount of DNA a cell is able to synthesize per unit of
time throughout S phase. The authors argue that E2F-depend... | Reviewers' comments:
Reviewer #1 (Remarks to the Author):
In this manuscript, Pennycook et al. intend to propose a new concept, called ‘replication capacity’,
which the authors define as the maximum amount of DNA a cell is able to synthesize per unit of
time throughout S phase. The authors argue that E2F-depend... | TPR | NC_BS_CBIO_010_RR1.txt | {
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0 | 0 | E2F-dependent transcription determines replication capacity and S phase length |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
In the revised manuscript, the authors have made a good effort to answer my previous comments
On the other hand, I still believe that the differences in the length of S phase (around 10% faster
in siE2F6) are too small and such modest differences can be the res... |
Reviewers' comments:
Reviewer #1 (Remarks to the Author):
In the revised manuscript, the authors have made a good effort to answer my previous comments
On the other hand, I still believe that the differences in the length of S phase (around 10% faster
in siE2F6) are too small and such modest differences can be the res... | TPR | NC_BS_CBIO_010_RR2.txt | {
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"role": "user"
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"content": "\nReviewers' comments:\nReviewer #1 (Remarks to the Author):\nIn the revised manuscript, the authors have made a good effort to answer my previous comments\nOn the other hand, I still believe that the differences in the length... | 2,020 | |||
0 | 0 | E2F-dependent transcription determines replication capacity and S phase length | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
I am now fully satisfied with the revisions. The authors have answered all of my questions. Anja Katrin Bielinsky
Reviewer #3 (Remarks to the Author):
I am now satisfied by the newly added data and authors' responses, and rec... | REVIEWERS' COMMENTS:
Reviewer #1 (Remarks to the Author):
Reviewer #2 (Remarks to the Author):
I am now fully satisfied with the revisions. The authors have answered all of my questions. Anja Katrin Bielinsky
Reviewer #3 (Remarks to the Author):
I am now satisfied by the newly added data and authors' responses, and rec... | TPR | NC_BS_CBIO_010_RR3.txt | {
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"content": "REVIEWERS' COMMENTS:\nReviewer #1 (Remarks to the Author):\nReviewer #2 (Remarks to the Author):\nI am now fully satisfied with the revisions. The authors have answered all of my questions. Anja Katrin Bielinsky\nReviewer #3 (... | 2,020 |
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