---
DOAJ_listed: '1'
_id: '17050'
abstract:
- lang: eng
text: The process of polymer condensation, i.e., the formation of bonds between
reactive end groups, is ubiquitous in both industry and biology. Here we study
generic systems undergoing polymer condensation in competition with cyclization.
Using a generalized Smoluchowski theory, molecular dynamics simulations and experiments
with DNA and ATP-consuming T4 ligase, we find that this system displays a transition,
from a ring-dominated regime with finite-length chains at infinite time to a linear-polymers-dominated
one with chains that keep growing in time. Finally, we show that fluids prepared
close to the transition may have widely different compositions and rheology at
large condensation times.
acknowledgement: D.M. acknowledges the support of the Royal Society via a University
Research Fellowship. This project has received support from the European Research
Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program
(Grant Agreement No. 947918 to D.M. and No. 677532 to M.L.). The authors acknowledge
insightful discussions with Daan Noordermeer and Antonio Valdes, who also kindly
gifted us with the 1288 plasmid.
article_number: '023189'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Maria
full_name: Panoukidou, Maria
last_name: Panoukidou
- first_name: Simon
full_name: Weir, Simon
last_name: Weir
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Yair Gutierrez
full_name: Fosado, Yair Gutierrez
last_name: Fosado
- first_name: Martin
full_name: Lenz, Martin
last_name: Lenz
- first_name: Davide
full_name: Michieletto, Davide
last_name: Michieletto
citation:
ama: Panoukidou M, Weir S, Sorichetti V, Fosado YG, Lenz M, Michieletto D. Runaway
transition in irreversible polymer condensation with cyclization. Physical
Review Research. 2024;6(2). doi:10.1103/PhysRevResearch.6.023189
apa: Panoukidou, M., Weir, S., Sorichetti, V., Fosado, Y. G., Lenz, M., & Michieletto,
D. (2024). Runaway transition in irreversible polymer condensation with cyclization.
Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.023189
chicago: Panoukidou, Maria, Simon Weir, Valerio Sorichetti, Yair Gutierrez Fosado,
Martin Lenz, and Davide Michieletto. “Runaway Transition in Irreversible Polymer
Condensation with Cyclization.” Physical Review Research. American Physical
Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.023189.
ieee: M. Panoukidou, S. Weir, V. Sorichetti, Y. G. Fosado, M. Lenz, and D. Michieletto,
“Runaway transition in irreversible polymer condensation with cyclization,” Physical
Review Research, vol. 6, no. 2. American Physical Society, 2024.
ista: Panoukidou M, Weir S, Sorichetti V, Fosado YG, Lenz M, Michieletto D. 2024.
Runaway transition in irreversible polymer condensation with cyclization. Physical
Review Research. 6(2), 023189.
mla: Panoukidou, Maria, et al. “Runaway Transition in Irreversible Polymer Condensation
with Cyclization.” Physical Review Research, vol. 6, no. 2, 023189, American
Physical Society, 2024, doi:10.1103/PhysRevResearch.6.023189.
short: M. Panoukidou, S. Weir, V. Sorichetti, Y.G. Fosado, M. Lenz, D. Michieletto,
Physical Review Research 6 (2024).
date_created: 2024-05-26T22:00:58Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-05-14T09:32:40Z
day: '01'
ddc:
- '530'
department:
- _id: AnSa
doi: 10.1103/PhysRevResearch.6.023189
external_id:
arxiv:
- '2210.14010'
file:
- access_level: open_access
checksum: 63a962d49ef1e21a3367d265784df14b
content_type: application/pdf
creator: dernst
date_created: 2024-05-27T06:37:01Z
date_updated: 2024-05-27T06:37:01Z
file_id: '17055'
file_name: 2024_PhysicalReviewResearch_Panoukidou.pdf
file_size: 1409416
relation: main_file
success: 1
file_date_updated: 2024-05-27T06:37:01Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '2'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Runaway transition in irreversible polymer condensation with cyclization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2024'
...
---
_id: '17051'
abstract:
- lang: eng
text: "Memory-hard functions (MHF) are functions whose evaluation provably requires\r\na
lot of memory. While MHFs are an unkeyed primitive, it is natural to consider
the\r\nnotion of trapdoor MHFs (TMHFs). A TMHF is like an MHF, but when sampling\r\nthe
public parameters one also samples a trapdoor which allows evaluating the\r\nfunction
much cheaper.\r\nBiryukov and Perrin (Asiacrypt’17) were the first to consider
TMHFs and put\r\nforth a candidate TMHF construction called Diodon that is based
on the Scrypt\r\nMHF (Percival, BSDCan’09). To allow for a trapdoor, Scrypt’s
initial hash chain\r\nis replaced by a sequence of squares in a group of unknown
order where the order of\r\nthe group is the trapdoor. For a length n sequence
of squares and a group of order\r\nN, Diodon’s cumulative memory complexity (CMC)
is O(n2log N) without the\r\ntrapdoor and O(n log(n) log(N)2) with knowledge of
it.\r\nWhile Scrypt is proven to be optimally memory-hard in the random oracle\r\nmodel
(Alwen et al., Eurocrypt’17), Diodon’s memory-hardness has not been\r\nproven
so far. In this work, we fill this gap by rigorously analyzing a specific\r\ninstantiation
of Diodon. We show that its CMC is lower bounded by Ω( n2log nlog N)\r\nwhich
almost matches the upper bound. Our proof is based Alwen et al.’s lower\r\nbound
on Scrypt’s CMC but requires non-trivial modifications due to the algebraic\r\nstructure
of Diodon. Most importantly, our analysis involves a more elaborate\r\ncompression
argument and a solvability criterion for certain systems of Diophantine\r\nequations."
acknowledgement: We thank the Eurocrypt reviewers for their thorough review and for
pointing out related works. This research was funded in whole or in part by the
Austrian Science Fund (FWF) 10.55776/F85.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Benedikt
full_name: Auerbach, Benedikt
id: D33D2B18-E445-11E9-ABB7-15F4E5697425
last_name: Auerbach
orcid: 0000-0002-7553-6606
- first_name: Christoph Ullrich
full_name: Günther, Christoph Ullrich
id: ec98511c-eb8e-11eb-b029-edd25d7271a1
last_name: Günther
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Auerbach B, Günther CU, Pietrzak KZ. Trapdoor memory-hard functions. In: 43rd
Annual International Conference on the Theory and Applications of Cryptographic
Techniques. Vol 14653. Springer Nature; 2024:315-344. doi:10.1007/978-3-031-58734-4_11'
apa: 'Auerbach, B., Günther, C. U., & Pietrzak, K. Z. (2024). Trapdoor memory-hard
functions. In 43rd Annual International Conference on the Theory and Applications
of Cryptographic Techniques (Vol. 14653, pp. 315–344). Zurich, Switzerland:
Springer Nature. https://doi.org/10.1007/978-3-031-58734-4_11'
chicago: Auerbach, Benedikt, Christoph Ullrich Günther, and Krzysztof Z Pietrzak.
“Trapdoor Memory-Hard Functions.” In 43rd Annual International Conference on
the Theory and Applications of Cryptographic Techniques, 14653:315–44. Springer
Nature, 2024. https://doi.org/10.1007/978-3-031-58734-4_11.
ieee: B. Auerbach, C. U. Günther, and K. Z. Pietrzak, “Trapdoor memory-hard functions,”
in 43rd Annual International Conference on the Theory and Applications of Cryptographic
Techniques, Zurich, Switzerland, 2024, vol. 14653, pp. 315–344.
ista: 'Auerbach B, Günther CU, Pietrzak KZ. 2024. Trapdoor memory-hard functions.
43rd Annual International Conference on the Theory and Applications of Cryptographic
Techniques. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS,
vol. 14653, 315–344.'
mla: Auerbach, Benedikt, et al. “Trapdoor Memory-Hard Functions.” 43rd Annual
International Conference on the Theory and Applications of Cryptographic Techniques,
vol. 14653, Springer Nature, 2024, pp. 315–44, doi:10.1007/978-3-031-58734-4_11.
short: B. Auerbach, C.U. Günther, K.Z. Pietrzak, in:, 43rd Annual International
Conference on the Theory and Applications of Cryptographic Techniques, Springer
Nature, 2024, pp. 315–344.
conference:
end_date: 2024-05-30
location: Zurich, Switzerland
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2024-05-26
corr_author: '1'
date_created: 2024-05-26T22:00:58Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-08T07:35:40Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-031-58734-4_11
external_id:
isi:
- '001274940200011'
intvolume: ' 14653'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2024/312
month: '05'
oa: 1
oa_version: Preprint
page: 315-344
project:
- _id: 34a34d57-11ca-11ed-8bc3-a2688a8724e1
grant_number: F8509
name: Security and Privacy by Design for Complex Systems
publication: 43rd Annual International Conference on the Theory and Applications of
Cryptographic Techniques
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031587337'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Trapdoor memory-hard functions
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14653
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17052'
abstract:
- lang: eng
text: Production of thermoelectric materials from solution-processed particles involves
the synthesis of particles, their purification and densification into pelletized
material. Chemical changes that occur during each one of these steps render them
performance determining. Particularly the purification steps, bypassed in conventional
solid-state synthesis, are the cause for large discrepancies among similar solution-processed
materials. In present work, the investigation focuses on a water-based surfactant
free solution synthesis of SnSe, a highly relevant thermoelectric material. We
show and rationalize that the number of leaching steps, purification solvent,
annealing, and annealing atmosphere have significant influence on the Sn : Se
ratio and impurity content in the powder. Such compositional changes that are
undetectable by conventional characterization techniques lead to distinct consolidated
materials with different types and concentration of defects. Additionally, the
profound effect on their transport properties is demonstrated. We emphasize that
understanding the chemistry and identifying key chemical species and their role
throughout the process is paramount for optimizing material performance. Furthermore,
we aim to demonstrate the necessity of comprehensive reporting of these steps
as a standard practice to ensure material reproducibility.
acknowledged_ssus:
- _id: EM-Fac
- _id: NMR
- _id: LifeSc
acknowledgement: ISTA and the Werner Siemens Foundation financially supported this
work. The Scientific Service Units (SSU) of ISTA supported this research through
resources provided by the Electron Microscopy Facility (EMF), NMR Facility and the
Lab Support Facility (LSF). Dr. Krishnendu Maji at ISTA aided in this work through
XRD analysis of the crystal phase of SnSe. Y.L. acknowledges funding from the European
Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie
grant agreement No. 754411, the National Natural Science Foundation of China (NSFC)
(Grants No. 22209034). M.C. received funding from the European Union's Horizon 2020
research and innovation program under the Marie Skłodowska-Curie Grant Agreement
No. 665385.
article_number: e202402628
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Christine
full_name: Fiedler, Christine
id: bd3fceba-dc74-11ea-a0a7-c17f71817366
last_name: Fiedler
- first_name: Mariano
full_name: Calcabrini, Mariano
id: 45D7531A-F248-11E8-B48F-1D18A9856A87
last_name: Calcabrini
orcid: 0000-0003-4566-5877
- first_name: Yu
full_name: Liu, Yu
id: 2A70014E-F248-11E8-B48F-1D18A9856A87
last_name: Liu
orcid: 0000-0001-7313-6740
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: Fiedler C, Calcabrini M, Liu Y, Ibáñez M. Unveiling crucial chemical processing
parameters influencing the performance of solution-processed inorganic thermoelectric
materials. Angewandte Chemie - International Edition. 2024;63(25). doi:10.1002/anie.202402628
apa: Fiedler, C., Calcabrini, M., Liu, Y., & Ibáñez, M. (2024). Unveiling crucial
chemical processing parameters influencing the performance of solution-processed
inorganic thermoelectric materials. Angewandte Chemie - International Edition.
Wiley. https://doi.org/10.1002/anie.202402628
chicago: Fiedler, Christine, Mariano Calcabrini, Yu Liu, and Maria Ibáñez. “Unveiling
Crucial Chemical Processing Parameters Influencing the Performance of Solution-Processed
Inorganic Thermoelectric Materials.” Angewandte Chemie - International Edition.
Wiley, 2024. https://doi.org/10.1002/anie.202402628.
ieee: C. Fiedler, M. Calcabrini, Y. Liu, and M. Ibáñez, “Unveiling crucial chemical
processing parameters influencing the performance of solution-processed inorganic
thermoelectric materials,” Angewandte Chemie - International Edition, vol.
63, no. 25. Wiley, 2024.
ista: Fiedler C, Calcabrini M, Liu Y, Ibáñez M. 2024. Unveiling crucial chemical
processing parameters influencing the performance of solution-processed inorganic
thermoelectric materials. Angewandte Chemie - International Edition. 63(25), e202402628.
mla: Fiedler, Christine, et al. “Unveiling Crucial Chemical Processing Parameters
Influencing the Performance of Solution-Processed Inorganic Thermoelectric Materials.”
Angewandte Chemie - International Edition, vol. 63, no. 25, e202402628,
Wiley, 2024, doi:10.1002/anie.202402628.
short: C. Fiedler, M. Calcabrini, Y. Liu, M. Ibáñez, Angewandte Chemie - International
Edition 63 (2024).
corr_author: '1'
date_created: 2024-05-26T22:00:58Z
date_published: 2024-06-17T00:00:00Z
date_updated: 2025-09-08T07:36:36Z
day: '17'
ddc:
- '540'
department:
- _id: MaIb
doi: 10.1002/anie.202402628
ec_funded: 1
external_id:
isi:
- '001223768400001'
pmid:
- '38623865'
file:
- access_level: open_access
checksum: 1572a0f4d2df55751761efeb2d11c7fc
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:12:07Z
date_updated: 2025-01-09T09:12:07Z
file_id: '18797'
file_name: 2024_AngewChemieIntern_Fiedler.pdf
file_size: 16347226
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:12:07Z
has_accepted_license: '1'
intvolume: ' 63'
isi: 1
issue: '25'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Angewandte Chemie - International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unveiling crucial chemical processing parameters influencing the performance
of solution-processed inorganic thermoelectric materials
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 63
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17053'
abstract:
- lang: eng
text: We introduce a formalization of ternary simulation as abstract interpretation
along with a widening operator to speed up convergence. With the same goal, we
present a subsumption algorithm that can determine termination earlier than the
usual approach using hash sets. Additionally, we introduce a narrowing operator
that utilizes recent advances in backbone extraction, allowing to increase the
overapproximation precision in simulation at any time. The experiments evaluate
the presented techniques in the context of hardware model checking.
acknowledgement: This work is supported by the Austrian Science Fund (FWF) under the
project W1255-N23, the LIT AI Lab funded by the State of Upper Austria, the ERC-2020-AdG
101020093 and by a gift from Intel Corporation.
article_processing_charge: No
author:
- first_name: Nils
full_name: Froleyks, Nils
last_name: Froleyks
- first_name: Zhengqi
full_name: Yu, Zhengqi
id: 20aa2ae8-f2f1-11ed-bbfa-8205053f1342
last_name: Yu
orcid: 0000-0002-4993-773X
- first_name: Armin
full_name: Biere, Armin
last_name: Biere
citation:
ama: 'Froleyks N, Yu E, Biere A. Ternary simulation as abstract interpretation (Work
in Progress). In: 27th Workshop on Methods and Description Languages for Modeling
and Verification of Circuits and Systems. ; 2024:148-151.'
apa: Froleyks, N., Yu, E., & Biere, A. (2024). Ternary simulation as abstract
interpretation (Work in Progress). In 27th Workshop on Methods and Description
Languages for Modeling and Verification of Circuits and Systems (pp. 148–151).
Kaiserslautern, Germany.
chicago: Froleyks, Nils, Emily Yu, and Armin Biere. “Ternary Simulation as Abstract
Interpretation (Work in Progress).” In 27th Workshop on Methods and Description
Languages for Modeling and Verification of Circuits and Systems, 148–51, 2024.
ieee: N. Froleyks, E. Yu, and A. Biere, “Ternary simulation as abstract interpretation
(Work in Progress),” in 27th Workshop on Methods and Description Languages
for Modeling and Verification of Circuits and Systems, Kaiserslautern, Germany,
2024, pp. 148–151.
ista: 'Froleyks N, Yu E, Biere A. 2024. Ternary simulation as abstract interpretation
(Work in Progress). 27th Workshop on Methods and Description Languages for Modeling
and Verification of Circuits and Systems. MBMV: Methods and Description Languages
for Modeling and Verification of Circuits and Systems, 148–151.'
mla: Froleyks, Nils, et al. “Ternary Simulation as Abstract Interpretation (Work
in Progress).” 27th Workshop on Methods and Description Languages for Modeling
and Verification of Circuits and Systems, 2024, pp. 148–51.
short: N. Froleyks, E. Yu, A. Biere, in:, 27th Workshop on Methods and Description
Languages for Modeling and Verification of Circuits and Systems, 2024, pp. 148–151.
conference:
end_date: 2024-02-15
location: Kaiserslautern, Germany
name: 'MBMV: Methods and Description Languages for Modeling and Verification of
Circuits and Systems'
start_date: 2024-02-14
date_created: 2024-05-26T22:00:58Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2026-01-05T14:05:35Z
day: '01'
department:
- _id: ToHe
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://cca.informatik.uni-freiburg.de/papers/FroleyksYuBiere-MBMV24.pdf
month: '02'
oa: 1
oa_version: Submitted Version
page: 148-151
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 27th Workshop on Methods and Description Languages for Modeling and Verification
of Circuits and Systems
publication_identifier:
isbn:
- '9783800762682'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ternary simulation as abstract interpretation (Work in Progress)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '17054'
abstract:
- lang: eng
text: Photoisomerization and photoluminescence are two distinct energy dissipation
pathways in light-driven molecular motors. The photoisomerization properties of
discrete molecular motors have been well established in solution, but their photoluminescent
properties have been rarely reported—especially in aggregates. Here, it is shown
that an overcrowded alkene-based molecular motor exhibits distinct dynamic properties
in solution and aggregate states, for example, gel and solid states. Despite the
poor emissive properties of molecular motors in solution, a bright emission is
observed in the aggregate states, including in gel and the crystalline solid.
The emission wavelength is highly dependent on the nature of the supramolecular
packing and order in the aggregates. As a result, the fluorescent color can be
readily tuned reversibly via mechanical grinding and vapor fuming, which provides
a new platform for developing multi-stimuli functional materials.
acknowledgement: This work was supported by the National Natural Science Foundation
of China (grant nos. 22220102004, 22025503), Shanghai Municipal Science and Technology
Major Project (grant no. 2018SHZDZX03), the Innovation Program of Shanghai Municipal
Education Commission (2023ZKZD40), the Fundamental Research Funds for the Central
Universities, the Program of Introducing Talents of Discipline to Universities (grant
no. B16017), Science and Technology Commission of Shanghai Municipality (grant no.
21JC1401700), and the Starry Night Science Fund of Zhejiang University Shanghai
Institute for Advanced Study (grant no. SN-ZJU-SIAS-006), China Scholarship Council
(CSC PhD Fellowship No. 202006745016 to Yahan Shan). The authors gratefully acknowledge
financial support from the Dutch Ministry of Education, Culture and Science (gravitation
program no. 024.001.035 to Ben L. Feringa). The authors thank Dr. Youxin Fu and
Dr. Alexander Ryabchun for the help with fluorescence quantum yield measurement,
Cristina Nitu for the help with photoisomerzation quantum yield measurement, Prof.
Wesley R. Browne for the help with fluorescence lifetime measurement, and Dr. Jianyu
Zhang for fruitful discussion and revising the manuscript.
article_number: e584
article_processing_charge: Yes
article_type: original
author:
- first_name: Yahan
full_name: Shan, Yahan
last_name: Shan
- first_name: Jinyu
full_name: Sheng, Jinyu
id: 639f0526-27c9-11ee-95a6-966cd7f102d8
last_name: Sheng
- first_name: Qi
full_name: Zhang, Qi
last_name: Zhang
- first_name: Marc C.A.
full_name: Stuart, Marc C.A.
last_name: Stuart
- first_name: Da Hui
full_name: Qu, Da Hui
last_name: Qu
- first_name: Ben L.
full_name: Feringa, Ben L.
last_name: Feringa
citation:
ama: Shan Y, Sheng J, Zhang Q, Stuart MCA, Qu DH, Feringa BL. Multi-state photoluminescent
properties of an overcrowded alkene-based molecular motor in aggregates. Aggregate.
2024;5(5). doi:10.1002/agt2.584
apa: Shan, Y., Sheng, J., Zhang, Q., Stuart, M. C. A., Qu, D. H., & Feringa,
B. L. (2024). Multi-state photoluminescent properties of an overcrowded alkene-based
molecular motor in aggregates. Aggregate. Wiley. https://doi.org/10.1002/agt2.584
chicago: Shan, Yahan, Jinyu Sheng, Qi Zhang, Marc C.A. Stuart, Da Hui Qu, and Ben
L. Feringa. “Multi-State Photoluminescent Properties of an Overcrowded Alkene-Based
Molecular Motor in Aggregates.” Aggregate. Wiley, 2024. https://doi.org/10.1002/agt2.584.
ieee: Y. Shan, J. Sheng, Q. Zhang, M. C. A. Stuart, D. H. Qu, and B. L. Feringa,
“Multi-state photoluminescent properties of an overcrowded alkene-based molecular
motor in aggregates,” Aggregate, vol. 5, no. 5. Wiley, 2024.
ista: Shan Y, Sheng J, Zhang Q, Stuart MCA, Qu DH, Feringa BL. 2024. Multi-state
photoluminescent properties of an overcrowded alkene-based molecular motor in
aggregates. Aggregate. 5(5), e584.
mla: Shan, Yahan, et al. “Multi-State Photoluminescent Properties of an Overcrowded
Alkene-Based Molecular Motor in Aggregates.” Aggregate, vol. 5, no. 5,
e584, Wiley, 2024, doi:10.1002/agt2.584.
short: Y. Shan, J. Sheng, Q. Zhang, M.C.A. Stuart, D.H. Qu, B.L. Feringa, Aggregate
5 (2024).
date_created: 2024-05-26T22:00:58Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-01-09T09:41:53Z
day: '01'
ddc:
- '540'
department:
- _id: RaKl
doi: 10.1002/agt2.584
file:
- access_level: open_access
checksum: 1e79dc81d0edf0b441ef661a1890bbf5
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T09:38:51Z
date_updated: 2025-01-09T09:38:51Z
file_id: '18804'
file_name: 2024_Aggregate_Shan.pdf
file_size: 2299084
relation: main_file
success: 1
file_date_updated: 2025-01-09T09:38:51Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '5'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Aggregate
publication_identifier:
eissn:
- 2692-4560
issn:
- 2766-8541
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multi-state photoluminescent properties of an overcrowded alkene-based molecular
motor in aggregates
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
_id: '17089'
abstract:
- lang: eng
text: How the coordination of neuronal spiking and brain rhythms between hippocampal
subregions supports memory function remains elusive. We studied the interregional
coordination of CA3 neuronal spiking with CA1 theta oscillations by recording
electrophysiological signals along the proximodistal axis of the hippocampus in
rats that were performing a high-memory-demand recognition memory task adapted
from humans. We found that CA3 population spiking occurs preferentially at the
peak of distal CA1 theta oscillations when memory was tested but only when previously
encountered stimuli were presented. In addition, decoding analyses revealed that
only population cell firing of proximal CA3 together with that of distal CA1 can
predict performance at test in the present non-spatial task. Overall, our work
demonstrates an important role for the synchronization of CA3 neuronal activity
with CA1 theta oscillations during memory testing.
acknowledgement: We would like to thank J. Maiwald for her assistance in animal behavior
training, experiments, and brain slice preparation; D. Koch for her assistance in
recording drive building and brain slicing; K. Kaefer and J. Wallenschus (IST Austria)
for their initial technical support; S. Mikulovich for her comments on an early
version of the manuscript; C. Reichert for his comments on SVM analyses; and J.
Pakan for English proofreading. This project is funded by the DFG (CRC 779 and CRC
1436).
article_number: '114276'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Shih Pi
full_name: Ku, Shih Pi
last_name: Ku
- first_name: Erika
full_name: Atucha, Erika
last_name: Atucha
- first_name: Nico
full_name: Alavi, Nico
last_name: Alavi
- first_name: Halla
full_name: Mulla-Osman, Halla
last_name: Mulla-Osman
- first_name: Rukhshona
full_name: Kayumova, Rukhshona
last_name: Kayumova
- first_name: Motoharu
full_name: Yoshida, Motoharu
last_name: Yoshida
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Magdalena M.
full_name: Sauvage, Magdalena M.
last_name: Sauvage
citation:
ama: Ku SP, Atucha E, Alavi N, et al. Phase locking of hippocampal CA3 neurons to
distal CA1 theta oscillations selectively predicts memory performance. Cell
Reports. 2024;43(6). doi:10.1016/j.celrep.2024.114276
apa: Ku, S. P., Atucha, E., Alavi, N., Mulla-Osman, H., Kayumova, R., Yoshida, M.,
… Sauvage, M. M. (2024). Phase locking of hippocampal CA3 neurons to distal CA1
theta oscillations selectively predicts memory performance. Cell Reports.
Elsevier. https://doi.org/10.1016/j.celrep.2024.114276
chicago: Ku, Shih Pi, Erika Atucha, Nico Alavi, Halla Mulla-Osman, Rukhshona Kayumova,
Motoharu Yoshida, Jozsef L Csicsvari, and Magdalena M. Sauvage. “Phase Locking
of Hippocampal CA3 Neurons to Distal CA1 Theta Oscillations Selectively Predicts
Memory Performance.” Cell Reports. Elsevier, 2024. https://doi.org/10.1016/j.celrep.2024.114276.
ieee: S. P. Ku et al., “Phase locking of hippocampal CA3 neurons to distal
CA1 theta oscillations selectively predicts memory performance,” Cell Reports,
vol. 43, no. 6. Elsevier, 2024.
ista: Ku SP, Atucha E, Alavi N, Mulla-Osman H, Kayumova R, Yoshida M, Csicsvari
JL, Sauvage MM. 2024. Phase locking of hippocampal CA3 neurons to distal CA1 theta
oscillations selectively predicts memory performance. Cell Reports. 43(6), 114276.
mla: Ku, Shih Pi, et al. “Phase Locking of Hippocampal CA3 Neurons to Distal CA1
Theta Oscillations Selectively Predicts Memory Performance.” Cell Reports,
vol. 43, no. 6, 114276, Elsevier, 2024, doi:10.1016/j.celrep.2024.114276.
short: S.P. Ku, E. Atucha, N. Alavi, H. Mulla-Osman, R. Kayumova, M. Yoshida, J.L.
Csicsvari, M.M. Sauvage, Cell Reports 43 (2024).
date_created: 2024-06-02T22:00:56Z
date_published: 2024-06-25T00:00:00Z
date_updated: 2025-09-08T07:42:25Z
day: '25'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.celrep.2024.114276
external_id:
isi:
- '001252792600001'
file:
- access_level: open_access
checksum: 9b43f8ca5e5a12ae96e3fb9df06385c1
content_type: application/pdf
creator: dernst
date_created: 2024-06-03T07:12:45Z
date_updated: 2024-06-03T07:12:45Z
file_id: '17096'
file_name: 2024_CellReports_Ku.pdf
file_size: 4371015
relation: main_file
success: 1
file_date_updated: 2024-06-03T07:12:45Z
has_accepted_license: '1'
intvolume: ' 43'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase locking of hippocampal CA3 neurons to distal CA1 theta oscillations selectively
predicts memory performance
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 43
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17090'
abstract:
- lang: eng
text: Primordial neutral atomic gas, mostly composed of hydrogen, is the raw material
for star formation in galaxies. However, there are few direct constraints on the
amount of neutral atomic hydrogen (H i) in galaxies at early cosmic times. We
analyzed James Webb Space Telescope (JWST) near-infrared spectroscopy of distant
galaxies, at redshifts ≳8. From a sample of 12 galaxies, we identified three that
show strong damped Lyman-α absorption due to H i in their local surroundings.
The galaxies are located at spectroscopic redshifts of 8.8, 10.2, and 11.4, corresponding
to 400 to 600 million years after the Big Bang. They have H i column densities
≳1022 cm−2, which is an order of magnitude higher than expected for a fully neutral
intergalactic medium, and constitute a gas-rich population of young star-forming
galaxies.
acknowledgement: K.E.H. acknowledges support from Carlsberg Foundation Reintegration
Fellowship grant CF21-0103. A.H. acknowledges support from the VILLUM FONDEN under
grant 37459. C.A.M. acknowledges support from the VILLUM FONDEN under grant 37459
and the Carlsberg Foundation under grant CF22-1322. N.R.T. was funded through Science
and Technology Facilities Council (STFC) consolidated grant ST/W000857/1. R.P.N.
acknowledges funding from JWST programs GO-1933 and GO-2279. R.P.N. was supported
by the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope
Science Institute, which is operated by the Association of Universities for Research
in Astronomy under NASA contract NAS5-26555. P.A.O. received funding from the Swiss
State Secretariat for Education, Research, and Innovation (SERI) under contract
number MB22.00072 and from the Swiss National Science Foundation (SNSF) through
project grant 200020_207349.
article_processing_charge: No
article_type: original
author:
- first_name: Kasper E.
full_name: Heintz, Kasper E.
last_name: Heintz
- first_name: Darach
full_name: Watson, Darach
last_name: Watson
- first_name: Gabriel
full_name: Brammer, Gabriel
last_name: Brammer
- first_name: Simone
full_name: Vejlgaard, Simone
last_name: Vejlgaard
- first_name: Anne
full_name: Hutter, Anne
last_name: Hutter
- first_name: Victoria B.
full_name: Strait, Victoria B.
last_name: Strait
- first_name: Jorryt J
full_name: Matthee, Jorryt J
id: 7439a258-f3c0-11ec-9501-9df22fe06720
last_name: Matthee
orcid: 0000-0003-2871-127X
- first_name: Pascal A.
full_name: Oesch, Pascal A.
last_name: Oesch
- first_name: Páll
full_name: Jakobsson, Páll
last_name: Jakobsson
- first_name: Nial R.
full_name: Tanvir, Nial R.
last_name: Tanvir
- first_name: Peter
full_name: Laursen, Peter
last_name: Laursen
- first_name: Rohan P.
full_name: Naidu, Rohan P.
last_name: Naidu
- first_name: Charlotte A.
full_name: Mason, Charlotte A.
last_name: Mason
- first_name: Meghana
full_name: Killi, Meghana
last_name: Killi
- first_name: Intae
full_name: Jung, Intae
last_name: Jung
- first_name: Tiger Yu Yang
full_name: Hsiao, Tiger Yu Yang
last_name: Hsiao
- first_name: Unknown
full_name: Abdurro’Uf, Unknown
last_name: Abdurro’Uf
- first_name: Dan
full_name: Coe, Dan
last_name: Coe
- first_name: Pablo Arrabal
full_name: Haro, Pablo Arrabal
last_name: Haro
- first_name: Steven L.
full_name: Finkelstein, Steven L.
last_name: Finkelstein
- first_name: Sune
full_name: Toft, Sune
last_name: Toft
citation:
ama: Heintz KE, Watson D, Brammer G, et al. Strong damped Lyman-a absorption in
young star-forming galaxies at redshifts 9 to 11. Science. 2024;384(6698):890-894.
doi:10.1126/science.adj0343
apa: Heintz, K. E., Watson, D., Brammer, G., Vejlgaard, S., Hutter, A., Strait,
V. B., … Toft, S. (2024). Strong damped Lyman-a absorption in young star-forming
galaxies at redshifts 9 to 11. Science. AAAS. https://doi.org/10.1126/science.adj0343
chicago: Heintz, Kasper E., Darach Watson, Gabriel Brammer, Simone Vejlgaard, Anne
Hutter, Victoria B. Strait, Jorryt J Matthee, et al. “Strong Damped Lyman-a Absorption
in Young Star-Forming Galaxies at Redshifts 9 to 11.” Science. AAAS, 2024.
https://doi.org/10.1126/science.adj0343.
ieee: K. E. Heintz et al., “Strong damped Lyman-a absorption in young star-forming
galaxies at redshifts 9 to 11,” Science, vol. 384, no. 6698. AAAS, pp.
890–894, 2024.
ista: Heintz KE, Watson D, Brammer G, Vejlgaard S, Hutter A, Strait VB, Matthee
JJ, Oesch PA, Jakobsson P, Tanvir NR, Laursen P, Naidu RP, Mason CA, Killi M,
Jung I, Hsiao TYY, Abdurro’Uf U, Coe D, Haro PA, Finkelstein SL, Toft S. 2024.
Strong damped Lyman-a absorption in young star-forming galaxies at redshifts 9
to 11. Science. 384(6698), 890–894.
mla: Heintz, Kasper E., et al. “Strong Damped Lyman-a Absorption in Young Star-Forming
Galaxies at Redshifts 9 to 11.” Science, vol. 384, no. 6698, AAAS, 2024,
pp. 890–94, doi:10.1126/science.adj0343.
short: K.E. Heintz, D. Watson, G. Brammer, S. Vejlgaard, A. Hutter, V.B. Strait,
J.J. Matthee, P.A. Oesch, P. Jakobsson, N.R. Tanvir, P. Laursen, R.P. Naidu, C.A.
Mason, M. Killi, I. Jung, T.Y.Y. Hsiao, U. Abdurro’Uf, D. Coe, P.A. Haro, S.L.
Finkelstein, S. Toft, Science 384 (2024) 890–894.
date_created: 2024-06-02T22:00:56Z
date_published: 2024-05-24T00:00:00Z
date_updated: 2025-09-08T07:43:13Z
day: '24'
department:
- _id: JoMa
doi: 10.1126/science.adj0343
external_id:
isi:
- '001230029500001'
pmid:
- '38781391'
intvolume: ' 384'
isi: 1
issue: '6698'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://figshare.com/articles/journal_contribution/Strong_damped_Lyman-_absorption_in_young_star-forming_galaxies_at_redshifts_9_to_11/26069122?file=47174584
month: '05'
oa: 1
oa_version: Submitted Version
page: 890-894
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong damped Lyman-a absorption in young star-forming galaxies at redshifts
9 to 11
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 384
year: '2024'
...
---
_id: '17091'
abstract:
- lang: eng
text: DNA sequences are connected to genes and functions in the developing and adult
brain
article_processing_charge: No
article_type: letter_note
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
citation:
ama: Novarino G, Bock C. Mapping the brain’s gene-regulatory maze. Science.
2024;384(6698):860-861. doi:10.1126/science.adp4663
apa: Novarino, G., & Bock, C. (2024). Mapping the brain’s gene-regulatory maze.
Science. AAAS. https://doi.org/10.1126/science.adp4663
chicago: Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory
Maze.” Science. AAAS, 2024. https://doi.org/10.1126/science.adp4663.
ieee: G. Novarino and C. Bock, “Mapping the brain’s gene-regulatory maze,” Science,
vol. 384, no. 6698. AAAS, pp. 860–861, 2024.
ista: Novarino G, Bock C. 2024. Mapping the brain’s gene-regulatory maze. Science.
384(6698), 860–861.
mla: Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.”
Science, vol. 384, no. 6698, AAAS, 2024, pp. 860–61, doi:10.1126/science.adp4663.
short: G. Novarino, C. Bock, Science 384 (2024) 860–861.
corr_author: '1'
date_created: 2024-06-02T22:00:57Z
date_published: 2024-05-24T00:00:00Z
date_updated: 2025-09-08T07:40:10Z
day: '24'
department:
- _id: GaNo
doi: 10.1126/science.adp4663
external_id:
isi:
- '001230076500007'
pmid:
- '38781359'
intvolume: ' 384'
isi: 1
issue: '6698'
language:
- iso: eng
month: '05'
oa_version: None
page: 860-861
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mapping the brain’s gene-regulatory maze
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 384
year: '2024'
...
---
_id: '17092'
abstract:
- lang: eng
text: Memories are thought to be stored in neural ensembles known as engrams that
are specifically reactivated during memory recall. Recent studies have found that
memory engrams of two events that happened close in time tend to overlap in the
hippocampus and the amygdala, and these overlaps have been shown to support memory
linking. It has been hypothesized that engram overlaps arise from the mechanisms
that regulate memory allocation itself, involving neural excitability, but the
exact process remains unclear. Indeed, most theoretical studies focus on synaptic
plasticity and little is known about the role of intrinsic plasticity, which could
be mediated by neural excitability and serve as a complementary mechanism for
forming memory engrams. Here, we developed a rate-based recurrent neural network
that includes both synaptic plasticity and neural excitability. We obtained structural
and functional overlap of memory engrams for contexts that are presented close
in time, consistent with experimental and computational studies. We then investigated
the role of excitability in memory allocation at the network level and unveiled
competitive mechanisms driven by inhibition. This work suggests mechanisms underlying
the role of intrinsic excitability in memory allocation and linking, and yields
predictions regarding the formation and the overlap of memory engrams.
acknowledgement: We thank Sadra Sadeh and Inês Completo Guerreiro for helpful comments
on the manuscript, Yosif Zaki and Denise J. Cai for useful feedback and members
of the Clopath lab for discussion and support. This work was supported by Biotechnology
and Biological Sciences Research Council (BB/N013956/1 awarded to C.C.), Wellcome
Trust (200790/Z/16/Z awarded to C.C.), the Simons Foundation (564408 awarded to
C.C.), and Engineering and Physical Sciences Research Council (EP/R035806/1 awarded
to C.C.).
article_number: e0846232024
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Geoffroy
full_name: Delamare, Geoffroy
last_name: Delamare
- first_name: Douglas
full_name: Feitosa Tomé, Douglas
id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2
last_name: Feitosa Tomé
- first_name: Claudia
full_name: Clopath, Claudia
last_name: Clopath
citation:
ama: Delamare G, Feitosa Tomé D, Clopath C. Intrinsic neural excitability biases
allocation and overlap of memory engrams. Journal of Neuroscience. 2024;44(21).
doi:10.1523/JNEUROSCI.0846-23.2024
apa: Delamare, G., Feitosa Tomé, D., & Clopath, C. (2024). Intrinsic neural
excitability biases allocation and overlap of memory engrams. Journal of Neuroscience.
Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0846-23.2024
chicago: Delamare, Geoffroy, Douglas Feitosa Tomé, and Claudia Clopath. “Intrinsic
Neural Excitability Biases Allocation and Overlap of Memory Engrams.” Journal
of Neuroscience. Society for Neuroscience, 2024. https://doi.org/10.1523/JNEUROSCI.0846-23.2024.
ieee: G. Delamare, D. Feitosa Tomé, and C. Clopath, “Intrinsic neural excitability
biases allocation and overlap of memory engrams,” Journal of Neuroscience,
vol. 44, no. 21. Society for Neuroscience, 2024.
ista: Delamare G, Feitosa Tomé D, Clopath C. 2024. Intrinsic neural excitability
biases allocation and overlap of memory engrams. Journal of Neuroscience. 44(21),
e0846232024.
mla: Delamare, Geoffroy, et al. “Intrinsic Neural Excitability Biases Allocation
and Overlap of Memory Engrams.” Journal of Neuroscience, vol. 44, no. 21,
e0846232024, Society for Neuroscience, 2024, doi:10.1523/JNEUROSCI.0846-23.2024.
short: G. Delamare, D. Feitosa Tomé, C. Clopath, Journal of Neuroscience 44 (2024).
date_created: 2024-06-02T22:00:57Z
date_published: 2024-05-22T00:00:00Z
date_updated: 2025-09-08T07:40:58Z
day: '22'
ddc:
- '570'
department:
- _id: TiVo
doi: 10.1523/JNEUROSCI.0846-23.2024
external_id:
isi:
- '001249681000008'
pmid:
- '38561228'
file:
- access_level: open_access
checksum: 4e19159800db605b802c721e4d4b1ffe
content_type: application/pdf
creator: dernst
date_created: 2024-06-03T06:34:21Z
date_updated: 2024-06-03T06:34:21Z
file_id: '17095'
file_name: 2024_JourNeuroscience_Delamare.pdf
file_size: 920354
relation: main_file
success: 1
file_date_updated: 2024-06-03T06:34:21Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '21'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intrinsic neural excitability biases allocation and overlap of memory engrams
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 44
year: '2024'
...
---
_id: '17093'
abstract:
- lang: eng
text: 'Federated Learning (FL) enables large-scale distributed training of machine
learning models, while still allowing individual nodes to maintain data locally.
However, executing FL at scale comes with inherent practical challenges: 1) heterogeneity
of the local node data distributions, 2) heterogeneity of node computational speeds
(asynchrony), but also 3) constraints in the amount of communication between the
clients and the server. In this work, we present the first variant of the classic
federated averaging (FedAvg) algorithm which, at the same time, supports data
heterogeneity, partial client asynchrony, and communication compression. Our algorithm
comes with a novel, rigorous analysis showing that, in spite of these system relaxations,
it can provide similar convergence to FedAvg in interesting parameter regimes.
Experimental results in the rigorous LEAF benchmark on setups of up to 300 nodes
show that our algorithm ensures fast convergence for standard federated tasks,
improving upon prior quantized and asynchronous approaches.'
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Hossein
full_name: Zakerinia, Hossein
id: 653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4
last_name: Zakerinia
- first_name: Shayan
full_name: Talaei, Shayan
last_name: Talaei
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. Communication-efficient
federated learning with data and client heterogeneity. In: Proceedings of the
27th International Conference on Artificial Intelligence and Statistics. Vol
238. ML Research Press; 2024:3448-3456.'
apa: 'Zakerinia, H., Talaei, S., Nadiradze, G., & Alistarh, D.-A. (2024). Communication-efficient
federated learning with data and client heterogeneity. In Proceedings of the
27th International Conference on Artificial Intelligence and Statistics (Vol.
238, pp. 3448–3456). Valencia, Spain: ML Research Press.'
chicago: Zakerinia, Hossein, Shayan Talaei, Giorgi Nadiradze, and Dan-Adrian Alistarh.
“Communication-Efficient Federated Learning with Data and Client Heterogeneity.”
In Proceedings of the 27th International Conference on Artificial Intelligence
and Statistics, 238:3448–56. ML Research Press, 2024.
ieee: H. Zakerinia, S. Talaei, G. Nadiradze, and D.-A. Alistarh, “Communication-efficient
federated learning with data and client heterogeneity,” in Proceedings of the
27th International Conference on Artificial Intelligence and Statistics, Valencia,
Spain, 2024, vol. 238, pp. 3448–3456.
ista: 'Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. 2024. Communication-efficient
federated learning with data and client heterogeneity. Proceedings of the 27th
International Conference on Artificial Intelligence and Statistics. AISTATS: Conference
on Artificial Intelligence and Statistics, PMLR, vol. 238, 3448–3456.'
mla: Zakerinia, Hossein, et al. “Communication-Efficient Federated Learning with
Data and Client Heterogeneity.” Proceedings of the 27th International Conference
on Artificial Intelligence and Statistics, vol. 238, ML Research Press, 2024,
pp. 3448–56.
short: H. Zakerinia, S. Talaei, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of
the 27th International Conference on Artificial Intelligence and Statistics, ML
Research Press, 2024, pp. 3448–3456.
conference:
end_date: 2024-05-04
location: Valencia, Spain
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2024-05-02
corr_author: '1'
date_created: 2024-06-02T22:00:57Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2024-10-09T21:08:57Z
day: '01'
department:
- _id: DaAl
- _id: ChLa
external_id:
arxiv:
- '2206.10032'
intvolume: ' 238'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2206.10032
month: '05'
oa: 1
oa_version: Preprint
page: 3448-3456
publication: Proceedings of the 27th International Conference on Artificial Intelligence
and Statistics
publication_identifier:
eissn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Communication-efficient federated learning with data and client heterogeneity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 238
year: '2024'
...
---
_id: '17098'
abstract:
- lang: eng
text: Turn-based discounted-sum games are two-player zero-sum games played on finite
directed graphs. The vertices of the graph are partitioned between player 1 and
player 2. Plays are infinite walks on the graph where the next vertex is decided
by a player that owns the current vertex. Each edge is assigned an integer weight
and the payoff of a play is the discounted-sum of the weights of the play. The
goal of player 1 is to maximize the discounted-sum payoff against the adversarial
player 2. These games lie in NP ∩ coNP and are among the rare combinatorial problems
that belong to this complexity class and the existence of a polynomial-time algorithm
is a major open question. Since breaking the general exponential barrier has been
a challenging problem, faster parameterized algorithms have been considered. If
the discount factor is expressed in unary, then discounted-sum games can be solved
in polynomial time. However, if the discount factor is arbitrary (or expressed
in binary), but the weights are in unary, none of the existing approaches yield
a sub-exponential bound. Our main result is a new analysis technique for a classical
algorithm (namely, the strategy iteration algorithm) that present a new runtime
bound which is [EQUATION] for game graphs with n vertices and absolute weights
of at most W. In particular, our result yields a deterministic sub-exponential
bound for games with weights that are constant or represented in unary.
acknowledgement: "This research was partially supported by the ERC CoG 863818 (ForM-SMArt)
grant.\r\n"
article_number: '6'
article_processing_charge: No
arxiv: 1
author:
- first_name: Ali
full_name: Asadi, Ali
id: 02d96aae-000e-11ec-b801-cadd0a5eefbb
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
citation:
ama: 'Asadi A, Chatterjee K, Svoboda J, Saona Urmeneta RJ. Deterministic sub-exponential
algorithm for discounted-sum games with unary weights. In: 39th Annual ACM/IEEE
Symposium on Logic in Computer Science. Association for Computing Machinery;
2024. doi:10.1145/3661814.3662080'
apa: 'Asadi, A., Chatterjee, K., Svoboda, J., & Saona Urmeneta, R. J. (2024).
Deterministic sub-exponential algorithm for discounted-sum games with unary weights.
In 39th Annual ACM/IEEE Symposium on Logic in Computer Science. Tallinn,
Estonia: Association for Computing Machinery. https://doi.org/10.1145/3661814.3662080'
chicago: Asadi, Ali, Krishnendu Chatterjee, Jakub Svoboda, and Raimundo J Saona
Urmeneta. “Deterministic Sub-Exponential Algorithm for Discounted-Sum Games with
Unary Weights.” In 39th Annual ACM/IEEE Symposium on Logic in Computer Science.
Association for Computing Machinery, 2024. https://doi.org/10.1145/3661814.3662080.
ieee: A. Asadi, K. Chatterjee, J. Svoboda, and R. J. Saona Urmeneta, “Deterministic
sub-exponential algorithm for discounted-sum games with unary weights,” in 39th
Annual ACM/IEEE Symposium on Logic in Computer Science, Tallinn, Estonia,
2024.
ista: 'Asadi A, Chatterjee K, Svoboda J, Saona Urmeneta RJ. 2024. Deterministic
sub-exponential algorithm for discounted-sum games with unary weights. 39th Annual
ACM/IEEE Symposium on Logic in Computer Science. LICS: Logic in Computer Science,
6.'
mla: Asadi, Ali, et al. “Deterministic Sub-Exponential Algorithm for Discounted-Sum
Games with Unary Weights.” 39th Annual ACM/IEEE Symposium on Logic in Computer
Science, 6, Association for Computing Machinery, 2024, doi:10.1145/3661814.3662080.
short: A. Asadi, K. Chatterjee, J. Svoboda, R.J. Saona Urmeneta, in:, 39th Annual
ACM/IEEE Symposium on Logic in Computer Science, Association for Computing Machinery,
2024.
conference:
end_date: 2024-07-11
location: Tallinn, Estonia
name: 'LICS: Logic in Computer Science'
start_date: 2024-07-08
corr_author: '1'
date_created: 2024-06-03T07:43:15Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2025-09-08T07:44:29Z
day: '08'
department:
- _id: KrCh
doi: 10.1145/3661814.3662080
ec_funded: 1
external_id:
arxiv:
- '2405.02479'
isi:
- '001275042100006'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.02479
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 39th Annual ACM/IEEE Symposium on Logic in Computer Science
publication_identifier:
eissn:
- 1043-6871
isbn:
- '9798400706608'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deterministic sub-exponential algorithm for discounted-sum games with unary
weights
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '17099'
abstract:
- lang: eng
text: "We study two-player zero-sum concurrent stochastic games with finite state
and action space played for an infinite number of steps. In every step, the two
players simultaneously and independently choose an action. Given the current state
and the chosen actions, the next state is obtained according to a stochastic transition
function. An objective is a measurable function on plays (or infinite trajectories)
of the game, and the value for an objective is the maximal expectation that the
player can guarantee against the adversarial player. We consider: (a) stateful-discounted
objectives, which are similar to the classical discounted-sum objectives, but
states are associated with different discount factors rather than a single discount
factor; and (b) parity objectives, which are a canonical representation for ω-regular
objectives. For stateful-discounted objectives, given an ordering of the discount
factors, the limit value is the limit of the value of the stateful-discounted
objectives, as the discount factors approach zero according to the given order.\r\nThe
computational problem we consider is the approximation of the value within an
arbitrary\r\nadditive error. The above problem is known to be in EXPSPACE for
the limit value of statefuldiscounted objectives and in PSPACE for parity objectives.
The best-known algorithms for both the above problems are at least exponential
time, with an exponential dependence on the number of states and actions. Our
main results for the value approximation problem for the limit value of stateful-discounted
objectives and parity objectives are as follows: (a) we establish TFNP[NP] complexity;
and (b) we present algorithms that improve the dependency on the number of actions
in the exponent from linear to logarithmic. In particular, if the number of states
is constant, our algorithms run in polynomial time."
acknowledgement: "This research was partially supported by ERC CoG 863818 (ForM-SMArt),
Austrian\r\nScience Fund (FWF) 10.55776/COE12, and French Agence Nationale de la
Recherche (ANR)\r\nANR-21-CE40-0020 (CONVERGENCE project)"
alternative_title:
- LIPIcs
article_number: '5'
article_processing_charge: No
arxiv: 1
author:
- first_name: Ali
full_name: Asadi, Ali
id: 02d96aae-000e-11ec-b801-cadd0a5eefbb
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
citation:
ama: 'Asadi A, Chatterjee K, Saona Urmeneta RJ, Svoboda J. Concurrent stochastic
games with stateful-discounted and parity objectives: Complexity and algorithms.
In: 44th IARCS Annual Conference on Foundations of Software Technology and
Theoretical Computer Science. Vol 323. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2024. doi:10.4230/LIPIcs.FSTTCS.2024.5'
apa: 'Asadi, A., Chatterjee, K., Saona Urmeneta, R. J., & Svoboda, J. (2024).
Concurrent stochastic games with stateful-discounted and parity objectives: Complexity
and algorithms. In 44th IARCS Annual Conference on Foundations of Software
Technology and Theoretical Computer Science (Vol. 323). Gujarat, India: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5'
chicago: 'Asadi, Ali, Krishnendu Chatterjee, Raimundo J Saona Urmeneta, and Jakub
Svoboda. “Concurrent Stochastic Games with Stateful-Discounted and Parity Objectives:
Complexity and Algorithms.” In 44th IARCS Annual Conference on Foundations
of Software Technology and Theoretical Computer Science, Vol. 323. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5.'
ieee: 'A. Asadi, K. Chatterjee, R. J. Saona Urmeneta, and J. Svoboda, “Concurrent
stochastic games with stateful-discounted and parity objectives: Complexity and
algorithms,” in 44th IARCS Annual Conference on Foundations of Software Technology
and Theoretical Computer Science, Gujarat, India, 2024, vol. 323.'
ista: 'Asadi A, Chatterjee K, Saona Urmeneta RJ, Svoboda J. 2024. Concurrent stochastic
games with stateful-discounted and parity objectives: Complexity and algorithms.
44th IARCS Annual Conference on Foundations of Software Technology and Theoretical
Computer Science. FSTTCS: Foundations of Software Technology and Theoretical Computer
Science, LIPIcs, vol. 323, 5.'
mla: 'Asadi, Ali, et al. “Concurrent Stochastic Games with Stateful-Discounted and
Parity Objectives: Complexity and Algorithms.” 44th IARCS Annual Conference
on Foundations of Software Technology and Theoretical Computer Science, vol.
323, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.FSTTCS.2024.5.'
short: A. Asadi, K. Chatterjee, R.J. Saona Urmeneta, J. Svoboda, in:, 44th IARCS
Annual Conference on Foundations of Software Technology and Theoretical Computer
Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.
conference:
end_date: 2024-12-18
location: Gujarat, India
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
start_date: 2024-12-16
corr_author: '1'
date_created: 2024-06-03T07:44:27Z
date_published: 2024-12-05T00:00:00Z
date_updated: 2025-12-02T13:40:52Z
day: '05'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.FSTTCS.2024.5
ec_funded: 1
external_id:
arxiv:
- '2405.02486'
isi:
- '001537516500005'
file:
- access_level: open_access
checksum: 5b544ab4692b93300b404435c036ddd4
content_type: application/pdf
creator: dernst
date_created: 2025-01-08T09:49:31Z
date_updated: 2025-01-08T09:49:31Z
file_id: '18777'
file_name: 2024_LIPIcs_Asadi.pdf
file_size: 847960
relation: main_file
success: 1
file_date_updated: 2025-01-08T09:49:31Z
has_accepted_license: '1'
intvolume: ' 323'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: 44th IARCS Annual Conference on Foundations of Software Technology and
Theoretical Computer Science
publication_identifier:
isbn:
- '9783959773553'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Concurrent stochastic games with stateful-discounted and parity objectives:
Complexity and algorithms'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 323
year: '2024'
...
---
_id: '17101'
abstract:
- lang: eng
text: "This paper considers a class of two-player zero-sum games on directed graphs
whose vertices are equipped with random payoffs of bounded support known by both
players.\r\nStarting from a fixed vertex, players take turns to move a token along
the edges of the graph.\r\nOn the one hand, for acyclic directed graphs of bounded
degree and sub-exponential expansion, we show that the value of the game converges
almost surely to a constant at an exponential rate dominated in terms of the expansion.\r\nOn
the other hand, for the infinite d-ary tree that does not fall into the previous
class of graphs, we show convergence at a double-exponential rate in terms of
the expansion."
acknowledgement: "This work was supported by the French Agence Nationale de la Recherche
(ANR) under references ANR-21-CE40-0020 (CONVERGENCE project) and ANR-20-CE40-0002
(GrHyDy), and by Fondecyt grant 1220174. This collaboration was mainly conducted
during a 1-year visit of Bruno Ziliotto to the Center for Mathematical Modeling
(CMM) at University of Chile in 2023,\r\nunder the IRL program of CNRS."
article_number: '2401.16252'
article_processing_charge: No
arxiv: 1
author:
- first_name: Luc
full_name: Attia, Luc
last_name: Attia
- first_name: Lyuben
full_name: Lichev, Lyuben
last_name: Lichev
- first_name: Dieter
full_name: Mitsche, Dieter
last_name: Mitsche
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Bruno
full_name: Ziliotto, Bruno
last_name: Ziliotto
citation:
ama: Attia L, Lichev L, Mitsche D, Saona Urmeneta RJ, Ziliotto B. Zero-sum random
games on directed graphs. arXiv. doi:10.48550/arXiv.2401.16252
apa: Attia, L., Lichev, L., Mitsche, D., Saona Urmeneta, R. J., & Ziliotto,
B. (n.d.). Zero-sum random games on directed graphs. arXiv. https://doi.org/10.48550/arXiv.2401.16252
chicago: Attia, Luc, Lyuben Lichev, Dieter Mitsche, Raimundo J Saona Urmeneta, and
Bruno Ziliotto. “Zero-Sum Random Games on Directed Graphs.” ArXiv, n.d.
https://doi.org/10.48550/arXiv.2401.16252.
ieee: L. Attia, L. Lichev, D. Mitsche, R. J. Saona Urmeneta, and B. Ziliotto, “Zero-sum
random games on directed graphs,” arXiv. .
ista: Attia L, Lichev L, Mitsche D, Saona Urmeneta RJ, Ziliotto B. Zero-sum random
games on directed graphs. arXiv, 2401.16252.
mla: Attia, Luc, et al. “Zero-Sum Random Games on Directed Graphs.” ArXiv,
2401.16252, doi:10.48550/arXiv.2401.16252.
short: L. Attia, L. Lichev, D. Mitsche, R.J. Saona Urmeneta, B. Ziliotto, ArXiv
(n.d.).
date_created: 2024-06-03T07:45:22Z
date_published: 2024-01-29T00:00:00Z
date_updated: 2024-06-03T07:50:29Z
day: '29'
department:
- _id: KrCh
doi: 10.48550/arXiv.2401.16252
external_id:
arxiv:
- '2401.16252'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2401.16252
month: '01'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Zero-sum random games on directed graphs
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
DOAJ_listed: '1'
_id: '17103'
abstract:
- lang: eng
text: Phytoalexin sakuranetin functions in resistance against rice blast. However,
the mechanisms underlying the effects of sakuranetin remains elusive. Here, we
report that rice lines expressing resistance (R) genes were found to contain high
levels of sakuranetin, which correlates with attenuated endocytic trafficking
of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates
the endocytosis of various PM proteins and the fungal effector PWL2. Moreover,
accumulation of the avirulence protein AvrCO39, resulting from uptake into rice
cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin.
Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that
this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin
is sufficient to convey resistance against rice blast. Our data reveals a mechanism
of rice against M. oryzae by increasing sakuranetin levels and repressing the
CME of pathogen effectors, which is distinct from the action of many R genes that
mainly function by modulating transcription.
acknowledgement: We thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese
Academy of Sciences) for his generous support with the sakuranetin measurement.
We thank International Rice Research Institute (IRRI) for provision of the rice
NILs. We thank Professor Zhongkai Zhang (Yunnan Academy of Agricultural Sciences)
for his generous support with subcellular structure observation of rice roots. We
thank Professor Barbara Valent (Kansas State University) for her generously provision
of the plasmid containing the PWL2 gene. We thank Professor Zuhua He (Chinese Academy
of Sciences) for the gift of the transgenic rice line expressing the Pigm gene,
OsNPR1-RNAi mutant line and ROD1-overexpression rice line. We thank Professor Yinong
Yang (The Pennsylvania State University) for provision of the rice line NahG. We
thank Professor Muyuan Zhu (Zhejiang University) for provision of the transgenic
plants overexpressing miR393a. We thank Professor Zhengge Zhu (Hebei Normal University)
for provision of the rice line overexpressing OsPIN3t-GFP. We thank Professor Yanhua
Qi (Zhejiang University) for provision of the arf12 mutant line. Thanks also go
to Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision
of the fungus M. oryzae strain Guy11 (AvrCo39-mRFP). This work was supported by
grants from the National Natural Science Foundation of China (Grant Nos. 32260085,
31460453, 31660501, 31860064, 31760500 and 31901870), the Major Special Program
for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005).
The project was also sponsored by SRF for ROCS, SEM (Grant No. [2013] 1792), the
Key Projects of Applied Basic Research Plan of Yunnan Province (Grant No. 2017FA018,
202301AS070082), the Major Science and Technology Project in Yunnan Province (202102AE090042,
202202AE090036 and 202102AE090017), the Young and Middle-Aged Academic and Technical
Leaders Reserve Talent Program in Yunnan Province (202205AC160076), the China Postdoctoral
Science Foundation (2019M653849XB) and the National Key Research and Development
Program of China (2023YFE0107500).
article_number: '3437'
article_processing_charge: Yes
article_type: original
author:
- first_name: Lihui
full_name: Jiang, Lihui
last_name: Jiang
- first_name: Xiaoyan
full_name: Zhang, Xiaoyan
last_name: Zhang
- first_name: Yiting
full_name: Zhao, Yiting
last_name: Zhao
- first_name: Haiyan
full_name: Zhu, Haiyan
last_name: Zhu
- first_name: Qijing
full_name: Fu, Qijing
last_name: Fu
- first_name: Xinqi
full_name: Lu, Xinqi
last_name: Lu
- first_name: Wuying
full_name: Huang, Wuying
last_name: Huang
- first_name: Xinyue
full_name: Yang, Xinyue
last_name: Yang
- first_name: Xuan
full_name: Zhou, Xuan
last_name: Zhou
- first_name: Lixia
full_name: Wu, Lixia
last_name: Wu
- first_name: Ao
full_name: Yang, Ao
last_name: Yang
- first_name: Xie
full_name: He, Xie
last_name: He
- first_name: Man
full_name: Dong, Man
last_name: Dong
- first_name: Ziai
full_name: Peng, Ziai
last_name: Peng
- first_name: Jing
full_name: Yang, Jing
last_name: Yang
- first_name: Liwei
full_name: Guo, Liwei
last_name: Guo
- first_name: Jiancheng
full_name: Wen, Jiancheng
last_name: Wen
- first_name: Huichuan
full_name: Huang, Huichuan
last_name: Huang
- first_name: Yong
full_name: Xie, Yong
last_name: Xie
- first_name: Shusheng
full_name: Zhu, Shusheng
last_name: Zhu
- first_name: Chengyun
full_name: Li, Chengyun
last_name: Li
- first_name: Xiahong
full_name: He, Xiahong
last_name: He
- first_name: Youyong
full_name: Zhu, Youyong
last_name: Zhu
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Yunlong
full_name: Du, Yunlong
last_name: Du
citation:
ama: Jiang L, Zhang X, Zhao Y, et al. Phytoalexin sakuranetin attenuates endocytosis
and enhances resistance to rice blast. Nature Communications. 2024;15.
doi:10.1038/s41467-024-47746-y
apa: Jiang, L., Zhang, X., Zhao, Y., Zhu, H., Fu, Q., Lu, X., … Du, Y. (2024). Phytoalexin
sakuranetin attenuates endocytosis and enhances resistance to rice blast. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-024-47746-y
chicago: Jiang, Lihui, Xiaoyan Zhang, Yiting Zhao, Haiyan Zhu, Qijing Fu, Xinqi
Lu, Wuying Huang, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances
Resistance to Rice Blast.” Nature Communications. Springer Nature, 2024.
https://doi.org/10.1038/s41467-024-47746-y.
ieee: L. Jiang et al., “Phytoalexin sakuranetin attenuates endocytosis and
enhances resistance to rice blast,” Nature Communications, vol. 15. Springer
Nature, 2024.
ista: Jiang L, Zhang X, Zhao Y, Zhu H, Fu Q, Lu X, Huang W, Yang X, Zhou X, Wu L,
Yang A, He X, Dong M, Peng Z, Yang J, Guo L, Wen J, Huang H, Xie Y, Zhu S, Li
C, He X, Zhu Y, Friml J, Du Y. 2024. Phytoalexin sakuranetin attenuates endocytosis
and enhances resistance to rice blast. Nature Communications. 15, 3437.
mla: Jiang, Lihui, et al. “Phytoalexin Sakuranetin Attenuates Endocytosis and Enhances
Resistance to Rice Blast.” Nature Communications, vol. 15, 3437, Springer
Nature, 2024, doi:10.1038/s41467-024-47746-y.
short: L. Jiang, X. Zhang, Y. Zhao, H. Zhu, Q. Fu, X. Lu, W. Huang, X. Yang, X.
Zhou, L. Wu, A. Yang, X. He, M. Dong, Z. Peng, J. Yang, L. Guo, J. Wen, H. Huang,
Y. Xie, S. Zhu, C. Li, X. He, Y. Zhu, J. Friml, Y. Du, Nature Communications 15
(2024).
date_created: 2024-06-03T08:54:50Z
date_published: 2024-04-23T00:00:00Z
date_updated: 2025-09-08T07:46:24Z
day: '23'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1038/s41467-024-47746-y
external_id:
isi:
- '001207290500013'
pmid:
- '38653755'
file:
- access_level: open_access
checksum: 80cb2f2c538e81064f4836b54bc313ca
content_type: application/pdf
creator: dernst
date_created: 2024-06-03T12:05:10Z
date_updated: 2024-06-03T12:05:10Z
file_id: '17110'
file_name: 2024_NatureComm_Jiang.pdf
file_size: 8013695
relation: main_file
success: 1
file_date_updated: 2024-06-03T12:05:10Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice
blast
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 15
year: '2024'
...
---
_id: '17104'
abstract:
- lang: eng
text: 'The homeostasis of epithelial tissue relies on a balance between the self-renewal
of stem cell populations, cellular differentiation, and loss. Although this balance
needs to be tightly regulated to avoid pathologies, such as tumor growth, the
regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue
steady-state are still poorly understood. Here, we develop a computational model
that incorporates basic assumptions of stem cell renewal into distinct populations
and mechanical interactions between cells. We find that the model generates unexpected
dynamic features: stem cells repel each other in the bulk tissue and are thus
found rather isolated, as in a number of in vivo contexts. By mapping the system
onto a gas of passive Brownian particles with effective repulsive interactions,
that arise from the generated flows of differentiated cells, we show that we can
quantitatively describe such stem cell distribution in tissues. The interaction
potential between a pair of stem cells decays exponentially with a characteristic
length that spans several cell sizes, corresponding to the volume of cells generated
per stem cell division. Our findings may help understanding the dynamics of normal
and cancerous epithelial tissues.'
acknowledgement: JE and JK gratefully acknowledge financial support from the Initiative
and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed
with computing resources granted by RWTH Aachen University under project ‘rwth0475’.
article_number: '097'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Johannes C.
full_name: Krämer, Johannes C.
last_name: Krämer
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Gerhard
full_name: Gompper, Gerhard
last_name: Gompper
- first_name: Jens
full_name: Elgeti, Jens
last_name: Elgeti
citation:
ama: Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation
in tissues caused by proliferating daughter cells. SciPost Physics. 2024;16(4).
doi:10.21468/scipostphys.16.4.097
apa: Krämer, J. C., Hannezo, E. B., Gompper, G., & Elgeti, J. (2024). Mechanically-driven
stem cell separation in tissues caused by proliferating daughter cells. SciPost
Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.16.4.097
chicago: Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti.
“Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter
Cells.” SciPost Physics. SciPost Foundation, 2024. https://doi.org/10.21468/scipostphys.16.4.097.
ieee: J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven
stem cell separation in tissues caused by proliferating daughter cells,” SciPost
Physics, vol. 16, no. 4. SciPost Foundation, 2024.
ista: Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem
cell separation in tissues caused by proliferating daughter cells. SciPost Physics.
16(4), 097.
mla: Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues
Caused by Proliferating Daughter Cells.” SciPost Physics, vol. 16, no.
4, 097, SciPost Foundation, 2024, doi:10.21468/scipostphys.16.4.097.
short: J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024).
date_created: 2024-06-03T08:58:44Z
date_published: 2024-04-08T00:00:00Z
date_updated: 2025-09-08T07:45:40Z
day: '08'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.21468/scipostphys.16.4.097
external_id:
arxiv:
- '2310.04272'
isi:
- '001202370200001'
file:
- access_level: open_access
checksum: 6fdeecd21c166db8dedb927ecc2e6025
content_type: application/pdf
creator: dernst
date_created: 2024-06-03T11:18:51Z
date_updated: 2024-06-03T11:18:51Z
file_id: '17109'
file_name: 2024_SciPostPhys_Kraemer.pdf
file_size: 4973291
relation: main_file
success: 1
file_date_updated: 2024-06-03T11:18:51Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: SciPost Physics
publication_identifier:
issn:
- 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanically-driven stem cell separation in tissues caused by proliferating
daughter cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2024'
...
---
_id: '17105'
abstract:
- lang: eng
text: The development of photoresponsive systems with non-invasive orthogonal control
by distinct wavelengths of light is still in its infancy. In particular, the design
of photochemically triggered-orthogonal systems integrated into solid materials
that enable multiple dynamic control over their properties remains a longstanding
challenge. Here, we report the orthogonal and reversible control of two types
of photoswitches in an integrated solid porous framework, that is, visible-light
responsive o-fluoroazobenzene and nitro-spiropyran motifs. The properties of the
constructed material can be selectively controlled by different wavelengths of
light thus generating four distinct states providing a basis for dynamic multifunctional
materials. Solid-state NMR spectroscopy demonstrated the selective transformation
of the azobenzene switch in the bulk, which in turn modulates N2 and CO2 adsorption.
acknowledgement: 'This work was supported from the following sources: China Scholarship
Council (CSC PhD Fellowship No. 201808330459 to J.S.), the Ministry of Education,
Culture and Science of the Netherlands (Gravitation Program No. 024.001.035 to BLF),
Financial support from The Netherlands Organization for Scientific Research (NWO-CW),
the European Research Council (ERC; advanced Grant No. 694345 to B.L.F.). PRIN (SHERPA
2020 No. H45F21003430001) and PRIN (HySTAR 2022 No. H53D23004720006) and Lombardy
Region for “Enhancing Photosynthesis” grant (2021-2023 No. H45F21002830007). W.D.
is grateful for financial support from Marie Skłodowska-Curie Actions (Individual
Fellowship No. 101027639). P.C. is grateful for the financial support provided by
the PRELUDIUM grant from the National Science Center Poland (Reg. No: 2023/49/N/ST5/01864).'
article_number: e202404878
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jinyu
full_name: Sheng, Jinyu
id: 639f0526-27c9-11ee-95a6-966cd7f102d8
last_name: Sheng
- first_name: Jacopo
full_name: Perego, Jacopo
last_name: Perego
- first_name: Silvia
full_name: Bracco, Silvia
last_name: Bracco
- first_name: Piotr
full_name: Cieciórski, Piotr
last_name: Cieciórski
- first_name: Wojciech
full_name: Danowski, Wojciech
last_name: Danowski
- first_name: Angiolina
full_name: Comotti, Angiolina
last_name: Comotti
- first_name: Ben L.
full_name: Feringa, Ben L.
last_name: Feringa
citation:
ama: Sheng J, Perego J, Bracco S, et al. Orthogonal photoswitching in a porous organic
framework. Angewandte Chemie International Edition. 2024;63(23). doi:10.1002/anie.202404878
apa: Sheng, J., Perego, J., Bracco, S., Cieciórski, P., Danowski, W., Comotti, A.,
& Feringa, B. L. (2024). Orthogonal photoswitching in a porous organic framework.
Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202404878
chicago: Sheng, Jinyu, Jacopo Perego, Silvia Bracco, Piotr Cieciórski, Wojciech
Danowski, Angiolina Comotti, and Ben L. Feringa. “Orthogonal Photoswitching in
a Porous Organic Framework.” Angewandte Chemie International Edition. Wiley,
2024. https://doi.org/10.1002/anie.202404878.
ieee: J. Sheng et al., “Orthogonal photoswitching in a porous organic framework,”
Angewandte Chemie International Edition, vol. 63, no. 23. Wiley, 2024.
ista: Sheng J, Perego J, Bracco S, Cieciórski P, Danowski W, Comotti A, Feringa
BL. 2024. Orthogonal photoswitching in a porous organic framework. Angewandte
Chemie International Edition. 63(23), e202404878.
mla: Sheng, Jinyu, et al. “Orthogonal Photoswitching in a Porous Organic Framework.”
Angewandte Chemie International Edition, vol. 63, no. 23, e202404878, Wiley,
2024, doi:10.1002/anie.202404878.
short: J. Sheng, J. Perego, S. Bracco, P. Cieciórski, W. Danowski, A. Comotti, B.L.
Feringa, Angewandte Chemie International Edition 63 (2024).
date_created: 2024-06-03T09:00:01Z
date_published: 2024-03-26T00:00:00Z
date_updated: 2025-04-23T07:48:28Z
day: '26'
ddc:
- '540'
department:
- _id: RaKl
doi: 10.1002/anie.202404878
external_id:
pmid:
- '38530132'
file:
- access_level: open_access
checksum: 7ecb0892051f6ed8f6a6f25baa47543a
content_type: application/pdf
creator: dernst
date_created: 2024-06-03T10:33:17Z
date_updated: 2024-06-03T10:33:17Z
file_id: '17107'
file_name: 2024_AngChemieInt_Sheng.pdf
file_size: 2363206
relation: main_file
success: 1
file_date_updated: 2024-06-03T10:33:17Z
has_accepted_license: '1'
intvolume: ' 63'
issue: '23'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Angewandte Chemie International Edition
publication_identifier:
eissn:
- 1521-3773
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Orthogonal photoswitching in a porous organic framework
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2024'
...
---
_id: '17111'
abstract:
- lang: eng
text: Membrane-associated protein phase separation plays critical roles in cell
biology, driving essential cellular phenomena from immune signaling to membrane
traffic. Importantly, by reducing dimensionality from three to two dimensions,
lipid bilayers can nucleate phase separation at far lower concentrations compared
with those required for phase separation in solution. How might other intracellular
lipid substrates, such as lipid droplets, contribute to nucleation of phase separation?
Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer
surrounding a core of neutral lipids, and they are energy storage organelles that
protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically
disordered proteins can undergo phase separation on the surface of synthetic and
cell-derived lipid droplets. Specifically, we find that the model disordered domains
FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on
the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions
between FUS LC proteins, increasing ionic strength drives an increase in its phase
separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the
electrostatic nature of its interprotein interactions. In both cases, protein-rich
phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate
molecular mobility indicative of a liquid-like state. Our results show that lipid
droplets can nucleate protein condensates, suggesting that protein phase separation
could be key in organizing biological processes involving lipid droplets.
article_processing_charge: No
article_type: original
author:
- first_name: Advika
full_name: Kamatar, Advika
last_name: Kamatar
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Feng
full_name: Yuan, Feng
last_name: Yuan
- first_name: Liping
full_name: Wang, Liping
last_name: Wang
- first_name: Eileen M.
full_name: Lafer, Eileen M.
last_name: Lafer
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
- first_name: Jeanne C.
full_name: Stachowiak, Jeanne C.
last_name: Stachowiak
- first_name: Sapun H.
full_name: Parekh, Sapun H.
last_name: Parekh
citation:
ama: Kamatar A, Bravo JPK, Yuan F, et al. Lipid droplets as substrates for protein
phase separation. Biophysical Journal. 2024;123(11):1494-1507. doi:10.1016/j.bpj.2024.03.015
apa: Kamatar, A., Bravo, J. P. K., Yuan, F., Wang, L., Lafer, E. M., Taylor, D.
W., … Parekh, S. H. (2024). Lipid droplets as substrates for protein phase separation.
Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2024.03.015
chicago: Kamatar, Advika, Jack Peter Kelly Bravo, Feng Yuan, Liping Wang, Eileen
M. Lafer, David W. Taylor, Jeanne C. Stachowiak, and Sapun H. Parekh. “Lipid Droplets
as Substrates for Protein Phase Separation.” Biophysical Journal. Elsevier,
2024. https://doi.org/10.1016/j.bpj.2024.03.015.
ieee: A. Kamatar et al., “Lipid droplets as substrates for protein phase
separation,” Biophysical Journal, vol. 123, no. 11. Elsevier, pp. 1494–1507,
2024.
ista: Kamatar A, Bravo JPK, Yuan F, Wang L, Lafer EM, Taylor DW, Stachowiak JC,
Parekh SH. 2024. Lipid droplets as substrates for protein phase separation. Biophysical
Journal. 123(11), 1494–1507.
mla: Kamatar, Advika, et al. “Lipid Droplets as Substrates for Protein Phase Separation.”
Biophysical Journal, vol. 123, no. 11, Elsevier, 2024, pp. 1494–507, doi:10.1016/j.bpj.2024.03.015.
short: A. Kamatar, J.P.K. Bravo, F. Yuan, L. Wang, E.M. Lafer, D.W. Taylor, J.C.
Stachowiak, S.H. Parekh, Biophysical Journal 123 (2024) 1494–1507.
date_created: 2024-06-04T06:41:03Z
date_published: 2024-06-04T00:00:00Z
date_updated: 2025-01-13T11:03:41Z
day: '04'
doi: 10.1016/j.bpj.2024.03.015
extern: '1'
external_id:
pmid:
- '38462838'
intvolume: ' 123'
issue: '11'
language:
- iso: eng
month: '06'
oa_version: None
page: 1494-1507
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lipid droplets as substrates for protein phase separation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 123
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17112'
abstract:
- lang: eng
text: The generation of cyclic oligoadenylates and subsequent allosteric activation
of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas
systems. In this work, we characterize a set of associated genes of a type III-B
system from Haliangium ochraceum that contains two caspase-like proteases, SAVED-CHAT
and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide–based
antiphage signaling system (CBASS). Cyclic tri–adenosine monophosphate (AMP)–induced
oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains,
which specifically cleave and activate PCaspase. Subsequently, activated PCaspase
cleaves a multitude of proteins, which results in a strong interference phenotype
in vivo in Escherichia coli. Taken together, our findings reveal how a CRISPR-Cas–based
detection of a target RNA triggers a cascade of caspase-associated proteolytic
activities.
acknowledgement: We thank R. Fregoso Ocampo for assistance with negative-stain EM
imaging. This work was funded by Dutch Research Council (NWO) VIDI grant VI.Vidi.203.074
(R.H.J.S.), NWO Spinoza grant SPI 93-537 (J.v.d.O.), European Research Council (ERC)
Advanced grant ERC-AdG-834279 (J.v.d.O.), ERC CoG grant 817834 (T.J.G.E.), NWO VICI
grant VI.C.192.016 (T.J.G.E.), Volkswagen Foundation grant 96725 (T.J.G.E.), National
Institute of General Medical Sciences of the National Institutes of Health grant
R35GM138348 (D.W.T.), Welch Foundation research grant F-1938 (D.W.T.), a Robert
J. Kleberg, Jr. And Helen C. Kleberg Foundation medical research grant (D.W.T.),
and American Cancer Society Research Scholar grant RSG-21-050-01-DMC (D.W.T.).
article_processing_charge: No
article_type: original
author:
- first_name: Jurre A.
full_name: Steens, Jurre A.
last_name: Steens
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Carl Raymund P.
full_name: Salazar, Carl Raymund P.
last_name: Salazar
- first_name: Caglar
full_name: Yildiz, Caglar
last_name: Yildiz
- first_name: Afonso M.
full_name: Amieiro, Afonso M.
last_name: Amieiro
- first_name: Stephan
full_name: Köstlbacher, Stephan
last_name: Köstlbacher
- first_name: Stijn H.P.
full_name: Prinsen, Stijn H.P.
last_name: Prinsen
- first_name: Constantinos
full_name: Patinios, Constantinos
last_name: Patinios
- first_name: Andreas
full_name: Bardis, Andreas
last_name: Bardis
- first_name: Arjan
full_name: Barendregt, Arjan
last_name: Barendregt
- first_name: Richard A.
full_name: Scheltema, Richard A.
last_name: Scheltema
- first_name: Thijs J.G.
full_name: Ettema, Thijs J.G.
last_name: Ettema
- first_name: John
full_name: van der Oost, John
last_name: van der Oost
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
- first_name: Raymond H.J.
full_name: Staals, Raymond H.J.
last_name: Staals
citation:
ama: Steens JA, Bravo JPK, Salazar CRP, et al. Type III-B CRISPR-Cas cascade of
proteolytic cleavages. Science. 2024;383(6682):512-519. doi:10.1126/science.adk0378
apa: Steens, J. A., Bravo, J. P. K., Salazar, C. R. P., Yildiz, C., Amieiro, A.
M., Köstlbacher, S., … Staals, R. H. J. (2024). Type III-B CRISPR-Cas cascade
of proteolytic cleavages. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.adk0378
chicago: Steens, Jurre A., Jack Peter Kelly Bravo, Carl Raymund P. Salazar, Caglar
Yildiz, Afonso M. Amieiro, Stephan Köstlbacher, Stijn H.P. Prinsen, et al. “Type
III-B CRISPR-Cas Cascade of Proteolytic Cleavages.” Science. American Association
for the Advancement of Science, 2024. https://doi.org/10.1126/science.adk0378.
ieee: J. A. Steens et al., “Type III-B CRISPR-Cas cascade of proteolytic
cleavages,” Science, vol. 383, no. 6682. American Association for the Advancement
of Science, pp. 512–519, 2024.
ista: Steens JA, Bravo JPK, Salazar CRP, Yildiz C, Amieiro AM, Köstlbacher S, Prinsen
SHP, Patinios C, Bardis A, Barendregt A, Scheltema RA, Ettema TJG, van der Oost
J, Taylor DW, Staals RHJ. 2024. Type III-B CRISPR-Cas cascade of proteolytic cleavages.
Science. 383(6682), 512–519.
mla: Steens, Jurre A., et al. “Type III-B CRISPR-Cas Cascade of Proteolytic Cleavages.”
Science, vol. 383, no. 6682, American Association for the Advancement of
Science, 2024, pp. 512–19, doi:10.1126/science.adk0378.
short: J.A. Steens, J.P.K. Bravo, C.R.P. Salazar, C. Yildiz, A.M. Amieiro, S. Köstlbacher,
S.H.P. Prinsen, C. Patinios, A. Bardis, A. Barendregt, R.A. Scheltema, T.J.G.
Ettema, J. van der Oost, D.W. Taylor, R.H.J. Staals, Science 383 (2024) 512–519.
date_created: 2024-06-04T06:41:26Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2025-09-24T08:31:45Z
day: '01'
doi: 10.1126/science.adk0378
extern: '1'
external_id:
pmid:
- '38301007'
intvolume: ' 383'
issue: '6682'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.06.23.546230
month: '02'
oa: 1
oa_version: Preprint
page: 512-519
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Type III-B CRISPR-Cas cascade of proteolytic cleavages
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 383
year: '2024'
...
---
_id: '17113'
abstract:
- lang: eng
text: CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement
for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA
target limits the number of editable genes. Recently developed Cas9 variants have
been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the
nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY
recognizes all potential PAM sequences remains unclear. Here, we combine structural
and biochemical approaches to determine how SpRY interrogates DNA and recognizes
target sites. Divergent PAM sequences can be accommodated through conformational
flexibility within the PAM-interacting region, which facilitates tight binding
to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than
for Streptococcus pyogenes Cas9, enabling us to directly
visualize multiple on-pathway intermediate states. Experiments with SpG position
it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on
the molecular mechanisms of PAMless genome editing.
article_number: '3663'
article_processing_charge: Yes
article_type: original
author:
- first_name: Grace N.
full_name: Hibshman, Grace N.
last_name: Hibshman
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Matthew M.
full_name: Hooper, Matthew M.
last_name: Hooper
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Hongshan
full_name: Zhang, Hongshan
last_name: Zhang
- first_name: Ilya J.
full_name: Finkelstein, Ilya J.
last_name: Finkelstein
- first_name: Kenneth A.
full_name: Johnson, Kenneth A.
last_name: Johnson
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Hibshman GN, Bravo JPK, Hooper MM, et al. Unraveling the mechanisms of PAMless
DNA interrogation by SpRY-Cas9. Nature Communications. 2024;15. doi:10.1038/s41467-024-47830-3
apa: Hibshman, G. N., Bravo, J. P. K., Hooper, M. M., Dangerfield, T. L., Zhang,
H., Finkelstein, I. J., … Taylor, D. W. (2024). Unraveling the mechanisms of PAMless
DNA interrogation by SpRY-Cas9. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-024-47830-3
chicago: Hibshman, Grace N., Jack Peter Kelly Bravo, Matthew M. Hooper, Tyler L.
Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David
W. Taylor. “Unraveling the Mechanisms of PAMless DNA Interrogation by SpRY-Cas9.”
Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47830-3.
ieee: G. N. Hibshman et al., “Unraveling the mechanisms of PAMless DNA interrogation
by SpRY-Cas9,” Nature Communications, vol. 15. Springer Nature, 2024.
ista: Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ,
Johnson KA, Taylor DW. 2024. Unraveling the mechanisms of PAMless DNA interrogation
by SpRY-Cas9. Nature Communications. 15, 3663.
mla: Hibshman, Grace N., et al. “Unraveling the Mechanisms of PAMless DNA Interrogation
by SpRY-Cas9.” Nature Communications, vol. 15, 3663, Springer Nature, 2024,
doi:10.1038/s41467-024-47830-3.
short: G.N. Hibshman, J.P.K. Bravo, M.M. Hooper, T.L. Dangerfield, H. Zhang, I.J.
Finkelstein, K.A. Johnson, D.W. Taylor, Nature Communications 15 (2024).
date_created: 2024-06-04T06:42:07Z
date_published: 2024-04-30T00:00:00Z
date_updated: 2024-10-14T12:34:26Z
day: '30'
doi: 10.1038/s41467-024-47830-3
extern: '1'
external_id:
pmid:
- '38688943'
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-024-47830-3
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...
---
_id: '17114'
abstract:
- lang: eng
text: CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize
CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for
destruction1–5. Target RNA cleavage at regular intervals
is characteristic of type III effector complexes6–8. Here,
we determine the structures of the Synechocystis type
III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein
type III effectors9,10, in pre- and post-cleavage states.
The structures show how multi-subunit fusion proteins in the effector are tethered
together in an unusual arrangement to assemble into an active and programmable
RNA endonuclease and how the effector utilizes a distinct mechanism for target
RNA seeding from other type III effectors. Using structural, biochemical, and
quantum/classical molecular dynamics simulation, we study the structure and dynamics
of the three catalytic sites, where a 2′-OH of the ribose on the target RNA acts
as a nucleophile for in line self-cleavage of the upstream scissile phosphate.
Strikingly, the arrangement at the catalytic residues of most type III complexes
resembles the active site of ribozymes, including the hammerhead, pistol, and
Varkud satellite ribozymes. Our work provides detailed molecular insight into
the mechanisms of RNA targeting and cleavage by an important intermediate in the
evolution of type III effector complexes.
article_number: '3324'
article_processing_charge: Yes
article_type: original
author:
- first_name: Evan A.
full_name: Schwartz, Evan A.
last_name: Schwartz
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Mohd
full_name: Ahsan, Mohd
last_name: Ahsan
- first_name: Luis A.
full_name: Macias, Luis A.
last_name: Macias
- first_name: Caitlyn L.
full_name: McCafferty, Caitlyn L.
last_name: McCafferty
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Jada N.
full_name: Walker, Jada N.
last_name: Walker
- first_name: Jennifer S.
full_name: Brodbelt, Jennifer S.
last_name: Brodbelt
- first_name: Giulia
full_name: Palermo, Giulia
last_name: Palermo
- first_name: Peter C.
full_name: Fineran, Peter C.
last_name: Fineran
- first_name: Robert D.
full_name: Fagerlund, Robert D.
last_name: Fagerlund
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Schwartz EA, Bravo JPK, Ahsan M, et al. RNA targeting and cleavage by the type
III-Dv CRISPR effector complex. Nature Communications. 2024;15. doi:10.1038/s41467-024-47506-y
apa: Schwartz, E. A., Bravo, J. P. K., Ahsan, M., Macias, L. A., McCafferty, C.
L., Dangerfield, T. L., … Taylor, D. W. (2024). RNA targeting and cleavage by
the type III-Dv CRISPR effector complex. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-024-47506-y
chicago: Schwartz, Evan A., Jack Peter Kelly Bravo, Mohd Ahsan, Luis A. Macias,
Caitlyn L. McCafferty, Tyler L. Dangerfield, Jada N. Walker, et al. “RNA Targeting
and Cleavage by the Type III-Dv CRISPR Effector Complex.” Nature Communications.
Springer Nature, 2024. https://doi.org/10.1038/s41467-024-47506-y.
ieee: E. A. Schwartz et al., “RNA targeting and cleavage by the type III-Dv
CRISPR effector complex,” Nature Communications, vol. 15. Springer Nature,
2024.
ista: Schwartz EA, Bravo JPK, Ahsan M, Macias LA, McCafferty CL, Dangerfield TL,
Walker JN, Brodbelt JS, Palermo G, Fineran PC, Fagerlund RD, Taylor DW. 2024.
RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature
Communications. 15, 3324.
mla: Schwartz, Evan A., et al. “RNA Targeting and Cleavage by the Type III-Dv CRISPR
Effector Complex.” Nature Communications, vol. 15, 3324, Springer Nature,
2024, doi:10.1038/s41467-024-47506-y.
short: E.A. Schwartz, J.P.K. Bravo, M. Ahsan, L.A. Macias, C.L. McCafferty, T.L.
Dangerfield, J.N. Walker, J.S. Brodbelt, G. Palermo, P.C. Fineran, R.D. Fagerlund,
D.W. Taylor, Nature Communications 15 (2024).
date_created: 2024-06-04T06:43:02Z
date_published: 2024-04-18T00:00:00Z
date_updated: 2024-06-04T07:05:26Z
day: '18'
doi: 10.1038/s41467-024-47506-y
extern: '1'
external_id:
pmid:
- '38637512'
intvolume: ' 15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-024-47506-y
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: RNA targeting and cleavage by the type III-Dv CRISPR effector complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2024'
...