---
_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'
fulldoi: https://doi.org/10.1145/3661814.3662080
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
fulldoi: https://doi.org/10.4230/LIPIcs.FSTTCS.2024.5
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'
fulldoi: https://doi.org/10.48550/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'
...
---
_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
fulldoi: https://doi.org/10.21468/scipostphys.16.4.097
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: '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'
fulldoi: https://doi.org/10.1016/j.bpj.2024.03.015
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'
fulldoi: https://doi.org/10.1126/science.adk0378
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'
fulldoi: https://doi.org/10.1038/s41467-024-47830-3
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'
fulldoi: https://doi.org/10.1038/s41467-024-47506-y
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'
...
---
_id: '17122'
abstract:
- lang: eng
text: "Background: Motor alterations and lowered physical activity are common in
affective disorders. Previous research has indicated a link between depressive
symptoms and declining muscle strength primarily focusing on the elderly but not
younger individuals. Thus, we aimed to evaluate the relationship between mood
and muscle strength in a sample of N = 73 young to middle-aged hospitalized patients
(18–49 years, mean age 30.7 years) diagnosed with major depressive, bipolar and
schizoaffective disorder, with a focus on moderating effects of psychopharmacotherapy.
The study was carried out as a prospective observational study at a German psychiatric
university hospital between September 2021 and March 2022.\r\nMethods: Employing
a standardized strength circuit consisting of computerized strength training devices,
we measured the maximal muscle strength (Fmax) using three repetitions maximum
across four muscle regions (abdomen, arm, back, leg) at three time points (t1-t3)
over four weeks accompanied by psychometric testing (MADRS, BPRS, YRMS) and blood
lipid profiling in a clinical setting. For analysis of psychopharmacotherapy,
medication was split into activating (AM) and inhibiting (IM) medication and dosages
were normalized by the respective WHO defined daily dose.\r\nResults: While we
observed a significant decrease of the MADRS score and increase of the relative
total Fmax (rTFmax) in the first two weeks (t1-t2) but not later (both p < .001),
we did not reveal a significant bivariate correlation between disease severity
(MADRS) and muscle strength (rTFmax) at any of the timepoints. Individuals with
longer disease history displayed reduced rTFmax (p = .048). IM was significantly
associated with decreased rTFmax (p = .032). Regression models provide a more
substantial effect of gender, age, and IM on muscle strength than the depressive
episode itself (p < .001).\r\nConclusions: The results of the study indicate that
disease severity and muscle strength are not associated in young to middle-aged
inpatients with affective disorders using a strength circuit as observational
measurement. Future research will be needed to differentiate the effect of medication,
gender, and age on muscle strength and to develop interventions for prevention
of muscle weakness, especially in younger patients with chronic affective illnesses."
acknowledgement: "This work was supported by the project ‘Fellows Ride’ of the Thomas
Lurz und Dieter Schneider Stiftung and by the ‘Würzburger Bündnis gegen Depression’
(to S.K.-S).\r\nOpen Access funding enabled and organized by Projekt DEAL."
article_number: '401'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Hannah
full_name: Ramming, Hannah
last_name: Ramming
- first_name: Linda
full_name: Theuerkauf, Linda
last_name: Theuerkauf
- first_name: Olaf
full_name: Hoos, Olaf
last_name: Hoos
- first_name: Katharina
full_name: Lichter, Katharina
id: 39302e62-fcfc-11ec-8196-8b01447dbd3d
last_name: Lichter
orcid: 0000-0002-1485-0351
- first_name: Sarah
full_name: Kittel-Schneider, Sarah
last_name: Kittel-Schneider
citation:
ama: Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. The association
between maximal muscle strength, disease severity and psychopharmacotherapy among
young to middle-aged inpatients with affective disorders – a prospective pilot
study. BMC Psychiatry. 2024;24. doi:10.1186/s12888-024-05849-2
apa: Ramming, H., Theuerkauf, L., Hoos, O., Lichter, K., & Kittel-Schneider,
S. (2024). The association between maximal muscle strength, disease severity and
psychopharmacotherapy among young to middle-aged inpatients with affective disorders
– a prospective pilot study. BMC Psychiatry. Springer Nature. https://doi.org/10.1186/s12888-024-05849-2
chicago: Ramming, Hannah, Linda Theuerkauf, Olaf Hoos, Katharina Lichter, and Sarah
Kittel-Schneider. “The Association between Maximal Muscle Strength, Disease Severity
and Psychopharmacotherapy among Young to Middle-Aged Inpatients with Affective
Disorders – a Prospective Pilot Study.” BMC Psychiatry. Springer Nature,
2024. https://doi.org/10.1186/s12888-024-05849-2.
ieee: H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, and S. Kittel-Schneider, “The
association between maximal muscle strength, disease severity and psychopharmacotherapy
among young to middle-aged inpatients with affective disorders – a prospective
pilot study,” BMC Psychiatry, vol. 24. Springer Nature, 2024.
ista: Ramming H, Theuerkauf L, Hoos O, Lichter K, Kittel-Schneider S. 2024. The
association between maximal muscle strength, disease severity and psychopharmacotherapy
among young to middle-aged inpatients with affective disorders – a prospective
pilot study. BMC Psychiatry. 24, 401.
mla: Ramming, Hannah, et al. “The Association between Maximal Muscle Strength, Disease
Severity and Psychopharmacotherapy among Young to Middle-Aged Inpatients with
Affective Disorders – a Prospective Pilot Study.” BMC Psychiatry, vol.
24, 401, Springer Nature, 2024, doi:10.1186/s12888-024-05849-2.
short: H. Ramming, L. Theuerkauf, O. Hoos, K. Lichter, S. Kittel-Schneider, BMC
Psychiatry 24 (2024).
date_created: 2024-06-09T22:01:01Z
date_published: 2024-05-29T00:00:00Z
date_updated: 2025-04-23T07:51:51Z
day: '29'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1186/s12888-024-05849-2
external_id:
pmid:
- '38811916'
file:
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checksum: 5df60d3c9388955c5b682ea34748d59d
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creator: dernst
date_created: 2024-06-10T10:44:26Z
date_updated: 2024-06-10T10:44:26Z
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file_name: 2024_BMCPsychiatry_Ramming.pdf
file_size: 2320147
relation: main_file
success: 1
file_date_updated: 2024-06-10T10:44:26Z
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intvolume: ' 24'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Psychiatry
publication_identifier:
eissn:
- 1471-244X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The association between maximal muscle strength, disease severity and psychopharmacotherapy
among young to middle-aged inpatients with affective disorders – a prospective pilot
study
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: 24
year: '2024'
...
---
APC_amount: 2570,79 EUR
OA_place: publisher
OA_type: hybrid
_id: '17123'
abstract:
- lang: eng
text: A key feature of many developmental systems is their ability to self-organize
spatial patterns of functionally distinct cell fates. To ensure proper biological
function, such patterns must be established reproducibly, by controlling and even
harnessing intrinsic and extrinsic fluctuations. While the relevant molecular
processes are increasingly well understood, we lack a principled framework to
quantify the performance of such stochastic self-organizing systems. To that end,
we introduce an information-theoretic measure for self-organized fate specification
during embryonic development. We show that the proposed measure assesses the total
information content of fate patterns and decomposes it into interpretable contributions
corresponding to the positional and correlational information. By optimizing the
proposed measure, our framework provides a normative theory for developmental
circuits, which we demonstrate on lateral inhibition, cell type proportioning,
and reaction–diffusion models of self-organization. This paves a way toward a
classification of developmental systems based on a common information-theoretic
language, thereby organizing the zoo of implicated chemical and mechanical signaling
processes.
acknowledgement: We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns,
Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo
for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS
Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship
(ALTF 343-2022). This research was performed in part at the Aspen Center for Physics,
which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical
Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon
and Betty Moore Foundation Grant No. 2919.02.
article_number: e2322326121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Brückner D, Tkačik G. Information content and optimization of self-organized
developmental systems. Proceedings of the National Academy of Sciences of the
United States of America. 2024;121(23). doi:10.1073/pnas.2322326121
apa: Brückner, D., & Tkačik, G. (2024). Information content and optimization
of self-organized developmental systems. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2322326121
chicago: Brückner, David, and Gašper Tkačik. “Information Content and Optimization
of Self-Organized Developmental Systems.” Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences,
2024. https://doi.org/10.1073/pnas.2322326121.
ieee: D. Brückner and G. Tkačik, “Information content and optimization of self-organized
developmental systems,” Proceedings of the National Academy of Sciences of
the United States of America, vol. 121, no. 23. National Academy of Sciences,
2024.
ista: Brückner D, Tkačik G. 2024. Information content and optimization of self-organized
developmental systems. Proceedings of the National Academy of Sciences of the
United States of America. 121(23), e2322326121.
mla: Brückner, David, and Gašper Tkačik. “Information Content and Optimization of
Self-Organized Developmental Systems.” Proceedings of the National Academy
of Sciences of the United States of America, vol. 121, no. 23, e2322326121,
National Academy of Sciences, 2024, doi:10.1073/pnas.2322326121.
short: D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of
the United States of America 121 (2024).
corr_author: '1'
date_created: 2024-06-09T22:01:02Z
date_published: 2024-06-04T00:00:00Z
date_updated: 2025-09-08T07:51:01Z
day: '04'
ddc:
- '570'
department:
- _id: EdHa
- _id: GaTk
doi: 10.1073/pnas.2322326121
external_id:
isi:
- '001244835000006'
pmid:
- '38819997'
file:
- access_level: open_access
checksum: 59797a75db7beb3721ed7a4d14c241f9
content_type: application/pdf
creator: dernst
date_created: 2024-06-10T10:27:37Z
date_updated: 2024-06-10T10:27:37Z
file_id: '17130'
file_name: 2024_PNAS_Brueckner.pdf
file_size: 12329234
relation: main_file
success: 1
file_date_updated: 2024-06-10T10:27:37Z
fulldoi: https://doi.org/10.1073/pnas.2322326121
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/dbrueckner/SelforgInformation
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/the-embryo-assembles-itself/
scopus_import: '1'
status: public
title: Information content and optimization of self-organized developmental systems
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: 121
year: '2024'
...
---
OA_type: closed access
_id: '17125'
abstract:
- lang: eng
text: We explore the potential of nanocrystals (a term used equivalently to nanoparticles)
as building blocks for nanomaterials, and the current advances and open challenges
for fundamental science developments and applications. Nanocrystal assemblies
are inherently multiscale, and the generation of revolutionary material properties
requires a precise understanding of the relationship between structure and function,
the former being determined by classical effects and the latter often by quantum
effects. With an emphasis on theory and computation, we discuss challenges that
hamper current assembly strategies and to what extent nanocrystal assemblies represent
thermodynamic equilibrium or kinetically trapped metastable states. We also examine
dynamic effects and optimization of assembly protocols. Finally, we discuss promising
material functions and examples of their realization with nanocrystal assemblies.
acknowledgement: This research was supported in part by the National Science Foundation
under Grant No. NSF PHY-1748958 to the Kavli Institute for Theoretical Physics.
The biophysics part of this paper was supported in part by the Gordon and Betty
Moore Foundation Grant No. 2919.02. CLB acknowledges the sponsorship of the Alexander
von Humboldt Foundation through the Humboldt Research Fellowship for postdoctoral
researchers, and the support of the Emerging Talents Initiative (ETI) and the EAM
Starting Grant (EAM-SG23-1) of the Competence Center Engineering of Advanced Materials
of the Friedrich-Alexander-Universität Erlangen-Nürnberg. CLB and ME acknowledge
the support of the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
Project-ID 416229255-SFB 1411. The research of AT was supported by the U.S. Department
of Energy (U.S. DOE), Office of Basic Energy Sciences, Division of Materials Sciences
and Engineering. Iowa State University operates Ames National Laboratory for the
U.S. DOE under Contract DE-AC02-07CH11358.
article_processing_charge: No
article_type: review
author:
- first_name: Carlos L.
full_name: Bassani, Carlos L.
last_name: Bassani
- first_name: Greg
full_name: Van Anders, Greg
last_name: Van Anders
- first_name: Uri
full_name: Banin, Uri
last_name: Banin
- first_name: Dmitry
full_name: Baranov, Dmitry
last_name: Baranov
- first_name: Qian
full_name: Chen, Qian
last_name: Chen
- first_name: Marjolein
full_name: Dijkstra, Marjolein
last_name: Dijkstra
- first_name: Michael S.
full_name: Dimitriyev, Michael S.
last_name: Dimitriyev
- first_name: Efi
full_name: Efrati, Efi
last_name: Efrati
- first_name: Jordi
full_name: Faraudo, Jordi
last_name: Faraudo
- first_name: Oleg
full_name: Gang, Oleg
last_name: Gang
- first_name: Nicola
full_name: Gaston, Nicola
last_name: Gaston
- first_name: Ramin
full_name: Golestanian, Ramin
last_name: Golestanian
- first_name: G. Ivan
full_name: Guerrero-Garcia, G. Ivan
last_name: Guerrero-Garcia
- first_name: Michael
full_name: Gruenwald, Michael
last_name: Gruenwald
- first_name: Amir
full_name: Haji-Akbari, Amir
last_name: Haji-Akbari
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Matthias
full_name: Karg, Matthias
last_name: Karg
- first_name: Tobias
full_name: Kraus, Tobias
last_name: Kraus
- first_name: Byeongdu
full_name: Lee, Byeongdu
last_name: Lee
- first_name: Reid C.
full_name: Van Lehn, Reid C.
last_name: Van Lehn
- first_name: Robert J.
full_name: Macfarlane, Robert J.
last_name: Macfarlane
- first_name: Bortolo M.
full_name: Mognetti, Bortolo M.
last_name: Mognetti
- first_name: Arash
full_name: Nikoubashman, Arash
last_name: Nikoubashman
- first_name: Saeed
full_name: Osat, Saeed
last_name: Osat
- first_name: Oleg V.
full_name: Prezhdo, Oleg V.
last_name: Prezhdo
- first_name: Grant M.
full_name: Rotskoff, Grant M.
last_name: Rotskoff
- first_name: Leonor
full_name: Saiz, Leonor
last_name: Saiz
- first_name: An Chang
full_name: Shi, An Chang
last_name: Shi
- first_name: Sara
full_name: Skrabalak, Sara
last_name: Skrabalak
- first_name: Ivan I.
full_name: Smalyukh, Ivan I.
last_name: Smalyukh
- first_name: Mario
full_name: Tagliazucchi, Mario
last_name: Tagliazucchi
- first_name: Dmitri V.
full_name: Talapin, Dmitri V.
last_name: Talapin
- first_name: Alexei V.
full_name: Tkachenko, Alexei V.
last_name: Tkachenko
- first_name: Sergei
full_name: Tretiak, Sergei
last_name: Tretiak
- first_name: David
full_name: Vaknin, David
last_name: Vaknin
- first_name: Asaph
full_name: Widmer-Cooper, Asaph
last_name: Widmer-Cooper
- first_name: Gerard C.L.
full_name: Wong, Gerard C.L.
last_name: Wong
- first_name: Xingchen
full_name: Ye, Xingchen
last_name: Ye
- first_name: Shan
full_name: Zhou, Shan
last_name: Zhou
- first_name: Eran
full_name: Rabani, Eran
last_name: Rabani
- first_name: Michael
full_name: Engel, Michael
last_name: Engel
- first_name: Alex
full_name: Travesset, Alex
last_name: Travesset
citation:
ama: 'Bassani CL, Van Anders G, Banin U, et al. Nanocrystal assemblies: Current
advances and open problems. ACS Nano. 2024;18(23):14791-14840. doi:10.1021/acsnano.3c10201'
apa: 'Bassani, C. L., Van Anders, G., Banin, U., Baranov, D., Chen, Q., Dijkstra,
M., … Travesset, A. (2024). Nanocrystal assemblies: Current advances and open
problems. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.3c10201'
chicago: 'Bassani, Carlos L., Greg Van Anders, Uri Banin, Dmitry Baranov, Qian Chen,
Marjolein Dijkstra, Michael S. Dimitriyev, et al. “Nanocrystal Assemblies: Current
Advances and Open Problems.” ACS Nano. American Chemical Society, 2024.
https://doi.org/10.1021/acsnano.3c10201.'
ieee: 'C. L. Bassani et al., “Nanocrystal assemblies: Current advances and
open problems,” ACS Nano, vol. 18, no. 23. American Chemical Society, pp.
14791–14840, 2024.'
ista: 'Bassani CL, Van Anders G, Banin U, Baranov D, Chen Q, Dijkstra M, Dimitriyev
MS, Efrati E, Faraudo J, Gang O, Gaston N, Golestanian R, Guerrero-Garcia GI,
Gruenwald M, Haji-Akbari A, Ibáñez M, Karg M, Kraus T, Lee B, Van Lehn RC, Macfarlane
RJ, Mognetti BM, Nikoubashman A, Osat S, Prezhdo OV, Rotskoff GM, Saiz L, Shi
AC, Skrabalak S, Smalyukh II, Tagliazucchi M, Talapin DV, Tkachenko AV, Tretiak
S, Vaknin D, Widmer-Cooper A, Wong GCL, Ye X, Zhou S, Rabani E, Engel M, Travesset
A. 2024. Nanocrystal assemblies: Current advances and open problems. ACS Nano.
18(23), 14791–14840.'
mla: 'Bassani, Carlos L., et al. “Nanocrystal Assemblies: Current Advances and Open
Problems.” ACS Nano, vol. 18, no. 23, American Chemical Society, 2024,
pp. 14791–840, doi:10.1021/acsnano.3c10201.'
short: C.L. Bassani, G. Van Anders, U. Banin, D. Baranov, Q. Chen, M. Dijkstra,
M.S. Dimitriyev, E. Efrati, J. Faraudo, O. Gang, N. Gaston, R. Golestanian, G.I.
Guerrero-Garcia, M. Gruenwald, A. Haji-Akbari, M. Ibáñez, M. Karg, T. Kraus, B.
Lee, R.C. Van Lehn, R.J. Macfarlane, B.M. Mognetti, A. Nikoubashman, S. Osat,
O.V. Prezhdo, G.M. Rotskoff, L. Saiz, A.C. Shi, S. Skrabalak, I.I. Smalyukh, M.
Tagliazucchi, D.V. Talapin, A.V. Tkachenko, S. Tretiak, D. Vaknin, A. Widmer-Cooper,
G.C.L. Wong, X. Ye, S. Zhou, E. Rabani, M. Engel, A. Travesset, ACS Nano 18 (2024)
14791–14840.
date_created: 2024-06-09T22:01:02Z
date_published: 2024-05-30T00:00:00Z
date_updated: 2025-09-08T07:52:37Z
day: '30'
department:
- _id: MaIb
doi: 10.1021/acsnano.3c10201
external_id:
isi:
- '001236199900001'
pmid:
- '38814908'
fulldoi: https://doi.org/10.1021/acsnano.3c10201
intvolume: ' 18'
isi: 1
issue: '23'
language:
- iso: eng
month: '05'
oa_version: None
page: 14791-14840
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
issn:
- 1936-0851
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Nanocrystal assemblies: Current advances and open problems'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 18
year: '2024'
...
---
_id: '17126'
abstract:
- lang: eng
text: "Functional encryption (FE) is a primitive where the holder of a master secret
key can control which functions a user can evaluate on encrypted data. It is a
powerful primitive that even implies indistinguishability obfuscation (iO), given
sufficiently compact ciphertexts (Ananth-Jain, CRYPTO’15 and Bitansky-Vaikuntanathan,
FOCS’15). However, despite being extensively studied, there are FE schemes, such
as function-hiding inner-product FE (Bishop-Jain-Kowalczyk, AC’15, Abdalla-Catalano-Fiore-Gay-Ursu,
CRYPTO’18) and compact quadratic FE (Baltico-Catalano-Fiore-Gay, Lin, CRYPTO’17),
that can be only realized using pairings. This raises the question if there are
some mathematical barriers that hinder us from realizing these FE schemes from
other assumptions.\r\n\r\nIn this paper, we study the difficulty of constructing
lattice-based compact FE. We generalize the impossibility results of Ünal (EC’20)
for lattice-based function-hiding FE, and extend it to the case of compact FE.
Concretely, we prove lower bounds for lattice-based compact FE schemes which meet
some (natural) algebraic restrictions at encryption and decryption, and have ciphertexts
of linear size and secret keys of minimal degree. We see our results as important
indications of why it is hard to construct lattice-based FE schemes for new functionalities,
and which mathematical barriers have to be overcome."
acknowledgement: We want to thank the anonymous reviewers of TCC and Eurocrypt for
their very helpful comments and suggestions. This work has received funding from
the Austrian Science Fund (FWF) and netidee SCIENCE via grant P31621-N38 (PROFET).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Erkan
full_name: Tairi, Erkan
last_name: Tairi
- first_name: Akin
full_name: Ünal, Akin
id: f6b56fb6-dc63-11ee-9dbf-f6780863a85a
last_name: Ünal
orcid: 0000-0002-8929-0221
citation:
ama: 'Tairi E, Ünal A. Lower bounds for lattice-based compact functional encryption.
In: Advances in Cryptology – EUROCRYPT 2024. Vol 14652. Springer Nature;
2024:249-279. doi:10.1007/978-3-031-58723-8_9'
apa: 'Tairi, E., & Ünal, A. (2024). Lower bounds for lattice-based compact functional
encryption. In Advances in Cryptology – EUROCRYPT 2024 (Vol. 14652, pp.
249–279). Zurich, Switzerland: Springer Nature. https://doi.org/10.1007/978-3-031-58723-8_9'
chicago: Tairi, Erkan, and Akin Ünal. “Lower Bounds for Lattice-Based Compact Functional
Encryption.” In Advances in Cryptology – EUROCRYPT 2024, 14652:249–79.
Springer Nature, 2024. https://doi.org/10.1007/978-3-031-58723-8_9.
ieee: E. Tairi and A. Ünal, “Lower bounds for lattice-based compact functional encryption,”
in Advances in Cryptology – EUROCRYPT 2024, Zurich, Switzerland, 2024,
vol. 14652, pp. 249–279.
ista: 'Tairi E, Ünal A. 2024. Lower bounds for lattice-based compact functional
encryption. Advances in Cryptology – EUROCRYPT 2024. EUROCRYPT: Theory and Applications
of Cryptographic Techniques, LNCS, vol. 14652, 249–279.'
mla: Tairi, Erkan, and Akin Ünal. “Lower Bounds for Lattice-Based Compact Functional
Encryption.” Advances in Cryptology – EUROCRYPT 2024, vol. 14652, Springer
Nature, 2024, pp. 249–79, doi:10.1007/978-3-031-58723-8_9.
short: E. Tairi, A. Ünal, in:, Advances in Cryptology – EUROCRYPT 2024, Springer
Nature, 2024, pp. 249–279.
conference:
end_date: 2024-05-30
location: Zurich, Switzerland
name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques'
start_date: 2024-05-26
date_created: 2024-06-09T22:01:03Z
date_published: 2024-05-08T00:00:00Z
date_updated: 2025-09-08T07:48:18Z
day: '08'
department:
- _id: KrPi
doi: 10.1007/978-3-031-58723-8_9
external_id:
isi:
- '001278247600009'
fulldoi: https://doi.org/10.1007/978-3-031-58723-8_9
intvolume: ' 14652'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2023/719.pdf
month: '05'
oa: 1
oa_version: Submitted Version
page: 249-279
publication: Advances in Cryptology – EUROCRYPT 2024
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031587221'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lower bounds for lattice-based compact functional encryption
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14652
year: '2024'
...
---
_id: '17128'
abstract:
- lang: eng
text: The onset of turbulence in pipe flow has defied detailed understanding ever
since the first observations of the spatially heterogeneous nature of the transition.
Recent theoretical studies and experiments in simpler, shear-driven flows suggest
that the onset of turbulence is a directed-percolation non-equilibrium phase transition,
but whether these findings are generic and also apply to open or pressure-driven
flows is unknown. In pipe flow, the extremely long time scales near the transition
make direct observations of critical behaviour virtually impossible. Here we find
a technical solution to that limitation and show that the universality class of
the transition is directed percolation, from which a jammed phase of puffs emerges
above the critical point. Our method is to experimentally characterize all pairwise
interactions between localized patches of turbulence puffs and use these interactions
as input for renormalization group and computer simulations of minimal models
that extrapolate to long length and time scales. The strong interactions in the
jamming regime enable us to explicitly measure the turbulent fraction and confirm
model predictions. Our work shows that directed-percolation scaling applies beyond
simple closed shear flows and underscores how statistical mechanics can lead to
profound, quantitative and predictive insights on turbulent flows and their phases.
acknowledgement: We gratefully acknowledge the assistance of J. M. Lopez with DNSs
at an early stage of this work. This work was partially supported by two grants
from the Simons Foundation (grant nos. 662985 (N.G.) and 662960 (B.H.)) and by Ministry
of Science and Technology, Taiwan (grant nos. MOST 109-2112-M-001-017-MY3 and MOST
111-2112-M-001-027-MY3 (H.-Y.S.)). Part of this work was performed using computing
resources of CRIANN (Normandy, France).
article_processing_charge: No
article_type: original
author:
- first_name: Grégoire M
full_name: Lemoult, Grégoire M
id: 4787FE80-F248-11E8-B48F-1D18A9856A87
last_name: Lemoult
- first_name: Mukund
full_name: Vasudevan, Mukund
id: 3C5A959A-F248-11E8-B48F-1D18A9856A87
last_name: Vasudevan
- first_name: Hong Yan
full_name: Shih, Hong Yan
last_name: Shih
- first_name: Gaute
full_name: Linga, Gaute
last_name: Linga
- first_name: Joachim
full_name: Mathiesen, Joachim
last_name: Mathiesen
- first_name: Nigel
full_name: Goldenfeld, Nigel
last_name: Goldenfeld
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Lemoult GM, Vasudevan M, Shih HY, et al. Directed percolation and puff jamming
near the transition to pipe turbulence. Nature Physics. 2024;20:1339-1345.
doi:10.1038/s41567-024-02513-0
apa: Lemoult, G. M., Vasudevan, M., Shih, H. Y., Linga, G., Mathiesen, J., Goldenfeld,
N., & Hof, B. (2024). Directed percolation and puff jamming near the transition
to pipe turbulence. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02513-0
chicago: Lemoult, Grégoire M, Mukund Vasudevan, Hong Yan Shih, Gaute Linga, Joachim
Mathiesen, Nigel Goldenfeld, and Björn Hof. “Directed Percolation and Puff Jamming
near the Transition to Pipe Turbulence.” Nature Physics. Springer Nature,
2024. https://doi.org/10.1038/s41567-024-02513-0.
ieee: G. M. Lemoult et al., “Directed percolation and puff jamming near the
transition to pipe turbulence,” Nature Physics, vol. 20. Springer Nature,
pp. 1339–1345, 2024.
ista: Lemoult GM, Vasudevan M, Shih HY, Linga G, Mathiesen J, Goldenfeld N, Hof
B. 2024. Directed percolation and puff jamming near the transition to pipe turbulence.
Nature Physics. 20, 1339–1345.
mla: Lemoult, Grégoire M., et al. “Directed Percolation and Puff Jamming near the
Transition to Pipe Turbulence.” Nature Physics, vol. 20, Springer Nature,
2024, pp. 1339–45, doi:10.1038/s41567-024-02513-0.
short: G.M. Lemoult, M. Vasudevan, H.Y. Shih, G. Linga, J. Mathiesen, N. Goldenfeld,
B. Hof, Nature Physics 20 (2024) 1339–1345.
corr_author: '1'
date_created: 2024-06-09T22:01:03Z
date_published: 2024-08-01T00:00:00Z
date_updated: 2025-09-08T07:50:20Z
day: '01'
department:
- _id: BjHo
doi: 10.1038/s41567-024-02513-0
external_id:
isi:
- '001232300600001'
fulldoi: https://doi.org/10.1038/s41567-024-02513-0
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 1339-1345
project:
- _id: 238598C6-32DE-11EA-91FC-C7463DDC885E
grant_number: '662960'
name: Revisiting the Turbulence Problem Using Statistical Mechanics
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Directed percolation and puff jamming near the transition to pipe turbulence
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
OA_place: publisher
_id: '17133'
abstract:
- lang: eng
text: "An ideal quantum computer relies on qubits capable of performing fast gate
operations and\r\nmaintaining strong interconnections while preserving their quantum
coherence. Since the\r\ninception of experimental eforts toward building a quantum
computer, the community has\r\nfaced challenges in engineering such a system.
Among the various methods of implementing a\r\nquantum computer, superconducting
qubits have shown fast gates close to tens of nanoseconds,\r\nwith the state-of-the-art
reaching a coherence of a few milliseconds. However, achieving\r\nsimultaneously
long lifetimes with fast qubit operations poses an inherent paradox. Qubits\r\nwith
high coherence require isolation from the environment, while fast operation necessitates\r\nstrong
coupling of the qubit. This thesis approaches this issue by proposing the idea
of\r\nengineering superconducting qubits capable of transitioning between operating
in a protected\r\nregime, where the qubit is completely isolated from the environment,
and coupling to the\r\ncommunication channels as needed. In this direction, we
use the geometric superinductor to\r\nscan the parameter space of rf-SQUID devices,
searching for a regime where we can take the\r\nqubit protection to its extreme.\r\n\r\nThis
leads us to the inductively shunted transmon (IST) regime, characterized by EJ
/EC ≫ 1\r\nand EJ /EL ≫ 1, where the circuit potential exhibits a double well
with a large barrier\r\nseparating the local ground states of each quantum well.
In this regime, although it is\r\nanticipated that the two quantum wells would
be isolated from each other, we observe single\r\nfuxon tunneling between them.
The interplay of the cavity photons and the fuxon transition\r\nforms a rich physical
system, containing resonance conditions that allow the preparation of the\r\nfuxon
ground or excited states. This enables us to study the relaxation rate of such
transition\r\nand show that it can be as large as 3.6 hours. Dynamically controlling
the barrier height\r\nbetween the two quantum wells allows for controllable coupling,
which scales exponentially,\r\nfor a qubit encoded in two fuxon states.\r\nThe
0-π qubit is one of the very few known superconducting circuit types that ofers
exponential\r\nprotection from both relaxation and dephasing simultaneously. However,
this qubit is not\r\nexempt from the fact that such protection comes at the expense
of complex readout and\r\ncontrol. In this thesis, we propose a way to controllably
break the circuit symmetry, the\r\nkey reason for the protection, to momentarily
restore the ability to control and manipulate\r\nthe qubit. An asymmetry in capacitances
and inductances in the 0-π circuit is detrimental\r\nsince they lead to coupling
of the protected state to the thermally occupied parasitic mode\r\nof the circuit.
However, here we try to exploit a controlled asymmetry in Josephson energies\r\nand
show that this can be used as a tunable coupler between the protected states.
In the\r\nfuture, this should allow to perform gate operations by dynamically
controlling the asymmetry\r\ninstead of driving the protected transition with
microwave pulses. Therefore, we believe that\r\nthe proposed method can make the
use of protected qubits more practical in experimental\r\nrealizations of quantum
computing."
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Farid
full_name: Hassani, Farid
id: 2AED110C-F248-11E8-B48F-1D18A9856A87
last_name: Hassani
orcid: 0000-0001-6937-5773
citation:
ama: Hassani F. Superconducting qubits capable of dynamic switching between protected
and high-speed control regimes. 2024. doi:10.15479/at:ista:17133
apa: Hassani, F. (2024). Superconducting qubits capable of dynamic switching
between protected and high-speed control regimes. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:17133
chicago: Hassani, Farid. “Superconducting Qubits Capable of Dynamic Switching between
Protected and High-Speed Control Regimes.” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/at:ista:17133.
ieee: F. Hassani, “Superconducting qubits capable of dynamic switching between protected
and high-speed control regimes,” Institute of Science and Technology Austria,
2024.
ista: Hassani F. 2024. Superconducting qubits capable of dynamic switching between
protected and high-speed control regimes. Institute of Science and Technology
Austria.
mla: Hassani, Farid. Superconducting Qubits Capable of Dynamic Switching between
Protected and High-Speed Control Regimes. Institute of Science and Technology
Austria, 2024, doi:10.15479/at:ista:17133.
short: F. Hassani, Superconducting Qubits Capable of Dynamic Switching between Protected
and High-Speed Control Regimes, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-06-11T18:20:05Z
date_published: 2024-06-11T00:00:00Z
date_updated: 2026-04-15T06:43:02Z
day: '11'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoFi
doi: 10.15479/at:ista:17133
file:
- access_level: open_access
checksum: 258c353d47fa37ea63ea43b1e10a34a0
content_type: application/pdf
creator: fhassani
date_created: 2024-06-12T07:53:19Z
date_updated: 2024-06-20T11:52:22Z
file_id: '17137'
file_name: Thesis_main_final.pdf
file_size: 28370759
relation: main_file
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checksum: deffa5d0db88093f74812fa71520d5e1
content_type: text/x-tex
creator: fhassani
date_created: 2024-06-12T07:54:27Z
date_updated: 2024-06-12T07:54:27Z
file_id: '17138'
file_name: Thesis_main.tex
file_size: 445735
relation: source_file
file_date_updated: 2024-06-20T11:52:22Z
fulldoi: https://doi.org/10.15479/at:ista:17133
has_accepted_license: '1'
keyword:
- Quantum information
- Qubits
- Superconducting devices
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '161'
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
- _id: bdb108fd-d553-11ed-ba76-83dc74a9864f
grant_number: F07105
name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration
of Superconducting Quantum Circuits
publication_identifier:
isbn:
- 978-3-99078-040-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '13227'
relation: part_of_dissertation
status: public
- id: '9928'
relation: part_of_dissertation
status: public
- id: '8755'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
title: Superconducting qubits capable of dynamic switching between protected and high-speed
control regimes
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
_id: '17136'
abstract:
- lang: eng
text: "This paper focuses on Majority Dynamics in sparse graphs, in particular,
as a\r\ntool to study internal cuts. It is known that, in Majority Dynamics on
a finite\r\ngraph, each vertex eventually either comes to a fixed state, or oscillates
with\r\nperiod two. The empirical evidence acquired by simulations suggests that
for\r\nrandom odd-regular graphs, approximately half of the vertices end up\r\noscillating
with high probability. We notice a local symmetry between\r\noscillating and non-oscillating
vertices, that potentially can explain why the\r\nfraction of the oscillating
vertices is concentrated around $\\frac{1}{2}$. In\r\nour simulations, we observe
that the parts of random odd-regular graph under\r\nMajority Dynamics with high
probability do not contain $\\lceil \\frac{d}{2}\r\n\\rceil$-cores at any timestep,
and thus, one cannot use Majority Dynamics to\r\nprove that internal cuts exist
in odd-regular graphs almost surely. However, we\r\nsuggest a modification of
Majority Dynamics, that yields parts with desired\r\ncores with high probability."
acknowledgement: "I am grateful to Matthew Kwan for setting the problem, providing
useful literature,\r\nfruitful discussions, text review, mentorship, general encouragement
and support."
article_number: '2406.07026'
article_processing_charge: No
arxiv: 1
author:
- first_name: Pavel
full_name: Arkhipov, Pavel
id: b25f2ab2-1fed-11ee-8599-fe02d211784f
last_name: Arkhipov
citation:
ama: 'Arkhipov P. Majority dynamics and internal partitions of random regular graphs:
Experimental results. arXiv. doi:10.48550/arXiv.2406.07026'
apa: 'Arkhipov, P. (n.d.). Majority dynamics and internal partitions of random regular
graphs: Experimental results. arXiv. https://doi.org/10.48550/arXiv.2406.07026'
chicago: 'Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random
Regular Graphs: Experimental Results.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2406.07026.'
ieee: 'P. Arkhipov, “Majority dynamics and internal partitions of random regular
graphs: Experimental results,” arXiv. .'
ista: 'Arkhipov P. Majority dynamics and internal partitions of random regular graphs:
Experimental results. arXiv, 2406.07026.'
mla: 'Arkhipov, Pavel. “Majority Dynamics and Internal Partitions of Random Regular
Graphs: Experimental Results.” ArXiv, 2406.07026, doi:10.48550/arXiv.2406.07026.'
short: P. Arkhipov, ArXiv (n.d.).
date_created: 2024-06-12T07:01:52Z
date_published: 2024-06-11T00:00:00Z
date_updated: 2024-06-17T10:45:32Z
day: '11'
department:
- _id: GradSch
doi: 10.48550/arXiv.2406.07026
external_id:
arxiv:
- '2406.07026'
fulldoi: https://doi.org/10.48550/arXiv.2406.07026
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2406.07026
month: '06'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: 'Majority dynamics and internal partitions of random regular graphs: Experimental
results'
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
_id: '17139'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Waleed
full_name: Khalid, Waleed
id: 097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1
last_name: Khalid
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core
is requested? In: ASHPC24 - Austrian-Slovenian HPC Meeting 2024. EuroCC
Austria; 2024:46. doi:10.25365/phaidra.463'
apa: 'Schlögl, A., Khalid, W., Elefante, S., & Stadlbauer, S. (2024). How much
memory per CPU core is requested? In ASHPC24 - Austrian-Slovenian HPC Meeting
2024 (p. 46). Grundlsee, Austria: EuroCC Austria. https://doi.org/10.25365/phaidra.463'
chicago: Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer.
“How Much Memory per CPU Core Is Requested?” In ASHPC24 - Austrian-Slovenian
HPC Meeting 2024, 46. EuroCC Austria, 2024. https://doi.org/10.25365/phaidra.463.
ieee: A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per
CPU core is requested?,” in ASHPC24 - Austrian-Slovenian HPC Meeting 2024,
Grundlsee, Austria, 2024, p. 46.
ista: 'Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per
CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian
HPC Meeting, 46.'
mla: Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” ASHPC24
- Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46, doi:10.25365/phaidra.463.
short: A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian
HPC Meeting 2024, EuroCC Austria, 2024, p. 46.
conference:
end_date: 2024-06-13
location: Grundlsee, Austria
name: 'ASHPC: Austrian-Slovenian HPC Meeting'
start_date: 2024-06-10
date_created: 2024-06-14T09:06:36Z
date_published: 2024-06-13T00:00:00Z
date_updated: 2024-06-17T09:40:37Z
day: '13'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.25365/phaidra.463
file:
- access_level: open_access
checksum: f7d3dded6df2dcdb4818904cf2e1c183
content_type: application/pdf
creator: dernst
date_created: 2024-06-17T09:36:51Z
date_updated: 2024-06-17T09:36:51Z
file_id: '17153'
file_name: 2024_ASHPC_Schloegl.pdf
file_size: 206746
relation: main_file
success: 1
file_date_updated: 2024-06-17T09:36:51Z
fulldoi: https://doi.org/10.25365/phaidra.463
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '46'
publication: ASHPC24 - Austrian-Slovenian HPC Meeting 2024
publication_identifier:
isbn:
- '9783200096455'
publication_status: published
publisher: EuroCC Austria
quality_controlled: '1'
status: public
title: How much memory per CPU core is requested?
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_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17141'
abstract:
- lang: eng
text: The TIR1/AFB–Aux/IAA–ARF canonical auxin signaling pathway is widely accepted
to (de)active transcriptional regulation, thus controlling auxin-associated developmental
processes. However, the theme of a rapid auxin response has emerged since the
2018 Auxins and Cytokinin in Plant Development conference. To date, a few signaling
components have been identified to mediate both slow and rapid auxin responses,
which unveils the complexity of auxin signaling.
acknowledgement: "We thank other lab members for their critical comments on this manuscript.
We also thank the editor and reviewers for their constructive comments to improve
our manuscript. We apologize to authors whose important work we could not include
due to space limitations.\r\nThis work is supported by funding from Jiangxi Agricultural
University (9232308314) and the Science and Technology Department of Jiangxi Province
(20223BCJ25037) to HBH, and the Science and Technology Department of Jiangxi Province
(20202ACB215002) to SYP."
article_number: erae246
article_processing_charge: No
article_type: original
author:
- first_name: Zilin
full_name: Zhang, Zilin
last_name: Zhang
- first_name: Huihuang
full_name: Chen, Huihuang
id: 83c96512-15b2-11ec-abd3-b7eede36184f
last_name: Chen
- first_name: Shuaiying
full_name: Peng, Shuaiying
last_name: Peng
- first_name: Huibin
full_name: Han, Huibin
last_name: Han
citation:
ama: Zhang Z, Chen H, Peng S, Han H. Slow and rapid auxin responses in Arabidopsis.
Journal of Experimental Botany. 2024;75(18). doi:10.1093/jxb/erae246
apa: Zhang, Z., Chen, H., Peng, S., & Han, H. (2024). Slow and rapid auxin responses
in Arabidopsis. Journal of Experimental Botany. Oxford University Press.
https://doi.org/10.1093/jxb/erae246
chicago: Zhang, Zilin, Huihuang Chen, Shuaiying Peng, and Huibin Han. “Slow and
Rapid Auxin Responses in Arabidopsis.” Journal of Experimental Botany.
Oxford University Press, 2024. https://doi.org/10.1093/jxb/erae246.
ieee: Z. Zhang, H. Chen, S. Peng, and H. Han, “Slow and rapid auxin responses in
Arabidopsis,” Journal of Experimental Botany, vol. 75, no. 18. Oxford University
Press, 2024.
ista: Zhang Z, Chen H, Peng S, Han H. 2024. Slow and rapid auxin responses in Arabidopsis.
Journal of Experimental Botany. 75(18), erae246.
mla: Zhang, Zilin, et al. “Slow and Rapid Auxin Responses in Arabidopsis.” Journal
of Experimental Botany, vol. 75, no. 18, erae246, Oxford University Press,
2024, doi:10.1093/jxb/erae246.
short: Z. Zhang, H. Chen, S. Peng, H. Han, Journal of Experimental Botany 75 (2024).
date_created: 2024-06-15T19:50:15Z
date_published: 2024-09-27T00:00:00Z
date_updated: 2025-09-08T07:57:50Z
day: '27'
ddc:
- '580'
department:
- _id: GradSch
- _id: JiFr
doi: 10.1093/jxb/erae246
external_id:
isi:
- '001270051200001'
pmid:
- '38794966'
file:
- access_level: open_access
checksum: 91b9435ed0f6640809c7588df19abf2f
content_type: application/pdf
creator: dernst
date_created: 2025-01-02T10:26:22Z
date_updated: 2025-01-02T10:26:22Z
file_id: '18720'
file_name: 2024_JourExperimentalBotany_Zhang.pdf
file_size: 763097
relation: main_file
success: 1
file_date_updated: 2025-01-02T10:26:22Z
fulldoi: https://doi.org/10.1093/jxb/erae246
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Experimental Botany
publication_identifier:
issn:
- 0022-0957
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Slow and rapid auxin responses in Arabidopsis
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: 75
year: '2024'
...
---
APC_amount: 6081,83 EUR
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '17142'
abstract:
- lang: eng
text: Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected
individuals share strikingly similar and correlated behavioural traits that include
perceptual and sensory processing challenges. Notably, the severity of these sensory
symptoms is often predictive of the expression of other autistic traits. However,
the origin of these perceptual deficits remains largely elusive. Here, we show
a recurrent impairment in visual threat perception that is similarly impaired
in 3 independent mouse models of ASD with different molecular aetiologies. Interestingly,
this deficit is associated with reduced avoidance of threatening environments—a
nonperceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation,
we define the molecular mechanism. We show that the perceptual impairment is caused
by a potassium channel (Kv1)-mediated hypoexcitability in a subcortical node essential
for the initiation of escape responses, the dorsal periaqueductal grey (dPAG).
Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance
deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore,
we show that different molecular mechanisms converge on similar behavioural phenotypes
by demonstrating that the autism models Cul3 and Ptchd1, despite having similar
behavioural phenotypes, differ in their functional and molecular alteration. Our
findings reveal a link between rapid perception controlled by subcortical pathways
and appropriate learned interactions with the environment and define a nondevelopmental
source of such deficits in ASD.
acknowledgement: 'This work was supported by a European Research Council Starting
Grant 756502 (MJ). '
article_number: e3002668
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author:
- first_name: Laura
full_name: Burnett, Laura
id: 3B717F68-F248-11E8-B48F-1D18A9856A87
last_name: Burnett
orcid: 0000-0002-8937-410X
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Olga
full_name: Symonova, Olga
id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87
last_name: Symonova
orcid: 0000-0003-2012-9947
- first_name: Tomas
full_name: Masson, Tomas
id: 93ac43e8-8599-11eb-9b86-f6efb0a4c207
last_name: Masson
orcid: 0000-0002-2634-6283
- first_name: Tomas A
full_name: Vega Zuniga, Tomas A
id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87
last_name: Vega Zuniga
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
citation:
ama: Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments
in visual perception and place avoidance across different autism models are driven
by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS
Biology. 2024;22. doi:10.1371/journal.pbio.3002668
apa: Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A.,
Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual
perception and place avoidance across different autism models are driven by periaqueductal
grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. Public
Library of Science. https://doi.org/10.1371/journal.pbio.3002668
chicago: Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas
A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino,
and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and
Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey
Hypoexcitability in Setd5 Haploinsufficient Mice.” PLoS Biology. Public
Library of Science, 2024. https://doi.org/10.1371/journal.pbio.3002668.
ieee: L. Burnett et al., “Shared behavioural impairments in visual perception
and place avoidance across different autism models are driven by periaqueductal
grey hypoexcitability in Setd5 haploinsufficient mice,” PLoS Biology, vol.
22. Public Library of Science, 2024.
ista: Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras
X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments
in visual perception and place avoidance across different autism models are driven
by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS
Biology. 22, e3002668.
mla: Burnett, Laura, et al. “Shared Behavioural Impairments in Visual Perception
and Place Avoidance across Different Autism Models Are Driven by Periaqueductal
Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” PLoS Biology, vol.
22, e3002668, Public Library of Science, 2024, doi:10.1371/journal.pbio.3002668.
short: L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X.
Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, PLoS Biology 22
(2024).
corr_author: '1'
date_created: 2024-06-16T22:01:05Z
date_published: 2024-06-10T00:00:00Z
date_updated: 2025-09-08T07:57:11Z
day: '10'
ddc:
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department:
- _id: RySh
- _id: GaNo
- _id: MaJö
doi: 10.1371/journal.pbio.3002668
ec_funded: 1
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call_identifier: H2020
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url: https://doi.org/10.5281/zenodo.11130587
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scopus_import: '1'
status: public
title: Shared behavioural impairments in visual perception and place avoidance across
different autism models are driven by periaqueductal grey hypoexcitability in Setd5
haploinsufficient mice
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: 22
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...
---
_id: '17143'
abstract:
- lang: eng
text: "This paper deals with local criteria for the convergence to a global minimiser
for gradient flow trajectories and their discretisations. To obtain quantitative
estimates on the speed of convergence, we consider variations on the classical
Kurdyka–Łojasiewicz inequality for a large class of parameter functions. Our assumptions
are given in terms of the initial data, without any reference to an equilibrium
point. The main results are convergence statements for gradient flow curves and
proximal point sequences to a global minimiser, together with sharp quantitative
estimates on the speed of convergence. These convergence results apply in the
general setting of lower semicontinuous functionals on complete metric spaces,
generalising recent results for smooth functionals on Rn. While the non-smooth
setting covers very general spaces, it is also useful for (non)-smooth functionals
on Rn.\r\n."
acknowledgement: The authors gratefully acknowledges support by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No. 716117). This research was funded in part by the Austrian Science
Fund (FWF) project 10.55776/ESP208. This research was funded in part by the Austrian
Science Fund (FWF) project 10.55776/F65
article_processing_charge: No
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arxiv: 1
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
- first_name: Francesco
full_name: Pedrotti, Francesco
id: d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c
last_name: Pedrotti
citation:
ama: Dello Schiavo L, Maas J, Pedrotti F. Local conditions for global convergence
of gradient flows and proximal point sequences in metric spaces. Transactions
of the American Mathematical Society. 2024;377(6):3779-3804. doi:10.1090/tran/9156
apa: Dello Schiavo, L., Maas, J., & Pedrotti, F. (2024). Local conditions for
global convergence of gradient flows and proximal point sequences in metric spaces.
Transactions of the American Mathematical Society. American Mathematical
Society. https://doi.org/10.1090/tran/9156
chicago: Dello Schiavo, Lorenzo, Jan Maas, and Francesco Pedrotti. “Local Conditions
for Global Convergence of Gradient Flows and Proximal Point Sequences in Metric
Spaces.” Transactions of the American Mathematical Society. American Mathematical
Society, 2024. https://doi.org/10.1090/tran/9156.
ieee: L. Dello Schiavo, J. Maas, and F. Pedrotti, “Local conditions for global convergence
of gradient flows and proximal point sequences in metric spaces,” Transactions
of the American Mathematical Society, vol. 377, no. 6. American Mathematical
Society, pp. 3779–3804, 2024.
ista: Dello Schiavo L, Maas J, Pedrotti F. 2024. Local conditions for global convergence
of gradient flows and proximal point sequences in metric spaces. Transactions
of the American Mathematical Society. 377(6), 3779–3804.
mla: Dello Schiavo, Lorenzo, et al. “Local Conditions for Global Convergence of
Gradient Flows and Proximal Point Sequences in Metric Spaces.” Transactions
of the American Mathematical Society, vol. 377, no. 6, American Mathematical
Society, 2024, pp. 3779–804, doi:10.1090/tran/9156.
short: L. Dello Schiavo, J. Maas, F. Pedrotti, Transactions of the American Mathematical
Society 377 (2024) 3779–3804.
date_created: 2024-06-16T22:01:06Z
date_published: 2024-06-01T00:00:00Z
date_updated: 2026-04-07T13:00:02Z
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doi: 10.1090/tran/9156
ec_funded: 1
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isi: 1
issue: '6'
language:
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main_file_link:
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url: https://doi.org/10.48550/arXiv.2304.05239
month: '06'
oa: 1
oa_version: Preprint
page: 3779-3804
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call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
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grant_number: F6504
name: Taming Complexity in Partial Differential Systems
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grant_number: E208
name: Configuration Spaces over Non-Smooth Spaces
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
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issn:
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publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
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scopus_import: '1'
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title: Local conditions for global convergence of gradient flows and proximal point
sequences in metric spaces
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user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 377
year: '2024'
...