---
OA_place: repository
OA_type: green
_id: '20050'
abstract:
- lang: eng
text: We prove upper bounds on the L∞-Wasserstein distance from optimal transport
between strongly log-concave probability densities and log-Lipschitz perturbations.
In the simplest setting, such a bound amounts to a transport-information inequality
involving the L∞-Wasserstein metric and the relative L∞-Fisher information. We
show that this inequality can be sharpened significantly in situations where the
involved densities are anisotropic. Our proof is based on probabilistic techniques
using Langevin dynamics. As an application of these results, we obtain sharp exponential
rates of convergence in Fisher’s infinitesimal model from quantitative genetics,
generalising recent results by Calvez, Poyato, and Santambrogio in dimension 1
to arbitrary dimensions.
acknowledgement: This research was funded in part by the Austrian Science Fund (FWF)
project 10.55776/F65 and the Austrian Academy of Science, DOC fellowship nr. 26293.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- 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: Khudiakova K, Maas J, Pedrotti F. L∞-optimal transport of anisotropic log-concave
measures and exponential convergence in Fisher’s infinitesimal model. The Annals
of Applied Probability. 2025;35(3):1913-1940. doi:10.1214/25-aap2162
apa: Khudiakova, K., Maas, J., & Pedrotti, F. (2025). L∞-optimal transport of
anisotropic log-concave measures and exponential convergence in Fisher’s infinitesimal
model. The Annals of Applied Probability. Institute of Mathematical Statistics.
https://doi.org/10.1214/25-aap2162
chicago: Khudiakova, Kseniia, Jan Maas, and Francesco Pedrotti. “L∞-Optimal Transport
of Anisotropic Log-Concave Measures and Exponential Convergence in Fisher’s Infinitesimal
Model.” The Annals of Applied Probability. Institute of Mathematical Statistics,
2025. https://doi.org/10.1214/25-aap2162.
ieee: K. Khudiakova, J. Maas, and F. Pedrotti, “L∞-optimal transport of anisotropic
log-concave measures and exponential convergence in Fisher’s infinitesimal model,”
The Annals of Applied Probability, vol. 35, no. 3. Institute of Mathematical
Statistics, pp. 1913–1940, 2025.
ista: Khudiakova K, Maas J, Pedrotti F. 2025. L∞-optimal transport of anisotropic
log-concave measures and exponential convergence in Fisher’s infinitesimal model.
The Annals of Applied Probability. 35(3), 1913–1940.
mla: Khudiakova, Kseniia, et al. “L∞-Optimal Transport of Anisotropic Log-Concave
Measures and Exponential Convergence in Fisher’s Infinitesimal Model.” The
Annals of Applied Probability, vol. 35, no. 3, Institute of Mathematical Statistics,
2025, pp. 1913–40, doi:10.1214/25-aap2162.
short: K. Khudiakova, J. Maas, F. Pedrotti, The Annals of Applied Probability 35
(2025) 1913–1940.
corr_author: '1'
date_created: 2025-07-21T08:13:54Z
date_published: 2025-06-01T00:00:00Z
date_updated: 2025-09-30T14:12:48Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/25-aap2162
external_id:
arxiv:
- '2402.04151'
isi:
- '001523520000012'
intvolume: ' 35'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2402.04151
month: '06'
oa: 1
oa_version: Preprint
page: 1913-1940
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
publication: The Annals of Applied Probability
publication_identifier:
issn:
- 1050-5164
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
related_material:
record:
- id: '17352'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: L∞-optimal transport of anisotropic log-concave measures and exponential convergence
in Fisher’s infinitesimal model
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20051'
abstract:
- lang: eng
text: "We revisit the majority problem in the population protocol communication
model, as first studied by Angluin et al. (Distributed Computing 2008). We consider
a more general version of this problem known as plurality consensus, which has
already been studied intensively in the literature. In this problem, each node
in a system of n nodes, has initially one of k different opinions, and they need
to agree on the (relative) majority opinion. In particular, we consider the important
and intensively studied model of Undecided State Dynamics.\r\nOur main contribution
is an almost tight lower bound on the stabilization time: we prove that there
exists an initial configuration, even with bias \\Delta = \\omega(\\sqrt{n\\log
n}), where stabilization requires \\Omega(kn\\log \\frac {\\sqrt n} {k \\log n})
interactions, or equivalently, \\Omega(k\\log \\frac {\\sqrt n} {k \\log n}) parallel
time for any k = o\\left(\\frac {\\sqrt n}{\\log n}\\right). This bound is tight
for any k \\le n^{\\frac 1 2 - \\epsilon}, where \\epsilon >0 can be any small
constant, as Amir et al.~(PODC'23) gave a O(k\\log n) parallel time upper bound
for k = O\\left(\\frac {\\sqrt n} {\\log ^2 n}\\right)."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/I5862,grant
DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with\r\nadditional funding from
the netidee SCIENCE Stiftung, 2020–2024\r\nand the German Research Foundation (DFG),
grant 470029389\r\n(FlexNets)."
article_processing_charge: Yes (via OA deal)
arxiv: 1
author:
- first_name: Antoine
full_name: El-Hayek, Antoine
id: 888a098e-fcac-11ee-aff7-d347be57b725
last_name: El-Hayek
orcid: 0000-0003-4268-7368
- first_name: Robert
full_name: Elsässer, Robert
last_name: Elsässer
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'El-Hayek A, Elsässer R, Schmid S. An almost tight lower bound for plurality
consensus with undecided state dynamics in the population protocol model. In:
Proceedings of the ACM Symposium on Principles of Distributed Computing.
Association for Computing Machinery; 2025. doi:10.1145/3732772.3733505'
apa: 'El-Hayek, A., Elsässer, R., & Schmid, S. (2025). An almost tight lower
bound for plurality consensus with undecided state dynamics in the population
protocol model. In Proceedings of the ACM Symposium on Principles of Distributed
Computing. Huatulco, Mexico: Association for Computing Machinery. https://doi.org/10.1145/3732772.3733505'
chicago: El-Hayek, Antoine, Robert Elsässer, and Stefan Schmid. “An Almost Tight
Lower Bound for Plurality Consensus with Undecided State Dynamics in the Population
Protocol Model.” In Proceedings of the ACM Symposium on Principles of Distributed
Computing. Association for Computing Machinery, 2025. https://doi.org/10.1145/3732772.3733505.
ieee: A. El-Hayek, R. Elsässer, and S. Schmid, “An almost tight lower bound for
plurality consensus with undecided state dynamics in the population protocol model,”
in Proceedings of the ACM Symposium on Principles of Distributed Computing,
Huatulco, Mexico, 2025.
ista: 'El-Hayek A, Elsässer R, Schmid S. 2025. An almost tight lower bound for plurality
consensus with undecided state dynamics in the population protocol model. Proceedings
of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on
Principles of Distributed Computing.'
mla: El-Hayek, Antoine, et al. “An Almost Tight Lower Bound for Plurality Consensus
with Undecided State Dynamics in the Population Protocol Model.” Proceedings
of the ACM Symposium on Principles of Distributed Computing, Association for
Computing Machinery, 2025, doi:10.1145/3732772.3733505.
short: A. El-Hayek, R. Elsässer, S. Schmid, in:, Proceedings of the ACM Symposium
on Principles of Distributed Computing, Association for Computing Machinery, 2025.
conference:
end_date: 2025-06-20
location: Huatulco, Mexico
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2025-06-16
corr_author: '1'
date_created: 2025-07-21T08:16:15Z
date_published: 2025-06-13T00:00:00Z
date_updated: 2025-10-16T13:08:45Z
day: '13'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.1145/3732772.3733505
ec_funded: 1
external_id:
arxiv:
- '2505.02765'
isi:
- '001525534800066'
file:
- access_level: open_access
checksum: 52976d226f3f691aa519d71c1c718fa5
content_type: application/pdf
creator: dernst
date_created: 2025-08-04T09:10:55Z
date_updated: 2025-08-04T09:10:55Z
file_id: '20115'
file_name: 2025_PODC_ElHayek.pdf
file_size: 2200347
relation: main_file
success: 1
file_date_updated: 2025-08-04T09:10:55Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: Proceedings of the ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- ' 9798400718854'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: An almost tight lower bound for plurality consensus with undecided state dynamics
in the population protocol model
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
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20052'
abstract:
- lang: eng
text: "This paper revisits a fundamental distributed computing problem in the population
protocol model. Provided n agents each starting with an input color in [k], the
relative majority problem asks to find the predominant color. In the population
protocol model, at each time step, a scheduler selects two agents that first learn
each other's states and then update their states based on what they learned.\r\nWe
present the Circles protocol that solves the relative majority problem with k3
states. It is always-correct under weakly fair scheduling. Not only does it improve
upon the best known upper bound of O(k7), but it also shows a strikingly simpler
design inspired by energy minimization in chemical settings."
acknowledgement: 'This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/I5982,
and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung,
2020–2024 and the German Research Foundation (DFG), grant 470029389 (FlexNets). '
article_processing_charge: No
author:
- first_name: Tom-Lukas
full_name: Breitkopf, Tom-Lukas
last_name: Breitkopf
- first_name: Julien
full_name: Dallot, Julien
last_name: Dallot
- first_name: Antoine
full_name: El-Hayek, Antoine
id: 888a098e-fcac-11ee-aff7-d347be57b725
last_name: El-Hayek
orcid: 0000-0003-4268-7368
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
citation:
ama: 'Breitkopf T-L, Dallot J, El-Hayek A, Schmid S. Brief announcement: Minimizing
energy solves relative majority with a cubic number of states in population protocols.
In: Proceedings of the ACM Symposium on Principles of Distributed Computing.
Association for Computing Machinery; 2025:549-552. doi:10.1145/3732772.3733512'
apa: 'Breitkopf, T.-L., Dallot, J., El-Hayek, A., & Schmid, S. (2025). Brief
announcement: Minimizing energy solves relative majority with a cubic number of
states in population protocols. In Proceedings of the ACM Symposium on Principles
of Distributed Computing (pp. 549–552). Huatulco, Mexico: Association for
Computing Machinery. https://doi.org/10.1145/3732772.3733512'
chicago: 'Breitkopf, Tom-Lukas, Julien Dallot, Antoine El-Hayek, and Stefan Schmid.
“Brief Announcement: Minimizing Energy Solves Relative Majority with a Cubic Number
of States in Population Protocols.” In Proceedings of the ACM Symposium on
Principles of Distributed Computing, 549–52. Association for Computing Machinery,
2025. https://doi.org/10.1145/3732772.3733512.'
ieee: 'T.-L. Breitkopf, J. Dallot, A. El-Hayek, and S. Schmid, “Brief announcement:
Minimizing energy solves relative majority with a cubic number of states in population
protocols,” in Proceedings of the ACM Symposium on Principles of Distributed
Computing, Huatulco, Mexico, 2025, pp. 549–552.'
ista: 'Breitkopf T-L, Dallot J, El-Hayek A, Schmid S. 2025. Brief announcement:
Minimizing energy solves relative majority with a cubic number of states in population
protocols. Proceedings of the ACM Symposium on Principles of Distributed Computing.
PODC: Symposium on Principles of Distributed Computing, 549–552.'
mla: 'Breitkopf, Tom-Lukas, et al. “Brief Announcement: Minimizing Energy Solves
Relative Majority with a Cubic Number of States in Population Protocols.” Proceedings
of the ACM Symposium on Principles of Distributed Computing, Association for
Computing Machinery, 2025, pp. 549–52, doi:10.1145/3732772.3733512.'
short: T.-L. Breitkopf, J. Dallot, A. El-Hayek, S. Schmid, in:, Proceedings of the
ACM Symposium on Principles of Distributed Computing, Association for Computing
Machinery, 2025, pp. 549–552.
conference:
end_date: 2025-06-20
location: Huatulco, Mexico
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2025-06-16
corr_author: '1'
date_created: 2025-07-21T08:17:04Z
date_published: 2025-06-13T00:00:00Z
date_updated: 2026-02-16T11:46:37Z
day: '13'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.1145/3732772.3733512
ec_funded: 1
external_id:
isi:
- '001525534800069'
file:
- access_level: open_access
checksum: e99679ffb28877b7cea4d54860302790
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T07:32:01Z
date_updated: 2025-08-05T07:32:01Z
file_id: '20123'
file_name: 2025_PODC_Breitkopf.pdf
file_size: 549706
relation: main_file
success: 1
file_date_updated: 2025-08-05T07:32:01Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 549-552
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: Proceedings of the ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9798400718854'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: 'Brief announcement: Minimizing energy solves relative majority with a cubic
number of states in population protocols'
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
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20053'
abstract:
- lang: eng
text: "Liquid democracy is a transitive vote delegation mechanism over voting graphs.
It enables each voter to delegate their vote(s) to another better-informed voter,
with the goal of collectively making a better decision. The question of whether
liquid democracy outperforms direct voting has been previously studied in the
context of local delegation mechanisms (where voters can only delegate to someone
in their neighbourhood) and binary decision problems. It has previously been shown
that it is impossible for local delegation mechanisms to outperform direct voting
in general graphs. This raises the question: for which classes of graphs do local
delegation mechanisms yield good results?\r\nIn this work, we analyse (1) properties
of specific graphs and (2) properties of local delegation mechanisms on these
graphs, determining where local delegation actually outperforms direct voting.
We show that a critical graph property enabling liquid democracy is that the voting
outcome of local delegation mechanisms preserves a sufficient amount of variance,
thereby avoiding situations where delegation falls behind direct voting1. These
insights allow us to prove our main results, namely that there exist local delegation
mechanisms that perform no worse and in fact quantitatively better than direct
voting in natural graph topologies like complete, random d-regular, and bounded
degree graphs, lending a more nuanced perspective to previous impossibility results."
acknowledgement: This work was partially supported by MOE-T2EP20122-0014 (DataDriven
Distributed Algorithms), German Research Foundation (DFG) project ReNO (SPP 2378)
from 2023-2027, ERC CoG 863818 (ForMSMArt) and Austrian Science Fund (FWF) 10.55776/COE12.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Seth
full_name: Gilbert, Seth
last_name: Gilbert
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
orcid: 0009-0001-3676-4809
citation:
ama: 'Chatterjee K, Gilbert S, Schmid S, Svoboda J, Yeo MX. When is liquid democracy
possible?: On the manipulation of variance. In: Proceedings of the ACM Symposium
on Principles of Distributed Computing. Association for Computing Machinery;
2025:241-251. doi:10.1145/3732772.3733544'
apa: 'Chatterjee, K., Gilbert, S., Schmid, S., Svoboda, J., & Yeo, M. X. (2025).
When is liquid democracy possible?: On the manipulation of variance. In Proceedings
of the ACM Symposium on Principles of Distributed Computing (pp. 241–251).
Huatulco, Mexico: Association for Computing Machinery. https://doi.org/10.1145/3732772.3733544'
chicago: 'Chatterjee, Krishnendu, Seth Gilbert, Stefan Schmid, Jakub Svoboda, and
Michelle X Yeo. “When Is Liquid Democracy Possible?: On the Manipulation of Variance.”
In Proceedings of the ACM Symposium on Principles of Distributed Computing,
241–51. Association for Computing Machinery, 2025. https://doi.org/10.1145/3732772.3733544.'
ieee: 'K. Chatterjee, S. Gilbert, S. Schmid, J. Svoboda, and M. X. Yeo, “When is
liquid democracy possible?: On the manipulation of variance,” in Proceedings
of the ACM Symposium on Principles of Distributed Computing, Huatulco, Mexico,
2025, pp. 241–251.'
ista: 'Chatterjee K, Gilbert S, Schmid S, Svoboda J, Yeo MX. 2025. When is liquid
democracy possible?: On the manipulation of variance. Proceedings of the ACM Symposium
on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed
Computing, 241–251.'
mla: 'Chatterjee, Krishnendu, et al. “When Is Liquid Democracy Possible?: On the
Manipulation of Variance.” Proceedings of the ACM Symposium on Principles of
Distributed Computing, Association for Computing Machinery, 2025, pp. 241–51,
doi:10.1145/3732772.3733544.'
short: K. Chatterjee, S. Gilbert, S. Schmid, J. Svoboda, M.X. Yeo, in:, Proceedings
of the ACM Symposium on Principles of Distributed Computing, Association for Computing
Machinery, 2025, pp. 241–251.
conference:
end_date: 2025-06-20
location: Huatulco, Mexico
name: 'PODC: Symposium on Principles of Distributed Computing'
start_date: 2025-06-16
corr_author: '1'
date_created: 2025-07-21T08:18:26Z
date_published: 2025-06-13T00:00:00Z
date_updated: 2026-02-16T11:46:51Z
day: '13'
ddc:
- '000'
department:
- _id: KrCh
- _id: KrPi
doi: 10.1145/3732772.3733544
ec_funded: 1
external_id:
isi:
- '001525534800030'
file:
- access_level: open_access
checksum: cd628fe54d96e9fc6cc789bb8145422b
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T07:15:31Z
date_updated: 2025-08-05T07:15:31Z
file_id: '20122'
file_name: 2025_PODC_Chatterjee.pdf
file_size: 783297
relation: main_file
success: 1
file_date_updated: 2025-08-05T07:15:31Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2025/745
month: '06'
oa: 1
oa_version: Published Version
page: 241-251
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the ACM Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9798400718854'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: 'When is liquid democracy possible?: On the manipulation of variance'
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
year: '2025'
...
---
_id: '20054'
article_number: '220'
article_processing_charge: No
author:
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
citation:
ama: 'Horta S. Solid state diffusion in metal-semiconductors core-shell nanoparticle.
In: Proceedings of the MATSUS Spring 2025 Conference. Fundació de la comunitat
valenciana SCITO; 2025. doi:10.29363/nanoge.matsusspring.2025.220'
apa: 'Horta, S. (2025). Solid state diffusion in metal-semiconductors core-shell
nanoparticle. In Proceedings of the MATSUS Spring 2025 Conference. Sevilla,
Spain: Fundació de la comunitat valenciana SCITO. https://doi.org/10.29363/nanoge.matsusspring.2025.220'
chicago: Horta, Sharona. “Solid State Diffusion in Metal-Semiconductors Core-Shell
Nanoparticle.” In Proceedings of the MATSUS Spring 2025 Conference. Fundació
de la comunitat valenciana SCITO, 2025. https://doi.org/10.29363/nanoge.matsusspring.2025.220.
ieee: S. Horta, “Solid state diffusion in metal-semiconductors core-shell nanoparticle,”
in Proceedings of the MATSUS Spring 2025 Conference, Sevilla, Spain, 2025.
ista: 'Horta S. 2025. Solid state diffusion in metal-semiconductors core-shell nanoparticle.
Proceedings of the MATSUS Spring 2025 Conference. MATSUS: Materials for Sustainable
Development Conference, 220.'
mla: Horta, Sharona. “Solid State Diffusion in Metal-Semiconductors Core-Shell Nanoparticle.”
Proceedings of the MATSUS Spring 2025 Conference, 220, Fundació de la comunitat
valenciana SCITO, 2025, doi:10.29363/nanoge.matsusspring.2025.220.
short: S. Horta, in:, Proceedings of the MATSUS Spring 2025 Conference, Fundació
de la comunitat valenciana SCITO, 2025.
conference:
end_date: 2025-03-07
location: Sevilla, Spain
name: 'MATSUS: Materials for Sustainable Development Conference'
start_date: 2025-03-03
corr_author: '1'
date_created: 2025-07-21T08:22:29Z
date_published: 2025-03-03T00:00:00Z
date_updated: 2025-09-23T09:04:03Z
day: '03'
department:
- _id: MaIb
doi: 10.29363/nanoge.matsusspring.2025.220
language:
- iso: eng
month: '03'
oa_version: None
publication: Proceedings of the MATSUS Spring 2025 Conference
publication_status: published
publisher: Fundació de la comunitat valenciana SCITO
quality_controlled: '1'
status: public
title: Solid state diffusion in metal-semiconductors core-shell nanoparticle
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_type: closed access
_id: '20055'
abstract:
- lang: eng
text: Supercrystals represent three-dimensional orderings of colloidal nanocrystals
(NCs), showcasing collective properties in photonics, phononics, and electronics
applications.1,2 Recent studies have shown that such assemblies are directly produced
during nanocrystal reactions.3–6 However, a fundamental understanding of in situ
formed supercrystals that withstand typical NC purification processes remains
underexplored, which is important for further use. Herein, we report the reaction
precursor-mediated formation of stable PbTe supercrystals. Rationalizing the formation
of these assemblies through small-angle x-ray scattering (SAXS) measurements,
we unveil their formation mechanism. Our findings reveal that the supercrystal
formation occurs in the presence of an excess of lead oleates in the crude solution.
It should be noted that the formed supercrystals can be stabilized under specific
conditions determined by the lead oleate cluster concentration, content of trioctylphosphine
telluride (TOP-Te), NC size and the need of an annealing step at mild conditions.
Furthermore, this approach allows for the continuous growth of a secondary phase
within the supercrystal; for example in the case of PbTe supercrystals, a PbS
shell can be grown on each PbTe NC constituent, resulting in core-shell PbTe-PbS
supercrystals. Our work elucidates that reaction precursors play an important
role in in situ SC formation and stabilization, implying the possibility of applying
this knowledge to other NC reactions.
acknowledged_ssus:
- _id: EM-Fac
- _id: NMR
- _id: LifeSc
acknowledgement: ISTA and the Werner Siemens Foundation financially supported this
work. The Scientific Service Units (SSU) of ISTA supported this research through
resources provided by the Electron Microscopy Facility (EMF), NMR Facility and the
Lab Support Facility (LSF).
article_number: '173'
article_processing_charge: No
author:
- first_name: Seungho
full_name: Lee, Seungho
id: BB243B88-D767-11E9-B658-BC13E6697425
last_name: Lee
orcid: 0000-0002-6962-8598
- first_name: Daniel
full_name: Balazs, Daniel
id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E
last_name: Balazs
orcid: 0000-0001-7597-043X
- first_name: Sharona
full_name: Horta, Sharona
id: 03a7e858-01b1-11ec-8b71-99ae6c4a05bc
last_name: Horta
- first_name: Aiswarya
full_name: Rayaroth Puthiyaveettil, Aiswarya
id: 8aceb01b-8972-11ed-ae7b-d5fe53775add
last_name: Rayaroth Puthiyaveettil
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
citation:
ama: 'Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. Reaction precursor-mediated
formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case.
In: Proceedings of the MATSUS Spring 2025 Conference. Fundació de la comunitat
valenciana SCITO; 2025. doi:10.29363/nanoge.matsusspring.2025.173'
apa: 'Lee, S., Balazs, D., Horta, S., Rayaroth Puthiyaveettil, A., & Ibáñez,
M. (2025). Reaction precursor-mediated formation of stable supercrystals in colloidal
nanocrystal synthesis: PbTe case. In Proceedings of the MATSUS Spring 2025
Conference. Sevilla, Spain: Fundació de la comunitat valenciana SCITO. https://doi.org/10.29363/nanoge.matsusspring.2025.173'
chicago: 'Lee, Seungho, Daniel Balazs, Sharona Horta, Aiswarya Rayaroth Puthiyaveettil,
and Maria Ibáñez. “Reaction Precursor-Mediated Formation of Stable Supercrystals
in Colloidal Nanocrystal Synthesis: PbTe Case.” In Proceedings of the MATSUS
Spring 2025 Conference. Fundació de la comunitat valenciana SCITO, 2025. https://doi.org/10.29363/nanoge.matsusspring.2025.173.'
ieee: 'S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, and M. Ibáñez, “Reaction
precursor-mediated formation of stable supercrystals in colloidal nanocrystal
synthesis: PbTe case,” in Proceedings of the MATSUS Spring 2025 Conference,
Sevilla, Spain, 2025.'
ista: 'Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. 2025. Reaction
precursor-mediated formation of stable supercrystals in colloidal nanocrystal
synthesis: PbTe case. Proceedings of the MATSUS Spring 2025 Conference. MATSUS:
Materials for Sustainable Development Conference, 173.'
mla: 'Lee, Seungho, et al. “Reaction Precursor-Mediated Formation of Stable Supercrystals
in Colloidal Nanocrystal Synthesis: PbTe Case.” Proceedings of the MATSUS Spring
2025 Conference, 173, Fundació de la comunitat valenciana SCITO, 2025, doi:10.29363/nanoge.matsusspring.2025.173.'
short: S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, M. Ibáñez, in:,
Proceedings of the MATSUS Spring 2025 Conference, Fundació de la comunitat valenciana
SCITO, 2025.
conference:
end_date: 2025-03-07
location: Sevilla, Spain
name: 'MATSUS: Materials for Sustainable Development Conference'
start_date: 2025-03-03
corr_author: '1'
date_created: 2025-07-21T08:33:20Z
date_published: 2025-03-15T00:00:00Z
date_updated: 2026-02-19T09:25:57Z
day: '15'
department:
- _id: MaIb
- _id: LifeSc
doi: 10.29363/nanoge.matsusspring.2025.173
language:
- iso: eng
month: '03'
oa_version: None
project:
- _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A
name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of
Semiconductors for Waste Heat Recovery'
publication: Proceedings of the MATSUS Spring 2025 Conference
publication_status: published
publisher: Fundació de la comunitat valenciana SCITO
quality_controlled: '1'
status: public
title: 'Reaction precursor-mediated formation of stable supercrystals in colloidal
nanocrystal synthesis: PbTe case'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20056'
abstract:
- lang: eng
text: Theoretical studies have shown that stochasticity can affect the dynamics
of ecosystems in counterintuitive ways. However, without knowing the equations
governing the dynamics of populations or ecosystems, it is difficult to ascertain
the role of stochasticity in real datasets. Therefore, the inverse problem of
inferring the governing stochastic equations from datasets is important. Here,
we present an equation discovery methodology that takes time series data of state
variables as input and outputs a stochastic differential equation. We achieve
this by combining traditional approaches from stochastic calculus with the equation
discovery techniques. We demonstrate the generality of the method via several
applications. First, we deliberately choose various stochastic models with fundamentally
different governing equations, yet they produce nearly identical steady-state
distributions. We show that we can recover the correct underlying equations, and
thus infer the structure of their stability, accurately from the analysis of time
series data alone. We demonstrate our method on two real-world datasets—fish schooling
and single-cell migration—that have vastly different spatiotemporal scales and
dynamics. We illustrate various limitations and potential pitfalls of the method
and how to overcome them via diagnostic measures. Finally, we provide our open-source
code via a package named PyDaDDy (Python Library for Data-Driven Dynamics).
acknowledgement: V.G. acknowledges support from the Science and Engi-neering Research
Board, Department of Biotechnology,and the Indo-French Centre for the Promotion
of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of
Science and Technology (DST) In-novation in Science Pursuit for Inspired Research
(IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral
fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B.
acknowledges support from the NOMIS Founda-tion and an European Molecular Biology
Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge
support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar,
Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments
on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada
translation of the title and abstract.Data-Driven Model Discovery E115
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Arshed
full_name: Nabeel, Arshed
last_name: Nabeel
- first_name: Ashwin
full_name: Karichannavar, Ashwin
last_name: Karichannavar
- first_name: Shuaib
full_name: Palathingal, Shuaib
last_name: Palathingal
- first_name: Jitesh
full_name: Jhawar, Jitesh
last_name: Jhawar
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Danny
full_name: Raj M, Danny
last_name: Raj M
- first_name: Vishwesha
full_name: Guttal, Vishwesha
last_name: Guttal
citation:
ama: Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical
equations from ecological time series data. The American Naturalist. 2025;205(4):E100-E117.
doi:10.1086/734083
apa: Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj
M, D., & Guttal, V. (2025). Discovering stochastic dynamical equations from
ecological time series data. The American Naturalist. University of Chicago
Press. https://doi.org/10.1086/734083
chicago: Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar,
David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical
Equations from Ecological Time Series Data.” The American Naturalist. University
of Chicago Press, 2025. https://doi.org/10.1086/734083.
ieee: A. Nabeel et al., “Discovering stochastic dynamical equations from
ecological time series data,” The American Naturalist, vol. 205, no. 4.
University of Chicago Press, pp. E100–E117, 2025.
ista: Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal
V. 2025. Discovering stochastic dynamical equations from ecological time series
data. The American Naturalist. 205(4), E100–E117.
mla: Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological
Time Series Data.” The American Naturalist, vol. 205, no. 4, University
of Chicago Press, 2025, pp. E100–17, doi:10.1086/734083.
short: A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj
M, V. Guttal, The American Naturalist 205 (2025) E100–E117.
date_created: 2025-07-21T08:37:27Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-09-30T14:14:43Z
day: '01'
department:
- _id: EdHa
doi: 10.1086/734083
external_id:
arxiv:
- '2205.02645'
isi:
- '001433250500001'
pmid:
- '40179429'
intvolume: ' 205'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2205.02645
month: '04'
oa: 1
oa_version: Preprint
page: E100-E117
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: The American Naturalist
publication_identifier:
eissn:
- 1537-5323
issn:
- 0003-0147
publication_status: published
publisher: University of Chicago Press
quality_controlled: '1'
related_material:
record:
- id: '20121'
relation: software
status: public
status: public
title: Discovering stochastic dynamical equations from ecological time series data
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 205
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20077'
abstract:
- lang: eng
text: Hyaluronic acid (HA) is a key extracellular matrix component of vertebrates,
where it mediates cell adhesion, immune regulation, and tissue remodeling through
its interaction with specific receptors. Although HA has been detected in a few
invertebrate species, the lack of fundamental components of the molecular HA pathway
poses relevant objections about its functional role in these species. Mining genomic
and transcriptomic data, we considered the conservation of the gene locus encoding
for the extracellular link protein (XLINK) in marine mussels as well as its expression
patterns. Structural and phylogenetic analyses were undertaken to evaluate possible
similarities with vertebrate orthologs and to infer the origin of this gene in
invertebrates. Biochemical analysis was used to quantify HA in tissues of Mytilus
galloprovincialis. As a result, we confirm that the mussel can produce HA (up
to 1.02 ng/mg in mantle) and that its genome encodes two XLINK gene loci. These
loci are conserved in Mytilidae species and show a complex evolutionary path.
Mussel XLINK genes appeared to be expressed during developmental stages in three
mussel species, ranking in the top 100 expressed genes in M. trossulus at 17 h
post-fertilization. In conclusion, the presence of HA and an active gene with
the potential to bind HA suggests that mussels have the potential to synthesize
and use HA and are among the few invertebrates encoding this gene.
acknowledgement: 'This research was funded by the Italian Ministry of University and
Research (MIUR), grant ID: P2022JEEMT (Developing a tool for the study of haplotype
diversity in Mytilus galloprovincialis (HAMIGA)).'
article_number: '930'
article_processing_charge: Yes
article_type: original
author:
- first_name: Umberto
full_name: Rosani, Umberto
last_name: Rosani
- first_name: Nehir
full_name: Altan, Nehir
last_name: Altan
- first_name: Paola
full_name: Venier, Paola
last_name: Venier
- first_name: Enrico
full_name: Bortoletto, Enrico
last_name: Bortoletto
- first_name: Nicola
full_name: Volpi, Nicola
last_name: Volpi
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. Ancestral origin
and functional expression of a hyaluronic acid pathway complement in mussels.
Biology. 2025;14(8). doi:10.3390/biology14080930
apa: Rosani, U., Altan, N., Venier, P., Bortoletto, E., Volpi, N., & Bernecky,
C. (2025). Ancestral origin and functional expression of a hyaluronic acid pathway
complement in mussels. Biology. MDPI. https://doi.org/10.3390/biology14080930
chicago: Rosani, Umberto, Nehir Altan, Paola Venier, Enrico Bortoletto, Nicola Volpi,
and Carrie Bernecky. “Ancestral Origin and Functional Expression of a Hyaluronic
Acid Pathway Complement in Mussels.” Biology. MDPI, 2025. https://doi.org/10.3390/biology14080930.
ieee: U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, and C. Bernecky,
“Ancestral origin and functional expression of a hyaluronic acid pathway complement
in mussels,” Biology, vol. 14, no. 8. MDPI, 2025.
ista: Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. 2025. Ancestral
origin and functional expression of a hyaluronic acid pathway complement in mussels.
Biology. 14(8), 930.
mla: Rosani, Umberto, et al. “Ancestral Origin and Functional Expression of a Hyaluronic
Acid Pathway Complement in Mussels.” Biology, vol. 14, no. 8, 930, MDPI,
2025, doi:10.3390/biology14080930.
short: U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, C. Bernecky, Biology
14 (2025).
date_created: 2025-07-25T08:28:26Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2025-09-30T14:10:07Z
day: '24'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.3390/biology14080930
external_id:
isi:
- '001557922100001'
file:
- access_level: open_access
checksum: f5e059e66803fa54249c1db029aef0f6
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T09:11:09Z
date_updated: 2025-07-31T09:11:09Z
file_id: '20097'
file_name: 2025_Biology_Rosani.pdf
file_size: 1885781
relation: main_file
success: 1
file_date_updated: 2025-07-31T09:11:09Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Biology
publication_identifier:
issn:
- 2079-7737
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Ancestral origin and functional expression of a hyaluronic acid pathway complement
in mussels
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: 14
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20078'
abstract:
- lang: eng
text: 'Let A be an abelian variety defined over a number field K, E/K be an elliptic
curve, and ϕ : A → Em be an isogeny defined over K. Let P ∈ A(K) be such that
ϕ(P)=(Q1,..., Qm) with RankZ(⟨Q1,...,Qm⟩)=1. We will study a divisibility sequence
related to the point P and show its relation with elliptic divisibility sequences.'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Stefan
full_name: Barańczuk, Stefan
last_name: Barańczuk
- first_name: Bartosz
full_name: Naskręcki, Bartosz
last_name: Naskręcki
- first_name: Matteo
full_name: Verzobio, Matteo
id: 7aa8f170-131e-11ed-88e1-a9efd01027cb
last_name: Verzobio
orcid: 0000-0002-0854-0306
citation:
ama: Barańczuk S, Naskręcki B, Verzobio M. Divisibility sequences related to abelian
varieties isogenous to a power of an elliptic curve. Journal of Number Theory.
2025;279:170-183. doi:10.1016/j.jnt.2025.06.001
apa: Barańczuk, S., Naskręcki, B., & Verzobio, M. (2025). Divisibility sequences
related to abelian varieties isogenous to a power of an elliptic curve. Journal
of Number Theory. Elsevier. https://doi.org/10.1016/j.jnt.2025.06.001
chicago: Barańczuk, Stefan, Bartosz Naskręcki, and Matteo Verzobio. “Divisibility
Sequences Related to Abelian Varieties Isogenous to a Power of an Elliptic Curve.”
Journal of Number Theory. Elsevier, 2025. https://doi.org/10.1016/j.jnt.2025.06.001.
ieee: S. Barańczuk, B. Naskręcki, and M. Verzobio, “Divisibility sequences related
to abelian varieties isogenous to a power of an elliptic curve,” Journal of
Number Theory, vol. 279. Elsevier, pp. 170–183, 2025.
ista: Barańczuk S, Naskręcki B, Verzobio M. 2025. Divisibility sequences related
to abelian varieties isogenous to a power of an elliptic curve. Journal of Number
Theory. 279, 170–183.
mla: Barańczuk, Stefan, et al. “Divisibility Sequences Related to Abelian Varieties
Isogenous to a Power of an Elliptic Curve.” Journal of Number Theory, vol.
279, Elsevier, 2025, pp. 170–83, doi:10.1016/j.jnt.2025.06.001.
short: S. Barańczuk, B. Naskręcki, M. Verzobio, Journal of Number Theory 279 (2025)
170–183.
corr_author: '1'
date_created: 2025-07-27T22:01:25Z
date_published: 2025-07-23T00:00:00Z
date_updated: 2025-09-30T14:09:38Z
day: '23'
department:
- _id: TiBr
doi: 10.1016/j.jnt.2025.06.001
external_id:
arxiv:
- '2309.09699'
isi:
- '001541172400002'
intvolume: ' 279'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jnt.2025.06.001
month: '07'
oa: 1
oa_version: Published Version
page: 170-183
publication: Journal of Number Theory
publication_identifier:
issn:
- 0022-314X
publication_status: epub_ahead
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divisibility sequences related to abelian varieties isogenous to a power of
an elliptic curve
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 279
year: '2025'
...
---
OA_type: closed access
_id: '20079'
abstract:
- lang: eng
text: "Research question: Is LINC01638 involved in regulation of epithelial-to-mesenchymal
transition (EMT) in endometriosis?\r\nDesign: A prospective patient cohort study
was combined with functional experiments in the 12Z endometriosis epithelial cell
line to investigate the role of LINC01638 in endometriosis. Eutopic endometrial
samples were collected by curettage, and ectopic endometrial lesion samples were
collected by laparoscopic surgery from 24 control patients and 41 patients with
endometriosis. The phenotype of 12Z cells was assessed following LINC01638 knockdown
using siRNA, performing proliferation, adhesion, migration and invasion assays,
as well as assessing apoptosis and cell cycle changes with flow cytometry assays.
In order to assess the relationship between LINC01638 and histone deacetylase
class 1 enzyme (HDAC1), LINC01638 knockdown was combined with HDAC inhibition
with the specific HDAC inhibitor romidepsin.\r\nResults: LINC01638 was up-regulated
in the epithelial layer of endometriotic lesions, and LINC01638 knockdown in 12Z
cells led to reduced proliferation, adhesion, migration and invasion. The reduction
in proliferation was associated with increased p21 and p27 expression, and G1
phase arrest. Further analysis of LINC01638 control and knockdown cells revealed
that a number of transcription factors associated with EMT are down-regulated
in knockdown cells, along with the cytoskeleton regulatory gene RHOB, while HDAC1
was up-regulated. Chromatin immunoprecipitation analysis and HDAC1 inhibitory
treatment combined with LINC01638 knockdown indicated that LINC01638 regulates
RHOB expression via HDAC1-mediated promoter deacetylation. RHOB is up-regulated
in the epithelial layer of endometriotic lesions compared with eutopic endometrium,
supporting a role in the disease.\r\nConclusions: LINC01638 is an epigenetic regulator
of the pathogenesis of endometriosis, promoting proliferation and EMT of endometriotic
lesions."
acknowledgement: "The authors wish to thank all the participants and health professionals
involved in this study. In addition, the authors wish to thank technical assistants
Barbara Widmar, Matthias Witzmann-Stern and Isabella Haslinger for their work assisting
with this study; and Simon Hippenmeyer for access to bioinformatic infrastructure
and resources.\r\nOpen access funding was provided by the Medical University of
Vienna."
article_number: '104942'
article_processing_charge: No
article_type: original
author:
- first_name: Iveta
full_name: Yotova, Iveta
last_name: Yotova
- first_name: Katharina
full_name: Proestling, Katharina
last_name: Proestling
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Lisa
full_name: Rainer, Lisa
last_name: Rainer
- first_name: Leonie
full_name: Kaup, Leonie
last_name: Kaup
- first_name: Jana
full_name: Heine, Jana
last_name: Heine
- first_name: Lejla
full_name: Sandrieser, Lejla
last_name: Sandrieser
- first_name: René
full_name: Wenzl, René
last_name: Wenzl
- first_name: Quanah J.
full_name: Hudson, Quanah J.
last_name: Hudson
citation:
ama: Yotova I, Proestling K, Pauler F, et al. LINC01638 promotes epithelial-to-mesenchymal
transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression.
Reproductive Biomedicine Online. 2025;51(3). doi:10.1016/j.rbmo.2025.104942
apa: Yotova, I., Proestling, K., Pauler, F., Rainer, L., Kaup, L., Heine, J., …
Hudson, Q. J. (2025). LINC01638 promotes epithelial-to-mesenchymal transition
in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression.
Reproductive Biomedicine Online. Elsevier. https://doi.org/10.1016/j.rbmo.2025.104942
chicago: Yotova, Iveta, Katharina Proestling, Florian Pauler, Lisa Rainer, Leonie
Kaup, Jana Heine, Lejla Sandrieser, René Wenzl, and Quanah J. Hudson. “LINC01638
Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells
by up-Regulating RHOB via HDAC1 Suppression.” Reproductive Biomedicine Online.
Elsevier, 2025. https://doi.org/10.1016/j.rbmo.2025.104942.
ieee: I. Yotova et al., “LINC01638 promotes epithelial-to-mesenchymal transition
in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression,”
Reproductive Biomedicine Online, vol. 51, no. 3. Elsevier, 2025.
ista: Yotova I, Proestling K, Pauler F, Rainer L, Kaup L, Heine J, Sandrieser L,
Wenzl R, Hudson QJ. 2025. LINC01638 promotes epithelial-to-mesenchymal transition
in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression.
Reproductive Biomedicine Online. 51(3), 104942.
mla: Yotova, Iveta, et al. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition
in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.”
Reproductive Biomedicine Online, vol. 51, no. 3, 104942, Elsevier, 2025,
doi:10.1016/j.rbmo.2025.104942.
short: I. Yotova, K. Proestling, F. Pauler, L. Rainer, L. Kaup, J. Heine, L. Sandrieser,
R. Wenzl, Q.J. Hudson, Reproductive Biomedicine Online 51 (2025).
date_created: 2025-07-27T22:01:25Z
date_published: 2025-07-17T00:00:00Z
date_updated: 2025-09-30T14:10:46Z
day: '17'
department:
- _id: SiHi
doi: 10.1016/j.rbmo.2025.104942
external_id:
isi:
- '001549819000002'
pmid:
- '40680553'
intvolume: ' 51'
isi: 1
issue: '3'
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: Reproductive Biomedicine Online
publication_identifier:
eissn:
- 1472-6491
issn:
- 1472-6483
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial
cells by up-regulating RHOB via HDAC1 suppression
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 51
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20080'
abstract:
- lang: eng
text: "Introduction: Acid-growth theory has been postulated in the 70s to explain
the rapid elongation of plant cells in response to the hormone auxin. More recently,
it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting
acidification of the apoplast is the principal mechanism by which auxin and other
hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances,
the impact of this acidification on the mechanical properties of the cell wall
remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of
Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate
hormone-induced tissue elongation and local changes in cell wall mechanical properties.
Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase
(PME), along with calcium chelators, we investigate the effect of pectin modification
in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification
of apoplast is necessary and sufficient to induce cell elongation through promoting
cell wall softening. Moreover, we show that enhanced PME activity can induce both
cell wall softening or stiffening in extracellular calcium dependent-manner and
that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion:
Our results confirm a dual role of PME in plant cell elongation. However, further
investigation is needed to assess the status of pectin following short- or long-term
PME treatments in order to determine if pectin methyl-esterification might promote
its degradation as well as the role of PME inhibitors upon PME induction."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
acknowledgement: "The author(s) declare that financial support was received for the
research and/or publication of this article. This work was supported by grants from
the European Research Council (Starting Independent Research Grant ERC-2007-Stg-
207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe
acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge
CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127).
We gratefully acknowledge support by the Scientific Service Units at ISTA, including
the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler
for the efforts to establish immunodetection method."
article_number: '1612366'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Nikola
full_name: Zarevski, Nikola
id: 18e95355-e05a-11ea-a9c0-8fba1b89e83a
last_name: Zarevski
- first_name: Jan
full_name: Pribyl, Jan
last_name: Pribyl
- first_name: Petr
full_name: Skládal, Petr
last_name: Skládal
- 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: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl
esterase activity in the regulation of plant cell wall biophysical properties.
Frontiers in Plant Science. 2025;16. doi:10.3389/fpls.2025.1612366
apa: Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P.,
Hannezo, E. B., & Benková, E. (2025). Dual role of pectin methyl esterase
activity in the regulation of plant cell wall biophysical properties. Frontiers
in Plant Science. Frontiers Media. https://doi.org/10.3389/fpls.2025.1612366
chicago: Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl,
Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl
Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.”
Frontiers in Plant Science. Frontiers Media, 2025. https://doi.org/10.3389/fpls.2025.1612366.
ieee: M. Gallemi et al., “Dual role of pectin methyl esterase activity in
the regulation of plant cell wall biophysical properties,” Frontiers in Plant
Science, vol. 16. Frontiers Media, 2025.
ista: Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB,
Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation
of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366.
mla: Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the
Regulation of Plant Cell Wall Biophysical Properties.” Frontiers in Plant Science,
vol. 16, 1612366, Frontiers Media, 2025, doi:10.3389/fpls.2025.1612366.
short: M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B.
Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).
corr_author: '1'
date_created: 2025-07-27T22:01:26Z
date_published: 2025-07-04T00:00:00Z
date_updated: 2025-09-30T14:08:22Z
day: '04'
ddc:
- '580'
department:
- _id: EdHa
- _id: EvBe
- _id: CaGu
doi: 10.3389/fpls.2025.1612366
ec_funded: 1
external_id:
isi:
- '001530690900001'
pmid:
- '40688689'
file:
- access_level: open_access
checksum: 9e6b8b53ba56d4a24a9bd91cf6d2dc58
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T07:28:54Z
date_updated: 2025-07-31T07:28:54Z
file_id: '20093'
file_name: 2025_FrontiersPlantSc_Gallemi.pdf
file_size: 3665187
relation: main_file
success: 1
file_date_updated: 2025-07-31T07:28:54Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664-462X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dual role of pectin methyl esterase activity in the regulation of plant cell
wall biophysical properties
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: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20081'
abstract:
- lang: eng
text: 'Information measures can be constructed from Rényi divergences much like
mutual information from Kullback-Leibler divergence. One such information measure
is known as Sibson α-mutual information and has received renewed attention recently
in several contexts: concentration of measure under dependence, statistical learning,
hypothesis testing, and estimation theory. In this paper, we survey and extend
the state of the art. In particular, we introduce variational representations
for Sibson α-mutual information and employ them in each described context to derive
novel results. Namely, we produce generalized Transportation-Cost inequalities
and Fano-type inequalities. We also present an overview of known applications,
spanning from learning theory and Bayesian risk to universal prediction.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Amedeo Roberto
full_name: Esposito, Amedeo Roberto
id: 9583e921-e1ad-11ec-9862-cef099626dc9
last_name: Esposito
- first_name: Michael
full_name: Gastpar, Michael
last_name: Gastpar
- first_name: Ibrahim
full_name: Issa, Ibrahim
last_name: Issa
citation:
ama: Esposito AR, Gastpar M, Issa I. Sibson α-mutual information and its variational
representations. IEEE Transactions on Information Theory. 2025. doi:10.1109/TIT.2025.3587340
apa: Esposito, A. R., Gastpar, M., & Issa, I. (2025). Sibson α-mutual information
and its variational representations. IEEE Transactions on Information Theory.
IEEE. https://doi.org/10.1109/TIT.2025.3587340
chicago: Esposito, Amedeo Roberto, Michael Gastpar, and Ibrahim Issa. “Sibson α-Mutual
Information and Its Variational Representations.” IEEE Transactions on Information
Theory. IEEE, 2025. https://doi.org/10.1109/TIT.2025.3587340.
ieee: A. R. Esposito, M. Gastpar, and I. Issa, “Sibson α-mutual information and
its variational representations,” IEEE Transactions on Information Theory.
IEEE, 2025.
ista: Esposito AR, Gastpar M, Issa I. 2025. Sibson α-mutual information and its
variational representations. IEEE Transactions on Information Theory.
mla: Esposito, Amedeo Roberto, et al. “Sibson α-Mutual Information and Its Variational
Representations.” IEEE Transactions on Information Theory, IEEE, 2025,
doi:10.1109/TIT.2025.3587340.
short: A.R. Esposito, M. Gastpar, I. Issa, IEEE Transactions on Information Theory
(2025).
date_created: 2025-07-27T22:01:26Z
date_published: 2025-07-11T00:00:00Z
date_updated: 2026-02-16T11:49:40Z
day: '11'
department:
- _id: MaMo
doi: 10.1109/TIT.2025.3587340
external_id:
arxiv:
- '2405.08352'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2405.08352
month: '07'
oa: 1
oa_version: Preprint
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: epub_ahead
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sibson α-mutual information and its variational representations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20098'
abstract:
- lang: eng
text: Climate change is causing wildfires to become more frequent and intense. While
predicting burned areas using bioclimatic and anthropogenic factors is an active
research area, few studies have examined what drives the economic damages of wildfires.
Our study aims to fill this gap by analyzing key factors influencing global economic
wildfire damages and projecting future damages under three shared socioeconomic
pathways (SSPs). We apply regression analyses to identify significant predictors
of economic wildfire damages at country levels and use the fitted model to project
future damages under SSP126, SSP245, and SSP370. Results show that the human vulnerability
index (HVI), reflecting socioeconomic conditions, is the strongest predictor of
historical wildfire damages, followed by water vapor pressure deficit during the
fire season and population density around forested areas. We found high population
density to be associated with lower damages. These findings contrast with studies
of burned areas, where climate factors are more dominant. Our model projects that
by 2070, average global economic wildfire damages will be three times higher under
SSP370 than SSP126. Our model also shows that following SSP126 not only reduces
wildfire damages but also lessens the inequalities in damage distribution across
countries. This pathway’s dual focus on equitable socioeconomic progress and climate
action potentially enhances a country’s resilience that helps mitigate wildfire
damages. Our analyses also indicate that strong socioeconomic development can
offset wildfire damages associated with climate hazards, although this is less
certain under SSP370. SSP126’s integrated approach improves both socioeconomic
conditions and limits global warming, providing substantial benefits to less developed
countries while still reducing damages in developed nations, despite their already
low HVI scores. Our work complements existing research on burned areas and underscores
the importance of sustainable development and international collaboration in reducing
the economic damages of wildfires.
acknowledgement: We thank Marina Andrijevic, Giacomo Falchetta, Samuel Lüthi, Caroline
Muller, Carl Schleussner, and Adriano Vinca for providing useful ideas and feedback
for this work. YLH is supported by funding from the European Union’s Horizon 2020
research and innovation programme under the Marie Skłodowska‐Curie Grant No. 101034413.
EB, MW, and YQ are supported by the European Union’s Horizon Europe research and
innovation programme under Grant Agreement No. 101081369 (SPARCCLE). We also thank
the two anonymous reviewers for providing helpful feedback that greatly improved
this manuscript.
article_number: '035005'
article_processing_charge: Yes
article_type: original
author:
- first_name: Yi-Ling
full_name: Hwong, Yi-Ling
id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22
last_name: Hwong
orcid: 0000-0001-9281-3479
- first_name: Edward
full_name: Byers, Edward
last_name: Byers
- first_name: Michaela
full_name: Werning, Michaela
last_name: Werning
- first_name: Yann
full_name: Quilcaille, Yann
last_name: Quilcaille
citation:
ama: 'Hwong Y-L, Byers E, Werning M, Quilcaille Y. Sustainable development key to
limiting climate change-driven wildfire damages. Environmental Research: Climate.
2025;4(3). doi:10.1088/2752-5295/adec11'
apa: 'Hwong, Y.-L., Byers, E., Werning, M., & Quilcaille, Y. (2025). Sustainable
development key to limiting climate change-driven wildfire damages. Environmental
Research: Climate. IOP Publishing. https://doi.org/10.1088/2752-5295/adec11'
chicago: 'Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Sustainable
Development Key to Limiting Climate Change-Driven Wildfire Damages.” Environmental
Research: Climate. IOP Publishing, 2025. https://doi.org/10.1088/2752-5295/adec11.'
ieee: 'Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Sustainable development
key to limiting climate change-driven wildfire damages,” Environmental Research:
Climate, vol. 4, no. 3. IOP Publishing, 2025.'
ista: 'Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Sustainable development
key to limiting climate change-driven wildfire damages. Environmental Research:
Climate. 4(3), 035005.'
mla: 'Hwong, Yi-Ling, et al. “Sustainable Development Key to Limiting Climate Change-Driven
Wildfire Damages.” Environmental Research: Climate, vol. 4, no. 3, 035005,
IOP Publishing, 2025, doi:10.1088/2752-5295/adec11.'
short: 'Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, Environmental Research:
Climate 4 (2025).'
corr_author: '1'
date_created: 2025-07-31T14:03:16Z
date_published: 2025-07-15T00:00:00Z
date_updated: 2025-08-04T07:46:33Z
day: '15'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1088/2752-5295/adec11
ec_funded: 1
file:
- access_level: open_access
checksum: ca679496767021e792b0378c48fdee8c
content_type: application/pdf
creator: dernst
date_created: 2025-08-04T07:38:14Z
date_updated: 2025-08-04T07:38:14Z
file_id: '20108'
file_name: 2025_EnvironResearchClimate_Hwong.pdf
file_size: 2807041
relation: main_file
success: 1
file_date_updated: 2025-08-04T07:38:14Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: 'Environmental Research: Climate'
publication_identifier:
eissn:
- 2752-5295
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '20107'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Sustainable development key to limiting climate change-driven wildfire damages
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: 4
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20099'
abstract:
- lang: eng
text: The hippocampus, critical for learning and memory, is dogmatically described
as a trisynaptic circuit where dentate gyrus granule cells (GCs), CA3 pyramidal
neurons (PNs), and CA1 PNs are serially connected. However, CA3 also forms an
autoassociative network, and its PNs have diverse morphologies, intrinsic properties,
and GC input levels. How PN subtypes compose this recurrent network is unknown.
To determine the synaptic arrangement of identified CA3 PNs, we combine multicellular
patch-clamp recording and post hoc morphological analysis in mouse hippocampal
slices. PNs can be divided into distinct “superficial” and “deep” subclasses,
the latter including previously reported “athorny” cells. Subclasses have distinct
input-output transformations and asymmetric connectivity, which is more abundant
from superficial to deep PNs, splitting CA3 locally into two parallel recurrent
networks. Coincident spontaneous inhibition occurs frequently within but not between
subclasses, implying subclass-specific inhibitory innervation. Our results suggest
two separately controlled sublayers for parallel information processing in hippocampal
CA3.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
- _id: M-Shop
acknowledgement: We thank Andrea Navas-Olive and Rebecca J. Morse-Mora for critically
reading an earlier version of the manuscript. We also thank Florian Marr and Christina
Altmutter for excellent technical assistance, Alois Schlögl for programming and
data-handling assistance, Todor Asenov for technical support, and Eleftheria Kralli-Beller
for manuscript editing. This research was supported by the Scientific Services Units
(SSUs) of ISTA. We are particularly grateful for assistance from the Imaging and
Optics Facility, Preclinical Facility, Lab Support Facility, and Miba Machine Shop.
The project received funding from the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement no.
692692 to P.J., Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635
to J.F.W., and an ISTplus Fellowship through Marie Skłodowska-Curie grant agreement
no. 754411 to V.V.-B.), the Austrian Science Fund (P 36232-B, PAT 4178023, and Cluster
of Excellence 10.55776/COE16 to P.J.), and a CONACyT fellowship (289638 to V.V.-B.)
and was supported by a non-stipendiary EMBO fellowship (ALTF 756–2020 to J.F.W.).
article_number: '116080'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Watson J, Vargas Barroso VM, Jonas PM. Cell-specific wiring routes information
flow through hippocampal CA3. Cell Reports. 2025;44(8). doi:10.1016/j.celrep.2025.116080
apa: Watson, J., Vargas Barroso, V. M., & Jonas, P. M. (2025). Cell-specific
wiring routes information flow through hippocampal CA3. Cell Reports. Elsevier.
https://doi.org/10.1016/j.celrep.2025.116080
chicago: Watson, Jake, Victor M Vargas Barroso, and Peter M Jonas. “Cell-Specific
Wiring Routes Information Flow through Hippocampal CA3.” Cell Reports.
Elsevier, 2025. https://doi.org/10.1016/j.celrep.2025.116080.
ieee: J. Watson, V. M. Vargas Barroso, and P. M. Jonas, “Cell-specific wiring routes
information flow through hippocampal CA3,” Cell Reports, vol. 44, no. 8.
Elsevier, 2025.
ista: Watson J, Vargas Barroso VM, Jonas PM. 2025. Cell-specific wiring routes information
flow through hippocampal CA3. Cell Reports. 44(8), 116080.
mla: Watson, Jake, et al. “Cell-Specific Wiring Routes Information Flow through
Hippocampal CA3.” Cell Reports, vol. 44, no. 8, 116080, Elsevier, 2025,
doi:10.1016/j.celrep.2025.116080.
short: J. Watson, V.M. Vargas Barroso, P.M. Jonas, Cell Reports 44 (2025).
corr_author: '1'
date_created: 2025-08-03T22:01:30Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-09-30T14:12:02Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.celrep.2025.116080
ec_funded: 1
external_id:
isi:
- '001544472300002'
file:
- access_level: open_access
checksum: 556ff9760661ecd23949d75031043b1f
content_type: application/pdf
creator: dernst
date_created: 2025-08-04T06:53:07Z
date_updated: 2025-08-04T06:53:07Z
file_id: '20106'
file_name: 2025_CellReports_Watson.pdf
file_size: 27695214
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intvolume: ' 44'
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- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9
call_identifier: H2020
grant_number: '101026635'
name: Synaptic computations of the hippocampal CA3 circuitry
- _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5
grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell-specific wiring routes information flow through hippocampal CA3
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 44
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20100'
abstract:
- lang: eng
text: A key step in protein structure prediction involves the detection of co-evolving
pairs of residues, a signal for spatial proximity. This information is gleaned
from multiple sequence alignment and underscores Alphafold’s structure prediction
for almost every known protein. A simple means to create proteins beyond those
found in nature, is by unnaturally fusing together two known proteins or protein
parts. Here we demonstrate that structured peptides are predicted with significantly
reduced accuracy when added to the terminal ends of scaffold proteins. Appending
the multiple sequence alignment for the individual peptide tags to that of the
scaffold protein often restores prediction accuracy. This work suggests that this
windowed multiple sequence alignment approach can be a useful tool for predicting
the structure of fused, chimeric proteins.
acknowledgement: AM acknowledges the financial support of the Helmsley Fellowships
Program for Sustainability and Health. AMB is supported by the Schmidt Chair in
Artificial Intelligence.
article_processing_charge: Yes
article_type: original
author:
- first_name: Sanketh
full_name: Vedula, Sanketh
id: 94f2fe44-70fa-11f0-b76b-92922c09452b
last_name: Vedula
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Ailie
full_name: Marx, Ailie
last_name: Marx
citation:
ama: Vedula S, Bronstein AM, Marx A. Improving prediction accuracy in chimeric proteins
with windowed multiple sequence alignment. Computational and Structural Biotechnology
Journal. 2025;27:3292-3298. doi:10.1016/j.csbj.2025.07.039
apa: Vedula, S., Bronstein, A. M., & Marx, A. (2025). Improving prediction accuracy
in chimeric proteins with windowed multiple sequence alignment. Computational
and Structural Biotechnology Journal. Elsevier. https://doi.org/10.1016/j.csbj.2025.07.039
chicago: Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Improving Prediction
Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” Computational
and Structural Biotechnology Journal. Elsevier, 2025. https://doi.org/10.1016/j.csbj.2025.07.039.
ieee: S. Vedula, A. M. Bronstein, and A. Marx, “Improving prediction accuracy in
chimeric proteins with windowed multiple sequence alignment,” Computational
and Structural Biotechnology Journal, vol. 27. Elsevier, pp. 3292–3298, 2025.
ista: Vedula S, Bronstein AM, Marx A. 2025. Improving prediction accuracy in chimeric
proteins with windowed multiple sequence alignment. Computational and Structural
Biotechnology Journal. 27, 3292–3298.
mla: Vedula, Sanketh, et al. “Improving Prediction Accuracy in Chimeric Proteins
with Windowed Multiple Sequence Alignment.” Computational and Structural Biotechnology
Journal, vol. 27, Elsevier, 2025, pp. 3292–98, doi:10.1016/j.csbj.2025.07.039.
short: S. Vedula, A.M. Bronstein, A. Marx, Computational and Structural Biotechnology
Journal 27 (2025) 3292–3298.
date_created: 2025-08-03T22:01:31Z
date_published: 2025-06-27T00:00:00Z
date_updated: 2025-11-27T14:09:59Z
day: '27'
ddc:
- '000'
- '570'
department:
- _id: AlBr
doi: 10.1016/j.csbj.2025.07.039
external_id:
isi:
- '001583543100001'
file:
- access_level: open_access
checksum: 78d01f30fc1dc11dd2bd1d7bb7ac8a62
content_type: application/pdf
creator: dernst
date_created: 2025-08-04T06:25:23Z
date_updated: 2025-08-04T06:25:23Z
file_id: '20104'
file_name: 2025_CompStrucBiotechJour_Vedula.pdf
file_size: 6609770
relation: main_file
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file_date_updated: 2025-08-04T06:25:23Z
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intvolume: ' 27'
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language:
- iso: eng
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oa: 1
oa_version: Published Version
page: 3292-3298
publication: Computational and Structural Biotechnology Journal
publication_identifier:
eissn:
- 2001-0370
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/sankethvedula/AFChimera
record:
- id: '20103'
relation: software
status: public
scopus_import: '1'
status: public
title: Improving prediction accuracy in chimeric proteins with windowed multiple sequence
alignment
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: 27
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20101'
abstract:
- lang: eng
text: 'Evading imminent threat from predators is critical for animal survival. Effective
defensive strategies can vary, even between closely related species. However,
the neural basis of such species-specific behaviours remains poorly understood1,2,3,4.
Here we find that two sister species of deer mice (genus Peromyscus)5 show different
responses to the same looming stimulus: Peromyscus maniculatus, which occupies
densely vegetated habitats, predominantly escapes, whereas the open field specialist,
Peromyscus polionotus, briefly freezes. This difference arises from species-specific
escape thresholds, is largely context-independent, and can be triggered by both
visual and auditory threat stimuli. Using immunohistochemistry and electrophysiological
recordings, we find that although visual threat activates the superior colliculus
in both species, the role of the dorsal periaqueductal grey (dPAG) in driving
behaviour differs. Whereas dPAG activity scales with running speed in P. maniculatus,
neural activity in the dPAG of P. polionotus correlates poorly with movement,
including during visually triggered escape. Moreover, optogenetic activation of
dPAG neurons elicits acceleration in P. maniculatus but not in P. polionotus,
and their chemogenetic inhibition during a looming stimulus delays escape onset
in P. maniculatus to match that of P. polionotus. Together, we trace species-specific
escape thresholds to a central circuit node, downstream of peripheral sensory
neurons, localizing an ecologically relevant behavioural difference to a specific
region of the mammalian brain.'
acknowledgement: The authors thank M. Yilmaz, M. Meister, M. Joesch and T. Branco
for advice on the behavioural experiments; C. Dulac, V. Bitsikas, E. Diel and J.
Chen for advice on the immunohistochemistry and RNAscope experiments; J. Greenwood
and E. Soucy for technical and engineering help; A. Chrzanowska for help and advice
on optogenetic experiments; A. Calzoni for help aligning histological sections to
a brain atlas; S. Worthington for statistical advice; P. Gonçalves for advice with
the electrophysiology analysis; I. Vlaemick for help with whole cell experiments;
R. Hellmiss for figure design; B. Sabatini, V. Stempel, K. Tyssowski and N. Sanguinetti
for feedback on the manuscript; and Y. M. Lee and A. Tomcho for photos of P. maniculatus
and P. leucopus habitats (Fig. 1). F.B. was supported by an HHMI International Student
Research Fellowship, a Grant-in-Aid of the American Society of Mammalogy, a Herchel
Smith Graduate Fellowship, a Robert A. Chapman Memorial Scholarship, and a Joan
Brockman Williamson Fellowship. This project received funding from the European
Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie
grant agreement 665501 and by the FWO (12S7917N and 12S7920N) to K.R. and from European
Research Council (ERC) (grant agreement 101075848) to K.R. V.T. was supported by
a Harvard PRISE fellowship and a Harvard Museum of Comparative Zoology grant for
undergraduate research. K.F. is supported by the FWO (G094616N and G091719N) and
the NIH (1R01EY032101). This work was supported by the Howard Hughes Medical Institute,
of which H.E.H. was an Investigator.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Felix
full_name: Baier, Felix
last_name: Baier
- first_name: Katja
full_name: Reinhard, Katja
last_name: Reinhard
- first_name: Bram
full_name: Nuttin, Bram
last_name: Nuttin
- first_name: Arnau
full_name: Sans-Dublanc, Arnau
last_name: Sans-Dublanc
- first_name: Chen
full_name: Liu, Chen
last_name: Liu
- first_name: Victoria
full_name: Tong, Victoria
last_name: Tong
- first_name: Julie Stefanie
full_name: Murmann, Julie Stefanie
id: 1d390868-f128-11eb-9611-a0ca5f7833b5
last_name: Murmann
- first_name: Keimpe
full_name: Wierda, Keimpe
last_name: Wierda
- first_name: Karl
full_name: Farrow, Karl
last_name: Farrow
- first_name: Hopi E.
full_name: Hoekstra, Hopi E.
last_name: Hoekstra
citation:
ama: Baier F, Reinhard K, Nuttin B, et al. The neural basis of species-specific
defensive behaviour in Peromyscus mice. Nature. 2025;645:439-447. doi:10.1038/s41586-025-09241-2
apa: Baier, F., Reinhard, K., Nuttin, B., Sans-Dublanc, A., Liu, C., Tong, V., …
Hoekstra, H. E. (2025). The neural basis of species-specific defensive behaviour
in Peromyscus mice. Nature. Springer Nature. https://doi.org/10.1038/s41586-025-09241-2
chicago: Baier, Felix, Katja Reinhard, Bram Nuttin, Arnau Sans-Dublanc, Chen Liu,
Victoria Tong, Julie Stefanie Murmann, Keimpe Wierda, Karl Farrow, and Hopi E.
Hoekstra. “The Neural Basis of Species-Specific Defensive Behaviour in Peromyscus
Mice.” Nature. Springer Nature, 2025. https://doi.org/10.1038/s41586-025-09241-2.
ieee: F. Baier et al., “The neural basis of species-specific defensive behaviour
in Peromyscus mice,” Nature, vol. 645. Springer Nature, pp. 439–447, 2025.
ista: Baier F, Reinhard K, Nuttin B, Sans-Dublanc A, Liu C, Tong V, Murmann JS,
Wierda K, Farrow K, Hoekstra HE. 2025. The neural basis of species-specific defensive
behaviour in Peromyscus mice. Nature. 645, 439–447.
mla: Baier, Felix, et al. “The Neural Basis of Species-Specific Defensive Behaviour
in Peromyscus Mice.” Nature, vol. 645, Springer Nature, 2025, pp. 439–47,
doi:10.1038/s41586-025-09241-2.
short: F. Baier, K. Reinhard, B. Nuttin, A. Sans-Dublanc, C. Liu, V. Tong, J.S.
Murmann, K. Wierda, K. Farrow, H.E. Hoekstra, Nature 645 (2025) 439–447.
date_created: 2025-08-03T22:01:31Z
date_published: 2025-07-23T00:00:00Z
date_updated: 2026-01-05T11:38:40Z
day: '23'
ddc:
- '570'
department:
- _id: GradSch
doi: 10.1038/s41586-025-09241-2
external_id:
pmid:
- '40702175'
file:
- access_level: open_access
checksum: 7ea846a7a49b3b2a248f6a27ab13d591
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T07:39:45Z
date_updated: 2025-12-30T07:39:45Z
file_id: '20884'
file_name: 2025_Nature_Baier.pdf
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file_date_updated: 2025-12-30T07:39:45Z
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month: '07'
oa: 1
oa_version: Published Version
page: 439-447
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
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relation: research_data
status: public
scopus_import: '1'
status: public
title: The neural basis of species-specific defensive behaviour in Peromyscus mice
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 645
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20102'
abstract:
- lang: eng
text: 'Speciation is rarely observable directly. A way forward is to compare pairs
of ecotypes that evolved in parallel in similar contexts but have reached different
degrees of reproductive isolation. Such comparisons are possible in the marine
snail Littorina saxatilis by contrasting barriers to gene flow between parallel
ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved
to withstand either crab predation or wave action. Here, we explore transects
spanning contact zones between the Crab and the Wave ecotypes using low-coverage
whole-genome sequencing, morphological and behavioural traits. Despite parallel
phenotypic divergence, distinct patterns of differentiation between the ecotypes
emerged: a continuous cline in Sweden indicating a weak barrier to gene flow,
but two highly genetically and phenotypically divergent, and partly spatially
overlapping clusters in Spain suggesting a much stronger barrier to gene flow.
The absence of Spanish early-generation hybrids supported strong isolation, but
a low level of gene flow is evident from molecular data. In both countries, highly
differentiated loci were located in both shared and country-specific chromosomal
inversions but were also present in collinear regions. Despite being considered
the same species and showing similar levels of phenotypic divergence, the Spanish
ecotypes are much closer to full reproductive isolation than the Swedish ones.
Barriers to gene flow of very different strengths between ecotypes within the
same species might be explained by dissimilarities in the spatial arrangement
of habitats, the selection gradients or the ages of the systems.'
acknowledgement: 'This study was supported by European Research Council grant 693030-BARRIERS
to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese
Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021)
to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU
(ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and
ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación
de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’
and Norwegian Research Council RCN, project 315287 to AMW.'
article_number: e70025
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Francesca
full_name: Raffini, Francesca
last_name: Raffini
- first_name: Aurélien
full_name: De Jode, Aurélien
last_name: De Jode
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Zuzanna B.
full_name: Zagrodzka, Zuzanna B.
last_name: Zagrodzka
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Juan
full_name: Galindo, Juan
last_name: Galindo
- first_name: Emilio
full_name: Rolán-Alvarez, Emilio
last_name: Rolán-Alvarez
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic
architecture between parallel ecotypes at two different points on the speciation
continuum in a marine snail. Molecular Ecology. 2025;34(21). doi:10.1111/mec.70025
apa: Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram,
A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.70025
chicago: Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna
B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K.
Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes
at Two Different Points on the Speciation Continuum in a Marine Snail.” Molecular
Ecology. Wiley, 2025. https://doi.org/10.1111/mec.70025.
ieee: F. Raffini et al., “Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail,” Molecular Ecology, vol. 34, no. 21. Wiley, 2025.
ista: Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo
J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail. Molecular Ecology. 34(21), e70025.
mla: Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture
between Parallel Ecotypes at Two Different Points on the Speciation Continuum
in a Marine Snail.” Molecular Ecology, vol. 34, no. 21, e70025, Wiley,
2025, doi:10.1111/mec.70025.
short: F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram,
J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025).
date_created: 2025-08-03T22:01:31Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2025-12-30T09:25:45Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.70025
external_id:
isi:
- '001538172800001'
file:
- access_level: open_access
checksum: ec01edda64cfbc6cbc8adf300f719644
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T09:25:17Z
date_updated: 2025-12-30T09:25:17Z
file_id: '20906'
file_name: 2025_MolecEcology_Raffini.pdf
file_size: 2767745
relation: main_file
success: 1
file_date_updated: 2025-12-30T09:25:17Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '21'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phenotypic divergence and genomic architecture between parallel ecotypes at
two different points on the speciation continuum in a marine snail
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: 34
year: '2025'
...
---
OA_place: repository
_id: '20103'
abstract:
- lang: eng
text: Official implementation, windowed MSAs, and the predictions as reported in
the manuscript titled "Improving Prediction Accuracy in Chimeric Proteins with
Windowed Multiple Sequence Alignment". (2025-06-27)
article_processing_charge: No
author:
- first_name: Sanketh
full_name: Vedula, Sanketh
id: 94f2fe44-70fa-11f0-b76b-92922c09452b
last_name: Vedula
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Ailie
full_name: Marx, Ailie
last_name: Marx
citation:
ama: 'Vedula S, Bronstein AM, Marx A. Replication Data for: “Improving Prediction
Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” 2025.
doi:10.7910/DVN/DYEBVM'
apa: 'Vedula, S., Bronstein, A. M., & Marx, A. (2025). Replication Data for:
“Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence
Alignment.” Harvard Dataverse. https://doi.org/10.7910/DVN/DYEBVM'
chicago: 'Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Replication Data
for: ‘Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple
Sequence Alignment.’” Harvard Dataverse, 2025. https://doi.org/10.7910/DVN/DYEBVM.'
ieee: 'S. Vedula, A. M. Bronstein, and A. Marx, “Replication Data for: ‘Improving
Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.’”
Harvard Dataverse, 2025.'
ista: 'Vedula S, Bronstein AM, Marx A. 2025. Replication Data for: ‘Improving Prediction
Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment’, Harvard
Dataverse, 10.7910/DVN/DYEBVM.'
mla: 'Vedula, Sanketh, et al. Replication Data for: “Improving Prediction Accuracy
in Chimeric Proteins with Windowed Multiple Sequence Alignment.” Harvard Dataverse,
2025, doi:10.7910/DVN/DYEBVM.'
short: S. Vedula, A.M. Bronstein, A. Marx, (2025).
date_created: 2025-08-04T06:18:55Z
date_published: 2025-06-27T00:00:00Z
date_updated: 2025-11-27T14:09:58Z
day: '27'
ddc:
- '000'
department:
- _id: AlBr
doi: 10.7910/DVN/DYEBVM
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.7910/DVN/DYEBVM
month: '06'
oa: 1
oa_version: Published Version
publisher: Harvard Dataverse
related_material:
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relation: used_for_analysis_in
status: public
status: public
title: 'Replication Data for: "Improving Prediction Accuracy in Chimeric Proteins
with Windowed Multiple Sequence Alignment"'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20107'
abstract:
- lang: eng
text: 'This repository contains the data and scripts required to reproduce the results
of the manuscript "Sustainable Development Key to Limiting Climate Change-Driven
Wildfire Damages" submitted to the Environmental Research Climate Journal (ERCL). '
article_processing_charge: No
author:
- first_name: Yi-Ling
full_name: Hwong, Yi-Ling
id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22
last_name: Hwong
orcid: 0000-0001-9281-3479
- first_name: Edward
full_name: Byers, Edward
last_name: Byers
- first_name: Michaela
full_name: Werning, Michaela
last_name: Werning
- first_name: Yann
full_name: Quilcaille, Yann
last_name: Quilcaille
citation:
ama: Hwong Y-L, Byers E, Werning M, Quilcaille Y. Data - Sustainable Development
Key to Limiting Climate Change-Driven Wildfire Damages. 2025. doi:10.5281/ZENODO.13988679
apa: Hwong, Y.-L., Byers, E., Werning, M., & Quilcaille, Y. (2025). Data - Sustainable
Development Key to Limiting Climate Change-Driven Wildfire Damages. Zenodo. https://doi.org/10.5281/ZENODO.13988679
chicago: Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Data
- Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.”
Zenodo, 2025. https://doi.org/10.5281/ZENODO.13988679.
ieee: Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Data - Sustainable
Development Key to Limiting Climate Change-Driven Wildfire Damages.” Zenodo, 2025.
ista: Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Data - Sustainable Development
Key to Limiting Climate Change-Driven Wildfire Damages, Zenodo, 10.5281/ZENODO.13988679.
mla: Hwong, Yi-Ling, et al. Data - Sustainable Development Key to Limiting Climate
Change-Driven Wildfire Damages. Zenodo, 2025, doi:10.5281/ZENODO.13988679.
short: Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, (2025).
corr_author: '1'
date_created: 2025-08-04T07:34:39Z
date_published: 2025-05-21T00:00:00Z
date_updated: 2025-08-04T07:46:33Z
day: '21'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.5281/ZENODO.13988679
ec_funded: 1
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.15409324
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publisher: Zenodo
related_material:
record:
- id: '20098'
relation: used_in_publication
status: public
status: public
title: Data - Sustainable Development Key to Limiting Climate Change-Driven Wildfire
Damages
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: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20116'
abstract:
- lang: eng
text: Auxin regulates various aspects of plant growth and development by modulating
the transcription of target genes through the degradation of auxin/indole-3-acetic
acid (Aux/IAA) repressors via the 26S proteasome. Proteasome regulator 1 (PTRE1),
a positive regulator of proteasome activity, has been implicated in auxin-mediated
proteasome suppression; however, the mechanism by which auxin modulates PTRE1
function remains unclear. Here, we demonstrate that auxin promotes the interaction
between germin-like protein 1 (GLP1) and PTRE1, facilitating PTRE1 retention at
the plasma membrane. The relocation of PTRE1 results in reduced nuclear 26S proteasome
activity, and thus the attenuated Aux/IAA degradation and altered Aux/IAA homeostasis,
ultimately resulting in suppressed auxin-mediated transcriptional regulation.
Our findings uncover a previously uncharacterized regulatory axis in auxin signaling
that controls Aux/IAA protein stability, functioning alongside the TIR1- and TRANSMEMBRANE
KINASE 1 (TMK1)-mediated pathways, and highlight the coordination of auxin signaling
from the cell surface to the nucleus via auxin-induced PTRE1 relocation, which
fine-tunes Aux/IAA protein homeostasis and auxin responses.
acknowledgement: The study was supported by the National Natural Science Foundation
of China (NSFC; 32230011, 91954206, and 31721001). We thank Dr. Deli Lin (Shanghai
Jiao Tong University) for kind help with the laser confocal microscope observation
and the Arabidopsis Biological Resource Center (ABRC) for providing T-DNA insertional
mutants.
article_number: '116056'
article_processing_charge: Yes
article_type: original
author:
- first_name: Faqing
full_name: Xu, Faqing
last_name: Xu
- first_name: Yongqiang
full_name: Yu, Yongqiang
last_name: Yu
- first_name: Bin
full_name: Guan, Bin
id: 56aad729-cca2-11ed-a45a-9b4138991a48
last_name: Guan
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Zhihong
full_name: Xu, Zhihong
last_name: Xu
- first_name: Hongwei
full_name: Xue, Hongwei
last_name: Xue
citation:
ama: Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. Germin-like protein 1 interacts with
proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA homeostasis.
Cell Reports. 2025;44(8). doi:10.1016/j.celrep.2025.116056
apa: Xu, F., Yu, Y., Guan, B., Xu, T., Xu, Z., & Xue, H. (2025). Germin-like
protein 1 interacts with proteasome regulator 1 to regulate auxin signaling by
controlling Aux/IAA homeostasis. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2025.116056
chicago: Xu, Faqing, Yongqiang Yu, Bin Guan, Tongda Xu, Zhihong Xu, and Hongwei
Xue. “Germin-like Protein 1 Interacts with Proteasome Regulator 1 to Regulate
Auxin Signaling by Controlling Aux/IAA Homeostasis.” Cell Reports. Elsevier,
2025. https://doi.org/10.1016/j.celrep.2025.116056.
ieee: F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, and H. Xue, “Germin-like protein 1 interacts
with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA
homeostasis,” Cell Reports, vol. 44, no. 8. Elsevier, 2025.
ista: Xu F, Yu Y, Guan B, Xu T, Xu Z, Xue H. 2025. Germin-like protein 1 interacts
with proteasome regulator 1 to regulate auxin signaling by controlling Aux/IAA
homeostasis. Cell Reports. 44(8), 116056.
mla: Xu, Faqing, et al. “Germin-like Protein 1 Interacts with Proteasome Regulator
1 to Regulate Auxin Signaling by Controlling Aux/IAA Homeostasis.” Cell Reports,
vol. 44, no. 8, 116056, Elsevier, 2025, doi:10.1016/j.celrep.2025.116056.
short: F. Xu, Y. Yu, B. Guan, T. Xu, Z. Xu, H. Xue, Cell Reports 44 (2025).
date_created: 2025-08-04T13:39:11Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2025-09-30T14:13:45Z
day: '24'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.celrep.2025.116056
external_id:
isi:
- '001542038500001'
pmid:
- '40714631'
file:
- access_level: open_access
checksum: 3c43e040a4a7a65ec67ae1d2bb81261a
content_type: application/pdf
creator: dernst
date_created: 2025-08-05T06:15:09Z
date_updated: 2025-08-05T06:15:09Z
file_id: '20120'
file_name: 2025_CellReports_Xu.pdf
file_size: 24178018
relation: main_file
success: 1
file_date_updated: 2025-08-05T06:15:09Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Germin-like protein 1 interacts with proteasome regulator 1 to regulate auxin
signaling by controlling Aux/IAA homeostasis
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 44
year: '2025'
...