---
OA_place: repository
OA_type: green
_id: '20723'
abstract:
- lang: eng
text: Information-flow interfaces is a formalism recently proposed for specifying,
composing, and refining system-wide security requirements. In this work, we show
how the widely used concept of security lattices provides a natural semantic interpretation
for information-flow interfaces.
acknowledgement: This project was funded in part by the Austrian Science Fund (FWF)
SFB project SpyCoDe F8502 and by the ERC-2020-AdG 101020093.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana
full_name: Oliveira da Costa, Ana
id: f347ec37-6676-11ee-b395-a888cb7b4fb4
last_name: Oliveira da Costa
orcid: 0000-0002-8741-5799
citation:
ama: 'Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. Information-Flow
Interfaces and Security Lattices. In: Engineering Safe and Trustworthy Cyber
Physical Systems. Vol 15471. Cham: Springer Nature; 2025:251-263. doi:10.1007/978-3-031-97537-0_15'
apa: 'Bartocci, E., Henzinger, T. A., Nickovic, D., & Oliveira da Costa, A.
(2025). Information-Flow Interfaces and Security Lattices. In Engineering Safe
and Trustworthy Cyber Physical Systems (Vol. 15471, pp. 251–263). Cham: Springer
Nature. https://doi.org/10.1007/978-3-031-97537-0_15'
chicago: 'Bartocci, Ezio, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da
Costa. “Information-Flow Interfaces and Security Lattices.” In Engineering
Safe and Trustworthy Cyber Physical Systems, 15471:251–63. Cham: Springer
Nature, 2025. https://doi.org/10.1007/978-3-031-97537-0_15.'
ieee: 'E. Bartocci, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Information-Flow
Interfaces and Security Lattices,” in Engineering Safe and Trustworthy Cyber
Physical Systems, vol. 15471, Cham: Springer Nature, 2025, pp. 251–263.'
ista: 'Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. 2025.Information-Flow
Interfaces and Security Lattices. In: Engineering Safe and Trustworthy Cyber Physical
Systems. LNCS, vol. 15471, 251–263.'
mla: Bartocci, Ezio, et al. “Information-Flow Interfaces and Security Lattices.”
Engineering Safe and Trustworthy Cyber Physical Systems, vol. 15471, Springer
Nature, 2025, pp. 251–63, doi:10.1007/978-3-031-97537-0_15.
short: E. Bartocci, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, in:, Engineering
Safe and Trustworthy Cyber Physical Systems, Springer Nature, Cham, 2025, pp.
251–263.
corr_author: '1'
date_created: 2025-12-01T15:44:58Z
date_published: 2025-10-02T00:00:00Z
date_updated: 2025-12-09T07:57:55Z
day: '02'
department:
- _id: ToHe
doi: 10.1007/978-3-031-97537-0_15
ec_funded: 1
external_id:
arxiv:
- '2406.14374'
fulldoi: https://doi.org/10.1007/978-3-031-97537-0_15
intvolume: ' 15471'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2406.14374
month: '10'
oa: 1
oa_version: Preprint
page: 251-263
place: Cham
project:
- _id: 34a1b658-11ca-11ed-8bc3-c75229f0241e
grant_number: F8502
name: Interface Theory for Security and Privacy
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Engineering Safe and Trustworthy Cyber Physical Systems
publication_identifier:
eisbn:
- '9783031975370'
eissn:
- 1611-3349
isbn:
- '9783031975363'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Information-Flow Interfaces and Security Lattices
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15471
year: '2025'
...
---
APC_amount: 5599.52 EUR
OA_place: publisher
OA_type: hybrid
_id: '20727'
abstract:
- lang: eng
text: Acoustic levitation provides a unique method for manipulating small particles
as it completely evades effects from gravity, container walls, or physical handling.
These advantages make it a tantalizing platform for studying complex phenomena
in many-particle systems. In most standing-wave traps, however, particles interact
via acoustic scattering forces that cause them to merge into a single dense object.
Here, we introduce a complementary approach that combines acoustic levitation
with electrostatic charging to assemble, adapt, and activate complex, separated
many-particle systems. The key idea is to superimpose electrostatic repulsion
on the intrinsic acoustic attraction, rendering a so-called “mermaid” potential
where interactions are attractive at short range and repulsive at long range.
By controlling the attraction–repulsion balance, we can levitate expanded structures
where all particles are separated, collapsed structures where they are in contact,
and hybrid ones consisting of both expanded and collapsed components. We find
that collapsed and expanded structures are inherently stable, whereas hybrid ones
exhibit transient stability governed by acoustically unstable dimers. Furthermore,
we show how electrostatics allow us to adapt between configurations on the fly,
either by quasistatic discharge or discrete up/down charge steps. Finally, we
demonstrate how large structures experience selective energy pumping from the
acoustic field—thrusting some particles into motion while others remain stationary—leading
to complex dynamics including coupled rotations and oscillations. Our approach
establishes a design space beyond acoustic collapse, offering possibilities to
study many-particle systems with complex interactions, while suggesting pathways
toward scalable integration into materials processing and other applications.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: We thank Dustin Kleckner, Jack-William Barotta, and Daniel M. Harris
for insightful discussions. We acknowledge the Miba machine shop at the Institute
of Science and Technology Austria for instrumentation support. M.C.H. and C.P.G.
acknowledge funding by the Gesellschaft für Forschungsförderung Niederösterreich
under project FTI23-G-011.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Sue
full_name: Shi, Sue
id: 5c5b9247-15b2-11ec-abd3-fd958715639c
last_name: Shi
- first_name: Maximilian
full_name: Hübl, Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- first_name: Galien M
full_name: Grosjean, Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
citation:
ama: Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. Electrostatics overcome
acoustic collapse to assemble, adapt, and activate levitated matter. Proceedings
of the National Academy of Sciences. 2025;122(50):e2516865122. doi:10.1073/pnas.2516865122
apa: Shi, S., Hübl, M., Grosjean, G. M., Goodrich, C. P., & Waitukaitis, S.
R. (2025). Electrostatics overcome acoustic collapse to assemble, adapt, and activate
levitated matter. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.2516865122
chicago: Shi, Sue, Maximilian Hübl, Galien M Grosjean, Carl Peter Goodrich, and
Scott R Waitukaitis. “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt,
and Activate Levitated Matter.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2516865122.
ieee: S. Shi, M. Hübl, G. M. Grosjean, C. P. Goodrich, and S. R. Waitukaitis, “Electrostatics
overcome acoustic collapse to assemble, adapt, and activate levitated matter,”
Proceedings of the National Academy of Sciences, vol. 122, no. 50. National
Academy of Sciences, p. e2516865122, 2025.
ista: Shi S, Hübl M, Grosjean GM, Goodrich CP, Waitukaitis SR. 2025. Electrostatics
overcome acoustic collapse to assemble, adapt, and activate levitated matter.
Proceedings of the National Academy of Sciences. 122(50), e2516865122.
mla: Shi, Sue, et al. “Electrostatics Overcome Acoustic Collapse to Assemble, Adapt,
and Activate Levitated Matter.” Proceedings of the National Academy of Sciences,
vol. 122, no. 50, National Academy of Sciences, 2025, p. e2516865122, doi:10.1073/pnas.2516865122.
short: S. Shi, M. Hübl, G.M. Grosjean, C.P. Goodrich, S.R. Waitukaitis, Proceedings
of the National Academy of Sciences 122 (2025) e2516865122.
corr_author: '1'
date_created: 2025-12-07T23:02:00Z
date_published: 2025-12-16T00:00:00Z
date_updated: 2026-05-20T08:41:15Z
day: '16'
ddc:
- '530'
department:
- _id: ScWa
- _id: CaGo
doi: 10.1073/pnas.2516865122
external_id:
arxiv:
- '2507.01739'
file:
- access_level: open_access
checksum: c40dc4c909724b9d1146636612e8821a
content_type: application/pdf
creator: dernst
date_created: 2025-12-09T12:45:53Z
date_updated: 2025-12-09T12:45:53Z
file_id: '20744'
file_name: 2025_PNAS_Shi.pdf
file_size: 10621381
relation: main_file
success: 1
file_date_updated: 2025-12-09T12:45:53Z
fulldoi: https://doi.org/10.1073/pnas.2516865122
has_accepted_license: '1'
intvolume: ' 122'
issue: '50'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: e2516865122
project:
- _id: 8dd93da8-16d5-11f0-9cad-d2c70200d9a5
grant_number: FTI23-G-011
name: Dynamically reconfigurable self-assembly with triangular DNA-origami bricks
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/science-is-like-magic-just-real/
record:
- id: '20749'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Electrostatics overcome acoustic collapse to assemble, adapt, and activate
levitated matter
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: 122
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20728'
abstract:
- lang: eng
text: Glaciers are often located in steep mountain settings and avalanches from
surrounding slopes can strongly influence snow accumulation patterns on their
surface. This effect has however never been quantified for more than a few glaciers
and the impact on the future evolution of glaciers is unclear. We coupled an avalanche
and a glacier model to estimate the contribution of avalanches to the accumulation
of all glaciers in the world and how this affects their evolution throughout the
21st century. Globally, 3% of the snow accumulation on glaciers comes from avalanches
and 1% is removed by avalanches. This net contribution varies between regions
and glaciers, with a maximum of 15% for New Zealand. Accounting for avalanches
modifies the altitudinal pattern of glacier mass balance and the projected evolution
of individual glaciers. The main effects include (1) a longer persistence of small
glaciers, with for example three times more ice retained by glaciers smaller than
1 km2 in Central Europe under a low-emission scenario, and (2) an increased sensitivity
of high-elevation accumulation zones to future warming. We anticipate the relative
influence of avalanches to increase in the future and advocate for a better monitoring
of this process and representation in glacier models.
acknowledgement: This project has received funding from the Swiss National Science
Foundation (SNSF) under the Postdoc. Mobility programme, grant agreement P500PN_210739,
CAIRN (MK), “Contribution of avalanches to glacier mass balance”, and grant agreement
P5R5PN_225605, CAIRN-GLOBAL (MK), “Contribution of avalanches to glacier mass balance
at the global scale”. The authors would like to acknowledge the OGGM community for
the extensive online documentation, data resources (OGGM-shop) and computing infrastructure
that were used as part of this study.
article_number: '10122'
article_processing_charge: Yes
article_type: original
author:
- first_name: Marin
full_name: Kneib, Marin
last_name: Kneib
- first_name: Fabien
full_name: Maussion, Fabien
last_name: Maussion
- first_name: Fanny
full_name: Brun, Fanny
last_name: Brun
- first_name: Guillem
full_name: Carcanade, Guillem
last_name: Carcanade
- first_name: Daniel
full_name: Farinotti, Daniel
last_name: Farinotti
- first_name: Matthias
full_name: Huss, Matthias
last_name: Huss
- first_name: Marit
full_name: Van Tiel, Marit
last_name: Van Tiel
- first_name: Achille
full_name: Jouberton, Achille
id: f2426a39-920b-11f0-ac40-cbeda2086b9c
last_name: Jouberton
- first_name: Patrick
full_name: Schmitt, Patrick
last_name: Schmitt
- first_name: Lilian
full_name: Schuster, Lilian
last_name: Schuster
- first_name: Amaury
full_name: Dehecq, Amaury
last_name: Dehecq
- first_name: Nicolas
full_name: Champollion, Nicolas
last_name: Champollion
citation:
ama: Kneib M, Maussion F, Brun F, et al. Topographically-controlled contribution
of avalanches to glacier mass balance in the 21st century. Nature Communications.
2025;16. doi:10.1038/s41467-025-65608-z
apa: Kneib, M., Maussion, F., Brun, F., Carcanade, G., Farinotti, D., Huss, M.,
… Champollion, N. (2025). Topographically-controlled contribution of avalanches
to glacier mass balance in the 21st century. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-025-65608-z
chicago: Kneib, Marin, Fabien Maussion, Fanny Brun, Guillem Carcanade, Daniel Farinotti,
Matthias Huss, Marit Van Tiel, et al. “Topographically-Controlled Contribution
of Avalanches to Glacier Mass Balance in the 21st Century.” Nature Communications.
Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65608-z.
ieee: M. Kneib et al., “Topographically-controlled contribution of avalanches
to glacier mass balance in the 21st century,” Nature Communications, vol.
16. Springer Nature, 2025.
ista: Kneib M, Maussion F, Brun F, Carcanade G, Farinotti D, Huss M, Van Tiel M,
Jouberton A, Schmitt P, Schuster L, Dehecq A, Champollion N. 2025. Topographically-controlled
contribution of avalanches to glacier mass balance in the 21st century. Nature
Communications. 16, 10122.
mla: Kneib, Marin, et al. “Topographically-Controlled Contribution of Avalanches
to Glacier Mass Balance in the 21st Century.” Nature Communications, vol.
16, 10122, Springer Nature, 2025, doi:10.1038/s41467-025-65608-z.
short: M. Kneib, F. Maussion, F. Brun, G. Carcanade, D. Farinotti, M. Huss, M. Van
Tiel, A. Jouberton, P. Schmitt, L. Schuster, A. Dehecq, N. Champollion, Nature
Communications 16 (2025).
date_created: 2025-12-07T23:02:00Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2025-12-09T12:38:44Z
day: '01'
ddc:
- '550'
department:
- _id: FrPe
doi: 10.1038/s41467-025-65608-z
external_id:
pmid:
- '41298449'
file:
- access_level: open_access
checksum: 5d8e420caa8259b67801f7c87e318d2e
content_type: application/pdf
creator: dernst
date_created: 2025-12-09T12:37:14Z
date_updated: 2025-12-09T12:37:14Z
file_id: '20740'
file_name: 2025_NatureComm_Kneib.pdf
file_size: 2749558
relation: main_file
success: 1
file_date_updated: 2025-12-09T12:37:14Z
fulldoi: https://doi.org/10.1038/s41467-025-65608-z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topographically-controlled contribution of avalanches to glacier mass balance
in the 21st century
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: 16
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20729'
abstract:
- lang: eng
text: 'Persistence modules (defined as a sequence of vector spaces and linear maps
between them) are a key tool in topological data analysis. They are easy to interpret
and fast to compute. However, when considering persistence maps (i.e. maps between
persistence modules), these properties are lost. We propose a new invariant for
persistence maps consisting of a partial matching such that: it is easy to interpret,
it is more discriminative than the image of the persistence map, and can be calculated
with cubical complexity.'
acknowledgement: Álvaro Torras-Casas contract is funded by the French Agence Nationale
de la Recherche through the project reference ANR-22-CPJ1-0047-01. Rocio Gonzalez-Diaz
is partially funded by the European Union under grant agreement no. 101070028-2
(REXASI-PRO).
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rocio
full_name: Gonzalez-Diaz, Rocio
last_name: Gonzalez-Diaz
- first_name: Manuel
full_name: Soriano Trigueros, Manuel
id: 15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8
last_name: Soriano Trigueros
orcid: 0000-0003-2449-1433
- first_name: Alvaro
full_name: Torras-Casas, Alvaro
last_name: Torras-Casas
citation:
ama: 'Gonzalez-Diaz R, Soriano Trigueros M, Torras-Casas A. Additive partial matchings
for persistent homology. In: Proceedings of the 2025 International Symposium
on Symbolic and Algebraic Computation. Association for Computing Machinery;
2025:188-196. doi:10.1145/3747199.3747561'
apa: 'Gonzalez-Diaz, R., Soriano Trigueros, M., & Torras-Casas, A. (2025). Additive
partial matchings for persistent homology. In Proceedings of the 2025 International
Symposium on Symbolic and Algebraic Computation (pp. 188–196). Guanajuato,
Mexico: Association for Computing Machinery. https://doi.org/10.1145/3747199.3747561'
chicago: Gonzalez-Diaz, Rocio, Manuel Soriano Trigueros, and Alvaro Torras-Casas.
“Additive Partial Matchings for Persistent Homology.” In Proceedings of the
2025 International Symposium on Symbolic and Algebraic Computation, 188–96.
Association for Computing Machinery, 2025. https://doi.org/10.1145/3747199.3747561.
ieee: R. Gonzalez-Diaz, M. Soriano Trigueros, and A. Torras-Casas, “Additive partial
matchings for persistent homology,” in Proceedings of the 2025 International
Symposium on Symbolic and Algebraic Computation, Guanajuato, Mexico, 2025,
pp. 188–196.
ista: 'Gonzalez-Diaz R, Soriano Trigueros M, Torras-Casas A. 2025. Additive partial
matchings for persistent homology. Proceedings of the 2025 International Symposium
on Symbolic and Algebraic Computation. ISSAC: International Symposium on Symbolic
and Algebraic Computation, 188–196.'
mla: Gonzalez-Diaz, Rocio, et al. “Additive Partial Matchings for Persistent Homology.”
Proceedings of the 2025 International Symposium on Symbolic and Algebraic Computation,
Association for Computing Machinery, 2025, pp. 188–96, doi:10.1145/3747199.3747561.
short: R. Gonzalez-Diaz, M. Soriano Trigueros, A. Torras-Casas, in:, Proceedings
of the 2025 International Symposium on Symbolic and Algebraic Computation, Association
for Computing Machinery, 2025, pp. 188–196.
conference:
end_date: 2025-08-01
location: Guanajuato, Mexico
name: 'ISSAC: International Symposium on Symbolic and Algebraic Computation'
start_date: 2025-07-28
corr_author: '1'
date_created: 2025-12-07T23:02:01Z
date_published: 2025-11-10T00:00:00Z
date_updated: 2025-12-09T13:46:42Z
day: '10'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1145/3747199.3747561
file:
- access_level: open_access
checksum: 1c299cca165a20e2518afe4fda63dbf1
content_type: application/pdf
creator: dernst
date_created: 2025-12-09T13:43:17Z
date_updated: 2025-12-09T13:43:17Z
file_id: '20751'
file_name: 2025_ISSAC_GonzalezDiaz.pdf
file_size: 761617
relation: main_file
success: 1
file_date_updated: 2025-12-09T13:43:17Z
fulldoi: https://doi.org/10.1145/3747199.3747561
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 188-196
publication: Proceedings of the 2025 International Symposium on Symbolic and Algebraic
Computation
publication_identifier:
isbn:
- '9798400720758'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Additive partial matchings for persistent homology
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
PlanS_conform: '1'
_id: '20730'
abstract:
- lang: eng
text: Radio-frequency measurements could satisfy DiVincenzo’s readout criterion
in future large-scale solid-state quantum processors, as they allow for high bandwidths
and frequency multiplexing. However, the scalability potential of this readout
technique can only be leveraged if quantum device tuning is performed using exclusively
radio-frequency measurements, that is, without resorting to current measurements.
We demonstrate an algorithm that performs automatic coarse tuning of double quantum
dots with only radio-frequency measurements by exploiting their bandwidth and
impedance matching. The tuning was completed within a few minutes with minimal
prior knowledge about the device. Our results show that it is possible to eliminate
the need for transport measurements for quantum-dot tuning, paving the way for
more scalable device architectures.
acknowledged_ssus:
- _id: NanoFab
acknowledgement: We thank Nicholas Sim for providing help with the rf cavities and
David Craig for his feedback on the paper. This work was supported by the Royal
Society (URF-R1-191150), the EPSRC National Quantum Technology Hub in Networked
Quantum Information Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1),
EPSRC Platform Grant (EP/R029229/1), the European Research Council (Grant Agreement
948932), the Scientific Service Units of IST Austria through resources provided
by the nanofabrication facility, the FWF-P 30207, and FWF-I 05060 projects, and
Grant No. FQXi-IAF19-01 from the Foundational Questions Institute Fund, a donor-advised
fund of Silicon Valley Community Foundation.
article_number: '054030'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Barnaby
full_name: Van Straaten, Barnaby
last_name: Van Straaten
- first_name: Federico
full_name: Fedele, Federico
last_name: Fedele
- first_name: Florian
full_name: Vigneau, Florian
last_name: Vigneau
- first_name: Joseph
full_name: Hickie, Joseph
last_name: Hickie
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Natalia
full_name: Ares, Natalia
last_name: Ares
citation:
ama: Van Straaten B, Fedele F, Vigneau F, et al. All-rf-based coarse-tuning algorithm
for quantum devices using machine learning. Physical Review Applied. 2025;24(5).
doi:10.1103/v11m-dbhm
apa: Van Straaten, B., Fedele, F., Vigneau, F., Hickie, J., Jirovec, D., Ballabio,
A., … Ares, N. (2025). All-rf-based coarse-tuning algorithm for quantum devices
using machine learning. Physical Review Applied. American Physical Society.
https://doi.org/10.1103/v11m-dbhm
chicago: Van Straaten, Barnaby, Federico Fedele, Florian Vigneau, Joseph Hickie,
Daniel Jirovec, Andrea Ballabio, Daniel Chrastina, Giovanni Isella, Georgios Katsaros,
and Natalia Ares. “All-Rf-Based Coarse-Tuning Algorithm for Quantum Devices Using
Machine Learning.” Physical Review Applied. American Physical Society,
2025. https://doi.org/10.1103/v11m-dbhm.
ieee: B. Van Straaten et al., “All-rf-based coarse-tuning algorithm for quantum
devices using machine learning,” Physical Review Applied, vol. 24, no.
5. American Physical Society, 2025.
ista: Van Straaten B, Fedele F, Vigneau F, Hickie J, Jirovec D, Ballabio A, Chrastina
D, Isella G, Katsaros G, Ares N. 2025. All-rf-based coarse-tuning algorithm for
quantum devices using machine learning. Physical Review Applied. 24(5), 054030.
mla: Van Straaten, Barnaby, et al. “All-Rf-Based Coarse-Tuning Algorithm for Quantum
Devices Using Machine Learning.” Physical Review Applied, vol. 24, no.
5, 054030, American Physical Society, 2025, doi:10.1103/v11m-dbhm.
short: B. Van Straaten, F. Fedele, F. Vigneau, J. Hickie, D. Jirovec, A. Ballabio,
D. Chrastina, G. Isella, G. Katsaros, N. Ares, Physical Review Applied 24 (2025).
date_created: 2025-12-07T23:02:01Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2025-12-09T14:49:35Z
day: '01'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1103/v11m-dbhm
file:
- access_level: open_access
checksum: 9906b32c7e3c79ed13d05ef88ff15586
content_type: application/pdf
creator: dernst
date_created: 2025-12-09T13:34:38Z
date_updated: 2025-12-09T13:34:38Z
file_id: '20748'
file_name: 2025_PhysReviewApplied_vanStraaten.pdf
file_size: 5754118
relation: main_file
success: 1
file_date_updated: 2025-12-09T13:34:38Z
fulldoi: https://doi.org/10.1103/v11m-dbhm
has_accepted_license: '1'
intvolume: ' 24'
issue: '5'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
- _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1
grant_number: I05060
name: High impedance circuit quantum electrodynamics with hole spins
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
record:
- id: '20750'
relation: research_data
status: public
scopus_import: '1'
status: public
title: All-rf-based coarse-tuning algorithm for quantum devices using machine learning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20731'
abstract:
- lang: eng
text: The adult human brain, under resting conditions, consumes approximately 20%
of total body glucose, a demand that is even higher during the first decade of
life. The brain metabolic landscape is intricately regulated throughout development,
and each cell type exhibits distinct metabolic signatures at each specific stage.
This picture becomes even more intricate when considering that metabolism is dynamically
modulated to sustain critical biological processes, such as cell proliferation
and differentiation and synaptic activity–dependent processes. The orchestration
between metabolic regulation and the aforementioned physiological processes often
relies on metabolism-dependent changes in the epigenetic landscape, which shape
gene expression patterns to trigger selected downstream biological responses.
Perturbations of brain metabolic pathways are frequently the cause of severe neurodevelopmental
disorders. This review explores the latest insights into the regulation of brain
metabolism in health and disease.
acknowledgement: Funding provided by the European Union (grant 101057429) to G.N.
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Domenico
full_name: Marano, Domenico
id: 3b004c42-803f-11ed-ab7e-ecee8f08bd58
last_name: Marano
- first_name: Vittoria
full_name: Mariano, Vittoria
id: ee829c33-edb3-11ed-b4fb-c020aaca4b01
last_name: Mariano
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: 'Marano D, Mariano V, Novarino G. Fueling the mind: Brain metabolism in health
and neurodevelopmental disorders. Annual Review of Genetics. 2025;59:415-434.
doi:10.1146/annurev-genet-111523-102424'
apa: 'Marano, D., Mariano, V., & Novarino, G. (2025). Fueling the mind: Brain
metabolism in health and neurodevelopmental disorders. Annual Review of Genetics.
Annual Reviews. https://doi.org/10.1146/annurev-genet-111523-102424'
chicago: 'Marano, Domenico, Vittoria Mariano, and Gaia Novarino. “Fueling the Mind:
Brain Metabolism in Health and Neurodevelopmental Disorders.” Annual Review
of Genetics. Annual Reviews, 2025. https://doi.org/10.1146/annurev-genet-111523-102424.'
ieee: 'D. Marano, V. Mariano, and G. Novarino, “Fueling the mind: Brain metabolism
in health and neurodevelopmental disorders,” Annual Review of Genetics,
vol. 59. Annual Reviews, pp. 415–434, 2025.'
ista: 'Marano D, Mariano V, Novarino G. 2025. Fueling the mind: Brain metabolism
in health and neurodevelopmental disorders. Annual Review of Genetics. 59, 415–434.'
mla: 'Marano, Domenico, et al. “Fueling the Mind: Brain Metabolism in Health and
Neurodevelopmental Disorders.” Annual Review of Genetics, vol. 59, Annual
Reviews, 2025, pp. 415–34, doi:10.1146/annurev-genet-111523-102424.'
short: D. Marano, V. Mariano, G. Novarino, Annual Review of Genetics 59 (2025) 415–434.
corr_author: '1'
date_created: 2025-12-07T23:02:01Z
date_published: 2025-11-03T00:00:00Z
date_updated: 2025-12-09T12:55:11Z
day: '03'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1146/annurev-genet-111523-102424
external_id:
pmid:
- '40902207'
file:
- access_level: open_access
checksum: 1000228dc9aca3d48e92605607a99c41
content_type: application/pdf
creator: dernst
date_created: 2025-12-09T12:53:09Z
date_updated: 2025-12-09T12:53:09Z
file_id: '20745'
file_name: 2025_AnnualRevGenetics_Marano.pdf
file_size: 3629986
relation: main_file
success: 1
file_date_updated: 2025-12-09T12:53:09Z
fulldoi: https://doi.org/10.1146/annurev-genet-111523-102424
has_accepted_license: '1'
intvolume: ' 59'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 415-434
pmid: 1
project:
- _id: 349d1832-11ca-11ed-8bc3-d79b574010e0
grant_number: '101057429'
name: Reducing the impact of major environmental challenges on mental health
publication: Annual Review of Genetics
publication_identifier:
eissn:
- 1545-2948
issn:
- 0066-4197
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Fueling the mind: Brain metabolism in health and neurodevelopmental disorders'
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: 59
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20732'
abstract:
- lang: eng
text: 'We investigate the real-time dynamics of a quenched quantum impurity immersed
in a one-dimensional ultracold Fermi gas, focusing on the breakdown of the adiabatic
Born-Oppenheimer approximation due to nonadiabatic effects. Despite a sizable
impurity-bath mass imbalance, increasing interactions induce strong nonadiabatic
couplings, disrupting adiabatic motion and enabling population transfer between
the adiabatic potential energy curves. These transitions are governed by conical
intersections arising from the pseudo Jahn-Teller effect, dynamically shaping
the impurity''s motion through the bath. Using ab initio simulations via the multilayer
multiconfiguration time-dependent Hartree method and a multichannel Born-Oppenheimer
framework, we track the impurity''s evolution and directly prove the dynamical
manifestation of the pseudo Jahn-Teller effect. We analyze two key scenarios:
(i) a small initial shift, where a single avoided crossing drives transitions,
and (ii) a large shift, where multiple avoided crossings lead to enhanced nonadiabaticity,
self-trapping, and energy redistribution. Our findings establish ultracold fermionic
few-body systems as tunable platforms for studying nonadiabatic quantum dynamics,
opening new avenues for controlled impurity transport in strongly correlated environments.'
acknowledgement: 'This work has been funded by the Cluster of Excellence “Advanced
Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project
ID 390715994. G.K.M. has received funding from the Austrian Science Fund (FWF) [DOI:
10.55776/F1004].'
article_number: '033088'
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: A.
full_name: Becker, A.
last_name: Becker
- first_name: Georgios
full_name: Koutentakis, Georgios
id: d7b23d3a-9e21-11ec-b482-f76739596b95
last_name: Koutentakis
- first_name: P.
full_name: Schmelcher, P.
last_name: Schmelcher
citation:
ama: Becker A, Koutentakis G, Schmelcher P. Dynamical probe of the pseudo Jahn-Teller
effect in one-dimensional confined fermions. Physical Review Research.
2025;7(3). doi:10.1103/2fr6-b59y
apa: Becker, A., Koutentakis, G., & Schmelcher, P. (2025). Dynamical probe of
the pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical
Review Research. American Physical Society. https://doi.org/10.1103/2fr6-b59y
chicago: Becker, A., Georgios Koutentakis, and P. Schmelcher. “Dynamical Probe of
the Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical
Review Research. American Physical Society, 2025. https://doi.org/10.1103/2fr6-b59y.
ieee: A. Becker, G. Koutentakis, and P. Schmelcher, “Dynamical probe of the pseudo
Jahn-Teller effect in one-dimensional confined fermions,” Physical Review Research,
vol. 7, no. 3. American Physical Society, 2025.
ista: Becker A, Koutentakis G, Schmelcher P. 2025. Dynamical probe of the pseudo
Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research.
7(3), 033088.
mla: Becker, A., et al. “Dynamical Probe of the Pseudo Jahn-Teller Effect in One-Dimensional
Confined Fermions.” Physical Review Research, vol. 7, no. 3, 033088, American
Physical Society, 2025, doi:10.1103/2fr6-b59y.
short: A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 7 (2025).
corr_author: '1'
date_created: 2025-12-07T23:02:02Z
date_published: 2025-07-01T00:00:00Z
date_updated: 2025-12-09T14:16:15Z
day: '01'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/2fr6-b59y
external_id:
arxiv:
- '2503.09835'
file:
- access_level: open_access
checksum: b9f5ccd6957759b0e578bc817a050532
content_type: application/pdf
creator: dernst
date_created: 2025-12-09T14:14:46Z
date_updated: 2025-12-09T14:14:46Z
file_id: '20754'
file_name: 2025_PhysReviewResearch_Becker.pdf
file_size: 2878032
relation: main_file
success: 1
file_date_updated: 2025-12-09T14:14:46Z
fulldoi: https://doi.org/10.1103/2fr6-b59y
has_accepted_license: '1'
intvolume: ' 7'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3
grant_number: F100403
name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamical probe of the pseudo Jahn-Teller effect in one-dimensional confined
fermions
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: 7
year: '2025'
...
---
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20733'
abstract:
- lang: eng
text: The conversion of thermal energy into work is usually more efficient in the
slow-driving regime, where the power output is vanishingly small. Efficient work
extraction for fast-driving protocols remains an outstanding challenge at the
nanoscale, where fluctuations play a significant role. In this Letter, we use
a quantum-dot Szilard engine to extract work from thermal fluctuations with maximum
efficiency over two decades of driving speed. We design and implement a family
of optimized protocols ranging from the slow- to the fast-driving regime, and
we measure the engine's efficiency as well as the mean and variance of its power
output in each case. These optimized protocols exhibit significant improvements
in power and efficiency compared to the naive approach. Our results also show
that, when optimizing for efficiency, boosting the power output of a Szilard engine
inevitably comes at the cost of increased power fluctuations.
acknowledgement: We thank Georgios Katsaros for providing the device for this experiment.
K.A. and N.A. acknowledge the support provided by funding from the Engineering and
Physical Sciences Research Council IAA (Grant No. EP/X525777/1). N.A. acknowledges
support from the European Research Council (Grant Agreement No. 948932) and the
Royal Society (URF-R1-191150). A.R. is supported by the Swiss National Science Foundation
through a Postdoc. Mobility (Grant No. P500PT 225461). M.T.M. is supported by a
Royal Society University Research Fellowship. M.P.-L. is supported by the Grant
RYC2022-036958-I funded by the Spanish MICIU/AEI/10.13039/501100011033 and by ESF+.
This project is cofunded by the European Union and UK Research & Innovation (Quantum
Flagship project ASPECTS, Grant Agreement No. 101080167). However, views and opinions
expressed are those of the authors only and do not necessarily reflect those of
the European Union, Research Executive Agency, or UK Research & Innovation. Neither
the European Union nor UK Research & Innovation can be held responsible for them.
article_number: L032017
article_processing_charge: Yes
article_type: letter_note
arxiv: 1
author:
- first_name: Kushagra
full_name: Aggarwal, Kushagra
last_name: Aggarwal
- first_name: Alberto
full_name: Rolandi, Alberto
last_name: Rolandi
- first_name: Yikai
full_name: Yang, Yikai
last_name: Yang
- first_name: Joseph
full_name: Hickie, Joseph
last_name: Hickie
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Mark T.
full_name: Mitchison, Mark T.
last_name: Mitchison
- first_name: Martí
full_name: Perarnau-Llobet, Martí
last_name: Perarnau-Llobet
- first_name: Natalia
full_name: Ares, Natalia
last_name: Ares
citation:
ama: Aggarwal K, Rolandi A, Yang Y, et al. Rapid optimal work extraction from a
quantum-dot information engine. Physical Review Research. 2025;7(3). doi:10.1103/q3dx-kyqj
apa: Aggarwal, K., Rolandi, A., Yang, Y., Hickie, J., Jirovec, D., Ballabio, A.,
… Ares, N. (2025). Rapid optimal work extraction from a quantum-dot information
engine. Physical Review Research. American Physical Society. https://doi.org/10.1103/q3dx-kyqj
chicago: Aggarwal, Kushagra, Alberto Rolandi, Yikai Yang, Joseph Hickie, Daniel
Jirovec, Andrea Ballabio, Daniel Chrastina, et al. “Rapid Optimal Work Extraction
from a Quantum-Dot Information Engine.” Physical Review Research. American
Physical Society, 2025. https://doi.org/10.1103/q3dx-kyqj.
ieee: K. Aggarwal et al., “Rapid optimal work extraction from a quantum-dot
information engine,” Physical Review Research, vol. 7, no. 3. American
Physical Society, 2025.
ista: Aggarwal K, Rolandi A, Yang Y, Hickie J, Jirovec D, Ballabio A, Chrastina
D, Isella G, Mitchison MT, Perarnau-Llobet M, Ares N. 2025. Rapid optimal work
extraction from a quantum-dot information engine. Physical Review Research. 7(3),
L032017.
mla: Aggarwal, Kushagra, et al. “Rapid Optimal Work Extraction from a Quantum-Dot
Information Engine.” Physical Review Research, vol. 7, no. 3, L032017,
American Physical Society, 2025, doi:10.1103/q3dx-kyqj.
short: K. Aggarwal, A. Rolandi, Y. Yang, J. Hickie, D. Jirovec, A. Ballabio, D.
Chrastina, G. Isella, M.T. Mitchison, M. Perarnau-Llobet, N. Ares, Physical Review
Research 7 (2025).
date_created: 2025-12-07T23:02:02Z
date_published: 2025-07-01T00:00:00Z
date_updated: 2025-12-09T14:07:49Z
day: '01'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.1103/q3dx-kyqj
external_id:
arxiv:
- '2412.06916'
file:
- access_level: open_access
checksum: 66f2b572a36a7b5fe611a7639a8b6f12
content_type: application/pdf
creator: dernst
date_created: 2025-12-09T14:05:56Z
date_updated: 2025-12-09T14:05:56Z
file_id: '20753'
file_name: 2025_PhysReviewResearch_Aggarwal.pdf
file_size: 536624
relation: main_file
success: 1
file_date_updated: 2025-12-09T14:05:56Z
fulldoi: https://doi.org/10.1103/q3dx-kyqj
has_accepted_license: '1'
intvolume: ' 7'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Physical Review Research
publication_identifier:
eissn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://doi.org/10.5281/zenodo.14516009
scopus_import: '1'
status: public
title: Rapid optimal work extraction from a quantum-dot information engine
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: 7
year: '2025'
...
---
OA_place: publisher
OA_type: diamond
PlanS_conform: '1'
_id: '20734'
abstract:
- lang: eng
text: We consider the problem of parameter estimation in a high-dimensional generalized
linear model. Spectral methods obtained via the principal eigenvector of a suitable
data-dependent matrix provide a simple yet surprisingly effective solution. However,
despite their wide use, a rigorous performance characterization, as well as a
principled way to preprocess the data, are available only for unstructured (i.i.d.
Gaussian and Haar orthogonal) designs. In contrast, real-world data matrices are
highly structured and exhibit non-trivial correlations. To address the problem,
we consider correlated Gaussian designs capturing the anisotropic nature of the
features via a covariance matrix Σ. Our main result is a precise asymptotic characterization
of the performance of spectral estimators. This allows us to identify the optimal
preprocessing that minimizes the number of samples needed for parameter estimation.
Surprisingly, such preprocessing is universal across a broad set of designs, which
partly addresses a conjecture on optimal spectral estimators for rotationally
invariant models. Our principled approach vastly improves upon previous heuristic
methods, including for designs common in computational imaging and genetics. The
proposed methodology, based on approximate message passing, is broadly applicable
and opens the way to the precise characterization of spiked matrices and of the
corresponding spectral methods in a variety of settings.
acknowledgement: "This work was done when Y. Z. and H. C. J. were at the Institute
of Science and Technology Austria. Y. Z. thanks Hugo Latourelle-Vigeant for bringing
[53] to the authors’ attention.\r\nY. Z. and M. M. are partially supported by the
2019 Lopez-Loreta Prize and by the Interdisciplinary Projects Committee (IPC) at
ISTA. H. C. J. is supported by the ERC Advanced Grant “RMTBeyond” No. 101020331."
article_processing_charge: No
article_type: original
author:
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
- first_name: Hong Chang
full_name: Ji, Hong Chang
last_name: Ji
- first_name: Ramji
full_name: Venkataramanan, Ramji
last_name: Venkataramanan
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: Zhang Y, Ji HC, Venkataramanan R, Mondelli M. Spectral estimators for structured
generalized linear models via approximate message passing. Mathematical Statistics
and Learning. 2025;8(3-4):193-304. doi:10.4171/MSL/52
apa: Zhang, Y., Ji, H. C., Venkataramanan, R., & Mondelli, M. (2025). Spectral
estimators for structured generalized linear models via approximate message passing.
Mathematical Statistics and Learning. EMS Press. https://doi.org/10.4171/MSL/52
chicago: Zhang, Yihan, Hong Chang Ji, Ramji Venkataramanan, and Marco Mondelli.
“Spectral Estimators for Structured Generalized Linear Models via Approximate
Message Passing.” Mathematical Statistics and Learning. EMS Press, 2025.
https://doi.org/10.4171/MSL/52.
ieee: Y. Zhang, H. C. Ji, R. Venkataramanan, and M. Mondelli, “Spectral estimators
for structured generalized linear models via approximate message passing,” Mathematical
Statistics and Learning, vol. 8, no. 3–4. EMS Press, pp. 193–304, 2025.
ista: Zhang Y, Ji HC, Venkataramanan R, Mondelli M. 2025. Spectral estimators for
structured generalized linear models via approximate message passing. Mathematical
Statistics and Learning. 8(3–4), 193–304.
mla: Zhang, Yihan, et al. “Spectral Estimators for Structured Generalized Linear
Models via Approximate Message Passing.” Mathematical Statistics and Learning,
vol. 8, no. 3–4, EMS Press, 2025, pp. 193–304, doi:10.4171/MSL/52.
short: Y. Zhang, H.C. Ji, R. Venkataramanan, M. Mondelli, Mathematical Statistics
and Learning 8 (2025) 193–304.
corr_author: '1'
date_created: 2025-12-07T23:02:02Z
date_published: 2025-09-02T00:00:00Z
date_updated: 2025-12-09T13:53:31Z
day: '02'
ddc:
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doi: 10.4171/MSL/52
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date_updated: 2025-12-09T13:50:03Z
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file_name: 2025_MathStatLearning_Zhang.pdf
file_size: 1379626
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success: 1
file_date_updated: 2025-12-09T13:50:03Z
fulldoi: https://doi.org/10.4171/MSL/52
has_accepted_license: '1'
intvolume: ' 8'
issue: 3-4
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 193-304
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Mathematical Statistics and Learning
publication_identifier:
eissn:
- 2520-2324
issn:
- 2520-2316
publication_status: published
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spectral estimators for structured generalized linear models via approximate
message passing
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)
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user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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year: '2025'
...
---
OA_place: publisher
_id: '20737'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: "I also want to thank ISTA and the Austrian Science Fund FWF SFB
F78 (F7805) for financially\r\nsupporting my research."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
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full_name: Casado Polanco, Raquel
id: 15240fc1-dbcd-11ea-9d1d-ac5a786425fd
last_name: Casado Polanco
orcid: 0000-0001-8293-4568
citation:
ama: Casado Polanco R. Role of NOTCH signaling in radial glial progenitor lineage
progression. 2025. doi:10.15479/AT-ISTA-20737
apa: Casado Polanco, R. (2025). Role of NOTCH signaling in radial glial progenitor
lineage progression. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20737
chicago: Casado Polanco, Raquel. “Role of NOTCH Signaling in Radial Glial Progenitor
Lineage Progression.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20737.
ieee: R. Casado Polanco, “Role of NOTCH signaling in radial glial progenitor lineage
progression,” Institute of Science and Technology Austria, 2025.
ista: Casado Polanco R. 2025. Role of NOTCH signaling in radial glial progenitor
lineage progression. Institute of Science and Technology Austria.
mla: Casado Polanco, Raquel. Role of NOTCH Signaling in Radial Glial Progenitor
Lineage Progression. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20737.
short: R. Casado Polanco, Role of NOTCH Signaling in Radial Glial Progenitor Lineage
Progression, Institute of Science and Technology Austria, 2025.
corr_author: '1'
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ddc:
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department:
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- _id: SiHi
doi: 10.15479/AT-ISTA-20737
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file_size: 78207207
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creator: rcasadop
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date_updated: 2025-12-11T09:28:04Z
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embargo_to: open_access
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file_name: 2025_CasadoPolanco_Raquel_Thesis.pdf
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relation: main_file
file_date_updated: 2025-12-11T11:18:37Z
fulldoi: https://doi.org/10.15479/AT-ISTA-20737
has_accepted_license: '1'
keyword:
- NOTCH
- radial glial progenitor
- lineage progression
- cortical development
language:
- iso: eng
month: '12'
oa_version: Published Version
page: '133'
project:
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F7805
name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular
Mechanisms of Neural Stem Cell Lineage Progression
publication_identifier:
isbn:
- 978-3-99078-072-5
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
title: Role of NOTCH signaling in radial glial progenitor lineage progression
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20749'
abstract:
- lang: eng
text: Datasets and code for publication "Electrostatics overcome acoustic collapse
to assemble, adapt, and activate levitated matter"
article_processing_charge: No
author:
- first_name: Sue
full_name: Shi, Sue
id: 5c5b9247-15b2-11ec-abd3-fd958715639c
last_name: Shi
citation:
ama: Shi S. Datasets and code for manuscript “Electrostatics overcome acoustic collapse
to assemble, adapt, and activate levitated matter.” 2025. doi:10.5281/ZENODO.15752991
apa: Shi, S. (2025). Datasets and code for manuscript “Electrostatics overcome acoustic
collapse to assemble, adapt, and activate levitated matter.” Zenodo. https://doi.org/10.5281/ZENODO.15752991
chicago: Shi, Sue. “Datasets and Code for Manuscript ‘Electrostatics Overcome Acoustic
Collapse to Assemble, Adapt, and Activate Levitated Matter.’” Zenodo, 2025. https://doi.org/10.5281/ZENODO.15752991.
ieee: S. Shi, “Datasets and code for manuscript ‘Electrostatics overcome acoustic
collapse to assemble, adapt, and activate levitated matter.’” Zenodo, 2025.
ista: Shi S. 2025. Datasets and code for manuscript ‘Electrostatics overcome acoustic
collapse to assemble, adapt, and activate levitated matter’, Zenodo, 10.5281/ZENODO.15752991.
mla: Shi, Sue. Datasets and Code for Manuscript “Electrostatics Overcome Acoustic
Collapse to Assemble, Adapt, and Activate Levitated Matter.” Zenodo, 2025,
doi:10.5281/ZENODO.15752991.
short: S. Shi, (2025).
contributor:
- first_name: Maximilian
id: 5eb8629e-15b2-11ec-abd3-e6f3e5e01f32
last_name: Hübl
- first_name: Galien M
id: 0C5FDA4A-9CF6-11E9-8939-FF05E6697425
last_name: Grosjean
orcid: 0000-0001-5154-417X
corr_author: '1'
date_created: 2025-12-09T13:36:16Z
date_published: 2025-11-10T00:00:00Z
date_updated: 2026-05-20T08:41:14Z
day: '10'
ddc:
- '530'
department:
- _id: ScWa
- _id: CaGo
doi: 10.5281/ZENODO.15752991
fulldoi: https://doi.org/10.5281/ZENODO.15752991
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/ZENODO.15752991
month: '11'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '20727'
relation: used_in_publication
status: public
status: public
title: Datasets and code for manuscript "Electrostatics overcome acoustic collapse
to assemble, adapt, and activate levitated matter"
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'
...
---
OA_place: repository
OA_type: green
_id: '20750'
article_processing_charge: No
author:
- first_name: Barnaby
full_name: Van Straaten, Barnaby
last_name: Van Straaten
- first_name: Federico
full_name: Fedele, Federico
last_name: Fedele
- first_name: Florian
full_name: Vigneau, Florian
last_name: Vigneau
- first_name: Joseph
full_name: Hickie, Joseph
last_name: Hickie
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Natalia
full_name: Ares, Natalia
last_name: Ares
citation:
ama: Van Straaten B, Fedele F, Vigneau F, et al. All rf-based tuning algorithm for
quantum devices using machine learning. 2025. doi:10.5281/ZENODO.17352653
apa: Van Straaten, B., Fedele, F., Vigneau, F., Hickie, J., Jirovec, D., Chrastina,
D., … Ares, N. (2025). All rf-based tuning algorithm for quantum devices using
machine learning. Zenodo. https://doi.org/10.5281/ZENODO.17352653
chicago: Van Straaten, Barnaby, Federico Fedele, Florian Vigneau, Joseph Hickie,
Daniel Jirovec, Daniel Chrastina, Giovanni Isella, and Natalia Ares. “All Rf-Based
Tuning Algorithm for Quantum Devices Using Machine Learning.” Zenodo, 2025. https://doi.org/10.5281/ZENODO.17352653.
ieee: B. Van Straaten et al., “All rf-based tuning algorithm for quantum
devices using machine learning.” Zenodo, 2025.
ista: Van Straaten B, Fedele F, Vigneau F, Hickie J, Jirovec D, Chrastina D, Isella
G, Ares N. 2025. All rf-based tuning algorithm for quantum devices using machine
learning, Zenodo, 10.5281/ZENODO.17352653.
mla: Van Straaten, Barnaby, et al. All Rf-Based Tuning Algorithm for Quantum
Devices Using Machine Learning. Zenodo, 2025, doi:10.5281/ZENODO.17352653.
short: B. Van Straaten, F. Fedele, F. Vigneau, J. Hickie, D. Jirovec, D. Chrastina,
G. Isella, N. Ares, (2025).
date_created: 2025-12-09T13:36:29Z
date_published: 2025-10-14T00:00:00Z
date_updated: 2025-12-09T14:49:36Z
day: '14'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.5281/ZENODO.17352653
fulldoi: https://doi.org/10.5281/ZENODO.17352653
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.17352653
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '20730'
relation: used_in_publication
status: public
status: public
title: All rf-based tuning algorithm for quantum devices using machine learning
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'
...
---
_id: '20780'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analysed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find the
majority of turnovers happened in the group Schizophora, which tend to have fewer
genes on the F element (the chromosome homologous to the ancestral insect X chromosome)
than lower dipterans, a factor previously hypothesized to facilitate turnover.
Most derived X chromosomes have higher GC content than autosomes, consistent with
a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene
movement out of the X is detected for most of these new X chromosomes, and many
of these moved genes have high testis expression in Drosophila, suggesting that
out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome
turnovers in Diptera. 2025. doi:10.15479/AT-ISTA-20780
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2025). Causes and consequences
of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-20780
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes
and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20780.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences
of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria,
2025.
ista: Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome
turnovers in Diptera, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20780.
mla: Layana Franco, Lorena Alexandra, et al. Causes and Consequences of Sex-Chromosome
Turnovers in Diptera. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20780.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025).
corr_author: '1'
date_created: 2025-12-10T23:40:14Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-06-10T08:27:48Z
department:
- _id: BeVi
doi: 10.15479/AT-ISTA-20780
file:
- access_level: open_access
checksum: 251e7aab01917c2ad2fbccf465492ea1
content_type: application/zip
creator: llayanaf
date_created: 2025-12-11T10:47:15Z
date_updated: 2025-12-11T10:47:15Z
file_id: '20799'
file_name: Perl_scripts.zip
file_size: 4575
relation: main_file
success: 1
- access_level: open_access
checksum: daf1c03149dd170b14e5c8e109ee3c77
content_type: application/zip
creator: llayanaf
date_created: 2025-12-11T10:52:17Z
date_updated: 2025-12-11T10:52:17Z
file_id: '20800'
file_name: Supplementary_Datasets.zip
file_size: 19052849
relation: main_file
success: 1
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checksum: 658d6e95a361b0a3db058b7b4e1733d4
content_type: application/zip
creator: llayanaf
date_created: 2025-12-11T10:52:11Z
date_updated: 2025-12-11T10:52:11Z
file_id: '20801'
file_name: Supplementary_Tables.zip
file_size: 566476
relation: main_file
success: 1
- access_level: open_access
checksum: 2a2b92eb9fade0015719190596a8c5b7
content_type: text/plain
creator: llayanaf
date_created: 2025-12-11T11:00:53Z
date_updated: 2025-12-11T11:00:53Z
file_id: '20802'
file_name: README.txt
file_size: 1204
relation: main_file
success: 1
file_date_updated: 2025-12-11T11:00:53Z
fulldoi: https://doi.org/10.15479/AT-ISTA-20780
has_accepted_license: '1'
keyword:
- Schizophora
- sex chromosomes
- sex-chromosome turnover
- Diptera
- genomic features
- out-of-X movement.
month: '12'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Causes and consequences of sex-chromosome turnovers in Diptera
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
user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2025'
...
---
APC_amount: 5651,35 EUR
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20795'
abstract:
- lang: eng
text: The tropical climate variability is characterized by various oscillations
across a range of timescales. Oscillations that imprint the tropical mean state
are generally attributed to slow processes, such as the seasonal cycle or interannual
variability. Here, we identify a pronounced tropics-wide intraseasonal oscillation
(TWISO) in satellite observations and reanalyses. This oscillation, with a period
of 30 to 60 d, is evident across multiple variables and involves interactions
between convection, radiation, surface fluxes, and large-scale circulation. It
is primarily manifested as convective perturbations in the tropical Indo-Pacific
warm pool accompanied by oscillations in the large-scale tropical overturning
circulation. Here, we examine the relationship between TWISO, the Madden–Julian
Oscillation (MJO), and the instability of radiative-convective equilibrium. Certain
phases of TWISO coincide with specific phases of the MJO, suggesting a potential
connection between the two. However, although the MJO can amplify the oscillation
amplitude of TWISO, it is not essential for TWISO to occur. Finally, due to its
broad manifestation across the tropics, TWISO potentially exerts widespread influence
on tropical weather and climate at regional scales.
acknowledgement: 'J.B. acknowledges funding from the European Union’s Horizon 2020
research and innovation programme under the Marie Skłodowska-Curie grant (grant
agreement No. 101034413). S.B. acknowledges funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (Project
Mesoscale organization of tropical convection, grant agreement No 101098063). D.T.
acknowledges funding from the Japan Society for the Promotion of Science (JSPS)
(Project JSPS Grants-in-Aid for Scientific Research, grant No. JP24K22893). C.M.
gratefully acknowledges funding from the ERC under the European Union’s Horizon
2020 research and innovation program (Project organisation of CLoUdS, and implications
for Tropical cyclones and for the Energetics of the tropics, in current and in a
waRming climate, grant agreement No. 805041). We thank Martin Singh, Steven Sherwood,
Bjorn Stevens, and Lokahith Agasthya for helpful discussions. JSPS Core-to-Core
Program, “International Core-to-Core Project on Global Storm Resolving Analysis”
(Grant Number: JPJSCCA20220001)'
article_number: e2511549122
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jiawei
full_name: Bao, Jiawei
id: bb9a7399-fefd-11ed-be3c-ae648fd1d160
last_name: Bao
- first_name: Sandrine
full_name: Bony, Sandrine
last_name: Bony
- first_name: Daisuke
full_name: Takasuka, Daisuke
last_name: Takasuka
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: Bao J, Bony S, Takasuka D, Muller CJ. Tropics-wide intraseasonal oscillations.
Proceedings of the National Academy of Sciences. 2025;122(48). doi:10.1073/pnas.2511549122
apa: Bao, J., Bony, S., Takasuka, D., & Muller, C. J. (2025). Tropics-wide intraseasonal
oscillations. Proceedings of the National Academy of Sciences. National
Academy of Sciences. https://doi.org/10.1073/pnas.2511549122
chicago: Bao, Jiawei, Sandrine Bony, Daisuke Takasuka, and Caroline J Muller. “Tropics-Wide
Intraseasonal Oscillations.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2511549122.
ieee: J. Bao, S. Bony, D. Takasuka, and C. J. Muller, “Tropics-wide intraseasonal
oscillations,” Proceedings of the National Academy of Sciences, vol. 122,
no. 48. National Academy of Sciences, 2025.
ista: Bao J, Bony S, Takasuka D, Muller CJ. 2025. Tropics-wide intraseasonal oscillations.
Proceedings of the National Academy of Sciences. 122(48), e2511549122.
mla: Bao, Jiawei, et al. “Tropics-Wide Intraseasonal Oscillations.” Proceedings
of the National Academy of Sciences, vol. 122, no. 48, e2511549122, National
Academy of Sciences, 2025, doi:10.1073/pnas.2511549122.
short: J. Bao, S. Bony, D. Takasuka, C.J. Muller, Proceedings of the National Academy
of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-12-11T10:41:13Z
date_published: 2025-12-02T00:00:00Z
date_updated: 2026-05-20T08:11:56Z
day: '02'
ddc:
- '550'
department:
- _id: CaMu
doi: 10.1073/pnas.2511549122
ec_funded: 1
external_id:
pmid:
- '41284872'
file:
- access_level: open_access
checksum: 093a8685170e4a1de9176f68ee449493
content_type: application/pdf
creator: dernst
date_created: 2025-12-15T09:17:33Z
date_updated: 2025-12-15T09:17:33Z
file_id: '20822'
file_name: 2025_PNAS_Bao.pdf
file_size: 30890293
relation: main_file
success: 1
file_date_updated: 2025-12-15T09:17:33Z
fulldoi: https://doi.org/10.1073/pnas.2511549122
has_accepted_license: '1'
intvolume: ' 122'
issue: '48'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: 629205d8-2b32-11ec-9570-e1356ff73576
call_identifier: H2020
grant_number: '805041'
name: Organization of CLoUdS, and implications of Tropical cyclones and for the
Energetics of the tropics, in current and waRming climate
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/hidden-in-plain-sight/
scopus_import: '1'
status: public
title: Tropics-wide intraseasonal oscillations
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: 122
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20796'
abstract:
- lang: eng
text: Rapid prophase chromosome movements ensure faithful alignment of the parental
homologous chromosomes and successful synapsis formation during meiosis. These
movements are driven by cytoplasmic forces transmitted to the nuclear periphery,
where chromosome ends are attached through transmembrane proteins. During many
developmental stages a specific genome architecture with chromatin nuclear periphery
contacts mediates specific gene expression. Whether chromatin is removed from
the nuclear periphery as a consequence of chromosome motions or by a specific
mechanism is not fully understood. Here, we identify a mechanism to remove chromatin
from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation
of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early
prophase of meiosis. Interfering with chromatin removal delays chromosome pairing,
impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis.
Long read sequencing reveals deletions and duplications in offspring lacking VRK-1
underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability
in gametes during rapid chromosome movements.
acknowledgement: We are grateful to Monique Zetka, Nicola Silva, and Yumi Kim, Needhi
Bhalla, George Krohne and Rueyling Lin for providing reagents; Scott Kennedy for
sharing the multiplexed FISH library; and members of the Max Perutz Labs’ BioOptics
facility (Irmgard Fischer, Josef Gotzmann, Thomas Peterbauer, Clara Bodner, and
Nick Wedige) for training and support in image acquisition. We also thank the members
of the NGS facility at the Vienna Biocenter. This work was funded by the Austrian
Science Fund (FWF) SFB projects F 8805-B (VJ), https://doi.org/10.55776/F88, F 8809-B
(ITB), and F8810-B (BV). We are also grateful to members of the V. Jantsch laboratory
for helpful discussions. Some strains were provided by the Caenorhabditis Genetics
Center, which is funded by the National Institutes of Health Office of Research
Infrastructure Programs (P40OD010440).
article_number: '10446'
article_processing_charge: Yes
article_type: original
author:
- first_name: Dimitra
full_name: Paouneskou, Dimitra
last_name: Paouneskou
- first_name: Antoine
full_name: Baudrimont, Antoine
last_name: Baudrimont
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Angela
full_name: Graf, Angela
last_name: Graf
- first_name: Shehab
full_name: Moukbel Ali Aldawla, Shehab
last_name: Moukbel Ali Aldawla
- first_name: Claudia
full_name: Kölbl, Claudia
last_name: Kölbl
- first_name: Irene
full_name: Tiemann-Boege, Irene
last_name: Tiemann-Boege
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Verena
full_name: Jantsch, Verena
last_name: Jantsch
citation:
ama: Paouneskou D, Baudrimont A, Kelemen RK, et al. BAF-1–VRK-1 mediated release
of meiotic chromosomes from the nuclear periphery is important for genome integrity.
Nature Communications. 2025;16. doi:10.1038/s41467-025-65420-9
apa: Paouneskou, D., Baudrimont, A., Kelemen, R. K., Elkrewi, M. N., Graf, A., Moukbel
Ali Aldawla, S., … Jantsch, V. (2025). BAF-1–VRK-1 mediated release of meiotic
chromosomes from the nuclear periphery is important for genome integrity. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-025-65420-9
chicago: Paouneskou, Dimitra, Antoine Baudrimont, Réka K Kelemen, Marwan N Elkrewi,
Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz
Vicoso, and Verena Jantsch. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes
from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications.
Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65420-9.
ieee: D. Paouneskou et al., “BAF-1–VRK-1 mediated release of meiotic chromosomes
from the nuclear periphery is important for genome integrity,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: Paouneskou D, Baudrimont A, Kelemen RK, Elkrewi MN, Graf A, Moukbel Ali Aldawla
S, Kölbl C, Tiemann-Boege I, Vicoso B, Jantsch V. 2025. BAF-1–VRK-1 mediated release
of meiotic chromosomes from the nuclear periphery is important for genome integrity.
Nature Communications. 16, 10446.
mla: Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes
from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications,
vol. 16, 10446, Springer Nature, 2025, doi:10.1038/s41467-025-65420-9.
short: D. Paouneskou, A. Baudrimont, R.K. Kelemen, M.N. Elkrewi, A. Graf, S. Moukbel
Ali Aldawla, C. Kölbl, I. Tiemann-Boege, B. Vicoso, V. Jantsch, Nature Communications
16 (2025).
date_created: 2025-12-11T10:45:06Z
date_published: 2025-11-25T00:00:00Z
date_updated: 2025-12-15T09:28:37Z
day: '25'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1038/s41467-025-65420-9
external_id:
pmid:
- '41290579'
file:
- access_level: open_access
checksum: a952f7ea050242b79008540de49a0e61
content_type: application/pdf
creator: dernst
date_created: 2025-12-15T09:25:51Z
date_updated: 2025-12-15T09:25:51Z
file_id: '20823'
file_name: 2025_NatureComm_Paouneskou.pdf
file_size: 8096309
relation: main_file
success: 1
file_date_updated: 2025-12-15T09:25:51Z
fulldoi: https://doi.org/10.1038/s41467-025-65420-9
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery
is important for genome integrity
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: 16
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '20816'
abstract:
- lang: eng
text: "Background: DNA methylation (DNAm) can regulate gene expression, and its
genome-wide patterns (epigenetic scores or EpiScores) can act as biomarkers for
complex traits. The relative stability of methylation profiles may enable better
assessment of chronic exposures compared to single time-point protein measures.
We present the first large-scale epigenetic study of the highly-abundant serum
proteome measured via ultra-high throughput mass spectrometry in 14,671 samples
from the Generation Scotland cohort. We further demonstrate the first large-scale
comparison of protein EpiScores and their respective proteins as predictors of
incident cardiovascular disease.\r\n\r\nResults: Marginal epigenome-wide association
models, adjusting for age, sex, measurement batch, estimated white cell proportions,
BMI, smoking and methylation principal components, reveal 15,855 significant CpG
– protein associations across 125 of 133 proteins PBonferroni < 2.71 × 10-10.
Bayesian epigenome-wide association studies of the same 133 proteins reveal 697
CpG-Protein associations (posterior inclusion probability > 0.95). 112 protein
EpiScores correlate significantly with their respective protein in a holdout test-set.
Of these, sixteen associate significantly with incident all-cause cardiovascular
disease (Nevents=191) compared to one measured protein.\r\n\r\nConclusions: We
highlight a complex interplay between the blood-based methylome and proteome.
Importantly, we show that protein EpiScores correlate with measured proteins and
demonstrate that the, as-yet understudied, high-abundance proteome may yield clinically
relevant biomarkers. The protein EpiScores demonstrate more significant associations
with cardiovascular disease than directly measured proteins, suggesting their
potential as clinical biomarkers for monitoring or predicting disease risk. We
suggest that biomarker development could be enhanced by the consideration of protein
EpiScores alongside measured proteins."
acknowledgement: "Generation Scotland received core support from the Chief Scientist
Office of the Scottish Government Health Directorates [CZD/16/6] and the Scottish
Funding Council [HR03006] and is currently supported by the Wellcome Trust [216767/Z/19/Z].
Genotyping of the Generation Scotland samples was carried out by the Genetics Core
Laboratory at the Edinburgh Clinical Research Facility, University of Edinburgh,
Scotland and was funded by the Medical Research Council UK and the Wellcome Trust
(Wellcome Trust Strategic Award “STratifying Resilience and Depression Longitudinally”
(STRADL) Reference 104036/Z/14/Z). The DNA methylation profiling and analysis was
supported by Wellcome Investigator Award 220857/Z/20/Z and Grant 104036/Z/14/Z (PI:
Prof AM McIntosh) and through funding from NARSAD (Ref: 27404; awardee: Dr DM Howard)
and the Royal College of Physicians of Edinburgh (Sim Fellowship; Awardee: Prof
HC Whalley).\r\nJAR is a University of Edinburgh Clinical Academic Track PhD student,
supported by the Wellcome Trust (319878/Z/24/Z). ADC was supported by a Medical
Research Council PhD Studentship in Precision Medicine with funding from the Medical
Research Council Doctoral Training Program and the University of Edinburgh College
of Medicine and Veterinary Medicine. HMS is a student on the University of Edinburgh
Translational Neuroscience PhD programme funded by the Wellcome Trust (218493/Z/19/Z).
CH was funded by MRC Human Genetics Unit program (QTL in Health and Disease) (grant
U.MC_UU_00007/10). S.R.C. is supported by a Sir Henry Dale Fellowship jointly funded
by the Wellcome Trust and the Royal Society (221890/Z/20/Z). JM and REM were supported
by Alzheimer’s Society project grant AS-PG-19b-010."
article_number: '417'
article_processing_charge: Yes
article_type: original
author:
- first_name: Josephine A.
full_name: Robertson, Josephine A.
last_name: Robertson
- first_name: Jakub
full_name: Bajzik, Jakub
id: b995e25b-8c4b-11ed-a6d8-f71b7bcd6122
last_name: Bajzik
- first_name: Spyros
full_name: Vernardis, Spyros
last_name: Vernardis
- first_name: Aleksandra D.
full_name: Chybowska, Aleksandra D.
last_name: Chybowska
- first_name: Daniel L.
full_name: Mccartney, Daniel L.
last_name: Mccartney
- first_name: Arturas
full_name: Grauslys, Arturas
last_name: Grauslys
- first_name: Jure
full_name: Mur, Jure
last_name: Mur
- first_name: Hannah M.
full_name: Smith, Hannah M.
last_name: Smith
- first_name: Archie
full_name: Campbell, Archie
last_name: Campbell
- first_name: Camilla
full_name: Drake, Camilla
last_name: Drake
- first_name: Hannah
full_name: Grant, Hannah
last_name: Grant
- first_name: Jamie
full_name: Pearce, Jamie
last_name: Pearce
- first_name: Tom C.
full_name: Russ, Tom C.
last_name: Russ
- first_name: Poppy
full_name: Adkin, Poppy
last_name: Adkin
- first_name: Matthew
full_name: White, Matthew
last_name: White
- first_name: Charles
full_name: Brigden, Charles
last_name: Brigden
- first_name: Christoph B.
full_name: Messner, Christoph B.
last_name: Messner
- first_name: David J.
full_name: Porteous, David J.
last_name: Porteous
- first_name: Caroline
full_name: Hayward, Caroline
last_name: Hayward
- first_name: Simon R.
full_name: Cox, Simon R.
last_name: Cox
- first_name: Aleksej
full_name: Zelezniak, Aleksej
last_name: Zelezniak
- first_name: Markus
full_name: Ralser, Markus
last_name: Ralser
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Riccardo E.
full_name: Marioni, Riccardo E.
last_name: Marioni
citation:
ama: Robertson JA, Bajzik J, Vernardis S, et al. Methylome-wide association studies
and epigenetic biomarker development for 133 mass spectrometry-assessed circulating
proteins in 14,671 Generation Scotland participants. Genome Biology. 2025;26.
doi:10.1186/s13059-025-03892-0
apa: Robertson, J. A., Bajzik, J., Vernardis, S., Chybowska, A. D., Mccartney, D.
L., Grauslys, A., … Marioni, R. E. (2025). Methylome-wide association studies
and epigenetic biomarker development for 133 mass spectrometry-assessed circulating
proteins in 14,671 Generation Scotland participants. Genome Biology. Springer
Nature. https://doi.org/10.1186/s13059-025-03892-0
chicago: Robertson, Josephine A., Jakub Bajzik, Spyros Vernardis, Aleksandra D.
Chybowska, Daniel L. Mccartney, Arturas Grauslys, Jure Mur, et al. “Methylome-Wide
Association Studies and Epigenetic Biomarker Development for 133 Mass Spectrometry-Assessed
Circulating Proteins in 14,671 Generation Scotland Participants.” Genome Biology.
Springer Nature, 2025. https://doi.org/10.1186/s13059-025-03892-0.
ieee: J. A. Robertson et al., “Methylome-wide association studies and epigenetic
biomarker development for 133 mass spectrometry-assessed circulating proteins
in 14,671 Generation Scotland participants,” Genome Biology, vol. 26. Springer
Nature, 2025.
ista: Robertson JA, Bajzik J, Vernardis S, Chybowska AD, Mccartney DL, Grauslys
A, Mur J, Smith HM, Campbell A, Drake C, Grant H, Pearce J, Russ TC, Adkin P,
White M, Brigden C, Messner CB, Porteous DJ, Hayward C, Cox SR, Zelezniak A, Ralser
M, Robinson MR, Marioni RE. 2025. Methylome-wide association studies and epigenetic
biomarker development for 133 mass spectrometry-assessed circulating proteins
in 14,671 Generation Scotland participants. Genome Biology. 26, 417.
mla: Robertson, Josephine A., et al. “Methylome-Wide Association Studies and Epigenetic
Biomarker Development for 133 Mass Spectrometry-Assessed Circulating Proteins
in 14,671 Generation Scotland Participants.” Genome Biology, vol. 26, 417,
Springer Nature, 2025, doi:10.1186/s13059-025-03892-0.
short: J.A. Robertson, J. Bajzik, S. Vernardis, A.D. Chybowska, D.L. Mccartney,
A. Grauslys, J. Mur, H.M. Smith, A. Campbell, C. Drake, H. Grant, J. Pearce, T.C.
Russ, P. Adkin, M. White, C. Brigden, C.B. Messner, D.J. Porteous, C. Hayward,
S.R. Cox, A. Zelezniak, M. Ralser, M.R. Robinson, R.E. Marioni, Genome Biology
26 (2025).
date_created: 2025-12-14T23:02:04Z
date_published: 2025-12-08T00:00:00Z
date_updated: 2025-12-15T13:19:41Z
day: '08'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1186/s13059-025-03892-0
external_id:
pmid:
- '41361833'
file:
- access_level: open_access
checksum: 7c92919af1b5820d01e91e08906a411f
content_type: application/pdf
creator: dernst
date_created: 2025-12-15T13:18:07Z
date_updated: 2025-12-15T13:18:07Z
file_id: '20825'
file_name: 2025_GenomeBiology_Robertson.pdf
file_size: 2206991
relation: main_file
success: 1
file_date_updated: 2025-12-15T13:18:07Z
fulldoi: https://doi.org/10.1186/s13059-025-03892-0
has_accepted_license: '1'
intvolume: ' 26'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1474-760X
issn:
- 1474-7596
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Methylome-wide association studies and epigenetic biomarker development for
133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland
participants
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: 26
year: '2025'
...
---
APC_amount: 4910,08 EUR
OA_place: publisher
OA_type: gold
_id: '8125'
abstract:
- lang: eng
text: "Biological memory is known to be flexible—memory formation and recall depend
on factors such as the behavioral context of the organism. However, this property
is often ignored in associative memory models, leaving it unclear how memories
can be organized and recalled when subject to contextual control. Because of the
lack of a rigorous analytical framework, it is also unknown how contextual control
affects memory stability, storage capacity, and information content. Here, we
bring the dynamic nature of memory to the fore by introducing a novel model of
associative memory, which we refer to as the context-modular memory network. In
our model, stored memory patterns are associated to one of several background
network states, or contexts. Memories are accessible when their corresponding
context is active, and are otherwise inaccessible. Context modulates the effective
network connectivity by imposing a specific\r\nconfiguration of neuronal and synaptic
gating—gated neurons (synapses) have their activity (weights) momentarily silenced,
thereby reducing interference from memories belonging to other contexts. Memory
patterns are randomly and independently chosen, while neuronal and synaptic gates
may be selected randomly or optimized through a process of contextual synaptic
refinement. Through analytic and numerical results, we show that context-modular
memory networks can exhibit both improved memory capacity and differential control
of memory stability with random gating (especially for neuronal gating). For contextual
synaptic refinement, we devise a method in which synapses are gated off for a
given context if they destabilize the memory patterns in that context, drastically
improving memory capacity and enabling even more precise control over memory stability.
Notably, synaptic refinement allows for patterns to be\r\naccessible in multiple
contexts, stabilizing memory patterns even for weight matrices that alone do not
contain any information about the memory patterns, such as Gaussian random matrices.
Overall, our model integrates recent ideas about context-dependent memory organization
with classic associative memory models and proposes a rigorous theory which can
act as a framework for future work. Furthermore, our work carries important implications
for the understanding of biological memory storage and recall in the brain, such
as highlighting an intriguing trade-off between memory capacity and accessibility."
acknowledgement: "We thank Helen Barron, Vezha Boboeva, Adam Packer, João Sacramento,
Andrew Saxe, Misha Tsodyks, and Friedemann Zenke for helpful comments at various
stages of this work, and Rubem Erichsen, Jr. for carefully reading the manuscript
and valuable comments. This work was\r\nsupported by a Sir Henry Dale Fellowship
by the Wellcome Trust and the Royal Society [No. WT100000 (W. F. P., E. J. A., and
T. P. V.)], a Wellcome Trust Senior Research Fellowship [No. 214316/Z/18/Z (E. J.
A. and T. P. V.)], and a Research Project Grant by the Leverhulme Trust\r\n[No.
RPG-2016-446 (E. J. A.)]. "
article_number: '011057'
article_processing_charge: Yes
article_type: original
author:
- first_name: William F.
full_name: Podlaski, William F.
last_name: Podlaski
orcid: 0000-0001-6619-7502
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
orcid: 0000-0001-7184-7311
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in
associative memory networks with context-dependent neuronal and synaptic gating.
Physical Review X. 2025;15. doi:10.1103/PhysRevX.15.011057
apa: Podlaski, W. F., Agnes, E. J., & Vogels, T. P. (2025). High capacity and
dynamic accessibility in associative memory networks with context-dependent neuronal
and synaptic gating. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.15.011057
chicago: Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity
and Dynamic Accessibility in Associative Memory Networks with Context-Dependent
Neuronal and Synaptic Gating.” Physical Review X. American Physical Society,
2025. https://doi.org/10.1103/PhysRevX.15.011057.
ieee: W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic
accessibility in associative memory networks with context-dependent neuronal and
synaptic gating,” Physical Review X, vol. 15. American Physical Society,
2025.
ista: Podlaski WF, Agnes EJ, Vogels TP. 2025. High capacity and dynamic accessibility
in associative memory networks with context-dependent neuronal and synaptic gating.
Physical Review X. 15, 011057.
mla: Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative
Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” Physical
Review X, vol. 15, 011057, American Physical Society, 2025, doi:10.1103/PhysRevX.15.011057.
short: W.F. Podlaski, E.J. Agnes, T.P. Vogels, Physical Review X 15 (2025).
corr_author: '1'
date_created: 2020-07-16T12:24:28Z
date_published: 2025-03-13T00:00:00Z
date_updated: 2026-05-06T12:44:27Z
day: '13'
ddc:
- '530'
department:
- _id: TiVo
doi: 10.1103/PhysRevX.15.011057
external_id:
isi:
- '001451378900002'
file:
- access_level: open_access
checksum: 1f27ee469ab51a3e1ce1e2df0022e81d
content_type: application/pdf
creator: dernst
date_created: 2025-03-20T12:47:17Z
date_updated: 2025-03-20T12:47:17Z
file_id: '19432'
file_name: 2025_PhysReviewX_Podlaski.pdf
file_size: 1373704
relation: main_file
success: 1
file_date_updated: 2025-03-20T12:47:17Z
fulldoi: https://doi.org/10.1103/PhysRevX.15.011057
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
locked: '1'
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: c084a126-5a5b-11eb-8a69-d75314a70a87
grant_number: 214316/Z/18/Z
name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent
neuronal networks.
publication: Physical Review X
publication_identifier:
eissn:
- 2160-3308
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/wpodlaski/contextual-memory-nets
scopus_import: '1'
status: public
title: High capacity and dynamic accessibility in associative memory networks with
context-dependent neuronal and synaptic gating
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: 15
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '8616'
abstract:
- lang: eng
text: The brain vasculature supplies neurons with glucose and oxygen, but little
is known about how vascular plasticity contributes to brain function. Using longitudinal
in vivo imaging, we report that a substantial proportion of blood vessels in the
adult mouse brain sporadically occlude and regress. Their regression proceeds
through sequential stages of blood-flow occlusion, endothelial cell collapse,
relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels
are found to be widespread in mouse, monkey and human brains. We further reveal
that blood vessel regression cause a reduction of neuronal activity due to a dysfunction
in mitochondrial metabolism and glutamate production. Our results elucidate the
mechanism of vessel regression and its role in neuronal function in the adult
brain.
acknowledgement: 'The project was initiated in the Jan lab at UCSF. We thank Lily
Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing
MADM-7 mice and Rolf A Brekken for VEGF-antibodies. Drs. Yuanquan Song (UPenn),
Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang
U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s
Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics,
Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion.
Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.)
for critical reading. We acknowledge the assistance of the CIBR Imaging core. We
also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the
Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support
Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart
Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.;
National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key
Research and Development Program of China (2016YFE0125400)to F.H.;National Natural
Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation
of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865)
to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake
University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670
and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780
to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking
Outside the Box Award.'
article_number: '5840'
article_processing_charge: Yes
article_type: original
author:
- first_name: Xiaofei
full_name: Gao, Xiaofei
last_name: Gao
- first_name: Jun-Liszt
full_name: Li, Jun-Liszt
last_name: Li
- first_name: Xingjun
full_name: Chen, Xingjun
last_name: Chen
- first_name: Bo
full_name: Ci, Bo
last_name: Ci
- first_name: Fei
full_name: Chen, Fei
last_name: Chen
- first_name: Nannan
full_name: Lu, Nannan
last_name: Lu
- first_name: Bo
full_name: Shen, Bo
last_name: Shen
- first_name: Lijun
full_name: Zheng, Lijun
last_name: Zheng
- first_name: Jie-Min
full_name: Jia, Jie-Min
last_name: Jia
- first_name: Yating
full_name: Yi, Yating
last_name: Yi
- first_name: Shiwen
full_name: Zhang, Shiwen
last_name: Zhang
- first_name: Ying-Chao
full_name: Shi, Ying-Chao
last_name: Shi
- first_name: Kaibin
full_name: Shi, Kaibin
last_name: Shi
- first_name: Nicholas E
full_name: Propson, Nicholas E
last_name: Propson
- first_name: Yubin
full_name: Huang, Yubin
last_name: Huang
- first_name: Katherine
full_name: Poinsatte, Katherine
last_name: Poinsatte
- first_name: Zhaohuan
full_name: Zhang, Zhaohuan
last_name: Zhang
- first_name: Yuanlei
full_name: Yue, Yuanlei
last_name: Yue
- first_name: Dale B
full_name: Bosco, Dale B
last_name: Bosco
- first_name: Ying-mei
full_name: Lu, Ying-mei
last_name: Lu
- first_name: Shi-bing
full_name: Yang, Shi-bing
last_name: Yang
- first_name: Ralf H.
full_name: Adams, Ralf H.
last_name: Adams
- first_name: Volkhard
full_name: Lindner, Volkhard
last_name: Lindner
- first_name: Fen
full_name: Huang, Fen
last_name: Huang
- first_name: Long-Jun
full_name: Wu, Long-Jun
last_name: Wu
- first_name: Hui
full_name: Zheng, Hui
last_name: Zheng
- first_name: Feng
full_name: Han, Feng
last_name: Han
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ann M.
full_name: Stowe, Ann M.
last_name: Stowe
- first_name: Bo
full_name: Peng, Bo
last_name: Peng
- first_name: Marta
full_name: Margeta, Marta
last_name: Margeta
- first_name: Xiaoqun
full_name: Wang, Xiaoqun
last_name: Wang
- first_name: Qiang
full_name: Liu, Qiang
last_name: Liu
- first_name: Jakob
full_name: Körbelin, Jakob
last_name: Körbelin
- first_name: Martin
full_name: Trepel, Martin
last_name: Trepel
- first_name: Hui
full_name: Lu, Hui
last_name: Lu
- first_name: Bo O.
full_name: Zhou, Bo O.
last_name: Zhou
- first_name: Hu
full_name: Zhao, Hu
last_name: Zhao
- first_name: Wenzhi
full_name: Su, Wenzhi
last_name: Su
- first_name: Robert M.
full_name: Bachoo, Robert M.
last_name: Bachoo
- first_name: Woo-ping
full_name: Ge, Woo-ping
last_name: Ge
citation:
ama: Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel
regression in the brain. Nature Communications. 2025;16. doi:10.1038/s41467-025-60308-0
apa: Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (2025). Reduction
of neuronal activity mediated by blood-vessel regression in the brain. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-025-60308-0
chicago: Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo
Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression
in the Brain.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-025-60308-0.
ieee: X. Gao et al., “Reduction of neuronal activity mediated by blood-vessel
regression in the brain,” Nature Communications, vol. 16. Springer Nature,
2025.
ista: Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y,
Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco
DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer
S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou
BO, Zhao H, Su W, Bachoo RM, Ge W. 2025. Reduction of neuronal activity mediated
by blood-vessel regression in the brain. Nature Communications. 16, 5840.
mla: Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel
Regression in the Brain.” Nature Communications, vol. 16, 5840, Springer
Nature, 2025, doi:10.1038/s41467-025-60308-0.
short: X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M.
Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte,
Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang,
L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X.
Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo,
W. Ge, Nature Communications 16 (2025).
date_created: 2020-10-06T08:58:59Z
date_published: 2025-07-01T00:00:00Z
date_updated: 2025-09-04T07:08:37Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1038/s41467-025-60308-0
ec_funded: 1
external_id:
isi:
- '001523450500035'
file:
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checksum: f59748cb67232cfb210035d9aef60836
content_type: application/pdf
creator: dernst
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isi: 1
language:
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month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reduction of neuronal activity mediated by blood-vessel regression in the brain
tmp:
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legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
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short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '17459'
abstract:
- lang: eng
text: Atopic dermatitis (AD) is the most common chronic inflammatory skin disease
worldwide. AD is a highly complex disease with different subtypes. Many elements
of AD pathophysiology have been described, but if/how they interact with each
other or which mechanisms are important in which patients is still unclear. Langerhans
cells (LCs) are antigen-presenting cells (APCs) in the epidermis. Depending on
the context, they can act either pro- or anti-inflammatory. Many different studies
have investigated LCs in the context of AD and found them to be connected to all
major mechanisms of AD pathophysiology. As APCs, LCs recruit other immune cells
and shape the immune response, especially adaptive immunity via polarization of
T cells. As sentinel cells, LCs are primary sensors of the skin microbiome and
are important for the decision of immunity versus tolerance. LCs are also involved
with the integrity of the skin barrier by influencing tight junctions. Finally,
LCs are important cells in the neuro-immune crosstalk in the skin. In this review,
we provide an overview about the many different roles of LCs in AD. Understanding
LCs might bring us closer to a more complete understanding of this highly complex
disease. Potentially, modulating LCs might offer new options for targeted therapies
for AD patients.
acknowledgement: This work was supported by the CK-CARE of the KühneFoundation, Switzerland;
the China Scholarship Counciland Shanghai Biocelline Enterprise Co. Ltd, China.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yi
full_name: Pan, Yi
last_name: Pan
- first_name: Mathias
full_name: Hochgerner, Mathias
last_name: Hochgerner
- first_name: Malgorzata Anna
full_name: Cichon, Malgorzata Anna
id: d63197a3-c188-11ed-9387-8d33a3f13871
last_name: Cichon
- first_name: Theresa
full_name: Benezeder, Theresa
last_name: Benezeder
- first_name: Thomas
full_name: Bieber, Thomas
last_name: Bieber
- first_name: Peter
full_name: Wolf, Peter
last_name: Wolf
citation:
ama: 'Pan Y, Hochgerner M, Cichon MA, Benezeder T, Bieber T, Wolf P. Langerhans
cells: Central players in the pathophysiology of atopic dermatitis. Journal
of the European Academy of Dermatology and Venereology. 2025;39(2):278-289.
doi:10.1111/jdv.20291'
apa: 'Pan, Y., Hochgerner, M., Cichon, M. A., Benezeder, T., Bieber, T., & Wolf,
P. (2025). Langerhans cells: Central players in the pathophysiology of atopic
dermatitis. Journal of the European Academy of Dermatology and Venereology.
Wiley. https://doi.org/10.1111/jdv.20291'
chicago: 'Pan, Yi, Mathias Hochgerner, Malgorzata Anna Cichon, Theresa Benezeder,
Thomas Bieber, and Peter Wolf. “Langerhans Cells: Central Players in the Pathophysiology
of Atopic Dermatitis.” Journal of the European Academy of Dermatology and Venereology.
Wiley, 2025. https://doi.org/10.1111/jdv.20291.'
ieee: 'Y. Pan, M. Hochgerner, M. A. Cichon, T. Benezeder, T. Bieber, and P. Wolf,
“Langerhans cells: Central players in the pathophysiology of atopic dermatitis,”
Journal of the European Academy of Dermatology and Venereology, vol. 39,
no. 2. Wiley, pp. 278–289, 2025.'
ista: 'Pan Y, Hochgerner M, Cichon MA, Benezeder T, Bieber T, Wolf P. 2025. Langerhans
cells: Central players in the pathophysiology of atopic dermatitis. Journal of
the European Academy of Dermatology and Venereology. 39(2), 278–289.'
mla: 'Pan, Yi, et al. “Langerhans Cells: Central Players in the Pathophysiology
of Atopic Dermatitis.” Journal of the European Academy of Dermatology and Venereology,
vol. 39, no. 2, Wiley, 2025, pp. 278–89, doi:10.1111/jdv.20291.'
short: Y. Pan, M. Hochgerner, M.A. Cichon, T. Benezeder, T. Bieber, P. Wolf, Journal
of the European Academy of Dermatology and Venereology 39 (2025) 278–289.
date_created: 2024-08-25T22:01:07Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-05-19T13:58:50Z
day: '01'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1111/jdv.20291
external_id:
isi:
- '001292894900001'
pmid:
- '39157943'
file:
- access_level: open_access
checksum: 12555ddb3490daf10b8d44e334e7312e
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T09:59:37Z
date_updated: 2025-04-16T09:59:37Z
file_id: '19583'
file_name: 2025_JEADV_Pan.pdf
file_size: 457698
relation: main_file
success: 1
file_date_updated: 2025-04-16T09:59:37Z
fulldoi: https://doi.org/10.1111/jdv.20291
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 278-289
pmid: 1
publication: Journal of the European Academy of Dermatology and Venereology
publication_identifier:
eissn:
- 1468-3083
issn:
- 0926-9959
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Langerhans cells: Central players in the pathophysiology of atopic dermatitis'
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: 39
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18154'
abstract:
- lang: eng
text: 'In 1976, Deligne and Lusztig realized the representation theory of finite
groups of Lie type inside étale cohomology of certain algebraic varieties. Recently,
a p-adic version of this theory started to emerge: there are p-adic Deligne–Lusztig
spaces, whose cohomology encodes representation theoretic information for p-adic
groups – for instance, it partially realizes the local Langlands correspondence
with characteristic zero coefficients. However, the parallel case of coefficients
of positive characteristic ℓ≠p has not been inspected so far. The purpose of
this article is to initiate such an inspection. In particular, we relate cohomology
of certain p-adic Deligne–Lusztig spaces to Vignéras''s modular local Langlands
correspondence for GLn.'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Jakub
full_name: Löwit, Jakub
id: e3b80ae2-eb8e-11eb-b029-9aef4a9108a0
last_name: Löwit
citation:
ama: Löwit J. On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn.
Journal of Algebra. 2025;663(2):81-118. doi:10.1016/j.jalgebra.2024.08.033
apa: Löwit, J. (2025). On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties
for GLn. Journal of Algebra. Elsevier. https://doi.org/10.1016/j.jalgebra.2024.08.033
chicago: Löwit, Jakub. “On modulo ℓ Cohomology of P-Adic Deligne–Lusztig Varieties
for GLn.” Journal of Algebra. Elsevier, 2025. https://doi.org/10.1016/j.jalgebra.2024.08.033.
ieee: J. Löwit, “On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for
GLn,” Journal of Algebra, vol. 663, no. 2. Elsevier, pp. 81–118, 2025.
ista: Löwit J. 2025. On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties
for GLn. Journal of Algebra. 663(2), 81–118.
mla: Löwit, Jakub. “On modulo ℓ Cohomology of P-Adic Deligne–Lusztig Varieties for
GLn.” Journal of Algebra, vol. 663, no. 2, Elsevier, 2025, pp. 81–118,
doi:10.1016/j.jalgebra.2024.08.033.
short: J. Löwit, Journal of Algebra 663 (2025) 81–118.
corr_author: '1'
date_created: 2024-09-29T22:01:37Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-02-27T12:32:40Z
day: '01'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1016/j.jalgebra.2024.08.033
external_id:
arxiv:
- '2404.11176'
isi:
- '001325207800001'
file:
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checksum: eb240e93c178e48429ad918c9058f1fe
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T08:57:57Z
date_updated: 2025-01-13T08:57:57Z
file_id: '18830'
file_name: 2024_JourAlgebra_Loewit.pdf
file_size: 731175
relation: main_file
success: 1
file_date_updated: 2025-01-13T08:57:57Z
fulldoi: https://doi.org/10.1016/j.jalgebra.2024.08.033
has_accepted_license: '1'
intvolume: ' 663'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 81-118
publication: Journal of Algebra
publication_identifier:
eissn:
- 1090-266X
issn:
- 0021-8693
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: On modulo ℓ cohomology of p-adic Deligne–Lusztig varieties for GLn
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: 663
year: '2025'
...