---
_id: '14243'
abstract:
- lang: eng
text: 'Two-player zero-sum "graph games" are central in logic, verification, and
multi-agent systems. The game proceeds by placing a token on a vertex of a graph,
and allowing the players to move it to produce an infinite path, which determines
the winner or payoff of the game. Traditionally, the players alternate turns in
moving the token. In "bidding games", however, the players have budgets and in
each turn, an auction (bidding) determines which player moves the token. So far,
bidding games have only been studied as full-information games. In this work we
initiate the study of partial-information bidding games: we study bidding games
in which a player''s initial budget is drawn from a known probability distribution.
We show that while for some bidding mechanisms and objectives, it is straightforward
to adapt the results from the full-information setting to the partial-information
setting, for others, the analysis is significantly more challenging, requires
new techniques, and gives rise to interesting results. Specifically, we study
games with "mean-payoff" objectives in combination with "poorman" bidding. We
construct optimal strategies for a partially-informed player who plays against
a fully-informed adversary. We show that, somewhat surprisingly, the "value" under
pure strategies does not necessarily exist in such games.'
acknowledgement: This research was supported in part by ISF grant no.1679/21, by the
ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.
article_processing_charge: No
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Ismael R
full_name: Jecker, Ismael R
id: 85D7C63E-7D5D-11E9-9C0F-98C4E5697425
last_name: Jecker
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable
budgets. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence.
Vol 37. ; 2023:5464-5471. doi:10.1609/aaai.v37i5.25679'
apa: Avni, G., Jecker, I. R., & Zikelic, D. (2023). Bidding graph games with
partially-observable budgets. In Proceedings of the 37th AAAI Conference on
Artificial Intelligence (Vol. 37, pp. 5464–5471). Washington, DC, United States.
https://doi.org/10.1609/aaai.v37i5.25679
chicago: Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with
Partially-Observable Budgets.” In Proceedings of the 37th AAAI Conference on
Artificial Intelligence, 37:5464–71, 2023. https://doi.org/10.1609/aaai.v37i5.25679.
ieee: G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable
budgets,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence,
Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.
ista: 'Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable
budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI:
Conference on Artificial Intelligence vol. 37, 5464–5471.'
mla: Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.”
Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol.
37, no. 5, 2023, pp. 5464–71, doi:10.1609/aaai.v37i5.25679.
short: G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference
on Artificial Intelligence, 2023, pp. 5464–5471.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2023-08-27T22:01:18Z
date_published: 2023-06-27T00:00:00Z
date_updated: 2025-03-31T16:01:08Z
day: '27'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i5.25679
ec_funded: 1
external_id:
arxiv:
- '2211.13626'
intvolume: ' 37'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1609/aaai.v37i5.25679
month: '06'
oa: 1
oa_version: Published Version
page: 5464-5471
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Proceedings of the 37th AAAI Conference on Artificial Intelligence
publication_identifier:
isbn:
- '9781577358800'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bidding graph games with partially-observable budgets
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2023'
...
---
_id: '14244'
abstract:
- lang: eng
text: "In this paper, we determine the motivic class — in particular, the weight
polynomial and conjecturally the Poincaré polynomial — of the open de Rham space,
defined and studied by Boalch, of certain moduli spaces of irregular meromorphic
connections on the trivial rank \r\n bundle on P1. The computation is by motivic
Fourier transform. We show that the result satisfies the purity conjecture, that
is, it agrees with the pure part of the conjectured mixed Hodge polynomial of
the corresponding wild character variety. We also identify the open de Rham spaces
with quiver varieties with multiplicities of Yamakawa and Geiss–Leclerc–Schröer.
We finish with constructing natural complete hyperkähler metrics on them, which
in the four-dimensional cases are expected to be of type ALF."
acknowledgement: We would like to thank Gergely Bérczy, Roger Bielawski, Philip Boalch,
Sergey Cherkis, Andrew Dancer, Brent Doran, Eloïse Hamilton, Frances Kirwan, Bernard
Leclerc, Emmanuel Letellier, Alessia Mandini, Maxence Mayrand, András Némethi, Szilárd
Szabó, and Daisuke Yamakawa for discussions related to the paper. We especially
thank the referee for an extensive list of very careful comments. At various stages
of this project, the authors were supported by the Advanced Grant “Arithmetic and
physics of Higgs moduli spaces” no. 320593 of the European Research Council, by
grant no. 153627 and NCCR SwissMAP, both funded by the Swiss National Science Foundation
as well as by EPF Lausanne and IST Austria. In the final stages of this project,
MLW was supported by SFB/TR 45 “Periods, moduli and arithmetic of algebraic varieties,”
subproject M08-10 “Moduli of vector bundles on higher-dimensional varieties.” DW
was also supported by the Fondation Sciences Mathématiques de Paris, as well as
public grants overseen by the Agence national de la recherche (ANR) of France as
part of the Investissements d'avenir program, under reference numbers ANR-10-LABX-0098
and ANR-15-CE40-0008 (Défigéo).
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
orcid: 0000-0002-9582-2634
- first_name: Michael Lennox
full_name: Wong, Michael Lennox
last_name: Wong
- first_name: Dimitri
full_name: Wyss, Dimitri
last_name: Wyss
citation:
ama: Hausel T, Wong ML, Wyss D. Arithmetic and metric aspects of open de Rham spaces.
Proceedings of the London Mathematical Society. 2023;127(4):958-1027. doi:10.1112/plms.12555
apa: Hausel, T., Wong, M. L., & Wyss, D. (2023). Arithmetic and metric aspects
of open de Rham spaces. Proceedings of the London Mathematical Society.
Wiley. https://doi.org/10.1112/plms.12555
chicago: Hausel, Tamás, Michael Lennox Wong, and Dimitri Wyss. “Arithmetic and Metric
Aspects of Open de Rham Spaces.” Proceedings of the London Mathematical Society.
Wiley, 2023. https://doi.org/10.1112/plms.12555.
ieee: T. Hausel, M. L. Wong, and D. Wyss, “Arithmetic and metric aspects of open
de Rham spaces,” Proceedings of the London Mathematical Society, vol. 127,
no. 4. Wiley, pp. 958–1027, 2023.
ista: Hausel T, Wong ML, Wyss D. 2023. Arithmetic and metric aspects of open de
Rham spaces. Proceedings of the London Mathematical Society. 127(4), 958–1027.
mla: Hausel, Tamás, et al. “Arithmetic and Metric Aspects of Open de Rham Spaces.”
Proceedings of the London Mathematical Society, vol. 127, no. 4, Wiley,
2023, pp. 958–1027, doi:10.1112/plms.12555.
short: T. Hausel, M.L. Wong, D. Wyss, Proceedings of the London Mathematical Society
127 (2023) 958–1027.
corr_author: '1'
date_created: 2023-08-27T22:01:18Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-04-14T09:12:46Z
day: '01'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.1112/plms.12555
ec_funded: 1
external_id:
arxiv:
- '1807.04057'
isi:
- '001049312700001'
file:
- access_level: open_access
checksum: 2af4d2d6a8ae42f7d3fba0188e79ae82
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:56:00Z
date_updated: 2024-01-30T12:56:00Z
file_id: '14910'
file_name: 2023_ProcLondonMathSoc_Hausel.pdf
file_size: 651335
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:56:00Z
has_accepted_license: '1'
intvolume: ' 127'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 958-1027
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
- _id: 25E6C798-B435-11E9-9278-68D0E5697425
grant_number: '153627'
name: Arithmetic quantization of character and quiver varities
publication: Proceedings of the London Mathematical Society
publication_identifier:
eissn:
- 1460-244X
issn:
- 0024-6115
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arithmetic and metric aspects of open de Rham spaces
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: 127
year: '2023'
...
---
_id: '14245'
abstract:
- lang: eng
text: We establish effective counting results for lattice points in families of
domains in real, complex and quaternionic hyperbolic spaces of any dimension.
The domains we focus on are defined as product sets with respect to an Iwasawa
decomposition. Several natural diophantine problems can be reduced to counting
lattice points in such domains. These include equidistribution of the ratio of
the length of the shortest solution (x,y) to the gcd equation bx−ay=1 relative
to the length of (a,b), where (a,b) ranges over primitive vectors in a disc whose
radius increases, the natural analog of this problem in imaginary quadratic number
fields, as well as equidistribution of integral solutions to the diophantine equation
defined by an integral Lorentz form in three or more variables. We establish an
effective rate of convergence for these equidistribution problems, depending on
the size of the spectral gap associated with a suitable lattice subgroup in the
isometry group of the relevant hyperbolic space. The main result underlying our
discussion amounts to establishing effective joint equidistribution for the horospherical
component and the radial component in the Iwasawa decomposition of lattice elements.
acknowledgement: The authors thank the referee for important comments which led to
significant improvements is the presentation of several results in the paper. They
also thank Ami Paz for preparing the figures for this paper. Horesh thanks Ami Paz
and Yakov Karasik for helpful discussions. Nevo thanks John Parker and Rene Rühr
for providing some very useful references. Nevo is supported by ISF Grant No. 2095/15.
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Tal
full_name: Horesh, Tal
id: C8B7BF48-8D81-11E9-BCA9-F536E6697425
last_name: Horesh
- first_name: Amos
full_name: Nevo, Amos
last_name: Nevo
citation:
ama: 'Horesh T, Nevo A. Horospherical coordinates of lattice points in hyperbolic
spaces: Effective counting and equidistribution. Pacific Journal of Mathematics.
2023;324(2):265-294. doi:10.2140/pjm.2023.324.265'
apa: 'Horesh, T., & Nevo, A. (2023). Horospherical coordinates of lattice points
in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal
of Mathematics. Mathematical Sciences Publishers. https://doi.org/10.2140/pjm.2023.324.265'
chicago: 'Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points
in Hyperbolic Spaces: Effective Counting and Equidistribution.” Pacific Journal
of Mathematics. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.324.265.'
ieee: 'T. Horesh and A. Nevo, “Horospherical coordinates of lattice points in hyperbolic
spaces: Effective counting and equidistribution,” Pacific Journal of Mathematics,
vol. 324, no. 2. Mathematical Sciences Publishers, pp. 265–294, 2023.'
ista: 'Horesh T, Nevo A. 2023. Horospherical coordinates of lattice points in hyperbolic
spaces: Effective counting and equidistribution. Pacific Journal of Mathematics.
324(2), 265–294.'
mla: 'Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in
Hyperbolic Spaces: Effective Counting and Equidistribution.” Pacific Journal
of Mathematics, vol. 324, no. 2, Mathematical Sciences Publishers, 2023, pp.
265–94, doi:10.2140/pjm.2023.324.265.'
short: T. Horesh, A. Nevo, Pacific Journal of Mathematics 324 (2023) 265–294.
corr_author: '1'
date_created: 2023-08-27T22:01:18Z
date_published: 2023-07-26T00:00:00Z
date_updated: 2024-10-09T21:06:46Z
day: '26'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.2140/pjm.2023.324.265
external_id:
arxiv:
- '1612.08215'
isi:
- '001047690500001'
file:
- access_level: open_access
checksum: a675b53cfb31fa46be1e879b7e77fe8c
content_type: application/pdf
creator: dernst
date_created: 2023-09-05T07:26:17Z
date_updated: 2023-09-05T07:26:17Z
file_id: '14267'
file_name: 2023_PacificJourMaths_Horesh.pdf
file_size: 654895
relation: main_file
success: 1
file_date_updated: 2023-09-05T07:26:17Z
has_accepted_license: '1'
intvolume: ' 324'
isi: 1
issue: '2'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 265-294
publication: Pacific Journal of Mathematics
publication_identifier:
eissn:
- 1945-5844
issn:
- 0030-8730
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Horospherical coordinates of lattice points in hyperbolic spaces: Effective
counting and equidistribution'
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: 324
year: '2023'
...
---
_id: '14246'
abstract:
- lang: eng
text: The model of a ring threaded by the Aharonov-Bohm flux underlies our understanding
of a coupling between gauge potentials and matter. The typical formulation of
the model is based upon a single particle picture, and should be extended when
interactions with other particles become relevant. Here, we illustrate such an
extension for a particle in an Aharonov-Bohm ring subject to interactions with
a weakly interacting Bose gas. We show that the ground state of the system can
be described using the Bose-polaron concept—a particle dressed by interactions
with a bosonic environment. We connect the energy spectrum to the effective mass
of the polaron, and demonstrate how to change currents in the system by tuning
boson-particle interactions. Our results suggest the Aharonov-Bohm ring as a platform
for studying coherence and few- to many-body crossover of quasi-particles that
arise from an impurity immersed in a medium.
acknowledgement: "Open Access funding enabled and organized by Projekt DEAL.\r\nWe
would like to thank Jonas Jager for sharing his data with us in the early stages
of this project. We thank Joachim Brand and Ray Yang for sharing with us data from
Yang et al.46. This work has received funding from the DFG Project no. 413495248
[VO 2437/1-1] (F.B., H.-W.H., A.G.V.). We acknowledge support from the Deutsche
Forschungsgemeinschaft (DFG - German Research Foundation) and the Open Access Publishing
Fund of the Technical University of Darmstadt."
article_number: '224'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Hans-Werner
full_name: Hammer, Hans-Werner
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. Emergence of a Bose polaron
in a small ring threaded by the Aharonov-Bohm flux. Communications Physics.
2023;6. doi:10.1038/s42005-023-01281-2
apa: Brauneis, F., Ghazaryan, A., Hammer, H.-W., & Volosniev, A. (2023). Emergence
of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications
Physics. Springer Nature. https://doi.org/10.1038/s42005-023-01281-2
chicago: Brauneis, Fabian, Areg Ghazaryan, Hans-Werner Hammer, and Artem Volosniev.
“Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.”
Communications Physics. Springer Nature, 2023. https://doi.org/10.1038/s42005-023-01281-2.
ieee: F. Brauneis, A. Ghazaryan, H.-W. Hammer, and A. Volosniev, “Emergence of a
Bose polaron in a small ring threaded by the Aharonov-Bohm flux,” Communications
Physics, vol. 6. Springer Nature, 2023.
ista: Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. 2023. Emergence of a Bose
polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics.
6, 224.
mla: Brauneis, Fabian, et al. “Emergence of a Bose Polaron in a Small Ring Threaded
by the Aharonov-Bohm Flux.” Communications Physics, vol. 6, 224, Springer
Nature, 2023, doi:10.1038/s42005-023-01281-2.
short: F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics
6 (2023).
corr_author: '1'
date_created: 2023-08-28T12:36:49Z
date_published: 2023-08-22T00:00:00Z
date_updated: 2024-10-09T21:06:47Z
day: '22'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1038/s42005-023-01281-2
external_id:
arxiv:
- '2301.10488'
isi:
- '001052577500002'
file:
- access_level: open_access
checksum: 6edfc59b0ee7dc406d0968b05236e83d
content_type: application/pdf
creator: dernst
date_created: 2023-09-05T08:45:49Z
date_updated: 2023-09-05T08:45:49Z
file_id: '14268'
file_name: 2023_CommPhysics_Brauneis.pdf
file_size: 855960
relation: main_file
success: 1
file_date_updated: 2023-09-05T08:45:49Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Communications Physics
publication_identifier:
issn:
- 2399-3650
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2023'
...
---
_id: '14253'
abstract:
- lang: eng
text: Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM)
are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration
of intracellular signaling machinery near ER-PM junctions allows these domains
to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular
compartmentalization of protein kinase A (PKA) signaling also regulates essential
cellular functions, however, no specific association between PKA and ER-PM junctional
domains is known. Here, we show that in brain neurons type I PKA is directed to
Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific
anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and
ER-resident VAP proteins results in the concentration of type I PKA between stacked
ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome
enables reciprocal regulation between PKA and Ca2+ signaling machinery to support
Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal
ER-PM junctions support a receptor-independent form of PKA signaling driven by
membrane depolarization and intracellular Ca2+, allowing conversion of information
encoded in electrical signals into biochemical changes universally recognized
throughout the cell.
acknowledgement: We thank Kayla Templeton and Peter Turcanu for technical assistance,
Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin
Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn
Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for
assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful
discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also
thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used
in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648
(J.S.T.), and F32NS108519 (N.C.V.).
article_number: '5231'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicholas C.
full_name: Vierra, Nicholas C.
last_name: Vierra
- first_name: Luisa
full_name: Ribeiro-Silva, Luisa
last_name: Ribeiro-Silva
- first_name: Michael
full_name: Kirmiz, Michael
last_name: Kirmiz
- first_name: Deborah
full_name: Van Der List, Deborah
last_name: Van Der List
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Olivia A.
full_name: Mack, Olivia A.
last_name: Mack
- first_name: James
full_name: Carroll, James
last_name: Carroll
- first_name: Elodie
full_name: Le Monnier, Elodie
id: 3B59276A-F248-11E8-B48F-1D18A9856A87
last_name: Le Monnier
- first_name: Sue A.
full_name: Aicher, Sue A.
last_name: Aicher
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: James S.
full_name: Trimmer, James S.
last_name: Trimmer
citation:
ama: Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions
couple excitation to Ca2+-activated PKA signaling. Nature Communications.
2023;14. doi:10.1038/s41467-023-40930-6
apa: Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P.,
Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple
excitation to Ca2+-activated PKA signaling. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-023-40930-6
chicago: Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der
List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma
Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature
Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40930-6.
ieee: N. C. Vierra et al., “Neuronal ER-plasma membrane junctions couple
excitation to Ca2+-activated PKA signaling,” Nature Communications, vol.
14. Springer Nature, 2023.
ista: Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA,
Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma
membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications.
14, 5231.
mla: Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation
to Ca2+-Activated PKA Signaling.” Nature Communications, vol. 14, 5231,
Springer Nature, 2023, doi:10.1038/s41467-023-40930-6.
short: N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A.
Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature
Communications 14 (2023).
date_created: 2023-09-03T22:01:14Z
date_published: 2023-08-26T00:00:00Z
date_updated: 2025-09-09T12:50:49Z
day: '26'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1038/s41467-023-40930-6
external_id:
isi:
- '001064563400013'
pmid:
- '37633939'
file:
- access_level: open_access
checksum: 6ab8aab4e957f626a09a1c73db3388fb
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T06:50:07Z
date_updated: 2023-09-06T06:50:07Z
file_id: '14270'
file_name: 2023_NatureComm_Vierra.pdf
file_size: 9412549
relation: main_file
success: 1
file_date_updated: 2023-09-06T06:50:07Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '08'
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: Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA
signaling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14
year: '2023'
...
---
_id: '14254'
abstract:
- lang: eng
text: In [10] Nam proved a Lieb–Thirring Inequality for the kinetic energy of a
fermionic quantum system, with almost optimal (semi-classical) constant and a
gradient correction term. We present a stronger version of this inequality, with
a much simplified proof. As a corollary we obtain a simple proof of the original
Lieb–Thirring inequality.
acknowledgement: J.P.S. thanks the Institute of Science and Technology Austria for
the hospitality and support during a visit where this work was done. J.P.S. was
also partially supported by the VILLUM Centre of Excellence for the Mathematics
of Quantum Theory (QMATH) (grant No. 10059).
article_number: '110129'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan Philip
full_name: Solovej, Jan Philip
last_name: Solovej
citation:
ama: Seiringer R, Solovej JP. A simple approach to Lieb-Thirring type inequalities.
Journal of Functional Analysis. 2023;285(10). doi:10.1016/j.jfa.2023.110129
apa: Seiringer, R., & Solovej, J. P. (2023). A simple approach to Lieb-Thirring
type inequalities. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.110129
chicago: Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring
Type Inequalities.” Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.110129.
ieee: R. Seiringer and J. P. Solovej, “A simple approach to Lieb-Thirring type inequalities,”
Journal of Functional Analysis, vol. 285, no. 10. Elsevier, 2023.
ista: Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities.
Journal of Functional Analysis. 285(10), 110129.
mla: Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring
Type Inequalities.” Journal of Functional Analysis, vol. 285, no. 10, 110129,
Elsevier, 2023, doi:10.1016/j.jfa.2023.110129.
short: R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (2023).
corr_author: '1'
date_created: 2023-09-03T22:01:14Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2024-10-09T21:06:47Z
day: '15'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2023.110129
external_id:
arxiv:
- '2303.04504'
isi:
- '001071552300001'
file:
- access_level: open_access
checksum: 28e424ad91be6219e9d321054ce3a412
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T14:15:16Z
date_updated: 2024-01-30T14:15:16Z
file_id: '14915'
file_name: 2023_JourFunctionalAnalysis_Seiringer.pdf
file_size: 232934
relation: main_file
success: 1
file_date_updated: 2024-01-30T14:15:16Z
has_accepted_license: '1'
intvolume: ' 285'
isi: 1
issue: '10'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Functional Analysis
publication_identifier:
eissn:
- 1096-0783
issn:
- 0022-1236
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A simple approach to Lieb-Thirring type inequalities
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: 285
year: '2023'
...
---
_id: '14255'
abstract:
- lang: eng
text: Toscana virus is a major cause of arboviral disease in humans in the Mediterranean
basin during summer. However, early virus-host cell interactions and entry mechanisms
remain poorly characterized. Investigating iPSC-derived human neurons and cell
lines, we found that virus binding to the cell surface was specific, and 50% of
bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes
and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration
required intact late endosomes and occurred within 30 min following internalization.
Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane
fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of
virions to the slightly acidic pH in early endosomes. Strikingly, the particles
remained infectious after entering late endosomes with a pH below the fusion threshold.
Overall, our study establishes Toscana virus as a late-penetrating virus and reveals
an atypical use of vacuolar acidity by this virus to enter host cells.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: "We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR
Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform
(IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg.
The sand fly cell lines were supplied by the Tick Cell Biobank at the University
of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs)
of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis
work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft
(DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding
(grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This
work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de
Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated
by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was
supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award,
a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by
a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1)
and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the
Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1)
and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered
by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are
grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003),
the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for
awarding fellowships to Q.X., J.C., and H.A.A., respectively."
article_number: e1011562
article_processing_charge: Yes
article_type: original
author:
- first_name: Jana
full_name: Koch, Jana
last_name: Koch
- first_name: Qilin
full_name: Xin, Qilin
last_name: Xin
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Alicia
full_name: Schäfer, Alicia
last_name: Schäfer
- first_name: Nina
full_name: Rolfs, Nina
last_name: Rolfs
- first_name: Holda A.
full_name: Anagho, Holda A.
last_name: Anagho
- first_name: Aiste
full_name: Kudulyte, Aiste
last_name: Kudulyte
- first_name: Lea
full_name: Woltereck, Lea
last_name: Woltereck
- first_name: Susann
full_name: Kummer, Susann
last_name: Kummer
- first_name: Joaquin
full_name: Campos, Joaquin
last_name: Campos
- first_name: Zina M.
full_name: Uckeley, Zina M.
last_name: Uckeley
- first_name: Lesley
full_name: Bell-Sakyi, Lesley
last_name: Bell-Sakyi
- first_name: Hans Georg
full_name: Kräusslich, Hans Georg
last_name: Kräusslich
- first_name: Florian Km
full_name: Schur, Florian Km
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Claudio
full_name: Acuna, Claudio
last_name: Acuna
- first_name: Pierre Yves
full_name: Lozach, Pierre Yves
last_name: Lozach
citation:
ama: Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical
use of vacuolar acidity to enter host cells. PLoS Pathogens. 2023;19(8).
doi:10.1371/journal.ppat.1011562
apa: Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach,
P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar
acidity to enter host cells. PLoS Pathogens. Public Library of Science.
https://doi.org/10.1371/journal.ppat.1011562
chicago: Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A.
Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical
Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens. Public Library
of Science, 2023. https://doi.org/10.1371/journal.ppat.1011562.
ieee: J. Koch et al., “The phenuivirus Toscana virus makes an atypical use
of vacuolar acidity to enter host cells,” PLoS Pathogens, vol. 19, no.
8. Public Library of Science, 2023.
ista: Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck
L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna
C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar
acidity to enter host cells. PLoS Pathogens. 19(8), e1011562.
mla: Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of
Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens, vol. 19, no. 8,
e1011562, Public Library of Science, 2023, doi:10.1371/journal.ppat.1011562.
short: J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte,
L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich,
F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).
date_created: 2023-09-03T22:01:14Z
date_published: 2023-08-14T00:00:00Z
date_updated: 2025-04-15T08:24:50Z
day: '14'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1371/journal.ppat.1011562
external_id:
isi:
- '001050846300004'
pmid:
- '37578957'
file:
- access_level: open_access
checksum: 47ca3bb54b27f28b05644be0ad064bc6
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T06:41:52Z
date_updated: 2023-09-06T06:41:52Z
file_id: '14269'
file_name: 2023_PloSPathogens_Koch.pdf
file_size: 4458336
relation: main_file
success: 1
file_date_updated: 2023-09-06T06:41:52Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: PLoS Pathogens
publication_identifier:
eissn:
- 1553-7374
issn:
- 1553-7366
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to
enter host cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '14256'
abstract:
- lang: eng
text: "Context. Space asteroseismology is revolutionizing our knowledge of the internal
structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries
of signatures of strong magnetic fields in the core of red giant stars. The key
signature for such a detection is the asymmetry these fields induce in the frequency
splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate
the ability of the observed asymmetries of the frequency splittings of dipolar
mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods.
We used the powerful analytical Racah-Wigner algebra used in quantum mechanics
to characterize the geometrical couplings of dipolar mixed oscillation modes with
various realistically plausible topologies of fossil magnetic fields. We also
computed the induced perturbation of their frequencies.\r\nResults. First, in
the case of an oblique magnetic dipole, we provide the exact analytical expression
of the asymmetry as a function of the angle between the rotation and magnetic
axes. Its value provides a direct measure of this angle. Second, considering a
combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry
is blind to the unraveling of the relative strength and sign of each component.
Finally, in the case of a given multipole, we show that a negative asymmetry is
a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar
mixed modes provide a key bit of information on the geometrical topology of deep
fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints
should therefore be combined with spectropolarimetric observations and numerical
simulations, which aim to predict the more probable stable large-scale geometries."
acknowledgement: The authors are grateful to the referee for her/his detailed and
constructive report, which has allowed us to improve our article. S. M. acknowledges
support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU).
We thank R. A. Garcia for fruitful discussions and suggestions.
article_number: L9
article_processing_charge: Yes (in subscription journal)
article_type: letter_note
arxiv: 1
author:
- first_name: S.
full_name: Mathis, S.
last_name: Mathis
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
citation:
ama: 'Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed
modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics.
2023;676. doi:10.1051/0004-6361/202346832'
apa: 'Mathis, S., & Bugnet, L. A. (2023). Asymmetries of frequency splittings
of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy
and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202346832'
chicago: 'Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings
of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy
and Astrophysics. EDP Sciences, 2023. https://doi.org/10.1051/0004-6361/202346832.'
ieee: 'S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar
mixed modes: A window on the topology of deep magnetic fields,” Astronomy and
Astrophysics, vol. 676. EDP Sciences, 2023.'
ista: 'Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar
mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics.
676, L9.'
mla: 'Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings
of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” Astronomy
and Astrophysics, vol. 676, L9, EDP Sciences, 2023, doi:10.1051/0004-6361/202346832.'
short: S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).
date_created: 2023-09-03T22:01:15Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-09-06T11:05:58Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.1051/0004-6361/202346832
external_id:
arxiv:
- '2306.11587'
isi:
- '001046037700007'
file:
- access_level: open_access
checksum: 7b30d26fb2b7bcb5b5be1414950615f9
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T07:13:19Z
date_updated: 2023-09-06T07:13:19Z
file_id: '14271'
file_name: 2023_AstronomyAstrophysics_Mathis.pdf
file_size: 458120
relation: main_file
success: 1
file_date_updated: 2023-09-06T07:13:19Z
has_accepted_license: '1'
intvolume: ' 676'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Astronomy and Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Asymmetries of frequency splittings of dipolar mixed modes: A window on the
topology of deep magnetic fields'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 676
year: '2023'
...
---
_id: '14258'
abstract:
- lang: eng
text: There is currently little evidence that the genetic basis of human phenotype
varies significantly across the lifespan. However, time-to-event phenotypes are
understudied and can be thought of as reflecting an underlying hazard, which is
unlikely to be constant through life when values take a broad range. Here, we
find that 74% of 245 genome-wide significant genetic associations with age at
natural menopause (ANM) in the UK Biobank show a form of age-specific effect.
Nineteen of these replicated discoveries are identified only by our modeling framework,
which determines the time dependency of DNA-variant age-at-onset associations
without a significant multiple-testing burden. Across the range of early to late
menopause, we find evidence for significantly different underlying biological
pathways, changes in the signs of genetic correlations of ANM to health indicators
and outcomes, and differences in inferred causal relationships. We find that DNA
damage response processes only act to shape ovarian reserve and depletion for
women of early ANM. Genetically mediated delays in ANM were associated with increased
relative risk of breast cancer and leiomyoma at all ages and with high cholesterol
and heart failure for late-ANM women. These findings suggest that a better understanding
of the age dependency of genetic risk factor relationships among health indicators
and outcomes is achievable through appropriate statistical modeling of large-scale
biobank data.
acknowledgement: This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181)
and by core funding from the Institute of Science and Technology Austria. K.L. and
R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank
computations were performed in the High-Performance Computing Center, University
of Tartu. We thank Triin Laisk for her valuable insights and comments that helped
greatly. We would like to acknowledge the participants and investigators of UK Biobank
and Estonian Biobank studies. This project uses UK Biobank data under project number
35520.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Sven E.
full_name: Ojavee, Sven E.
last_name: Ojavee
- first_name: Liza
full_name: Darrous, Liza
last_name: Darrous
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Kristi
full_name: Läll, Kristi
last_name: Läll
- first_name: Krista
full_name: Fischer, Krista
last_name: Fischer
- first_name: Reedik
full_name: Mägi, Reedik
last_name: Mägi
- first_name: Zoltan
full_name: Kutalik, Zoltan
last_name: Kutalik
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
citation:
ama: Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific
biological mechanisms governing human ovarian aging. American Journal of Human
Genetics. 2023;110(9):1549-1563. doi:10.1016/j.ajhg.2023.07.006
apa: Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., …
Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms
governing human ovarian aging. American Journal of Human Genetics. Elsevier.
https://doi.org/10.1016/j.ajhg.2023.07.006
chicago: Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer,
Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into
the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” American
Journal of Human Genetics. Elsevier, 2023. https://doi.org/10.1016/j.ajhg.2023.07.006.
ieee: S. E. Ojavee et al., “Genetic insights into the age-specific biological
mechanisms governing human ovarian aging,” American Journal of Human Genetics,
vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023.
ista: Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson
MR. 2023. Genetic insights into the age-specific biological mechanisms governing
human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563.
mla: Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological
Mechanisms Governing Human Ovarian Aging.” American Journal of Human Genetics,
vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:10.1016/j.ajhg.2023.07.006.
short: S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik,
M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563.
corr_author: '1'
date_created: 2023-09-03T22:01:15Z
date_published: 2023-09-07T00:00:00Z
date_updated: 2025-09-09T12:51:20Z
day: '07'
ddc:
- '570'
department:
- _id: MaRo
doi: 10.1016/j.ajhg.2023.07.006
external_id:
isi:
- '001074842500001'
pmid:
- '37543033'
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issue: '9'
language:
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month: '09'
oa: 1
oa_version: Published Version
page: 1549-1563
pmid: 1
publication: American Journal of Human Genetics
publication_identifier:
eissn:
- 1537-6605
issn:
- 0002-9297
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic insights into the age-specific biological mechanisms governing human
ovarian aging
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 110
year: '2023'
...
---
_id: '14259'
abstract:
- lang: eng
text: "We provide a learning-based technique for guessing a winning strategy in
a parity game originating from an LTL synthesis problem. A cheaply obtained guess
can be useful in several applications. Not only can the guessed strategy be applied
as best-effort in cases where the game’s huge size prohibits rigorous approaches,
but it can also increase the scalability of rigorous LTL synthesis in several
ways. Firstly, checking whether a guessed strategy is winning is easier than constructing
one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy
iteration faster than constructing one from scratch. Thirdly, the guess can be
used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn
contrast to previous works, we (i) reflect the highly structured logical information
in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata
translations, and (ii) learn to reflect it properly by learning from previously
solved games, bringing the solving process closer to human-like reasoning."
acknowledgement: This research was funded in part by the German Research Foundation
(DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Maximilian
full_name: Prokop, Maximilian
last_name: Prokop
- first_name: Sabine
full_name: Rieder, Sabine
last_name: Rieder
citation:
ama: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies
in LTL synthesis by semantic learning. In: 35th International Conference on
Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20'
apa: 'Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing
winning policies in LTL synthesis by semantic learning. In 35th International
Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris,
France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20'
chicago: Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder.
“Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th
International Conference on Computer Aided Verification , 13964:390–414. Springer
Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20.
ieee: J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning
policies in LTL synthesis by semantic learning,” in 35th International Conference
on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414.
ista: 'Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies
in LTL synthesis by semantic learning. 35th International Conference on Computer
Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.'
mla: Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic
Learning.” 35th International Conference on Computer Aided Verification ,
vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20.
short: J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International
Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-03T22:01:16Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2025-09-09T12:52:34Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37706-8_20
external_id:
isi:
- '001310786500020'
file:
- access_level: open_access
checksum: ed66278b61bb869e1baba3d9b9081271
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T08:25:50Z
date_updated: 2023-09-06T08:25:50Z
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file_name: 2023_LNCS_CAV_Kretinsky.pdf
file_size: 428354
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success: 1
file_date_updated: 2023-09-06T08:25:50Z
has_accepted_license: '1'
intvolume: ' 13964'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 390-414
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guessing winning policies in LTL synthesis by semantic 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: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13964
year: '2023'
...
---
_id: '14260'
abstract:
- lang: eng
text: "This paper presents Lincheck, a new practical and user-friendly framework
for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck
provides a simple and declarative way to write concurrent tests: instead of describing
how to perform the test, users specify what to test by declaring all the operations
to examine; the framework automatically handles the rest. As a result, tests written
with Lincheck are concise and easy to understand. The framework automatically
generates a set of concurrent scenarios, examines them using stress-testing or
bounded model checking, and verifies that the results of each invocation are correct.
Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow
trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo
the best of our knowledge, Lincheck is the first production-ready tool on the
JVM that offers such a simple way of writing concurrent tests, without requiring
special skills or expertise. We successfully integrated Lincheck in the development
process of several large projects, such as Kotlin Coroutines, and identified new
bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque
and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is
used in most of the synchronization primitives. We believe that Lincheck can significantly
improve the quality and productivity of concurrent algorithms research and development
and become the state-of-the-art tool for checking their correctness."
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Alexander
full_name: Fedorov, Alexander
id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6
last_name: Fedorov
- first_name: Maria
full_name: Sokolova, Maria
last_name: Sokolova
- first_name: Dmitry
full_name: Tsitelov, Dmitry
last_name: Tsitelov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical
framework for testing concurrent data structures on JVM. In: 35th International
Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:156-169.
doi:10.1007/978-3-031-37706-8_8'
apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A.
(2023). Lincheck: A practical framework for testing concurrent data structures
on JVM. In 35th International Conference on Computer Aided Verification
(Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8'
chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and
Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data
Structures on JVM.” In 35th International Conference on Computer Aided Verification
, 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8.'
ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck:
A practical framework for testing concurrent data structures on JVM,” in 35th
International Conference on Computer Aided Verification , Paris, France, 2023,
vol. 13964, pp. 156–169.'
ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck:
A practical framework for testing concurrent data structures on JVM. 35th International
Conference on Computer Aided Verification . CAV: Computer Aided Verification,
LNCS, vol. 13964, 156–169.'
mla: 'Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent
Data Structures on JVM.” 35th International Conference on Computer Aided Verification
, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.'
short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th
International Conference on Computer Aided Verification , Springer Nature, 2023,
pp. 156–169.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-03T22:01:16Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2025-09-09T12:51:52Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: GradSch
doi: 10.1007/978-3-031-37706-8_8
external_id:
isi:
- '001310786500008'
file:
- access_level: open_access
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content_type: application/pdf
creator: dernst
date_created: 2023-09-06T08:16:25Z
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file_name: 2023_LNCS_Koval.pdf
file_size: 421408
relation: main_file
success: 1
file_date_updated: 2023-09-06T08:16:25Z
has_accepted_license: '1'
intvolume: ' 13964'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 156-169
publication: '35th International Conference on Computer Aided Verification '
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377051'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14995'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Lincheck: A practical framework for testing concurrent data structures on JVM'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13964
year: '2023'
...
---
_id: '14261'
abstract:
- lang: eng
text: In this work, a generalized, adapted Numerov implementation capable of determining
band structures of periodic quantum systems is outlined. Based on the input potential,
the presented approach numerically solves the Schrödinger equation in position
space at each momentum space point. Thus, in addition to the band structure, the
method inherently provides information about the state functions and probability
densities in position space at each momentum space point considered. The generalized,
adapted Numerov framework provided reliable estimates for a variety of increasingly
complex test suites in one, two, and three dimensions. The accuracy of the proposed
methodology was benchmarked against results obtained for the analytically solvable
Kronig-Penney model. Furthermore, the presented numerical solver was applied to
a model potential representing a 2D optical lattice being a challenging application
relevant, for example, in the field of quantum computing.
acknowledgement: Financial supports for this work via a PhD scholarship for J. Gamper
issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike
Tanzer) are gratefully acknowledged. The computational results presented have been
achieved (in part) using the HPC infrastructure of the University of Innsbruck.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jakob
full_name: Gamper, Jakob
last_name: Gamper
- first_name: Florian
full_name: Kluibenschedl, Florian
id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9
last_name: Kluibenschedl
- first_name: Alexander K.H.
full_name: Weiss, Alexander K.H.
last_name: Weiss
- first_name: Thomas S.
full_name: Hofer, Thomas S.
last_name: Hofer
citation:
ama: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave
functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems.
Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707
apa: Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & Hofer, T. S. (2023).
Accessing position space wave functions in band structure calculations of periodic
systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional
quantum problems. Journal of Physical Chemistry Letters. American Chemical
Society. https://doi.org/10.1021/acs.jpclett.3c01707
chicago: Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas
S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations
of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-,
Two-, and Three-Dimensional Quantum Problems.” Journal of Physical Chemistry
Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707.
ieee: J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position
space wave functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems,”
Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical
Society, pp. 7395–7403, 2023.
ista: Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space
wave functions in band structure calculations of periodic systems - a generalized,
adapted numerov implementation for one-, two-, and three-dimensional quantum problems.
Journal of Physical Chemistry Letters. 14(33), 7395–7403.
mla: Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure
Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation
for One-, Two-, and Three-Dimensional Quantum Problems.” Journal of Physical
Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403,
doi:10.1021/acs.jpclett.3c01707.
short: J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical
Chemistry Letters 14 (2023) 7395–7403.
date_created: 2023-09-03T22:01:16Z
date_published: 2023-08-11T00:00:00Z
date_updated: 2023-09-06T11:04:31Z
day: '11'
ddc:
- '530'
- '540'
department:
- _id: GradSch
doi: 10.1021/acs.jpclett.3c01707
external_id:
isi:
- '001048165800001'
pmid:
- '37566743'
file:
- access_level: open_access
checksum: 637454e2b3a357498d8d622d241c4bf6
content_type: application/pdf
creator: dernst
date_created: 2023-09-06T07:32:39Z
date_updated: 2023-09-06T07:32:39Z
file_id: '14272'
file_name: 2023_JourPhysChemistry_Gamper.pdf
file_size: 4986859
relation: main_file
success: 1
file_date_updated: 2023-09-06T07:32:39Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '33'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 7395-7403
pmid: 1
publication: Journal of Physical Chemistry Letters
publication_identifier:
eissn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accessing position space wave functions in band structure calculations of periodic
systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional
quantum problems
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2023'
...
---
_id: '14277'
abstract:
- lang: eng
text: Living tissues are characterized by an intrinsically mechanochemical interplay
of active physical forces and complex biochemical signaling pathways. Either feature
alone can give rise to complex emergent phenomena, for example, mechanically driven
glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion
instabilities. An important question is how to quantitatively assess the contribution
of these different cues to the large-scale dynamics of biological materials. We
address this in Madin-Darby canine kidney (MDCK) monolayers, considering both
mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling
activity and cellular density as well as a mechanically active tissue rheology
via a self-propelled vertex model. We show that the relative strength of active
migration forces to mechanochemical couplings controls a transition from a uniform
active glass to periodic spatiotemporal waves. We parametrize the model from published
experimental data sets on MDCK monolayers and use it to make new predictions on
the correlation functions of cellular dynamics and the dynamics of topological
defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers
are best described by an intermediary parameter region in which both mechanochemical
couplings and noisy active propulsion have a strong influence on the dynamics.
Finally, we study how tissue rheology and ERK waves produce feedback on one another
and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical
waves at both the local and global levels.
acknowledgement: We thank all members of the Hannezo group for discussions and suggestions,
as well as Sound Wai Phow for technical assistance. This work received funding from
the European Research Council under the EU Horizon 2020 research and innovation
program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and
the Ministry of Education under the Research Centres of Excellence program through
the MBI at NUS.
article_number: '013001'
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel R
full_name: Boocock, Daniel R
id: 453AF628-F248-11E8-B48F-1D18A9856A87
last_name: Boocock
orcid: 0000-0002-1585-2631
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning
and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001
apa: Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between
mechanochemical patterning and glassy dynamics in cellular monolayers. PRX
Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001
chicago: Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay
between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.”
PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001.
ieee: D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical
patterning and glassy dynamics in cellular monolayers,” PRX Life, vol.
1, no. 1. American Physical Society, 2023.
ista: Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical
patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.
mla: Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and
Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001,
American Physical Society, 2023, doi:10.1103/prxlife.1.013001.
short: D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).
corr_author: '1'
date_created: 2023-09-06T08:30:59Z
date_published: 2023-07-20T00:00:00Z
date_updated: 2025-04-14T07:52:27Z
day: '20'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1103/prxlife.1.013001
ec_funded: 1
file:
- access_level: open_access
checksum: f881d98c89eb9f1aa136d7b781511553
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:30:50Z
date_updated: 2023-09-15T06:30:50Z
file_id: '14335'
file_name: 2023_PRXLife_Boocock.pdf
file_size: 2559520
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:30:50Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: PRX Life
publication_identifier:
issn:
- 2835-8279
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Interplay between mechanochemical patterning and glassy dynamics in cellular
monolayers
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: 1
year: '2023'
...
---
_id: '14279'
abstract:
- lang: eng
text: "The zip file includes source data used in the manuscript \"CCR7 acts as both
a sensor and a sink for CCL19 to coordinate collective leukocyte migration\",
as well as a representative Jupyter notebook to reproduce the main figures. Please
see the preprint on bioRxiv and the DOI link there to access the final published
version. Note the title change between the preprint and the published manuscript.\r\nA
sample script for particle-based simulations of collective chemotaxis by self-generated
gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb)
to generate exemplary cell trajectories. A detailed description of the simulation
setup is provided in the supplementary information of the manuscipt."
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
citation:
ama: Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink
for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960
apa: Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960
chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023.
https://doi.org/10.5281/ZENODO.8133960.
ieee: M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and
a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.
ista: Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor
and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.
mla: Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor
and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo,
2023, doi:10.5281/ZENODO.8133960.
short: M.C. Ucar, (2023).
corr_author: '1'
date_created: 2023-09-06T08:39:25Z
date_published: 2023-07-11T00:00:00Z
date_updated: 2025-04-15T06:54:33Z
day: '11'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.5281/ZENODO.8133960
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8133960
month: '07'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14274'
relation: used_in_publication
status: public
status: public
title: Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19
to coordinate collective leukocyte migration"
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: '2023'
...
---
_id: '14313'
abstract:
- lang: eng
text: To respond to auxin, the chief orchestrator of their multicellularity, plants
evolved multiple receptor systems and signal transduction cascades. Despite decades
of research, however, we are still lacking a satisfactory synthesis of various
auxin signaling mechanisms. The chief discrepancy and historical controversy of
the field is that of rapid and slow auxin effects on plant physiology and development.
How is it possible that ions begin to trickle across the plasma membrane as soon
as auxin enters the cell, even though the best-characterized transcriptional auxin
pathway can take effect only after tens of minutes? Recently, unexpected progress
has been made in understanding this and other unknowns of auxin signaling. We
provide a perspective on these exciting developments and concepts whose general
applicability might have ramifications beyond auxin signaling.
acknowledgement: The opening quote is not intended to reflect any political views
of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld
or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote
led to both public and academic debates on the concept of known and unknown unknowns,
which can be applied to the recent unexpected developments in the auxin signaling
field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation
and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain
for discussion of Greek mythology.
article_number: '102443'
article_processing_charge: No
article_type: review
author:
- first_name: Lukas
full_name: Fiedler, Lukas
id: 7c417475-8972-11ed-ae7b-8b674ca26986
last_name: Fiedler
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. Current
Opinion in Plant Biology. 2023;75(10). doi:10.1016/j.pbi.2023.102443'
apa: 'Fiedler, L., & Friml, J. (2023). Rapid auxin signaling: Unknowns old and
new. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2023.102443'
chicago: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and
New.” Current Opinion in Plant Biology. Elsevier, 2023. https://doi.org/10.1016/j.pbi.2023.102443.'
ieee: 'L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” Current
Opinion in Plant Biology, vol. 75, no. 10. Elsevier, 2023.'
ista: 'Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current
Opinion in Plant Biology. 75(10), 102443.'
mla: 'Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.”
Current Opinion in Plant Biology, vol. 75, no. 10, 102443, Elsevier, 2023,
doi:10.1016/j.pbi.2023.102443.'
short: L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).
corr_author: '1'
date_created: 2023-09-10T22:01:11Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-09-09T12:54:16Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2023.102443
external_id:
isi:
- '001080095300001'
pmid:
- '37666097'
file:
- access_level: open_access
checksum: 1c476c3414d2dfb0c85db0cb6cfd8a28
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:03:20Z
date_updated: 2023-11-02T17:03:20Z
file_id: '14482'
file_name: Fiedler CurrOpinOlantBiol 2023_revised.pdf
file_size: 737872
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:03:20Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Rapid auxin signaling: Unknowns old and new'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 75
year: '2023'
...
---
_id: '14314'
abstract:
- lang: eng
text: The execution of cognitive functions requires coordinated circuit activity
across different brain areas that involves the associated firing of neuronal assemblies.
Here, we tested the circuit mechanism behind assembly interactions between the
hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording
neuronal populations during a rule-switching task. We identified functionally
coupled CA1-mPFC cells that synchronized their activity beyond that expected from
common spatial coding or oscillatory firing. When such cell pairs fired together,
the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent
theta firing phases, independent of the theta timing of their CA1 counterpart.
These functionally connected CA1-mPFC cells formed interconnected assemblies.
While firing together with their CA1 assembly partners, mPFC cells fired along
specific theta sequences. Our results suggest that upregulated theta oscillatory
firing of mPFC cells can signal transient interactions with specific CA1 assemblies,
thus enabling distributed computations.
acknowledgement: We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on
an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS
(grant 607616).
article_number: '113015'
article_processing_charge: Yes
article_type: original
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports.
2023;42(9). doi:10.1016/j.celrep.2023.113015
apa: Nardin, M., Käfer, K., Stella, F., & Csicsvari, J. L. (2023). Theta oscillations
as a substrate for medial prefrontal-hippocampal assembly interactions. Cell
Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113015
chicago: Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari.
“Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly
Interactions.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113015.
ieee: M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as
a substrate for medial prefrontal-hippocampal assembly interactions,” Cell
Reports, vol. 42, no. 9. Elsevier, 2023.
ista: Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate
for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9),
113015.
mla: Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal
Assembly Interactions.” Cell Reports, vol. 42, no. 9, 113015, Elsevier,
2023, doi:10.1016/j.celrep.2023.113015.
short: M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).
corr_author: '1'
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-26T00:00:00Z
date_updated: 2025-09-09T12:53:32Z
day: '26'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.celrep.2023.113015
ec_funded: 1
external_id:
isi:
- '001068779200001'
pmid:
- '37632747'
file:
- access_level: open_access
checksum: ca77a304fb813c292550b8604b0fb41d
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T07:12:46Z
date_updated: 2023-09-15T07:12:46Z
file_id: '14337'
file_name: 2023_CellPress_Nardin.pdf
file_size: 4879455
relation: main_file
success: 1
file_date_updated: 2023-09-15T07:12:46Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: inter-and intracellular signalling in schizophrenia
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Theta oscillations as a substrate for medial prefrontal-hippocampal assembly
interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 42
year: '2023'
...
---
_id: '14315'
abstract:
- lang: eng
text: During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly
demolish the nuclear pore complex. However, for poorly understood reasons, caspases
are also activated during cell differentiation. Here, we show that sublethal activation
of caspases during myogenesis results in the transient proteolysis of four peripheral
Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective,
and we identified in an unbiased manner several classes of cytoplasmic, plasma
membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC
trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic
reticulum stress. Our results suggest that caspases can reversibly modulate nuclear
transport activity, which allows them to function as agents of cell differentiation
and adaptation at sublethal levels.
acknowledgement: 'We thank the members of the Hetzer laboratory, Tony Hunter (Salk),
Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital)
for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin
(Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto
and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra
Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing
mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical
Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH),
and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC).
This work was also supported by the Mass Spectrometry Core of the Salk Institute
with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine.
We thank Jolene Diedrich and Antonio Pinto for technical support.'
article_number: RP89066
article_processing_charge: Yes
article_type: original
author:
- first_name: Ukrae H.
full_name: Cho, Ukrae H.
last_name: Cho
- first_name: Martin W
full_name: Hetzer, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: Hetzer
orcid: 0000-0002-2111-992X
citation:
ama: Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation
and endoplasmic reticulum stress. eLife. 2023;12. doi:10.7554/eLife.89066
apa: Cho, U. H., & Hetzer, M. (2023). Caspase-mediated nuclear pore complex
trimming in cell differentiation and endoplasmic reticulum stress. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.89066
chicago: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex
Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife.
eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.89066.
ieee: U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress,” eLife, vol. 12.
eLife Sciences Publications, 2023.
ista: Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in
cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.
mla: Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming
in Cell Differentiation and Endoplasmic Reticulum Stress.” ELife, vol.
12, RP89066, eLife Sciences Publications, 2023, doi:10.7554/eLife.89066.
short: U.H. Cho, M. Hetzer, ELife 12 (2023).
corr_author: '1'
date_created: 2023-09-10T22:01:11Z
date_published: 2023-09-04T00:00:00Z
date_updated: 2024-10-09T21:06:57Z
day: '04'
ddc:
- '570'
department:
- _id: MaHe
doi: 10.7554/eLife.89066
external_id:
pmid:
- '37665327'
file:
- access_level: open_access
checksum: db24bf3d595507387b48d3799c33e289
content_type: application/pdf
creator: dernst
date_created: 2023-09-15T06:59:10Z
date_updated: 2023-09-15T06:59:10Z
file_id: '14336'
file_name: 2023_eLife_Cho.pdf
file_size: 3703097
relation: main_file
success: 1
file_date_updated: 2023-09-15T06:59:10Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Caspase-mediated nuclear pore complex trimming in cell differentiation and
endoplasmic reticulum stress
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: 12
year: '2023'
...
---
_id: '14316'
abstract:
- lang: eng
text: Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport.
In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted
to generate distinct transport vesicles at the trans-Golgi network (TGN), and
the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories
for these adaptors. Recently, we showed that vesicle transport from the TGN is
crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p
are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However,
these observations were incompatible with previous studies showing that these
adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall
mechanism responsible for regulation of Vps21p activity remains ambiguous. Here,
we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated
Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired
transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to
the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA
adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and
Ypt32p were found to have partially overlapping functions for recruitment of AP-1
and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors
for Vps21p activation in the TGN–endosome trafficking pathway.
article_number: jcs261448
article_processing_charge: No
article_type: original
author:
- first_name: Makoto
full_name: Nagano, Makoto
last_name: Nagano
- first_name: Kaito
full_name: Aoshima, Kaito
last_name: Aoshima
- first_name: Hiroki
full_name: Shimamura, Hiroki
last_name: Shimamura
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Junko Y.
full_name: Toshima, Junko Y.
last_name: Toshima
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct
role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 2023;136(17). doi:10.1242/jcs.261448
apa: Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &
Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p
activation in the TGN-endosome trafficking pathway. Journal of Cell Science.
The Company of Biologists. https://doi.org/10.1242/jcs.261448
chicago: Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko
Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors
for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of
Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.261448.
ieee: M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J.
Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation
in the TGN-endosome trafficking pathway,” Journal of Cell Science, vol.
136, no. 17. The Company of Biologists, 2023.
ista: Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023.
Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome
trafficking pathway. Journal of Cell Science. 136(17), jcs261448.
mla: Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for
Vps21p Activation in the TGN-Endosome Trafficking Pathway.” Journal of Cell
Science, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:10.1242/jcs.261448.
short: M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima,
Journal of Cell Science 136 (2023).
date_created: 2023-09-10T22:01:12Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-09-09T12:56:46Z
day: '01'
department:
- _id: DaSi
doi: 10.1242/jcs.261448
external_id:
isi:
- '001112832300005'
pmid:
- '37539494'
intvolume: ' 136'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.27.534325
month: '09'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the
TGN-endosome trafficking pathway
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 136
year: '2023'
...
---
_id: '14317'
abstract:
- lang: eng
text: "Markov decision processes can be viewed as transformers of probability distributions.
While this view is useful from a practical standpoint to reason about trajectories
of distributions, basic reachability and safety problems are known to be computationally
intractable (i.e., Skolem-hard) to solve in such models. Further, we show that
even for simple examples of MDPs, strategies for safety objectives over distributions
can require infinite memory and randomization.\r\nIn light of this, we present
a novel overapproximation approach to synthesize strategies in an MDP, such that
a safety objective over the distributions is met. More precisely, we develop a
new framework for template-based synthesis of certificates as affine distributional
and inductive invariants for safety objectives in MDPs. We provide two algorithms
within this framework. One can only synthesize memoryless strategies, but has
relative completeness guarantees, while the other can synthesize general strategies.
The runtime complexity of both algorithms is in PSPACE. We implement these algorithms
and show that they can solve several non-trivial examples."
acknowledgement: This work was supported in part by the ERC CoG 863818 (FoRM-SMArt)
and the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project
EQuaVE and SERB Matrices grant MTR/2018/00074.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: S.
full_name: Akshay, S.
last_name: Akshay
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Tobias
full_name: Meggendorfer, Tobias
id: b21b0c15-30a2-11eb-80dc-f13ca25802e1
last_name: Meggendorfer
orcid: 0000-0002-1712-2165
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers:
Affine invariant synthesis for safety objectives. In: International Conference
on Computer Aided Verification. Vol 13966. Springer Nature; 2023:86-112. doi:10.1007/978-3-031-37709-9_5'
apa: 'Akshay, S., Chatterjee, K., Meggendorfer, T., & Zikelic, D. (2023). MDPs
as distribution transformers: Affine invariant synthesis for safety objectives.
In International Conference on Computer Aided Verification (Vol. 13966,
pp. 86–112). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_5'
chicago: 'Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic.
“MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.”
In International Conference on Computer Aided Verification, 13966:86–112.
Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_5.'
ieee: 'S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution
transformers: Affine invariant synthesis for safety objectives,” in International
Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966,
pp. 86–112.'
ista: 'Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution
transformers: Affine invariant synthesis for safety objectives. International
Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 13966, 86–112.'
mla: 'Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis
for Safety Objectives.” International Conference on Computer Aided Verification,
vol. 13966, Springer Nature, 2023, pp. 86–112, doi:10.1007/978-3-031-37709-9_5.'
short: S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International
Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2025-09-09T12:56:00Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_5
ec_funded: 1
external_id:
isi:
- '001310805600005'
file:
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checksum: f143c8eedf609f20f2aad2eeb496d53f
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:46:43Z
date_updated: 2023-09-20T08:46:43Z
file_id: '14349'
file_name: 2023_LNCS_Akshay.pdf
file_size: 531745
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success: 1
file_date_updated: 2023-09-20T08:46:43Z
has_accepted_license: '1'
intvolume: ' 13966'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 86-112
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: International Conference on Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'MDPs as distribution transformers: Affine invariant synthesis for safety objectives'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13966
year: '2023'
...
---
_id: '14318'
abstract:
- lang: eng
text: "Probabilistic recurrence relations (PRRs) are a standard formalism for describing
the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider
the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime
T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims
at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem,
the classical and most well-known approach is the cookbook method by Karp (JACM
1994), while other approaches are mostly limited to deriving tail bounds of specific
PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach
for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing
time and random passed sizes observe discrete or (piecewise) uniform distribution
and whose recursive call is either a single procedure call or a divide-and-conquer.
We first establish a theoretical approach via Markov’s inequality, and then instantiate
the theoretical approach with a template-based algorithmic approach via a refined
treatment of exponentiation. Experimental evaluation shows that our algorithmic
approach is capable of deriving tail bounds that are (i) asymptotically tighter
than Karp’s method, (ii) match the best-known manually-derived asymptotic tail
bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor)
than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover,
our algorithmic approach handles all examples (including realistic PRRs such as
QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing
that our approach is efficient in practice."
acknowledgement: We thank Prof. Bican Xia for valuable information on the exponential
theory of reals. The work is partially supported by the National Natural Science
Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt),
the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa
Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Yican
full_name: Sun, Yican
last_name: Sun
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic
recurrence relations. In: Computer Aided Verification. Vol 13966. Springer
Nature; 2023:16-39. doi:10.1007/978-3-031-37709-9_2'
apa: 'Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2023). Automated
tail bound analysis for probabilistic recurrence relations. In Computer Aided
Verification (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_2'
chicago: Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady.
“Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In Computer
Aided Verification, 13966:16–39. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_2.
ieee: Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound
analysis for probabilistic recurrence relations,” in Computer Aided Verification,
Paris, France, 2023, vol. 13966, pp. 16–39.
ista: 'Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis
for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer
Aided Verification, LNCS, vol. 13966, 16–39.'
mla: Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence
Relations.” Computer Aided Verification, vol. 13966, Springer Nature, 2023,
pp. 16–39, doi:10.1007/978-3-031-37709-9_2.
short: Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification,
Springer Nature, 2023, pp. 16–39.
conference:
end_date: 2023-07-22
location: Paris, France
name: 'CAV: Computer Aided Verification'
start_date: 2023-07-17
date_created: 2023-09-10T22:01:12Z
date_published: 2023-07-17T00:00:00Z
date_updated: 2025-09-09T12:55:28Z
day: '17'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-031-37709-9_2
ec_funded: 1
external_id:
isi:
- '001310805600002'
file:
- access_level: open_access
checksum: 42917e086f8c7699f3bccf84f74fe000
content_type: application/pdf
creator: dernst
date_created: 2023-09-20T08:24:47Z
date_updated: 2023-09-20T08:24:47Z
file_id: '14348'
file_name: 2023_LNCS_Sun.pdf
file_size: 624647
relation: main_file
success: 1
file_date_updated: 2023-09-20T08:24:47Z
has_accepted_license: '1'
intvolume: ' 13966'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 16-39
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Computer Aided Verification
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783031377082'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/boyvolcano/PRR
scopus_import: '1'
status: public
title: Automated tail bound analysis for probabilistic recurrence relations
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13966
year: '2023'
...