---
_id: '14240'
abstract:
- lang: eng
text: This paper introduces a novel method for simulating large bodies of water
as a height field. At the start of each time step, we partition the waves into
a bulk flow (which approximately satisfies the assumptions of the shallow water
equations) and surface waves (which approximately satisfy the assumptions of Airy
wave theory). We then solve the two wave regimes separately using appropriate
state-of-the-art techniques, and re-combine the resulting wave velocities at the
end of each step. This strategy leads to the first heightfield wave model capable
of simulating complex interactions between both deep and shallow water effects,
like the waves from a boat wake sloshing up onto a beach, or a dam break producing
wave interference patterns and eddies. We also analyze the numerical dispersion
created by our method and derive an exact correction factor for waves at a constant
water depth, giving us a numerically perfect re-creation of theoretical water
wave dispersion patterns.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We thank Georg Sperl for helping with early research for this paper,
Mickael Ly and Yi-Lu Chen for proofreading, and members of the ISTA Visual Computing
Group for general feedback. This project was funded in part by the European Research
Council (ERC Consolidator Grant 101045083 CoDiNA).\r\nThe motorboat and sailboat
were modeled by Sergei and the palmtrees by YadroGames. The environment map was
created by Emil Persson."
article_number: '83'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Wojtan C. Generalizing shallow water simulations with dispersive
surface waves. ACM Transactions on Graphics. 2023;42(4). doi:10.1145/3592098
apa: Jeschke, S., & Wojtan, C. (2023). Generalizing shallow water simulations
with dispersive surface waves. ACM Transactions on Graphics. Association
for Computing Machinery. https://doi.org/10.1145/3592098
chicago: Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations
with Dispersive Surface Waves.” ACM Transactions on Graphics. Association
for Computing Machinery, 2023. https://doi.org/10.1145/3592098.
ieee: S. Jeschke and C. Wojtan, “Generalizing shallow water simulations with dispersive
surface waves,” ACM Transactions on Graphics, vol. 42, no. 4. Association
for Computing Machinery, 2023.
ista: Jeschke S, Wojtan C. 2023. Generalizing shallow water simulations with dispersive
surface waves. ACM Transactions on Graphics. 42(4), 83.
mla: Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations
with Dispersive Surface Waves.” ACM Transactions on Graphics, vol. 42,
no. 4, 83, Association for Computing Machinery, 2023, doi:10.1145/3592098.
short: S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023).
corr_author: '1'
date_created: 2023-08-27T22:01:17Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2025-04-14T08:01:13Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3592098
external_id:
isi:
- '001044671300049'
file:
- access_level: open_access
checksum: 1d178bb2f8011d9f5aedda6427e18c7a
content_type: video/mp4
creator: sjeschke
date_created: 2023-12-21T12:26:40Z
date_updated: 2023-12-21T12:26:40Z
file_id: '14704'
file_name: PaperVideo_final.mp4
file_size: 511572575
relation: main_file
success: 1
- access_level: open_access
checksum: a49b2e744d5cd1276bb8b2e0ce6dc638
content_type: application/pdf
creator: dernst
date_created: 2024-01-02T09:34:27Z
date_updated: 2024-01-02T09:34:27Z
file_id: '14725'
file_name: 2023_ACMToG_Jeschke.pdf
file_size: 7469177
relation: main_file
success: 1
file_date_updated: 2024-01-02T09:34:27Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088
grant_number: '101045083'
name: Computational Discovery of Numerical Algorithms for Animation and Simulation
of Natural Phenomena
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Generalizing shallow water simulations with dispersive surface waves
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: 42
year: '2023'
...
---
_id: '14241'
abstract:
- lang: eng
text: We present a technique to optimize the reflectivity of a surface while preserving
its overall shape. The naïve optimization of the mesh vertices using the gradients
of reflectivity simulations results in undesirable distortion. In contrast, our
robust formulation optimizes the surface normal as an independent variable that
bridges the reflectivity term with differential rendering, and the regularization
term with as-rigid-as-possible elastic energy. We further adaptively subdivide
the input mesh to improve the convergence. Consequently, our method can minimize
the retroreflectivity of a wide range of input shapes, resulting in sharply creased
shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by
changing the reward for the direction of the outgoing light directions, our method
can be applied to other reflectivity design tasks, such as the optimization of
architectural walls to concentrate light in a specific region. We have tested
the proposed method using light-transport simulations and real-world 3D-printed
objects.
acknowledgement: "The authors would like to thank Yuki Koyama and Takeo Igarashi for
early discussions, and Yuta Yaguchi for support in 3D printing. This research is
partially supported by the Israel Science Foundation grant number 1390/19.\r\n"
article_number: '20'
article_processing_charge: No
arxiv: 1
author:
- first_name: Kenji
full_name: Tojo, Kenji
last_name: Tojo
- first_name: Ariel
full_name: Shamir, Ariel
last_name: Shamir
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
citation:
ama: 'Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization
as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association
for Computing Machinery; 2023. doi:10.1145/3588432.3591542'
apa: 'Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper:
Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference
Proceedings. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3588432.3591542'
chicago: 'Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth
Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023
Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.'
ieee: 'K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity
optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings,
Los Angeles, CA, United States, 2023.'
ista: 'Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity
optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH:
Computer Graphics and Interactive Techniques Conference, 20.'
mla: 'Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface
Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for
Computing Machinery, 2023, doi:10.1145/3588432.3591542.'
short: K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference
Proceedings, Association for Computing Machinery, 2023.
conference:
end_date: 2023-08-10
location: Los Angeles, CA, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2023-08-06
corr_author: '1'
date_created: 2023-08-27T22:01:17Z
date_published: 2023-07-23T00:00:00Z
date_updated: 2025-09-09T12:49:15Z
day: '23'
department:
- _id: BeBi
doi: 10.1145/3588432.3591542
external_id:
arxiv:
- '2305.05944'
isi:
- '001117690500020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2305.05944
month: '07'
oa: 1
oa_version: Preprint
publication: SIGGRAPH 2023 Conference Proceedings
publication_identifier:
isbn:
- '9798400701597'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Stealth shaper: Reflectivity optimization as surface stylization'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2023'
...
---
_id: '14242'
abstract:
- lang: eng
text: We study the problem of training and certifying adversarially robust quantized
neural networks (QNNs). Quantization is a technique for making neural networks
more efficient by running them using low-bit integer arithmetic and is therefore
commonly adopted in industry. Recent work has shown that floating-point neural
networks that have been verified to be robust can become vulnerable to adversarial
attacks after quantization, and certification of the quantized representation
is necessary to guarantee robustness. In this work, we present quantization-aware
interval bound propagation (QA-IBP), a novel method for training robust QNNs.
Inspired by advances in robust learning of non-quantized networks, our training
algorithm computes the gradient of an abstract representation of the actual network.
Unlike existing approaches, our method can handle the discrete semantics of QNNs.
Based on QA-IBP, we also develop a complete verification procedure for verifying
the adversarial robustness of QNNs, which is guaranteed to terminate and produce
a correct answer. Compared to existing approaches, the key advantage of our verification
procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate
experimentally that our approach significantly outperforms existing methods and
establish the new state-of-the-art for training and certifying the robustness
of QNNs.
acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093, 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. Research
was sponsored by the United\r\nStates Air Force Research Laboratory and the United
States Air Force Artificial Intelligence Accelerator and was accomplished under
Cooperative Agreement Number FA8750-19-2-\r\n1000. The views and conclusions contained
in this document are those of the authors and should not be interpreted as representing
the official policies, either expressed or implied,\r\nof the United States Air
Force or the U.S. Government. The U.S. Government is authorized to reproduce and
distribute reprints for Government purposes notwithstanding any copyright\r\nnotation
herein. The research was also funded in part by the AI2050 program at Schmidt Futures
(Grant G-22-63172) and Capgemini SE."
article_processing_charge: No
arxiv: 1
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
citation:
ama: 'Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks.
In: Proceedings of the 37th AAAI Conference on Artificial Intelligence.
Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973.
doi:10.1609/aaai.v37i12.26747'
apa: 'Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D.
(2023). Quantization-aware interval bound propagation for training certifiably
robust quantized neural networks. In Proceedings of the 37th AAAI Conference
on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United
States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747'
chicago: Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger,
and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably
Robust Quantized Neural Networks.” In Proceedings of the 37th AAAI Conference
on Artificial Intelligence, 37:14964–73. Association for the Advancement of
Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i12.26747.
ieee: M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks,”
in Proceedings of the 37th AAAI Conference on Artificial Intelligence,
Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.
ista: 'Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware
interval bound propagation for training certifiably robust quantized neural networks.
Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference
on Artificial Intelligence vol. 37, 14964–14973.'
mla: Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for
Training Certifiably Robust Quantized Neural Networks.” Proceedings of the
37th AAAI Conference on Artificial Intelligence, vol. 37, no. 12, Association
for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:10.1609/aaai.v37i12.26747.
short: M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings
of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement
of Artificial Intelligence, 2023, pp. 14964–14973.
conference:
end_date: 2023-02-14
location: Washington, DC, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2023-02-07
date_created: 2023-08-27T22:01:17Z
date_published: 2023-06-26T00:00:00Z
date_updated: 2025-03-31T16:01:08Z
day: '26'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1609/aaai.v37i12.26747
ec_funded: 1
external_id:
arxiv:
- '2211.16187'
intvolume: ' 37'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.16187
month: '06'
oa: 1
oa_version: Preprint
page: 14964-14973
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
- _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
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantization-aware interval bound propagation for training certifiably robust
quantized neural networks
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: '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: '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'
file:
- access_level: open_access
checksum: 4108b031dc726ae6b4a5ae7e021ba188
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T13:20:35Z
date_updated: 2024-01-30T13:20:35Z
file_id: '14912'
file_name: 2023_AJHG_Ojavee.pdf
file_size: 2551276
relation: main_file
success: 1
file_date_updated: 2024-01-30T13:20:35Z
has_accepted_license: '1'
intvolume: ' 110'
isi: 1
issue: '9'
language:
- iso: eng
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: '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: 2026-06-18T17:34:48Z
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: '14281'
abstract:
- lang: eng
text: In nature, proteins that switch between two conformations in response to environmental
stimuli structurally transduce biochemical information in a manner analogous to
how transistors control information flow in computing devices. Designing proteins
with two distinct but fully structured conformations is a challenge for protein
design as it requires sculpting an energy landscape with two distinct minima.
Here we describe the design of “hinge” proteins that populate one designed state
in the absence of ligand and a second designed state in the presence of ligand.
X-ray crystallography, electron microscopy, double electron-electron resonance
spectroscopy, and binding measurements demonstrate that despite the significant
structural differences the two states are designed with atomic level accuracy
and that the conformational and binding equilibria are closely coupled.
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Philip J. Y.
full_name: Leung, Philip J. Y.
last_name: Leung
- first_name: Maxx H.
full_name: Tessmer, Maxx H.
last_name: Tessmer
- first_name: Adam
full_name: Broerman, Adam
last_name: Broerman
- first_name: Cullen
full_name: Demakis, Cullen
last_name: Demakis
- first_name: Acacia F.
full_name: Dishman, Acacia F.
last_name: Dishman
- first_name: Arvind
full_name: Pillai, Arvind
last_name: Pillai
- first_name: Abbas
full_name: Idris, Abbas
last_name: Idris
- first_name: David
full_name: Juergens, David
last_name: Juergens
- first_name: Justas
full_name: Dauparas, Justas
last_name: Dauparas
- first_name: Xinting
full_name: Li, Xinting
last_name: Li
- first_name: Paul M.
full_name: Levine, Paul M.
last_name: Levine
- first_name: Mila
full_name: Lamb, Mila
last_name: Lamb
- first_name: Ryanne K.
full_name: Ballard, Ryanne K.
last_name: Ballard
- first_name: Stacey R.
full_name: Gerben, Stacey R.
last_name: Gerben
- first_name: Hannah
full_name: Nguyen, Hannah
last_name: Nguyen
- first_name: Alex
full_name: Kang, Alex
last_name: Kang
- first_name: Banumathi
full_name: Sankaran, Banumathi
last_name: Sankaran
- first_name: Asim K.
full_name: Bera, Asim K.
last_name: Bera
- first_name: Brian F.
full_name: Volkman, Brian F.
last_name: Volkman
- first_name: Jeff
full_name: Nivala, Jeff
last_name: Nivala
- first_name: Stefan
full_name: Stoll, Stefan
last_name: Stoll
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive
two-state hinge proteins. Science. 2023;381(6659):754-760. doi:10.1126/science.adg7731
apa: Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis,
C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state
hinge proteins. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.adg7731
chicago: Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman,
Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive
Two-State Hinge Proteins.” Science. American Association for the Advancement
of Science, 2023. https://doi.org/10.1126/science.adg7731.
ieee: F. M. Praetorius et al., “Design of stimulus-responsive two-state hinge
proteins,” Science, vol. 381, no. 6659. American Association for the Advancement
of Science, pp. 754–760, 2023.
ista: Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai
A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben
SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker
D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659),
754–760.
mla: Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge
Proteins.” Science, vol. 381, no. 6659, American Association for the Advancement
of Science, 2023, pp. 754–60, doi:10.1126/science.adg7731.
short: F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F.
Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M.
Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F.
Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.
date_created: 2023-09-06T12:04:23Z
date_published: 2023-08-17T00:00:00Z
date_updated: 2023-11-07T12:42:09Z
day: '17'
doi: 10.1126/science.adg7731
extern: '1'
external_id:
pmid:
- '37590357'
intvolume: ' 381'
issue: '6659'
language:
- iso: eng
month: '08'
oa_version: None
page: 754-760
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Design of stimulus-responsive two-state hinge proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 381
year: '2023'
...
---
_id: '14294'
abstract:
- lang: eng
text: Growth factors and cytokines signal by binding to the extracellular domains
of their receptors and drive association and transphosphorylation of the receptor
intracellular tyrosine kinase domains, initiating downstream signaling cascades.
To enable systematic exploration of how receptor valency and geometry affects
signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using
repeat protein building blocks that can be modularly extended. By incorporating
a de novo designed fibroblast growth-factor receptor (FGFR) binding module into
these scaffolds, we generated a series of synthetic signaling ligands that exhibit
potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation.
The high specificity of the designed agonists reveal distinct roles for two FGFR
splice variants in driving endothelial and mesenchymal cell fates during early
vascular development. The ability to incorporate receptor binding domains and
repeat extensions in a modular fashion makes our designed scaffolds broadly useful
for probing and manipulating cellular signaling pathways.
article_processing_charge: No
author:
- first_name: Natasha I
full_name: Edman, Natasha I
last_name: Edman
- first_name: Rachel L
full_name: Redler, Rachel L
last_name: Redler
- first_name: Ashish
full_name: Phal, Ashish
last_name: Phal
- first_name: Thomas
full_name: Schlichthaerle, Thomas
last_name: Schlichthaerle
- first_name: Sanjay R
full_name: Srivatsan, Sanjay R
last_name: Srivatsan
- first_name: Ali
full_name: Etemadi, Ali
last_name: Etemadi
- first_name: Seong
full_name: An, Seong
last_name: An
- first_name: Andrew
full_name: Favor, Andrew
last_name: Favor
- first_name: Devon
full_name: Ehnes, Devon
last_name: Ehnes
- first_name: Zhe
full_name: Li, Zhe
last_name: Li
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Max
full_name: Gordon, Max
last_name: Gordon
- first_name: Wei
full_name: Yang, Wei
last_name: Yang
- first_name: Brian
full_name: Coventry, Brian
last_name: Coventry
- first_name: Derrick R
full_name: Hicks, Derrick R
last_name: Hicks
- first_name: Longxing
full_name: Cao, Longxing
last_name: Cao
- first_name: Neville
full_name: Bethel, Neville
last_name: Bethel
- first_name: Piper
full_name: Heine, Piper
last_name: Heine
- first_name: Analisa N
full_name: Murray, Analisa N
last_name: Murray
- first_name: Stacey
full_name: Gerben, Stacey
last_name: Gerben
- first_name: Lauren
full_name: Carter, Lauren
last_name: Carter
- first_name: Marcos
full_name: Miranda, Marcos
last_name: Miranda
- first_name: Babak
full_name: Negahdari, Babak
last_name: Negahdari
- first_name: Sangwon
full_name: Lee, Sangwon
last_name: Lee
- first_name: Cole
full_name: Trapnell, Cole
last_name: Trapnell
- first_name: Lance
full_name: Stewart, Lance
last_name: Stewart
- first_name: Damian C
full_name: Ekiert, Damian C
last_name: Ekiert
- first_name: Joseph
full_name: Schlessinger, Joseph
last_name: Schlessinger
- first_name: Jay
full_name: Shendure, Jay
last_name: Shendure
- first_name: Gira
full_name: Bhabha, Gira
last_name: Bhabha
- first_name: Hannele
full_name: Ruohola-Baker, Hannele
last_name: Ruohola-Baker
- first_name: David
full_name: Baker, David
last_name: Baker
citation:
ama: Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and
vascular differentiation using designed oligomeric assemblies. bioRxiv.
doi:10.1101/2023.03.14.532666
apa: Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R.,
Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies. bioRxiv. https://doi.org/10.1101/2023.03.14.532666
chicago: Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle,
Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling
and Vascular Differentiation Using Designed Oligomeric Assemblies.” BioRxiv,
n.d. https://doi.org/10.1101/2023.03.14.532666.
ieee: N. I. Edman et al., “Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies,” bioRxiv. .
ista: Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An
S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks
DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari
B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha
G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular
differentiation using designed oligomeric assemblies. bioRxiv, 10.1101/2023.03.14.532666.
mla: Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular
Differentiation Using Designed Oligomeric Assemblies.” BioRxiv, doi:10.1101/2023.03.14.532666.
short: N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi,
S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry,
D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M.
Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger,
J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.).
date_created: 2023-09-06T12:31:49Z
date_published: 2023-03-15T00:00:00Z
date_updated: 2023-11-07T12:21:58Z
day: '15'
doi: 10.1101/2023.03.14.532666
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.03.14.532666
month: '03'
oa: 1
oa_version: Preprint
publication: bioRxiv
publication_status: submitted
status: public
title: Modulation of FGF pathway signaling and vascular differentiation using designed
oligomeric assemblies
type: preprint
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:
- access_level: open_access
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
relation: main_file
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'
...